WO2025248505A1 - Methods for treating endometrial and ovarian hyperproliferative disorders - Google Patents

Abstract

The current disclosure provides novel treatments for endometrial and ovarian hyperproliferative disorders, such as endometriosis, certain cancers, and benign hyperproliferation in female reproductive tissues. According, aspects of the disclosure relate to a method for treating endometrial or ovarian hyperproliferative disorders in a subject, the method comprising administration of a modulator of LMTK3 to the subject. The disclosure further describes nucleic acids encoding peptides of the disclosure and host cells and compositions comprising the nucleic acids or peptides of the disclosure.

Description

DESCRIPTION METHODS FOR TREATING ENDOMETRIAL AND OVARIAN HYPERPROLIFERATIVE DISORDERS CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims priority to and the benefit of U.S. Provisional Application No.63/654,661, filed May 31, 2024, the contents of which is incorporated herein by reference in its entirety. SEQUENCE LISTING [0002] The instant application contains a Sequence Listing which has been submitted in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on May 30, 2025, is named “TMPLP0014WO.xml” and is 50,528 bytes in size. BACKGROUND I. Field of the Invention [0003] This invention relates to the field of medicine and molecular biology. II. Background [0004] It is estimated that about 21,750 women will receive a new diagnosis of ovarian cancer and about 13,940 women will die from ovarian cancer in the year of 2020. Ovarian cancer ranks fifth in cancer deaths among women, accounting for more deaths than any other cancer of the female reproductive system. A woman's risk of getting ovarian cancer during her lifetime is about 1 in 78. Her lifetime chance of dying from ovarian cancer is about 1 in 108. These statistics don’t count low malignant potential ovarian tumors. Because there are no screening tests for ovarian cancer, and symptoms are often subtle, most ovarian cancer cases are diagnosed at a more advanced stage. [0005] For stages II, III, or IV ovarian cancer, surgery is typically performed prior to chemotherapy in order to remove the tumor, both ovaries, and affected organs and lymph nodes throughout the body. After surgery, the majority of patients will start a personalized chemotherapy plan, including one or more chemotherapy drugs. Sometimes, once a diagnosis of ovarian cancer has been made by a biopsy, a few cycles of chemotherapy are given first in order to make surgery more successful and less complicated. Chemotherapy is then completed

TMPL14WO_spec.docx - 1 - after surgery. There are some targeted or biologic therapies available for ovarian cancer. Despite the advances in ovarian cancer therapies, the 5-year relative survival rate is less than 50%. Therefore, there is a need for additional ovarian cancer therapeutics. SUMMARY [0006] The current disclosure provides treatment, composition and methods for hyperproliferative disorders, such as endometriosis, certain cancers, and benign hyperproliferation in female reproductive tissues. Accordingly, aspects of the disclosure relate to a method for treating endometrial or ovarian hyperproliferative disorders in a subject, the method comprising administration of a modulator of LMTK3 to the subject. Further aspects relate to an amino acid peptide comprising the sequence of one of SEQ ID NOS:1-30. Yet further aspects relate to an amino acid peptide comprising the consensus sequence: WVG- [S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L]-[A/N]-X-[N/V]-[N/L/R]-[E/Y]-X-[R/V], wherein x is any amino acid. Also provided is an amino acid peptide comprising the consensus sequence: WVG-[S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L/D]-[A/N/E]-X-[N/V/Y]-[N/L/R]-[E/Y/D]-X- [R/V/D/L]. The sequence of WVG-[S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L]-[A/N]-X-[N/V]- [N/L/R]-[E/Y]-X-[R/V] may include or exclude one or more of SEQ ID NOS:1-30. The disclosure further describes nucleic acids encoding peptides of the disclosure and host cells and compositions comprising the nucleic acids or peptides of the disclosure. Further aspects relate to a method of making a peptide of the disclosure, the method comprising expressing a nucleic acid of the disclosure in a host cell. Also provided is a method of making a peptide of the disclosure comprising chemically synthesizing the peptide. The peptides and compositions of the disclosure may be administered to a subject for treating a hyperproliferative disorder in the subject. [0007] The disclosure also provides for an expression construct comprising nucleic acids of the disclosure, such as nucleic acids encoding LMTK3 modulators. Host cells comprising the expression construct are also described. Methods include a method for making a peptide comprising incubating the host cell under conditions for expression of the peptide from the expression construct. Expression constructs include viral and non-viral vectors. [0008] Aspects of the disclosure also relate to a method for evaluating a subject comprising detecting LMTK3 in a biological sample from the subject. A further aspect relates to a method for treating a subject for cancer comprising treating a subject having a biological sample that was determined to have low expression of LMTK3 with chemotherapy and/or radiotherapy. A further aspect relates to a method for treating a subject for cancer comprising treating a subject

TMPL14WO_spec.docx - 2 - having a biological sample that was determined to have high expression of LMTK3 with the combination of i) a LMTK3 modulator and ii) chemotherapy and/or radiotherapy. A yet further aspect relates to a method of prognosing a subject with cancer or predicting a therapeutic response to chemotherapy or radiation therapy comprising: a) measuring LMTK3 expression level in a biological sample from the subject; b) comparing the measured level to control level or control samples; and c) prognosing the subject or predicting a therapeutic response based on the measured level of LMTK3. [0009] The disclosure also describes methods for treating an LMTK3+ hyperproliferative disorder comprising contacting LMTK3+ cells with an LMTK3+ modulator that binds to and inhibits LMTK3. In some embodiments, the LMTK3+ hyperproliferative disorder is an LMTK3+ cancer. The methods of the disclosure include reducing LMTK3+ cancer cells in a subject in need thereof. The disclosure also relates to inhibiting progression of LMTK3+ cancers in a subject in need thereof. The methods also include reducing tumor size in a subject in need thereof. Methods also include treating, inhibiting, or reducing an ovarian cancer tumor. Methods also include treating, reducing, or inhibiting the growth of endometrial tissue. It is specifically contemplated that one or more of these aspects may be excluded. [0010] The methods of the disclosure may include extension of the subject's life by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 30 years (or any range derivable therein); decrease or delay in the neoplastic development of the disease; decrease in hyperproliferation; reduction in tumor growth; delay of metastases or reduction in number of metastases; reduction in cancer cell number or tumor cell proliferation rate; decrease or delay in progression of neoplastic development from a premalignant condition; and a decrease in pain to the subject that can be attributed to the subject's condition. The reduction, decrease, or delay may be a reduction of at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, or 80%, or any derivable range therein. Methods of the disclosure may also increase the overall survival rate, the progression- free survival rate, and/or recurrence-free survival rate. The increase may be by at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, or 80%, or any derivable range therein. [0011] Also provided are kits comprising for detecting LMTK3 expression in a biological sample from the subject. The kits may comprise at least one LMTK3 detection agent, such as probes or primers for detecting LMTK3 nucleic acids and/or antibodies or LMTK3 binding polypeptides for detecting LMTK3 polypeptides. [0012] The hyperproliferative disorder may include or exclude a cancer. Hyperproliferative disorders include or exclude pre-cancer and dysplasia. The hyperproliferative disorder may include or exclude an endometrial or ovarian

TMPL14WO_spec.docx - 3 - hyperproliferative disorder. The hyperproliferative disorder may comprise a cancer that is positive for the expression of LMTK3. The hyperproliferative disorder may include or exclude a gynecologic cancer such as cervical, ovarian, uterine, vaginal, or vulvar cancer. The hyperproliferative disorder may comprise ovarian cancer. The hyperproliferative disorder may comprise glioblastoma, breast cancer, lung cancer, liver cancer, prostate cancer, bladder cancer, colorectal cancer, or thyroid cancer. The hyperproliferative disorder may comprise endometriosis. The hyperproliferative disorder may comprise a cancerous tumor. The tumor may be of any histotypes or of a specific histotype, such as HGSC (High grade serous carcinomas, MC (Mucinous carcinomas), EC (Endometroid carcinomas) and CCC (Clear cell carcinomas). [0013] The hyperproliferative disorder may also include or exclude a benign tumor, such as a fibroid or polyp in the uterus, ovaries, or fallopian tubes. Other hyperproliferative disorders include or exclude benign tumors such as endometriomas, adenomyosis, ovarian cysts, and uterine leiomyomas. [0014] The modulator may inhibit LMTK3 by directly inhibiting its activity or by inhibiting it’s binding to another cellular molecule. The modulator may comprise a peptide modulator. In some embodiments, the peptide modulator is a peptide comprising an N-terminal WVG motif that is capable of binding to and inhibiting LMTK3. The peptide modulator may comprise the consensus sequence: WVG-[S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L]-[A/N]-X-[N/V]- [N/L/R]-[E/Y]-X-[R/V], wherein x is any amino acid. The peptide modulator may comprise the consensus sequence of: WVG-[S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L]-[A/N]-X-[N/V]-[N/L/R]- [E/Y]-X-[R/V]-XXX. The peptide modulator may comprise the consensus sequence of WVG- [S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L/D]-[A/N/E]-X-[N/V/Y]-[N/L/R]-[E/Y/D]-X-[R/V/D/L]. “X” in the consensus sequence can be any amino acid. X may include or exclude one or more of alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, or valine. X may be a D stereoisomer amino acid. X may be a L sterioisomer amino acid. [0015] The peptide may be of a certain length. In some embodiments, the peptide is, is at least, or is at most 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,

TMPL14WO_spec.docx - 4 - 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, or 200 amino acids in length (or any derivable range therein). In some embodiments, the peptide is 3-50, 3-20, 5-20, 10-20 or 15-20 amino acids in length. The peptide may be seventeen amino acids in length. The peptide may comprise the amino acid sequence of one of SEQ ID NOS:1-30, or an amino acid sequence with at least 80% sequence identity to one of SEQ ID NOS:1-30, or a fragment thereof. The peptide may comprise an amino acid sequence with at least 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% sequence identity to one of SEQ ID NOS:1-30. The peptide may comprise only D, only L, or both D and L amino acid stereoisomers. The peptide may comprise both D and L amino acid stereoisomers. The peptide may comprise one or more D amino acid stereoisomers. The peptide may comprise, comprise at least, or comprise at most, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 D or L amino acid stereoisomers. The amino acid at position 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, and/or 17 may be a D stereoisomer. The amino acid at position 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, and/or 17 may be a L stereoisomer. The peptide may comprise at least one amino acid residue of Trp, Leu, Arg, and/or Ala and wherein the at least one of Trp, Leu, Arg, and/or Ala is a D amino acid stereoisomer. The amino acid at position 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, and/or 17 (including combinations thereof) may be a D amino acid stereoisomer or is a L amino acid stereoisomer. The peptide may be synthetic. The peptide may be a natural protein or peptide. The peptide may or may not comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more modifications (or any range derivable therein). The modification may comprise an acetate molecule at the terminus of the peptide. The terminus may be the carboxy or amino terminus. The peptide modulator may comprise an acetate molecule at the carboxy terminus of the peptide. [0016] The modulator may also be an anti-LMTK3 antibody or antigen binding fragment thereof. The modulator may inhibit the phosphorylation activity of LMTK3. The modulator may include or exclude one that inhibits the interaction of LMKT3 and an integrin protein. Also included or excluded are oligonucleotide modulators. The modulator may comprise an isolated oligonucleotide that hybridizes with a nucleic acid molecule encoding the LMKT3 gene. The oligonucleotide modulator may include or exclude an siRNA, a double stranded RNA, a short hairpin RNA, or an antisense oligonucleotide. The modulator may be an LMTK3

TMPL14WO_spec.docx - 5 - inhibitor. The inhibitor may or may not inhibit one or more activities of the LMTK3 protein, such as a binding activity or an enzymatic activity. The LMTK3 modulator may or may not inhibit the expression of the LMTK3 protein. The anti-LMTK3 antibody may include or exclude one that does not bind to CD11b. The anti-LMTK3 antibody may bind to CD11b with a KD of or a KD of less than 10^-1, 10^-2, 10^-3, 10^-4, 10^-5, 10^-6, 10^-7, 10^-8, 10^-9, 10^-10, 10^-11, 10^-12, 10^-13, 10^-14, or 10^-15 M (or any derivable range therein). The anti-LMTK3 antibody may bind to LMTK3 with a K_D of, a K_D of at least, or a K_D of at most 10^-4, 10^-5, 10^-6, 10^-7, 10^-8, 10^-9, 10- ¹⁰, 10^-11, 10^-12, 10^-13, 10^-14, or 10^-15 M (or any derivable range therein). [0017] The subject may be or not be one that has cancer or hyperproliferative cells that are positive for expression of LMTK3. The subject may include or exclude one that has ovarian, fallopian, cervical, or uterine tissues that are positive for expression of LMTK3. The subject may include or exclude one that has glioblastoma, breast, lung, liver, prostate, bladder, colorectal, or thyroid tumor cells that are positive for expression of LMTK3. The subject may include or exclude one that has been determined to have LMTK3 positive cells. The subject may be further defined as a human subject. The subject may be a female subject. The subject may be a male subject The subject may include or exclude a subject on hormone therapy. The hormone therapy may comprise or exclude contraception or hormone replacement therapy. The female subject may include or exclude an adolescent, perimenopausal, or menopausal female. The subject may include or exclude one that has received one or more prior therapies to treat the hyperproliferative disorder. The subject may include or exclude one that has been determined to be a non-responder or resistant to the one or more prior therapies. The one or more therapies may include or exclude an immunotherapy. The immunotherapy may include or exclude a checkpoint inhibitor therapy. The immunotherapy may include or exclude Pembrolizumab. The prior therapy may also include or exclude be an additional agent described herein. The one or more prior therapies may include or exclude a targeted antibody. The targeted antibody in the methods and compositions of the disclosure may include or exclude Bevacizumab. The prior therapy may include or exclude a chemotherapy. The chemotherapy may include or exclude a platinum-based chemotherapy, a taxane-based chemotherapy, or a combination thereof. The chemotherapy may include or exclude carboplatin, paclitaxel, or a combination thereof. The method may exclude, include, comprise, or further comprise administration of an additional agent. The additional agent may exclude or include a platinum-based chemotherapy, a taxane-based chemotherapy, or a combination thereof. Platinum-based chemotherapies useful in the methods and compositions of the disclosure include or exclude cisplatin, oxaliplatin, nedaplatin, triplatin tetranitrate,

TMPL14WO_spec.docx - 6 - phenanthriplatin, picoplatin, satraplatin, and carboplatin. Taxane-based chemotherapies useful in the methods and compositions of the disclosure include or exclude paclitaxel, docetaxel, and cabazitaxel. The additional agent may comprise cisplatin. The subject may include or exclude one that is sensitive or has been determined to be sensitive to platinum-based chemotherapy and/or taxane based chemotherapy. The platinum-based chemotherapy may include or exclude carboplatin and/or the taxane-based chemotherapy comprises paclitaxel. The additional agent may include or exclude a PARP inhibitor, a targeted antibody, or combinations thereof. The PARP inhibitor may include or exclude olaparib or niraparib. The subject may include or exclude one that is or has been determined to be resistant to platinum-based chemotherapy and/or taxane based chemotherapy. The subject may include or exclude one that is administered a LMTK3 modulator in combination with platinum-based chemotherapy when the subject is or has been determined to be sensitive to platinum-based chemotherapy. The subject may be one that is administered the LMTK3 modulator in combination with a PARP inhibitor when the subject has been determined to be resistant to platinum-based chemotherapy or in platinum resistant refractory subjects. The subject may be one that is administered the LMTK3 modulator in combination with a PARP inhibitor and bevacizumab when the subject has been determined to be resistant to platinum-based chemotherapy or in platinum resistant refractory subjects. [0018] The cancer may include or exclude a stage I, II, III, or IV cancer, such as a stage I, II, III, or IV cancer. The cancer may include or exclude metastatic cancer. The cancer may include or exclude recurrent cancer. The cancer may include or exclude non-metastatic cancer. The cancer may include or exclude non-recurrent cancer. [0019] Compositions of the disclosure may include or exclude additional agents described herein. The composition may include or exclude a chemotherapeutic agent, a PARP inhibitor, a targeted antibody, or combinations thereof. Immunotherapies, chemotherapies, targeted antibodies, and additional agents may be any molecule described herein, such as a platinum- based chemotherapeutic agent, a taxane based chemotherapeutic agent, a PARP inhibitor, olaparib, niraparib, bevacizumab, cisplatin, oxaliplatin, nedaplatin, triplatin tetranitrate, phenanthriplatin, picoplatin, satraplatin, carboplatin, paclitaxel, docetaxel, and cabazitaxel. [0020] Exemplary biological samples of the disclosure include serum, biopsy, plasma, or tissue sample. The biological sample may include or exclude one described herein, such as those described in “sample preparation” section. Detecting LMTK3 may include or exclude detecting LMTK3 protein or LMTK3 mRNA.

TMPL14WO_spec.docx - 7 - [0021] The subject or patient of the methods of the disclosure may be one who has been diagnosed with cancer. The subject may include or exclude one that is suspected of having a cancer but has not been diagnosed. The subject may be one that has been diagnosed with stage I cancer, diagnosed with stage II cancer, diagnosed with stage III cancer, or diagnosed with stage IV cancer. The subject may be one that has been diagnosed with metastatic cancer or has not been diagnosed with metastatic cancer. The subject may be one that has been diagnosed with recurrent cancer or has not been diagnosed with recurrent cancer. The cancer may comprise or exclude breast, ovarian, or head and neck cancer. The cancer may comprise or exclude one that is listed herein. [0022] Detecting LMTK3 may comprise or exclude quantitating the expression level of LMTK3. The expression level of LMTK3 may be normalized. Methods of the disclosure also include or exclude comparing the evaluated, measured, or determined expression level of LMTK3 to a control. The evaluated, measured, or determined expression level of LMTK3 may be determined to be greater than a control. The evaluated, measured, or determined expression level of LMTK3 may be determined to be less than the control. The evaluated, measured, or determined expression level of LMTK3 may be determined to be not significantly different than the control. The control may comprise the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with stage I, II, III, or IV cancer. The control may comprise the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject without cancer. The control may comprise the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with a favorable prognosis or from a subject that has a chemotherapy-responsive or radiotherapy–responsive cancer. The control may comprise the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with an unfavorable prognosis or from a subject that has a chemotherapy- resistant or radiotherapy–resistant cancer. [0023] Methods of the disclosure may also comprise or further comprise treating the subject based on the detection of LMTK3. The treatment may comprise exclude chemotherapy and wherein chemotherapy comprises doxorubicin, epirubicin, paclitaxel, docetaxel, 5- fluorouracil, capecitabine, cyclophosphamide, carboplatin, and combinations thereof. The treatment may comprise doxorubicin. The treatment may excludes doxorubicin, epirubicin, paclitaxel, docetaxel, 5-fluorouracil, capecitabine, cyclophosphamide, carboplatin, and combinations thereof. The treatment may comprise chemotherapy and wherein the chemotherapy comprises cisplatin, carboplatin, paclitaxel, docetaxel, albumin bound

TMPL14WO_spec.docx - 8 - paclitaxel, altretamine, capecitabine, cyclophosphamide, etoposide, gemcitabine, ifosfamide, irinotecan, liposomal doxorubicin, melphalan, pemetrexed, topotecan, vinorelbine, or combinations thereof. The treatment may excludes cisplatin, carboplatin, paclitaxel, docetaxel, albumin bound paclitaxel, altretamine, capecitabine, cyclophosphamide, etoposide, gemcitabine, ifosfamide, irinotecan, liposomal doxorubicin, melphalan, pemetrexed, topotecan, vinorelbine, or combinations thereof. The subject may include or exclude one that has been determined to have a favorable prognosis and/or treated with chemotherapy or radiation therapy when the biological sample from the subject was determined to have low expression of LMTK3 or an expression level that is lower than or not significantly different than the level of LMTK3 expression that is representative of the expression level in a biological sample from a subject with a favorable prognosis or from a subject that has a chemotherapy- responsive or radiotherapy–responsive cancer. The treatment may exclude a LMTK3 modulator. The subject may include or exclude one that is determined to have an unfavorable prognosis and/or treated with the combination of i) a LMTK3 modulator and ii) chemotherapy and/or radiotherapy when the biological sample from the subject was determined to have high expression of LMTK3 or an expression level that is higher than or not significantly different than the level of LMTK3 expression that is representative of the expression level in a biological sample from a subject with an unfavorable prognosis or from a subject that has a chemotherapy- resistant or radiotherapy–resistant cancer. [0024] The biological sample from the subject may include or exclude one that was determined to have low expression of LMTK3 or an expression level that is lower than or not significantly different than the level of LMTK3 expression that is representative of the expression level in a biological sample from a subject with a favorable prognosis or from a subject that has a chemotherapy-responsive or radiotherapy–responsive cancer. The biological sample from the subject may be one that was determined to have high expression of LMTK3 or an expression level that is higher than or not significantly different than the level of LMTK3 expression that is representative of the expression level in a biological sample from a subject with an unfavorable prognosis or from a subject that has a chemotherapy-resistant or radiotherapy–resistant cancer. In some aspects, "high" expression means expression that is, is at least, or is at most 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10, 11, 12, 13, 14, 15, 16, 17, 18,

TMPL14WO_spec.docx - 9 - 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100-fold or greater (or any range derivable therein) compared to a normalized or representative level of expression of a control. [0025] Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the measurement or quantitation method. [0026] The use of the word “a” or “an” when used in conjunction with the term “comprising” may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” [0027] The phrase “and/or” means “and” or “or”. To illustrate, A, B, and/or C includes: A alone, B alone, C alone, a combination of A and B, a combination of A and C, a combination of B and C, or a combination of A, B, and C. In other words, “and/or” operates as an inclusive or. [0028] The words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. [0029] The compositions and methods for their use can “comprise,” “consist essentially of,” or “consist of” any of the ingredients or steps disclosed throughout the specification. Compositions and methods “consisting essentially of” any of the ingredients or steps disclosed limits the scope of the claim to the specified materials or steps which do not materially affect the basic and novel characteristic of the claimed invention. As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. It is contemplated that embodiments described herein in the context of the term “comprising” may also be implemented in the context of the term “consisting of” or “consisting essentially of.” [0030] It is specifically contemplated that any limitation discussed with respect to one embodiment of the invention may apply to any other embodiment of the invention. Furthermore, any composition of the invention may be used in any method of the invention,

TMPL14WO_spec.docx - 10 - and any method of the invention may be used to produce or to utilize any composition of the invention. Aspects of an embodiment set forth in the Examples are also embodiments that may be implemented in the context of embodiments discussed elsewhere in a different Example or elsewhere in the application, such as in the Summary of Invention, Detailed Description of the Embodiments, Claims, and description of Figure Legends. [0031] Any method in the context of a therapeutic, diagnostic, or physiologic purpose or effect may also be described in “use” claim language such as “Use of” any compound, composition, or agent discussed herein for achieving or implementing a described therapeutic, diagnostic, or physiologic purpose or effect. [0032] Use of the one or more sequences or compositions may be employed based on any of the methods described herein. Other embodiments are discussed throughout this application. Any embodiment discussed with respect to one aspect of the disclosure applies to other aspects of the disclosure as well and vice versa. [0033] Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description. BRIEF DESCRIPTION OF THE DRAWINGS [0034] The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein. [0035] FIG. 1: Tissue microarrays utilizing LMTK3 monoclonal antibody on ovarian cancer paraffin blocks from various histology. [0036] FIG.2A-B: (A) LMTK3 peptide hits have a very strong, N-terminal wVG- motif, unlike the library as a whole. ”Consensus motif “wVG-[S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L]- [A/N]-x-[N/V]-[N/L/R]-[E/Y]-x-[r/V]-x-xx”. There is reduced amino acid diversity in this peptide library, with a strong overrepresentation of C-terminal G/S/l/a/V, so the “motif” at positions 16 and 17 is most likely from the bias in the library. (B) Binding for LMTK3 was generally low but a number of peptides bound with good signal-to-noise (S/N) ratios and did not bind GST.

