[go: up one dir, main page]

WO2025072849A1 - Peptides présentables par le cmh associés au diabète de type 1 - Google Patents

Peptides présentables par le cmh associés au diabète de type 1 Download PDF

Info

Publication number
WO2025072849A1
WO2025072849A1 PCT/US2024/049097 US2024049097W WO2025072849A1 WO 2025072849 A1 WO2025072849 A1 WO 2025072849A1 US 2024049097 W US2024049097 W US 2024049097W WO 2025072849 A1 WO2025072849 A1 WO 2025072849A1
Authority
WO
WIPO (PCT)
Prior art keywords
amino acids
mhc
seq
presentable
composition
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
PCT/US2024/049097
Other languages
English (en)
Inventor
Ryan NISTLER
William Edward RUFF
Jan KIESELOW
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Repertoire Immune Medicines Inc
Original Assignee
Repertoire Immune Medicines Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Repertoire Immune Medicines Inc filed Critical Repertoire Immune Medicines Inc
Publication of WO2025072849A1 publication Critical patent/WO2025072849A1/fr
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0008—Antigens related to auto-immune diseases; Preparations to induce self-tolerance
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P5/00—Drugs for disorders of the endocrine system
    • A61P5/48—Drugs for disorders of the endocrine system of the pancreatic hormones
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/53—DNA (RNA) vaccination
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/57—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2
    • A61K2039/577—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2 tolerising response
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/70—Multivalent vaccine
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/70539—MHC-molecules, e.g. HLA-molecules

