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WO2021241981A1 - Composition pour la prévention ou le traitement du cancer - Google Patents

Composition pour la prévention ou le traitement du cancer Download PDF

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Publication number
WO2021241981A1
WO2021241981A1 PCT/KR2021/006493 KR2021006493W WO2021241981A1 WO 2021241981 A1 WO2021241981 A1 WO 2021241981A1 KR 2021006493 W KR2021006493 W KR 2021006493W WO 2021241981 A1 WO2021241981 A1 WO 2021241981A1
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cancer
znf667
acta2
head
rna
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Korean (ko)
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정재호
신민규
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Industry Academic Cooperation Foundation of Yonsei University
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Industry Academic Cooperation Foundation of Yonsei University
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/713—Double-stranded nucleic acids or oligonucleotides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents

Definitions

  • An object of the present invention is to provide a composition capable of preventing or treating gastric cancer among cancers, or inhibiting invasiveness or metastasis of gastric cancer cells.
  • Cancer is a cell mass composed of undifferentiated cells that proliferate indefinitely while ignoring the necessary condition in the tissue, unlike normal cells, which can proliferate and suppress regularly and in a controlled manner according to individual needs.
  • Such unrestricted proliferation of cancer cells infiltrates into surrounding tissues and, in more severe cases, metastasizes to other organs of the body, causing severe pain and eventually death.
  • Cancer is broadly classified into blood cancer and solid cancer, and occurs in almost all parts of the body, such as stomach cancer, pancreatic cancer, breast cancer, oral cancer, liver cancer, uterine cancer, esophageal cancer, and skin cancer.
  • therapeutic agents are being used for the treatment of specific cancers, surgery, radiation therapy, and anticancer drug treatment using chemotherapeutic agents that inhibit cell proliferation are the main methods up to now.
  • chemotherapeutic agents since it is not a targeted therapy, the biggest problem with existing chemotherapeutic agents is the side effects and drug resistance due to cytotoxicity, which is a major factor that ultimately causes the treatment to fail despite the initial successful response to the anticancer agent. Therefore, in order to overcome the limitations of these chemotherapeutic agents, there is a continuous need to develop targeted therapeutics with a clear anticancer mechanism.
  • Gastric cancer is the third leading cause of cancer-related death and ranks fourth among the most common cancers.
  • personalized pharmaceuticals clinically and biologically close molecular analysis is required.
  • understanding of biological complexity has been improved through omics studies of gastric cancer at the whole genome level, and in particular, prognosis using biomarkers and responsiveness to adjuvant chemotherapy through analysis of mRNA gene expression data.
  • Great advances have been made in forecasting.
  • Molecular profiling at different levels in gastric cancer is expected to lead to the development of personalized treatment strategies.
  • lncRNA long non-coding RNA
  • the lncRNA acts as an important substance in the path of cancer, and is related to the development and progression of cancer.
  • the lncRNA is a transcript of 200 or more nucleotides without protein-coding potential. They have a higher number of constituent nucleotides than the protein-coding gene, are restricted to specific cell/tissue types to a greater extent than mRNA, and are promising as cancer-type specific therapeutic targets.
  • RNA-targeting Nucleic acid-based (RNA-targeting) therapeutics have shown clinical success in several diseases and preclinical success in some cancers by targeting lncRNA. However, there have been no reports of lncRNA targets in gastric cancer, and sufficient studies have not been conducted on their clinical relevance and biological functions.
  • One object of the present invention is to provide a composition capable of preventing or treating cancer.
  • Another object of the present invention is to provide a composition capable of inhibiting the invasiveness or metastasis of cancer.
  • Another object of the present invention is to provide a composition that can overcome resistance to anticancer drugs.
  • ZNF667-AS1 ZNF667 Antisense RNA 1 (Head To Head)
  • RP11-572C15.6 FENDRR (FOXF1 Adjacent Non-Coding Developmental Regulatory RNA)
  • ACTA2-AS1 ACTA2 Antisense RNA 1
  • a pharmaceutical composition for preventing or treating cancer comprising an expression inhibitor specific to at least one of them as an active ingredient.
  • ZNF667-AS1, RP11-572C15.6, FENDRR and comprising an expression inhibitor specific to at least one of ACTA2-AS1 as an active ingredient, a pharmaceutical composition for inhibiting invasiveness or metastasis of cancer it's about
  • a pharmaceutical composition for overcoming resistance of resistant cancer comprising an expression inhibitor specific to at least one of ZNF667-AS1, RP11-572C15.6, FENDRR and ACTA2-AS1 as an active ingredient it's about
  • ZNF667-AS1, RP11-572C15.6, FENDRR, and containing an expression inhibitor specific for at least one of ACTA2-AS1 as an active ingredient, resistant or metastatic cancer prevention or treatment It relates to a pharmaceutical composition.