TMPL14WO_spec.docx - 11 - [0037] FIG.3. LMTK3 monoclonal antibody and the top 2 LMTK3 specific peptides are cytotoxic to both sensitive and chemoresistant ovarian cancer cells. Cytotoxicity was determined in human macrophages, as well as in sensitive and chemoresistant EOC cell lines by the MTT Cell Proliferation Assay. Significant cytotoxicity was observed in both sensitive and chemoresistant ovarian cancer cells as compared to their isotype controls and as compared to macrophages. [0038] FIG. 4. Orthotopic human ovarian cancer mouse model, which utilizes mCherry labeled-OCSC1-F2 human ovarian cancer cells grown intra-peritoneally (i.p) in athymic nude mice. (ROI) area allows quantification of i.p. tumor burden and thus allow evaluation of treatment efficacy in real-time. [0039] FIG.5. (A) The orthotopic human ovarian cancer mouse model recapitulates the clinical profile observed in patients. (B) 1st-line treatment with Taxol (i.e. Paclitaxel (PTX) in castor oil; 12 mg/kg q3d x 4 doses) induces a “complete response” as determined by (C) the absence of mCherry signal at the end of treatment. [0040] FIG. 6. Synergy of the LMTK3 antibody (5 and 10 ug/ml) was determined following combination of LMTK3 antibody with increasing doses of cisplatin (0.1, 0.5, 1.0 uM) and analyzed by the automated calculation of combination index (CI) where CI<1 is synergistic, CI=1 is additive, and CI>1 is antagonistic. [0041] FIG. 7A-7B. Ovarian cancer cell lines, A2780 (FIG. 7A bottom), MDAH (FIG. 7A top), SKOV-3 (FIG.7B top) and normal ovarian cell lines, HOSPIC and NOEC (FIG.7B bottom) were seeded on a 6-well plate (approx. 300,000 cells/well). After cells reached confluence (approx. 1 million cells/well) cells were treated with LMTK3-SiRNA and scrambled SiRNA (10, 20, and 40 nM) for 21 hours at 37 degree Celsius. Cells were washed, trypsinized, and seeded into 96-well plate in triplicates and subjected to the MTT assay to determine cell viability. [0042] FIG. 8. In the METABRIC cohort, consisting of 1904 breast cancer patients, LMTK3 expression was significantly predictive of overall survival in a Kaplan Meier analysis. [0043] FIG. 9. In the TCGA ovarian cancer cohort, consisting of 303 patients, a high LMTK3 expression was associated with a reduced survival. The Kaplan-Meier analysis did however not reach statistical significance. [0044] FIG.10 shows the expression of LMTK3 RNA in tumor tissue vs normal tissue for different cancer forms. [0045] FIG. 11. Body weight means of mice groups before starting the treatment protocol. Mean ± SD was 24.2±1.8 for Vehicle, 24.1±2.1 for Peptide #1, 24,2±2.3 for Peptide

TMPL14WO_spec.docx - 12 - #2, 24.7±2.9 for Peptide #3, 23.9±2.4 for Cisplatin. No statistically significant differences were observed between groups (one-way ANOVA test, p=0.994). [0046] FIG. 12. Mice body weight mean during treatment. No statistically significant differences in body weight were found between groups (two-way RMANOVA test, p=0.670). [0047] FIG.13 (A-E). Location and appearance of A2780 cell-line derived orthotopic tumors. One representative mouse from each treatment group showing A2780 cell-line derived ovarian tumor: (A) Vehicle, mouse E1, (B) Peptide #1, mouse B2, (C) Peptide #2, mouse B3, (D) Peptide #3, mouse C4, (E) Cisplatin, mouse D5. White arrows point to the tumors, which grew in the right ovary of each mouse. [0048] FIG.14 (A-E). Gross pathology of A2780 cell-line derived orthotopic tumors. One representative tumor from each treatment group: (A) Vehicle, mouse B1, (B) Peptide #1, mouse B2, (C) Peptide #2, mouse B3, (D) Peptide #3, mouse F4, (E) Cisplatin, mouse D5. White arrows point to the tumors, which grew in the right ovary of each mouse. [0049] FIG.15 (A-C). A2780 cell-line derived peritoneal implants. Representative sites of A2780 tumor implants in the peritoneal cavity. Mesentery (A), Kidney (B), Diaphragm (C). White arrows point to the peritoneal implants. [0050] FIG.16. Tumor weight at sacrifice after 8 doses of Vehicle, Peptide #1, Peptide #2, Peptide #3 or Cisplatin. Statistically significant differences were observed between groups (one-way ANOVA test **, p=0.006). Bonferroni post-hoc test found statistically significant differences between vehicle and cisplatin. [0051] FIG. 17A-17C. Results from IHC staining of LMTK3 in 197 human ovarian carcinomas from various stages and histotype revealed cytoplasmic and nuclear localization of LMTK3. High cytoplasmic LMTK3 staining significantly correlated with poor prognosis. P<0.01. [0052] FIG.18. shows peptide characterization. [0053] FIG.19 shows body weight, liver weight, and spleen weight after peptide treatment. No statistically significant differences in body weight were found between groups (two-way RMANOVA test, p=0.864). [0054] FIG. 20 (A-H) shows histological sections of the brain (A), heart (B), lung (C), esophagus (D), kidney (E), stomach (F), adrenal gland (G), and liver (H) after peptide treatment. No statistically significant differences in body weight were found between groups (One-way ANOVA test, p=0.283 for liver weight, and p=0.439 for spleen weight). [0055] FIG. 21A-21B shows LMTK3 siRNA treatment in various cell lines. FIG. 21A: Targeting LMTK3 in ovarian cancer cell lines and normal epithelial ovarian cells by LMTK3

TMPL14WO_spec.docx - 13 - specific siRNA. Treatment of 10nM, 20nM, and 40nM of LMTK3 siRNA for 24 hours was performed in each cell line. For comparison, untreated cells and cells treated with 40 nM of Silencer Negative Control siRNA was performed. Viability of cells was determined by the TACS MTT proliferation assay kit, P<0.05. FIG.21B: Caspase-3 activity was determined by the Caspase-3 Colorimetric Activity Assay Kit in MDAH-2774 and SKOV-3 ovarian cancer cell lines treated with 10 ug/ml of LMTK3BP 1(P1) and peptide 2 (P2) for 24 hours. [0056] FIG.22 shows the proposed mechanism of action. DETAILED DESCRIPTION OF THE INVENTION [0057] Shown herein and in the examples of the application is a study is to evaluate Lemur Tyrosine Kinase 3 (LMTK3) as a specific target for the treatment of ovarian cancer. LMTK3 belongs to a family of regulated serine/threonine tyrosine kinases with three structurally related isoforms, LMTK1, LMTK2, and LMTK3. They were reported to be localized to the nucleus, cytoplasm, transmembrane and in the extracellular space. Both nuclear and cytoplasmic LMTK3 expression was shown to correlate with tumor grade and patient survival in some cancers. The inventors have utilized the MTT assay to test the killing efficacy of targeting LMTK3 by monoclonal antibody, siRNA, and specific LMTK3 binding peptides (LMTK3BP) in various ovarian cancer cell lines. They have also used orthotopic xenograft mouse model of ovarian cancer to test the efficacy of specific LMTK3BP in vivo. Immunohistochemistry (IHC) using LMTK3 monoclonal antibody was performed on formalin-fixed paraffin embedded specimens collected from 204 phase 1 and 2 ovarian cancer patients. Treatment with LMTK3 specific monoclonal antibody, siRNA, and specific LMTK3 binding peptides significantly induced killing of both chemosensitive and chemoresistant ovarian cancer cells without affecting normal cells. Moreover, this killing is synergistic with both cisplatin and Taxotere treatment. More importantly, LMTK3BP 2 mg/kg IV dose given 3 times a week for 3 weeks showed a 35% tumor reduction. This is significant as cisplatin alone showed 45% tumor reduction under the same conditions. Results from IHC LMTK3 staining from stages 1 and 2 patients within 15 years of diagnosis revealed a higher cytoplasmic to nuclear localization of LMTK3 that correlates with worse prognosis (P<0.01). In conclusion, the results from this study highlights the importance of targeting LMTK3 as a potential treatment for ovarian cancer and hyperproliferative disorders. I. LMTK3 modulators A. Peptides and Polypeptide Modulators

TMPL14WO_spec.docx - 14 - Exemplary modulator polypeptides include those in the table below: Table 1: Peptide Modulators of LMTK3** SEQ ID NO Peptide sequence 1 WVGPYSLAHNLEYRDAG 2 WVGSVAYNYRDSGVASG 3 DGAEWSNQAYNEYWRDA 4 WVGSYSDAPNNERDALG 5 WVGGSVLAENLYRDSAG 6 WVGSEYSFAVNSFENRS 7 WVGESFADNFEYNRHAS 8 WVGSVADNFYRDALGVS 9 WVGYSHAYDNQRDALGL 10 WVGSFSGAHVNGYNRDV 11 WVGPSGFAYHNYWRDAV 12 WVGPSVAEHNRYRVVAS 13 WVGQSLAYNLFRDVAVA 14 WVGSGSLSGANLGERHL 15 WVGEYSLANNLEWRHLG 16 wVGPYSlAHNlEYrDaG 17 wVGSVAYNYrDSGVaSG 18 DGaEwSNQAYNEYwrDa 19 wVGSYSDAPNNErDalG 20 wVGGSVlAENlYrDSaG 21 wVGSEYSFAVNSFENrS 22 wVGESFADNFEYNrHaS 23 wVGSVADNFYrDalGVS 24 wVGYSHAYDNQrDalGl 25 wVGSFSGAHVNGYNrDV 26 wVGPSGFAYHNYwrDaV 27 wVGPSVAEHNrYrVVaS 28 wVGQSlAYNlFrDVaVa 29 wVGSGSlSGANlGErHl

TMPL14WO_spec.docx - 15 - 30 wVGEYSlANNlEwrHlG **Lowercase indicates D-amino acid stereoisomers. [0058] As used herein, a “protein” or “polypeptide” refers to a molecule comprising at least five amino acid residues. As used herein, the term “wild-type” refers to the endogenous version of a molecule that occurs naturally in an organism. In some embodiments, wild-type versions of a protein or polypeptide are employed, however, in many embodiments of the disclosure, a modified protein or polypeptide is employed to generate an immune response. The terms described above may be used interchangeably. A “modified protein” or “modified polypeptide” or a “variant” refers to a protein or polypeptide whose chemical structure, particularly its amino acid sequence, is altered with respect to the wild-type protein or polypeptide. In some embodiments, a modified/variant protein or polypeptide has at least one modified activity or function (recognizing that proteins or polypeptides may have multiple activities or functions). It is specifically contemplated that a modified/variant protein or polypeptide may be altered with respect to one activity or function yet retain a wild-type activity or function in other respects, such as immunogenicity. [0059] Where a protein is specifically mentioned herein, it is in general a reference to a native (wild-type) or recombinant (modified) protein or, optionally, a protein in which any signal sequence has been removed. The protein may be isolated directly from the organism of which it is native, produced by recombinant DNA/exogenous expression methods, or produced by solid-phase peptide synthesis (SPPS) or other in vitro methods. In particular embodiments, there are isolated nucleic acid segments and recombinant vectors incorporating nucleic acid sequences that encode a polypeptide (e.g., an antibody or fragment thereof). The term “recombinant” may be used in conjunction with a polypeptide or the name of a specific polypeptide, and this generally refers to a polypeptide produced from a nucleic acid molecule that has been manipulated in vitro or that is a replication product of such a molecule. [0060] In certain embodiments the size of a peptide or protein of the disclosure may comprise, but is not limited to, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 amino acid residues or greater, and any range derivable therein. It is contemplated that polypeptides may be mutated by truncation, rendering them shorter than their corresponding wild-type form, also, they might be altered by fusing or conjugating a heterologous protein or polypeptide sequence with a particular function (e.g., for targeting or localization, for enhanced immunogenicity, for purification purposes, etc.). As used herein, the term “domain” refers to any distinct functional

TMPL14WO_spec.docx - 16 - or structural unit of a protein or polypeptide, and generally refers to a sequence of amino acids with a structure or function recognizable by one skilled in the art. [0061] The polypeptides and peptides of the disclosure may include 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (or any derivable range therein) or more variant amino acids substitutions or be at least 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% (or any derivable range therein) similar, identical, or homologous with at least, or at most 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 contiguous amino acids or nucleic acids, or any range derivable therein, of SEQ ID NO:1- 30. [0062] In some embodiments, the peptide or polypeptide may comprise amino acids 1 to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17, (or any derivable range therein) of SEQ ID NOS:1-30. [0063] In some embodiments, the peptide or polypeptide may comprise amino acids 1 to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17, (or any derivable range therein) of SEQ ID NOS:1-30 and have, have at least, or have at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 (or any derivable range therein) contiguous amino acids of SEQ ID NOS:1-30 that are at least, at most, or exactly 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% (or any derivable range therein) similar, identical, or homologous with one of SEQ ID NOS:1-30. [0064] In some embodiments, the peptide or polypeptide may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17, (or any derivable range therein) contiguous amino acids of SEQ ID NOs:1-30. [0065] In some embodiments, the peptide or polypeptide may comprise, may comprise at least, may comprise at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 (or any derivable range therein) contiguous amino acids of SEQ ID NOS:1-30 that are at least, at most, or exactly 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% (or any derivable range therein) similar, identical, or homologous with one of SEQ ID NOS:1-30. [0066] In some aspects there is a peptide or polypeptide starting at position 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 of any of SEQ ID NOS:1-30 and comprising, comprising at least, or comprising

TMPL14WO_spec.docx - 17 - at most 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 (or any derivable range therein) contiguous amino acids or nucleotides of any of SEQ ID NOS:1-30. [0067] The peptide or polypeptide may comprise, may comprise at least, or may comprise at most 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (or any derivable range therein) amino acid substitutions relative to SEQ ID NOS:1-30. The peptide or polypeptide may comprise, may comprise at least, or may comprise at most 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (or any derivable range therein) amino acid substitutions, and the substitution(s) may be at position 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, and/or 17 relative to SEQ ID NOS:1-30. The substitution at position(s) , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, and/or 17 may be with an alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, or valine. [0068] The nucleotide as well as the protein, polypeptide, and peptide sequences for various genes have been previously disclosed, and may be found in the recognized computerized databases. Two commonly used databases are the National Center for Biotechnology Information’s Genbank and GenPept databases (on the World Wide Web at ncbi.nlm.nih.gov/) and The Universal Protein Resource (UniProt; on the World Wide Web at uniprot.org). The coding regions for these genes may be amplified and/or expressed using the techniques disclosed herein or as would be known to those of ordinary skill in the art. [0069] It is contemplated that in compositions of the disclosure, there is between about 0.001 mg and about 10 mg of total polypeptide, peptide, and/or protein per ml. The concentration of protein in a composition can be about, at least about or at most about 0.001, 0.010, 0.050, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, 10.0 mg/ml or more (or any range derivable therein). B. LMTK3 inhibitory oligonucleotides [0070] In some aspects, the disclosure relates to inhibitory oligonucleotides that inhibit the gene expression of LMTK3. Examples of an inhibitory oligonucleotides include but are not limited to siRNA (small interfering RNA), short hairpin RNA (shRNA), double-stranded RNA, an antisense oligonucleotide, a ribozyme and a oligonucleotide encoding thereof. An inhibitory oligonucleotide may inhibit the transcription of a gene or prevent the translation of a gene transcript in a cell. An inhibitory oligonucleotide acid may be from 16 to 1000 nucleotides long, and in certain embodiments from 18 to 100 nucleotides long. The oligonucleotide may have at least or may have at most 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,

TMPL14WO_spec.docx - 18 - 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 50, 60, 70, 80, or 90 (or any range derivable therein) nucleotides. The oligonucleotide may be DNA, RNA, or a cDNA that encodes an inhibitory RNA. [0071] As used herein, “isolated” means altered or removed from the natural state through human intervention. For example, an siRNA naturally present in a living animal is not “isolated,” but a synthetic siRNA, or an siRNA partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated siRNA can exist in substantially purified form, or can exist in a non-native environment such as, for example, a cell into which the siRNA has been delivered. [0072] Inhibitory oligonucleotides are well known in the art. For example, siRNA and double-stranded RNA have been described in U.S. Patents 6,506,559 and 6,573,099, as well as in U.S. Patent Publications 2003/0051263, 2003/0055020, 2004/0265839, 2002/0168707, 2003/0159161, and 2004/0064842, all of which are herein incorporated by reference in their entirety. [0073] Particularly, an inhibitory oligonucleotide may be capable of decreasing the expression of LMTK3 by at least 10%, 20%, 30%, or 40%, more particularly by at least 50%, 60%, or 70%, and most particularly by at least 75%, 80%, 90%, 95%, 99%, or 100% more or any range or value in between the foregoing. [0074] In further embodiments, there are synthetic oligonucleotides that are LMTK3 inhibitors. An inhibitor may be between 17 to 25 nucleotides in length and comprises a 5’ to 3’ sequence that is at least 90% complementary to the 5’ to 3’ sequence of a mature LMTK3 mRNA. In certain embodiments, an inhibitor molecule is 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length, or any range derivable therein. Moreover, an inhibitor molecule has a sequence (from 5’ to 3’) that is or is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9 or 100% complementary, or any range derivable therein, to the 5’ to 3’ sequence of a mature LMTK3 mRNA, particularly a mature, naturally occurring mRNA. One of skill in the art could use a portion of the probe sequence that is complementary to the sequence of a mature mRNA as the sequence for an mRNA inhibitor. Moreover, that portion of the probe sequence can be altered so that it is still 90% complementary to the sequence of a mature mRNA. [0075] In some embodiments, the inhibitory oligonucleotide is an analog and my include modifications, particularly modifications that increase nuclease resistance, improve binding affinity, and/or improve binding specificity. For example, when the sugar portion of a nucleoside or nucleotide is replaced by a carbocyclic moiety, it is no longer a sugar. Moreover,

TMPL14WO_spec.docx - 19 - when other substitutions, such a substitution for the inter-sugar phosphodiester linkage are made, the resulting material is no longer a true species. All such compounds are considered to be analogs. Throughout this specification, reference to the sugar portion of a nucleic acid species shall be understood to refer to either a true sugar or to a species taking the structural place of the sugar of wild type nucleic acids. Moreover, reference to inter-sugar linkages shall be taken to include moieties serving to join the sugar or sugar analog portions in the fashion of wild type nucleic acids. [0076] The present disclosure concerns modified oligonucleotides, i.e., oligonucleotide analogs or oligonucleosides, and methods for effecting the modifications. These modified oligonucleotides and oligonucleotide analogs may exhibit increased chemical and/or enzymatic stability relative to their naturally occurring counterparts. Extracellular and intracellular nucleases generally do not recognize and therefore do not bind to the backbone-modified compounds. When present as the protonated acid form, the lack of a negatively charged backbone may facilitate cellular penetration. [0077] The modified internucleoside linkages are intended to replace naturally-occurring phosphodiester-5’-methylene linkages with four atom linking groups to confer nuclease resistance and enhanced cellular uptake to the resulting compound. [0078] Modifications may be achieved using solid supports which may be manually manipulated or used in conjunction with a DNA synthesizer using methodology commonly known to those skilled in DNA synthesizer art. Generally, the procedure involves functionalizing the sugar moieties of two nucleosides which will be adjacent to one another in the selected sequence. In a 5’ to 3’ sense, an “upstream” synthon such as structure H is modified at its terminal 3’ site, while a “downstream” synthon such as structure H1 is modified at its terminal 5’ site. [0079] Oligonucleosides linked by hydrazines, hydroxylarnines, and other linking groups can be protected by a dimethoxytrityl group at the 5’-hydroxyl and activated for coupling at the 3’-hydroxyl with cyanoethyldiisopropyl-phosphite moieties. These compounds can be inserted into any desired sequence by standard, solid phase, automated DNA synthesis techniques. One of the most popular processes is the phosphoramidite technique. Oligonucleotides containing a uniform backbone linkage can be synthesized by use of CPG- solid support and standard nucleic acid synthesizing machines such as Applied Biosystems Inc. 380B and 394 and Milligen/Biosearch 7500 and 8800s. The initial nucleotide (number 1 at the 3’-terminus) is attached to a solid support such as controlled pore glass. In sequence specific

TMPL14WO_spec.docx - 20 - order, each new nucleotide is attached either by manual manipulation or by the automated synthesizer system. [0080] Free amino groups can be alkylated with, for example, acetone and sodium cyanoboro hydride in acetic acid. The alkylation step can be used to introduce other, useful, functional molecules on the macromolecule. Such useful functional molecules include but are not limited to reporter molecules, RNA cleaving groups, groups for improving the pharmacokinetic properties of an oligonucleotide, and groups for improving the pharmacodynamic properties of an oligonucleotide. Such molecules can be attached to or conjugated to the macromolecule via attachment to the nitrogen atom in the backbone linkage. Alternatively, such molecules can be attached to pendent groups extending from a hydroxyl group of the sugar moiety of one or more of the nucleotides. Examples of such other useful functional groups are provided by WO1993007883, which is herein incorporated by reference, and in other of the above-referenced patent applications. [0081] Solid supports may include any of those known in the art for polynucleotide synthesis, including controlled pore glass (CPG), oxalyl controlled pore glass, TentaGel Support—an aminopolyethyleneglycol derivatized support or Poros —a copolymer of polystyrene/divinylbenzene. Attachment and cleavage of nucleotides and oligonucleotides can be effected via standard procedures. As used herein, the term solid support further includes any linkers (e.g., long chain alkyl amines and succinyl residues) used to bind a growing oligonucleoside to a stationary phase such as CPG. In some embodiments, the oligonucleotide may be further defined as having one or more locked nucleotides, ethylene bridged nucleotides, peptide nucleic acids, or a 5’(E)-vinyl-phosphonate (VP) modification. In some embodiments, the oligonucleotides has one or more phosphorothioated DNA or RNA bases. C. LMTK3 antibodies [0082] In certain embodiments, an antibody or a fragment thereof that binds to at least a portion of LMTK3 protein and modulates LMTK3 activity, such as its binding activity, enzymatic activity, or binding specificity. [0083] Aspects of the disclosure relate to antibodies comprising a heavy or light chain, or fragments thereof. The term “antibody” refers to an intact immunoglobulin of any isotype, or a fragment thereof that can compete with the intact antibody for specific binding to the target antigen, and includes chimeric, humanized, fully human, and bispecific antibodies. As used herein, the terms “antibody” or “immunoglobulin” are used interchangeably and refer to any of several classes of structurally related proteins that function as part of the immune response

TMPL14WO_spec.docx - 21 - of an animal, including IgG, IgD, IgE, IgA, IgM, and related proteins, as well as polypeptides comprising antibody CDR domains that retain antigen-binding activity. [0084] The term “antigen” refers to a molecule or a portion of a molecule capable of being bound by a selective binding agent, such as an antibody. An antigen may possess one or more epitopes that are capable of interacting with different antibodies. [0085] The term “epitope” includes any region or portion of molecule capable eliciting an immune response by binding to an immunoglobulin or to a T-cell receptor. Epitope determinants may include chemically active surface groups such as amino acids, sugar side chains, phosphoryl or sulfonyl groups, and may have specific three-dimensional structural characteristics and/or specific charge characteristics. Generally, antibodies specific for a particular target antigen will preferentially recognize an epitope on the target antigen within a complex mixture. [0086] The epitope regions of a given polypeptide can be identified using many different epitope mapping techniques are well known in the art, including: x-ray crystallography, nuclear magnetic resonance spectroscopy, site-directed mutagenesis mapping, protein display arrays, see, e.g., Epitope Mapping Protocols, (Johan Rockberg and Johan Nilvebrant, Ed., 2018) Humana Press, New York, N.Y. Such techniques are known in the art and described in, e.g., U.S. Pat. No. 4,708,871; Geysen et al. Proc. Natl. Acad. Sci. USA 81:3998-4002 (1984); Geysen et al. Proc. Natl. Acad. Sci. USA 82:178-182 (1985); Geysen et al. Molec. Immunol. 23:709-715 (1986). Additionally, antigenic regions of proteins can also be predicted and identified using standard antigenicity and hydropathy plots. [0087] The term “immunogenic sequence” means a molecule that includes an amino acid sequence of at least one epitope such that the molecule is capable of stimulating the production of antibodies in an appropriate host. The term “immunogenic composition” means a composition that comprises at least one immunogenic molecule (e.g., an antigen or carbohydrate). [0088] An intact antibody is generally composed of two full-length heavy chains and two full-length light chains, but in some instances may include fewer chains, such as antibodies naturally occurring in camelids that may comprise only heavy chains. Antibodies as disclosed herein may be derived solely from a single source or may be “chimeric,” that is, different portions of the antibody may be derived from two different antibodies. For example, the variable or CDR regions may be derived from a rat or murine source, while the constant region is derived from a different animal source, such as a human. The antibodies or binding fragments may be produced in hybridomas, by recombinant DNA techniques, or by enzymatic or

TMPL14WO_spec.docx - 22 - chemical cleavage of intact antibodies. Unless otherwise indicated, the term “antibody” includes derivatives, variants, fragments, and muteins thereof, examples of which are described below (Sela-Culang et al., Front Immunol.2013; 4: 302; 2013). [0089] The term “light chain” includes a full-length light chain and fragments thereof having sufficient variable region sequence to confer binding specificity. A full-length light chain has a molecular weight of around 25,000 Daltons and includes a variable region domain (abbreviated herein as VL), and a constant region domain (abbreviated herein as CL). There are two classifications of light chains, identified as kappa (κ) and lambda (λ). The term “VL fragment” means a fragment of the light chain of a monoclonal antibody that includes all or part of the light chain variable region, including CDRs. A VL fragment can further include light chain constant region sequences. The variable region domain of the light chain is at the amino-terminus of the polypeptide. [0090] The term “heavy chain” includes a full-length heavy chain and fragments thereof having sufficient variable region sequence to confer binding specificity. A full-length heavy chain has a molecular weight of around 50,000 Daltons and includes a variable region domain (abbreviated herein as VH), and three constant region domains (abbreviated herein as CH1, CH2, and CH3). The term “VH fragment” means a fragment of the heavy chain of a monoclonal antibody that includes all or part of the heavy chain variable region, including CDRs. A VH fragment can further include heavy chain constant region sequences. The number of heavy chain constant region domains will depend on the isotype. The VH domain is at the amino-terminus of the polypeptide, and the CH domains are at the carboxy-terminus, with the CH3 being closest to the —COOH end. The isotype of an antibody can be IgM, IgD, IgG, IgA, or IgE and is defined by the heavy chains present of which there are five classifications: mu (μ), delta (δ), gamma (γ), alpha (α), or epsilon (ε) chains, respectively. IgG has several subtypes, including, but not limited to, IgG1, IgG2, IgG3, and IgG4. IgM subtypes include IgM1 and IgM2. IgA subtypes include IgA1 and IgA2. [0091] Antibodies can be whole immunoglobulins of any isotype or classification, chimeric antibodies, or hybrid antibodies with specificity to two or more antigens. They may also be fragments (e.g., F(abʹ)2, Fabʹ, Fab, Fv, and the like), including hybrid fragments. An immunoglobulin also includes natural, synthetic, or genetically engineered proteins that act like an antibody by binding to specific antigens to form a complex. The term antibody includes genetically engineered or otherwise modified forms of immunoglobulins, such as the following:

TMPL14WO_spec.docx - 23 - [0092] The term “monomer” means an antibody containing only one Ig unit. Monomers are the basic functional units of antibodies. The term “dimer” means an antibody containing two Ig units attached to one another via constant domains of the antibody heavy chains (the Fc, or fragment crystallizable, region). The complex may be stabilized by a joining (J) chain protein. The term “multimer” means an antibody containing more than two Ig units attached to one another via constant domains of the antibody heavy chains (the Fc region). The complex may be stabilized by a joining (J) chain protein. [0093] The term “bivalent antibody” means an antibody that comprises two antigen- binding sites. The two binding sites may have the same antigen specificities or they may be bi- specific, meaning the two antigen-binding sites have different antigen specificities. [0094] Bispecific antibodies are a class of antibodies that have two paratopes with different binding sites for two or more distinct epitopes. In some embodiments, bispecific antibodies can be biparatopic, wherein a bispecific antibody may specifically recognize a different epitope from the same antigen. In some embodiments, bispecific antibodies can be constructed from a pair of different single domain antibodies termed “nanobodies”. Single domain antibodies are sourced and modified from cartilaginous fish and camelids. Nanobodies can be joined together by a linker using techniques typical to a person skilled in the art; such methods for selection and joining of nanobodies are described in PCT Publication No. WO2015044386A1, No. WO2010037838A2, and Bever et al., Anal Chem. 86:7875–7882 (2014), each of which are specifically incorporated herein by reference in their entirety. [0095] Bispecific antibodies can be constructed as: a whole IgG, Fab′2, Fab′PEG, a diabody, or alternatively as scFv. Diabodies and scFvs can be constructed without an Fc region, using only variable domains, potentially reducing the effects of anti-idiotypic reaction. Bispecific antibodies may be produced by a variety of methods including, but not limited to, fusion of hybridomas or linking of Fab′ fragments. See, e.g., Songsivilai and Lachmann, Clin. Exp. Immunol.79:315-321 (1990); Kostelny et al., J. Immunol. 148:1547-1553 (1992), each of which are specifically incorporated by reference in their entirety. [0096] In certain aspects, the antigen-binding domain may be multispecific or heterospecific by multimerizing with VH and VL region pairs that bind a different antigen. For example, the antibody may bind to, or interact with, (a) a cell surface antigen, (b) an Fc receptor on the surface of an effector cell, or (c) at least one other component. Accordingly, aspects may include, but are not limited to, bispecific, trispecific, tetraspecific, and other multispecific antibodies or antigen-binding fragments thereof that are directed to epitopes and to other targets, such as Fc receptors on effector cells.