Definitions

  • T1D Type 1 Diabetes
  • APCs antigen-presenting cells
  • T1D Type 1 Diabetes
  • T1D is a prevalent chronic disease with about 1.6 million adult and pediatric patients in the United States, and about 64,000 new cases diagnosed per year.
  • T1D is an autoimmune disease characterized by T-cell-mediated destruction of pancreatic ⁇ cells, resulting in a deficiency of insulin synthesis and secretion.
  • T1D To manage the disease, patients are dependent on insulin substitution therapy for the rest of their lives. To date, there is no cure for T1D.
  • the standard of care treatment for T1D includes administration of insulin, metformin, Pramlintide (SYMLIN ® ), blood pressure drugs, cholesterol medications, and aspirin, as well as exercise and diet.
  • the first and only disease modifying drug for T1D was FDA approved in 2022 for the delay of T1D, TZIELD TM , no other disease modifying therapy is approved for T1D.
  • TZIELD TM no other disease modifying therapy is approved for T1D.
  • T1D damages the heart and blood vessels, mainly by promoting high blood pressure and atherosclerosis that can lead to other diabetes-related complications, such as heart disease, chronic kidney disease, nerve damage, and other problems with feet, oral health, vision, hearing, and mental health. Accordingly, there remains a need for new treatments for these patients.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide, which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in Table 1A, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide, which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide as set forth in Table 2A, Table 2B, or Table 3, or (ii) the amino acid sequence comprising the MHC-presentable peptide, which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide, which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8, or (ii) the amino acid sequence comprising the MHC-presentable peptide, which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 6.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 6 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence set forth in SEQ ID NO: 9.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 10 SEQ ID NO: 11, or SEQ ID NO: 12, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 10.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 10 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 13.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 14, SEQ ID NO: 15, or SEQ ID NO: 16, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the least 8 amino acids of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 14.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 14 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 17.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 18, SEQ ID NO: 19, or SEQ ID NO: 20, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC
  • composition for use the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 18.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 18 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 21.
  • the present disclosure provides, a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 22, SEQ ID NO: 23, or SEQ ID NO: 24, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 22.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 22 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 25.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 26, SEQ ID NO: 27, or SEQ ID NO: 28, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence as
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 26.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 26 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC- presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 29.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 30, SEQ ID NO: 31, or SEQ ID NO: 32, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 30.
  • the MHC-presentable peptide sequence set forth in SEQ ID NO: 30 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 33.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 34, SEQ ID NO: 35, or SEQ ID NO: 36, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids)
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 34.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 34 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 37.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of sequence at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide as set forth in SEQ ID NO: 38, SEQ ID NO: 39, or SEQ ID NO: 40, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids)
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 38.
  • the MHC-presentable peptide sequence set forth in SEQ ID NO: 38 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 41.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 42, SEQ ID NO: 43, or SEQ ID NO: 44, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids)
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 42.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 42 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 45.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 46, SEQ ID NO: 47, or SEQ ID NO: 48, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 46.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 46 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 49.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 50, SEQ ID NO: 51, or SEQ ID NO: 52, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids)
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 50.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 50 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 53.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 54, SEQ ID NO: 55, or SEQ ID NO: 56, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids)
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 54.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 54 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 57.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 58, SEQ ID NO: 59, or SEQ ID NO: 60, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 58.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 58 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence set forth in SEQ ID NO: 61.
  • the present disclosure provides a composition for use in inducing a tolerizing immune response in a subject in need thereof, the composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 62, SEQ ID NO: 63, or SEQ ID NO: 64, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 62.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 62 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence set forth in SEQ ID NO: 65.
  • the MHC-presentable peptide in the amino acid sequence is less than 35 amino acids, less than 34 amino acids, less than 33 amino acids, less than 32 amino acids, less than 31 amino acids, less than 30 amino acids, less than 29 amino acids, less than 28 amino acids, less than 27 amino acids, less than 26 amino acids, less than 25 amino acids, less than 24 amino acids, less than 23 amino acids, less than 22 amino acids, less than 21 amino acids, less than 20 amino acids, less than 19 amino acids, less than 18 amino acids, less than 17 amino acids, less than 16 amino acids, less than 15 amino acids, less than 14 amino acids, less than 13 amino acids, less than 12 amino acids, less than 11 amino acids, less than 10 amino acids, or less than 9 amino acids.
  • the MHC-presentable peptide in the amino acid sequence consists of 9 amino acids, 10 amino acids, 11 amino acids, 12 amino acids, 13 amino acids, 14 amino acids, 15 amino acids, 16 amino acids, 17 amino acids, 18 amino acids, 19 amino acids, 20 amino acids, 21 amino acids, 22 amino acids, 23 amino acids, 24 amino acids, 25 amino acids, 26 amino acids, 27 amino acids, 28 amino acids, 29 amino acids, 30 amino acids, 31 amino acids, 32 amino acids, 33 amino acids, 34 amino acids, or 35 amino acids.
  • the MHC-presentable peptide in the amino acid sequence has 8-35 amino acids, 9-35, 10-35, 11-35, 12-35, 13-35, 14-35, 15-35, 8-34, 9-34, 10-34, 11-34, 12-34, 13-34, 14-34, 15-34, 8-33, 9-33, 10-33, 11-33, 12-33, 13-33, 14-33, 15- 33, 8-32, 9-32, 10-32, 11-32, 12-32, 13-32, 14-32, 15-32, 8-31, 9-31, 10-31, 11-31, 12-31, 13-31, 14-31, or 15-31 amino acids.
  • the amino acid sequence further comprises a second MHC-presentable peptide that is heterologous to the MHC-presentable peptide. In some aspects, the amino acid sequence further comprises a third MHC-presentable peptide, a fourth MHC- presentable peptide, a fifth MHC-presentable peptide, a sixth MHC-presentable peptide, a seventh MHC-presentable peptide, a ninth MHC-presentable peptide, a tenth MHC-presentable peptide, an 11th MHC-presentable peptide, a 12th MHC-presentable peptide, a 13th MHC-presentable peptide, a 14th MHC-presentable peptide, a 15th MHC-presentable peptide, a 16th MHC- presentable peptide, a 17th MHC-presentable peptide, an 18th MHC-presentable peptide, a 19th MHC-presentable peptide, a 20th MHC-
  • the amino acid sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 26, SEQ ID NO: 30, SEQ ID NO: 34, SEQ ID NO: 38, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 54, SEQ ID NO: 54, SEQ ID NO: 58, or SEQ ID NO: 62.
  • the present disclosure provides a composition
  • a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide, which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide as set forth in Table 2A, Table 2B, or Table 3, or (ii) the amino acid sequence comprising the MHC-presentable peptide, which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the present disclosure provides a composition
  • a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide, which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8, or (ii) the amino acid sequence comprising the MHC-presentable peptide, which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence set forth in SEQ ID NO: 9.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 10, SEQ ID NO: 11, or SEQ ID NO: 12, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 14.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 14 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 17.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 18, SEQ ID NO: 19, or SEQ ID NO: 20, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 18.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 18 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 21.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 22, SEQ ID NO: 23, or SEQ ID NO: 24, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 22.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 22 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 25.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 26, SEQ ID NO: 27, or SEQ ID NO: 28, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 26.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 26 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 29.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 30, SEQ ID NO: 31, or SEQ ID NO: 32, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 30.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 30 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 33.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 34, SEQ ID NO: 35, or SEQ ID NO: 36, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 34.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 34 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 37.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of sequence at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide as set forth in SEQ ID NO: 38, SEQ ID NO: 39, or SEQ ID NO: 40, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 38.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 38 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 41.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth SEQ ID NO: 42, SEQ ID NO: 43, or SEQ ID NO: 44, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 42.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 42 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 45.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 46, SEQ ID NO: 47, or SEQ ID NO: 48, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 46.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 46 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 49.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 50, SEQ ID NO: 51, or SEQ ID NO: 52, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 50.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 50 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 53.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 54, SEQ ID NO: 55, or SEQ ID NO: 56, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 54.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 54 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 57.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 58, SEQ ID NO: 59, or SEQ ID NO: 60, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 58.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 58 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence set forth in SEQ ID NO: 61.
  • the present disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 62, SEQ ID NO: 63, or SEQ ID NO: 64, or (ii) the amino acid sequence comprising the MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 62.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 62 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence set forth in SEQ ID NO: 65.
  • the MHC-presentable peptide in the amino acid sequence is less than 35 amino acids, less than 34 amino acids, less than 33 amino acids, less than 32 amino acids, less than 31 amino acids, less than 30 amino acids, less than 29 amino acids, less than 28 amino acids, less than 27 amino acids, less than 26 amino acids, less than 25 amino acids, less than 24 amino acids, less than 23 amino acids, less than 22 amino acids, less than 21 amino acids, less than 20 amino acids, less than 19 amino acids, less than 18 amino acids, less than 17 amino acids, less than 16 amino acids, less than 15 amino acids, less than 14 amino acids, less than 13 amino acids, less than 12 amino acids, less than 11 amino acids, less than 10 amino acids, or less than 9 amino acids.
  • the MHC-presentable peptide in the amino acid sequence consists of 9 amino acids, 10 amino acids, 11 amino acids, 12 amino acids, 13 amino acids, 14 amino acids, 15 amino acids, 16 amino acids, 17 amino acids, 18 amino acids, 19 amino acids, 20 amino acids, 21 amino acids, 22 amino acids, 23 amino acids, 24 amino acids, 25 amino acids, 26 amino acids, 27 amino acids, 28 amino acids, 29 amino acids, 30 amino acids, 31 amino acids, 32 amino acids, 33 amino acids, 34 amino acids, or 35 amino acids.
  • the MHC-presentable peptide in the amino acid sequence has 8-35 amino acids, 9-35, 10-35, 11-35, 12-35, 13-35, 14-35, 15-35, 8-34, 9-34, 10-34, 11-34, 12-34, 13-34, 14-34, 15-34, 8-33, 9-33, 10-33, 11-33, 12-33, 13-33, 14-33, 15- 33, 8-32, 9-32, 10-32, 11-32, 12-32, 13-32, 14-32, 15-32, 8-31, 9-31, 10-31, 11-31, 12-31, 13-31, 14-31, or 15-31 amino acids.
  • the MHC-presentable peptide amino acid sequence further comprises a second MHC-presentable peptide that is heterologous to the MHC-presentable peptide.
  • the amino acid sequence further comprises a third MHC-presentable peptide, a fourth MHC-presentable peptide, a fifth MHC-presentable peptide, a sixth MHC- presentable peptide, a seventh MHC-presentable peptide, a ninth MHC-presentable peptide, a tenth MHC-presentable peptide, an 11th MHC-presentable peptide, a 12th MHC-presentable peptide, a 13th MHC-presentable peptide, a 14th MHC-presentable peptide, a 15th MHC-presentable peptide, a 16th MHC-presentable peptide, a 17th MHC-presentable peptide, an 18th MHC- presentable peptide, a 19th MHC-presentable peptide
  • the amino acid sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 26, SEQ ID NO: 30, SEQ ID NO: 34, SEQ ID NO: 38, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 54, SEQ ID NO: 54, SEQ ID NO: 58, or SEQ ID NO: 62.
  • the amino acid sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 7, SEQ ID NO: 11, SEQ ID NO: 15, SEQ ID NO: 19, SEQ ID NO: 23, SEQ ID NO: 27, SEQ ID NO: 31, SEQ ID NO: 35, SEQ ID NO: 39, SEQ ID NO: 43, SEQ ID NO: 47, SEQ ID NO: 51, SEQ ID NO: 55, SEQ ID NO: 59, or SEQ ID NO: 65.
  • the amino acid sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 8, SEQ ID NO: 12, SEQ ID NO: 16, SEQ ID NO: 20, SEQ ID NO: 24, SEQ ID NO: 28, SEQ ID NO: 32, SEQ ID NO: 36, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, or SEQ ID NO: 66.
  • the amino acid sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 17, SEQ ID NO: 21, SEQ ID NO: 25, SEQ ID NO: 29, SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 41, SEQ ID NO: 45, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 57, SEQ ID NO: 61, or SEQ ID NO: 67.
  • the MHC-presentable peptide is specific to HLA-DQ2.5 and/or HLA- DQ8.
  • the amino acid sequence induces a tolerizing immune response.
  • the tolerizing immune response is against Type 1 Diabetes.
  • the immune response comprises (i) an induction of antigen-specific T cell tolerance, (ii) an increase in Treg cells (e.g., CD4+ Treg cells or FOXP3+ Treg cells), (iii) inhibition of autoimmunity, (iv) an induction of anergy of effector T cells, (e.g., CD4+ T effector cells), (v) inhibition of cytokine production, (vi) a decrease in a pro-inflammatory cytokine, (vii) an increase in an immunosuppressive cytokine, (viii) a suppression of CD8+ effector cells, (ix) an increase of LAG3+ CD49b+ Tr1 cells, or any combination thereof.
  • Treg cells e.g., CD4+ Treg cells or FOXP3+ Treg cells
  • an induction of anergy of effector T cells e.g., CD4+ T effector cells
  • the immune response comprises an increase in the number of Treg cells, e.g., FOXP3+ Treg cells. In some aspects, the immune response comprises an increase of Type 1 Regulatory (Tr1) cells. In some aspects, the immune response comprises a decrease of a pro-inflammatory cytokine, wherein the pro- inflammatory cytokine comprises Interferon- ⁇ , Interleukin-1, Interleukin-2, Interleukin-12, Interleukin-16, Interleukin-17, Interleukin-18, Interleukin-21, Interleukin-22, Interleukin-23, Tumor Necrosis Factor- ⁇ , or any combination thereof.
  • the pro-inflammatory cytokine comprises Interferon- ⁇ , Interleukin-1, Interleukin-2, Interleukin-12, Interleukin-16, Interleukin-17, Interleukin-18, Interleukin-21, Interleukin-22, Interleukin-23, Tumor Necrosis Factor- ⁇ , or any combination thereof.
  • the immune response comprises an increase of an immunosupressive cytokine, wherein the immunosuppressive cytokine comprises Interleukin-1R ⁇ , Interleukin-4, Interleukin-10, Interleukin-11, Interleukin-13, Tumor Growth Factor- ⁇ , Interleukin-33, Interleukin-35, Interleukin-37, or any combination thereof.
  • the immunosuppressive cytokine comprises Interleukin-1R ⁇ , Interleukin-4, Interleukin-10, Interleukin-11, Interleukin-13, Tumor Growth Factor- ⁇ , Interleukin-33, Interleukin-35, Interleukin-37, or any combination thereof.
  • At least one MHC-presentable peptide is derived from a protein comprising Chromogranin-A (CHGA), Carboxypeptidase A1(CPA1), C1orf127 protein (C1orf127), Early growth response protein 4 (EGR4), Glutamate decarboxylase 2 (GAD2), Vitamin D-binding protein (GC), Guanine nucleotide-binding protein G(s) subunit alpha isoform XLas (GNAS), Glucose-6-phosphatase 2 (G6PC2 (IGRP)), Insulin (INS), Potassium channel subfamily K member 16 (KCNK16), Kinesin-like protein KIF1A (KIF1A), Neuroendocrine convertase 2 (PCSK2), Pancreas/duodenum homeobox protein 1 (PDX1), Proton-coupled zinc antiporter SLC30A8 (SLC30A8), or any combination thereof.
  • CHGA Chromogranin-A
  • C1
  • the nucleotide sequence comprises an RNA, DNA, or any combination thereof. In some aspects, the nucleotide sequence comprises an mRNA. [0044] In some aspects, one or more of the MHC-presentable peptides are an MHC class II peptide. In some aspects, all of the MHC-presentable peptides are MHC class II peptides. In some aspects, one or more of the MHC-presentable peptides are an MHC class I peptide. In some aspects, two or more MHC-presentable peptides are a combination of an MHC class I peptide and an MHC class II peptide.
  • the nucleotide sequence comprises a single open reading frame that encodes one or more MHC-presentable peptides. In some aspects, the single open reading frame encodes all MHC-presentable peptides in the amino acid sequence. In some aspects, the nucleotide sequence comprises one or more open reading frames that encode one or more MHC-presentable peptides. In some aspects, the nucleotide sequence comprises a plurality of open reading frames that encodes one or more MHC-presentable peptides. In some aspects, the amino acid sequence encoded by the nucleotide sequence further comprises MHC-presentable peptides directly linked to each other without a linker.
  • the amino acid sequence comprising the MHC- presentable peptides further comprises a linker between two MHC-presentable peptides.
  • the linker comprises a single amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids.
  • the linker comprises a flexible linker.
  • the linker comprises a cleavable linker.
  • the linker comprises an amino acid sequence selected from the group consisting of the linkers set forth in Table 4.
  • two or more of the MHC-presentable peptides comprise amino acid sequences of different lengths.
  • one or more of the MHC-presentable peptides comprises a flank region at the N terminus (N terminus flank) and/or the C terminus (C terminus flank) of the MHC-presentable peptides.
  • the total length of the amino acid sequence comprises 50-100 amino acids, 100-200 amino acids, 200-300 amino acids, 300-400 amino acids, 400-500 amino acids, 500-600 amino acids, 600-700 amino acids, 700-800 amino acids, 800-900 amino acids, 900-1000 amino acids, 1000-1100 amino acids, or 1100-1200 amino acids.
  • the nucleotide sequence further comprises a 5’ UTR. In some aspects, the nucleotide sequence further comprises a 3’ UTR.
  • the nucleotide sequence further comprises a poly-A tail. In some aspects, the nucleotide sequence further comprises a cap structure. In some aspects, the cap structure comprises a 5' cap structure, a 5' cap-0 structure, a 5' cap-l structure, or a 5' cap-2 structure. In some aspects, the nucleotide sequence comprises a nucleic acid having at least one chemical modification. In some aspects, the chemical modification is in the nucleic acid base, in the nucleic acid sugar, or in the nucleic acid backbone.
  • the chemical modification in the base comprises pseudouridine, Nl-methylpseudouridine, Nl-ethylpseudouridine, 2-thiouridine, 4'-thiouridine, 5- methylcytosine, 2-thio-l-methyl-l-deaza-pseudouridine, 2-thio-1-methyl-pseudouridine, 2-thio-5- aza-uridine, 2-thio-dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-pseudouridine, 4- methoxy-2-thio-pseudouridine, 4-methoxy-pseudouridine, 4-thio-l -methyl-pseudouridine, 4-thio- pseudouridine, 5-aza-uridine, dihydropseudouridine, 5-methyluridine, 5-methyluridine, 5- methoxyuridine, or 2'-0-methyl uridine.
  • the chemical modification in the sugar comprises Locked Nucleic Acid (LNA); 2'-O-alkyl-RNA; 2'-amino-DNA; 2'-fluoro-DNA; arabino nucleic acid (ANA); 2'-fluoro-ANA, hexitol nucleic acid (HNA), intercalating nucleic acid (INA), constrained ethyl nucleic acid (cEt), 2'-O-methyl nucleic acid (2'-OMe), or 2'-O-methoxyethyl nucleic acid (2'-MOE).
  • LNA Locked Nucleic Acid
  • 2'-O-alkyl-RNA 2'-amino-DNA
  • 2'-fluoro-DNA arabino nucleic acid
  • ANA arabino nucleic acid
  • INA intercalating nucleic acid
  • cEt constrained ethyl nucleic acid
  • 2'-OMe 2'-O-methyl nucleic acid
  • the chemical modifications in the backbone comprises a phosphorodiamidate morpholino oligomer (PMO) and/or phosphorothioate (PS) modification.
  • the MHC-presentable peptides are encoded by a nucleotide sequence. In some aspects, all the MHC-presentable peptides are encoded by a single nucleotide sequence. In some aspects, all the MHC-presentable peptides are encoded by at least two heterologous nucleotide sequences. [0046] In some aspects, all of the MHC-presentable peptides are derived from one or more Type 1 Diabetes (T1D) antigens.
  • T1D Type 1 Diabetes
  • one or more of the MHC-presentable peptides are derived from an antigen specific to a subject having Type 1 Diabetes (“subject specific T1D antigen”). In some aspects, one or more of the MHC-presentable peptides are immunogenic.
  • the nucleotide sequence or the amino acid sequence is delivered by a delivery agent.
  • the delivery agent is capable of delivering the nucleotide sequence or the amino acid sequence to a target cell.
  • the delivery agent comprises a liposome, a lipid nanoparticle, an exosome, a lipid-like particle, a lipoplex, a microvesicle, a vector, or any combination thereof.
  • the delivery agent comprises a nanoparticle.
  • the target cell is a pancreatic cell, a dendritic cell, a macrophage, a B cell, or a non- professional antigen presenting cell.
  • the target cell is a tolerogenic cell.
  • the tolerogenic cell is a cell in the liver, optionally selected from a liver sinusoidal endothelial cell, a MARCO+ Kupffer cell, and a monocyte-derived macrophage.
  • the tolerogenic cell is a cell in the spleen, optionally selected from a marginal zone macrophage, a metallophilic macrophage, and a marginal zone dendritic cell.
  • the target cell is a pancreatic cell.
  • the delivery agent has a negative zeta potential.
  • the delivery agent comprises a ligand that binds the target cell.
  • the present disclosure provides an MHC complex comprising an MHC class I or II molecule and an MHC-presentable peptide comprising at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in Table 1A.
  • the present disclosure provides an MHC complex comprising an MHC class I or II molecule and an MHC-presentable peptide encoded by the nucleotide sequence in the composition.
  • MHC complex comprises an MHC class I molecule only, an MHC class II molecule only, or both an MHC class I molecule and an MHC class II molecule.
  • APC antigen presenting cell
  • the present disclosure provides a pharmaceutical composition comprising the composition, the MHC complex, or the antigen presenting cell, and a pharmaceutically acceptable excipient.
  • the composition for use further comprising administering an immunomodulator.
  • the composition further comprises an immunomodulator.
  • the immunomodulator is encoded by a nucleotide sequence.
  • the immunomodulator is encoded by the same nucleotide sequence that encodes the MHC-presentable peptides.
  • the immunomodulator comprises an immunomodulatory cytokine or a nucleic acid encoding the immunomodulatory cytokine.
  • the immunomodulatory cytokine comprises IL-2, IL-10, TGF- ⁇ , IL-37, IL-27, IL-35, CXCL11, CCL17, OX40L/Jagged- 1, Vasoactive Intestinal MHC-presentable peptide (VIP), or any combination thereof.
  • the immunomodulatory cytokine comprises an IL-2 protein that preferentially activates the IL-2R ⁇ receptor complex relative to the IL-2R ⁇ receptor complex. In some aspects, the immunomodulatory cytokine comprises an IL-10 protein. In some aspects, the immunomodulatory cytokine comprises a TGF- ⁇ protein. In some aspects, the immunomodulator comprises or further comprises a nucleic acid encoding an intracellular or transmembrane immunomodulatory protein.
  • the intracellular or transmembrane immunomodulatory protein comprises PD-L1, PD-L2, ICOS ligand, ILT3, ILT4, BTLA, Fas, CD39, indoleamine 2,3-dioxygenase 1 (IDO1), CHUK, Ikkb, GILZ, or any combination thereof.
  • the immunomodulator comprises an immunomodulatory compound.
  • the immunomodulatory compound comprises vitamin A, vitamin D, adenosine, kynurenine, 2-(1' H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE), fingolimod (FTY720), interferon beta-1a, interferon beta-1b, glatiramer acetate, mitoxantrone, natalizumab, or any combination thereof.
  • the immunomodulator is in or on the delivery agent.
  • the present disclosure provides a kit comprising the composition for use, the composition, the MHC complex, the antigen presenting cell, or the pharmaceutical composition, and instructions for use.
  • the present disclosure provides a method of increasing CD4+ Treg cells in a subject in need thereof comprising administering the composition or the pharmaceutical composition to the subject. In some aspects, the present disclosure provides a method of decreasing CD8+ Treg cells in a subject in need thereof comprising administering the composition or the pharmaceutical composition to the subject. In some aspects, the present disclosure provides a method of increasing Type 1 Regulatory (Tr1) cells or inducing T-regulatory 35 (iTr35) cells in a subject in need thereof comprising administering the or the pharmaceutical composition to the subject. In some aspects, the present disclosure provides a method of increasing LAG3+CD49b+ Tr1 cells in a subject in need thereof comprising administering the composition or the pharmaceutical composition to the subject.
  • Tr1 Type 1 Regulatory
  • iTr35 T-regulatory 35
  • the present disclosure provides a method of inducing an anergy of T effector cells in a subject in need thereof comprising administering the composition or the pharmaceutical composition to the subject. In some aspects, the present disclosure provides a method of inducing an anergy of CD4+ T effector cells in a subject in need thereof comprising administering the composition or the pharmaceutical composition to the subject. In some aspects, the present disclosure provides a method of producing the composition, the MHC complex, the antigen presenting, or the pharmaceutical composition, comprising adding a nucleotide sequence encoding the MHC-presentable peptide in the nucleotide sequence.
  • the present disclosure provides a method of inducing a tolerizing immune response in a subject in need thereof, the method comprising administering to the subject an effective amount of the composition, the MHC complex, the antigen presenting cell, or the pharmaceutical composition.
  • the present disclosure provides a method of inducing a T cell response against Type 1 Diabetes in a subject in need thereof, the method comprising administering to the subject an effective amount of the composition, the MHC complex, the antigen presenting cell, or the pharmaceutical composition.