  • each of the ZNF667-AS1, RP11-572C15.6, FENDRR and ACTA2-AS1 is a long non-coding RNA gene (lncRNA), and the ZNF667-AS1 may be represented by SEQ ID NO: 1
  • the RP11-572C15.6 may be represented by SEQ ID NO: 2
  • the FENDRR may be represented by SEQ ID NO: 3
  • the ACTA2-AS1 may be represented by SEQ ID NO: 4, but is not limited thereto.
  • the ZNF667-AS1, RP11-572C15, FENDRR or ACTA2-AS1 specific expression inhibitor is an antisense nucleotide complementary to the gene, short interfering RNA (siRNA), short hairpin RNA (short RNA) It is preferable that at least one selected from the group consisting of hairpin RNA; shRNA) and ribozyme.
  • the "antisense nucleotide” binds (hybridizes) to the complementary base sequence of DNA, immature-mRNA, or mature mRNA as defined in Watson-Crick base pairing to disrupt the flow of genetic information from DNA to protein.
  • the nature of antisense nucleotides specific to a target sequence makes them exceptionally versatile. Since antisense nucleotides are long chains of monomeric units, they can be readily synthesized for the target RNA sequence. Many recent studies have demonstrated the usefulness of antisense nucleotides as biochemical means for studying target proteins (Rothenberg et al., J. Natl. Cancer Inst., 81:1539-1544, 1999).
  • antisense nucleotides Due to recent advances in oligonucleotide chemistry and nucleotide synthesis with improved cell line adsorption, target binding affinity and nuclease resistance, the use of antisense nucleotides can be considered as a new type of inhibitor.
  • the "siRNA” and “shRNA” are nucleic acid molecules capable of mediating RNA interference or gene silencing, and because they can inhibit the expression of a target gene, an efficient gene knockdown method or gene therapy used in a way shRNA is a single-stranded oligonucleotide that forms a hairpin structure by bonding between complementary sequences. In vivo, the shRNA is cut by a dicer and a small RNA fragment of 21 to 25 nucleotides in size. siRNA, which is a double-stranded oligonucleotide, and can specifically bind to mRNA having a complementary sequence to inhibit expression.
  • shRNA and siRNA to use may be determined by a person skilled in the art, and if the mRNA sequences targeted by them are the same, a similar expression reduction effect can be expected.
  • it specifically acts on ZNF667-AS1, RP11-572C15, FENDRR or ACTA2-AS1 to cut ZNF667-AS1, RP11-572C15, FENDRR or ACTA2-AS1 LncRNA molecules to interfere with RNA (RNAi, RNA interference) By inducing the phenomenon, it is possible to inhibit the ZNF667-AS1, RP11-572C15, FENDRR or ACTA2-AS1.
  • siRNA can be synthesized chemically or enzymatically.
  • the method for preparing siRNA is not particularly limited, and methods known in the art may be used. For example, a method for synthesizing siRNA directly chemically, a method for synthesizing siRNA using in vitro transcription, a method for cleaving long double-stranded RNA synthesized by in vitro transcription using an enzyme; Expression method through intracellular delivery of an shRNA expression plasmid or viral vector and expression method through intracellular delivery of a PCR (polymerase chain reaction)-induced siRNA expression cassette (cassette), but are not limited thereto.
  • a method for synthesizing siRNA directly chemically a method for synthesizing siRNA using in vitro transcription, a method for cleaving long double-stranded RNA synthesized by in vitro transcription using an enzyme
  • Expression method through intracellular delivery of an shRNA expression plasmid or viral vector and expression method through intracellular delivery of a PCR (polymerase chain reaction)-induced siRNA expression cassette (cassette), but are not limited thereto
  • the "ribozyme” refers to an RNA molecule having catalytic activity. Ribozymes having various activities are known, and the ribozymes of the gene include known or artificially generated ribozymes, and selectively ribozymes having target-specific RNA cleavage activity are prepared by known standard techniques. can be
  • the expression inhibitor is an expression inhibitor specific to the gene of ZNF667-AS1, and may be siRNA represented by SEQ ID NOs: 5 and 6, but is not limited thereto.
  • an expression inhibitor specific to at least one gene of ZNF667-AS1, RP11-572C15.6, FENDRR and ACTA2-AS1 can effectively inhibit the growth or proliferation of cancer cells, and furthermore, cancer cell invasiveness or Metastasis can also be effectively prevented or treated.