TMPL14WO_spec.docx - 24 - [0097] In some embodiments, multispecific antibodies can be used and directly linked via a short flexible polypeptide chain, using routine methods known in the art. One such example is diabodies that are bivalent, bispecific antibodies in which the VH and VL domains are expressed on a single polypeptide chain, and utilize a linker that is too short to allow for pairing between domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain creating two antigen binding sites. The linker functionality is applicable for embodiments of triabodies, tetrabodies, and higher order antibody multimers. (see, e.g., Hollinger et al., Proc Natl. Acad. Sci. USA 90:6444-6448 (1993); Polijak et al., Structure 2:1121-1123 (1994); Todorovska et al., J. Immunol. Methods 248:47-66 (2001)). [0098] Bispecific diabodies, as opposed to bispecific whole antibodies, may also be advantageous because they can be readily constructed and expressed in E. coli. Diabodies (and other polypeptides such as antibody fragments) of appropriate binding specificities can be readily selected using phage display (WO94/13804) from libraries. If one arm of the diabody is kept constant, for instance, with a specificity directed against a protein, then a library can be made where the other arm is varied and an antibody of appropriate specificity selected. Bispecific whole antibodies may be made by alternative engineering methods as described in Ridgeway et al., (Protein Eng., 9:616-621, 1996) and Krah et al., (N Biotechnol.39:167-173, 2017), each of which is hereby incorporated by reference in their entirety. [0099] Heteroconjugate antibodies are composed of two covalently linked monoclonal antibodies with different specificities. See, e.g., US Patent No.6,010,902, incorporated herein by reference in its entirety. [0100] The part of the Fv fragment of an antibody molecule that binds with high specificity to the epitope of the antigen is referred to herein as the “paratope.” The paratope consists of the amino acid residues that make contact with the epitope of an antigen to facilitate antigen recognition. Each of the two Fv fragments of an antibody is composed of the two variable domains, VH and VL, in dimerized configuration. The primary structure of each of the variable domains includes three hypervariable loops separated by, and flanked by, Framework Regions (FR). The hypervariable loops are the regions of highest primary sequences variability among the antibody molecules from any mammal. The term hypervariable loop is sometimes used interchangeably with the term “Complementarity Determining Region (CDR).” The length of the hypervariable loops (or CDRs) varies between antibody molecules. The framework regions of all antibody molecules from a given mammal have high primary sequence similarity/consensus. The consensus of framework regions can be used by one skilled in the art to identify both the framework regions and the hypervariable loops (or CDRs) which are

TMPL14WO_spec.docx - 25 - interspersed among the framework regions. The hypervariable loops are given identifying names which distinguish their position within the polypeptide, and on which domain they occur. CDRs in the VL domain are identified as L1, L2, and L3, with L1 occurring at the most distal end and L3 occurring closest to the CL domain. The CDRs may also be given the names CDR-1, CDR-2, and CDR-3. The L3 (CDR-3) is generally the region of highest variability among all antibody molecules produced by a given organism. The CDRs are regions of the polypeptide chain arranged linearly in the primary structure, and separated from each other by Framework Regions. The amino terminal (N-terminal) end of the VL chain is named FR1. The region identified as FR2 occurs between L1 and L2 hypervariable loops. FR3 occurs between L2 and L3 hypervariable loops, and the FR4 region is closest to the CL domain. This structure and nomenclature is repeated for the VH chain, which includes three CDRs identified as H1, H2 and H3. The majority of amino acid residues in the variable domains, or Fv fragments (VH and VL), are part of the framework regions (approximately 85%). The three dimensional, or tertiary, structure of an antibody molecule is such that the framework regions are more internal to the molecule and provide the majority of the structure, with the CDRs on the extrenal surface of the molecule. [0101] Several methods have been developed and can be used by one skilled in the art to identify the exact amino acids that constitute each of these regions. This can be done using any of a number of multiple sequence alignment methods and algorithms, which identify the conserved amino acid residues that make up the framework regions, therefore identifying the CDRs that may vary in length but are located between framework regions. Three commonly used methods have been developed for identification of the CDRs of antibodies: Kabat (as described in T. T. Wu and E. A. Kabat, “AN ANALYSIS OF THE SEQUENCES OF THE VARIABLE REGIONS OF BENCE JONES PROTEINS AND MYELOMA LIGHT CHAINS AND THEIR IMPLICATIONS FOR ANTIBODY COMPLEMENTARITY,” J Exp Med, vol. 132, no.2, pp.211–250, Aug.1970); Chothia (as described in C. Chothia et al., “Conformations of immunoglobulin hypervariable regions,” Nature, vol. 342, no. 6252, pp. 877–883, Dec. 1989); and IMGT (as described in M.-P. Lefranc et al., “IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains,” Developmental & Comparative Immunology, vol. 27, no. 1, pp. 55–77, Jan. 2003). These methods each include unique numbering systems for the identification of the amino acid residues that constitute the variable regions. In most antibody molecules, the amino acid residues that actually contact the epitope of the antigen occur in the CDRs, although in some cases, residues within the framework regions contribute to antigen binding.

TMPL14WO_spec.docx - 26 - [0102] One skilled in the art can use any of several methods to determine the paratope of an antibody. These methods include: 1) Computational predictions of the tertiary structure of the antibody/epitope binding interactions based on the chemical nature of the amino acid sequence of the antibody variable region and composition of the epitope; 2) Hydrogen- deuterium exchange and mass spectroscopy; 3) Polypeptide fragmentation and peptide mapping approaches in which one generates multiple overlapping peptide fragments from the full length of the polypeptide and evaluates the binding affinity of these peptides for the epitope; 4) Antibody Phage Display Library analysis in which the antibody Fab fragment encoding genes of the mammal are expressed by bacteriophage in such a way as to be incorporated into the coat of the phage. This population of Fab expressing phage are then allowed to interact with the antigen which has been immobilized or may be expressed in by a different exogenous expression system. Non-binding Fab fragments are washed away, thereby leaving only the specific binding Fab fragments attached to the antigen. The binding Fab fragments can be readily isolated and the genes which encode them determined. This approach can also be used for smaller regions of the Fab fragment including Fv fragments or specific VH and VL domains as appropriate. [0103] In certain aspects, affinity matured antibodies are enhanced with one or more modifications in one or more CDRs thereof that result in an improvement in the affinity of the antibody for a target antigen as compared to a parent antibody that does not possess those alteration(s). Certain affinity matured antibodies will have nanomolar or picomolar affinities for the target antigen. Affinity matured antibodies are produced by procedures known in the art, e.g., Marks et al., Bio/Technology 10:779 (1992) describes affinity maturation by VH and VL domain shuffling, random mutagenesis of CDR and/or framework residues employed in phage display is described by Rajpal et al., PNAS. 24: 8466-8471 (2005) and Thie et al., Methods Mol Biol. 525:309-22 (2009) in conjugation with computation methods as demonstrated in Tiller et al., Front. Immunol.8:986 (2017). [0104] Chimeric immunoglobulins are the products of fused genes derived from different species; “humanized” chimeras generally have the framework region (FR) from human immunoglobulins and one or more CDRs are from a non-human source. [0105] In certain aspects, portions of the heavy and/or light chain are identical or homologous to corresponding sequences from another particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so

TMPL14WO_spec.docx - 27 - long as they exhibit the desired biological activity. U.S. Pat. No.4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851 (1984). For methods relating to chimeric antibodies, see, e.g., U.S. Pat. No. 4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851- 6855 (1985), each of which are specifically incorporated herein by reference in their entirety. CDR grafting is described, for example, in U.S. Pat. Nos. 6,180,370, 5,693,762, 5,693,761, 5,585,089, and 5,530,101, which are all hereby incorporated by reference for all purposes. [0106] In some embodiments, minimizing the antibody polypeptide sequence from the non-human species optimizes chimeric antibody function and reduces immunogenicity. Specific amino acid residues from non-antigen recognizing regions of the non-human antibody are modified to be homologous to corresponding residues in a human antibody or isotype. One example is the “CDR-grafted” antibody, in which an antibody comprises one or more CDRs from a particular species or belonging to a specific antibody class or subclass, while the remainder of the antibody chain(s) is identical or homologous to a corresponding sequence in antibodies derived from another species or belonging to another antibody class or subclass. For use in humans, the V region composed of CDR1, CDR2, and partial CDR3 for both the light and heavy chain variance region from a non-human immunoglobulin, are grafted with a human antibody framework region, replacing the naturally occurring antigen receptors of the human antibody with the non-human CDRs. In some instances, corresponding non-human residues replace framework region residues of the human immunoglobulin. Furthermore, humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody to further refine performance. The humanized antibody may also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. See, e.g., Jones et al., Nature 321:522 (1986); Riechmann et al., Nature 332:323 (1988); Presta, Curr. Op. Struct. Biol. 2:593 (1992); Vaswani and Hamilton, Ann. Allergy, Asthma and Immunol.1:105 (1998); Harris, Biochem. Soc. Transactions 23; 1035 (1995); Hurle and Gross, Curr. Op. Biotech.5:428 (1994); Verhoeyen et al., Science 239:1534-36 (1988). [0107] Intrabodies are intracellularly localized immunoglobulins that bind to intracellular antigens as opposed to secreted antibodies, which bind antigens in the extracellular space. [0108] Polyclonal antibody preparations typically include different antibodies against different determinants (epitopes). In order to produce polyclonal antibodies, a host, such as a rabbit or goat, is immunized with the antigen or antigen fragment, generally with an adjuvant and, if necessary, coupled to a carrier. Antibodies to the antigen are subsequently collected from the sera of the host. The polyclonal antibody can be affinity purified against the antigen rendering it monospecific.

TMPL14WO_spec.docx - 28 - [0109] Monoclonal antibodies or “mAb” refer to an antibody obtained from a population of homogeneous antibodies from an exclusive parental cell, e.g., the population is identical except for naturally occurring mutations that may be present in minor amounts. Each monoclonal antibody is directed against a single antigenic determinant. 1. Functional Antibody Fragments and Antigen-Binding Fragments [0110] Certain aspects relate to antibody fragments, such as antibody fragments that bind to and modulate activity. The term functional antibody fragment includes antigen-binding fragments of an antibody that retain the ability to specifically bind to an antigen. These fragments are constituted of various arrangements of the variable region heavy chain (VH) and/or light chain (VL); and in some embodiments, include constant region heavy chain 1 (CHl) and light chain (CL). In some embodiments, theylack the Fc region constituted of heavy chain 2 (CH2) and 3 (CH3) domains. Embodiments of antigen binding fragments and the modifications thereof may include: (i) the Fab fragment type constituted with the VL, VH, CL, and CHl domains; (ii) the Fd fragment type constituted with the VH and CHl domains; (iii) the Fv fragment type constituted with the VH and VL domains; (iv) the single domain fragment type, dAb, (Ward, 1989; McCafferty et al., 1990; Holt et al., 2003) constituted with a single VH or VL domain; (v) isolated complementarity determining region (CDR) regions. Such terms are described, for example, in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, NY (1989); Molec. Biology and Biotechnology: A Comprehensive Desk Reference (Myers, R. A. (ed.), New York: VCH Publisher, Inc.); Huston et al., Cell Biophysics, 22:189-224 (1993); Pluckthun and Skerra, Meth. Enzymol., 178:497-515 (1989) and in Day, E. D., Advanced Immunochemistry, 2d ed., Wiley-Liss, Inc. New York, N.Y. (1990); Antibodies, 4:259-277 (2015). The citations in this paragraph are all incorporated by reference. [0111] Antigen-binding fragments also include fragments of an antibody that retain exactly, at least, or at most 1, 2, or 3 complementarity determining regions (CDRs) from a light chain variable region. Fusions of CDR-containing sequences to an Fc region (or a CH2 or CH3 region thereof) are included within the scope of this definition including, for example, scFv fused, directly or indirectly, to an Fc region are included herein. [0112] The term Fab fragment means a monovalent antigen-binding fragment of an antibody containing the VL, VH, CL and CH1 domains. The term Fab′ fragment means a monovalent antigen-binding fragment of a monoclonal antibody that is larger than a Fab fragment. For example, a Fab′ fragment includes the VL, VH, CL and CH1 domains and all or

TMPL14WO_spec.docx - 29 - part of the hinge region. The term F(ab′)2 fragment means a bivalent antigen-binding fragment of a monoclonal antibody comprising two Fab′ fragments linked by a disulfide bridge at the hinge region. An F(ab′)2 fragment includes, for example, all or part of the two VH and VL domains, and can further include all or part of the two CL and CH1 domains. [0113] The term Fd fragment means a fragment of the heavy chain of a monoclonal antibody, which includes all or part of the VH, including the CDRs. An Fd fragment can further include CH1 region sequences. [0114] The term Fv fragment means a monovalent antigen-binding fragment of a monoclonal antibody, including all or part of the VL and VH, and absent of the CL and CH1 domains. The VL and VH include, for example, the CDRs. Single-chain antibodies (sFv or scFv) are Fv molecules in which the VL and VH regions have been connected by a flexible linker to form a single polypeptide chain, which forms an antigen-binding fragment. Single chain antibodies are discussed in detail in International Patent Application Publication No. WO 88/01649 and U.S. Pat. Nos. 4,946,778 and 5,260,203, the disclosures of which are herein incorporated by reference. The term (scFv)2 means bivalent or bispecific sFv polypeptide chains that include oligomerization domains at their C-termini, separated from the sFv by a hinge region (Pack et al. 1992). The oligomerization domain comprises self-associating a- helices, e.g., leucine zippers, which can be further stabilized by additional disulfide bonds. (scFv)2 fragments are also known as “miniantibodies” or “minibodies.” [0115] A single domain antibody is an antigen-binding fragment containing only a VH or the VL domain. In some instances, two or more VH regions are covalently joined with a peptide linker to create a bivalent domain antibody. The two VH regions of a bivalent domain antibody may target the same or different antigens. [0116] Fragment Crystallizable Region, Fc [0117] A fragment crystallizable region (Fc region) contains two heavy chain fragments comprising the CH2 and CH3 domains of an antibody. The two heavy chain fragments are held together by two or more disulfide bonds and by hydrophobic interactions of the CH3 domains. The term “Fc polypeptide” as used herein includes native and mutein forms of polypeptides derived from the Fc region of an antibody. Truncated forms of such polypeptides containing the hinge region that promotes dimerization are included. [0118] Antigen-binding peptide scaffolds, such as complementarity-determining regions (CDRs), are used to generate protein-binding molecules in accordance with the embodiments. Generally, a person skilled in the art can determine the type of protein scaffold on which to graft at least one of the CDRs. It is known that scaffolds, optimally, must meet a number of

TMPL14WO_spec.docx - 30 - criteria such as: good phylogenetic conservation; known three-dimensional structure; small size; few or no post-transcriptional modifications; and/or be easy to produce, express, and purify. Skerra, J Mol Recognit, 13:167-87 (2000). [0119] The protein scaffolds can be sourced from, but not limited to: fibronectin type III FN3 domain (known as “monobodies”), fibronectin type III domain 10, lipocalin, anticalin, Z- domain of protein A of Staphylococcus aureus, thioredoxin A or proteins with a repeated motif such as the “ankyrin repeat”, the “armadillo repeat”, the “leucine-rich repeat” and the “tetratricopeptide repeat”. Such proteins are described in US Patent Publication Nos. 2010/0285564, 2006/0058510, 2006/0088908, 2005/0106660, and PCT Publication No. WO2006/056464, each of which are specifically incorporated herein by reference in their entirety. Scaffolds derived from toxins from scorpions, insects, plants, mollusks, etc., and the protein inhibiters of neuronal NO synthase (PIN) may also be used.

TMPL14WO_spec.docx - 31 - II. Additional Agents A. Immunostimulators [0120] In some embodiments, the method further comprises administration of an additional agent. In some embodiments, the additional agent is an immunostimulator. The term “immunostimulator” as used herein refers to a compound that can stimulate an immune response in a subject, and may include an adjuvant. In some embodiments, an immunostimulator is an agent that does not constitute a specific antigen, but can boost the strength and longevity of an immune response to an antigen. Such immunostimulators may include, but are not limited to stimulators of pattern recognition receptors, such as Toll-like receptors, RIG-1 and NOD-like receptors (NLR), mineral salts, such as alum, alum combined with monphosphoryl lipid (MPL) A of Enterobacteria, such as Escherihia coli, Salmonella minnesota, Salmonella typhimurium, or Shigella flexneri or specifically with MPL (ASO4), MPL A of above-mentioned bacteria separately, saponins, such as QS-21, Quil-A, ISCOMs, ISCOMATRIX, emulsions such as MF59, Montanide, ISA 51 and ISA 720, AS02 (QS21+squalene+MPL.), liposomes and liposomal formulations such as AS01, synthesized or specifically prepared microparticles and microcarriers such as bacteria-derived outer membrane vesicles (OMV) of N. gonorrheae, Chlamydia trachomatis and others, or chitosan particles, depot-forming agents, such as Pluronic block co-polymers, specifically modified or prepared peptides, such as muramyl dipeptide, aminoalkyl glucosaminide 4-phosphates, such as RC529, or proteins, such as bacterial toxoids or toxin fragments. [0121] In some embodiments, the additional agent comprises an agonist for pattern recognition receptors (PRR), including, but not limited to Toll-Like Receptors (TLRs), specifically TLRs 2, 3, 4, 5, 7, 8, 9 and/or combinations thereof. In some embodiments, additional agents comprise agonists for Toll-Like Receptors 3, agonists for Toll-Like Receptors 7 and 8, or agonists for Toll-Like Receptor 9; preferably the recited immunostimulators comprise imidazoquinolines; such as R848; adenine derivatives, such as those disclosed in U.S. Pat. No. 6,329,381, U.S. Published Patent Application 2010/0075995, or WO 2010/018132; immunostimulatory DNA; or immunostimulatory RNA. In some embodiments, the additional agents also may comprise immunostimulatory RNA molecules, such as but not limited to dsRNA, poly I:C or poly I:poly C12U (available as Ampligen.RTM., both poly I:C and poly I:polyC12U being known as TLR3 stimulants), and/or those disclosed in F. Heil et al., "Species-Specific Recognition of Single-Stranded RNA via Toll-like Receptor 7 and 8" Science 303(5663), 1526-1529 (2004); J. Vollmer et al., "Immune modulation by chemically

TMPL14WO_spec.docx - 32 - modified ribonucleosides and oligoribonucleotides" WO 2008033432 A2; A. Forsbach et al., "Immunostimulatory oligoribonucleotides containing specific sequence motif(s) and targeting the Toll-like receptor 8 pathway" WO 2007062107 A2; E. Uhlmann et al., "Modified oligoribonucleotide analogs with enhanced immunostimulatory activity" U.S. Pat. Appl. Publ. US 2006241076; G. Lipford et al., "Immunostimulatory viral RNA oligonucleotides and use for treating cancer and infections" WO 2005097993 A2; G. Lipford et al., "Immunostimulatory G,U-containing oligoribonucleotides, compositions, and screening methods" WO 2003086280 A2. In some embodiments, an additional agent may be a TLR-4 agonist, such as bacterial lipopolysaccharide (LPS), VSV-G, and/or HMGB-1. In some embodiments, additional agents may comprise TLR-5 agonists, such as flagellin, or portions or derivatives thereof, including but not limited to those disclosed in U.S. Pat. Nos.6,130,082, 6,585,980, and 7,192,725. [0122] In some embodiments, additional agents may be proinflammatory stimuli released from necrotic cells (e.g., urate crystals). In some embodiments, additional agents may be activated components of the complement cascade (e.g., CD21, CD35, etc.). In some embodiments, additional agents may be activated components of immune complexes. Additional agents also include complement receptor agonists, such as a molecule that binds to CD21 or CD35. In some embodiments, the complement receptor agonist induces endogenous complement opsonization of the synthetic nanocarrier. In some embodiments, immunostimulators are cytokines, which are small proteins or biological factors (in the range of 5 kD-20 kD) that are released by cells and have specific effects on cell-cell interaction, communication and behavior of other cells. In some embodiments, the cytokine receptor agonist is a small molecule, antibody, fusion protein, or aptamer. B. Immunotherapies [0123] In some embodiments, the additional therapy comprises a cancer immunotherapy. Cancer immunotherapy (sometimes called immuno-oncology, abbreviated IO) is the use of the immune system to treat cancer. Immunotherapies can be categorized as active, passive or hybrid (active and passive). These approaches exploit the fact that cancer cells often have molecules on their surface that can be detected by the immune system, known as tumour- associated antigens (TAAs); they are often proteins or other macromolecules (e.g. carbohydrates). Active immunotherapy directs the immune system to attack tumor cells by targeting TAAs. Passive immunotherapies enhance existing anti-tumor responses and include the use of monoclonal antibodies, lymphocytes and cytokines. Immumotherapies are known in the art, and some are described below.