  • the present disclosure provides a method of preventing or treating Type 1 Diabetes in a subject in need thereof, the method comprising administering to the subject an effective amount of the composition, the MHC complex, the antigen presenting cell, or the pharmaceutical composition.
  • the present disclosure provides a use of the composition, the MHC complex, the antigen presenting cell, or the pharmaceutical composition in the manufacture of a medicament for inducing a tolerizing immune response against Type 1 Diabetes.
  • the present disclosure provides a use of the composition, the MHC complex, the antigen presenting cell, or the pharmaceutical composition for use in the manufacture of a medicament for treating or preventing Type 1 Diabetes.
  • the composition, the MHC complex, the antigen presenting cell, the pharmaceutical composition, or the medicament is administered intravenously, subcutaneously, intramuscularly, intra-arterially, intra-articularly, intracardiacly, intradermally, intraperitoneally, intrathecally, or transdermally.
  • the present disclosure provides a means for inducing a tolerogenic immune response in a subject in need thereof, in combination with a pharmaceutically acceptable carrier.
  • the present disclosure provides a method of treating or preventing type I diabetes in a subject in need thereof comprising administering to the subject a means for inducing a tolerogenic immune response in combination with a pharmaceutically acceptable carrier.
  • FIG. 1 shows a schematic diagram of an exemplary mRNA construct (a string polynucleotide sequence) that expresses multiple MHC-presentable peptides when translated.
  • FIG.2 shows a schematic diagram of an exemplary epitope cassette to be included in a mRNA construct, such as the construct shown in FIG.1.
  • FIG.3 shows an exemplary plot demonstrating peptide presentation by MHC molecules identified by MEDi.
  • FIG.4 shows exemplary linker sequences as Table 4.
  • FIGs.5A-5B show the in vivo efficacy of an mRNA tolerizing vaccine in a Nonobese Diabetic (NOD) mouse model of Type 1 Diabetes.
  • FIG. 5A provides the blood glucose levels (mg/dL) in the mice following administration of a Lipid Particle Formulation containing KIF1a mRNA and tol105 mRNA (tolerizing mRNA).
  • FIG.5B provides the percent normal glucose in the NOD mice following administration of the Lipid Particle Formulation containing KIF1a mRNA and tol105 mRNA (tolerizing mRNA).
  • FIG.6A-6B shows exemplary plots showing the NetMHC and immunogenicity scores for tested epitopes.
  • FIG.6A shows the scores for HLA-DQ8 epitopes and
  • FIG.6B shows the scores for HLA-DQ2.5 epitopes.
  • DETAILED DESCRIPTION [0062] The present disclosure is based, in part, upon the identification of MHC-presentable peptides associated with Type 1 Diabetes (T1D) MHC risk alleles.
  • T1D-associated peptides comprising these MHC-presentable peptides can be used for inducing immune tolerance to cells (e.g., islet ⁇ cells) presenting these MHC-presentable peptides.
  • the terms “antigen-presenting cell” or “APC” refer to a cell or particle that elicits a cellular immune response by displaying a peptide presented by a major histocompatibility complex (MHC) on an outer surface of the cell or particle, for recognition by an immune cell such as a T cell.
  • MHC major histocompatibility complex
  • APCs include, e.g., professional APCs, such as dendritic cells, macrophages, Langerhans cells, and B cells, that express both class I and class II MHCs, and non- professional APCs (e.g., nucleated cells) that generally express only class I MHCs.
  • APCs also include artificial APCs (aAPCs), e.g., cells (e.g., drosophila cells) engineered to express an MHC that presents a peptide.
  • aAPCs artificial APCs
  • artificial APCs include particles (e.g., beads, nanoparticles, or liposomes) that present a peptide-MHC on the surface, configured such that the aAPC can prime or stimulate T cells in vitro, ex vivo, or in vivo.
  • exemplary aAPCs are known in the art and are described in Section V herein.
  • the term “delivery agent” refers to an agent capable of delivering a cargo (e.g., peptide, protein, nucleic acid, or other compounds) to a target cell, tissue, or organ.
  • a delivery agent may deliver a cargo into a target cell (e.g., cytosol or endosome of the target cell).
  • a delivery agent may deliver a cargo to the vicinity of a target cell in a target tissue, such that the cargo can bind to an outer surface of the target cell or be internalized into the target cell.
  • a delivery agent may, e.g., bind to the cargo or encapsulate the cargo.
  • Delivery agents include, for example, particles such as nanoparticles (e.g., lipid nanoparticles), exosomes, lipoplex, lipid-like particles, vectors, microvesicles, or liposomes (e.g., nanoliposomes).
  • the term “effective amount” refers to the amount of a compound (e.g., a compound of the present disclosure) sufficient to effect beneficial or desired results.
  • percent “identity” between a polypeptide sequence and a reference sequence is defined as the percentage of amino acid residues in the polypeptide sequence that are identical to the amino acid residues in the reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity.
  • percent “identity” between a nucleic acid sequence and a reference sequence is defined as the percentage of nucleotides in the nucleic acid sequence that are identical to the nucleotides in the reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity.
  • Alignment for purposes of determining percent sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, MEGALIGN (DNASTAR), CLUSTALW, CLUSTAL OMEGA, or MUSCLE software.
  • BLAST BLAST-2
  • ALIGN ALIGN
  • MEGALIGN MEGALIGN
  • CLUSTALW CLUSTAL OMEGA
  • MUSCLE software Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
  • the term “include,” “includes,” “including,” “have,” “has,” “having,” “contain,” “contains,” or “containing,” including grammatical equivalents thereof, should be understood generally as open-ended and non-limiting, for example, not excluding additional unrecited elements or steps, unless otherwise specifically stated or understood from the context.
  • the term “isolated” when used in reference to a biological substance means that the substance is not in its native state or is removed from at least a portion of other molecules associated or occurring with the substance in its native environment (e.g., within a cell or tissue) or in another environment (e.g., in a cell extract, extraction buffer, etc.).
  • an isolated biological substance e.g., a protein, peptide, nucleic acid, or cell
  • an isolated protein, peptide, nucleic acid, or cell can be at least 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% free of other molecules present in a natural or non-natural environment.
  • an isolated peptide is not present in a native composition of the peptide, e.g., in a cell comprising the peptide in its cytoplasm, or an isolated antigen-presenting cell (“APC”) is not present in a native environment of the APC, e.g., in a biological sample (e.g., tissue or body fluid sample) comprising the APC.
  • APC isolated antigen-presenting cell
  • MHC major histocompatibility complex
  • CD8 + e.g., cytotoxic
  • CD4 + e.g., helper
  • HLA human leukocyte antigen
  • Class I HLA protein is a heterodimer composed of a heavy ⁇ -chain and a smaller ⁇ -chain.
  • the ⁇ -chain is encoded by a variant HLA gene, and the ⁇ chain is an invariant ⁇ 2 microglobulin ( ⁇ 2m) polypeptide encoded by a separate region of the human genome.
  • Human MHC class II genes encode, for example, HLA-DM, HLA-DO, HLA-DP, HLA-DQ, and HLA-DR proteins.
  • Class II HLA protein is a heterodimer composed of ⁇ and ⁇ chains both encoded by variant HLA genes.
  • a HLA can include multiple serotypes (e.g., HLA-A*02, HLA-DPA1*02) each of which may include multiple alleles (e.g., HLA-DQ2.5 comprises alleles HLA-DQA1*0501 and DQB1*0201; and HLA-DQ8 comprises DQA1*0301 and DQB1*0302).
  • Nucleotide sequences and a gene map of human MHC are publicly available (e.g., The MHC sequencing consortium, Nature 401:921-923, 1999).
  • major histocompatibility complex and “MHC” also refer to the polymorphic glycoproteins encoded by the MHC class I or class II genes, where appropriate in the context, and proteins comprising variants thereof that bind MHC-presentable peptides (e.g., class I or class II peptides).
  • a class I MHC binds an MHC-presentable peptide in a groove formed by its ⁇ 1 domain and ⁇ 2 domain
  • a class II MHC binds an MHC-presentable peptide in a groove formed by its ⁇ 1 domain and ⁇ 1 domain.
  • soluble MHC refers to an extracellular fragment of an MHC comprising corresponding ⁇ 1 and ⁇ 2 domains that bind a class I MHC-presentable peptide or corresponding ⁇ 1 and ⁇ 1 domains that bind a class II MHC-presentable peptide, where the ⁇ 1 and ⁇ 2 domains or the ⁇ 1 and ⁇ 1 domains are derived from a naturally occurring MHC or a variant thereof.
  • pharmaceutical composition refers to the combination of an active agent with a carrier (e.g., a pharmaceutically acceptable carrier), inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo or ex vivo.
  • the term “pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, emulsions (e.g., such as an oil/water or water/oil emulsions), and various types of wetting agents.
  • the compositions also can include stabilizers and preservatives.
  • stabilizers and adjuvants see e.g., Adejare, Remington, The Science and Practice of Pharmacy (23rd Ed. 2020).
  • presentation agent refers to an agent (e.g., a cell or particle) that can bind a plurality of peptide-MHC complexes (e.g., a plurality of the same peptide-MHC complexes) for recognition by a TCR, e.g., a TCR expressed by a T cell.
  • Presentation agents include but are not limited to APCs (e.g., dendritic cells or macrophages), artificial APCs (e.g., engineered cells, nanoparticles, or liposomes), and multimerization domains linked to peptide- MHC complexes.
  • the terms “prime” and “priming,” in the context of antigen-presenting cells and T cells, refers to na ⁇ ve T cell clonal expansion, activation, and/or generation of memory T cells as a result of TCR engagement by a peptide presented by an MHC on an outer surface of an antigen-presenting cell.
  • the terms “subject” and “patient” are used interchangeably and refer to an organism to be treated by the methods and compositions described herein. Such organisms preferably include, but are not limited to, mammals (e.g., murines, simians, equines, bovines, porcines, canines, felines, and the like), and more preferably include humans.
  • target cell refers to a cell that can be targeted by a delivery agent.
  • a target cell may have a cell surface receptor (e.g., a TCR) that can be bound by the delivery agent, e.g., via a ligand present on the delivery agent that binds the cell surface receptor.
  • a target cell may be located in a specific tissue or organ (e.g., liver, lymph nodes, or spleen) that the delivery agent is enriched in or delivered to.
  • a target cell may comprise, e.g., an immune cell (e.g., dendritic cell or macrophage).
  • a cell composition is “substantially free” of a specified type of cells if this type of cells does not exceed 0.1%, 0.01%, or 0.001% of the total amount of cells in the composition.
  • the percentage of each cell type in a cell composition can be determined using a method known in the art. For example, immune cells are often characterized by cell type-specific markers (e.g., cell surface markers) and the amount of each cell type can be determined by flow cytometry.
  • the term “MHC-presentable peptide” refers to a peptide of an antigen protein presentable by a class I or class II MHC and do not encompass the full-length antigens or any isoforms thereof.
  • Peptides presentable by class I MHC proteins are typically 8-11 amino acids in length.
  • the peptide is located in the peptide-binding groove of the central region of the ⁇ 1/ ⁇ 2 domains of the class I MHC.
  • T cell peptides presentable by class II MHC proteins are typically 13-25 amino acids (e.g., 15-24 amino acids) in length.
  • the peptide is located in the peptide-binding groove formed by the ⁇ 1/ ⁇ 1 domains of the class II MHC.
  • MHC-presentable peptide can be smaller than the peptide sequences disclosed herein, e.g., eight contiguous amino acids, nine contiguous amino acids, ten contiguous amino acids, 11 contiguous amino acids, 12 contiguous amino acids, 13 contiguous amino acids, or 14 contiguous amino acids of a 15mer peptide disclosed herein (e.g., LWVPGAIGSPSQEAV (SEQ ID NO: 6)).
  • the term “MHC-presentable peptide” can refer to a contiguous amino acid sequence that contains the whole length (i.e., 15mer) of a peptide sequence in Table 1A or Table 1B and/or a contiguous amino acid sequence that can be longer than the peptide sequence disclosed in Table 1A or Table 1B. See Table 3 for example. Therefore, the “MHC-presentable peptide” can include additional amino acids that can be processed by antigen processing pathways to be presented on class I and/or class II MHC proteins.
  • the "MHC- presentable peptide” can include up to 10 additional amino acids at the N terminus and/or up to 10 amino acids at the C terminus of a peptide sequence in Table 1A or Table 1B.
  • the additional amino acids are the naturally occurring amino acids flanking a peptide sequence of Table 1A or Table 1B in an antigen sequence described herein.
  • the additional amino acids comprise a spacer sequence.
  • An MHC-presentable peptide is “immunogenic” if the MHC-presentable peptide activates a T cell and/or stimulates a T cell response in a subject, for example, as measured by the amount of total T cells and/or memory T cells, respectively, reactive to the MHC-presentable peptide.
  • the strength and duration of the T cell response e.g., proliferation or activation
  • Immunogenic MHC-presentable peptides can also be identified in a population of organisms (e.g., humans) with respect to the average strength and duration of T cell response to the peptides.
  • T cell receptor and “TCR” refer to a surface protein (e.g., a heterodimeric protein) of a T cell that allows the T cell to recognize an antigen and/or or a peptide thereof, typically presented by a major histocompatibility complex (MHC) (e.g., an MHC- presentable peptide), or a fragment of such a surface protein comprising at least its variable domains.
  • MHC major histocompatibility complex
  • TCRs are heterodimers comprising two different protein chains.
  • the TCR comprises an alpha ( ⁇ ) chain and a beta ( ⁇ ) chain.
  • Each chain in its native form, typically comprises two extracellular domains, a variable (V) domain and a constant (C) domain, the latter of which is membrane-proximal.
  • the variable domain of ⁇ -chain (V ⁇ ) and the variable domain of ⁇ -chain (V ⁇ ) each comprise three hypervariable regions that are also referred to as the complementarity determining regions (CDRs) such as CDR1, CDR2, and CDR3.
  • the CDRs are primarily responsible for contacting MHC-presentable peptides and thus define the specificity of the TCR, although, under certain circumstances, the CDR1 of the ⁇ -chain can interact with the N-terminal part of the antigen, and CDR1 of the ⁇ -chain interacts with the C- terminal part of the antigen.
  • the term “treating” includes any effect, e.g., lessening, reducing, modulating, ameliorating or eliminating, that results in the improvement of the condition, disease, disorder, and the like, or ameliorating a symptom thereof. It is understood that T1D can be diagnosed by assessing genetic, immunologic, and/or metabolic markers prior to symptomatic onset.
  • the term “treating” also includes prevention of symptomatic onset after observation of the predictive markers.
  • the term “vehicle” refers to an agent (e.g., delivery agent or presentation agent) that can bind or contain a biomolecule (e.g., a peptide, protein, or nucleic acid).
  • a vehicle can deliver a biomolecule to a target cell, tissue, or organ.
  • a vehicle can bind one or more peptide-MHC complexes for recognition by a TCR. It is contemplated that in certain aspects, the vehicle that binds or contains the biomolecule is not naturally occurring.
  • compositions specifying a percentage are by weight unless otherwise specified. Further, if a variable is not accompanied by a definition, then the previous definition of the variable controls.
  • T cell-mediated immune responses are generally employed to kill undesired cells, such as cancer cells and pathogen-infected cells. T cells reactive to autoantigens are generally removed by negative selection in the thymus, an organ that shrinks in adulthood. However, failure to remove autoreactive T cells, among other mechanisms, can lead to T cell attack of healthy cells or tissues, resulting in autoimmune diseases (e.g., T1D).
  • T cell immunity Unlike humoral immune responses, T cell immunity relies on T cell receptor (TCR) recognition of antigenic peptides presented by MHCs. While only particular MHC-presentable peptides of surface proteins allow targeting by neutralizing antibodies, many peptides can serve as targets of T cells. Peptides from antigens delivered endogenously to APCs (e.g., expressed in the APCs) are processed primarily for association with class I MHC. Peptides from antigens delivered exogenously to APCs (e.g., internalized by endosomes) are processed primarily for association with class II MHC. Thus, T cell immunity can be elicited towards antigen proteins having various physiological functions and localizations.
  • TCR T cell receptor
  • Peptides can be presented at different levels on MHC complexes, and this property is referred to herein as "presentability".
  • the presentability of a peptide can be determined by a number of methods comprising Mammalian MHC-presentable peptide Display (MEDi), prediction programs such as NetMHC, Mass Spectrometry, or any combination thereof.
  • MEDi Mammalian MHC-presentable peptide Display
  • peptides (Obermair et al., (2022) Sci. Adv.8, eabl5394)a peptide.
  • a peptide is defined as presentable (i.e., an "MHC-presentable peptide") if the peptide falls in the 50-100% quartile as measured by MEDi.
  • MHC-presentable peptides of a given antigen can be identified or selected by in silico methods, for example, as described in Schaap-Johansen et al., (2021) Front. Immunol. 12:712488 or in vitro experimental methods, for example MEDi, as described in Obermair et al., (2022) Sci. Adv.8, eabl5394. (see, e.g., WO2019197671).
  • these methods generally focus on MHC presentation, whereas the immunogenicity of an MHC-presentable peptide still needs to be determined empirically.
  • Various methods of identifying immunogenic MHC-presentable peptides have been described in the art.
  • MCR peptide-MHC- TCR fusion
  • a method has been developed to identify immunogenic MHC-presentable peptides from a library of peptide-MHC- TCR fusion (MCR) proteins using human-derived T cell receptors (see Kisielow et al., Nat. Immunol. (2019) 20:652–62; WO2016097334).
  • MCR protein includes a peptide, an extracellular domain of an MHC allele, and transmembrane and intracellular domains of a TCR.
  • Reporter T cells are engineered to constitutively express the library of MCR proteins and to express a reporter gene (e.g., GFP) under the control of a TCR-responsive transcription factor (e.g., NFAT).
  • GFP reporter gene
  • NFAT TCR-responsive transcription factor
  • a reporter T cell When contacting the reporter T cells and T cells from a patient sample, a reporter T cell expresses the reporter gene if the peptide and MHC of its MCR protein is recognized by a TCR of a patient T cell.
  • this system can be utilized also for identification of immunongenic MHC-presentable peptides in the library of MCRs that are associated with the disease.
  • this MCR screening platform has identified class I- restricted anti-cancer T cells in HPV positive oropharyngeal cancers (see McInnis et al., (2023) J Immunother Cancer 11:3).
  • MHC-presentable peptides of interest can be used to expand rare populations of MHC-presentable peptide-specific T cells, which allows for the identification of immunogenic and immuno prevalence of T cells at higher throughput relative to methods such as MCR.
  • MCR and autologous APC T cell expansion protocols are able to identify disease-relevant T cells, such as T1D-relevant T cells.
  • the ability of an MHC-presentable peptide to bind T cells can be assessed using a peptide-MHC multimer (e.g., tetramer) including the MHC-presentable peptide.
  • Such multimers incorporating the MHC-presentable peptide, a soluble fragment of MHC, and optionally a marker (e.g., fluorophore or barcode), can be produced by various methods in vitro, for example, as described in Jordan et al., J. Immunol. (2008) 180(1): 188–97, WO2021202727; and WO2021262872. Briefly, a T cell sample can be incubated with a library of peptide-MHC (“pMHC”) complex. The T cells that bind the pMHC can then be isolated and the peptides identified. The method can be conducted in a multiplex manner.
  • pMHC peptide-MHC
  • the method of producing an MHC multimer comprises (a) providing two or more MHC monomers, wherein each monomer comprises a conjugation moiety; (b) providing a multimerization domain, wherein each subunit of the multimerization domain comprises a conjugation moiety; (c) combining the MHC monomers and the multimerization domain under conditions sufficient for covalent conjugation between the MHC monomers and the multimerization domain to produce an MHC multimer.
  • an Enzyme-linked immunosorbent spot (ELISpot) assay can be used to test immunogenicity of a peptide.
  • ELISpot quantitatively measures the frequency of cells secreting cytokine out of a population of cells.
  • the ELISpot Assay is also a form of immunostaining since it is classified as a technique that uses antibodies to detect a protein analyte, with the word "analyte" as used herein, referring to any biological or chemical substance being identified or measured.
  • the ELISpot assay is a FluoroSpot assay.
  • the FluoroSpot assay is a variation of the ELISpot assay.
  • the FluoroSpot Assay uses fluorescence in order to analyze multiple analytes, meaning it can detect the secretion of more than one type of protein.
  • the ELISpot assay comprises the following steps. Cytokine specific monoclonal antibodies are first added to the wells of a plate. Next, the desired cells being observed and analyzed (e.g., T cells) are added to the wells and are subsequently treated with a potentially immune stimulating element (e.g., a candidate peptide), and cytokine secretion is measured.
  • a potentially immune stimulating element e.g., a candidate peptide
  • cytokine from activated cells will bind to antibody adjacent to the activated cell.
  • biotinylated cytokine-specific detection antibodies are then added to the well, followed by streptavidin-enzyme conjugation.
  • a substrate is then added to the wells, and is catalyzed by the enzyme conjugate forming an insoluble precipitate in the wells which form spots.
  • the substrate used in this step will depend on the type of enzyme used in the previous step.
  • the streptavidin enzyme substrate combination comprises streptavidin-ALP (streptavidin and alkaline phosphatase conjugate) and BCIP/NBT-plus (a mixture of 5-bromo-4-chloro-3-indolyl phosphate and nitroblue tetrazolium chloride).
  • the streptavidin enzyme substrate combination comprises streptavidin-HRP (streptavidin and horseradish peroxidase conjugate) and TMB (tetramethylbenzidine). The spots are then quantified manually under a microscope or by an automated ELISpot reader to calculate cytokine secretion.
  • the assay can detect the production of cytokines IFN- ⁇ , IL-2, TNF- alpha, IL-4, IL-5, and IL-13.
  • the first three cytokines are produced by Th1 cells, while the last three are produced by Th2 cells.
  • the production of cytokines as measured by ELISpot suggest the potentially immune stimulating element is immunogenic.
  • One of the challenges to developing T cell-directed T1D therapies is identification of strongly immunogenic MHC-presentable peptides that contribute to T1D pathogenesis and the determination of the frequency of T cells reacting to such MHC-presentable peptides.
  • the present disclosure provides the MHC-presentable peptides set forth in Table 1A, Table 1B, Table 2A, and/or 2B, and compositions comprising these MHC-presentable peptides, that may be useful in T cell-directed T1D therapies.
  • the MHC presentable peptides are presentable by HLA-DQ and/or HLA-DR serotypes.
  • the MHC-presentable peptides are presentable by known T1D-risk associated HLA serotypes, such as, HLA-DQ2, HLA- DQ8, HLA-DR3, and/or HLA-DR4.
  • the MHC-presentable peptides are presentable by known T1D-risk associated HLA haplotypes, such as, HLA-DQ2.5.
  • the MHC-presentable peptides are presentable by known T1D-risk associated HLA alleles, such as, HLA-DQA1, HLA-DQB1, HLA-DRA1, HLA-DRB1, or any combination thereof.
  • MHC-presentable peptides can be further characterized by their immunogenicity as determined by functional assays, such as ELISpot, using primary human CD4 T cells derived from donors expressing HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof.
  • Table 1A Exemplary MHC-presentable Peptides Associated with T1D [0097]
  • one or more of the MHC-presentable peptide sequences in Table 1A are presentale on T1D-risk associated HLA serotypes, such as, HLA-DQ2, HLA-DQ8, HLA-DR3, and/or HLA-DR4.
  • one or more of the MHC-presentable peptide sequences in Table 1A are presentale on T1D-risk associated HLA serotypes, such as, HLA-DQ2.5, HLA-DQ8, and/or HLA-DRB1 (e.g., HLA-DRB1*0401).
  • the MHC-presentable peptide sequences derived from or comprising any one of SEQ ID NO: 6 to SEQ ID NO: 175 and SEQ ID NO: 213 can be presentable on HLA-DQ8.
  • the MHC-presentable peptide sequences derived from or comprising any one of SEQ ID NO: 131 and SEQ ID NO: 176 to SEQ ID NO: 247 are presentable on HLA-DQ2.5. In some aspects, the MHC-presentable peptide sequences derived from or comprising any one of SEQ ID NO: 83 and SEQ ID NO: 176 are presentable on HLA-DRB1, e.g., HLA DRB1*0401. Table 1B. Exemplary MHC-presentable Peptides Associated with T1D.
  • one or more of the MHC-presentable peptide sequences on Table 1B are presentale on T1D-risk associated HLA serotypes, such as, HLA-DQ2, HLA-DQ8, HLA-DR3, and/or HLA-DRB1, e.g., DRB1*0401.
  • the MHC-presentable peptide sequences in Table 1B derived from or comprising any one of SEQ ID NO: 260 and SEQ ID NO: 278 are presentable on HLA-DRB1, e.g., HLA DRB1*0401.
  • Table 2A Exemplary MHC-presentable Peptide 19mers, 25mers, and 31mers. Table 2B.
  • MHC-presentable Peptides identified in at least 60% of donors are generated from selected antigens, e.g., Chromogranin-A (CHGA), Carboxypeptidase A1 (CPA1), C1orf127 protein (C1orf127), Early growth response protein 4 (EGR4), Glutamate decarboxylase 2 (GAD2), Vitamin D-binding protein (GC), Guanine nucleotide-binding protein G(s) subunit alpha isoform XLas (GNAS), Glucose-6-phosphatase 2 (G6PC2 (IGRP)), Insulin (INS), Potassium channel subfamily K member 16 (KCNK16), Kinesin-like protein KIF1A (KIF1A), Neuroendocrine convertase 2 (PCSK2), Pancreas/duodenum homeobox protein 1 (PDX1), Proton-coupled zinc antiport
  • selected antigens e.g., Chromogranin-A (CHGA), Car
  • the MHC-presentable peptide for the present disclosure can be derived from Chromogranin-A (CHGA), which is also known as parathyroid secretory protein 1, CHGA, CGA, chromogranin A, Chromogranin A, PHES, or PHE5.
  • Chromogranin A (CHGA) is found in secretory vesicles of neurons and endocrine cells. Specifically, CHGA is found in islet beta cell secretory granules in the pancreas and induces their generation.
  • CHGA protein is a precursor to three biologically active peptides; vasostatin, pancreastatin, and parastatin.
  • Chromogranin A has been identified as autoantigen in type 1 diabetes and CHGA expression is elevated in patients with pheochromocytomas.
  • a peptide fragment of ChgA located in the Vasostatin-1, namely ChgA29-42 has been identified as the antigenic MHC-presentable peptide recognized by diabetogenic BDC2.5 T cells from type 1 diabetes prone NOD mice.
  • CHGA may also play a role in cancer progression, such as pancreatic cancer and prostate cancer.
  • An exemplary accession number for Chromogranin A is P10645 (length: 457 aa). Additional accession numbers include B2R9E9, Q53FA8, Q6NR84, Q96E84, Q96GL7, Q9BQB5, and G3V2Q7.
  • P10645 (Length: 457) MRSAAVLALLLCAGQVTALPVNSPMNKGDTEVMKCIVEVISDTLSKPSPMPVSQECFETLRGDERILSILR HQNLLKELQDLALQGAKERAHQQKKHSGFEDELSEVLENQSSQAELKEAVEEPSSKDVMEKREDSKEAEKS GEATDGARPQALPEPMQESKAEGNNQAPGEEEEEEEEEEATNTHPPASLPSQKYPGPQAEGDSEGLSQGLVDR EKGLSAEPGWQAKREEEEEEEEEEEEEEEAEAGEEAVPEEEGPTVVLNPHPSLGYKEIRKGESRSEALAVDGAGKPG AEEAQDPEGKGEQEHSQQKEEEEEMAVVPQGLFRGGKSGELEQEEERLSKEWEDSKRWSKMDQLAKELTAE KRLEGQEEEEDNRDSSMKLSFRARAYGFRGPGPQLRRGWRPSSREDSLEAGLPLQ
  • A1 and A2 forms are monomeric proteins with different biochemical properties.
  • Carboxypeptidase A1 is a monomeric pancreatic exopeptidase. It is involved in zymogen inhibition.
  • An exemplary accession number is P15085. Additional accession numbers include A4D1M1, Q53XU0, Q9BS67, Q9UCF2, C9JQ63, C9JUF9, C9JUZ4, and S4R433.
  • P15085 A representative sequence (P15085) of the CPA1 is shown below: P15085 (Length: 419) MRGLLVLSVLLGAVFGKEDFVGHQVLRISVADEAQVQKVKELEDLEHLQLDFWRGPAHPGSPIDVRVPFPS IQAVKIFLESHGISYETMIEDVQSLLDEEQEQMFAFRSRARSTDTFNYATYHTLEEIYDFLDLLVAENPHL VSKIQIGNTYEGRPIYVLKFSTGGSKRPAIWIDTGIHSREWVTQASGVWFAKKITQDYGQDAAFTAILDTL DIFLEIVTNPDGFAFTHSTNRMWRKTRSHTAGSLCIGVDPNRNWDAGFGLSGASSNPCSETYHGKFANSEV EVKSIVDFVKDHGNIKAFISIHSYSQLLMYPYGYKTEPVPDQDELDQLSKAAVTALASLYGTKFNYGSIIK AIYQASGSTIDWTYSQGIKYSFTFELRD
  • C1orf127 is expressed in a variety of tissues, with the highest expression levels found in the stomach and pancreas. It is thought that the protein is excreted to the extracellular matrix and may be involved in development and adult homeostasis of the brain, skeletal muscle, testis, cardiac muscle, and the digestive system.
  • An exemplary accession number is G8JLG8. Additional accession numbers include A0AVG8, A6NKM7, Q5VXJ2, H0YBK5, H3BM07, K7EPZ7, B7ZLG7, B7ZLG9, and Q8N9H9 (and isoform Q8N9H9-2).