  • the term “cancer” refers to or refers to a physiological condition typically characterized by unregulated cell growth in mammals.
  • the cancer to be prevented or treated is gastric cancer, ovarian cancer, colorectal cancer, breast cancer, liver cancer, pancreatic cancer, cervical cancer, thyroid cancer, parathyroid cancer, non-small cell lung cancer, prostate cancer, Gallbladder cancer, biliary tract cancer, non-Hodgkin's lymphoma, Hodgkin's lymphoma, blood cancer, bladder cancer, kidney cancer, melanoma, colon cancer, bone cancer, skin cancer, head cancer, uterine cancer, rectal cancer, brain tumor, perianal cancer, fallopian tube carcinoma, endometrial carcinoma, Vaginal cancer, vulvar carcinoma, esophageal cancer, small intestine cancer, endocrine adenocarcinoma, adrenal cancer, soft tissue sarcoma, urethral cancer, penile cancer, ureter cancer, renal cell carcinoma, renal pelvi
  • resistant cancer refers to a cancer that exhibits extremely low sensitivity to cancer treatment drugs, particularly anticancer drugs, and does not show improvement, alleviation, alleviation, or treatment symptoms by treatment such as chemotherapy. do.
  • the drug-resistant cancer for cancer treatment may have resistance to a specific anticancer agent from the beginning, and did not initially show resistance, but due to long-time drug treatment, it no longer exhibits sensitivity to the same therapeutic agent due to genetic mutation in cancer cells. may occur.
  • the "drug for cancer treatment” or “anticancer agent” is not particularly limited in its type, but may preferably be a drug for the treatment of gastric cancer.
  • Specific examples include nitrogen mustard, imatinib, oxaliplatin, rituximab, erlotinib, neratinib, lapatinib, gefitinib, vandetanib, nirotinib, semasanib, bosutinib, axitinib, cediranib , restautinib, trastuzumab, gefitinib, bortezomib, sunitinib, carboplatin, sorafenib, bevacizumab, cisplatin, cetuximab, viscumalbum, asparaginase, tretinoin, hydroxycarba amide, dasatinib, estramustine, gemtuzumab ozogamicin, ibritum
  • the term "overcoming resistance” refers to an action of increasing the sensitivity of cancer cells that have acquired resistance to a cancer treatment drug, particularly an anticancer drug, to a drug for treatment with a specific drug.
  • the increase in sensitivity is the degree to which the concentration exhibiting effects such as growth inhibition and apoptosis of cancer cells that have acquired resistance is equal to or higher than the concentration exhibiting effects such as growth inhibition on non-resistant cancer cells means to reach Synonyms with overcoming the tolerance include "resistance suppression”, “resistance release”, “resistance release” and "sensitivity enhancement” and the like.
  • the term “metastasis cancer” refers to a cancer that is caused by cancer cells moving from a primary organ to another organ and proliferating.
  • the spread of cancer to other parts of the body can be largely divided into growth of cancer tissue from the primary cancer and directly invading surrounding organs, and distant metastasis along blood vessels or lymphatic vessels to other organs far away.
  • it may mean that the cancer has metastasized to the stomach organs from other primary cancers, but is not limited thereto.
  • prevention may include, without limitation, any action that blocks cancer symptoms or suppresses or delays cancer symptoms using the pharmaceutical composition of the present invention.
  • treatment may include, without limitation, any action in which cancer symptoms are improved or beneficial by examining the pharmaceutical composition of the present invention.
  • the pharmaceutical composition of the present invention may be used not only in the form of an anticancer agent, but also in the form of an adjuvant for the anticancer agent.
  • the pharmaceutical composition of the present invention may be additionally administered in combination with other anticancer agents, thereby further enhancing the growth inhibitory effect on cancer cells.
  • the anticancer agent includes nitrogen mustard, imatinib, oxaliplatin, 5FU, rituximab, erlotinib, neratinib, lapatinib, gefitinib, vandetanib, nirotinib, semasanib, bosutinib, axitinib, Cediranib, restautinib, trastuzumab, gefitinib, bortezomib, sunitinib, carboplatin, bevacizumab, cisplatin, cetuximab, viscumalbum, asparaginase, tretinoin, hydroxycarbamide , Dasatinib, estramustine, gemtuzumab ozogamicin, ibritumomab tuccetan, heptaplatin, methylaminolevulinic acid, amsacrine, alemtuzumab, procarba
  • the pharmaceutical composition may be characterized in the form of capsules, tablets, granules, injections, ointments, powders or drinks, and the pharmaceutical composition may be characterized in that it is targeted to humans.