TMPL14WO_spec.docx - 33 - 1. Inhibition of co-stimulatory molecules [0124] In some embodiments, the immunotherapy comprises an inhibitor of a co- stimulatory molecule. In some embodiments, the inhibitor comprises an inhibitor of B7-1 (CD80), B7-2 (CD86), CD28, ICOS, OX40 (TNFRSF4), 4-1BB (CD137; TNFRSF9), CD40L (CD40LG), GITR (TNFRSF18), and combinations thereof. Inhibitors include inhibitory antibodies, polypeptides, compounds, and nucleic acids. 2. Dendritic cell therapy [0125] Dendritic cell therapy provokes anti-tumor responses by causing dendritic cells to present tumor antigens to lymphocytes, which activates them, priming them to kill other cells that present the antigen. Dendritic cells are antigen presenting cells (APCs) in the mammalian immune system. In cancer treatment they aid cancer antigen targeting. One example of cellular cancer therapy based on dendritic cells is sipuleucel-T. [0126] One method of inducing dendritic cells to present tumor antigens is by vaccination with autologous tumor lysates or short peptides (small parts of protein that correspond to the protein antigens on cancer cells). These peptides are often given in combination with adjuvants (highly immunogenic substances) to increase the immune and anti-tumor responses. Other adjuvants include proteins or other chemicals that attract and/or activate dendritic cells, such as granulocyte macrophage colony-stimulating factor (GM-CSF). [0127] Dendritic cells can also be activated in vivo by making tumor cells express GM- CSF. This can be achieved by either genetically engineering tumor cells to produce GM-CSF or by infecting tumor cells with an oncolytic virus that expresses GM-CSF. [0128] Another strategy is to remove dendritic cells from the blood of a patient and activate them outside the body. The dendritic cells are activated in the presence of tumor antigens, which may be a single tumor-specific peptide/protein or a tumor cell lysate (a solution of broken down tumor cells). These cells (with optional adjuvants) are infused and provoke an immune response. [0129] Dendritic cell therapies include the use of antibodies that bind to receptors on the surface of dendritic cells. Antigens can be added to the antibody and can induce the dendritic cells to mature and provide immunity to the tumor. Dendritic cell receptors such as TLR3, TLR7, TLR8 or CD40 have been used as antibody targets.

TMPL14WO_spec.docx - 34 - 3. CAR-T cell therapy [0130] Chimeric antigen receptors (CARs, also known as chimeric immunoreceptors, chimeric T cell receptors or artificial T cell receptors) are engineered receptors that combine a new specificity with an immune cell to target cancer cells. Typically, these receptors graft the specificity of a monoclonal antibody onto a T cell. The receptors are called chimeric because they are fused of parts from different sources. CAR-T cell therapy refers to a treatment that uses such transformed cells for cancer therapy. [0131] The basic principle of CAR-T cell design involves recombinant receptors that combine antigen-binding and T-cell activating functions. The general premise of CAR-T cells is to artificially generate T-cells targeted to markers found on cancer cells. Scientists can remove T-cells from a person, genetically alter them, and put them back into the patient for them to attack the cancer cells. Once the T cell has been engineered to become a CAR-T cell, it acts as a “living drug”. CAR-T cells create a link between an extracellular ligand recognition domain to an intracellular signalling molecule which in turn activates T cells. The extracellular ligand recognition domain is usually a single-chain variable fragment (scFv). An important aspect of the safety of CAR-T cell therapy is how to ensure that only cancerous tumor cells are targeted, and not normal cells. The specificity of CAR-T cells is determined by the choice of molecule that is targeted. [0132] Exemplary CAR-T therapies include Tisagenlecleucel (Kymriah) and Axicabtagene ciloleucel (Yescarta). In some embodiments, the CAR-T therapy targets CD19. 4. Cytokine therapy [0133] Cytokines are proteins produced by many types of cells present within a tumor. They can modulate immune responses. The tumor often employs them to allow it to grow and reduce the immune response. These immune-modulating effects allow them to be used as drugs to provoke an immune response. Two commonly used cytokines are interferons and interleukins. [0134] Interferons are produced by the immune system. They are usually involved in anti- viral response, but also have use for cancer. They fall in three groups: type I (IFNα and IFNβ), type II (IFNγ) and type III (IFNλ). [0135] Interleukins have an array of immune system effects. IL-2 is an exemplary interleukin cytokine therapy.

TMPL14WO_spec.docx - 35 - 5. Adoptive T-cell therapy [0136] Adoptive T cell therapy is a form of passive immunization by the transfusion of T- cells (adoptive cell transfer). They are found in blood and tissue and usually activate when they find foreign pathogens. Specifically they activate when the T-cell's surface receptors encounter cells that display parts of foreign proteins on their surface antigens. These can be either infected cells, or antigen presenting cells (APCs). They are found in normal tissue and in tumor tissue, where they are known as tumor infiltrating lymphocytes (TILs). They are activated by the presence of APCs such as dendritic cells that present tumor antigens. Although these cells can attack the tumor, the environment within the tumor is highly immunosuppressive, preventing immune-mediated tumour death. [0137] Multiple ways of producing and obtaining tumour targeted T-cells have been developed. T-cells specific to a tumor antigen can be removed from a tumor sample (TILs) or filtered from blood. Subsequent activation and culturing is performed ex vivo, with the results reinfused. Activation can take place through gene therapy, or by exposing the T cells to tumor antigens. 6. Checkpoint Inhibitors and Combination Treatment [0138] In some embodiments, the additional therapy comprises immune checkpoint inhibitors. Certain embodiments are further described below. a. PD-1, PDL1, and PDL2 inhibitors [0139] PD-1 can act in the tumor microenvironment where T cells encounter an infection or tumor. Activated T cells upregulate PD-1 and continue to express it in the peripheral tissues. Cytokines such as IFN-gamma induce the expression of PDL1 on epithelial cells and tumor cells. PDL2 is expressed on macrophages and dendritic cells. The main role of PD-1 is to limit the activity of effector T cells in the periphery and prevent excessive damage to the tissues during an immune response. Inhibitors of the disclosure may block one or more functions of PD-1 and/or PDL1 activity. [0140] Alternative names for “PD-1” include CD279 and SLEB2. Alternative names for “PDL1” include B7-H1, B7-4, CD274, and B7-H. Alternative names for “PDL2” include B7- DC, Btdc, and CD273. In some embodiments, PD-1, PDL1, and PDL2 are human PD-1, PDL1 and PDL2. [0141] In some embodiments, the PD-1 inhibitor is a molecule that inhibits the binding of PD-1 to its ligand binding partners. In a specific aspect, the PD-1 ligand binding partners are

TMPL14WO_spec.docx - 36 - PDL1 and/or PDL2. In another embodiment, a PDL1 inhibitor is a molecule that inhibits the binding of PDL1 to its binding partners. In a specific aspect, PDL1 binding partners are PD-1 and/or B7-1. In another embodiment, the PDL2 inhibitor is a molecule that inhibits the binding of PDL2 to its binding partners. In a specific aspect, a PDL2 binding partner is PD-1. The inhibitor may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide. Exemplary antibodies are described in U.S. Patent Nos. 8,735,553, 8,354,509, and 8,008,449, all incorporated herein by reference. Other PD-1 inhibitors for use in the methods and compositions provided herein are known in the art such as described in U.S. Patent Application Nos. US2014/0294898, US2014/022021, and US2011/0008369, all incorporated herein by reference. [0142] In some embodiments, the PD-1 inhibitor is an anti-PD-1 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody). In some embodiments, the anti-PD- 1 antibody is selected from the group consisting of nivolumab, pembrolizumab, and pidilizumab. In some embodiments, the PD-1 inhibitor is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PDL1 or PDL2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence). In some embodiments, the PDL1 inhibitor comprises AMP- 224. Nivolumab, also known as MDX-1106-04, MDX- 1106, ONO-4538, BMS-936558, and OPDIVO®, is an anti-PD-1 antibody described in WO2006/121168. Pembrolizumab, also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA®, and SCH-900475, is an anti-PD-1 antibody described in WO2009/114335. Pidilizumab, also known as CT-011, hBAT, or hBAT-1, is an anti-PD-1 antibody described in WO2009/101611. AMP-224, also known as B7-DCIg, is a PDL2-Fc fusion soluble receptor described in WO2010/027827 and WO2011/066342. Additional PD-1 inhibitors include MEDI0680, also known as AMP-514, and REGN2810. [0143] In some embodiments, the immune checkpoint inhibitor is a PDL1 inhibitor such as Durvalumab, also known as MEDI4736, atezolizumab, also known as MPDL3280A, avelumab, also known as MSB00010118C, MDX-1105, BMS-936559, or combinations thereof. In certain aspects, the immune checkpoint inhibitor is a PDL2 inhibitor such as rHIgM12B7. [0144] In some embodiments, the inhibitor comprises the heavy and light chain CDRs or VRs of nivolumab, pembrolizumab, or pidilizumab. Accordingly, in one embodiment, the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of nivolumab, pembrolizumab, or pidilizumab, and the CDR1, CDR2 and CDR3 domains of the VL region of nivolumab, pembrolizumab, or pidilizumab. In another embodiment, the antibody competes

TMPL14WO_spec.docx - 37 - for binding with and/or binds to the same epitope on PD-1, PDL1, or PDL2 as the above- mentioned antibodies. In another embodiment, the antibody has at least about 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range therein) variable region amino acid sequence identity with the above-mentioned antibodies. b. CTLA-4, B7-1, and B7-2 [0145] Another immune checkpoint that can be targeted in the methods provided herein is the cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), also known as CD152. The complete cDNA sequence of human CTLA-4 has the Genbank accession number L15006. CTLA-4 is found on the surface of T cells and acts as an “off” switch when bound to B7-1 (CD80) or B7-2 (CD86) on the surface of antigen-presenting cells. CTLA4 is a member of the immunoglobulin superfamily that is expressed on the surface of Helper T cells and transmits an inhibitory signal to T cells. CTLA4 is similar to the T-cell co-stimulatory protein, CD28, and both molecules bind to B7-1 and B7-2 on antigen-presenting cells. CTLA-4 transmits an inhibitory signal to T cells, whereas CD28 transmits a stimulatory signal. Intracellular CTLA- 4 is also found in regulatory T cells and may be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules. Inhibitors of the disclosure may block one or more functions of CTLA-4, B7-1, and/or B7-2 activity. In some embodiments, the inhibitor blocks the CTLA-4 and B7-1 interaction. In some embodiments, the inhibitor blocks the CTLA-4 and B7-2 interaction. [0146] In some embodiments, the immune checkpoint inhibitor is an anti-CTLA-4 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide. [0147] Anti-human-CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-CTLA-4 antibodies can be used. For example, the anti- CTLA-4 antibodies disclosed in: US 8,119,129, WO 01/14424, WO 98/42752; WO 00/37504 (CP675,206, also known as tremelimumab; formerly ticilimumab), U.S. Patent No.6,207,156; Hurwitz et al., 1998; can be used in the methods disclosed herein. The teachings of each of the aforementioned publications are hereby incorporated by reference. Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used. For example, a humanized CTLA-4 antibody is described in International Patent Application No.

TMPL14WO_spec.docx - 38 - WO2001/014424, WO2000/037504, and U.S. Patent No.8,017,114; all incorporated herein by reference. [0148] A further anti-CTLA-4 antibody useful as a checkpoint inhibitor in the methods and compositions of the disclosure is ipilimumab (also known as 10D1, MDX- 010, MDX- 101, and Yervoy®) or antigen binding fragments and variants thereof (see, e.g., WO01/14424). [0149] In some embodiments, the inhibitor comprises the heavy and light chain CDRs or VRs of tremelimumab or ipilimumab. Accordingly, in one embodiment, the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of tremelimumab or ipilimumab, and the CDR1, CDR2 and CDR3 domains of the VL region of tremelimumab or ipilimumab. In another embodiment, the antibody competes for binding with and/or binds to the same epitope on PD-1, B7-1, or B7-2 as the above- mentioned antibodies. In another embodiment, the antibody has at least about 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range therein) variable region amino acid sequence identity with the above-mentioned antibodies. C. Oncolytic virus [0150] In some embodiments, the additional therapy comprises an oncolytic virus. An oncolytic virus is a virus that preferentially infects and kills cancer cells. As the infected cancer cells are destroyed by oncolysis, they release new infectious virus particles or virions to help destroy the remaining tumour. Oncolytic viruses are thought not only to cause direct destruction of the tumour cells, but also to stimulate host anti-tumour immune responses for long-term immunotherapy D. Polysaccharides [0151] In some embodiments, the additional therapy comprises polysaccharides. Certain compounds found in mushrooms, primarily polysaccharides, can up-regulate the immune system and may have anti-cancer properties. For example, beta-glucans such as lentinan have been shown in laboratory studies to stimulate macrophage, NK cells, T cells and immune system cytokines and have been investigated in clinical trials as immunologic adjuvants. E. Neoantigens [0152] In some embodiments, the additional therapy comprises neoantigen administration. Many tumors express mutations. These mutations potentially create new targetable antigens (neoantigens) for use in T cell immunotherapy. The presence of CD8+ T cells in cancer lesions,

TMPL14WO_spec.docx - 39 - as identified using RNA sequencing data, is higher in tumors with a high mutational burden. The level of transcripts associated with cytolytic activity of natural killer cells and T cells positively correlates with mutational load in many human tumors. F. Chemotherapies [0153] In some embodiments, the additional therapy comprises a chemotherapy. Suitable classes of chemotherapeutic agents include (a) Alkylating Agents, such as nitrogen mustards (e.g., mechlorethamine, cylophosphamide, ifosfamide, melphalan, chlorambucil), ethylenimines and methylmelamines (e.g., hexamethylmelamine, thiotepa), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomustine, chlorozoticin, streptozocin) and triazines (e.g., dicarbazine), (b) Antimetabolites, such as folic acid analogs (e.g., methotrexate), pyrimidine analogs (e.g., 5-fluorouracil, floxuridine, cytarabine, azauridine) and purine analogs and related materials (e.g., 6-mercaptopurine, 6-thioguanine, pentostatin), (c) Natural Products, such as vinca alkaloids (e.g., vinblastine, vincristine), epipodophylotoxins (e.g., etoposide, teniposide), antibiotics (e.g., dactinomycin, daunorubicin, doxorubicin, bleomycin, plicamycin and mitoxanthrone), enzymes (e.g., L-asparaginase), and biological response modifiers (e.g., Interferon-α), and (d) Miscellaneous Agents, such as platinum coordination complexes (e.g., cisplatin, carboplatin), substituted ureas (e.g., hydroxyurea), methylhydiazine derivatives (e.g., procarbazine), and adreocortical suppressants (e.g., taxol and mitotane). In some embodiments, cisplatin is a particularly suitable chemotherapeutic agent. [0154] Cisplatin has been widely used to treat cancers such as, for example, metastatic testicular or ovarian carcinoma, advanced bladder cancer, head or neck cancer, cervical cancer, lung cancer or other tumors. Cisplatin is not absorbed orally and must therefore be delivered via other routes such as, for example, intravenous, subcutaneous, intratumoral or intraperitoneal injection. Cisplatin can be used alone or in combination with other agents, with efficacious doses used in clinical applications including about 15 mg/m2 to about 20 mg/m2 for 5 days every three weeks for a total of three courses being contemplated in certain embodiments. In some embodiments, the amount of cisplatin delivered to the cell and/or subject in conjunction with the construct comprising an Egr-1 promoter operably linked to a polynucleotide encoding the therapeutic polypeptide is less than the amount that would be delivered when using cisplatin alone. [0155] Other suitable chemotherapeutic agents include antimicrotubule agents, e.g., Paclitaxel (“Taxol”) and doxorubicin hydrochloride (“doxorubicin”). The combination of an Egr-1 promoter/TNFα construct delivered via an adenoviral vector and doxorubicin was

TMPL14WO_spec.docx - 40 - determined to be effective in overcoming resistance to chemotherapy and/or TNF-α, which suggests that combination treatment with the construct and doxorubicin overcomes resistance to both doxorubicin and TNF-α. [0156] Doxorubicin is absorbed poorly and is preferably administered intravenously. In certain embodiments, appropriate intravenous doses for an adult include about 60 mg/m2 to about 75 mg/m2 at about 21-day intervals or about 25 mg/m2 to about 30 mg/m2 on each of 2 or 3 successive days repeated at about 3 week to about 4 week intervals or about 20 mg/m2 once a week. The lowest dose should be used in elderly patients, when there is prior bone- marrow depression caused by prior chemotherapy or neoplastic marrow invasion, or when the drug is combined with other myelopoietic suppressant drugs. [0157] Nitrogen mustards are another suitable chemotherapeutic agent useful in the methods of the disclosure. A nitrogen mustard may include, but is not limited to, mechlorethamine (HN2), cyclophosphamide and/or ifosfamide, melphalan (L-sarcolysin), and chlorambucil. Cyclophosphamide (CYTOXAN®) is available from Mead Johnson and NEOSTAR® is available from Adria), is another suitable chemotherapeutic agent. Suitable oral doses for adults include, for example, about 1 mg/kg/day to about 5 mg/kg/day, intravenous doses include, for example, initially about 40 mg/kg to about 50 mg/kg in divided doses over a period of about 2 days to about 5 days or about 10 mg/kg to about 15 mg/kg about every 7 days to about 10 days or about 3 mg/kg to about 5 mg/kg twice a week or about 1.5 mg/kg/day to about 3 mg/kg/day. Because of adverse gastrointestinal effects, the intravenous route is preferred. The drug also sometimes is administered intramuscularly, by infiltration or into body cavities. [0158] Additional suitable chemotherapeutic agents include pyrimidine analogs, such as cytarabine (cytosine arabinoside), 5-fluorouracil (fluouracil; 5-FU) and floxuridine (fluorode- oxyuridine; FudR).5-FU may be administered to a subject in a dosage of anywhere between about 7.5 to about 1000 mg/m2. Further, 5-FU dosing schedules may be for a variety of time periods, for example up to six weeks, or as determined by one of ordinary skill in the art to which this disclosure pertains. [0159] Gemcitabine diphosphate (GEMZAR®, Eli Lilly & Co., “gemcitabine”), another suitable chemotherapeutic agent, is recommended for treatment of advanced and metastatic pancreatic cancer, and will therefore be useful in the present disclosure for these cancers as well. [0160] The amount of the chemotherapeutic agent delivered to the patient may be variable. In one suitable embodiment, the chemotherapeutic agent may be administered in an amount

TMPL14WO_spec.docx - 41 - effective to cause arrest or regression of the cancer in a host, when the chemotherapy is administered with the construct. In other embodiments, the chemotherapeutic agent may be administered in an amount that is anywhere between 2 to 10,000 fold less than the chemotherapeutic effective dose of the chemotherapeutic agent. For example, the chemotherapeutic agent may be administered in an amount that is about 20 fold less, about 500 fold less or even about 5000 fold less than the chemotherapeutic effective dose of the chemotherapeutic agent. The chemotherapeutics of the disclosure can be tested in vivo for the desired therapeutic activity in combination with the construct, as well as for determination of effective dosages. For example, such compounds can be tested in suitable animal model systems prior to testing in humans, including, but not limited to, rats, mice, chicken, cows, monkeys, rabbits, etc. In vitro testing may also be used to determine suitable combinations and dosages, as described in the examples. G. Radiotherapy [0161] In some embodiments, the additional therapy or prior therapy comprises radiation, such as ionizing radiation. As used herein, “ionizing radiation” means radiation comprising particles or photons that have sufficient energy or can produce sufficient energy via nuclear interactions to produce ionization (gain or loss of electrons). An exemplary and preferred ionizing radiation is an x-radiation. Means for delivering x-radiation to a target tissue or cell are well known in the art. [0162] In some embodiments, the amount of ionizing radiation is greater than 20 Gy and is administered in one dose. In some embodiments, the amount of ionizing radiation is 18 Gy and is administered in three doses. In some embodiments, the amount of ionizing radiation is at least, at most, or exactly 2, 4, 6, 8, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 40 Gy (or any derivable range therein). In some embodiments, the ionizing radiation is administered in at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 does (or any derivable range therein). When more than one dose is administered, the does may be about 1, 4, 8, 12, or 24 hours or 1, 2, 3, 4, 5, 6, 7, or 8 days or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, or 16 weeks apart, or any derivable range therein. [0163] In some embodiments, the amount of IR may be presented as a total dose of IR, which is then administered in fractionated doses. For example, in some embodiments, the total dose is 50 Gy administered in 10 fractionated doses of 5 Gy each. In some embodiments, the total dose is 50-90 Gy, administered in 20-60 fractionated doses of 2-3 Gy each. In some

TMPL14WO_spec.docx - 42 - embodiments, the total dose of IR is at least, at most, or about 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 125, 130, 135, 140, or 150 (or any derivable range therein). In some embodiments, the total dose is administered in fractionated doses of at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 20, 25, 30, 35, 40, 45, or 50 Gy (or any derivable range therein. In some embodiments, at least, at most, or exactly 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 fractionated doses are administered (or any derivable range therein). In some embodiments, at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 (or any derivable range therein) fractionated doses are administered per day. In some embodiments, at least, at most, or exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 (or any derivable range therein) fractionated doses are administered per week. H. Surgery [0164] Approximately 60% of persons with cancer will undergo surgery of some type, which includes preventative, diagnostic or staging, curative, and palliative surgery. Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed and may be used in conjunction with other therapies, such as the treatment of the present embodiments, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy, and/or alternative therapies. Tumor resection refers to physical removal of at least part of a tumor. In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically-controlled surgery (Mohs’ surgery). [0165] Upon excision of part or all of cancerous cells, tissue, or tumor, a cavity may be formed in the body. Treatment may be accomplished by perfusion, direct injection, or local application of the area with an additional anti-cancer therapy. Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. These treatments may be of varying dosages as well.

TMPL14WO_spec.docx - 43 - I. Other Agents [0166] It is contemplated that other agents may be used in combination with certain aspects of the present embodiments to improve the therapeutic efficacy of treatment. These additional agents include agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adhesion, agents that increase the sensitivity of the hyperproliferative cells to apoptotic inducers, or other biological agents. Increases in intercellular signaling by elevating the number of GAP junctions would increase the anti-hyperproliferative effects on the neighboring hyperproliferative cell population. In other embodiments, cytostatic or differentiation agents can be used in combination with certain aspects of the present embodiments to improve the anti-hyperproliferative efficacy of the treatments. Inhibitors of cell adhesion are contemplated to improve the efficacy of the present embodiments. Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin. It is further contemplated that other agents that increase the sensitivity of a hyperproliferative cell to apoptosis, such as the antibody c225, could be used in combination with certain aspects of the present embodiments to improve the treatment efficacy. J. Analysis of Gene Expression Levels [0167] A gene shall be understood to be specifically expressed in a certain cell type if the expression level of said gene in said cell type is at least 2-fold, 5-fold, 10-fold, 100-fold, 1000- fold, or 10000-fold higher than in a reference cell type, or in a mixture of reference cell types. Reference cell types include non-cancerous tissue cells or a heterogeneous population of cancers. [0168] Comparison of multiple marker genes with a threshold level can be performed as follows: 1. The individual marker genes are compared to their respective threshold levels. 2. The number of marker genes, the expression level of which is above their respective threshold level, is determined. 3. If a marker genes is expressed above its respective threshold level, then the expression level of the marker gene is taken to be "above the threshold level". [0169] In certain aspects, the determination of expression levels is on a gene chip, such as an Affymetrix™ gene chip. In another aspect, the determination of expression levels is done by kinetic real time PCR. [0170] In certain aspects, the methods can relate to a system for performing such methods, the system comprising (a) apparatus or device for storing data on the biomarker level of the patient; (b) apparatus or device for determining the expression level of at least one marker gene

TMPL14WO_spec.docx - 44 - or activity; (c) apparatus or device for comparing the expression level of the first marker gene or activity with a predetermined first threshold value; (d) apparatus or device for determining the expression level of at least one second, third, fourth, 5th, 6th or more marker gene or activity and for comparing with a corresponding predetermined threshold; and (e) computing apparatus or device programmed to provide a unfavorable or poor prognosis or favorable prognosis based on the comparisons. [0171] The person skilled in the art readily appreciates that an unfavorable or poor prognosis can be given if the expression level of the first marker gene with the predetermined first threshold value indicates a tumor that is likely to recur or not respond well to standard therapies. [0172] The expression patterns can also be compared by using one or more ratios between the expression levels of different cancer biomarkers. Other suitable measures or indicators can also be employed for assessing the relationship or difference between different expression patterns. [0173] The expression levels of cancer biomarkers can be compared to reference expression levels using various methods. These reference levels can be determined using expression levels of a reference based on all cancer patients. Alternatively, it can be based on an internal reference such as a gene that is expressed in all cells. In some embodiments, the reference is a gene expressed in cancer cells at a higher level than any biomarker. Any comparison can be performed using the fold change or the absolute difference between the expression levels to be compared. One or more cancer biomarkers can be used in the comparison. It is contemplated that 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, and/or 11 biomarkers (or any range derivable therein) may be compared to each other and/or to a reference that is internal or external. A person of ordinary skill in the art would know how to do such comparisons. [0174] Comparisons or results from comparisons may reveal or be expressed as x-fold increase or decrease in expression relative to a standard or relative to another biomarker or relative to the same biomarker but in a different class of prognosis. In some embodiments, patients with a poor prognosis have a relatively high level of expression (overexpression) or relatively low level of expression (underexpression) when compared to patients with a better or favorable prognosis, or vice versa. [0175] Fold increases or decreases may be, be at least, or be at most 1-, 2-, 3-, 4-, 5-, 6-, 7- , 8-, 9-, 10-, 11-, 12-, 13-, 14-, 15-, 16-, 17-, 18-, 19-, 20-, 25-, 30-, 35-, 40-, 45-, 50-, 55-, 60- , 65-, 70-, 75-, 80-, 85-, 90-, 95-, 100- or more, or any range derivable therein. Alternatively, differences in expression may be expressed as a percent decrease or increase, such as at least