  • G8JLG8 The sequence of G8JLG8 (Length: 823) is shown below: MWGSPALAWAVWLACVQPTVFPWSLSFRSDTDKPSSAAEVLTEASSCWTDTVECFSDYMTLWIPRSHVEGL RRWLARTLHLPGTWRSPDHLDSSLAKCGYFLHLASDGDFLFRVQYSACFVQKEKANYRLEIRIFQKGVMGL ERSDRYIMKCPMLRSRLGQESVHCGPMFIQVSRPLPLWRDNRQTPWLLSLRGELVASLEDASLMGLYVDMN ATTVTVQSPRQGLLQRWEVLNTSAELLPLWLVSGHHAYSLEAACPPVSFQPESEVLVHIPKQRLGLVKRGS YIEETLSLRFLRVHQSNIFMVTENKDFVVVSIPAAGVLQVQRCQEVGGTPGTQAFYRVDLSLEFAEMAAPV LWTVESFFQCVGSGTESPASTAALRTTPSPPSPGPE
  • EGR4 Early growth response protein 4
  • EGR4 binds to DNA and is involved in the positive regulation of RNA polymerase II.
  • Diseases associated with EGR4 include Schizophrenia 19 and Neuropathy, Congenital Hypomyelinating 1, Autosomal Recessive.
  • An exemplary accession number is Q05215. Additional accession numbers include B2RAE3, G3V1T5, Q2Z1P5, and A0A0C4DG96.
  • the sequence of Q05215 (Length: 589) is: MAVARGVGSPEPAPPQLYKWGGCGLGEPGSALERRGAAARGRCGRARAPRLPDSFPRGECPKPGARAPRSV RCGEPLPPASPPPARPQAQRARPRAPHSRRRAMLHLSEFSEPDALLVKSTEGCCAEPSAELPRLPARDAPA ATGYPGAGDFLSWALNSCGASGDLADSCFLEGPAPTPPPGLSYSGSFFIQAVPEHPHDPEALFNLMSGILG LAPFPGPEAAASRSPLDAPFPAGSDALLPGPPDLYSPDLGAAPFPEAFWEASPCAGAPSQCLYEPQLSPPD VKPGLRAPPASPALDAVSAFKGPYAPWELLSVGAPGNCGSQGDYQAAPEARFPVIGTKIEDLLSISCPAEL PAVPANRLYPSGAYDAFPLAPGDLGEGAEGLPGLLTPPSGEGGSSGDGGEFLASTQPQLSPLGLRSAAAAD FPKPLVADIPGSSGVAAPPVPPPPPTPFPQAKARRKGRR
  • Glutamate decarboxylase 2 is an enzyme that in humans is encoded by the GAD2 gene. This gene encodes one of several forms of glutamic acid decarboxylase which catalyzes the decarboxylation of glutamate to gamma-aminobutyric acid (GABA). GAD2 encodes the islet specific glutamic acid decarboxylase (GAD65) and has been identified as an autoantibody eliciting an autoreactive T cell response in insulin-dependent diabetes. [0109] An exemplary accession number for GAD2 is Q05329. Additional accession numbers include Q9UD87, A0A3B3IU09, and Q5VZ31.
  • the sequence of Q05329 (Length: 585) is shown below: MASPGSGFWSFGSEDGSGDSENPGTARAWCQVAQKFTGGIGNKLCALLYGDAEKPAESGGSQPPRAAARKA ACACDQKPCSCSKVDVNYAFLHATDLLPACDGERPTLAFLQDVMNILLQYVVKSFDRSTKVIDFHYPNELL QEYNWELADQPQNLEEILMHCQTTLKYAIKTGHPRYFNQLSTGLDMVGLAADWLTSTANTNMFTYEIAPVF VLLEYVTLKKMREIIGWPGGSGDGIFSPGGAISNMYAMMIARFKMFPEVKEKGMAALPRLIAFTSEHSHFS LKKGAAALGIGTDSVILIKCDERGKMIPSDLERRILEAKQKGFVPFLVSATAGTTVYGAFDPLLAVADICK KYKIWMHVDAAWGGGLLMSRKHKWKLSGVERANSVTWNPHKMMGVPLQCSALLVREEGLMQNCN
  • Vitamin D-binding protein belongs to the albumin gene family, together with human serum albumin and alpha-fetoprotein. It is a multifunctional protein found in plasma, ascitic fluid, cerebrospinal fluid and on the surface of many cell types. It is able to bind the various forms of vitamin D including ergocalciferol (vitamin D2) and cholecalciferol (vitamin D3), the 25-hydroxylated forms (calcifediol), and the active hormonal product, 1,25-dihydroxyvitamin D (calcitriol). The major proportion of vitamin D in blood is bound to this protein. It transports vitamin D metabolites between skin, liver and kidney, and then on to the various target tissues.
  • Gc protein-derived macrophage activating factor it is a Macrophage Activating Factor (MAF) that has been tested for use as a cancer treatment that would activate macrophages against cancer cells.
  • MAF Macrophage Activating Factor
  • An exemplary accession number is P02774. Additional accession numbers include B4DPP2, D6RAK8, Q16309, Q16310, Q53F31, Q6GTG1, D6RBJ7, D6RF20, and D6RF35.
  • P02774 (Length: 474) MKRVLVLLLAVAFGHALERGRDYEKNKVCKEFSHLGKEDFTSLSLVLYSRKFPSGTFEQVSQLVKEVVSLT EACCAEGADPDCYDTRTSALSAKSCESNSPFPVHPGTAECCTKEGLERKLCMAALKHQPQEFPTYVEPTND EICEAFRKDPKEYANQFMWEYSTNYGQAPLSLLVSYTKSYLSMVGSCCTSASPTVCFLKERLQLKHLSLLT TLSNRVCSQYAAYGEKKSRLSNLIKLAQKVPTADLEDVLPLAEDITNILSKCCESASEDCMAKELPEHTVK LCDNLSTKNSKFEDCCQEKTAMDVFVCTYFMPAAQLPELPDVELPTNKDVCDPGNTKVMDKYTFELSRRTH LPEVFLSKVLEPTLKSLGECCDVEDSTTCFNAKGPLLKKELSSFIDKGQELCADYSENTFTEY
  • GNAS Guanine Nucleotide binding protein, Alpha Stimulating activity polypeptide
  • GNAS is encoded by the GNAS complex gene locus in humans, which has a highly complex imprinted expression pattern resulting in several transcript isoforms and alternative gene products.
  • GNAS is a key component of G protein-coupled receptor-regulated adenylyl cyclase signal transduction pathways. Traditional G protein-coupled receptor signaling proceeds primarily through Gs ⁇ -long and Gs ⁇ -short, the most abundant, ubiquitously-expressed protein products of this gene.
  • GNAS GNAS-associated diseases and disorders
  • diseases and disorders including Albright hereditary osteodystrophy, psuedohypoparathyroidism type Ia and Ib, pseudopseudohypoparathyroidism, McCune-Albright syndrome, Myxoma, progressive osseous heteroplasia, polyostotic fibrous dysplasia of bone, and some pituitary tumors.
  • An exemplary accession number is Q5JWF2 and the isoform sequences Q5JWF2-2 and Q5JWF2-3.
  • Additional accession numbers include A2A2S3, E1P5G3, O75684, O75685, Q5JW67, A0A0A0MR13, A0A590UJ46, A0A590UJ47, A0A590UJC9, A0A590UJF0, A0A590UJQ9, A0A590UJS2, A0A590UJX3, A0A590UJX6, A0A590UJY2, A0A590UK00, A0A590UK28, A0A7I2V5R6, A0A804HIH4, A0A8I5F5B5, A2A2R6, A2A2S1, B0AZR9, O95467, P84996, P63092, P63092-2, P63092-3, and P63092-4.
  • G6PC2 An exemplary accession number of G6PC2 is Q9NQR9 and isoforms Q9NQR9-2 and Q9NQR9-3.
  • Additional accession numbers include E9PAX2, Q6AHZ0, and C9IYU7.
  • the sequence of Q9NQR9 (Length: 355) is shown below: MDFLHRNGVLIIQHLQKDYRAYYTFLNFMSNVGDPRNIFFIYFPLCFQFNQTVGTKMIWVAVIGDWLNLIF KWILFGHRPYWWVQETQIYPNHSSPCLEQFPTTCETGPGSPSGHAMGASCVWYVMVTAALSHTVCGMDKFS ITLHRLTWSFLWSVFWLIQISVCISRVFIATHFPHQVILGVIGGMLVAEAFEHTPGIQTASLGTYLKTNLF LFLFAVGFYLLLRVLNIDLLWSVPIAKKWCANPDWIHIDTTPFAGLVRNLGVLFGLGFAINSEMFLLSCRG GNNYTLSFRLLCALTSLTILQLYHFLQIPTHEEHLFYVLSFCKSASIPLTVVAFIPYSVHMLMKQSGKKSQ (SEQ ID NO
  • I3WAC9 An exemplary accession number is I3WAC9. Additional accession numbers include P01308, F8WCM5, and Q5EEX2.
  • the sequence of I3WAC9 (Length: 110) is shown below: MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGG PGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN (SEQ ID NO.: 291)
  • Potassium channel subfamily K member 16 (KCNK16) is also known as: KCNK16, K2p16.1, TALK-1, TALK1, potassium two pore domain channel subfamily K member 16.
  • K2P16.1 Potassium channel subfamily K member 16 (K2P16.1) is encoded by the KCNK16 gene.
  • K2P16.1 is a member of the family of potassium channel proteins containing two pore-forming P domains and is predominantly expressed in the pancreas.
  • An exemplary accession number is Q96T55, and the secondary accession numbers include: B5TJL9, Q2M2N9, Q5TCF3, Q6X6Z3, Q6X6Z4, Q6X6Z5, D6RC57, and Q9H591.
  • Several isoforms of KCNK16 are known. One isoform has Accession no.
  • Kinesin-like protein KIF1A (KIF1A) is also known as: KIF1A, ATSV, C2orf20, HSN2C, MRD9, SPG30, UNC
  • Kinesin-like protein is a microtubule motorprotein involved in the transport of vesicles and organelles. KIF1A is highly expressed in neurons and is essential for neuronal survival, but is also lowly expressed in the heart, testes, pancrease, adrenal glands, and pituitary glands. KIF1A-mediated anterograde axonal transport is of critical importance for the development and maintenance of the nervous system. Mutations in KIF1A have been identified as associated with Hereditary Spastic Paraplegia (HSP), Nonsyndromic Intellectual Disability (NID), and Hereditary Sensory and Autonomic Neuropathy type II (HSAN II). An exemplary accession number is Q12756.
  • HSP Hereditary Spastic Paraplegia
  • NID Nonsyndromic Intellectual Disability
  • HSAN II Hereditary Sensory and Autonomic Neuropathy type II
  • Additional accession numbers include: B0I1S5, F5H045, O95068, Q13355, Q14752, Q2NKJ6, Q4LE42, Q53T78, Q59GH1, Q63Z40, Q6P1R9, Q7KZ57, A0A3B3IT28, A0A3B3ITE5, A0A3B3ITF7, A0A3B3ITK3, A0A3B3ITW4, A0A3B3ITW6, A0A3B3IU40, A0A3B3IUA1, A0A3F2YNW9, A0A6Q8PFJ8, A0A6Q8PFL2, A0A6Q8PFR1, A0A6Q8PFR5, A0A6Q8PGE4, A0A6Q8PGW8, A0A6Q8PH56, A0A6Q8PHQ5, C9JBH1, H7C0K6, H7C3Y8 and A0A6Q8PFE9.
  • PCSK2 Protein convertase 2
  • PCSK2 is a serine protease and proprotein convertase responsible for the first step in the maturation of many neuroendocrine peptides.
  • PCSK2 is involved in the conversion of proinsulin to insulin intermediates, and in glucagon biosynthesis.
  • Diseases associated with PCSK2 include Mahvash Disease and Insulinoma. Additionally, genetic polymorphisms in PCSK2 have been identified as risk alleles for Type 2 Diabetes.
  • An exemplary accession number is P16519 and isoforms P16519-2 and P16519-3.
  • accession numbers include: B1ANH9, B4DFQ3, Q14927, Q5JYQ1, Q8IWA8, Q9NQG3, Q9NUG1, or Q9UJC6.
  • the sequences for P16519 and isoforms P16519-2 and P16519- 3 areshown below: P16519 (Length: 638) MKGGCVSQWKAAAGFLFCVMVFASAERPVFTNHFLVELHKGGEDKARQVAAEHGFGVRKLPFAEGLYHFYH NGLAKAKRRRSLHHKQQLERDPRVKMALQQEGFDRKKRGYRDINEIDINMNDPLFTKQWYLINTGQADGTP GLDLNVAEAWELGYTGKGVTIGIMDDGIDYLHPDLASNYNAEASYDFSSNDPYPYPRYTDDWFNSHGTRCA GEVSAAANNNICGVGVAYNSKVAGIRMLDQPFMTDIIEASSISHMPQLIDIYSASWGPTDNGKTVDGPREL TL
  • Pdx1 is necessary for pancreatic development, including ⁇ -cell maturation, and duodenal differentiation.
  • Pdx1 is expressed by a population of cells in the posterior foregut region of the definitive endoderm, and Pdx1+ epithelial cells give rise to the developing pancreatic buds, and eventually, the whole of the pancreas—its exocrine, endocrine, and ductal cell populations.
  • Pancreatic Pdx1+ cells first arise at mouse embryonic day 8.5-9.0 (E8.5-9.0), and Pdx1 expression continues until E12.0-E12.5.
  • Soluble carrier family 30 member 8 is a zinc transporter involved in insulin secretion.
  • SLC30A8 is critical for the accumulation of zinc into beta cell secretory granules and the maintenance of insulin stored as tightly packaged hexamers. Twelve variants of the SLC30A8 gene have been identified as associated with increased risk of developing Type 2 diabetes. However, loss-of-function mutations appear to greatly reduce the risk of diabetes.
  • An exemplary accession number for SLC30A8 is Q8IWU4 and isoform Q8IWU4-2. Additional accession numbers include A0AVP9, A5YM39, B4DPE0, Q8TCL3, A0A096LNR0, A0A096LPF3, and E5RG87.
  • the composition comprises (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, or at least 15 amino acids of one or more MHC-presentable peptide sequences set forth in Table 1A or Table 1B (or for example, Table 2A (15mer) or Table 2B), or (ii) the amino acid sequence comprising an MHC-presentable peptide which comprises at least 8 amino acids, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, or at least 15 amino acids of one or more MHC-presentable peptide sequence set forth in Table 1A or Table 1B (or for example, Table 2A (15mer) or Table 2B).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 45.
  • the disclosure comprises a composion comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 46, SEQ ID NO: 47, or SEQ ID NO: 48, or (ii) the amino acid sequence comprising the MHC- presentable peptide which comprises, consists essentially of, or consists of the at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 46.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 46 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 49.
  • the disclosure comprises a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 50, SEQ ID NO: 51, or SEQ ID NO: 52, or (ii) the amino acid sequence comprising the MHC- presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 50.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 50 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 53.
  • the disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 54, SEQ ID NO: 55, or SEQ ID NO: 56, or (ii) the amino acid sequence comprising the MHC- presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 54.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 54 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence as set forth in SEQ ID NO: 57.
  • the disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 58, SEQ ID NO: 59, or SEQ ID NO: 60, or (ii) the amino acid sequence comprising the MHC- presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 58.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 58 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence set forth in SEQ ID NO: 61.
  • the disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 62, SEQ ID NO: 63, or SEQ ID NO: 64, or (ii) the amino acid sequence comprising the MHC- presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 62 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises, consists essentially of, or consists of the MHC- presentable peptide sequence set forth in SEQ ID NO: 65.
  • the disclosure provides a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of an MHC-presentable peptide sequence as set forth in SEQ ID NO: 66, SEQ ID NO: 67, or SEQ ID NO: 68, or (ii) the amino acid sequence comprising the MHC- presentable peptide which comprises, consists essentially of, or consists of at least 8 amino acids (or at least 13 amino acids, e.g., 13, 14, or 15 amino acids) of the MHC-presentable peptide sequence.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 66.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 66 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 70.
  • the MHC-presentable peptide in the amino acid sequence comprises at least 9 amino acids, at least 10 amino acids, at least 11 amino acids, at least 12 amino acids, at least 13 amino acids, at least 14 amino acids, or at least 15 amino acids of the MHC-presentable peptide sequence as set forth in SEQ ID NO: 74.
  • the MHC-presentable peptide in the amino acid sequence comprises the MHC-presentable peptide sequence set forth in SEQ ID NO: 74 and further comprises (i) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the N terminus, (ii) one amino acid, two amino acids, three amino acids, four amino acids, five amino acids, six amino acids, seven amino acids, eight amino acids, nine amino acids, or ten amino acids at the C terminus, or (iii) both (i) and (ii).
  • any MHC-presentable peptides described herein are capable of inducing a tolerizing immune response against Type I diabetes in a subject in need thereof.
  • the amino acid sequences comprising these MHC-presentable peptides are recognized herein as T1D-risk-associated peptides.
  • compositions comprising one or more of such MHC-presentable peptides or nucleotide sequence encoding the MHC-presentable peptides.
  • one or more of the MHC-presentable peptides in the amino acid sequence is less than 36 amino acids, less than 35 amino acids, less than 34 amino acids, less than 33 amino acids, less than 32 amino acids, less than 31 amino acids, less than 30 amino acids, less than 29 amino acids, less than 28 amino acids, less than 27 amino acids, less than 26 amino acids, less than 25 amino acids, less than 24 amino acids, less than 23 amino acids, less than 22 amino acids, less than 21 amino acids, less than 20 amino acids, less than 19 amino acids, less than 18 amino acids, less than 17 amino acids, less than 16 amino acids, less than 15 amino acids, less than 14 amino acids, less than 13 amino acids, less than 12 amino acids, less than 11 amino acids, less than 10 amino acids, or less than 9 amino acids.
  • all MHC- presentable peptides in the amino acid sequence consist of 9 amino acids, 10 amino acids, 11 amino acids, 12 amino acids, 13 amino acids, 14 amino acids, 15 amino acids, 16 amino acids, 17 amino acids, 18 amino acids, 19 amino acids, 20 amino acids, 21 amino acids, 22 amino acids, 23 amino acids, 24 amino acids, 25 amino acids, 26 amino acids, 27 amino acids, 28 amino acids, 29 amino acids, 30 amino acids, 31 amino acids, 32 amino acids, 33 amino acids, 34 aminio acids, or 35 amino acids.
  • one or more MHC-presentable peptides in the amino acid sequence have 8-35 amino acids, 9-35, 10-35, 11-35, 12-35, 13-35, 14-35, 15-35, 8-34, 9-34, 10-34, 11-34, 12-34, 13-34, 14-34, 15-34, 8-33, 9-33, 10-33, 11-33, 12-33, 13-33, 14-33, 15-33, 8-32, 9-32, 10- 32, 11-32, 12-32, 13-32, 14-32, 15-32, 8-31, 9-31, 10-31, 11-31, 12-31, 13-31, 14-31, or 15-31 amino acids.
  • all MHC-presentable peptides in the amino acid sequence have 8-35 amino acids, 9-35, 10-35, 11-35, 12-35, 13-35, 14-35, 15-35, 8-34, 9-34, 10-34, 11-34, 12-34, 13- 34, 14-34, 15-34, 8-33, 9-33, 10-33, 11-33, 12-33, 13-33, 14-33, 15-33, 8-32, 9-32, 10-32, 11-32, 12-32, 13-32, 14-32, 15-32, 8-31, 9-31, 10-31, 11-31, 12-31, 13-31, 14-31, or 15-31 amino acids.
  • the amino acid sequence further comprises a second MHC-presentable peptide that is heterologous to the MHC-presentable peptide.
  • the second MHC- presentable peptide is an MHC-presentable peptide disclosed herein. In some aspects the second MHC-presentable peptide is not disclosed herein.
  • the second MHC-presentable peptide is derived from an antigen selected from the group consisting of Chromogranin-A (CHGA), Carboxypeptidase A1(CPA1), C1orf127 protein (C1orf127), Early growth response protein 4 (EGR4), Glutamate decarboxylase 2 (GAD2), Vitamin D-binding protein (GC), Guanine nucleotide-binding protein G(s) subunit alpha isoform XLas (GNAS), Glucose-6-phosphatase 2 (G6PC2 (IGRP)), Insulin (INS), Potassium channel subfamily K member 16 (KCNK16), Kinesin- like protein KIF1A (KIF1A), Neuroendocrine convertase 2 (PCSK2), Pancreas/duodenum homeobox protein 1 (PDX1), Proton-coupled zinc antiporter SLC30A8 (SLC30A8), and any combination thereof.
  • CHGA Chromogranin-A
  • the amino acid sequence further comprises a third MHC-presentable peptide, a fourth MHC-presentable peptide, a fifth MHC-presentable peptide, a sixth MHC- presentable peptide, a seventh MHC-presentable peptide, a ninth MHC-presentable peptide, a tenth MHC-presentable peptide, an 11 th MHC-presentable peptide, a 12 th MHC-presentable peptide, a 13 th MHC-presentable peptide, a 14 th MHC-presentable peptide, a 15 th MHC-presentable peptide, a 16 th MHC-presentable peptide, a 17 th MHC-presentable peptide, an 18 th MHC-presentable peptide, a 19 th MHC-presentable peptide, a 20 th MHC-presentable peptide, a 21 st MHC-presentable peptide, a
  • any one of the additional MHC-presentable peptides comprises at least eight amino acids of one or more MHC-presentable peptide sequences in Tables 1A, 1B, 2A, 2B, and/or 3.
  • the amino acid sequence encoded by the nucleotide sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 26, SEQ ID NO: 30, SEQ ID NO: 34, SEQ ID NO: 38, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 54, SEQ ID NO: 54, SEQ ID NO: 58, and/or SEQ ID NO: 62 in any order.
  • the amino acid sequence encoded by the nucleotide sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 7, SEQ ID NO: 11, SEQ ID NO: 15, SEQ ID NO: 19, SEQ ID NO: 23, SEQ ID NO: 27, SEQ ID NO: 31, SEQ ID NO: 35, SEQ ID NO: 39, SEQ ID NO: 43, SEQ ID NO: 47, SEQ ID NO: 51, SEQ ID NO: 55, SEQ ID NO: 59, and/or SEQ ID NO: 65 in any order.
  • the amino acid sequence encoded by the nucleotide sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 8, SEQ ID NO: 12, SEQ ID NO: 16, SEQ ID NO: 20, SEQ ID NO: 24, SEQ ID NO: 28, SEQ ID NO: 32, SEQ ID NO: 36, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, and/or SEQ ID NO: 66 in any order.
  • the amino acid sequence encoded by the nucleotide sequence comprises the MHC-presentable peptide sequences as set forth in SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 17, SEQ ID NO: 21, SEQ ID NO: 25, SEQ ID NO: 29, SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 41, SEQ ID NO: 45, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 57, SEQ ID NO: 61, and/or SEQ ID NO: 67 in any order.
  • an amino acid sequence comprising variants of the MHC- presentable peptides, or a nucleotide sequence encoding the amino acid sequence.
  • an amino acid sequence, or a nucleotide sequence encoding the amino acid sequence can comprise an MHC-presentable peptide that differs by 1, 2, or 3 amino acids (e.g., substitutions, insertions, or deletions) relative to an MHC-presentable peptide disclosed herein.
  • a composition can comprise an amino acid sequence comprising an MHC-presentable peptide set forth in Tables 1 and/or 2, with the N-terminal or C-terminal amino acid deleted, or a nucleotide sequence encoding the amino acid sequence.
  • Such variants can be derived from, for example, mutant forms of the respective antigens that may be present in the human population.
  • MHC-presentable peptides are typically anchor residues forming a core sequence fitting to the binding groove of the MHC.
  • a skilled person in the art would be able to modify the amino acid sequences of an MHC-presentable peptide disclosed herein, by maintaining the known anchor residues, and determine whether such variants maintain the ability to bind the MHC.
  • the MHC anchor residues can be modified to improve binding of the peptide to the MHC, without affecting the remaining residues that interact with the cognate TCR.
  • amino acid sequences or nucleotide sequence encoding the amino acid sequence comprising the MHC-presentable peptides disclosed herein or their variants are useful for stimulating T cell immune responses in vitro, ex vivo, or in vivo.
  • the amino acid sequence encoded by the nucleotide sequence of the disclosure comprising an MHC-presentable peptide set forth in Table 1A, Table 1B, Table 2A, Table 2B and Table 3, or a variant of such MHC-presentable peptide is no more than 35 amino acids, no more than 30 amino acids, no more than 25 amino acids, no more than 20 amino acids, no more than 19 amino acids, no more than 18 amino acids, no more than 17 amino acids, no more than 16 amino acids, no more than 15 amino acids, or no more than 14 amino acids, in length.
  • the amino acid sequence encoded by the nucleotide sequence of the disclosure does not comprise more than 100 (e.g., more than 90, more than 80, more than 70, more than 60, more than 50, more than 40, more than 30, more than 25, more than 20, more than 19, more than 18, more than 17, more than 16, more than 15, more than 14, more than 13, more than 12, more than 11, more than 10, more than 9, or more than 8) contiguous amino acids of an antigen set forth in Tables 1A, 1B, 2A, 2B, and/or 3.
  • the amino acid sequence encoded by the nucleotide sequence of the disclosure comprises at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, or 100% of the entire length of the corresponding antigen.
  • an amino acid sequence encoded by the nucleotide sequence of the disclosure comprises two or more MHC-presentable peptides of the same antigen.
  • the two or more MHC-presentable peptides are partially overlapping, and the amino acid sequence encoded by the nucleotide sequence of the disclosure comprises the entire sequences of the two or more MHC-presentable peptides aligned.
  • the amino acid sequence encoded by the nucleotide sequence of the disclosure comprises an MHC-presentable peptide presentable by a class II MHC. In some aspects, the amino acid sequence encoded by the nucleotide sequence of the disclosure comprises a T cell MHC-presentable peptide presentable by a class I MHC. In some aspects, the amino acid sequence encoded by the nucleotide sequence of the disclosure comprises an MHC-presentable peptide presentable by a class II MHC and an MHC-presentable peptide presentable by a class I MHC.
  • an amino acid sequence encoded by the nucleotide sequence of the disclosure may further comprise a moiety (e.g., an amino acid sequence) that improves one or more characteristics of the MHC-presentable peptide or its manufacture or function.
  • the amino acid sequence (or a nucleotide sequence encoding the same) further comprises an amino acid sequence (or a nucleotide sequence) that facilitates delivery of the MHC-presentable peptide into an APC.
  • the amino acid sequence encoded by a nucleotide sequence of the disclosure comprises a cell penetrating peptide, which facilitates cell uptake in a manner that does not require a cell membrane protein.
  • the amino acid sequence encoded by a nucleotide sequence of the disclosure comprises a lipidation moiety, for example, to improve the half-live of the amino acid sequence.
  • Exemplary cell penetrating peptides are disclosed in the CPPsite 2.0 database (crdd.osdd.net/raghava/cppsite/), which includes more than 1,000 unique cell penetrating peptides.
  • the amino acid sequence encoded by a nucleotide sequence of the disclosure further comprises a binding moiety (e.g., an antibody or an antigen-binding fragment thereof) that targets an APC (e.g., professional APC).
  • a binding moiety e.g., an antibody or an antigen-binding fragment thereof
  • APC e.g., professional APC
  • targets of such binding moiety include CD11b, CD11c, CD18, CD24, CD1a, CD206, DC inhibitory receptor 2 (DCIR2), and DEC205.
  • the amino acid sequence encoded by a nucleotide sequence of the disclosure further comprises a moiety that improves immunogenicity of the MHC-presentable peptide.
  • the amino acid sequence encoded by a nucleotide sequence of the disclosure further comprises a heat shock protein-binding motif (see WO2019210055A2).
  • Amino acid sequences encoded by a nucleotide sequence of the disclosure can be synthesized by the translation machinery (optionally in combination of transcription machinery) of a cell either in the cell or in vitro.
  • an amino acid sequence and/or a nucleotide sequence of the disclosure can be chemically synthesized.
  • the amino acid sequence is modified or comprises a non-germline encoded peptide, for example, to comprise or mimic a post-translational modification (PTM) of the antigen protein when expressed in an APC.
  • PTM post-translational modification
  • Modified amino acid sequence comprise, but are not limited, to post-translational modifications (PTMs) and other non- germline encoded peptides as reviewed in (Mannering et al., (2019) Diabetologia 62:351-356, Doyle et al., (2014) Autoimmunity 47:220-233), such as defective ribosomal products (Kracht et al., (2017) Nat Med 23:501-507), peptide fusions (Babon et al., (2016) Nat Med 22:1482-1487, Delong et al., (2016) Science 351:711-714), amino acid substitutions or changes such as arginine to citrulline or deamidation (Babon et al., (2016) Nat Med 22:1482-1487, McLaughlin et al.,(2016) Clin Exp Immunol 185:133-140) that have been shown to be antigenic MHC-presentable peptides in Type I diabetes or other T cell-based studies.
  • modified peptides include vicinal disulfide bond (Mannering et al.,(2005) J Exp Med 202:1191-1197), glutamine to glutamic acid conversion (Lummel et al.,(2014) Diabetes 63:237-247), arginine to citrulline (Babon et al.,(2016) Nat Med 22:1482-1487, Azoury et al.,(2021) Diabetes 70:2879-2891), chlorination (Sidney et al.,(2018) BMC Immunol 19:12), oxidation (Sidney et al.,(2018) BMC Immunol 19:12), deamidation (Sidney et al.,(2018) BMC Immunol 19:12), alternative splicing (Jong et al.,(2013) Diabetologia 56:2651- 2658), carbonylation (Yang et al.,(2017) Antioxid Redox Signal 29:1415-1431), aspart
  • composition e.g., pharmaceutical composition
  • a composition comprising a plurality of different amino acid sequences or a plurality of different nucleotide sequences encoding the MHC-presentable peptides disclosed herein.
  • the composition comprises two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, 15 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 150 or more, 200 or more, or 300 or more different amino acid sequences comprising MHC-presentable peptides disclosed herein or nucleotide sequences encoding MHC-presentable peptides disclosed herein.
  • the composition comprises 5-500, 5-400, 5-300, 5-200, 5-150, 5-100, 5-90, 5-80, 5- 70, 5-60, 5-50, 5-40, 5-30, 5-20, 5-10, 10-500, 10-400, 10-300, 10-200, 10-150, 10-100, 10-90, 10- 80, 10-70, 10-60, 10-50, 10-40, 10-30, 10-20, 20-500, 20-400, 20-300, 20-200, 20-150, 20-100, 20-90, 20-80, 20-70, 20-60, 20-50, 20-40, 20-30, 30-500, 30-400, 30-300, 30-200, 30-150, 30-100, 30-90, 30-80, 30-70, 30-60, 30-50, 30-40, 40-500, 40-400, 40-300, 40-200, 40-150, 40-100, 40- 90, 40-80, 40-70, 40-60, 40-50, 50-500, 50-400, 50-300, 50-200, 50-150, 50-100, 50-90, 50-80, 50-70
  • the composition comprises a first amino acid sequence comprising an MHC-presentable peptide presentable by a class II MHC and a second amino acid sequence comprising an MHC-presentable peptide presentable by a class II MHC, optionally wherein the first and second amino acid sequence are different.
  • the composition comprises a first amino acid sequence comprising an MHC-presentable peptide presentable by a class II MHC and a second amino acid sequence comprising an MHC-presentable peptide presentable by a class I MHC, optionally wherein the first and second amino acid sequence are different.
  • a composition comprising a nucleotide sequence or an amino acid sequence disclosed herein, when presented by cognate MHC(s), is capable of stimulating a T cell response, for example, enhancing survival, proliferation, activation, and/or memory formation of one or more T cells, in a T cell population obtained from a subject (e.g., peripheral blood mononuclear cells from a human subject) under ex vivo or in vivo conditions.
  • a subject e.g., peripheral blood mononuclear cells from a human subject
  • the peptide is capable of stimulating a CD4 + T cell response.
  • the peptide- MHC complex can be a soluble complex, immobilized on a solid surface (e.g., bead or nanoparticle), or presented on the surface of an APC. Viability of T cells can be assessed by methods known in the art such as cell counting or dye exclusion assays (e.g., with trypan blue or propidium iodide).
  • Clonal T cell proliferation can be assessed by methods known in the art such as carboxyfluorescein succinimidyl ester (CFSE) dilution assay, Ki-67 staining, tritiated thymidine incorporation, BrdU incorporation (see Gratzner, Science (1982) 218(4571):474-75), or quantitation of ATP levels (e.g., with CellTiter-Glo Cell Viability assay).
  • CFSE carboxyfluorescein succinimidyl ester
  • T cell activation can be assessed by methods known in the art such as staining for cell surface markers (e.g., upregulation of CD69, CD27, CD137, CD154, CD25, CD44, or CD107a, or downregulation of CD62L or CCR7) or cytokines (e.g., IFN ⁇ or TNF ⁇ ) or detecting secretion of cytokine proteins (e.g., IFN ⁇ or TNF ⁇ ) or proteins associated with cytolytic activity (e.g., GranzymeB or Perforin).