TMPL14WO_spec.docx - 45 - or at most 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 300, 400, 500, 600, 700, 800, 900, 1000% difference, or any range derivable therein. [0176] Other ways to express relative expression levels are with normalized or relative numbers such as 0.001, 0.002, 0.003, 0.004, 0.005, 0.006, 0.007, 0.008, 0.009, 0.01, 0.02, 0.03. 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7. 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, or any range derivable therein. In some embodiments, the levels can be relative to a control. [0177] Algorithms, such as the weighted voting programs, can be used to facilitate the evaluation of biomarker levels. In addition, other clinical evidence can be combined with the biomarker-based test to reduce the risk of false evaluations. Other cytogenetic evaluations may be considered in some embodiments. [0178] Any biological sample from the patient that contains cancer cells may be used to evaluate the expression pattern of any biomarker discussed herein. In some embodiments, a biological sample from a tumor is used. Evaluation of the sample may involve, though it need not involve, panning (enriching) for cancer cells or isolating the cancer cells. K. Measurement of Gene Expression Using Nucleic Acids [0179] Testing methods based on differentially expressed gene products are well known in the art. In accordance with one aspect, the differential expression patterns of cancer biomarkers can be determined by measuring the levels of RNA transcripts of these genes, or genes whose expression is modulated by the these genes, in the patient’s cancer cells. Suitable methods for this purpose include, but are not limited to, RT-PCR, Northern Blot, in situ hybridization, Southern Blot, slot-blotting, nuclease protection assay and oligonucleotide arrays. [0180] In certain aspects, RNA isolated from cancer cells can be amplified to cDNA or cRNA before detection and/or quantitation. The isolated RNA can be either total RNA or mRNA. The RNA amplification can be specific or non-specific. Suitable amplification methods include, but are not limited to, reverse transcriptase PCR, isothermal amplification, ligase chain reaction, and Qbeta replicase. The amplified nucleic acid products can be detected and/or quantitated through hybridization to labeled probes. In some embodiments, detection

TMPL14WO_spec.docx - 46 - may involve fluorescence resonance energy transfer (FRET) or some other kind of quantum dots. [0181] Amplification primers or hybridization probes for a cancer biomarker can be prepared from the gene sequence or obtained through commercial sources, such as Affymatrix. In certain embodiments the gene sequence is identical or complementary to at least 8 contiguous nucleotides of the coding sequence. [0182] Sequences suitable for making probes/primers for the detection of their corresponding cancer biomarkers include those that are identical or complementary to all or part of the cancer biomarker genes described herein. These sequences are all nucleic acid sequences of cancer biomarkers. [0183] The use of a probe or primer of between 13 and 100 nucleotides, particularly between 17 and 100 nucleotides in length, or in some aspects up to 1-2 kilobases or more in length, allows the formation of a duplex molecule that is both stable and selective. Molecules having complementary sequences over contiguous stretches greater than 20 bases in length may be used to increase stability and/or selectivity of the hybrid molecules obtained. One may design nucleic acid molecules for hybridization having one or more complementary sequences of 20 to 30 nucleotides, or even longer where desired. Such fragments may be readily prepared, for example, by directly synthesizing the fragment by chemical means or by introducing selected sequences into recombinant vectors for recombinant production. [0184] In one embodiment, each probe/primer comprises at least 15 nucleotides. For instance, each probe can comprise at least or at most 20, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 400 or more nucleotides (or any range derivable therein). They may have these lengths and have a sequence that is identical or complementary to a gene described herein. Particularly, each probe/primer has relatively high sequence complexity and does not have any ambiguous residue (undetermined "n" residues). The probes/primers can hybridize to the target gene, including its RNA transcripts, under stringent or highly stringent conditions. In some embodiments, because each of the biomarkers has more than one human sequence, it is contemplated that probes and primers may be designed for use with each of these sequences. For example, inosine is a nucleotide frequently used in probes or primers to hybridize to more than one sequence. It is contemplated that probes or primers may have inosine or other design implementations that accommodate recognition of more than one human sequence for a particular biomarker. [0185] For applications requiring high selectivity, one will typically desire to employ relatively high stringency conditions to form the hybrids. For example, relatively low salt

TMPL14WO_spec.docx - 47 - and/or high temperature conditions, such as provided by about 0.02 M to about 0.10 M NaCl at temperatures of about 50°C to about 70°C. Such high stringency conditions tolerate little, if any, mismatch between the probe or primers and the template or target strand and would be particularly suitable for isolating specific genes or for detecting specific mRNA transcripts. It is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide. [0186] In another embodiment, the probes/primers for a gene are selected from regions which significantly diverge from the sequences of other genes. Such regions can be determined by checking the probe/primer sequences against a human genome sequence database, such as the Entrez database at the NCBI. One algorithm suitable for this purpose is the BLAST algorithm. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence to increase the cumulative alignment score. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. These parameters can be adjusted for different purposes, as appreciated by one of ordinary skill in the art. [0187] In one embodiment, quantitative RT-PCR (such as TaqMan, ABI) is used for detecting and comparing the levels of RNA transcripts in cancer samples. Quantitative RT- PCR involves reverse transcription (RT) of RNA to cDNA followed by relative quantitative PCR (RT-PCR). The concentration of the target DNA in the linear portion of the PCR process is proportional to the starting concentration of the target before the PCR was begun. By determining the concentration of the PCR products of the target DNA in PCR reactions that have completed the same number of cycles and are in their linear ranges, it is possible to determine the relative concentrations of the specific target sequence in the original DNA mixture. If the DNA mixtures are cDNAs synthesized from RNAs isolated from different tissues or cells, the relative abundances of the specific mRNA from which the target sequence was derived may be determined for the respective tissues or cells. This direct proportionality between the concentration of the PCR products and the relative mRNA abundances is true in the linear range portion of the PCR reaction. The final concentration of the target DNA in the

TMPL14WO_spec.docx - 48 - plateau portion of the curve is determined by the availability of reagents in the reaction mix and is independent of the original concentration of target DNA. Therefore, the sampling and quantifying of the amplified PCR products may be carried out when the PCR reactions are in the linear portion of their curves. In addition, relative concentrations of the amplifiable cDNAs may be normalized to some independent standard, which may be based on either internally existing RNA species or externally introduced RNA species. The abundance of a particular mRNA species may also be determined relative to the average abundance of all mRNA species in the sample. [0188] In one embodiment, the PCR amplification utilizes one or more internal PCR standards. The internal standard may be an abundant housekeeping gene in the cell or it can specifically be GAPDH, GUSB and β-2 microglobulin. These standards may be used to normalize expression levels so that the expression levels of different gene products can be compared directly. A person of ordinary skill in the art would know how to use an internal standard to normalize expression levels. [0189] A problem inherent in clinical samples is that they are of variable quantity and/or quality. This problem can be overcome if the RT-PCR is performed as a relative quantitative RT-PCR with an internal standard in which the internal standard is an amplifiable cDNA fragment that is similar or larger than the target cDNA fragment and in which the abundance of the mRNA encoding the internal standard is roughly 5-100 fold higher than the mRNA encoding the target. This assay measures relative abundance, not absolute abundance of the respective mRNA species. [0190] In another embodiment, the relative quantitative RT-PCR uses an external standard protocol. Under this protocol, the PCR products are sampled in the linear portion of their amplification curves. The number of PCR cycles that are optimal for sampling can be empirically determined for each target cDNA fragment. In addition, the reverse transcriptase products of each RNA population isolated from the various samples can be normalized for equal concentrations of amplifiable cDNAs. [0191] Nucleic acid arrays can also be used to detect and compare the differential expression patterns of cancer biomarkers in cancer cells. The probes suitable for detecting the corresponding cancer biomarkers can be stably attached to known discrete regions on a solid substrate. As used herein, a probe is "stably attached" to a discrete region if the probe maintains its position relative to the discrete region during the hybridization and the subsequent washes. Construction of nucleic acid arrays is well known in the art. Suitable substrates for making

TMPL14WO_spec.docx - 49 - polynucleotide arrays include, but are not limited to, membranes, films, plastics and quartz wafers. [0192] A nucleic acid array can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more different polynucleotide probes, which may hybridize to different and/or the same biomarkers. Multiple probes for the same gene can be used on a single nucleic acid array. Probes for other disease genes can also be included in the nucleic acid array. The probe density on the array can be in any range. In some embodiments, the density may be 50, 100, 200, 300, 400, 500 or more probes/cm2. [0193] Specifically contemplated are chip-based nucleic acid technologies such as those described by Hacia et al. (1996) and Shoemaker et al. (1996). Briefly, these techniques involve quantitative methods for analyzing large numbers of genes rapidly and accurately. By tagging genes with oligonucleotides or using fixed probe arrays, one can employ chip technology to segregate target molecules as high density arrays and screen these molecules on the basis of hybridization (see also, Pease et al., 1994; and Fodor et al, 1991). It is contemplated that this technology may be used in conjunction with evaluating the expression level of one or more cancer biomarkers with respect to diagnostic, prognostic, and treatment methods. [0194] Certain embodiments may involve the use of arrays or data generated from an array. Data may be readily available. Moreover, an array may be prepared in order to generate data that may then be used in correlation studies. [0195] An array generally refers to ordered macroarrays or microarrays of nucleic acid molecules (probes) that are fully or nearly complementary or identical to a plurality of mRNA molecules or cDNA molecules and that are positioned on a support material in a spatially separated organization. Macroarrays are typically sheets of nitrocellulose or nylon upon which probes have been spotted. Microarrays position the nucleic acid probes more densely such that up to 10,000 nucleic acid molecules can be fit into a region typically 1 to 4 square centimeters. Microarrays can be fabricated by spotting nucleic acid molecules, e.g., genes, oligonucleotides, etc., onto substrates or fabricating oligonucleotide sequences in situ on a substrate. Spotted or fabricated nucleic acid molecules can be applied in a high density matrix pattern of up to about 30 non-identical nucleic acid molecules per square centimeter or higher, e.g. up to about 100 or even 1000 per square centimeter. Microarrays typically use coated glass as the solid support, in contrast to the nitrocellulose-based material of filter arrays. By having an ordered array of complementing nucleic acid samples, the position of each sample can be tracked and linked to the original sample. A variety of different array devices in which a plurality of distinct nucleic acid probes are stably associated with the surface of a solid support are known to those of skill

TMPL14WO_spec.docx - 50 - in the art. Useful substrates for arrays include nylon, glass and silicon. Such arrays may vary in a number of different ways, including average probe length, sequence or types of probes, nature of bond between the probe and the array surface, e.g. covalent or non-covalent, and the like. The labeling and screening methods and the arrays are not limited in its utility with respect to any parameter except that the probes detect expression levels; consequently, methods and compositions may be used with a variety of different types of genes. [0196] Representative methods and apparatus for preparing a microarray have been described, for example, in U.S. Patent Nos. 5,143,854; 5,202,231; 5,242,974; 5,288,644; 5,324,633; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,432,049; 5,436,327; 5,445,934; 5,468,613; 5,470,710; 5,472,672; 5,492,806; 5,525,464; 5,503,980; 5,510,270; 5,525,464; 5,527,681; 5,529,756; 5,532,128; 5,545,531; 5,547,839; 5,554,501; 5,556,752; 5,561,071; 5,571,639; 5,580,726; 5,580,732; 5,593,839; 5,599,695; 5,599,672; 5,610;287; 5,624,711; 5,631,134; 5,639,603; 5,654,413; 5,658,734; 5,661,028; 5,665,547; 5,667,972; 5,695,940; 5,700,637; 5,744,305; 5,800,992; 5,807,522; 5,830,645; 5,837,196; 5,871,928; 5,847,219; 5,876,932; 5,919,626; 6,004,755; 6,087,102; 6,368,799; 6,383,749; 6,617,112; 6,638,717; 6,720,138, as well as WO 93/17126; WO 95/11995; WO 95/21265; WO 95/21944; WO 95/35505; WO 96/31622; WO 97/10365; WO 97/27317; WO 99/35505; WO 09923256; WO 09936760; WO0138580; WO 0168255; WO 03020898; WO 03040410; WO 03053586; WO 03087297; WO 03091426; WO03100012; WO 04020085; WO 04027093; EP 373203; EP 785280; EP 799897 and UK 8803000; the disclosures of which are all herein incorporated by reference. [0197] It is contemplated that the arrays can be high density arrays, such that they contain 100 or more different probes. It is contemplated that they may contain 1000, 16,000, 65,000, 250,000 or 1,000,000 or more different probes. The probes can be directed to targets in one or more different organisms. The oligonucleotide probes range from 5 to 50, 5 to 45, 10 to 40, or 15 to 40 nucleotides in length in some embodiments. In certain embodiments, the oligonucleotide probes are 20 to 25 nucleotides in length. [0198] The location and sequence of each different probe sequence in the array are generally known. Moreover, the large number of different probes can occupy a relatively small area providing a high density array having a probe density of generally greater than about 60, 100, 600, 1000, 5,000, 10,000, 40,000, 100,000, or 400,000 different oligonucleotide probes per cm². The surface area of the array can be about or less than about 1, 1.6, 2, 3, 4, 5, 6, 7, 8, 9, or 10 cm².

TMPL14WO_spec.docx - 51 - [0199] Moreover, a person of ordinary skill in the art could readily analyze data generated using an array. Such protocols include information found in WO 9743450; WO 03023058; WO 03022421; WO 03029485; WO 03067217; WO 03066906; WO 03076928; WO 03093810; WO 03100448A1, all of which are specifically incorporated by reference. [0200] In one embodiment, nuclease protection assays are used to quantify RNAs derived from the cancer samples. There are many different versions of nuclease protection assays known to those practiced in the art. The common characteristic that these nuclease protection assays have is that they involve hybridization of an antisense nucleic acid with the RNA to be quantified. The resulting hybrid double-stranded molecule is then digested with a nuclease that digests single-stranded nucleic acids more efficiently than double-stranded molecules. The amount of antisense nucleic acid that survives digestion is a measure of the amount of the target RNA species to be quantified. An example of a nuclease protection assay that is commercially available is the RNase protection assay manufactured by Ambion, Inc. (Austin, Tex.). L. Measurement of Gene Expression Using Proteins and Polypeptides [0201] In other embodiments, the differential expression patterns of cancer biomarkers can be determined by measuring the levels of polypeptides encoded by these genes in cancer cells. Methods suitable for this purpose include, but are not limited to, immunoassays such as ELISA, RIA, FACS, dot blot, Western Blot, immunohistochemistry, and antibody-based radioimaging. Protocols for carrying out these immunoassays are well known in the art. Other methods such as 2-dimensional SDS-polyacrylamide gel electrophoresis can also be used. These procedures may be used to recognize any of the polypeptides encoded by the cancer biomarker genes described herein. [0202] One example of a method suitable for detecting the levels of target proteins in peripheral blood samples is ELISA. In an exemplifying ELISA, antibodies capable of binding to the target proteins encoded by one or more cancer biomarker genes are immobilized onto a selected surface exhibiting protein affinity, such as wells in a polystyrene or polyvinylchloride microtiter plate. Then, cancer cell samples to be tested are added to the wells. After binding and washing to remove non-specifically bound immunocomplexes, the bound antigen(s) can be detected. Detection can be achieved by the addition of a second antibody which is specific for the target proteins and is linked to a detectable label. Detection may also be achieved by the addition of a second antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label. Before being added to the microtiter plate, cells in the peripheral blood samples can be lysed

TMPL14WO_spec.docx - 52 - using various methods known in the art. Proper extraction procedures can be used to separate the target proteins from potentially interfering substances. [0203] In another ELISA embodiment, the cancer cell samples containing the target proteins are immobilized onto the well surface and then contacted with the antibodies. After binding and washing to remove non-specifically bound immunocomplexes, the bound antigen is detected. Where the initial antibodies are linked to a detectable label, the immunocomplexes can be detected directly. The immunocomplexes can also be detected using a second antibody that has binding affinity for the first antibody, with the second antibody being linked to a detectable label. [0204] Another typical ELISA involves the use of antibody competition in the detection. In this ELISA, the target proteins are immobilized on the well surface. The labeled antibodies are added to the well, allowed to bind to the target proteins, and detected by means of their labels. The amount of the target proteins in an unknown sample is then determined by mixing the sample with the labeled antibodies before or during incubation with coated wells. The presence of the target proteins in the unknown sample acts to reduce the amount of antibody available for binding to the well and thus reduces the ultimate signal. [0205] Different ELISA formats can have certain features in common, such as coating, incubating or binding, washing to remove non-specifically bound species, and detecting the bound immunocomplexes. For instance, in coating a plate with either antigen or antibody, the wells of the plate can be incubated with a solution of the antigen or antibody, either overnight or for a specified period of hours. The wells of the plate are then washed to remove incompletely adsorbed material. Any remaining available surfaces of the wells are then "coated" with a nonspecific protein that is antigenically neutral with regard to the test samples. Examples of these nonspecific proteins include bovine serum albumin (BSA), casein and solutions of milk powder. The coating allows for blocking of nonspecific adsorption sites on the immobilizing surface and thus reduces the background caused by nonspecific binding of antisera onto the surface. [0206] In ELISAs, a secondary or tertiary detection means can also be used. After binding of a protein or antibody to the well, coating with a non-reactive material to reduce background, and washing to remove unbound material, the immobilizing surface is contacted with the control and/or clinical or biological sample to be tested under conditions effective to allow immunocomplex (antigen/antibody) formation. These conditions may include, for example, diluting the antigens and antibodies with solutions such as BSA, bovine gamma globulin (BGG) and phosphate buffered saline (PBS)/Tween and incubating the antibodies and antigens

TMPL14WO_spec.docx - 53 - at room temperature for about 1 to 4 hours or at 49°C overnight. Detection of the immunocomplex then requires a labeled secondary binding ligand or antibody, or a secondary binding ligand or antibody in conjunction with a labeled tertiary antibody or third binding ligand. [0207] After all of the incubation steps in an ELISA, the contacted surface can be washed so as to remove non-complexed material. For instance, the surface may be washed with a solution such as PBS/Tween, or borate buffer. Following the formation of specific immunocomplexes between the test sample and the originally bound material, and subsequent washing, the occurrence of the amount of immunocomplexes can be determined. [0208] To provide a detecting means, the second or third antibody can have an associated label to allow detection. In one embodiment, the label is an enzyme that generates color development upon incubating with an appropriate chromogenic substrate. Thus, for example, one may contact and incubate the first or second immunocomplex with a urease, glucose oxidase, alkaline phosphatase or hydrogen peroxidase-conjugated antibody for a period of time and under conditions that favor the development of further immunocomplex formation (e.g., incubation for 2 hours at room temperature in a PBS-containing solution such as PBS-Tween). [0209] After incubation with the labeled antibody, and subsequent to washing to remove unbound material, the amount of label is quantified, e.g., by incubation with a chromogenic substrate such as urea and bromocresol purple or 2,2'-azido-di-(3-ethyl)-benzhiazoline-6- sulfonic acid (ABTS) and hydrogen peroxide, in the case of peroxidase as the enzyme label. Quantitation can be achieved by measuring the degree of color generation, e.g., using a spectrophotometer. [0210] Another suitable method is RIA (radioimmunoassay). An example of RIA is based on the competition between radiolabeled-polypeptides and unlabeled polypeptides for binding to a limited quantity of antibodies. Suitable radiolabels include, but are not limited to, I125. In one embodiment, a fixed concentration of I125-labeled polypeptide is incubated with a series of dilution of an antibody specific to the polypeptide. When the unlabeled polypeptide is added to the system, the amount of the I125-polypeptide that binds to the antibody is decreased. A standard curve can therefore be constructed to represent the amount of antibody-bound I125- polypeptide as a function of the concentration of the unlabeled polypeptide. From this standard curve, the concentration of the polypeptide in unknown samples can be determined. Various protocols for conducting RIA to measure the levels of polypeptides in cancer cell samples are well known in the art.

TMPL14WO_spec.docx - 54 - [0211] Suitable antibodies include, but are not limited to, polyclonal antibodies, monoclonal antibodies, chimeric antibodies, humanized antibodies, single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. [0212] Antibodies can be labeled with one or more detectable moieties to allow for detection of antibody-antigen complexes. The detectable moieties can include compositions detectable by spectroscopic, enzymatic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical or chemical means. The detectable moieties include, but are not limited to, radioisotopes, chemiluminescent compounds, labeled binding proteins, heavy metal atoms, spectroscopic markers such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like. [0213] Protein array technology is discussed in detail in Pandey and Mann (2000) and MacBeath and Schreiber (2000), each of which is herein specifically incorporated by reference. These arrays typically contain thousands of different proteins or antibodies spotted onto glass slides or immobilized in tiny wells and allow one to examine the biochemical activities and binding profiles of a large number of proteins at once. To examine protein interactions with such an array, a labeled protein is incubated with each of the target proteins immobilized on the slide, and then one determines which of the many proteins the labeled molecule binds. In certain embodiments such technology can be used to quantitate a number of proteins in a sample, such as a cancer biomarker proteins. [0214] The basic construction of protein chips has some similarities to DNA chips, such as the use of a glass or plastic surface dotted with an array of molecules. These molecules can be DNA or antibodies that are designed to capture proteins. Defined quantities of proteins are immobilized on each spot, while retaining some activity of the protein. With fluorescent markers or other methods of detection revealing the spots that have captured these proteins, protein microarrays are being used as powerful tools in high-throughput proteomics and drug discovery. [0215] The earliest and best-known protein chip is the ProteinChip by Ciphergen Biosystems Inc. (Fremont, Calif.). The ProteinChip is based on the surface-enhanced laser desorption and ionization (SELDI) process. Known proteins are analyzed using functional assays that are on the chip. For example, chip surfaces can contain enzymes, receptor proteins, or antibodies that enable researchers to conduct protein-protein interaction studies, ligand binding studies, or immunoassays. With state-of-the-art ion optic and laser optic technologies,

TMPL14WO_spec.docx - 55 - the ProteinChip system detects proteins ranging from small peptides of less than 1000 Da up to proteins of 300 kDa and calculates the mass based on time-of-flight (TOF). [0216] The ProteinChip biomarker system is the first protein biochip-based system that enables biomarker pattern recognition analysis to be done. This system allows researchers to address important clinical questions by investigating the proteome from a range of crude clinical samples (i.e., laser capture microdissected cells, biopsies, tissue, urine, and serum). The system also utilizes biomarker pattern software that automates pattern recognition-based statistical analysis methods to correlate protein expression patterns from clinical samples with disease phenotypes. [0217] In other aspects, the levels of polypeptides in samples can be determined by detecting the biological activities associated with the polypeptides. If a biological function/activity of a polypeptide is known, suitable in vitro bioassays can be designed to evaluate the biological function/activity, thereby determining the amount of the polypeptide in the sample. III. Sample Preparation [0218] In certain aspects, methods involve obtaining a sample from a subject. The methods of obtaining provided herein may include methods of biopsy such as fine needle aspiration, core needle biopsy, vacuum assisted biopsy, incisional biopsy, excisional biopsy, punch biopsy, shave biopsy or skin biopsy. In certain embodiments the sample is obtained from a biopsy from ovarian or endometrial tissue by any of the biopsy methods previously mentioned. In other embodiments the sample may be obtained from any of the tissues provided herein that include but are not limited to non-cancerous or cancerous tissue and non-cancerous or cancerous tissue from the ovarian epithelium, fallopian epithelium, ovaries, cervix, fallopian tube, or uterus. Alternatively, the sample may be obtained from any other source including but not limited to blood, serum, plasma, sweat, hair follicle, buccal tissue, tears, menses, feces, or saliva. In certain aspects of the current methods, any medical professional such as a doctor, nurse or medical technician may obtain a biological sample for testing. Yet further, the biological sample can be obtained without the assistance of a medical professional. [0219] A sample may include but is not limited to, tissue, cells, or biological material from cells or derived from cells of a subject. The biological sample may be a heterogeneous or homogeneous population of cells or tissues. The biological sample may be obtained using any method known to the art that can provide a sample suitable for the analytical methods described herein. The sample may be obtained by non-invasive methods including but not limited to:

TMPL14WO_spec.docx - 56 - scraping of the skin or cervix, swabbing of the cheek, saliva collection, urine collection, feces collection, collection of menses, tears, or semen. [0220] The sample may be obtained by methods known in the art. In certain embodiments the samples are obtained by biopsy. In other embodiments the sample is obtained by swabbing, endoscopy, scraping, phlebotomy, or any other methods known in the art. In some cases, the sample may be obtained, stored, or transported using components of a kit of the present methods. In some cases, multiple samples, such as multiple plasma or serum samples may be obtained for diagnosis by the methods described herein. In other cases, multiple samples, such as one or more samples from one tissue type (for example ovaries or related tissues) and one or more samples from another specimen (for example serum) may be obtained for diagnosis by the methods. Samples may be obtained at different times are stored and/or analyzed by different methods. For example, a sample may be obtained and analyzed by routine staining methods or any other cytological analysis methods. [0221] In some embodiments the biological sample may be obtained by a physician, nurse, or other medical professional such as a medical technician, endocrinologist, cytologist, phlebotomist, radiologist, or a pulmonologist. The medical professional may indicate the appropriate test or assay to perform on the sample. In certain aspects a molecular profiling business may consult on which assays or tests are most appropriately indicated. In further aspects of the current methods, the patient or subject may obtain a biological sample for testing without the assistance of a medical professional, such as obtaining a whole blood sample, a urine sample, a fecal sample, a buccal sample, or a saliva sample. [0222] In other cases, the sample is obtained by an invasive procedure including but not limited to: biopsy, needle aspiration, blood draw, endoscopy, or phlebotomy. The method of needle aspiration may further include fine needle aspiration, core needle biopsy, vacuum assisted biopsy, or large core biopsy. In some embodiments, multiple samples may be obtained by the methods herein to ensure a sufficient amount of biological material. [0223] General methods for obtaining biological samples are also known in the art. Publications such as Ramzy, Ibrahim Clinical Cytopathology and Aspiration Biopsy 2001, which is herein incorporated by reference in its entirety, describes general methods for biopsy and cytological methods. [0224] In some embodiments of the present methods, the molecular profiling business may obtain the biological sample from a subject directly, from a medical professional, from a third party, or from a kit provided by a molecular profiling business or a third party. In some cases, the biological sample may be obtained by the molecular profiling business after the subject, a

TMPL14WO_spec.docx - 57 - medical professional, or a third party acquires and sends the biological sample to the molecular profiling business. In some cases, the molecular profiling business may provide suitable containers, and excipients for storage and transport of the biological sample to the molecular profiling business. [0225] In some embodiments of the methods described herein, a medical professional need not be involved in the initial diagnosis or sample acquisition. An individual may alternatively obtain a sample through the use of an over the counter (OTC) kit. An OTC kit may contain a means for obtaining said sample as described herein, a means for storing said sample for inspection, and instructions for proper use of the kit. In some cases, molecular profiling services are included in the price for purchase of the kit. In other cases, the molecular profiling services are billed separately. A sample suitable for use by the molecular profiling business may be any material containing tissues, cells, nucleic acids, genes, gene fragments, expression products, gene expression products, or gene expression product fragments of an individual to be tested. Methods for determining sample suitability and/or adequacy are provided. [0226] In some embodiments, the subject may be referred to a specialist such as an oncologist, surgeon, or endocrinologist. The specialist may likewise obtain a biological sample for testing or refer the individual to a testing center or laboratory for submission of the biological sample. In some cases the medical professional may refer the subject to a testing center or laboratory for submission of the biological sample. In other cases, the subject may provide the sample. In some cases, a molecular profiling business may obtain the sample. IV. Methods of treatment [0227] The compositions, peptides, and nucleic acids encoding the peptides of the disclosure may be used for the treatment of certain cancers. In some embodiments, the cancer is a LMTK3+ cancer. In some embodiments, the subject is one that has been determined to have a LMTK3+ cancer. In some embodiments, the cancer/cancer cells have an increased expression of LMTK3 compared to non-cancerous tissues of the same type. In some embodiments, the subject is one that has been determined to have increased expression of LMTK3 in cancer cells as compared to the expression of LMTK3 in non-cancerous cells. In some embodiments, the subject is one that has been determined to have increased LMTK3 localization in the cytoplasm of cancer cells as compared to the nucleus. [0228] The cancers amenable for treatment include, but are not limited to, cancers and tumors of all types, locations, sizes, and characteristics. The methods and compositions of the disclosure are suitable for treating, for example, pancreatic cancer, colon cancer, acute myeloid

TMPL14WO_spec.docx - 58 - leukemia, adrenocortical carcinoma, AIDS-related cancers, AIDS-related lymphoma, anal cancer, appendix cancer, astrocytoma, childhood cerebellar or cerebral basal cell carcinoma, bile duct cancer, extrahepatic bladder cancer, bone cancer, colorectal cancer, osteosarcoma/malignant fibrous histiocytoma, brainstem glioma, brain tumor, cerebellar astrocytoma brain tumor, cerebral astrocytoma/malignant glioma brain tumor, ependymoma brain tumor, medulloblastoma brain tumor, supratentorial primitive neuroectodermal tumors brain tumor, visual pathway and hypothalamic glioma, breast cancer, lymphoid cancer, bronchial adenomas/carcinoids, tracheal cancer, Burkitt lymphoma, carcinoid tumor, childhood carcinoid tumor, glioblastoma, neuroblastoma, gastrointestinal carcinoma of unknown primary, central nervous system lymphoma, primary cerebellar astrocytoma, childhood cerebral astrocytoma/malignant glioma, childhood cervical cancer, childhood cancers, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloproliferative disorders, cutaneous T-cell lymphoma, desmoplastic small round cell tumor, endometrial cancer, ependymoma, esophageal cancer, Ewing's, childhood extragonadal Germ cell tumor, extrahepatic bile duct cancer, eye Cancer, intraocular melanoma eye Cancer, retinoblastoma, gallbladder cancer, gastric (stomach) cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumor (GIST), germ cell tumor: extracranial, extragonadal, or ovarian, gestational trophoblastic tumor, glioma of the brain stem, glioma, childhood cerebral astrocytoma, childhood visual pathway and hypothalamic glioma, gastric carcinoid, hairy cell leukemia, head and neck cancer, heart cancer, hepatocellular (liver) cancer, Hodgkin lymphoma, hypopharyngeal cancer, hypothalamic and visual pathway glioma, childhood intraocular melanoma, islet cell carcinoma (endocrine pancreas), kaposi sarcoma, kidney cancer (renal cell cancer), laryngeal cancer , leukemia, acute lymphoblastic (also called acute lymphocytic leukemia) leukemia, acute myeloid (also called acute myelogenous leukemia) leukemia, chronic lymphocytic (also called chronic lymphocytic leukemia) leukemia, chronic myelogenous (also called chronic myeloid leukemia) leukemia, hairy cell lip and oral cavity cancer, liposarcoma, liver cancer (primary), non-small cell lung cancer, small cell lung cancer, lymphomas, AIDS-related lymphoma, Burkitt lymphoma, cutaneous T-cell lymphoma, Hodgkin lymphoma, Non-Hodgkin (an old classification of all lymphomas except Hodgkin's) lymphoma, primary central nervous system lymphoma, Waldenstrom macroglobulinemia, malignant fibrous histiocytoma of bone/osteosarcoma, childhood medulloblastoma, melanoma, intraocular (eye) melanoma, merkel cell carcinoma, adult malignant mesothelioma, childhood mesothelioma, metastatic squamous neck cancer, mouth cancer, multiple endocrine neoplasia syndrome, multiple myeloma/plasma cell neoplasm, mycosis fungoides,

TMPL14WO_spec.docx - 59 - myelodysplastic syndromes, myelodysplastic/myeloproliferative diseases, chronic myelogenous leukemia, adult acute myeloid leukemia, childhood acute myeloid leukemia, multiple myeloma, chronic myeloproliferative disorders, nasal cavity and paranasal sinus cancer, nasopharyngeal carcinoma, neuroblastoma, oral cancer, oropharyngeal cancer, osteosarcoma/malignant, fibrous histiocytoma of bone, ovarian cancer, ovarian epithelial cancer (surface epithelial-stromal tumor), ovarian germ cell tumor, ovarian low malignant potential tumor, pancreatic cancer, islet cell paranasal sinus and nasal cavity cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pheochromocytoma, pineal astrocytoma, pineal germinoma, pineoblastoma and supratentorial primitive neuroectodermal tumors, childhood pituitary adenoma, plasma cell neoplasia/multiple myeloma, pleuropulmonary blastoma, primary central nervous system lymphoma, prostate cancer, rectal cancer, renal cell carcinoma (kidney cancer), renal pelvis and ureter transitional cell cancer, retinoblastoma, rhabdomyosarcoma, childhood Salivary gland cancer Sarcoma, Ewing family of tumors, Kaposi sarcoma, soft tissue sarcoma, uterine sezary syndrome sarcoma, skin cancer (nonmelanoma), skin cancer (melanoma), skin carcinoma, Merkel cell small cell lung cancer, small intestine cancer, soft tissue sarcoma, squamous cell carcinoma. squamous neck cancer with occult primary, metastatic stomach cancer, supratentorial primitive neuroectodermal tumor, childhood T-cell lymphoma, testicular cancer, throat cancer, thymoma, childhood thymoma, thymic carcinoma, thyroid cancer, urethral cancer, uterine cancer, endometrial uterine sarcoma, vaginal cancer, visual pathway and hypothalamic glioma, childhood vulvar cancer, and wilms tumor (kidney cancer). V. Administration of Therapeutic Compositions [0229] The therapy provided herein may comprise administration of a combination of therapeutic agents, such as a first cancer therapy and a second cancer therapy. The therapies may be administered in any suitable manner known in the art. For example, the first and second cancer treatment may be administered sequentially (at different times) or concurrently (at the same time). In some embodiments, the first and second cancer treatments are administered in a separate composition. In some embodiments, the first and second cancer treatments are in the same composition. [0230] Embodiments of the disclosure relate to compositions and methods comprising therapeutic compositions. The different therapies may be administered in one composition or in more than one composition, such as 2 compositions, 3 compositions, or 4 compositions. Various combinations of the agents may be employed.

TMPL14WO_spec.docx - 60 - [0231] The therapeutic agents of the disclosure may be administered by the same route of administration or by different routes of administration. In some embodiments, the cancer therapy is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally. In some embodiments, the antibiotic is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally. The appropriate dosage may be determined based on the type of disease to be treated, severity and course of the disease, the clinical condition of the individual, the individual's clinical history and response to the treatment, and the discretion of the attending physician. [0232] The treatments may include various “unit doses.” Unit dose is defined as containing a predetermined-quantity of the therapeutic composition. The quantity to be administered, and the particular route and formulation, is within the skill of determination of those in the clinical arts. A unit dose need not be administered as a single injection but may comprise continuous infusion over a set period of time. In some embodiments, a unit dose comprises a single administrable dose. [0233] The quantity to be administered, both according to number of treatments and unit dose, depends on the treatment effect desired. An effective dose is understood to refer to an amount necessary to achieve a particular effect. In the practice in certain embodiments, it is contemplated that doses in the range from 10 mg/kg to 200 mg/kg can affect the protective capability of these agents. Thus, it is contemplated that doses include doses of about 0.1, 0.5, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, and 200, 300, 400, 500, 1000 µg/kg, mg/kg, µg/day, or mg/day or any range derivable therein. Furthermore, such doses can be administered at multiple times during a day, and/or on multiple days, weeks, or months. [0234] In certain embodiments, the effective dose of the pharmaceutical composition is one which can provide a blood level of about 1 µM to 150 µM. In another embodiment, the effective dose provides a blood level of about 4 µM to 100 µM.; or about 1 µM to 100 µM; or about 1 µM to 50 µM; or about 1 µM to 40 µM; or about 1 µM to 30 µM; or about 1 µM to 20 µM; or about 1 µM to 10 µM; or about 10 µM to 150 µM; or about 10 µM to 100 µM; or about 10 µM to 50 µM; or about 25 µM to 150 µM; or about 25 µM to 100 µM; or about 25 µM to 50 µM; or about 50 µM to 150 µM; or about 50 µM to 100 µM (or any range derivable therein).

TMPL14WO_spec.docx - 61 - In other embodiments, the dose can provide the following blood level of the agent that results from a therapeutic agent being administered to a subject: about, at least about, or at most about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 μM or any range derivable therein. In certain embodiments, the therapeutic agent that is administered to a subject is metabolized in the body to a metabolized therapeutic agent, in which case the blood levels may refer to the amount of that agent. Alternatively, to the extent the therapeutic agent is not metabolized by a subject, the blood levels discussed herein may refer to the unmetabolized therapeutic agent. [0235] Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment (alleviation of symptoms versus cure) and the potency, stability and toxicity of the particular therapeutic substance or other therapies a subject may be undergoing. [0236] It will be understood by those skilled in the art and made aware that dosage units of µg/kg or mg/kg of body weight can be converted and expressed in comparable concentration units of µg/ml or mM (blood levels), such as 4 µM to 100 µM. It is also understood that uptake is species and organ/tissue dependent. The applicable conversion factors and physiological assumptions to be made concerning uptake and concentration measurement are well-known and would permit those of skill in the art to convert one concentration measurement to another and make reasonable comparisons and conclusions regarding the doses, efficacies and results described herein. VI. Examples [0237] The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

TMPL14WO_spec.docx - 62 - Example 1: Treating Ovarian Cancer with LMTK3 modulators [0238] Utilizing a combination of mass spectroscopy and antibody epitope mapping with peptide microarray, the inventor has recently succeeded in identifying LMTK3 (lemur tyrosine kinase 3) as a tumor cell-specific target, that leads to cell death and reduced tumor growth through a novel mechanism. Through the process of identifying LMTK3 as a specific target to induce cytotoxicity of ovarian cancer cells, the inventor has characterized a number of peptides that specifically induced killing of ovarian cancer cells, but not normal cells. As with the LMTK3 antibody, the developed peptide appears not to be toxic to normal (non-immortalized) cells. [0239] LMTK3 belongs to a family of regulated serine/threonine tyrosine kinases with three structurally related isoforms, LMTK1, LMTK2, and LMTK3. They were reported to be localized to the nucleus, cytoplasm, transmembrane and in the extracellular space (1). Both nuclear and cytoplasmic LMTK3 expression were known to correlate with tumor grade and patient survival (1). LMTKs are known to play a major role in gene transcription and regulation and thus can affect cell proliferation/apoptosis, cell growth/differentiation, as well as cell migration (1). LMTK3 can act as a DNA binding protein that represses tumor suppressor-like genes further supporting the [0240] It is hypothesized that LMTK3 will be clinically revealed as a promising target for ovarian cancer drug development. [0241] The objective of this preclinical phase study is to determine the efficacy, safety and dose of the LMTK3 peptide(s) against ovarian cancer and recurrent ovarian cancer using orthotopic ovarian cancer xenograft animal model. Discovering potent and selective inhibitors of LMTK3 that will be used to pharmacologically validate LMTK3 as a novel target for ovarian cancer therapy that will have an important translational impact. Positioning of LMTK3 peptide(s) ultimately would be applicable in patients who are non-responders to therapy. The focus on ovarian cancer is the first of solid tumors given there are few therapies available. Therefore, LMTK3 peptide(s) would be positioned as potential for a second line treatment in combination with platinum-based chemotherapy in patients who are sensitive to platinum- based drugs or in combination with a PARP inhibitor in platinum resistant refractory patients plus/minus bevacizumab. [0242] Novel target – The inventor has developed a new approach and platform to target the tumor growth process, using a molecule to block a novel tumor cell-specific target (LMTK3) leading to cell death (apoptosis) and reduced tumor growth. The optimized molecule,

TMPL14WO_spec.docx - 63 - LMTK3 peptide(s), therefore may be classified as a breakthrough. The method chosen in this project therefore consists of developing a novel therapeutic candidate for an indication for which currently there is a large unmet medical need, with potential application in other estrogen receptors pathway affected cancers. [0243] Cancer specific target – LMTK3 peptide(s) directly and specifically targets apoptosis, a major determinant in uncontrolled cell growth in ovarian cancer. Throughout the project, profiling studies using tissue microarrays validated LMTK3 expression in subgroups of ovarian cancer patients (FIG.1). [0244] Little or no effect on healthy cells– Targeting LMTK3 with LMTK3 specific peptide(s) did not affect non-tumor cells in vitro (FIG. 3), thus potentially showing a better safety profile with less side effects compared to current treatment options. Many recently introduced targeted therapies still suffer from drawbacks. For instance, checkpoint inhibitors, expected to be the next big improvement in ovarian cancer treatment, are effective in only 30% of patients, and lead to severe side effects, because PD-(L)-1 inhibitors have strong systemic effects. [0245] Effect on cells resistant to chemotherapy and radiation therapy – LMTK3 peptide(s) was as effective in cells resistant to chemotherapy (e.g. docetaxel or cisplatin) as in sensitive cells (FIG. 3). This is particularly important in the treatment of ovarian cancer patients, who often experience recurrent disease, which is refractory to treatment. Further, determining effectiveness of LMTK3 peptide(s) on cells resistant to radiotherapy and sensitive to radiotherapy, may be valuable as well. [0246] Monoclonal antibody against the LMTK3 target was optimized for immunohistochemistry analysis. The inventor collected 206 ovarian tumors from stage I and II with long and short time survivors. Four different histotypes were included, HGSC (High grade serous carcinomas, MC (Mucinous carcinomas), EC (Endometroid carcinomas) and CCC (Clear cell carcinomas). Tissue microarray was performed using material from the ovarian paraffin blocks. Results showed LMTK3 staining across all tumor types (FIG.1). [0247] The inventor has characterized a number of LMTK3 specific peptides that specifically induced killing of ovarian cancer cells, but not normal cells (FIG. 2). Targeting LMTK3 with the novel LMTK3-specific peptides induced killing in all ovarian cancer cells but not in normal cells (FIG.3). [0248] Orthotopic ovarian cancer xenograft model: To test novel therapies the inventor developed an orthotopic human ovarian cancer mouse model, which utilizes mCherry labeled- OCSC1-F2 human ovarian cancer cells grown intra-peritoneally (i.p) in athymic nude mice

TMPL14WO_spec.docx - 64 - (14-18). (ROI) area allows quantification of i.p. tumor burden (FIG. 4) and thus allow evaluation of treatment efficacy in real-time. The model recapitulates tumor distribution observed in patients and demonstrates disseminated carcinomatosis and omental cake about 30 days after injection of cancer cells (FIG. 4). Similarly, the model recapitulates the clinical profile observed in patients.1st-line treatment with Taxol (i.e. Paclitaxel (PTX) in castor oil; 12 mg/kg q3d x 4 doses) induces a “complete response” as determined by the absence of mCherry signal at the end of treatment (FIG.5). However, when followed, recurrent disease is observed two weeks after the end of 1^st-line treatment (FIG.5). The same response is observed with Cisplatin.1st-line treatment with Cisplatin shows significant reduction in tumor growth but recurrence is eventually observed upon cessation of treatment (FIG. 5). Similar to the chemoresponse profile observed in patients (19-21), administration of Taxol as maintenance therapy did not curtail disease progression (FIG.4). Thus, this model can serve as a platform for the evaluation of novel therapies both as 1^st-line and for recurrent disease. [0249] Experimental design to determine MTD: 3 x 10⁶ mCherry+ OCSC1-F2 cells will be injected i.p. in athymic nude mice (day 0). On day 3, mice will be randomly assigned to Vehicle or 2.5 mg/kg LMTK3 peptide. Treatment will be given i.p. daily for 7 days. [0250] Tumor kinetics will be measured using mCherry ROI area. Animals will be monitored for toxicity by: 1) observation for piloerection, crouched posture, and impaired coordination of movement; 2) measurement of body weight; 3) determination of blood count (WBC count, RBC count, hemoglobin, hematocrit), renal function (urea and creatinine) and liver function (alkaline phosphatase and alanine aminotransferase). If no toxicity is observed with this dose, the dose will be doubled to establish MTD. [0251] Experimental design to test efficacy as monotherapy against primary disease: Tumors will be established as above and on day 3, animals will be randomly distributed to the following groups: 1) Vehicle; 2) peptide at MTD determined above; 3) Taxol (12 mg/kg q3d x 4 doses); and 4) Cisplatin (5 mg/kg q7d x 3 doses). Response will be monitored by live-imaging every 3 days and tumor burden will be quantified by measuring mCherry fluorescence ROI area. [0252] Endpoints will be: 1) tumor kinetics using mCherry ROI area; 2) progression free survival (PFS) - for complete responders (i.e. no detectable mCherry fluorescence by imaging at last day of treatment), PFS is defined as the number of days for recurrent tumors to reach ROI area = 2,000; for partial responders, PFS is defined as the number of days it took the measured ROI area at last day of treatment to double in size; 3) overall survival (OS) defined as the number of days ROI area = 100,000. This corresponds to 1.5 g of total i.p. tumor burden,

TMPL14WO_spec.docx - 65 - which is the maximum allowed tumor burden for this model. In control untreated mice, this usually occurs around day 30. [0253] Experimental design to test efficacy as maintenance treatment for recurrent disease: Tumors will be established as above and on day 3, animals will be randomly distributed to the groups defined in Table 3.1^st-line treatment with Taxol at 12 mg/kg q3d for 4 doses or Cisplatin (5 mg/kg q7d x 3 doses) will be administered. Maintenance treatment will commence 24 hours after the last dose of Taxol or Cisplatin using the MTD defined above. Response to treatment and endpoints will be the same as above for primary disease. Table 3 Group Number 1st-Line Treatment Maintenance Treatment 1 Vehicle Vehicle 2 Taxol/Cis Vehicle 3 Taxol/Cis Taxol 4 Taxol/Cis Peptide [0254] Statistical analysis: All continuous outcomes (i.e. tumor growth) will be checked for distributions and, if needed, will be transformed to meet normality assumptions.2-sample 2-sided t-test or one/two-way ANOVA followed by Holm’s post-hoc analysis will be used to compare 2 groups and 3 or more groups, respectively. Xenograft mouse models will be used to assess PFS and OS among the defined groups. The preliminary data yielded a median OS of 34 days for Cisplatin and PTX as well as a hazard ratio (HR) of 0.36 in OS between PTX vs. Control and Cisplatin vs. Control, which the inventor targeted for the sample size justification. Twenty-six mice per group will allow us to detect an HR of 0.36 between with 80% power using 1-sided log-rank test at a 5% level. [0255] In Vitro Validation: A series of 5~10 candidate peptides will be tested in vitro by DS Biotech, using 3D models established from patient-derived (PDX) tumor cells, which provide a clinically relevant measure of efficacy of the novel peptide. The 3D nature of the in vitro system allows the study of characteristics that cannot be tested in simple cell line systems, such as peptide tumor penetration and its effect on treatment efficacy, efficacy of peptides after relapse, and the effect of peptides on immune cells. This provides a better predictor for efficacy and reducing the number of animal experiments needed. The prediction of peptide efficacy will be further increased by matching the PDX derived materials from the 3D models with the PDX materials used for in vivo models. As such, a strong predictive patient derived in vitro + in vivo

TMPL14WO_spec.docx - 66 - screening platform will be established. Based on in vitro results, 5 molecules will be selected for in vivo experiments. Clinical translation will be further facilitated by Karmanos Cancer Institute testing in vitro efficacy of lead peptides in novel patient-derived 3D tumor models. [0256] Milestones and Alternative Approaches: The inventor has Developed a new approach and platform to target the ovarian tumor growth process, using a newly characterized peptide(s) to block a novel ovarian tumor cell-specific target (LMTK3) leading to cell death (apoptosis) and reduced tumor growth. In this preclinical phase of the study the inventor will utilize an orthotopic ovarian cancer xenograft animal model to determine the efficacy, safety and the dose of the newly characterized peptide(s) that block a novel ovarian cancer target, LMTK3. [0257] SUMMARY AND FUTURE DIRECTIONS: The aim of this phase of the study is to determine the efficacy, safety and the dose of the newly discovered peptide(s) that block a novel target, LMTK3 against ovarian cancer and recurrent ovarian cancer using orthotopic ovarian cancer xenograft animal model. Validating LMTK3 as a novel target for ovarian cancer therapy and discovering specific peptides to block LMTK3 will have translational impact. Positioning of LMTK3 peptide(s) ultimately would be applicable in patients who are non-responders to immunotherapy. The focus on ovarian cancer is the first of solid tumors given there are few therapies available. Therefore, LMTK3 peptide(s) would be positioned as potential for second line treatment in combination with platinum-based chemo in patient who are sensitive to platinum-based drugs or in combination with a PARP inhibitor in platinum resistant refractory patients plus/minus bevacizumab. The outcome of this proposal will serve as a foundation for a phase II study focusing on efficacy, dose and safety of LMTK3 peptide(s) in human. Example 2: LMTK3 expression for prognosis and prediction of therapeutic response in cancer patients. [0258] LMTK3 is a protein kinase and acts as a potent regulator of ESR1 in vitro. The inventor hypothesized that LMTK3 gene and protein expression will confer an unfavorable prognosis. LMTK3 may protect breast cancer cells from Doxorubicin induced double stranded DNA breaks[10]. Based on this, the inventor thinks it would be interesting to attempt to link LMTK3 expression to resistance to chemotherapy in ovarian cancer and to resistance to radiotherapy in breast cancer and head & neck cancer. FIGS.8-10 shows the results from gene expression cohort analysis.

TMPL14WO_spec.docx - 67 - [0259] In the METABRIC cohort, consisting of 1904 breast cancer patients, LMTK3 expression was significantly predictive of overall survival in a Kaplan Meier analysis (FIG.8). FIG.8 and the statistical analysis in Table 4 below shows that LMTK3 as a continuous variable is significantly associated with overall survival. Table 4: Univariable Cox regression analysis Variable Beta (SE) HR (95% CI) P LMTK3 0.13 (0.03) 1.14 (1.08, 1.22) <0.001 [0260] As shown in Table 5, LMTK3 remained significantly prognostic to overall survival when the Cox analysis was adjusted for age, Nottingham Prognostic Index (histological grade) and the number of lymph nodes examined positive. Table 5: Multivariable Cox regression analysis Variable Beta (SE) HR (95% CI) P LMTK3 0.08 (0.03) 1.08 (1.02, 1.15) 0.009 Age at diagnosis 0.04 (0.00) 1.04 (1.03, 1.04) <0.001 NPI 0.22 (0.03) 1.24 (1.17, 1.32) <0.001 Lymph nodes examined positive 0.04 (0.01) 1.04 (1.03, 1.06) <0.001 [0261] In the TCGA ovarian cancer cohort, consisting of 303 patients, a high LMTK3 expression was associated with a reduced survival. The Kaplan-Meier analysis did however not reach statistical significance (FIG. 9). As shown in Table 6, in univariable analysis, the continuous LMTK3 variable was significantly associated with overall survival. Table 6: Univariable Cox regression analysis Variable Beta (SE) HR (95% CI) P LMTK3 0.18 (0.07) 1.19 (1.03, 1.38) 0.02 [0262] As shown in Table 7, the significance of LMTK3 remained when adjusting for age.

TMPL14WO_spec.docx - 68 - Table 7: Multivariable cox regression analysis Variable Beta (SE) HR (95% CI) P LMTK3 0.21 (0.07) 1.24 (1.07, 1.43) 0.004 Years to birth 0.03 (0.01) 1.03 (1.01, 1.04) <0.001 [0263] LMTK3 mRNA expression is higher in tumor tissue compared to normal tissue in breast (BRCA) and ovarian (OV) cancer. [0264] FIG. 10 shows the protein analysis of the LMTK3 antibody using TMA from ovarian, breast and kidney cancers: The immunohistochemical hybridization pattern using LMTK3 on ovarian cancer showed that the LMTK3 is localized in the cytoplasm but not the cell nucleus of tumor cells. Intriguingly cytoplasmic LMTK3 expression correlates with poor survival (FIG. 17). There was no staining to the cell membrane. The stromal cells were negative. The proportion of hybridized tumor cells is 90%. The immunohistochemical hybridization pattern using LMTK3 on kidney cancer showed that the LMTK3 is localized in the cell nucleus (strong and distinct) and cytoplasm (less strong compared to the nucleus) of tumor cells. There was no staining to the cell membrane. The stromal cells were negative. The immunohistochemical hybridization pattern using LMTK3 on breast cancer showed that the LMTK3 is similar to ovarian cancer. Example 3: Efficacy of anti LMTK3 (Peptides #1, #2, and #3) in a A2780 cell line derived orthotopic xenograft model of ovarian cancer. [0265] The aim of this study is to evaluate the antitumor effect of three different anti- LMTK3 peptides (peptides #1, #2, and #3) in a A2780 cell-line derived orthotopic xenograft model of ovarian cancer. A. Materials and experimental methods 1. Animals [0266] The mice used were 5-week old female Mus musculus from the Athymic Nude- Foxn1nu strain. The body weight of the animals was 22-24g. Mice were kept in laminar flow rooms at constant temperature (20-24ºC) and humidity with 5 animals per cage. Cages were made of polycarbonate. The size of the cages were 300 mm x 180 mm x 150 mm. Bedding material used was corn cob, changed once per week. The animals had access to irradiation sterilized dry food and sterile drinking water during the entire study period. The cages were

TMPL14WO_spec.docx - 69 - labeled with number of animals, sex, strain, arrival date, treatment, study number, group number and starting date of the treatment. Animals were marked by ear coding. 2. Tumor implantation [0267] Mycoplasma-free A2780 cell fragments (approx. 40 mg) were implanted into the ovary of 40 mice to generate a A2780 cell line-derived orthotopic xenograft model of ovarian cancer. 3. Drug preparation [0268] Peptide #1: The lyophilized powder was suspended in DMSO to reach a concentration of 400 mg/ml. It was aliquoted (25 ul) and kept at -20ºC. Each day before injection, an aliquot was thawed and diluted with 2475 ul of PBS to reach a concentration of 4 mg/ml (1:100 dilution) for 40 mg/kg dose (volume: 10 ml/kg). DMSO concentration: 1% [0269] Peptide #2: The lyophilized powder was suspended in DMSO to reach a concentration of 50 mg/ml. It was aliquoted (100 ul) and kept at -20ºC. Each day before injection, an aliquot was thawed and diluted with 2400 ul of PBS to reach a concentration of 2 mg/ml (1:25 dilution) for 20 mg/kg dose (volume: 10 ml/kg). It was filtered with a sterile 0.25um filter. DMSO concentration: 4% [0270] Peptide #3: The lyophilized powder was suspended in DMSO to reach a concentration of 100 mg/ml. It was aliquoted (100 ul) and kept at -20ºC. Each day before injection, an aliquot was thawed and diluted with 2400 ul of PBS to reach a concentration of 4 mg/ml (1:25 dilution) for 40 mg/kg dose (volume: 10 ml/kg). DMSO concentration: 4% [0271] Vehicle: 4% DMSO in PBS. 4. Treatments [0272] Group A: Vehicle. 3 times/week. 3 weeks. Group B: Peptide #1. 40 mg/kg. IV. 3 times/week. 3 weeks. Group C: Peptide #2. 20 mg/kg. IV. 3 times/week. 3 weeks. Group D: Peptide #3. 40 mg/kg. IV. 3 times/week. 3 weeks. Group E: Cisplatin. 1.5 mg/kg. IV. 3 times/week.3 weeks. 5. Experimental endpoints [0273] Mice behavior, body weight, and general behavior were monitored during treatment. Weight loss of more than 20% of the total body weight, tumor mass of more than 2000 mm³, or any sign of suffering were the ethical endpoint criteria of the experiment.

TMPL14WO_spec.docx - 70 - 6. Ethical observations [0274] All procedures related to animal handling, care, and treatment in this study were performed according to the guidelines approved by the Ethical Committee of Animal Experimentation of the Parc Científic de Barcelona (PCB). The procedure applied was number 9928-P1 approved by the Generalitat de Catalunya (IP: Alberto Villanueva). B. Results [0275] At Day 3 post-implantation, 40 mice bearing orthotopic A2780 cell-line derived tumors were randomly assigned to receive different treatments (Table 1A). Table 1A. Treatment details for each group. Group N Treatment Dose Schedule Route Duration A 8 Vehicle -- 3 times/week IV 3 weeks B 8 Peptide#1 40 mg/kg 3 times/week IV 3 weeks C 8 Peptide#2 20 mg/kg 3 times/week IV 3 weeks D 8 Peptide#3 40 mg/kg 3 times/week IV 3 weeks E 8 Cisplatin 40 mg/kg 3 times/week IV 3 weeks [0276] Mice body weight means and standard deviations for treatment groups after randomization can be seen in FIG.11. [0277] Mice body weight mean evolution for each group during the experiment is shown in FIG.12. Raw data of mice body weights is captured in Table 2A. Table 2A. Mice body weight (g). Days post-implantation 1 3 5 8 10 12 15 17 19 ID 26.0 26.2 26.8 26.8 26.8 27.7 27.9 28.1 28.8 A1 24.2 24.8 25.4 25.9 25.5 26.2 26.1 26.6 27.9 B1 23.5 23.8 23.9 24.1 23.8 24.6 26.1 27.2 28.9 C1 22.1 22.3 22.8 22.8 23.1 24.1 24.7 25.3 27.0 D1 VEHICLE 24.6 25.1 25.3 25.0 25.5 26.6 27.0 27.5 30.4 E1 20.4 21.0 21.8 21.8 22.2 22.5 22.3 22.2 23.6 F1 24.5 24.8 25.3 25.6 25.4 26.9 27.6 29.5 31.3 G1 25.7 25.8 25.9 25.8 26.0 27.5 27.0 26.6 28.6 H1 Mean 23.9 24.2 24.7 24.7 24.8 25.8 26.1 26.6 28.3 SD 1.9 1.8 1.7 1.7 1.6 1.8 1.8 2.2 2.3 22.3 22.7 23.6 23.1 22.9 24.1 24.7 25.3 25.8 A2 24.9 25.1 25.2 25.4 25.1 25.9 26.8 27.4 29.2 B2 23.6 24.1 24.7 23.4 24.8 25.6 26.1 26.8 28.9 C2

TMPL14WO_spec.docx - 71 - 24.0 24.2 24.8 24.7 25.2 25.3 26.1 25.7 27.5 D2 Peptide #1 23.9 24.4 24.8 25.4 25.3 25.9 25.5 25.9 27.0 E2 23.8 24.1 24.5 24.4 24.8 25.3 25.9 26.0 26.7 F2 23.7 23.9 24.6 24.2 24.2 25.4 25.7 26.7 28.8 G2 23.9 24.3 24.8 24.2 24.8 25.1 25.2 24.8 26.2 H2 Mean 23.8 24.1 24.6 24.4 24.6 25.3 25.8 26.1 27.5 SD 0.7 0.7 0.5 0.8 0.8 0.6 0.6 0.9 1.3 22.7 23.0 25.1 26.3 25.9 27.2 25.8 24.6 24.4 A3 25.6 26.1 26.0 25.5 25.7 26.7 26.8 27.7 29.3 B3 23.5 23.7 24.3 24.5 24.7 25.3 25.8 25.9 27.4 C3 27.3 28.2 28.7 28.4 28.5 29.9 30.0 30.4 31.8 D3 Peptide #2 25.1 25.6 25.7 26.2 25.9 26.4 26.2 26.3 27.1 E3 20.9 21.0 20.6 20.8 21.3 21.4 21.7 21.8 22.4 F3 22.3 22.6 23.4 23.1 23.5 24.4 25.5 26.8* G3 22.8 23.1 23.8 24.3 23.8 24.6 24.9 25.5 26.8 H3 Mean 23.8 24.2 24.7 24.9 24.9 25.7 25.8 26.0 27.0 SD 2.1 2.3 2.3 2.3 2.1 2.5 2.3 2.7 3.1 21.4 21.6 21.9 22.7 22.3 23.6 23.2 23.3 24.6 A4 26.8 27.5 27.5 27.5 27.8 29.0 30.1 30.7 32.0 B4 21.0 22.4 22.4 22.2 22.3 23.3 23.7 24.4 25.2 C4 21.0 21.2 21.5 22.4 23.1 23.6 24.0 24.5 26.0 D4 Peptide #3 24.5 24.9 25.5 26.0 26.2 26.7 25.4 26.0 28.0 E4 27.6 28.2 28.3 28.6 28.2 29.0 29.1 29.6 32.1 F4 27.3 27.8 27.5 28.2 28.3 29.1 30.5 31.4 32.6 G4 23.7 24.0 24.6 24.7 25.2 25.9 25.1 24.5 26.5 H4 Mean 24.2 24.7 24.9 25.3 25.4 26.3 26.4 26.8 28.4 SD 2.8 2.9 2.7 2.7 2.6 2.6 3.0 3.2 3.3 23.5 23.8 24.3 24.6 24.1 24.7 24.9 25.0 26.0 A5 24.1 24.6 24.3 25.7 24.9 24.6 24.4 24.2 25.3 B5 25.9 26.4 26.3 26.5 26.7 27.0 27.3 27.5 28.5 C5 25.0 25.3 25.8 25.7 25.7 26.6 26.8 27.6 28.2 D5 Cisplatin 22.9 23.2 23.2 23.3 23.1 23.8 22.9 22.7 22.9 E5 23.6 23.8 24.2 24.0 23.7 24.4 24.5 24.3 25.5 F5 18.4 18.5 18.8 19.3 19.2 19.2 19.2 18.6 18.7 G5 25.2 25.4 25.8 25.4 25.9 26.9 25.4 25.1 26.4 H5 Mean 23.6 23.9 24.1 24.3 24.2 24.7 24.4 24.4 25.2 SD 2.3 2.4 2.4 2.3 2.3 2.5 2.5 2.9 3.2 [0278] On Day 17 post-implantation, one mouse (G3-peptide #2) had to be sacrificed for tumor overgrowth (>2000 mm³) accompanied by abdominal distension, internal hemorrhage, and lethargy.

TMPL14WO_spec.docx - 72 - [0279] On Day 19 post-implantation, the last treatment dose (8th dose) was administered for all mice, since most of them showed criteria for applying the ethical endpoint. One hour after treatment, all mice were sacrificed. [0280] During necropsy, it was observed that tumor grew in the right ovary and occupied practically the whole abdominal cavity (FIG. 13 and 14). Multiple peritoneal implants were also detected into the surface of different organs (mesentery, liver, diaphragm…) (FIG.15). [0281] All tumors were excised and weighted. Tumor weight for all treatment groups is shown in Table 3A. Table 3A.Tumor weights (g). Tumor weight (g) ID Tumor weight ID (g) 4,01 A1 6,64 A4 6,70 B1 7,19 B4 7,64 C1 7,61 C4 5,63 D1 5,09 D4 VEHICLE 7,72 E1 3,85 E4 3,50 F1 Peptide #3 6,78 F4 8,42 G1 4,07 G4 2,46 H1 4,09 H4 M_{ean 5,76} ^{Mean 5,67} S_{D 2,22} ^{SD 1,56} 5,40 A2 2,01 A5 5,09 B2 4,63 B5 6,54 C2 2,88 C5 2,64 D2 2,24 D5 Peptide #1 3,81 E2 Cisplatin 3,94 E5 4,98 F2 2,03 F5 5,14 G2 0,03 G5 1,56 H2 2,73 H5 M_{ean 4,40} ^{Mean 2,56} S_{D 1,62} ^{SD 1,38} 2,93 A3 5,82 B3 3,38 C3 2,95 D3 Peptide #2 0,19 E3 2,42 F3 5,72 G3 6,66 H3 Mean 3,76 SD 2,16

TMPL14WO_spec.docx - 73 - [0282] Statistically significant differences in tumor weight were detected between groups (FIG.16). The data with peptide 1 and 2 treatments showed a 24% and 35% tumor reduction, respectively. [0283] After weighting, tumors were divided in two halves: one half was collected and fixed in p-formaldehyde for histological analyses and the other half was snap frozen for molecular analyses. C. Conclusions [0284] In this study, Xenopat aimed at evaluating the antitumor effect and safety of three different anti-LMTK3 peptides (peptides #1, #2, and #3) in a A2780 cell-line derived orthotopic xenograft model of ovarian cancer. In terms of antitumor effect, Xenopat concludes that, although 40 mg/kg Peptide#1 and 20 mg/kg Peptide #2 given 3 times/week intravenously induced a 24% and 35% tumor reduction, respectively, only 1.5 mg/kg iv cisplatin was capable of significantly reducing tumor growth (56%). In terms of toxicity, all treatments were well tolerated with no detectable toxicologic effects. Example 4: Lemur Tyrosine Kinase 3 serves as a predictor of patient outcome and a target for the treatment of ovarian cancer [0285] The objective of these in vitro and in vivo studies was to validate Lemur Tyrosine Kinase 3 (LMTK3) as a specific target and predictor of clinical outcome in ovarian cancer. LMTK3 belongs to a family of regulated tyrosine kinases with three structurally related isoforms, LMTK1, LMTK2, and LMTK3. Both nuclear and cytoplasmic LMTK3 expressions correlated with tumor grade and patient survival in cancers such as breast and colorectal cancer. [0286] The inventors tested the clinical significance of the LMTK3 gene by immunohistochemistry (IHC) using LMTK3 monoclonal antibody on formalin-fixed paraffin- embedded sections (FFPE) collected from 204 early-stage (stage I-II) ovarian cancer patients. Results from this IHC LMTK3 study revealed a higher cytoplasmic to nuclear localization of LMTK3 correlated with worse overall survival (P<0.01). Further investigation of LMTK3’s prognostic value by screening LMTK3 signaling in 270 stage III-IV ovarian cancer patients is ongoing. The inventors utilized the MTT ((3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazolium bromide) assay for testing the killing efficacy of targeting LMTK3 by a monoclonal antibody, siRNA, and specific LMTK3 binding peptides (LMTK3BP) in ovarian cancer cell lines SKOV3, MDAH-2774, A2780, and TOV-21G. Treatment with LMTK3 specific monoclonal antibody, siRNA, and LMTK3BP significantly induced killing of both

TMPL14WO_spec.docx - 74 - chemosensitive and chemoresistant ovarian cancer cells without affecting normal cells in vitro. Moreover, the inventors observed this killing as synergistic with both Cisplatin and Taxotere treatment in vitro. Lastly, the inventors used an A2780 cell line derived orthotopic xenograft mouse model of ovarian cancer to test the efficacy of specific LMTK3BP in vivo. Strikingly, LMTK3BP 2 mg/kg IV dose given three times a week for three weeks showed a 35% tumor reduction. Furthermore, in vivo safety studies showed no signs of toxicity of the LMTK3BP, even at a very high dose of 40 mg/kg. Thus, with dose optimization in ongoing experiments, we could expect a higher efficacy. In conclusion, this study highlighted the importance of LMTK3 as a predictor of patient clinical outcome and potential target for treatment in ovarian cancer. [0287] Results from IHC LMTK3 study revealed a higher cytoplasmic to nuclear localization of LMTK3 correlated with worse overall survival (FIG. 17A-17C). The risk of death among patients with more cytoplasmic than nuclear LMTK3 was particularly high during the first years after diagnosis (FIG. 17A-17C). Targeting LMTK3 with our novel LMTK3- specific peptide 1 or 2 and/or LMTK3 antibody induced killing in commercially available chemosensitive and chemoresistant ovarian cancer cell lines A2780, SKOV-3, and TOV-21G, but not in normal cells (FIG. 3). Furthermore, this killing was synergistic with cisplatin and taxotere treatment (FIG. 6). Silencing LMTK3 gene expression decreased cell viability in a dose response manner in all ovarian cancer cell lines tested but not in normal epithelial ovarian cells (FIG. 21A). This killing is mediated by apoptosis as indicated by increased caspase-3 activity (FIG. 21B). Athymic mice given 2, 10, or 40 mg/kg LMTK3 peptide 1,2 and 3 intravenous injections 3 times/week for 3 weeks showed no signs of toxicity at any dose (FIG. 19). Testing with the lowest dose of the LMTK3BPs, 2 mg/kg, revealed a 24% and 35% tumor reduction, respectively (FIG. 19 and 16). Studies with increasing doses and combination of LMTK3BP in vivo are ongoing. [0288] FIG. 17 shows results from IHC staining of LMTK3 in 204 human ovarian carcinomas from various stages and histotype revealed cytoplasmic and nuclear localization of LMTK3. Cytoplasmic:nuclear LMTK3 ratio as a predictor of overall survival within 15 years of ovarian cancer diagnosis. High cytoplasmic LMTK3 staining significantly correlated with poor prognosis (P<0.01). [0289] In FIG. 3, cytotoxicity was determined in human macrophages, as well as in sensitive and chemoresistant EOC cell lines, A2780, SKOV-3, and TOV-21G, treated with 5 ug/ml and 10 ug/ml of isotype control, LMTK3 antibody, and LMTK3BP #1 and #2. Cytotoxicity was determined by the MTT Cell Proliferation Assay after a 24-hour treatment,

TMPL14WO_spec.docx - 75 - P<0.05. FIG. 6 shows a synergistic effect of LMTK3 peptide and chemotherapy in ovarian cancer. TOV21G and SKOV3 cancer cell lines and their chemoresistant counterparts were treated with a combination of LMTK3BP 1 and Cisplatin or Docettaxel for 24 hours. MTT assay was used to determine cytotoxicity after treatment. The Compusyn software was utilized to generate Chou-Talalay plots (X-axis: Fractional activity (Fa), reflects the fraction of cellular viability affected by treatment relative to controls; Y-axis: combination index (CI) with <1, =1, >1 indicating synergistic, additive, and antagonistic effects, respectively; each point represents a different combination of LMTK3 peptide concentration tested; experiments were performed in triplicate). [0290] FIG. 21A shows the targeting of LMTK3 in ovarian cancer cell lines and normal epithelial ovarian cells by LMTK3 specific siRNA. Treatment of 10nM, 20nM, and 40nM of LMTK3 siRNA for 24 hours was performed in each cell line. For comparison, untreated cells and cells treated with 40 nM of Silencer Negative Control siRNA was performed. Viability of cells was determined by the TACS MTT proliferation assay kit (P<0.05). In FIG. 21B, Caspase-3 activity was determined by the Caspase-3 Colorimetric Activity Assay Kit in MDAH-2774 and SKOV-3 ovarian cancer cell lines treated with 10 ug/ml of LMTK3BP 1(P1) and peptide 2 (P2) for 24 hours. [0291] FIG.19 shows the liver and spleen weight of mice were treated with 2, 10, and 40 mg/kg LMTKBP13 times/week for 3 weeks. No statistically significant differences in body weight were found between groups (One-way ANOVA test, p=0.283 for liver weight, and p=0.439 for spleen weight). Also shown in FIG.19 is the total mice body weight over 20 days with 2, 10, and 40 mg/kg LMTKBP1 treatment 3 times/week for 3 weeks. No statistically significant differences in body weight were found between groups (two-way RMANOVA test, p=0.864). FIG. 16 shows the tumor weight at sacrifice after 8 doses of Vehicle, Peptide #1, Peptide #2, Peptide #3 (Negative control), or Cisplatin. Statistically significant differences were observed between groups, except peptide 3 (one-way ANOVA test **, p=0.006). [0292] LMTK3 is reportedly required for cancer cell proliferation and survival, but is dispensable in the normal cells, providing a rationale for developing LMTK3-targeted therapeutics. In this study, the inventors have identified LMTK3 as a prognostic marker for ovarian cancer, as it significantly correlated with poor prognosis in early-stage ovarian cancer. They have also successfully identified LMTK3 specific peptides that induces in vitro and in vivo cytotoxic effects in ovarian cancer cells but not in normal cells. More importantly, LMTK3 peptides are shown to be safe at a high dose of 40 mg/kg, allowing maximizing efficacy.

TMPL14WO_spec.docx - 76 - * * * [0293] All of the methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

TMPL14WO_spec.docx - 77 - Table 2: LMTK3 Peptides

TMPL14WO_spec.docx - 78 - REFERENCES The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference. 1. F. Wendler, The LMTK-family of kinases: Emerging important players in cell physiology and disease pathogenesis. Biochim Biophys Acta Mol Basis Dis, (2018). 2. Y. Xu et al., LMTK3 Represses Tumor Suppressor-like Genes through Chromatin Remodeling in Breast Cancer. Cell Rep 12, 837-849 (2015). 3. K. Anbarasu, S. Jayanthi, Identification of curcumin derivatives as human LMTK3 inhibitors for breast cancer: a docking, dynamics, and MM/PBSA approach.3 Biotech 8, 228 (2018). 4. T. Wakatsuki et al., Prognostic role of lemur tyrosine kinase-3 germline polymorphisms in adjuvant gastric cancer in Japan and the United States. Mol Cancer Ther 12, 2261-2272 (2013). 5. H. Shi et al., Serum lemur tyrosine kinase 3 expression in colorectal cancer patients predicts cancer progression and prognosis. Med Oncol 30, 754 (2013). 6. L. R. Klug et al., LMTK3 is essential for oncogenic KIT expression in KIT-mutant GIST and melanoma. Oncogene 38, 1200-1210 (2019). 7. L. Lu, X. Yuan, Q. Zhang, H. Zhang, B. Shen, LMTK3 knockdown retards cell growth and invasion and promotes apoptosis in thyroid cancer. Mol Med Rep 15, 2015-2022 (2017). 8. G. Giamas et al., Kinome screening for regulators of the estrogen receptor identifies LMTK3 as a new therapeutic target in breast cancer. Nat Med 17, 715-719 (2011). 9. J. Stebbing et al., LMTK3 expression in breast cancer: association with tumor phenotype and clinical outcome. Breast Cancer Res Treat 132, 537-544 (2012). 10. G. M. Saed et al., Myeloperoxidase serves as a redox switch that regulates apoptosis in epithelial ovarian cancer. Gynecol Oncol 116, 276-281 (2010). 11. G. M. Saed et al., Novel expression of CD11b in epithelial ovarian cancer: Potential therapeutic target. Gynecol Oncol 148, 567-575 (2018). 12. Z. Wu et al., Development of immunoaffinity chromatographic method for Ara h 2 isolation. Protein expression and purification 131, 85-90 (2016). 13. G. M. Saed, M. P. Diamond, N. M. Fletcher, Updates of the role of oxidative stress in the pathogenesis of ovarian cancer. Gynecol Oncol 145, 595-602 (2017).