  • Memory T cell formation can be assessed by methods known in the art such as staining for cell surface markers (e.g., CD45RO, CD95, Sca1, CD62L, CD27, CD127, and CD44).
  • the composition is capable of enhancing survival, proliferation, activation, and/or memory formation of both CD8 + and CD4 + T cells.
  • the composition that is administered according to the disclosed methods further comprises an immunomodulator.
  • immunomodulators are disclosed elsewhere herein.
  • Nucleic acids encoding for the amino acid sequence and MHC-presentable peptides disclosed herein can be useful for treating and preventing T1D in a subject. Where the peptides or polypeptides constitute a fragment of the complete antigen protein, such tolerogenic nucleic acid compositions are also known as minigene vaccines.
  • At least one nucleotide sequence of the composition encodes a plurality of different peptides.
  • the nucleotide sequence can be engineered to insert protease cleavage sites and/or ribosomal skipping elements between the MHC-presentable peptides, such that the encoded MHC-presentable peptides are processed to produce separate MHC-presentable peptides.
  • Such polynucleotide constructs, also called “strings,” are useful as tolerogenic compositions (see, e.g., Velders et al., J. Immunol. (2001) 166:5366-73; Schubert et. al., Genome Medicine (2016) 8:9).
  • string construct or “string polynucleotide” used herein refers to a construct or a polynucleotide sequence that contains at least two MHC-presentable peptides and at least one cleavable linker between the two MHC-presentable peptides so that the translated product results in two MHC-presentable peptides separate from each other.
  • string polypeptide or “string amino acid sequence” used herein refers to an amino acid sequence that can be translated by a string construct or a string polynucleotide, but those string amino acid sequences may not be the translated product of the string polynucleotide because the cleavable linker(s) may have been cleaved during the translation or right after the translation, and the amino acid sequences may now be two sequences, each comprising one MHC-presentable peptide.
  • the composition comprises one or more polynucleotide constructs that encode one or more of the MHC-presentable peptides disclosed herein with one or more protease cleavage sites and/or ribosomal skipping elements between the MHC-presentable peptides. Both coding and non-coding strands can be incorporated into the composition.
  • the string refers to a polynucleotide chain that encodes a plurality of the MHC-presentable peptides in tandem.
  • the string encodes 2 to 100, 2 to 90, 2 to 80, 2 to 70, 2 to 60, 2 to 50, 2 to 40, 2 to 30, 2 to 20, 2 to 10, 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60, 10 to 50, 10 to 40, 10 to 30, 10 to 20, 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 20 to 30, 50 to 100, 50 to 90, 50 to 80, 50 to 70, or 50 to 60 peptides.
  • a string polynucleotide chain encodes a string amino acid sequence as disclosed in the following formula: E1-L1-E2-L2-E3-L3-E4-L4-E5-L5-E6-L6-E7-L7-E8-L8-E9-L9-E10 (I); E1-L1-E2-L2-E3-L3-E4-L4-E5-L5-E6-L6-E7-L7-E8-L8-E9-L9-E10-L10-E11 (II); E1-L1-E2-L2-E3-L3-E4-L4-E5-L5-E6-L6-E7-L7-E8-L8-E9-L9-E10-L10-E11-L11-E12 (III); E1-L1-E2-L2-E3-L3-E4-L4-E5-L5-E6-E7-L7-E
  • each MHC- presentable peptide in the string amino acid sequence is unique (different from each other).
  • all linkers are the same in the string amino acid sequence.
  • some linkers are different from each other.
  • the composition comprises (i) a string nucleotide sequence that encodes an amino acid sequence comprising one MHC-presentable peptide comprising at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 35 amino acids of one MHC-presentable peptide selected from the MHC- presentable peptides in Table 1A, Table 1B, Table 2A (15mer), or Table 2B (for example see Table 2A (19mer, 25mer, or 31mer) and Table 3)and another MHC-presentable peptide comprising at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 35 amino acids of one MHC-presentable peptide
  • the composition comprises (i) a string nucleotide sequence that encodes an amino acid sequence comprising at least three MHC-presentable peptides, at least four MHC-presentable peptides, at least five MHC-presentable peptides, at least six MHC-presentable peptides, at least seven MHC-presentable peptides, at least eight MHC- presentable peptides, at least ten MHC-presentable peptides, wherein at least one, two, three, four, five, six, seven, eight, nine, or ten of the MHC-presentable peptides comprieses at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, or at least 35 amino acids of one MHC-presentable peptide selected from the MHC-presentable peptides in Table 1A, Table 1B
  • the composition comprises (i) a string nucleotide sequence that encodes an amino acid sequence comprising about ten to about 30 MHC-presentable peptides (e.g., 10 to 20 MHC-presentable peptides, 10 to 25 MHC-presentable peptides, 15 to 20 MHC- presentable peptides, 15 to 25 MHC-presentable peptides, or 20 to 30 MHC-presentable peptides), wherein one or more, or all of the MHC-presentable peptides comprise at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, or at least 35 amino acids of the MHC-presentable peptides in Table 1A, Table 1B, Table 2A (15mer), or Table 2B (for example see Table 2A (19mer, 25mer, or 31mer) and Table 3).
  • the composition comprises (i) a string nucleotide sequence that encodes an amino acid sequence comprising about ten to about 30 MHC-presentable peptides (e.g., 10 to 20 MHC-presentable peptides, 10 to 25 MHC-presentable peptides, 15 to 20 MHC- presentable peptides, 15 to 25 MHC-presentable peptides, or 20 to 30 MHC-presentable peptides), wherein one or more, or all of the MHC-presentable peptides comprises at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, or at least 35 amino acids of the MHC-presentable peptides in Table 1A, Table 1B, Table 2A (15mer), or Table 2B (for example see Table 2A (19mer, 25mer, or 31mer) and Table 3).
  • the composition comprises (i) a string nucleotide sequence that encodes an amino acid sequence comprising about ten to about 30 MHC-presentable peptides (e.g., 10 to 20 MHC-presentable peptides, 10 to 25 MHC-presentable peptides, 15 to 20 MHC- presentable peptides, 15 to 25 MHC-presentable peptides, or 20 to 30 MHC-presentable peptides), wherein one or more of the MHC-presentable peptides comprise at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, or at least 35 amino acids of the MHC-presentable peptides in Table 1A, Table 1B, Table 2A (15mer), or Table 2B (for example see Table 2A (19mer, 25mer, or 31mer) and Table 3), and wherein
  • one or more of the heterologous MHC-presentable peptides are derived from an antigen known to be associated with T1D.
  • one or more of the heterologous MHC-presentable peptides are derived from Chromogranin-A (CHGA), Carboxypeptidase A1(CPA1), C1orf127 protein (C1orf127), Early growth response protein 4 (EGR4), Glutamate decarboxylase 2 (GAD2), Vitamin D-binding protein (GC), Guanine nucleotide-binding protein G(s) subunit alpha isoform XLas (GNAS), Glucose-6-phosphatase 2 (G6PC2 (IGRP)), Insulin (INS), Potassium channel subfamily K member 16 (KCNK16), Kinesin-like protein KIF1A (KIF1A), Neuroendocrine convertase 2 (PCSK2), Pancreas/duodenum homeobox protein 1 (PDX1), Pro
  • CHGA Ch
  • the peptides are arranged on a string to maximize recognition by HLA- DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof.
  • the MHC- presentable peptide-coding sequences in a string construct are flanked by one or more sequences selected for better cleavability for peptide presentation by MHCs, better expression, and/or improved translation in a cell in a subject.
  • the flanking sequences may comprise ribosomal skipping elements such as a T2A, P2A, F2A, or E2A sequence.
  • the one or more cleavage sequences are selected from the group consisting of FRAC (SEQ ID NO: 367), KRCF (SEQ ID NO: 368), KKRY (SEQ ID NO: 369), ARMA (SEQ ID NO: 370), RRSG (SEQ ID NO: 371), MRAC (SEQ ID NO: 372), KMCG (SEQ ID NO: 373), ARCA (SEQ ID NO: 374), KKQG (SEQ ID NO: 375), YRSY (SEQ ID NO: 376), SFMN (SEQ ID NO: 377), FKAA (SEQ ID NO: 378), KRNG (SEQ ID NO: 379), YNSF (SEQ ID NO: 380), KKNG (SEQ ID NO: 381), RRRG (SEQ ID NO: 382), KRYS (SEQ ID NO: 383), and ARYA (SEQ ID NO: 384).
  • FRAC SEQ ID NO: 367)
  • KRCF SEQ ID
  • the linker comprise any one of linkers in Table 4.
  • the amino acid sequences encoded by a string construct further comprises a signal protein sequence.
  • the string constructs may be mRNA.
  • a pharmaceutical composition may comprise one or more mRNA string constructs.
  • the tolerogenic composition is a DNA composition (e.g., tolerogenic DNA composition).
  • the DNA composition may comprise a DNA plasmid or a minicircle DNA encoding for one or more antigen peptides and/or MHC-presentable peptides disclosed herein.
  • the DNA plasmid can further comprise a promoter sequence and a backbone sequence.
  • the DNA composition can be formulated with nano-carriers to shield the DNA composition from degradation by DNases and other enzymes.
  • Suitable nano-carriers for DNA compositions are well known in the art and may include for example, nanoparticles, nanotubes, dendrimers, liposomes, foams, hydrogels, cubosomes, quantum dots, natural drug carriers, and exosomes.
  • the DNA composition is administered to a patient by intravenous injection, oral, or pulmonary administration.
  • the DNA composition can be applied topically via the skin or intramuscularly.
  • the DNA composition can be administered by intramuscular (IM) injection, subcutaneous injection, or intradermal injection.
  • IM intramuscular
  • the pDNA transfects cells in the subject, which can then undergo a type of programmed cell death known as apoptosis.
  • a cell that undergoes apoptosis releases small membrane-bound fragments that known as apoptotic bodies, which trigger the endocytosis of cellular debris by immature dendritic cells (iDC).
  • iDC immature dendritic cells
  • the activity of iDCs can then initiate the generation of exogenous antigens, which are exclusively presented by class II MHCs.
  • an administration route can also transfect APCs located near the injection site.
  • the tolerogenic composition is an RNA composition (e.g., tolerogenic RNA composition) encoding for one or more antigen peptides and/or MHC-presentable peptides disclosed herein.
  • the RNA composition is a messenger RNA (mRNA) composition.
  • the RNA composition optionally further comprises one or more chemical modifications.
  • the RNA composition can comprise a five-prime (5′) and a three- prime (3′) untranslated region (UTR), and can be further stabilized by 7-methylguanosine (m7G) 5′ cap and 3′ poly (A) tails respectively, and/or a suitable Poly(A) sequence.
  • the mRNA composition comprises modified nucleosides, for example Pseudouridine ( ⁇ ), N1- methylpseudouridine (m1 ⁇ ), and 5-methylcytidine (m5C).
  • the RNA composition comprises a self-amplifying RNA (saRNA), which further encodes an RNA-dependent RNA polymerase that can be translated in situ, thereby amplifying the peptide- or antigen-encoding sequence(s) in situ (see, e.g., Bloom et al., Gene Therapy (2021) 28:117–29).
  • the mRNA composition can be formulated into delivery agents, including but not limited to lipid nanoparticles, polymers, liposomes, and peptides.
  • delivery agents including but not limited to lipid nanoparticles, polymers, liposomes, and peptides.
  • the tolerogenic composition comprises both an antigen peptide and a nucleic acid coding for the peptide.
  • the antigen peptide and the nucleic acid are linked.
  • the pharmaceutical composition further comprises a delivery agent for delivering the nucleic acid(s) to a target cell (e.g., tolerogenic target cell).
  • a target cell e.g., tolerogenic target cell.
  • the target cell after internalizing the peptide(s), can present the peptide(s) on the cell surface with a cognate MHC (e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof), thereby to stimulate tolerogenic T cell responses.
  • Delivery agents for delivering nucleic acids to target cell include but are not limited to lipid nanoparticles (“LNPs”).
  • the delivery agent comprises an LNP.
  • the lipid comprises a cationic lipid, e.g., a ionizable cationic lipid.
  • the lipid forms a complex with and/or encapsulates the nucleic acid (e.g., RNA).
  • the ratio of positive charges to negative charges on the nanoparticles is 1.4:1 or less, and/or the zeta potential of the nanoparticles is 0 or less.
  • the ratio of positive charges to negative charges in the nanoparticles is between 1.4:1 and 1:8, for example, between 1.2:1 and 1:4, between 1:1 and 1:3, between 1:1.2 and 1:2, between 1:1.2 and 1:1.8, between 1:1.3 and 1:1.7, between 1:1.4 and 1:1.6, or about 1:1.5.
  • the zeta potential of the nanoparticles is -5 mV or less, -10 mV or less, -15 mV or less, -20 mV or less, or -25 mV or less. In some aspects, the zeta potential of the nanoparticle is -35 mV or greater, -30 mV or greater, or -25 mV or greater.
  • the nanoparticles have a zeta potential of -50 to 0 mV, for example, -40 to 0 mV, -30 to -10 mV.
  • positive charges are contributed by at least one cationic lipid present in the nanoparticles; negative charges are contributed by RNA and certain lipid components of the LNPs such as anionic helper lipids.
  • the nanoparticles comprise at least one helper lipid, such as a neutral lipid or an anionic lipid.
  • the nanoparticles are lipoplexes that comprise DOTMA and DOPE in a molar ratio of 10:0 to 1:9, for example, 8:2 to 3:7, or 7:3 to 5:5, and where the ratio of charges from positive charges in DOTMA to negative charges in RNA is 1.8:2 to 0.8:2, for example, 1.6:2 to 1:2, 1.4: 2 to 1.1:2, or about 1.2:2.
  • the nanoparticles are lipoplexes that comprise DOTMA and cholesterol in a molar ratio of 10: 0 to 1:9, for example, 8:2 to 3:7 or 7:3 to 5:5, and where the ratio of charges from positive charges in DOTMA to negative charges in RNA is 1.8:2 to 0.8:2, for example, 1.6:2 to 1:2, 1.4:2 to 1.1:2, or approximately 1.2:2.
  • the nanoparticles are lipoplexes that comprise DOTAP and DOPE in a molar ratio of 10:0 to 1:9, for example, 8:2 to 3:7 or 7:3 to 5:5, and where the ratio of charges from positive charges in DOTMA to negative charges in RNA is 1.8:2 to 0.8:2, for example, 1.6:2 to 1:2, 1.4:2 to 1.1:2, or approximately 1.2:2.
  • the nanoparticles are lipoplexes that comprise DOTMA and DOPE in a molar ratio of 2:1 to 1:2, for example, 2:1 to 1:1, and in which the ratio of positive charges in DOTMA to negative charges in RNA is 1.4:1 or less.
  • nanoparticles are lipoplexes that comprise DOTMA and cholesterol in a molar ratio of 2:1 to 1:2, for example, 2:1 to 1:1, and in which the ratio of positive charges in DOTMA to negative charges in RNA is 1.4:1 or less.
  • nanoparticles are lipoplexes that comprise DOTAP and DOPE in a molar ratio of 2:1 to 1:2, for example, 2:1 to 1:1, and in which the ratio of positive charges in DOTAP to negative charges in RNA is 1.4:1 or less.
  • the composition e.g., LNP composition
  • the tolerogenic nucleic acid composition further comprises one or more carriers or excipients. Exemplary excipients are described herein.
  • Nucleic acid compositions comprising such adjuvants, carriers, and/or excipients can be formulated by well-known conventional methods. These pharmaceutical compositions can be administered to the subject at a suitable dose. It is preferred that the pharmaceutically acceptable carrier be one which has no detrimental side effects or toxicity under the conditions of use.
  • a tolerogenic nucleic acid composition is sterile and produced according to GMP guidelines.
  • the tolerogenic composition is in the form of a lyophilized formulation or an aqueous solution.
  • the tolerogenic composition can be in dosages suspended in any appropriate pharmaceutical carrier in sufficient volume to carry the dosage.
  • the final volume typically will be at least 0.5 mL.
  • the upper limit is governed by the practicality of the amount to be administered, generally in the range of 0.5 mL to about 4.0 mL, such as 0.5 mL to about 2.0 mL.
  • the tolerogenic composition is administered to a patient enterally or parenterally.
  • the tolerogenic compositions are administered to a patient by intravenous, intramuscular, intratumoral, intradermal, intrajejunal, intraileal, intracolonic, or intrarectal administration.
  • the present disclosure also provides a protein complex comprising a peptide disclosed herein complexed with a cognate MHC (e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof).
  • a cognate MHC e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof.
  • the peptide, the cognate MHC, and the complex thereof are soluble.
  • the MHC is a class II MHC (e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof)
  • the protein complex comprises ⁇ 1 domain and ⁇ 1 domain of the class II MHC.
  • the protein complex further comprises ⁇ 2 domain and ⁇ 2 domain of the class II MHC.
  • the amino acid sequence is fused with at least one polypeptide of the class II MHC (e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof).
  • the first and second flexible linkers are peptide linkers, such that the single-chain construct can be produced recombinantly.
  • the amino acid sequence and/or the MHC e.g., as a single-chain construct
  • the multimerization increases the avidity of the pMHC, thereby to compensate for the often low affinity of pMHCs to cognate TCRs.
  • such multimer can be used to probe T cells or isolated TCRs to identify a TCR that binds the MHC-presentable peptide.
  • the multimerization domain comprises avidin or a variant thereof (e.g., streptavidin).
  • the complex further comprises a barcode, for example, a barcode nucleic acid conjugated with a biotin that binds a streptavidin that is fused with the peptide and/or MHC.
  • a pMHC multimer can comprise a plurality of the same pMHC. Alternatively, it can comprise a plurality of different pMHCs, e.g., two or more copies of a first pMHC and two or more copies of a second, different pMHC.
  • the multimerization domain comprises an antibody (e.g., IgG, IgM, IgA) Fc region or a fragment thereof that mediates multimerization.
  • the multimerization domain is a dimerization domain comprising an IgG (e.g., IgG4) Fc region or a fragment thereof that mediates dimerization (e.g., CH3 domain) (see Suarez et al., Transfus. Med.
  • the effector comprises an anti-inflammatory cytokine such as TGF ⁇ or IL-10, which promotes Treg phenotype and context-dependent immunosuppression effects.
  • the effector comprises an inducer of cell death.
  • the inducer of cell death is a TNF receptor superfamily agonist, such as FasL, an anti-Fas agonistic antibody or an antigen-binding fragment thereof, TRAIL, an agonistic anti-DR4 or anti- DR5 antibody or an antigen-binding fragment thereof.
  • the inducer of cell death is a cytotoxic agent such as a microtubule inhibitor or DNA damaging agent.
  • the present disclosure comprises a tolerizing vaccine composition that is capable of inducing antigen-specific immune tolerance to treat autoimmune diseases, e.g., T1D.
  • a tolerizing vaccine composition comprises a nucleotide sequence that encodes one or more MHC-presentable peptides derived from one or more antigens specific to a tissue or the amino acid sequence comprising the one or more MHC-presentable peptides, wherein the tissue represents the primary site of a disease or disorder, wherein the presentability of the MHC- presentable peptides in a risk-associated or highly prevalent HLA for the disease or disorder are experimentally measured or predicted.
  • the presentability is determined by MEDi, NetMHC, Mass Spectrometry, or any combination thereof, as disclosed elsewhere herein.
  • the disclosure comprises a method of inducing a tolerizing immune response against Type I Diabetes in a subject, comprising administering a nucleotide sequence that encodes an amino acid sequence comprising one or more MHC-presentable peptides to the subject, wherein at least one of the MHC-presentable peptides are specific to HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof.
  • the tolerizing immune response is against Type I diabetes.
  • the immune response comprises (i) an induction of antigen-specific T cell tolerance, (ii) an increase in Treg cells (e.g., CD4+ Treg cells or FOXP3+ Treg cells), (iii) inhibition of autoimmunity, (iv) an induction of anergy of effector T cells, (e.g., CD4+ T effector cells), (v) inhibition of cytokine production, (vi) a decrease in a pro-inflammatory cytokine, (vii) an increase in an immunosuppressive cytokine, (viii) a suppression of CD8+ effector cells, (ix) an increase of LAG3+ CD49b+ Type 1 Regulatory (Tr1) cells, or any combination thereof.
  • Treg cells e.g., CD4+ Treg cells or FOXP3+ Treg cells
  • an induction of anergy of effector T cells e.g., CD4+ T effector cells
  • inhibition of cytokine production e.g., CD
  • the immune response comprises a decrease of a pro-inflammatory cytokine, wherein the pro-inflammatory cytokine comprises Interferon ⁇ , Interferon beta-1a, Interferon alpha, (all subtypes), Interleukin-1 alpha, Interleukin-1 beta, Interleukin-2, Interleukin- 6, Interleukin-8, Interleukin-12, Interleukin-17, Interleukin-18, Interleukin-23, Tumor Necrosis Factor- ⁇ , Granulocyte-macrophage colony-stimulating factor, or any combination thereof.
  • the pro-inflammatory cytokine comprises Interferon ⁇ , Interferon beta-1a, Interferon alpha, (all subtypes), Interleukin-1 alpha, Interleukin-1 beta, Interleukin-2, Interleukin- 6, Interleukin-8, Interleukin-12, Interleukin-17, Interleukin-18, Interleukin-23, Tumor Necrosis Factor- ⁇ , Granulocyte-
  • the present disclosure provides a method of inducing a tolerizing immune response in a subject in need thereof, comprising administering to the subject a composition comprising (i) a nucleotide sequence that encodes an amino acid sequence comprising an MHC-presentable peptide as set forth in Tables 1A, 1B, 2A, 2B, and/or 3, or (ii) the amino acid sequence comprising the MHC-presentable peptide.
  • T1D Methods of Treating T1D
  • the present disclosure provides methods of treating T1D comprising administering a therapeutically effective amount of a pharmaceutical composition, tolerogenic composition, or APC, e.g., aAPC, disclosed herein to a subject in need thereof.
  • APC e.g., aAPC
  • the therapies disclosed herein are useful in treating symptomatic or pre-symptomatic T1D.
  • T1D disease progression is characterized by several stages of the disease that are characterized by a gradual loss of ⁇ -cell function over time. Stages include pre-stage 1, stage 1, stage 2, and stage 3. It is appreciated, however, that not all stages are present in all patients. In pre-stage 1, exposure to driving factors creates the conditions for ⁇ -cell autoimmunity to emerge.
  • random blood and fasting blood sugar tests can be performed.
  • a blood sample is taken at a random time and may be confirmed by repeat testing. Blood sugar values are expressed in milligrams per deciliter (mg/dL) or millimoles per liter (mmol/L). Regardless of the last meal, a random blood sugar level of 200 mg/dL (11.1 mmol/L) or higher suggests diabetes, especially when coupled with any of the signs and symptoms of diabetes, such as frequent urination and extreme thirst.
  • For the fasting blood sugar test a blood sample will be taken after an overnight fast.
  • a fasting blood sugar level less than 100 mg/dL (5.6 mmol/L) is normal.
  • a fasting blood sugar level from 100 to 125 mg/dL (5.6 to 6.9 mmol/L) is considered prediabetes. If the blood sugar level is 126 mg/dL (7 mmol/L) or higher on two separate tests, suggests diabetes.
  • Additional autoantibody tests for example for Islet Cell Cytoplasmic Autoantibodies (ICA), Glutamic Acid Decarboxylase Autoantibodies (GADA), Insulinoma-Associated-2 Autoantibodies (IA-2A), Insulin Autoantibodies (IAA) and/or Zinc Transporter-8 Autoantibodies (ZnT8)) can confirm T1D.
  • ICA Islet Cell Cytoplasmic Autoantibodies
  • GADA Glutamic Acid Decarboxylase Autoantibodies
  • IA-2A Insulinoma-Associated-2 Autoantibodies
  • IAA Insulin Autoantibodies
  • ZnT8 Zinc Transporter-8 Autoantibodies
  • the present disclosure provides a method of identifying an MHC- presentable peptide that is capable of inducing a tolerizing immune response in a subject in need thereof, comprising selecting an MHC-presentable peptide that is specific to HLA-DQ2.5. In some aspects, the disclosure provides a method of identifying an MHC-presentable peptide that is capable of inducing a tolerizing immune response in a subject in need thereof, comprising selecting an MHC-presentable peptide that is specific to HLA-DQ8.
  • the disclosure provides a method of identifying an MHC-presentable peptide that is capable of inducing a tolerizing immune response in a subject in need thereof, comprising selecting an MHC-presentable peptide that is specific to (or presentable by) HLA-DRB1.
  • the disclosure provides a method of identifying an MHC-presentable peptide that is capable of inducing a tolerizing immune response in a subject in need thereof, comprising selecting an MHC-presentable peptide that is presentable by both HLA-DQ2.5 and HLA-DQ8, both HLA-DQ2.5 and HLA-DRB1, both HLA- DQ8 and HLA-DRB1, or all three.
  • the APC is a tolerogenic APC.
  • APCs and tolerogenic APCs [0207]
  • the present disclosure provides tolerogenic antigen-presenting cells (APCs) or a population or composition (e.g., pharmaceutical composition) thereof.
  • APCs are a group of cells (e.g., immune cells) that mediate the cellular immune response by displaying endogenous and exogenous antigen complexed to major histocompatibility complexes (MHCs) class I and class II (“MHC I” and “MHC II”) on the cell surface for recognition by certain lymphocytes such as T cells.
  • MHCs major histocompatibility complexes
  • T cells lymphocytes
  • Tolerogenic APCs can be found in all tissues but are found in abundance in the skin, liver, spleen, and lymph nodes.
  • the tolerogenic APC expresses scavenger receptor MARCO, ILT-3, ILT-4, and/or CD52.
  • APCs include professional APCs and non-professional APCs.
  • Professional APCs include but are not limited to dendritic cells (DCs), macrophages, Langerhans cells, and B cells.
  • Non-professional APCs include but are not limited to endothelial cells, fibroblasts, certain cells in the liver, and lymph node stromal cells that are capable of expressing MHC I and MHC II proteins and can present exogenous antigens.
  • An APC can also be an artificial APC (e.g., drosophila cells) engineered to express an MHC that presents an MHC-presentable peptide.
  • artificial APCs for example, a bead, nanoparticle, or liposome, that presents a peptide- MHC on the surface.
  • artificial APCs can also be used to prime or stimulate T cells ex vivo or in vivo.
  • a function of dendritic cells (DCs) is to present antigens to T cells. Dendritic cells typically use two types of major histocompatibility complex (MHC) to display antigen peptides: MHC I and MHC II.
  • MHC major histocompatibility complex
  • MHC I trains CD8+ T-cells into cytotoxic, tumor-cell killers; and MHC II trains CD4+ T-cells into cytokine-producing helper cells. Clinical and pre-clinical data suggest that both T-cell types help to kill tumors.
  • the peptides presented by MHC I and MHC II are not necessarily the same between each other, or between patients.
  • Immature dendritic cells iDCs are characterized by high endocytic activity and low T-cell activation potential. Immature dendritic cells phagocytose pathogens and degrade their proteins into small pieces and upon maturation present those fragments at their cell surface using MHC molecules.
  • iDCs upregulate cell-surface receptors that act as co-receptors in T-cell activation such as CD80 (B7.1), CD86 (B7.2), and CD40, greatly enhancing their ability to activate T-cells.
  • iDCs Once iDCs have come into contact with a presentable antigen, iDCs become activated and mature into mature dendritic cells (mDCs), which in turn, can activate helper T-cells and cytotoxic T-cells as well as B-cells by presenting them with antigens derived from the pathogen, alongside non-antigen specific costimulatory signals.
  • mDCs mature dendritic cells
  • Tolerogenic DCs comprise several subsets of cells, for example VitD3-tolDC, Rapa-DC, DC10, Dex-tolDC, and ATDC. TolDCs induce tolerance via several contact-dependent and contact-independent mechanisms. TolDCs are generally characterized by low expression of costimulatory molecules (CD80, CD86, and CD83), upregulation of inhibitory and modulatory receptors, secretion of low pro-inflammatory and high levels of anti-inflammatory cytokines. TolDCs present antigens through normal T cell TCR and DC MHC interactions. However, mature tolerogenic DCs express high levels of CD86, which stimulates CD28 signaling to stabilize Treg cells (see Halliday et al., Front.
  • CD80, CD86, and CD83 costimulatory molecules
  • inhibitory and modulatory receptors secretion of low pro-inflammatory and high levels of anti-inflammatory cytokines.
  • TolDCs present antigens through normal T cell TCR and DC MHC interactions. However, mature tolerogenic DCs
  • a tolDC is generated by loading or pulsing an immature dendritic cell (iDC) in vitro with apoptotic bodies from a cell that expresses an autoantigen and/or presents an MHC-presentable peptide thereof (e.g., one or more MHC-presentable peptides disclosed herein) (see Marin-Gallen et al., Clin. Exp. Immunol. (2010) 160(2): 207–14).
  • iDC immature dendritic cell
  • a tolDC is generated by loading or pulsing an iDC in vitro with one or more MHC-presentable peptides of an autoantigen (e.g., one or more MHC- presentable peptides disclosed herein) and culturing the iDC under immunosuppressive conditions.
  • immunosuppressive conditions include but are not limited to presence of an agonist of an immune checkpoint protein (e.g., an agonistic anti-CTLA-4 antibody or an antigen-binding fragment thereof conjugated to an anti-CD11c antibody or an antigen-binding fragment thereof for coating the iDC).
  • an agonist of an immune checkpoint protein e.g., an agonistic anti-CTLA-4 antibody or an antigen-binding fragment thereof conjugated to an anti-CD11c antibody or an antigen-binding fragment thereof for coating the iDC.
  • Interaction tolDCs with T cells leads to inhibition of effector T cell responses and the induction of regulatory T cells (Tregs).
  • the target cell is a tolerogenic target cell in the spleen, such as a marginal zone macrophage, a metallophilic macrophage, or a marginal zone dendritic cell.
  • Marginal zone dendritic cells (Langerin + CD8 + DC) reside in the splenic marginal zone and are important for the regulation of tolerance toward cell-associated self-antigens. Markers for marginal zone DCs include CD8 and CD103.
  • dendritic cells can be generated in vivo or ex vivo from monocytes, sometimes referred to as monocyte-derived dendritic cells.
  • monocytes can transition from CD14+CD83- monocytes to CD14-CD83- immature DCs under the influence of IL-4 and GMCSF and then upregulate CD83 upon activation/maturation to become CD14-CD83+ mDC (see, e.g., Putz et al., Methods Mol Med. (2005) 109:71-82).
  • the transition from immature to mature DC is not instantaneous and requires some time, during which time the DCs undergo a maturing process. Some DCs may mature faster than others and thus, the population may be a mix of immature, maturing, semi-mature, and mature DCs, while the population as a whole is in the process of maturing.
  • PBMCs peripheral blood mononuclear cells
  • IL-4 interleukin 4
  • GM-CSF granulocyte- macrophage colony stimulating factor
  • TNF tumor necrosis factor
  • IL-6 IL-6
  • IL-1 ⁇ IL-1 ⁇
  • PGE2 tumor necrosis factor
  • Macrophages are effector cells of the innate immune system that phagocytose bacteria and secrete both pro-inflammatory and antimicrobial mediators.
  • macrophages play an important role in eliminating diseased and damaged cells through their programmed cell death.
  • M1 macrophages classically-activated (M1) macrophages
  • wound- healing macrophages also known as alternatively-activated (M2) macrophages
  • Mregs regulatory macrophages
  • Regulatory macrophages (Mregs) can provide a tolerogenic environment.
  • Marginal zone macrophages (MZM or MZM ⁇ ) and metallophilic macrophages (MMM ⁇ ) are a subset of specialized splenic macrophages that interact with apoptotic material entering the spleen from circulation.
  • Hepatic macrophages comprise a heterogeneous population of cells, for example, Kupffer cells (KCs), and recruited macrophages derived from peritoneal cavity as well as the bone marrow.
  • Hepatic macrophages can be tolerogenic antigen-presenting cells that inhibit T-cell activation by producing distinct sets of cytokines, chemokines, and mediators to maintain or resolve inflammation.
  • Markers for macrophages include CD11b/Integrin alpha M, CD14, CD68, Fc gamma RIII/CD16, Fc gamma RI/CD64, and CCR5.
  • the target cell is a tolerogenic target cell in the liver, such as a liver sinusoidal endothelial cell (LSEC), MARCO + Kupffer cell, or a monocyte-derived macrophage.
  • LSECs are in direct contact with blood and possess efficient endocytic pathways for exogenic antigen endocytosis.
  • Markers for LSECs include CD31, CD36, stabilin 1, 2, and B1, lipoprotein receptor-related protein-1, and certain C-type lectin receptors.
  • Type 1 LSEC are CD36hiCD32 ⁇ CD14 ⁇ LYVE-1 ⁇
  • Type 2 LSEC are LYVE- 1 + CD32hiCD14 + CD54 + CD36mid-lo.
  • LSECs are not only able to present exogenous antigen on MHC II but also on MHC I and are capable of antigen cross-presentation to CD8 + T cells. LSECs can upregulate the co-inhibitory molecule B7-H1 in CD8 + T-cells, and shift the balance from activation to tolerance induction in CD8 + T-cells.
  • Na ⁇ ve CD4 + T-cells primed by LSECs under steady state can differentiate into regulatory T-cells (Tregs) that lack the transcription factor Forkhead-Box-Protein P3 (FoxP3), which is normally expressed by Tregs generated by professional APCs.
  • Tregs regulatory T-cells
  • FoxP3 transcription factor Forkhead-Box-Protein P3
  • LSEC-induced CD25 low FoxP3 ⁇ T-cells are immune suppressive.
  • Hepatocytes are liver cells that can present exogenic antigens on MHC I and, in inflammatory conditions, MHC II molecules.
  • Lymph node stromal cells are a group of cells that include, for example, fibroblastic reticular cells, and lymphatic and blood endothelial cells. LNSCs can promote a tolerogenic CD4+ T cell compartment and can aid in the deletion of antigen-specific CD8+ T cells.
  • Markers for LNSCs comprise podoplanin (gp38) and PECAM-1 (CD31). Lymphatic endothelial cells have a high endocytic capacity, are capable of presenting exogenous antigens to T-cells on both MHC-I and MHC-II molecules, and mediate the deletion of autoreactive CD8+ T-cells.
  • the APC is an artificial APC, for example, a cell line engineered to express an MHC (see Turtle et al., Cancer J. (2010) 16(4): 374–81).
  • the cell line is a lymphoblast cell line (e.g., K562).
  • aAPCs are designed to mimic the temporal and spatial aspects of T cell-APC interactions.
  • Such artificial APCs can be used to activate T cells (e.g., Treg cells) that express a cognate TCR in vitro or in vivo.
  • Peptide loading [0220]
  • the APC composition disclosed herein is prepared by loading cells (e.g., monocytes and/or dendritic cells) with a composition disclosed herein, using the preloading method and/or the direct loading method.
  • Methods for peptide loading on APCs are known in the art, for example as described in WO2020/055931. Briefly, APCs such as monocytes, iDCs, and other non-mature DCs can be loaded with antigen peptides for presenting the incorporated MHC-presentable peptides on the cell surface.
  • monocytes and/or immature DCs are induced to internalize and proteolytically process the antigen peptides into shorter fragments (MHC-presentable peptides) for subsequent loading onto class I and class II MHCs and presentation to T cells.
  • the processed antigen peptides may be stored by the monocytes and/or immature DCs during the differentiation and/or maturation process and subsequently presented on the surface of mature DCs.
  • monocytes are incubated in the presence of one or more peptides prior to and/or during differentiation.
  • immature DCs are incubated in the presence of one or more peptides prior to and/or during maturation.
  • peptides can be directly loaded onto mature DCs. These peptides are directly loaded on the cell surface MHCs and are generally not shortened by intracellular processing. In some aspects, preloading of immature DCs and direct loading of mature DCs can be combined, resulting in a mixed population of pre-loaded and directly loaded mature DCs.
  • the APC composition disclosed herein can be prepared by nucleic acid transfection.
  • the APCs are prepared by transfecting a population of cells ex vivo with one or more nucleic acids encoding an antigen or a portion thereof (e.g., at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or 100% of the antigen).
  • Nucleic acids useful herein include DNA and RNA (e.g., mRNA), including modified forms thereof.
  • the nucleic acids transfected comprise mRNA, optionally mRNA having one or more chemical modifications. Nucleic acid compositions described herein are also contemplated for use in this ex vivo transfection method.
  • the APCs of the APC composition are derived from a single subject and thus, as a population, express up to two variants from the two alleles of each MHC genetic locus (e.g., HLA-A, HLA-B, HLA-C, HLA-DP, HLA-DQ, HLA-DR).
  • the APCs of the APC composition are pooled from a plurality of subjects and thus have greater MHC diversity.
  • the APCs of the APC composition present one or more MHC- presentable peptides disclosed herein.
  • the APCs present a plurality of different MHC-presentable peptides disclosed herein.
  • the APCs e.g., APCs derived from a single subject
  • the APCs (e.g., APCs derived from a single subject) present 5-100, 5-90, 5-80, 5-70, 5-60, 5-50, 5-40, 5-30, 5-20, 5-10, 10-100, 10-90, 10-80, 10-70, 10-60, 10-50, 10-40, 10-30, 10-20, 20-100, 20-90, 20-80, 20-70, 20-60, 20-50, 20-40, 20-30, 30-100, 30-90, 30-80, 30-70, 30-60, 30-50, 30- 40, 40-100, 40-90, 40-80, 40-70, 40-60, 40-50, 50-100, 50-90, 50-80, 50-70, 50-60, 60-100, 60- 90, 60-80, 60-70, 70-100, 70-90, 70-80, 80-100, 80-90, or 90-100 different MHC-presentable peptides disclosed herein.
  • the APCs present a first MHC-presentable peptide by a class I MHC and a second MHC-presentable peptide by a class II MHC. Without wishing to be bound by theory, it is contemplated that such APCs are capable of stimulating an immune response by both CD8 + and CD4 + T cells. [0225] In some aspects, at least 30, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% of the APCs in the APC composition present one or more MHC-presentable peptides disclosed herein.
  • the percentage of lymphocytes (e.g., T cells) relative to all cells in the APC composition is 20% or less, 10% or less, 5% or less, 4% or less, 3% or less, 2% or less, or 1% or less.
  • the APC composition is substantially free of lymphocytes (e.g., T cells).
  • lymphocytes e.g., T cells
  • the composition comprises an immunomodulator disclosed herein. It is contemplated that the immunomodulator may induce or stabilize a tolerogenic phenotype of the APC. IV.
  • the present disclosure provides a T cell composition comprising one or more T cells (e.g., regulatory T cells) that recognize one or more MHC-presentable peptides presented by HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof on an APC (e.g., artificial APC), e.g., MHC-presentable peptides as set forth in Tables 1A, 1B, 2A, 2B, and/or 3.
  • APC e.g., artificial APC
  • TCR engagement with an MHC presenting a cognate peptide is the first step and is termed “signal 1.”
  • T cells can be expanded by providing “signal 2,” which can be provided by, for example, the B7 family proteins B7.1 and B7.2 which interact with CD28, or the tumor necrosis factor receptor (TNFR) family ligands OX-40L, CD70, 4-1BBL, which interact with OX-40, CD27, and 4-1BB on the T cell, respectively.
  • Certain signal 2 interactions can be inhibitory to T cell expansion and effector function, such as the interaction of CTLA-4 with B7.1 or PD-1 with PD-L1 (B7.H1) or PD-L2 (B7-DC).
  • T cell priming and expansion are known in the art, e.g., co-culturing the lymphocyte-rich fraction of the PBMCs with the APCs disclosed herein to expand T cells that are reactive to the MHC-presentable peptides disclosed herein.
  • the APCs loaded with MHC-presentable peptides disclosed herein and prepared in accordance with the methods disclosed herein can be used to prime and expand certain T cells populations in vitro, ex vivo, and in vivo.
  • CD4 + and CD8 + Regulatory T Cells are characterized by the expression of certain cell surface molecules such as the T cell receptor (TCR), a multiprotein complex that is involved in MHC binding.
  • TCR T cell receptor
  • the T cells are derived from blood, bone marrow, lymphoid organs (e.g., lymph nodes or spleen), or tumor biopsies from a subject. These cells typically are primary cells, such as those isolated directly from a subject and/or tissue isolated from a subject. Other exemplary sources of T cells include T cell derived from stem cells, such as multipotent and pluripotent stem cells, including induced pluripotent stem cells (iPSCs). Stem cells can be directly isolated from a subject such as from cord blood, blood, or tissue. iPSCs can be derived from any cell type that can be used to produce iPSCs.
  • iPSCs induced pluripotent stem cells
  • iPSCs can also be derived from a cell bank, and used to generate an allogeneic T cell product.
  • the T cells disclosed herein can be from a T cell subpopulation defined by function, activation state, maturity, potential for differentiation, expansion, recirculation, localization, and/or persistence capacities, antigen specificity, type of antigen receptor, presence in a particular organ or compartment, marker or cytokine secretion profile, and/or degree of differentiation. Included within this subpopulation of T cells are, for example, CD4 + T cells and CD8 + T cells.
  • Regulatory T (Treg) cells are a specialized subpopulation of T cells that act to suppress immune response, thereby maintaining homeostasis and self-tolerance.
  • Tregs are able to inhibit T cell proliferation and cytokine production and play a critical role in preventing autoimmunity.
  • Treg cells can be CD4 + Treg cells or CD8 + Treg cells.
  • CD4+ T cells are now commonly divided into two distinct lineages: CD4 + Treg cells and CD4 + conventional T helper (Th) cells.
  • Th cells control the adaptive immunity by activating, in an antigen-specific fashion, other effector cells such as CD8+ cytotoxic T cells, B cells and macrophages.
  • CD4 + Treg cells are defined as CD4 + T cells in charge of suppressing potentially deleterious activities of Th cells. Therefore, in some aspects, the present composition is capable of increasing a population of CD4 + Treg cells.
  • Molecular markers are essential tools for defining and for analyzing a subpopulation of immune cells.
  • the most widely used markers for Treg cells are CD4, CD25, cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), glucocorticoid-induced tumour necrosis factor receptor family-related gene (GITR), lymphocyte activation gene-3 (LAG-3), CD127, and forkhead/winged-helix transcription factor box P3 (Foxp3).
  • CTLA-4 cytotoxic T lymphocyte-associated antigen 4
  • GITR glucocorticoid-induced tumour necrosis factor receptor family-related gene
  • LAG-3 lymphocyte activation gene-3
  • CD127 forkhead/winged-helix transcription factor box P3
  • Foxp3 transcription factor is considered the most reliable marker for Treg cells. Tissue distribution analysis has shown that Foxp3 is mostly present in lymphoid tissues.
  • Foxp3 is highly restricted to ⁇ T cells, and almost undetectable in B cells, ⁇ T cells, natural killer (NK) cells, macrophages and dendritic cells (DC).
  • the expression of Foxp3 is mostly restricted to CD4+ T cells, but some CD8+ T cells do express Foxp3 as well.
  • Foxp3 is essential for T-cell functions and defective Foxp3 leads to lethal immune dysregulation. It has been suggested that Foxp3 may act as a repressor of transcription with the function of regulating the amplitude of the response of CD4+ T cells to activation. It has also been proposed that all human CD4+ and CD8+ T cells may upregulate Foxp3 and acquire suppressive properties upon activation.
  • Treg cells like all CD4+ T cells, possess a somatically-rearranged TCR, which allows specific recognition of antigenic peptides in the context of MHC class II molecules. Activation of conventional Th cells requires specific antigen recognition by the TCR and one would expect Treg cells to follow the same rule.
  • CD4 + Treg cells need to be first activated via the TCR to become suppressive. This implies that (1) CD4 + Treg-cell activation is antigen-specific; and (2) the suppressive activity of CD4 + Treg cells is triggered in an antigen-specific fashion. The same requirement for antigen seems to apply for Treg functions in vivo, since the proliferation of CD4 + Treg cells in lymph nodes was shown to be antigen-dependent. In the non-obese diabetic mouse model for type 1 diabetes, CD4 + Treg cells specific for a pancreatic autoantigen were much more efficient at preventing diabetes than polyclonal Treg cells.
  • pancreas- specific Treg cells could only prevent diabetes when the Treg antigen was present in vivo in the pancreas.
  • destructive autoimmune gastritis could be prevented by transfer of stomach- specific Treg cells, but not with polyclonal Treg cells.
  • Treg cells which are in charge of maintaining self-tolerance, would be self-reactive. Supporting this hypothesis, self-reactive Treg cells have been observed in various mouse models for autoimmune diseases. For instance, Treg cells specific for the insulin B chain or for a pancreatic islet autoantigen protected against type 1 diabetes.
  • CD8 + Treg cells possess important immunosuppressive functions. They can target antigen-activated CD4 + helper T cells with their cytotoxic activity, thereby suppressing the activity of the CD4 + helper T cells.
  • CD8 + Treg cells can function by secreting various inhibitory cytokines and chemokines, including IL-10, transforming growth factor (TGF)- ⁇ , IL-16, IFN- ⁇ and chemokine (C-C motif) ligand 4, that can render APCs tolerogenic.
  • TGF transforming growth factor
  • C-C motif chemokine
  • subpopulations of CD8 + Treg cells are characterized by several surface markers. In humans, the most prevalent are CD8 + CD28 – Treg cells that exhibit age-dependent accumulation in human and sub-populations of CD8 + CD122 + CD49d + T reg cells that express both PD-1 and IL-10 and suppress alloantigen-induced transplant rejections.
  • CD8 + Treg cells can be primed and/or expanded by induction of CD8 + T cells, preferably na ⁇ ve CD8+ T cells or natural regulatory CD8+ T cells, in vitro.
  • Conditions for priming and/or expanding CD8 + Treg cells include but are not limited to TGF- ⁇ and IL-2, or IL-15 and IL-2, in the presence of APCs or anti-CD3/CD28 antibodies.
  • Tolerogenic small molecules such as rapamycin, cyclosporin A, methylprednisolone, or tacrolimus, can also be included in the cell culture for priming and/or expanding CD8 + Treg cells.
  • the present disclosure provides a population of T cells that recognize one or more MHC-presentable peptides disclosed herein.
  • the T cells include one or more subsets of T cells, such as a whole T cell population, CD8 + cells, CD4 + cells, or subpopulations and combinations thereof.
  • the T cells can be harvested from blood, bone marrow, lymphoid organs (e.g., lymph nodes), or tumor biopsies from a subject.
  • the T cells are harvested from a cell culture.
  • the T cells can be purified before further culturing and expansion or can be used in a mixture with other cells.
  • the primary T cells and stem cell derived T cells can be used fresh or frozen.
  • the T cells can be maintained in ex vivo culture in the presence of one or more cytokines, such as IL-15 and/or IL-12, and optionally one or more of IL-21, IL-7, IL-2, IL- 10, and IL-6.
  • cytokines such as IL-15 and/or IL-12
  • IL-21, IL-7, IL-2, IL- 10, and IL-6 are also provided herein.
  • a composition or population disclosed herein is enriched for such T cells.
  • the CD4+ cells in the composition or population recognize one or more MHC-presentable peptides disclosed herein.
  • cell compositions comprising the T cells disclosed herein.
  • the cell composition has been enriched for T cells (e.g., CD4 + Treg cells).
  • the enrichment can produce a composition in which at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% of the cells in the composition are T cells (e.g., CD4 + Treg cells).
  • the T cells e.g., CD8 + Treg cells
  • the T cells express endogenous TCRs that bind one or more MHC-presentable peptides disclosed herein.
  • the T cells can be prepared by priming with an APC presenting the MHC-presentable peptides (e.g., an APC composition disclosed herein in Section III) ex vivo or in vivo.
  • T cells can be obtained from a blood sample of a subject (e.g., a patient) by apheresis.
  • a lymphocyte-rich fraction and a monocyte-rich fraction can be acquired by elutriating peripheral blood mononuclear cells (PBMCs) of the subject.
  • the monocyte-rich fraction can then be used to prepare antigen-presenting cells (APCs) for priming T cells, which can be obtained from the lymphocyte-rich fraction.
  • the APC composition used for priming T cells is derived from the same subject as the T cells.
  • the APCs prepared in accordance with a method disclosed herein can be used to prime and expand T cells directed to the one or more selected antigen ex vivo, the method comprising co-culturing of the APCs with the T cells.
  • a lymphocyte-rich fraction of PBMCs can be co-cultured with the tolerogenic APCs disclosed herein (e.g., at a ratio between about 1:1 to about 40:1) to expand T cells that are reactive to the one or more MHC-presentable peptides.
  • T cells directed to the one or more MHC-presentable peptides presented on the APCs preferentially expand and enrich during the co-culturing process, resulting in a primed and expanded T cell composition directed to the one or more MHC-presentable peptides.
  • the T cell composition may be re-stimulated by the same population of antigen-pulsed APCs.
  • the T cell composition may be re-stimulated by another population of APCs pulsed by the same antigens or peptides (e.g., a fresh population of APCs produced by the same method as those used in initial stimulation).
  • the primed and expanded Treg cells are CD8+ CD122 hi CD49d/f+, CD8+ CD28-, CD8+ CD103+ CD25 hi , CD8+ FOXP3+, CD8+ FOXP3+ Helios+, or CD8+ CD45RC low .
  • the resulting expanded and primed T cells can be used for various purposes (e.g., in T cell therapies as further disclosed herein).
  • V. PHARMACEUTICAL COMPOSITIONS AND THERAPEUTIC METHODS Disclosed herein are pharmaceutical compositions that contain one or more peptides, nucleic acids, APCs, T cells, or fusion proteins described herein that are useful for treating T1D.
  • compositions described herein include but are not limited to peptide compositions, nucleic acid compositions, presentation agents (e.g., APCs and artificial APCs), and T cell compositions. Also disclosed are therapeutic uses of these pharmaceutical compositions.
  • Tolerogenic Compositions [0251] The T1D-associated MHC-presentable peptides disclosed herein or any nucleotide sequence encoding the MHC-presentable peptides are useful as tolerogenic compositions for treating and preventing T1D in a subject.
  • the present disclosure provides a pharmaceutical composition (e.g., tolerogenic composition) comprising one or more MHC-presentable peptides disclosed herein, an amino acid sequence encoding the MHC-presentable peptides, or one or more nucleotide sequences encoding the one or more MHC-presentable peptides or the amino acid sequence.
  • the MHC-presentable peptide(s) are delivered to a target cell.
  • the pharmaceutical composition further comprises a vehicle, e.g., a delivery agent, for delivering the T1D-associated peptide(s) to a target cell (e.g., tolerogenic target cell), a pancreatic cell.
  • the target cell after internalizing the peptide(s), can present the peptide(s) on the cell surface with a cognate MHC (e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof), thereby to stimulate tolerogenic T cell responses.
  • Delivery agents for delivering peptides to target cell include but are not limited to nanoparticles, liposomes, virus-like particles, and red blood cells.
  • the delivery agent may also reduce susceptibility of the peptides to proteolytic degradation.
  • the delivery agent comprises a nanoparticle.
  • the nanoparticle is a polymeric nanoparticle composed of poly(lactide-co-glycolide) (PLG or PLGA) (Jamison et al., J. Immunol. (2019) 203(1) 48:57), polylactic acid (PLA) (Ruan et al., J. Control Release (2016) 279: 306-315), or poly( ⁇ -caprolactone) (PCL) (Kim et al., Polymers (Basel) (2019) 11(2): 288).
  • the polymeric nanoparticle is an amphiphilic block copolymer where at least one block is hydrophobic and one block is hydrophilic and the block copolymer self- assembles in an aqueous solution.
  • the amphiphilic block copolymer can be a di-block A-B, tri- block A-B-A or a graft copolymer and can form polymeric micelles.
  • the hydrophobic portion of the block copolymer forms the core of micelles, while the hydrophilic portion forms the shell or the corona.
  • the commonly used hydrophilic blocks are poly(ethylene glycol), poly(N-vinyl pyrrolidine) (PVP), polysialic acid (PSA) (Lei et al., Chem Sci. (2021) 12(18):6449-6457), and poly (N-isopropyl acrylamide) (pNIPAAm) among others.
  • Hydrophobic blocks can comprise poly(propylene oxide) (PPO), PCL, PLGA, poly(L-lactide), poly(L-lysine) (Luo et al., J. Control Release (2013) 170(2): 259-67) poly(L-aspartic acid) (pAsp) (Kagaya et al., Gene Ther (2012) 19(1): 61-9), and poly(L-histidine) (pHis) (Wu et al., Biomaterials (2013) 34(4):1213-22).
  • PPO poly(propylene oxide)
  • PCL poly(L-lactide)
  • poly(L-lysine) Lio et al., J. Control Release (2013) 170(2): 259-67
  • poly(L-aspartic acid) pAsp)
  • pHis poly(L-histidine)
  • the nanoparticle is a phospholipid micelle, where the hydrophobic block of polymeric micelles can be short, phospholipid residues like disteroyl phosphatidyl ethanolamine (DSPE) conjugated chemically to hydrophilic blocks like mPEG to form mPEG-DSPE micelles (Banerjee et al., Nanomedicine (2013) 9(6):722-8; Kumar et al., ACS Infect Dis. (2019) 5(3): 443-453).
  • DSPE disteroyl phosphatidyl ethanolamine
  • Polymeric nanoparticles can be formed by the double emulsion or nanoprecipitation methods.
  • the nanoparticle is a gold particle with a layer of thiol-poly-ethylene glycol (PEG) (Yeste et al., Sci Signal. (2016) 9(433): ra61).
  • the gold nanoparticle is 60 nm in diameter.
  • the nanoparticle is a liposome or a nanoliposome prepared by the thin- film hydration or ethanol injection method (Kenison et al., Proc. Natl. Acad. Sci. (2020) 117(50): 32017-32028, WO2019/165436 A1).
  • the nanoparticle comprises a polystyrene particle or a polystyrene microsphere.
  • Peptides can be encapsulated within the nanoparticles either by passive loading through spontaneous self-assembly (Luo et al., J Control Release. (2013) 10:170(2):259-67, Kenison et al., Proc. Natl. Acad. Sci.
  • nanocarriers (2020) 117(50): 32017-32028, Pujol- Autonell et al., PLoS One (2015) 10(6): e0127057), electrostatically attached to the nanocarrier through interaction of opposite charges on the antigen and nanoparticle, physically adsorbed to nanoparticles (US2018/0071376 A1) or can be covalently attached to nanoparticle surface using well-defined conjugation chemistries as described in Bioconjugate Techniques, 3 rd edition by Greg T Hermanson, Academic Press Inc. 2013)(US 2019/0282707 A1).
  • the nanoparticles may incorporate functional groups for further reaction. Functional groups include electrophiles or nucleophiles which can conveniently react with other molecules.
  • the nanoparticle has a diameter that makes the particle suitable for systemic, in particular parenteral, administration of nucleic acids or peptides, typically a diameter less than 1,000 nanometers (nm). In some aspects, the nanoparticle has a diameter of less than 600 nm.
  • the nanoparticle has a diameter of less than 400 nm. In some aspects, the nanoparticle has a diameter in the range of 50 to 1,000 nm, for example, 50 to 900 nm, 50 to 800 nm, 50 to 700 nm, 50 to 600 nm, 50 to 500 nm, 50 to 400 nm, 50 to 300 nm, 50 to 200 nm, 50 to 100 nm, 100 to 1,000 nm, 100 to 900 nm, 100 to 800 nm, 100 to 700 nm, 100 to 600 nm, 100 to 500 nm, 100 to 400 nm, 100 to 300 nm, 100 to 200 nm, 150 to 1,000 nm, 150 to 900 nm, 150 to 800 nm, 150 to 700 nm, 150 to 600 nm, 150 to 500 nm, 150 to 400 nm, 150 to 300 nm, 150 to 200 nm, 150 to 1,000 nm, 150 to 900 nm, 150 to 800 n
  • the nanoparticle has a diameter in the range of 250 to 550 nm, 300 to 500 nm, or 200 to 400 nm.
  • Nanoparticles can be targeted to certain cells (e.g., tolerogenic cells) by various means. Tolerogenic APCs can be found in the liver and spleen. Accordingly, in some aspects, the nanoparticle preferentially targets the liver. In some aspects, the nanoparticle preferentially targets the spleen, for example, by having a negative zeta potential (see WO 2013/192532, US 2019/0282707 A1, Kranz et al., Nature (2016) 534(7607): 396-401).
  • the nanoparticle comprises an apoptotic body surrogate (see WO2013/184976).
  • the nanoparticle comprises one or more apoptotic signaling molecules selected from annexin-1, annexin-5, milk fat globule-EGF-factor 8 (MFG-E8), calreticulin, phosphatidylserine, CD47, oxidized LDL, Fas-ligand and TNF.
  • the nanoparticle can be targeted to immune cells based on its particle size (Thorp et al., Front Immunol.(2020) 11:945, US 2019/0282707 A1).
  • the nanoparticle has a particle size of at least 200 nm, which allows particles to accumulate predominantly in the red pulp of the spleen and preferentially interact with immune cells therein.
  • a particle size of 200 nm has been shown to preferentially accumulate in late endosomal or lysosomal compartments, making them ideal for immunomodulatory properties, as cargo movement through the late endosomal compartment via intracellular endosomal receptors is an important step for engaging adaptive and innate immune processes (Rejman et al., Biochem J. (2004) 377(Pt 1): 159-69, Gleeson., Semin Cell Dev Biol. (2014)31: 64-72).
  • the particle has a diameter in the range of 50-800 nm, for example, 50-700 nm, 50-600 nm, 50-500 nm, 50-400 nm, 50-300 nm, 50-200 nm, 50-150 nm, 50-100 nm, 50-90 nm, 50-80 nm, 50-70 nm, 50-60 nm, 100-800 nm, 100-700 nm, 100-600 nm, 100-500 nm, 100-400 nm, 100-300 nm, 100- 200 nm, 100-150 nm, 150-800 nm, 150-700 nm, 150-600 nm, 150-500 nm, 150-400 nm, 150-300 nm, 150-250 nm, 150-200 nm, 200-800 nm, 200-700 nm, 200-600 nm, 200-500 nm, 200-400 nm, 200-300
  • the nanoparticle comprises a ligand (e.g., an antibody or an antigen- binding fragment thereof) that binds an antigen of a target cell (e.g., tolerogenic cell).
  • the ligand comprises an antibody that binds such an antigen or an antigen-binding fragment thereof.
  • the delivery agent comprises a liposome. See, e.g., U.S. Patents Nos: 4,235,871; 5,000,887; 5,395,619; 4,837,028; U.S. Patent Applications Nos: US 2016/0324779A1, US 2020/0405642A1, and EP Patent No: EP3,095,440.
  • Liposomes are lipid bilayer spherical membranes that provide both hydrophilic and hydrophobic environments.
  • the liposome is a multilamellar liposomes/vesicles (MLV), an oligolamellar vesicles (OLV), a multilamellar liposomes/vesicles (MVV), or an unilamellar vesicles (ULV).
  • the liposome comprises neutral lipids or negatively charged lipids.
  • the liposome comprises dilaurylphosphotidylcholine (DLPC), dimyristoyl phosphotidylcholine (DMPC), dipalmitoylphosphotidylcholine (DPPC), dioleolylphosphotidyl choline (DOPC), dilaurylphosphotidylethanolamine (DLPE), dipalmitoylphosphotidylcholine (DPPC), distearoylphosphotidylcholine (DSPC), dioleolylphosphotidylcholine (DOPC), dimyristoyl phosphotidylethanolamine (DMPE), distearoylphosphotidylethanolamine (DSPE), dilaurylphosphotidylglycerol (DLPG), dicetylphosphate (DCP), dioleoylphosphatidylethanolamine (DOPE), 1,2-dioleoyl-3 trimethylammoniumpropane (DOTAP), di