TMPL14WO_spec.docx - 79 - 14. A. B. Alvero et al., TRX-E-002-1 Induces c-Jun-Dependent Apoptosis in Ovarian Cancer Stem Cells and Prevents Recurrence In Vivo. Mol Cancer Ther 15, 1279-1290 (2016). 15. A. B. Alvero et al., Novel approach for the detection of intraperitoneal micrometastasis using an ovarian cancer mouse model. Sci Rep 7, 40989 (2017). 16. C. Cardenas et al., Adipocyte microenvironment promotes Bclxl expression and confers chemoresistance in ovarian cancer cells. Apoptosis 22, 558-569 (2017). 17. V. Craveiro et al., Phenotypic modifications in ovarian cancer stem cells following Paclitaxel treatment. Cancer Med 2, 751-762 (2013). 18. J. Pizzonia et al., Multimodality animal rotation imaging system (Mars) for in vivo detection of intraperitoneal tumors. Am J Reprod Immunol 67, 84-90 (2012). 19. S. B. Kaye, Chemotherapy for recurrent ovarian cancer. Lancet 361, 2094-2095 (2003). 20. P. DiSilvestro, A. Alvarez Secord, Maintenance treatment of recurrent ovarian cancer: Is it ready for prime time? Cancer Treat Rev 69, 53-65 (2018). 21. D. K. Armstrong, Relapsed ovarian cancer: challenges and management strategies for a chronic disease. Oncologist 7 Suppl 5, 20-28 (2002). 22. Jiang, T., et al., LMTK3 promotes tumorigenesis in bladder cancer via the ERK/MAPK pathway. FEBS Open Bio, 2020.10(10): p.2107-2121. 23. Asano, T., et al., High expression of LMTK3 is an independent factor indicating a poor prognosis in estrogen receptor alpha-positive breast cancer patients. Jpn J Clin Oncol, 2014.44(10): p.889-97. 24. Xu, Y., et al., The kinase LMTK3 promotes invasion in breast cancer through GRB2- mediated induction of integrin beta(1). Sci Signal, 2014.7(330): p. ra58. 25. Cairns, J., et al., The lncRNA MIR2052HG regulates ERalpha levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1. Breast Cancer Res, 2019.21(1): p. 47. 26. Stebbing, J., et al., LMTK3 confers chemo-resistance in breast cancer. Oncogene, 2018.37(23): p.3113-3130.

TMPL14WO_spec.docx - 80 -

Claims

WHAT IS CLAIMED: 1. A method for treating a hyperproliferative disorder in a subject, the method comprising administering a peptide of SEQ ID NO:1 to the subject.

2. A method for treating endometrial or ovarian hyperproliferative disorders in a subject, the method comprising administration of a modulator of LMTK3 to the subject.

3. The method of claim 2, wherein the hyperproliferative disorder comprises ovarian cancer.

4. The method of claim 2, wherein the hyperproliferative disorder comprises endometriosis.

5. The method of any one of claims 2-4, wherein the modulator comprises a peptide modulator, and wherein the peptide modulator comprises an N-terminal WVG motif that is capable of binding to and inhibiting LMTK3.

6. The method of claim 5, wherein the peptide modulator comprises the consensus sequence: WVG-[S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L]-[A/N]-X-[N/V]-[N/L/R]-[E/Y]-X-[R/V], wherein x is any amino acid.

7. The amino acid peptide of claim 5, wherein the consensus sequence comprises WVG- [S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L/D]-[A/N/E]-X-[N/V/Y]-[N/L/R]-[E/Y/D]-X-[R/V/D/L].

8. The method of any one of claims 2-7, wherein the peptide is 10-20 amino acids in length.

9. The method of claim 8, wherein the peptide is seventeen amino acids in length.

10. The method of any one of claims 5-9, wherein the peptide comprises the amino acid sequence of one of SEQ ID NOS:1-30, or an amino acid sequence with at least 80% sequence identity to one of SEQ ID NOS:1-30, or a fragment thereof.

11. The method of any one of claims 5-10, wherein the peptide comprises both D and L amino acid stereoisomers.

12. The method of any one of claims 5-10, wherein the peptide comprises one or more D amino acid stereoisomers.

13. The method of claim 11 or 12, wherein the peptide comprises at least one amino acid residue of Trp, Leu, Arg, and/or Ala and wherein the at least one of Trp, Leu, Arg, and/or Ala is a D amino acid stereoisomer.

14. The method of any one of claims 5-13, wherein the peptide modulator comprises a modification.

15. The method of claim 14, wherein the modification comprises an acetate molecule at the terminus of the peptide.

TMPL14WO_spec.docx - 81 -

16. The method of claim 15, wherein the modification comprises an acetate molecule at the carboxy terminus of the peptide.

17. The method of claim 2, wherein the modulator comprises an anti-LMTK3 antibody.

18. The method of claim 17, wherein the anti-LMTK3 does not bind to CD11b.

19. The method of any one of claims 2-18, wherein the modulator inhibits the phosphorylation activity of LMTK3.

20. The method of any one of claims 2-19, wherein the modulator inhibits the interaction of LMKT3 and an integrin protein.

21. The method of claim 2, wherein the modulator comprises an oligonucleotide modulator.

22. The method of claim 21, wherein the modulator comprises an isolated oligonucleotide that hybridizes with a nucleic acid molecule encoding the LMKT3 gene.

23. The method of claim 21 or 22, wherein the LMTK3 modulator is an siRNA, a double stranded RNA, a short hairpin RNA, or an antisense oligonucleotide.

24. The method of any one of claims 2-23, wherein the subject has ovarian or endometrial cells that are positive for expression of LMTK3.

25. The method of any one of claims 2-24, wherein the subject has been determined to have LMTK3 positive cells.

26. The method of any one of claims 2-25, wherein the subject is female.

27. The method of any one of claims 2-26, wherein the subject is on hormone therapy.

28. The method of claim 27, wherein the hormone therapy comprises contraception or hormone replacement therapy.

29. The method of any one of claims 26-28, wherein the female is an adolescent, perimenopausal, or menopausal female.

30. The method of any one of claims 2-29, wherein the subject has received one or more prior therapies to treat the hyperproliferative disorder.

31. The method of claim 30, wherein the subject has been determined to be a non-responder or resistant to the one or more prior therapies.

32. The method of claim 30 or 31, wherein the one or more prior therapies comprise an immunotherapy.

33. The method of claim 32, wherein the immunotherapy comprises a checkpoint inhibitor.

34. The method of claim 33, wherein the immunotherapy comprises Pembrolizumab.

35. The method of any one of claims 30-34, wherein the one or more prior therapies comprises a targeted antibody.

36. The method of claim 35, wherein the targeted antibody comprises Bevacizumab.

TMPL14WO_spec.docx - 82 -

37. The method of any one of claims 30-36, wherein the one or more prior therapies comprises a chemotherapy.

38. The method of claim 37, wherein the chemotherapy comprises a platinum-based chemotherapy, a taxane-based chemotherapy, or a combination thereof.

39. The method of claim 38, wherein the chemotherapy comprises carboplatin, paclitaxel, or a combination thereof.

40. The method of any one of claims 2-39, wherein the method comprises administration of an additional agent.

41. The method of claim 40, wherein the additional agent comprises a platinum-based chemotherapy, a taxane-based chemotherapy, or a combination thereof.

42. The method of claim 40, wherein the additional agent comprises cisplatin.

43. The method of claim 41 or 42, wherein the subject is sensitive or has been determined to be sensitive to platinum-based chemotherapy and/or taxane based chemotherapy.

44. The method of claim 43, wherein the platinum-based chemotherapy comprises carboplatin and/or the taxane-based chemotherapy comprises paclitaxel.

45. The method of any one of claims 40-44, wherein the additional agent comprises a PARP inhibitor, a targeted antibody, or combinations thereof.

46. The method of claim 45, wherein the PARP inhibitor comprises olaparib or niraparib.

47. The method of claim 45, wherein the targeted antibody comprises bevacizumab.

48. The method of any one of claims 45-47, wherein the subject is or has been determined to be resistant to platinum-based chemotherapy and/or taxane based chemotherapy.

49. The method of any of claims 3-48, wherein the ovarian cancer comprises stage I, II, III, or IV ovarian cancer.

50. The method of any one of claims 3-49, wherein the ovarian cancer comprises metastatic ovarian cancer.

51. An amino acid peptide comprising the sequence of one of SEQ ID NOS:1-30.

52. An amino acid peptide comprising the consensus sequence: WVG-[S/E/P]-[S/Y/V/E]- [S/A/V]-[A/L]-[A/N]-X-[N/V]-[N/L/R]-[E/Y]-X-[R/V], wherein x is any amino acid.

53. The amino acid peptide of claim 52, wherein the consensus sequence comprises WVG- [S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L]-[A/N]-X-[N/V]-[N/L/R]-[E/Y]-X-[R/V]-XXX.

54. An amino acid peptide comprising the consensus sequence: WVG-[S/E/P]-[S/Y/V/E]- [S/A/V]-[A/L/D]-[A/N/E]-X-[N/V/Y]-[N/L/R]-[E/Y/D]-X-[R/V/D/L].

55. The peptide of any one of claims 51-54, wherein the peptide is synthetic.

TMPL14WO_spec.docx - 83 -

56. The peptide of any one of claims 51-55, wherein the peptide is 10-20 amino acids in length.

57. The peptide of any one of claims 51-56, wherein the peptide is seventeen amino acids in length.

58. The peptide of any one of claims 51-57, wherein the peptide comprises the amino acid sequence of SEQ ID NO:1 or 15, or an amino acid sequence with at least 80% sequence identity to SEQ ID NO:1 or 15, or a fragment thereof.

59. The peptide of any one of claims 51-58, wherein the peptide comprises both D and L amino acid stereoisomers.

60. The peptide of any one of claims 51-59, wherein the peptide comprises one or more D amino acid stereoisomers.

61. The peptide of claim 59 or 60, wherein the peptide comprises at least one amino acid residue of Trp, Leu, Arg, and/or Ala and wherein the at least one of Trp, Leu, Arg, and/or Ala is a D amino acid stereoisomer.

62. The peptide of any one of claims 51-61, wherein the peptide comprises a modification.

63. The peptide of claim 62, wherein the modification comprises an acetate molecule at the terminus of the peptide.

64. The peptide of claim 63, wherein the modification comprises an acetate molecule at the carboxy terminus of the peptide.

65. A polypeptide comprising the peptide of any one of claims 51-64.

66. A composition comprising the peptide of any one of claims 51-64 or the polypeptide of claim 65.

67. The composition of claim 66, wherein the composition further comprises an additional agent.

68. The composition of claim 67, wherein the additional agent comprises a chemotherapeutic agent, a PARP inhibitor, a targeted antibody, or combinations thereof.

69. The composition of claim 68, wherein the additional agent comprises a chemotherapeutic agent and wherein the chemotherapeutic agent comprises a platinum-based chemotherapeutic agent, a taxane based chemotherapeutic agent, or combinations thereof.

70. The composition of claim 69, wherein the platinum-based chemotherapeutic agent comprises carboplatin and/or the taxane-based chemotherapeutic agent comprises paclitaxel.

71. The composition of claim 69, wherein the additional agent comprises cisplatin.

TMPL14WO_spec.docx - 84 -

72. The composition of any one of claims 68-71, wherein the composition comprises a PARP inhibitor, and wherein the PARP inhibitor comprises olaparib, niraparib, or combinations thereof.

73. The composition of any one of claims 68-72, wherein the composition comprises a targeted antibody and wherein the targeted antibody comprises bevacizumab.

74. A nucleic acid encoding the peptide of any one of claims 51-64.

75. A method of making the peptide of any one of claims 51-64, the method comprising expressing the nucleic acid of claim 74 in a host cell.

76. A method of making the peptide of any one of claims 51-64, the method comprising chemically synthesizing the peptide.

77. A method for treating a hyperproliferative disorder in a subject, the method comprising administering the peptide of any one of claims 51-64 or the composition of any one of claims 66-73 to the subject.

78. The method of claim 77, wherein the hyperproliferative disorder comprises an endometrial or ovarian hyperproliferative disorder.

79. The method of claim 77 or 78, wherein the hyperproliferative disorder comprises cancer.

80. The method of claim 79, wherein the cancer comprises ovarian cancer.

81. The method of claim 79, wherein the cancer comprises glioblastoma, breast cancer, lung cancer, liver cancer, prostate cancer, bladder cancer, colorectal cancer, or thyroid cancer.

82. The method of claim 78, wherein the hyperproliferative disorder comprises endometriosis.

83. The method of any one of claims 77-82, wherein the hyperproliferative disorders is positive for expression of LMTK3.

84. The method of any one of claims 77-83, wherein the subject has been determined to have LMTK3 positive ovarian or endometrial cells.

85. The method of any one of claims 77-84, wherein the subject is female.

86. The method of any one of claims 77-85, wherein the subject is on hormone therapy.

87. The method of claim 86, wherein the hormone therapy comprises contraception or hormone replacement therapy.

88. The method of any one of claims 85-87, wherein the female is an adolescent, perimenopausal, or menopausal female.

89. The method of any one of claims 77-88, wherein the subject has received one or more prior therapies to treat the hyperproliferative disorder.

TMPL14WO_spec.docx - 85 -

90. The method of claim 89, wherein the subject has been determined to be a non-responder or resistant to the one or more prior therapies.

91. The method of claim 89 or 90, wherein the one or more prior therapies comprise an immunotherapy.

92. The method of claim 91 wherein the immunotherapy comprises a checkpoint inhibitor.

93. The method of claim 92, wherein the immunotherapy comprises Pembrolizumab.

94. The method of any one of claims 89-93, wherein the one or more prior therapies comprises a targeted antibody.

95. The method of claim 94, wherein the targeted antibody comprises Bevacizumab.

96. The method of any one of claims 89-95, wherein the one or more prior therapies comprises a chemotherapy.

97. The method of claim 96, wherein the chemotherapy comprises a platinum-based chemotherapy, a taxane-based chemotherapy, or a combination thereof.

98. The method of claim 97, wherein the chemotherapy comprises carboplatin, paclitaxel, or a combination thereof.

99. The method of any one of claims 77-98, wherein the method comprises administration of an additional agent.

100. The method of claim 99, wherein the additional agent comprises a platinum-based chemotherapy, a taxane-based chemotherapy, or a combination thereof.

101. The method of claim 99, wherein the additional agent comprises cisplatin.

102. The method of claim 100 or 101, wherein the subject is sensitive or has been determined to be sensitive to platinum-based chemotherapy and/or taxane based chemotherapy.

103. The method of claim 102, wherein the platinum-based chemotherapy comprises carboplatin and/or the taxane-based chemotherapy comprises paclitaxel.

104. The method of any one of claims 99-103, wherein the additional agent comprises a PARP inhibitor, a targeted antibody, or combinations thereof.

105. The method of claim 104, wherein the PARP inhibitor comprises olaparib or niraparib.

106. The method of claim 104 or 105, wherein the targeted antibody comprises bevacizumab.

107. The method of any one of claims 104-106, wherein the subject is or has been determined to be resistant to platinum-based chemotherapy and/or taxane based chemotherapy.

108. The method of any of claims 80-107, wherein the ovarian cancer comprises stage I, II, III, or IV ovarian cancer.

TMPL14WO_spec.docx - 86 -

109. The method of any one of claims 80-108, wherein the ovarian cancer comprises metastatic ovarian cancer.

110. A method for evaluating a subject comprising detecting LMTK3 in a biological sample from the subject.

111. The method of claim 110, wherein the biological sample comprises serum, biopsy, plasma, or tissue sample.

112. The method of any one of claims 110-111, wherein detecting LMTK3 comprises detecting LMTK3 protein or LMTK3 mRNA.

113. The method of any one of claims 110-112, wherein the subject has or is suspected of having cancer.

114. The method of claim 113, wherein the cancer comprises breast, ovarian, or head and neck cancer.

115. The method of any one of claims 110-114, wherein the subject is female.

116. The method of any one of claims 110-115, wherein the subject is on hormone therapy.

117. The method of claim 116, wherein the hormone therapy comprises contraception or hormone replacement therapy.

118. The method of any one of claims 115-117, wherein the female is an adolescent, perimenopausal, or menopausal female.

119. The method of any one of claims 110-118, wherein detecting LMTK3 comprises quantitating the expression level of LMTK3.

120. The method of claim 119, wherein the expression level of LMTK3 is normalized.

121. The method of claim 119 or 120, wherein the expression level of LMTK3 is compared to a control.

122. The method of claim 121, wherein the expression level of LMTK3 is determined to be greater than the control.

123. The method of claim 121, wherein the expression level of LMTK3 is determined to be less than the control.

124. The method of any one of claims 121-123, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with stage I, II, III, or IV cancer.

125. The method of any one of claims 121-123, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject without cancer.

TMPL14WO_spec.docx - 87 -

126. The method of any one of claims 121-123, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with a favorable prognosis or from a subject that has a chemotherapy-responsive or radiotherapy–responsive cancer.

127. The method of any one of claims 121-123, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with an unfavorable prognosis or from a subject that has a chemotherapy-resistant or radiotherapy–resistant cancer.

128. The method of any one of claims 110-127, wherein the method further comprises treating the subject based on the detection of LMTK3.

129. A method for treating a subject for cancer comprising treating a subject having a biological sample that was determined to have low expression of LMTK3 with chemotherapy and/or radiotherapy.

130. A method for treating a subject for cancer comprising treating a subject having a biological sample that was determined to have high expression of LMTK3 with the combination of i) a LMTK3 modulator and ii) chemotherapy and/or radiotherapy.

131. The method of claim 129 or 130, wherein the biological sample comprises serum, a biopsy, plasma, or tissue sample.

132. The method of any one of claims 129-131, wherein LMTK3 protein or mRNA was detected in the biological sample from the subject.

133. The method of any one of claims 129-132, wherein the subject has or is suspected of having cancer.

134. The method of claim 133, wherein the cancer comprises breast, ovarian, or head and neck cancer.

135. The method of any one of claim 129-134, wherein the expression level of LMTK3 was a normalized level of expression of LMTK3.

136. The method of any one of claims 129-135, wherein the expression level of LMTK3 was high or low compared to a control.

137. The method of claim 136, wherein the expression level of LMTK3 is determined to be higher than the control.

138. The method of claim 136, wherein the expression level of LMTK3 is determined to be lower than the control.

TMPL14WO_spec.docx - 88 -

139. The method of any one of claims 136-138, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with stage I, II, III, or IV cancer.

140. The method of any one of claims 136-138, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject without cancer.

141. The method of any one of claims 136-138, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with a favorable prognosis or from a subject that has a chemotherapy- responsive or radiotherapy–responsive cancer.

142. The method of any one of claims 136-138, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with an unfavorable prognosis or from a subject that has a chemotherapy-resistant or radiotherapy–resistant cancer.

143. The method of claim 129 or 131-136, wherein the biological sample from the subject was determined to have low expression of LMTK3 or an expression level that is lower than or not significantly different than the level of LMTK3 expression that is representative of the expression level in a biological sample from a subject with a favorable prognosis or from a subject that has a chemotherapy-responsive or radiotherapy–responsive cancer.

144. The method of any one of claims 130-143, wherein the biological sample from the subject was determined to have high expression of LMTK3 or an expression level that is higher than or not significantly different than the level of LMTK3 expression that is representative of the expression level in a biological sample from a subject with an unfavorable prognosis or from a subject that has a chemotherapy-resistant or radiotherapy– resistant cancer.

145. The method of any one of claims 129-144, wherein the cancer comprises breast cancer.

146. The method of claim 145, wherein the treatment comprises chemotherapy and wherein chemotherapy comprises doxorubicin, epirubicin, paclitaxel, docetaxel, 5- fluorouracil, capecitabine, cyclophosphamide, carboplatin, and combinations thereof.

147. The method of any one of claims 129-144, wherein the cancer comprises ovarian cancer.

148. The method of claim 147, wherein the treatment comprises chemotherapy and wherein the chemotherapy comprises cisplatin, carboplatin, paclitaxel, docetaxel, albumin

TMPL14WO_spec.docx - 89 - bound paclitaxel, altretamine, capecitabine, cyclophosphamide, etoposide, gemcitabine, ifosfamide, irinotecan, liposomal doxorubicin, melphalan, pemetrexed, topotecan, vinorelbine, or combinations thereof.

149. A method of prognosing a subject with cancer or predicting a therapeutic response to chemotherapy or radiation therapy comprising: a) measuring LMTK3 expression level in a biological sample from the subject; b) comparing the measured level to control level or control samples; and c) prognosing the subject or predicting a therapeutic response based on the measured level of LMTK3.

150. The method of claim 149, wherein the biological sample comprises serum, biopsy, plasma, or tissue sample.

151. The method of any one of claims 149-150, wherein measuring LMTK3 comprises measuring LMTK3 protein or LMTK3 mRNA in the biological sample.

152. The method of any one of claims 149-151, wherein the subject has or is suspected of having cancer.

153. The method of claim 152, wherein the cancer comprises breast, ovarian, or head and neck cancer.

154. The method of any one of claims 149-153, wherein measuring LMTK3 comprises quantitating the expression level of LMTK3.

155. The method of claim 154, wherein the expression level of LMTK3 is normalized.

156. The method of any one of claims 149-155, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with stage I, II, III, or IV cancer.

157. The method of any one of claims 149-155, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject without cancer.

158. The method of any one of claims 149-155, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with a favorable prognosis or from a subject that has a chemotherapy- responsive or radiotherapy–responsive cancer.

159. The method of any one of claims 149-155, wherein the control comprises the expression level of LMTK3 that is representative of the expression level in a biological sample from a subject with an unfavorable prognosis or from a subject that has a chemotherapy-resistant or radiotherapy–resistant cancer.

TMPL14WO_spec.docx - 90 -

160. The method of any one of claims 149-159, wherein the method further comprises treating the subject based on the detection of LMTK3.

161. The method of claim 160, wherein the subject is treated with chemotherapy or radiation therapy when the biological sample from the subject was determined to have low expression of LMTK3 or an expression level that is lower than or not significantly different than the level of LMTK3 expression that is representative of the expression level in a biological sample from a subject with a favorable prognosis or from a subject that has a chemotherapy-responsive or radiotherapy–responsive cancer.

162. The method of claim 161, wherein the treatment excludes a LMTK3 modulator.

163. The method of claim 160, wherein the subject is treated with the combination of i) a LMTK3 modulator and ii) chemotherapy and/or radiotherapy when the biological sample from the subject was determined to have high expression of LMTK3 or an expression level that is higher than or not significantly different than the level of LMTK3 expression that is representative of the expression level in a biological sample from a subject with an unfavorable prognosis or from a subject that has a chemotherapy-resistant or radiotherapy– resistant cancer.

164. The method of any one of claims 149-163, wherein the cancer comprises breast cancer.

165. The method of claim 164, wherein the treatment comprises chemotherapy and wherein chemotherapy comprises doxorubicin, epirubicin, paclitaxel, docetaxel, 5- fluorouracil, capecitabine, cyclophosphamide, carboplatin, and combinations thereof.

166. The method of any one of claims 149-163, wherein the cancer comprises ovarian cancer.

167. The method of claim 166, wherein the treatment comprises chemotherapy and wherein the chemotherapy comprises cisplatin, carboplatin, paclitaxel, docetaxel, albumin bound paclitaxel, altretamine, capecitabine, cyclophosphamide, etoposide, gemcitabine, ifosfamide, irinotecan, liposomal doxorubicin, melphalan, pemetrexed, topotecan, vinorelbine, or combinations thereof.

168. The method of any one of claims 130-167, wherein the modulator comprises a peptide modulator.

169. The method of claim 168, wherein the peptide modulator comprises the consensus sequence: WVG-[S/E/P]-[S/Y/V/E]-[S/A/V]-[A/L]-[A/N]-X-[N/V]-[N/L/R]-[E/Y]-X-[R/V], wherein x is any amino acid.

TMPL14WO_spec.docx - 91 -

170. The method of claim 168, wherein the consensus sequence comprises WVG-[S/E/P]- [S/Y/V/E]-[S/A/V]-[A/L/D]-[A/N/E]-X-[N/V/Y]-[N/L/R]-[E/Y/D]-X-[R/V/D/L].

171. The method of any one of claims 110-170, wherein the peptide is 10-20 amino acids in length.

172. The method of claim 171, wherein the peptide is seventeen amino acids in length.

173. The method of any one of claims 168-172, wherein the peptide comprises the amino acid sequence of one of SEQ ID NOS:1-30, or an amino acid sequence with at least 80% sequence identity to one of SEQ ID NOS:1-30, or a fragment thereof.

174. The method of any one of claims 168-173, wherein the peptide comprises both D and L amino acid stereoisomers.

175. The method of any one of claims 168-173, wherein the peptide comprises one or more D amino acid stereoisomers.

176. The method of claim 174 or 175, wherein the peptide comprises at least one amino acid residue of Trp, Leu, Arg, and/or Ala and wherein the at least one of Trp, Leu, Arg, and/or Ala is a D amino acid stereoisomer.

177. The method of any one of claims 168-173, wherein the peptide comprises a modification.

178. The method of claim 177, wherein the modification comprises an acetate molecule at the terminus of the peptide.

179. The method of claim 178, wherein the modification comprises an acetate molecule at the carboxy terminus of the peptide.

180. The method of claim 110, wherein the modulator comprises an anti-LMTK3 antibody.

181. The method of claim 180, wherein the anti-LMTK3 does not bind to CD11b.

182. The method of any one of claims 110-181, wherein the modulator inhibits the phosphorylation activity of LMTK3.

183. The method of any one of claims 110-182, wherein the modulator inhibits the interaction of LMKT3 and an integrin protein.

184. The method of claim 110, wherein the modulator comprises an oligonucleotide modulator.

185. The method of claim 184, wherein the modulator comprises an isolated oligonucleotide that hybridizes with a nucleic acid molecule encoding the LMKT3 gene.

TMPL14WO_spec.docx - 92 -