  • the liposome comprises L- ⁇ -egg phosphatidylcholine (EPC) and/or L- ⁇ -egg phosphatidylglycerol (EPG).
  • the liposomes comprise 1,2-dioleoyl-sn-glycero3-phospho-L-serine (DOPS), 1,2-didodecanoyl-sn-glycero-3-phosphocholine (DLPC), and cholesterol.
  • DOPS 1,2-dioleoyl-sn-glycero3-phospho-L-serine
  • DLPC 1,2-didodecanoyl-sn-glycero-3-phosphocholine
  • the liposomes are negatively charged.
  • the liposomes are nanoliposomes.
  • the diameter of the liposome is 50-500 nm, for example, 50-400 nm, 50-300 nm, 50-200 nm, 50-100 nm, 100-500 nm, 100-400 nm, 100-300 nm, 100-200 nm, 200-500 nm, 200-400 nm, 200-300 nm, 300-500 nm, 300- 400 nm, or 400-500 nm.
  • Liposomes can be targeted to target cells (e.g., tolerogenic cells) by various means.
  • the liposome comprises phosphatidylserine.
  • the liposome comprises a ligand (e.g., an antibody an antigen-binding fragment thereof) that binds an antigen of a target cell (e.g., tolerogenic cell), as disclosed above in connection with nanoparticles.
  • the delivery agent comprises a targeting domain (e.g., a natural ligand, an antibody or an antigen-binding fragment thereof) that binds a receptor that is specifically or preferentially expressed on tolerogenic APCs, relative to immunogenic APCs.
  • exemplary receptors include but are not limited to MARCO, ILT-3, ILT-4, and CD52.
  • Additional receptors comprise Clec9A, an anti-C-type lectin (e.g., DC-SIGN, Mannose receptor (MR), or macrophage galactose-type C-type lectin (MGL)), dendritic cell immunoreceptor (DCIR), DCIR2, DEC205 (CD205), Langerin (CD207), and Sialic-acid binding immunoglobulin-type lectin (Siglec).
  • an anti-C-type lectin e.g., DC-SIGN, Mannose receptor (MR), or macrophage galactose-type C-type lectin (MGL)
  • DCIR dendritic cell immunoreceptor
  • DCIR2 DCIR2, DEC205 (CD205), Langerin (CD207)
  • CD207 Sialic-acid binding immunoglobulin-type lectin
  • Siglec Sialic-acid binding immunoglobulin-type lectin
  • the delivery agent comprises a erythroid cell such as a red
  • the erythroid cell is an enucleated mature red blood cell that lacks a nucleus. In some aspects, the erythroid cell is CD47-negative.
  • Tolerance to ingested antigens is an essential feature required for normal homeostasis and maintenance of barrier function in the gastrointestinal tract. Therefore, oral tolerance is another means of suppressing T cell immunity.
  • the delivery agent comprises a carrier for delivering a peptide to the small intestine, for example, a coating that renders resistance to degradation in the low pH and the presence of proteolytic enzymes in the stomach.
  • a peptide composition suitable for oral administration without a delivery agent for example, if the peptide is designed and/or chemically modified to resist degradation in the stomach.
  • the pharmaceutical composition e.g., tolerogenic composition, nanoparticle composition, liposome composition, etc.
  • the pharmaceutical composition further comprises an immunomodulator or a nucleotide sequence encoding the immunomodulator.
  • An immunomodulator can be an immunosuppressor, which reduces effector cell (e.g., cytotoxic T cell) activity, or an immunostimulator, which promotes T cell anergy or exhaustion (e.g., described in Kwong et al., Immunology & Cell Biology (2021) 99: 486–495, and Linsley et al., Curr Opin Endocrinol Diabetes Obes (2019) 26:213–218) It is contemplated that the immunomodulator, when delivered to or expressed by the target cell, may induce or stabilize a tolerogenic, anergic, or exhausted status of the target cell or a cell in the vicinity.
  • effector cell e.g., cytotoxic T cell
  • an immunostimulator which promotes T cell anergy or exhaustion (e.g., described in Kwong et al., Immunology & Cell Biology (2021) 99: 486–495, and Linsley et al., Curr Opin Endocri
  • the immunomodulator comprises an immunomodulatory cytokine, for example, an immunomodulatory cytokine selected from IL-2, IL-10, TGF- ⁇ , IL-37, IL-27, IL-35, IL-31, Vasoactive Intestinal Peptide (VIP), and variants thereof.
  • the immunomodulatory cytokine is a mutant IL-2 that preferentially activates the IL-2R ⁇ receptor complex relative to the IL-2R ⁇ receptor complex (see, e.g., Ghelani et al., Front. Immunol. (2020) 11:1106; Khoryati et al., Sci Immunol. (2020) 5(50):eaba5264).
  • the immunomodulator comprises a nucleic acid encoding an immunomodulatory cytokine.
  • the immunomodulator comprises a nucleic acid encoding an intracellular or transmembrane immunomodulatory protein, for example, an immunomodulatory protein selected from PD-L1, PD-L2, ICOS ligand, ILT3, ILT4, BTLA, Fas, CD39, and indoleamine 2,3-dioxygenase 1 (IDO1), heme oxygenase 1, HLA-G, CD95L, galectin- 1, and DC-SIGN.
  • an immunomodulatory protein selected from PD-L1, PD-L2, ICOS ligand, ILT3, ILT4, BTLA, Fas, CD39, and indoleamine 2,3-dioxygenase 1 (IDO1), heme oxygenase 1, HLA-G, CD95L, galectin- 1, and DC-SIGN.
  • the immunomodulator comprises an immunomodulatory compound, for example, an immunomodulatory compound selected from vitamin A, vitamin D (e.g., 1 ⁇ ,25-dihydroxyvitamin D3, a.k.a. calcitriol), adenosine, kynurenine, retinoic acid, rapamycin, dexamethasone, corticosteroids, and a AhR ligand such as 2-(1' H-indole-3'-carbonyl)- thiazole-4-carboxylic acid methyl ester (ITE).
  • the immunomodulator provides a tolerogenic signal to an APC (e.g., dendritic cell, macrophage).
  • APC e.g., dendritic cell, macrophage
  • the immunomodulator comprises a ligand (for example a carbohydrate ligand) or an antibody to APC receptors, for example, Clec9A, an anti-C-type lectin (e.g., DC-SIGN, Mannose receptor (MR), or macrophage galactose-type C-type lectin (MGL)), dendritic cell immunoreceptor (DCIR), DCIR2, DEC205 (CD205), Langerin (CD207), and Sialic-acid binding immunoglobulin-type lectin (Siglec).
  • the immunomodulator can be delivered to the target cell by the delivery agent, for example, where the immunomodulator is present in or on the delivery agent.
  • the immunomodulator can be encapsulated or otherwise contained in the delivery agent, or covalently or non-covalently attached to an outer or inner surface of the delivery agent.
  • the immunomodulator is disposed in the delivery agent.
  • the tolerogenic composition further comprises a pharmaceutically acceptable carrier, excipient, or stabilizer (see, e.g., Adeboye Adejare, Remington: The Science and Practice of Pharmacy (23d ed. 2020)).
  • Suitable carriers are well known in the art and may include for example, nanoparticles, nanotubes, dendrimers, liposomes, foams, hydrogels, cubosomes, quantum dots, natural drug carriers, exosomes, and macrophages.
  • Acceptable carriers, excipients, or stabilizers are nontoxic to the recipients at the dosages and concentrations, and may comprise phosphate buffered saline solutions, water, emulsions, such as oil/water emulsions, various types of wetting agents, and sterile solutions.
  • the carrier or excipient comprises buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as Mercury((o-carboxyphenyl)thio)ethyl sodium salt (THIO E SAL), octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine
  • compositions comprising such carrier, excipients, or stabilizers can be formulated by well-known conventional methods.
  • the tolerogenic composition is formulated to have a pH in the range of about 4.5 to about 9.0, including for example pH ranges of about any one of 5.0 to about 8.0, about 6.5 to about 7.5, or about 6.5 to about 7.0.
  • the tolerogenic composition can also be made to be isotonic with blood by the addition of a suitable tonicity modifier, such as glycerol.
  • the tolerogenic composition is formulated as a liquid or the liquid is dried for a solid preparation (for example by spray drying or lyophilization).
  • cryoprotectants include, but are not limited to DMSO, sugars like trehalose and sucrose, polysaccharides, like starch and dextran, or proteins. Solid preparations allow for a long storage time of the tolerogenic composition. Lyophilized preparations of the tolerogenic composition can be stored in bulk or in ready-made doses for use such as in a vial.
  • the pharmaceutical composition e.g., a tolerogenic composition, is in the form of a lyophilized formulation or an aqueous solution.
  • the pharmaceutical composition e.g., a tolerogenic composition
  • a tolerogenic composition is administered to a patient enterally or parenterally.
  • the tolerogenic composition can be administered to a patient by oral, sublingual, gastric, or rectal administration.
  • the tolerogenic composition can administered to a patient by intravenous, intramuscular, intratumoral, intradermal, intrajejunal, intraileal, intracolonic, or intrarectal administration.
  • the tolerogenic composition can be also delivered by subcutaneous axillary and/or inguinal injection.
  • T1D-associated peptides disclosed herein can be presented by cognate MHCs (e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof) to form peptide-MHC (pMHC) complexes.
  • MHCs e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof
  • pMHC peptide-MHC
  • the pMHC complexes bind T cells that are prevalent in T1D patients, and are thus useful for targeting T cells (e.g., Treg cells and Tr1 cells) for treating and preventing T1D in a subject.
  • a vehicle e.g., a presentation agent
  • a vehicle e.g., a presentation agent
  • a presentation agent can be used to multimerize or cluster pMHC complexes to increase their binding avidity.
  • the present disclosure provides a composition (e.g., pharmaceutical composition) comprising a plurality of pMHC complexes disclosed herein bound to a presentation agent.
  • Useful presentation agents when bound to the pMHC complexes, can form, e.g., antigen-presenting cells (APCs), artificial APCs, or soluble complexes such as multimerized pMHC complexes.
  • APCs antigen-presenting cells
  • APCs artificial APCs
  • soluble complexes such as multimerized pMHC complexes.
  • the composition comprises an APC (e.g., dendritic cell, cultured cell line, artificial APC, nanoparticle, bead, liposome, or lipid bilayer scaffold) displaying MHC- presentable peptides disclosed herein presented by cognate MHC (e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof) molecules on an outer surface of the APC.
  • APCs are useful for eliciting a tolerogenic immune response, thereby to treat or prevent T1D in a subject.
  • the MHC-presentable peptide is presented by a soluble MHC, such as a soluble pMHC fusion protein disclosed herein (see the “Soluble MHC Complexes” subsection of Section II above).
  • the APC e.g., dendritic cell
  • the APC is a cell genetically engineered to silence or knock out a gene that mediates an immunostimulatory or inflammatory response (e.g., allograft inflammatory factor-1 (AIF1), see Elizondo et al., J.
  • AIF1 allograft inflammatory factor-1
  • the tolerogenic APC composition can be formulated in a carrier solution and stored frozen in a cell cryopreservation medium.
  • Cell cryopreservation media are known in the art, for example buffer solutions with varying amounts of DMSO such as CRYOSTOR® CS5 or CRYOSTOR® CS10.
  • the tolerogenic APC composition can then be administered to the subject after thawing. It is contemplated that the APC can be an autologous cell, i.e., from a subject to be treated with the tolerogenic APC composition.
  • Examples of artificial APCs useful in the present disclosure are known in the art.
  • the artificial APC comprises a cultured cell line presenting one or more MHC-presentable peptides disclosed herein.
  • the cell line can be engineered to express an MHC, e.g., HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof.
  • the cell line comprises the K562 human erythromyeloid cell line or the murine NIH/3T3 fibroblast line.
  • T cells can be co-cultured with the engineered cell line for a certain period of time before harvesting.
  • the cell line can be engineered to further express a molecule that provides signal 2, for example B7 family proteins, OX-40L, CD70, or 4-1BBL.
  • the artificial APC comprises a nanoparticle presenting one or more MHC-presentable peptides disclosed herein.
  • the nanoparticle can be coated with a pMHC or a soluble pMHC complex (see Perica et al., BBA Molecular Cell Research (2015) 1853(4):781-90), e.g., a T1D-associated peptide presented by HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof.
  • the nanoparticle can comprise various materials, for example, a gold particle with a layer of thiol-poly-ethylene glycol (PEG), a irondextran nanoparticle, or an iron oxide nanoparticle (e.g., a superparamagnetic iron oxide nanoparticle) (see Tsai et al., Immunity (2010) 32(4):568-80; Clemente-Casares et al., Nature (2016) 530(7591): 434-40; Umeshappa et al., Nat Commun.(2019) 10(1): 2150; Umeshappa et al., J Clin Invest.
  • PEG thiol-poly-ethylene glycol
  • irondextran nanoparticle e.g., a superparamagnetic iron oxide nanoparticle
  • the artificial APC comprises a bead presenting one or more MHC- presentable peptides disclosed herein.
  • the nanoparticle is engineered to present an MHC, for example HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof.
  • the bead comprises sepharose or latex (polystyrene) beads or irondextran microparticles (see e.g., Perica et al., BBA Molecular Cell Research (2015) 1853(4):781-790).
  • the bead is a biodegradable bead, made for example from biodegradable polymers, such as poly (lactic acid) (PLA), poly (glycolic acid) (PGA), and their co-polymer, and poly (lactic-co-glycolic acid) (PLGA).
  • PLA poly (lactic acid)
  • PGA poly (glycolic acid)
  • PLGA poly (lactic-co-glycolic acid)
  • the artificial APC comprises a liposome or a lipid bilayer scaffold presenting one or more MHC-presentable peptides disclosed herein.
  • the liposome or a lipid bilayer scaffold is engineered to present an MHC, for example HLA-DQ2.5, HLA-DQ8, HLA-DRB1, or any combination thereof.
  • the lipid bilayer scaffold is a APC- mimetic scaffold (APC-ms).
  • APC-ms APC- mimetic scaffold
  • the lipid bilayer is supported by mesoporous silica micro-rods.
  • the micro-rods are coated with a cytokine, a lipid bilayer, an MHC and a molecule that provides signal 2 (see e.g., Cheung et al., Nature Biotechnology (2016) 36: 160–169).
  • the liposome is an aryl hydrocarbon receptor-activating nanoliposome (AhR-NLP) (see e.g., Kenison et al., PNAS (2020) 117(50):32017-32018 and Rothhammer et al., Nature Reviews Immunology (2019) 19:184-197).
  • AhR-NLP aryl hydrocarbon receptor-activating nanoliposome
  • Another example of an aAPC is described in Li et al., J Clin Invest (2021) 131(23):e141051, and comprises covalently tethered peptide-MHC modules and immunomodulators linked to an Fc domain scaffold.
  • the resulting construct can be used in vitro or in vivo to modulate T cells, for example, by injecting into a patient to stimulate or modulate T cells in the patient.
  • the nanoparticle has a diameter that makes the particle suitable for administration, for example, systemic, in particular parenteral, administration. Nanoparticles typically have a diameter less than 1,000 nanometers (nm). In some aspects, the nanoparticle has a diameter of less than 600 nm. In some aspects, the nanoparticle has a diameter of less than 400 nm.
  • the nanoparticle has a diameter in the range of 50 to 1,000 nm, for example, 50 to 900 nm, 50 to 800 nm, 50 to 700 nm, 50 to 600 nm, 50 to 500 nm, 50 to 400 nm, 50 to 300 nm, 50 to 200 nm, 50 to 100 nm, 100 to 1,000 nm, 100 to 900 nm, 100 to 800 nm, 100 to 700 nm, 100 to 600 nm, 100 to 500 nm, 100 to 400 nm, 100 to 300 nm, 100 to 200 nm, 150 to 1,000 nm, 150 to 900 nm, 150 to 800 nm, 150 to 700 nm, 150 to 600 nm, 150 to 500 nm, 150 to 400 nm, 150 to 300 nm, 150 to 200 nm, 200 to 1,000 nm, 150 to 900 nm, 150 to 800 nm, 150 to 700 nm, 150 to 600 nm, 150 to 500
  • the composition further comprises an immunomodulator. It is contemplated that the pMHC complex bound to the presentation agent is targeted to T cells that express cognate TCRs.
  • the immunomodulator when delivered to an outer surface of the target T cell or internalized by the target T cell, can suppress survival, proliferation, activation, and/or memory formation of the target T cells. Immunomodulators can also be designed to modulate other immune cells in the microenvironment.
  • the immunomodulator is conjugated to the pMHC complex or the presentation agent, either covalently or noncovalently. In a specific aspect, the immunomodulator is coated on an outer surface of the presentation agent.
  • the immunomodulator can also be expressed by the APC.
  • the immunomodulator comprises an immunomodulatory cytokine, for example IL-2, IL-10, TGF- ⁇ , IL-37, IL-27, IL-35, IL-31, and Vasoactive Intestinal Peptide (VIP), or variants and fragments thereof.
  • the cytokine variant is a variant with altered binding affinity to its cognate receptor, for example the cytokine comprises IL-2, and the IL-2 comprises a variant with reduced or no binding affinity for CD25/IL-2R ⁇ .
  • the cytokine has at least 95%, 96%, 97%, 98%, 99%, or 100% identity to a wild type human cytokine.
  • the cytokine comprises a cytokine fused with another protein, such as a cytokine antibody fusion or cytokine receptor fusion (for example IL-15/IL-15R ⁇ fusion).
  • the immunomodulator comprises a protein providing a co-inhibitory signal 2 to T cells, for example PD-L1, PD-L2, ICOS ligand, CD80, CD86, ILT3, ILT4, Fas, CD39, and indoleamine 2,3-dioxygenase 1 (IDO1).
  • the immunomodulator comprises an agonist of an immunomodulatory receptor of a T cell, for example, PD-1, 4-1BB, CTLA-4, BTLA, LAG-3, TIM-3, TIGIT, CD2, or CD3.
  • the immunomodulator comprises the extracellular portion of a natural ligand of the immunomodulatory receptor of a T cell (e.g., PD- L1 or PD-L2) or a functional fragment thereof, or an agonistic antibody that binds the immunomodulatory receptor of a T cell (e.g., anti-PD-1 antibody, e.g., novolumab or pembrolizumab, or an anti-CTLA-4 antibody, e.g., ipilimumab) or an antigen-binding fragment thereof.
  • a natural ligand of the immunomodulatory receptor of a T cell e.g., PD- L1 or PD-L2
  • an agonistic antibody that binds the immunomodulatory receptor of a T cell e.
  • the immunomodulator inhibits the CD80/CD86-CD28 signaling.
  • the immunomodulator comprises an extracellular fragment of CTLA-4 (for example abatacept or belatacept), an antagonistic ligand or antibody to CD80 or CD86, or an antigen-binding fragment thereof.
  • CTLA-4 for example abatacept or belatacept
  • an antagonistic ligand or antibody to CD80 or CD86 or an antigen-binding fragment thereof.
  • the immunomodulator provides a tolerogenic signal to an APC (e.g., dendritic cell, macrophage), which may be present in the microenvironment.
  • APC e.g., dendritic cell, macrophage
  • the immunomodulator comprises a tolerogenic compound, for example vitamin D3, retinoic acid, rapamycin, dexamethasone, corticosteroids, ligands of the aryl hydrocarbon receptor (AhR), or specific cytokines (such as IL-10, TGF ⁇ ).
  • a tolerogenic compound for example vitamin D3, retinoic acid, rapamycin, dexamethasone, corticosteroids, ligands of the aryl hydrocarbon receptor (AhR), or specific cytokines (such as IL-10, TGF ⁇ ).
  • the immunomodulator comprises a ligand (for example a carbohydrate ligand) or an antibody to APC receptors, for example, Clec9A, an anti-C-type lectin (e.g., DC-SIGN, Mannose receptor (MR), or macrophage galactose-type C- type lectin (MGL)), dendritic cell immunoreceptor (DCIR), DCIR2, DEC205 (CD205), Langerin (CD207), and a Sialic-acid binding immunoglobulin-type lectin (Siglec) protein.
  • the pMHC-presentation agent composition further comprises one or more carriers, excipients, and/or stabilizers.
  • the pMHC-presentation agent composition is administered to a patient by intravenous, intramuscular, intratumoral, or intradermal administration.
  • T Cell Therapies [0281] The T cell compositions disclosed herein are useful as T cell therapies (e.g., adoptive T cell therapy). Accordingly, in another aspect, the present disclosure provides a T cell therapy comprising one or more T cell compositions disclosed herein (see Section IV above). In some aspects, the T cell therapy is a Treg cell therapy. [0282] In certain aspects, the T cell therapy is autologous, i.e., T cells obtained from a patient, after in vitro culture, are administered to the same patient.
  • the T cell therapy is allogeneic, optionally wherein the T cells are genetically engineered to inactivate a component of class II MHC (e.g., ⁇ 2).
  • the T cell compositions comprises T cells that express T cell mimetics disclosed herein.
  • the T cell therapy can further comprise one or more carriers, excipients, and/or stabilizers. Exemplary carriers, excipients, and stabilizers are described herein. VI. DIAGNOSTIC METHODS [0285] Information about the immunogenic MHC-presentable peptides associated with T1D can be used to diagnose or predict T1D in a subject.
  • compositions and methods disclosed herein are used to guide clinical decision making, e.g., identification of prognostic factors, monitoring of treatment response or disease progression, or implementation of preventative measures.
  • Information about the immunogenic MHC-presentable peptides associated with T1D can also be used to determine whether a subject may elicit a more desirable immune response to one therapeutic agent over another.
  • a subject having CD8+ T cells e.g., cytotoxic T cells
  • a therapy that comprises the MHC-presentable peptide and/or a nucleic acid encoding the MHC-presentable peptide.
  • Samples for making the assessment can be harvested for example from blood, body fluid, saliva, stool, or a tissue biopsy of a patient.
  • the samples can be analyzed the presence and/or amount of T cells reactive with the MHC-presentable peptides using a peptide-MHC tetramer or multimer-assay, an Enzyme Linked Immuno Spot Assay (ELISpot), or an Activation Induced Marker (AIM) assay.
  • the methods can be conducted in a multiplex manner. For example, a sample of T cells from a patient can be contacted with a peptide-MHC multimer library comprising a plurality of the MHC-presentable peptides disclosed herein, and T cells in the sample that binds to at least one member of the peptide-MHC multimer library can be identified.
  • the method can further comprise determining the sequence of the peptide(s) loaded onto the MHC multimer(s) to which the T cell binds, to thereby determine the antigenic specificity of the T cell response in the patient. It is contemplated that such a method can be conducted on a plurality of patients, and the resulting information can be used to identify a patient subpopulation having an antigen-specific T cell response of interest.
  • compositions are described as having, including, or comprising specific components, or where processes and methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are compositions of the present disclosure that consist essentially of, or consist of, the recited components, and that there are processes and methods according to the present disclosure that consist essentially of, or consist of, the recited processing steps.
  • compositions are described as having, including, or comprising specific components, or where processes and methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are compositions of the present disclosure that consist essentially of, or consist of, the recited components, and that there are processes and methods according to the present disclosure that consist essentially of, or consist of, the recited processing steps.
  • Example 1 Antigen Selection and Library Generation
  • 43 antigens were selected for study. These were selected from a potential list of thousands of antigens known to be expressed and potentially enriched in beta cells, which incorporate potentially millions of MHC-presentable peptides.
  • RNA sequencing datasets from the Genotype Tissue Expression (GTEx) project and from a study of pancreatic cell-type-specific gene expression (www.gtexportal.org/home/datasets, Nica et al. (2013) Genome Res 23:1554-1562.
  • GTEx Genotype Tissue Expression
  • peptides were selected to represent equal weightings within and across antigens, for example long antigens that have well-presented peptides such as Kinesin-like protein produce a larger absolute number of peptides relative to shorter, poorly-presented peptide regions, such as insulin.
  • IFN ⁇ ELISpot was performed on overlapping pools of peptides that allowed for the identification of immunogenic peptides. Peptides showing immunogenicity in 60% or more of donors are listed in Table 2B. [0300] The immunogenicity scores of the tested peptides were compared to their NetMHC scores as shown in FIG.6.
  • FIG.6A shows the scores for HLA-DQ8 epitopes and FIG.6B shows the scores for HLA-DQ2.5 epitopes.
  • This data shows that there is no real correlation between the NetMHC Elution score and the immunogenicity scoring. This suggests that NetMHC alone cannot be used to infer immunogenicity, and that with NetMHC alone one would not readily select the peptides identified herein.
  • Example 4. CIPHER Analysis [0301] The CIPHER platform (described in WO2021262872) leverages peptide-MHC multimers.
  • Such multimers incorporating an MHC-presentable peptide, a soluble fragment of MHC, and optionally a marker can be produced by various methods in vitro, for example, as described in Jordan et al., J. Immunol. (2008) 180(1): 188–97, WO2021202727;WO2021262872. Briefly, a T cell sample can be incubated with a library of peptide-MHC (“pMHC”) complex. The T cells that bind the pMHC can then be isolated, and the peptides that are complexed with the pMHC can be identified. The method can be conducted in a multiplex manner.
  • pMHC peptide-MHC
  • a plurality of barcoded pMHC multimers can be contacted with T cells in parallel, followed by replicating each TCR-encoding nucleic acid in a hydrogel linked with a barcode (see, e.g., WO2020142724 and WO2021138588, incorporated herein by reference).
  • This screening technique allows the determination of immunopravelence as well as cognate MHC- presentable peptide specificity and HLA restriction of a T cell ex vivo.
  • CIPHER to identify the TCRs from immunoreactive T cells in order to further define the phenotype and frequency of peptide-specific T cells.
  • a T1D vaccine will be prepared as an mRNA cassette that expresses peptides determined to be immunogenic see Table 3. This vaccine will be used to transfect antigen presenting cells (APCs) that express the relevant MHC, i.e. DQ2, DQ8, DQ2 and DQ8 etc. These transfected APCs will be co-cultured with primary human T cells that recombinantly express T cell receptors demonstrated to react to peptides in the vaccine. After incubation of up to 5 days the T cells will be harvested and analyzed for Treg phenotype and expansion.
  • APCs antigen presenting cells
  • Tregs were generated and expanded to specific MHC-presentable peptides in the vaccine, we will compare the harvested T cells to control T cells expressing the specific TCRs but co-cultured with APCs expressing irrelevant peptides and/or to T cells expressing irrelevant TCRs co-cultured with the T1D vaccine.
  • Example 6 Methods of Treating T1D in vivo [0303] 10 to 20 MHC-presentable peptides will be selected to prepare an mRNA vaccine.
  • T1D non-obese diabetic
  • NOD non-obese diabetic
  • This mRNA vaccine or control mRNA vaccine composed of irrelevant peptides will be administered to 8-10 week old NOD mice, after the expected start of T1D pathogenesis, i.e., after the induction of pathogenic T cells therefore providing a therapeutic benefit.
  • mice treated with the mRNA vaccine will be compared to control treated mice for development of diabetes, survival, and T cell phenotype and function. It is expected that mice treated with the T1D mRNA vaccine will have decreased rates of diabetes, increased survival, and increased overall and peptide-specific Tregs with functional suppressive capacity.
  • Example 7. In vivo Efficacy in NOD Mouse Model of Type 1 Diabetes [0304] NOD mice were immunized intravenously once a week for five weeks starting when the mice were 6 weeks of age.
  • the tolerizing vaccine (tolerizing mRNA) used in this experiment used a Lipid Particle Formulation as follows: • Formulation 1: Lipid Particle Formulation with tol105 mRNA and KIF1a mRNA (20 ⁇ g of each, 40 ⁇ g total) • Formulation 2: Lipid Particle Formulation with tol105 mRNA, KIF1a mRNA, and IL- 10HA mRNA (20 ⁇ g of each, 60 ⁇ g total) • Formulation 3: Lipid Particle Formulation with no mRNA, dosed at a lipid equivalence to the 60 ⁇ g dose of formulation 2.
  • Tol105 is a construct made using literature epitopes described in Podojil, JR, et al., “Tolerogenic Immune-Modifying Nanoparticles Encapsulating Multiple Recombinant Pancreatic ⁇ Cell Proteins Prevent Onset and Progression of Type 1 Diabetes in Nonobese Diabetic Mice,” J Immunol. (Aug 1 2022):209(3):465-75. doi: 10.4049/jimmunol.2200208. Epub 2022 Jun 20. PMID: 35725270; PMCID: PMC9339508.
  • the KIF1a mRNA consists of two overlapping DECODE class I epitopes with flanks.
  • mice were monitored for blood glucose levels once a week. Hyperglycemia was indicated when blood glucose levels exceeded 200mg/dL glucose and diabetes was indicated when blood glucose levels exceeded 400mg/dL. Diabetic mice were euthanized and their spleens and pancreas collected. All remaining mice on study were euthanized when the mice were 30 weeks of age and spleen and pancreas collected. Results from the study are provided in FIGs. 5A-B. This Example shows that the mRNA tolerizing vaccine reduces hyperglycemia in NOD mice.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Veterinary Medicine (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Chemical & Material Sciences (AREA)
  • Immunology (AREA)
  • Public Health (AREA)
  • Medicinal Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Animal Behavior & Ethology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Diabetes (AREA)
  • Endocrinology (AREA)
  • Rheumatology (AREA)
  • Microbiology (AREA)
  • Mycology (AREA)
  • Epidemiology (AREA)
  • Peptides Or Proteins (AREA)

Abstract

L'invention concerne des peptides présentables par le CMH associés au diabète de type 1. L'invention concerne également des cellules présentatrices d'antigène présentant de tels peptides présentables par le CMH, des lymphocytes T réactifs à de tels peptides présentables par le CMH, ainsi que des compositions et des thérapies associées.
PCT/US2024/049097 2023-09-29 2024-09-27 Peptides présentables par le cmh associés au diabète de type 1 Pending WO2025072849A1 (fr)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US202363587028P 2023-09-29 2023-09-29
US63/587,028 2023-09-29
US202463619403P 2024-01-10 2024-01-10
US63/619,403 2024-01-10

Publications (1)

Publication Number Publication Date
WO2025072849A1 true WO2025072849A1 (fr) 2025-04-03

Family

ID=93099759

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2024/049097 Pending WO2025072849A1 (fr) 2023-09-29 2024-09-27 Peptides présentables par le cmh associés au diabète de type 1

Country Status (1)

Country Link
WO (1) WO2025072849A1 (fr)

Citations (20)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4235871A (en) 1978-02-24 1980-11-25 Papahadjopoulos Demetrios P Method of encapsulating biologically active materials in lipid vesicles
US4837028A (en) 1986-12-24 1989-06-06 Liposome Technology, Inc. Liposomes with enhanced circulation time
US5000887A (en) 1988-05-17 1991-03-19 Liposome Technology, Inc. Preparation of uniform-size liposomes
US5395619A (en) 1993-03-03 1995-03-07 Liposome Technology, Inc. Lipid-polymer conjugates and liposomes
WO2013184976A2 (fr) 2012-06-06 2013-12-12 Northwestern University Compositions et procédés d'induction d'une tolérance spécifique d'antigène
WO2013192532A2 (fr) 2012-06-21 2013-12-27 Northwestern University Particules conjuguées à des peptides
WO2016097334A1 (fr) 2014-12-19 2016-06-23 ETH Zürich Récepteurs antigéniques chimères et leurs procédés d'utilisation
US20160324779A1 (en) 2003-09-17 2016-11-10 Rodos Biotarget Gmbh Targeted Lipid-Drug Formulations for Delivery of Drugs to Myeloid and Lymphoid Immune Cells
EP3095440A1 (fr) 2015-05-19 2016-11-23 PLS-Design GmbH Immunothérapie spécifique d'un antigène à l'aide de liposomes de tolérance
US20180071376A1 (en) 2015-03-23 2018-03-15 The Brigham And Women`S Hospital, Inc. Tolerogenic nanoparticles for treating diabetes mellitus
WO2019133881A1 (fr) 2017-12-29 2019-07-04 Rubius Therapeutics, Inc. Édition génique et modulation transcriptionnelle ciblée pour modifier des cellules érythroïdes
WO2019165436A1 (fr) 2018-02-26 2019-08-29 Antolrx Liposomes tolérogènes et leurs procédés d'utilisation
US20190282707A1 (en) 2015-12-23 2019-09-19 Cour Pharmaceuticals Development Company, Inc Covalent polymer-antigen conjugated particles
WO2019197671A1 (fr) 2018-04-12 2019-10-17 ETH Zürich Affichage de peptide du cmh de mammifère en tant qu'outil de sélection d'épitope pour la conception d'un vaccin
WO2019210055A2 (fr) 2018-04-26 2019-10-31 Agenus Inc. Compositions peptidiques de liaison à une protéine de choc thermique (hsp) et leurs méthodes d'utilisation
WO2020055931A1 (fr) 2018-09-10 2020-03-19 Torque Therapeutics, Inc. Lymphocytes t spéciphiques d'un antigène et leurs méthodes de fabrication et d'utilisation
WO2020142724A1 (fr) 2019-01-04 2020-07-09 Cogen Immune Medicine, Inc. Banques de peptides et leurs méthodes d'utilisation
WO2021138588A1 (fr) 2020-01-03 2021-07-08 Repertoire Immune Medicines, Inc. Compositions d'hydrogels et leurs procédés d'utilisation
WO2021202727A2 (fr) 2020-03-31 2021-10-07 Repertoire Immune Medicines, Inc. Bibliothèques de multimères de cmh de peptide échangeables et à codes-barres
WO2021262872A2 (fr) 2020-06-24 2021-12-30 Repertoire Immune Medicines, Inc. Constructions d'expression de multimères du cmh et leurs utilisations

Patent Citations (22)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4235871A (en) 1978-02-24 1980-11-25 Papahadjopoulos Demetrios P Method of encapsulating biologically active materials in lipid vesicles
US4837028A (en) 1986-12-24 1989-06-06 Liposome Technology, Inc. Liposomes with enhanced circulation time
US5000887A (en) 1988-05-17 1991-03-19 Liposome Technology, Inc. Preparation of uniform-size liposomes
US5395619A (en) 1993-03-03 1995-03-07 Liposome Technology, Inc. Lipid-polymer conjugates and liposomes
US20160324779A1 (en) 2003-09-17 2016-11-10 Rodos Biotarget Gmbh Targeted Lipid-Drug Formulations for Delivery of Drugs to Myeloid and Lymphoid Immune Cells
WO2013184976A2 (fr) 2012-06-06 2013-12-12 Northwestern University Compositions et procédés d'induction d'une tolérance spécifique d'antigène
US20200046816A1 (en) 2012-06-06 2020-02-13 Northwestern University Compositions and Methods for Antigen-Specific Tolerance
WO2013192532A2 (fr) 2012-06-21 2013-12-27 Northwestern University Particules conjuguées à des peptides
WO2016097334A1 (fr) 2014-12-19 2016-06-23 ETH Zürich Récepteurs antigéniques chimères et leurs procédés d'utilisation
US20180071376A1 (en) 2015-03-23 2018-03-15 The Brigham And Women`S Hospital, Inc. Tolerogenic nanoparticles for treating diabetes mellitus
EP3095440A1 (fr) 2015-05-19 2016-11-23 PLS-Design GmbH Immunothérapie spécifique d'un antigène à l'aide de liposomes de tolérance
US20190282707A1 (en) 2015-12-23 2019-09-19 Cour Pharmaceuticals Development Company, Inc Covalent polymer-antigen conjugated particles
WO2019133881A1 (fr) 2017-12-29 2019-07-04 Rubius Therapeutics, Inc. Édition génique et modulation transcriptionnelle ciblée pour modifier des cellules érythroïdes
US20200405642A1 (en) 2018-02-26 2020-12-31 AnTolRx, Inc. Tolerogenic liposomes and methods of use thereof
WO2019165436A1 (fr) 2018-02-26 2019-08-29 Antolrx Liposomes tolérogènes et leurs procédés d'utilisation
WO2019197671A1 (fr) 2018-04-12 2019-10-17 ETH Zürich Affichage de peptide du cmh de mammifère en tant qu'outil de sélection d'épitope pour la conception d'un vaccin
WO2019210055A2 (fr) 2018-04-26 2019-10-31 Agenus Inc. Compositions peptidiques de liaison à une protéine de choc thermique (hsp) et leurs méthodes d'utilisation
WO2020055931A1 (fr) 2018-09-10 2020-03-19 Torque Therapeutics, Inc. Lymphocytes t spéciphiques d'un antigène et leurs méthodes de fabrication et d'utilisation
WO2020142724A1 (fr) 2019-01-04 2020-07-09 Cogen Immune Medicine, Inc. Banques de peptides et leurs méthodes d'utilisation
WO2021138588A1 (fr) 2020-01-03 2021-07-08 Repertoire Immune Medicines, Inc. Compositions d'hydrogels et leurs procédés d'utilisation
WO2021202727A2 (fr) 2020-03-31 2021-10-07 Repertoire Immune Medicines, Inc. Bibliothèques de multimères de cmh de peptide échangeables et à codes-barres
WO2021262872A2 (fr) 2020-06-24 2021-12-30 Repertoire Immune Medicines, Inc. Constructions d'expression de multimères du cmh et leurs utilisations

Non-Patent Citations (72)

* Cited by examiner, † Cited by third party
Title
AZOURY ET AL., DIABETES, vol. 70, 2021, pages 2879 - 2891
AZOURY MARIE ELIANE ET AL: "Peptides Derived From Insulin Granule Proteins Are Targeted by CD8+ T Cells Across MHC Class I Restrictions in Humans and NOD Mice", DIABETES, vol. 69, no. 12, 14 September 2020 (2020-09-14), pages 2678 - 2690, XP093232560, ISSN: 0012-1797, Retrieved from the Internet <URL:https://journals.org/diabetes/diabetes/article-pdf/69/12/2678/434710/db200013.pdf> DOI: 10.2337/db20-0013 *
BABON ET AL., NAT MED, vol. 22, 2016, pages 1482 - 1487
BABON ET AL., NATA1ED, vol. 22, 2016, pages 1482 - 1487
BANERJEE ET AL., NANOMEDICINE, vol. 9, no. 6, 2013, pages 722 - 8
BLOOM ET AL., GENE THERAPY, vol. 28, 2021, pages 117 - 29
CHEUNG ET AL., NATURE BIOTECHNOLOGY, vol. 36, 2018, pages 160 - 169
CLEMENTE-CASARES ET AL., NATURE, vol. 530, no. 7591, 2016, pages 434 - 401
COBBOLD ET AL., SCI TRANSL MED, vol. 5, no. 203, 2013, pages 203 - 125
DELOTIC ET AL., SCIENCE, vol. 351, 2016, pages 711 - 714
DOYLE ET AL., AUTOIMMUNITY, vol. 46, 2013, pages 6 - 13
DOYLE ET AL., AUTOIMMUNITY, vol. 47, 2014, pages 220 - 233
EIZIRIK ET AL., PLOS GENET, vol. 8, 2012, pages e1002552
ELIZONDO ET AL., J. LEUKOC. BIOL, vol. 105, no. 1, 2019, pages 123 - 30
GONZALEZ-DUQUE ET AL., CELL METAB, vol. 28, 2018, pages 946 - 960
GRATZNER, SCIENCE, vol. 218, no. 4571, 1982, pages 474 - 75
HALLIDAY ET AL., FRONT. IMMUNOL, vol. 11, 2020, pages 600000
JA.NIISON ET AL., J. IMMUNOL, vol. 203, no. 1, 2019, pages 48 - 57
JAMES EDDIE A. ET AL: "T-Cell Epitopes and Neo-epitopes in Type 1 Diabetes: A Comprehensive Update and Reappraisal", DIABETES, vol. 69, no. 7, 15 June 2020 (2020-06-15), pages 1311 - 1335, XP093232417, ISSN: 0012-1797, Retrieved from the Internet <URL:https://journals.org/diabetes/diabetes/article-pdf/69/7/1311/435627/dbi190022.pdf> DOI: 10.2337/dbi19-0022 *
JAMES ET AL., DIABETES, vol. 69, 2020, pages 1311 - 1335
JONG ET AL., DIABETOLOGIA, vol. 56, 2013, pages 2651 - 2658
JORDAN ET AL., J. IMMUNOL, vol. 180, no. 1, 2008, pages 188 - 97
JORDAN ET AL., J. IMMUNOL., vol. 180, no. 1, 2008, pages 188 - 97
KAGAYA ET AL., GENE THER, vol. 19, no. 1, 2012, pages 61 - 9
KENISON ET AL., PNAS, vol. 117, no. 50, 2020, pages 32017 - 32018
KENISON ET AL., PROC. NATL. ACAD. SCI., vol. 117, no. 50, 2020, pages 32017 - 32028
KHORYATI ET AL., SCI IMMUNOL, vol. 5, no. 50, 2020, pages eaba5264
KIM ET AL., POLYMERS, vol. 11, no. 2, 2019, pages 288
KISIELOW ET AL., NAT. IMMUNOL, vol. 20, 2019, pages 652 - 62
KRACHT ET AL., NAT MED, vol. 23, 2017, pages 501 - 507
KUMAR ET AL., ACS INFECT DIS, vol. 5, no. 3, 2019, pages 443 - 453
KWONG ET AL., IMMUNOLOGY & CELL BIOLOGY, vol. 99, 2021, pages 486 - 495
LEI ET AL., CHEM SCI, vol. 12, no. 18, 2021, pages 6449 - 6457
LI ET AL., J CLIN INVEST, vol. 131, no. 23, 2021, pages e141051
LINSLEY ET AL., CURR OPIN ENDOCRINOL DIABETES OBES, vol. 26, 2019, pages 213 - 218
LUMMEL ET AL., DIABETES, vol. 63, 2014, pages 237 - 247
LUO ET AL., J CONTROL RELEASE, vol. 10, no. 170, 2013, pages 259 - 67
LUO ET AL., J. CONTROL RELEASE, vol. 170, no. 2, 2013, pages 259 - 67
MANNERING ET AL., DIABETOLOGIA, vol. 62, 2019, pages 351 - 356
MANNERING ET AL., J EXP MED, vol. 202, 2005, pages 1191 - 1197
MARIN-GALLEN ET AL., CLIN. EXP. IMMUNOL, vol. 160, no. 2, 2010, pages 207 - 14
MCINNIS ET AL., J IMMUNOTHER CANCER, vol. 11, 2023, pages 3
MCLAUGHLIN ET AL., CLIN EXP IMMUNOL, vol. 185, pages 133 - 140
MEHRFELD ET AL., FRONT. IMMUNOL, vol. 9, 2018, pages 635
MEI ET AL., MOL CELL PROTEOMICS, vol. 19, 2020, pages 1236 - 1247
MIAO, L ET AL., MOLECULAR CANCER, vol. 20, 2021, pages 41
NATURE, vol. 401, 1999, pages 921 - 923
NICA ET AL., GENOME RES, vol. 23, 2013, pages 1554 - 1562
OBERMAIR ET AL., SCI. ADV, vol. 8, 2022, pages eabl5394
PERICA ET AL., BBA MOLECULAR CELL RESEARCH, vol. 1853, no. 4, 2015, pages 781 - 790
PODOJIL JOSEPH R. ET AL: "Tolerogenic Immune-Modifying Nanoparticles Encapsulating Multiple Recombinant Pancreatic [beta] Cell Proteins Prevent Onset and Progression of Type 1 Diabetes in Nonobese Diabetic Mice", JOURNAL OF IMMUNOLOGY, vol. 209, no. 3, 1 August 2022 (2022-08-01), pages 465 - 475, XP093232443, ISSN: 0022-1767, Retrieved from the Internet <URL:https://journals.aai.org/jimmunol/article-pdf/209/3/465/1641271/ji2200208.pdf> DOI: 10.4049/jimmunol.2200208 *
PODOJIL, JR ET AL.: "Tolerogenic Immune-Modifying Nanoparticles Encapsulating Multiple Recombinant Pancreatic β Cell Proteins Prevent Onset and Progression of Type 1 Diabetes in Nonobese Diabetic Mice", J IMMUNOL., vol. 209, no. 3, 1 August 2022 (2022-08-01), pages 465 - 75
PUJOL-AUTONELL ET AL., PLOS ONE, vol. 10, no. 6, 2015, pages e0127057
PUTZ ET AL., METHODS MOL MED, vol. 109, 2005, pages 71 - 82
REJMAN ET AL., BIOCHEM J, vol. 377, no. 1, 2004, pages 159 - 69
REYNISSON ET AL., NUCLEIC ACIDS RES, vol. 48, 2020, pages 449 - 454
ROTHHAMMER ET AL., NATURE REVIEWS IMMUNOLOGY, vol. 19, 2019, pages 184 - 197
RUAN ET AL., J. CONTROL RELEASE, vol. 279, 2018, pages 306 - 315
SCHAAP-JOHANSEN ET AL., FRONT. IMMUNOL, vol. 12, 2021, pages 712488
SCHUBERT, GENOME MEDICINE, vol. 8, 2016, pages 9
SEMIN CELL DEV BIOL, vol. 31, 2014, pages 64 - 72
SIDNEY ET AL., BMC IMMUNOL, vol. 19, 2018, pages 12
SUAREZ ET AL., TRANSFUS. MED. HEMOTHER, vol. 47, 2020, pages 464 - 71
THORP ET AL., FRONT IMMUNOL, vol. 11, 2020, pages 945
TSAI ET AL., IMMUNITY, vol. 32, no. 4, 2010, pages 568 - 80
TURTLE ET AL., CANCER J, vol. 16, no. 4, 2010, pages 374 - 81
UMESHAPPA ET AL., J CLIN INVEST., vol. 130, no. 4, 2020, pages 1823 - 29
UMESHAPPA ET AL., NAT COMMUN, vol. 10, no. 1, 2019, pages 2150
VELDERS ET AL., J. IMMUNOL., vol. 166, 2001, pages 5366 - 73
WU ET AL., BIOMATERIALS, vol. 34, no. 4, 2013, pages 1213 - 22
YANG ET AL., ANTIOXID REDOX SIGNAL, vol. 29, 2017, pages 1415 - 1431
YESTE ET AL., SCI SIGNAL, vol. 9, no. 433, 2016, pages ra61

Similar Documents

Publication Publication Date Title
Gangadaran et al. The emerging role of exosomes in innate immunity, diagnosis and therapy
Yi et al. Surface engineered polymersomes for enhanced modulation of dendritic cells during cardiovascular immunotherapy
US11186825B2 (en) Compositions and methods for evaluating and modulating immune responses by detecting and targeting POU2AF1
JP6763832B2 (ja) 感染症、自己免疫疾患、同種因子に対する免疫応答、アレルギー性疾患、腫瘍、移植片拒絶反応、および、遺伝子療法または遺伝子ワクチン接種のために使用されるウイルスベクターに対する免疫応答の予防および／または治療における使用のための免疫原性ペプチド
EP3368689B1 (fr) Compositions d&#39;évaluation et de modulation des réponses immunitaires à l&#39;aide de signatures génétiques de cellules immunitaires
TW202024120A (zh) 靶向樹突狀細胞之胞外囊泡及其用途
US20200121727A1 (en) Methods and compositions for treating skeletal muscular dystrophy
US20220251200A1 (en) Extracellular vesicles targeting t cells and uses thereof
Wu et al. Spleen‐targeted neoantigen DNA vaccine for personalized immunotherapy of hepatocellular carcinoma
AU2024200560B2 (en) Immunogenic peptides specific to BCMA and TACI antigens for treatment of cancer
US20140286906A1 (en) Use of igf-1 in the modulation of treg cell activity and the treatment and prevention of autoimmune disorders or diseases
EP4499117A1 (fr) Compositions et procédés pour activation de cellules immunitaires
JP2013544243A (ja) 動脈瘤の治療及び／又は予防のための免疫調節方法及びシステム
JP2014516913A (ja) 高血圧の治療及び／又は予防のための免疫調節方法及びシステム
WO2024026452A1 (fr) Épitopes de lymphocytes t associés au diabète de type 1
US20200010530A1 (en) Methods and reagents to treat autoimmune diseases and allergy
Cai et al. Dendritic cells and antigen-specific immunotherapy in autoimmune rheumatic diseases
JP6283809B2 (ja) Ｉ型糖尿病の予防又は治療のための製剤
Mondanelli et al. Islet antigen-pulsed dendritic cells expressing ectopic IL-35Ig protect nonobese diabetic mice from autoimmune diabetes
WO2025072849A1 (fr) Peptides présentables par le cmh associés au diabète de type 1
Wang et al. Nanoparticle platform preferentially targeting liver sinusoidal endothelial cells induces tolerance in CD4+ T cell-mediated disease models
EP3609912B1 (fr) Procédés de production de peptides, polypeptides ou cellules pour moduler l&#39;immunité
CN112011833A (zh) 筛选和分离肿瘤新生抗原的方法
US20200331976A1 (en) Multivalent Antigens Stimulating TH1 and TH2
Zhang et al. Lipid-mediated insertion of Toll-like receptor (TLR) ligands for facile immune cell engineering

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 24790081

Country of ref document: EP

Kind code of ref document: A1