  • the pharmaceutical composition of the present invention is not limited thereto, but each can be formulated in the form of oral dosage forms such as powders, granules, capsules, tablets, aqueous suspensions, external preparations, suppositories, and sterile injection solutions according to conventional methods.
  • the pharmaceutical composition of the present invention may include a pharmaceutically acceptable carrier.
  • Pharmaceutically acceptable carriers may include binders, lubricants, disintegrants, excipients, solubilizers, dispersants, stabilizers, suspending agents, dyes, fragrances, etc. for oral administration, and in the case of injections, buffers, preservatives, pain-freezing agents A topical agent, solubilizer, isotonic agent, stabilizer, etc.
  • the dosage form of the pharmaceutical composition of the present invention can be prepared in various ways by mixing with a pharmaceutically acceptable carrier as described above.
  • a pharmaceutically acceptable carrier as described above.
  • it can be prepared in the form of tablets, troches, capsules, elixirs, suspensions, syrups, wafers, etc., and in the case of injections, it can be prepared in the form of unit dose ampoules or multiple doses. have.
  • it can be formulated as a solution, suspension, tablet, capsule, sustained release formulation, and the like.
  • suitable carriers, excipients and diluents for formulation include lactose, dextrose, sucrose, sorbitol, mannitol, xylitol, erythritol, malditol, starch, acacia gum, alginate, gelatin, calcium phosphate, calcium silicate, Cellulose, methyl cellulose, microcrystalline cellulose, polyvinylpyrrolidone, water, methylhydroxybenzoate, propylhydroxybenzoate, talc, magnesium stearate or mineral oil may be used.
  • it may further include a filler, an anti-agglomeration agent, a lubricant, a wetting agent, a flavoring agent, an emulsifier, a preservative, and the like.
  • the route of administration of the pharmaceutical composition according to the present invention is not limited thereto, but oral, intravenous, intramuscular, intraarterial, intramedullary, intrathecal, intracardiac, transdermal, subcutaneous, intraperitoneal, intranasal, intestinal, topical , sublingual or rectal. Oral or parenteral administration is preferred.
  • parenteral includes subcutaneous, intradermal, intravenous, intramuscular, intraarticular, intrasynovial, intrasternal, intrathecal, intralesional and intracranial injection or infusion techniques.
  • the pharmaceutical composition of the present invention may also be administered in the form of a suppository for rectal administration.
  • the pharmaceutical composition of the present invention depends on several factors including the activity of the specific compound used, age, weight, general health, sex, formula, administration time, administration route, excretion rate, drug formulation, and the severity of the specific disease to be prevented or treated.
  • the dosage of the pharmaceutical composition may vary depending on the patient's condition, weight, disease severity, drug form, administration route and period, but may be appropriately selected by those skilled in the art, and 0.0001 to 50 mg/day kg or 0.001 to 50 mg/kg. Administration may be administered once a day, or may be administered in several divided doses. The above dosage does not limit the scope of the present invention in any way.
  • the pharmaceutical composition according to the present invention may be formulated as pills, dragees, capsules, solutions, gels, syrups, slurries, and suspensions.
  • ZNF667-AS1 ZNF667 Antisense RNA 1 (Head To Head)
  • RP11-572C15.6 FENDRR (FOXF1 Adjacent Non-Coding Developmental Regulatory RNA)
  • ACTA2 Antisense RNA a method for preventing or treating cancer, comprising administering an effective amount of an expression inhibitor specific for at least one of -AS1 (ACTA2 Antisense RNA 1).
  • cancer comprising administering to an individual in need of administration an expression inhibitor specific for at least one of ZNF667-AS1, RP11-572C15.6, FENDRR and ACTA2-AS1 in an effective amount It relates to a method for inhibiting invasive or metastatic infiltration.
  • an anticancer agent comprising administering to an individual in need of administration, an expression inhibitor specific for at least one of ZNF667-AS1, RP11-572C15.6, FENDRR and ACTA2-AS1 in an effective amount It relates to a method of enhancing sensitivity to
  • the "individual” refers to an individual having cancer or suspected of having cancer, and refers to mammals including mice, livestock, etc. do.
  • composition according to the present invention when used, it is possible to effectively prevent, ameliorate or treat gastric cancer among cancers, as well as inhibit the invasiveness and metastasis of cancer cells, particularly gastric cancer cells.
  • composition of the present invention when used, it is possible to overcome resistance of resistant cancer by enhancing sensitivity to anticancer agents, and furthermore, to prevent or treat resistant cancer.
  • Each data is presented in matrix form, with rows representing individual genes and columns representing each tissue.
  • each cell represents the expression level of a gene in an individual tissue, and red and green represent the relative high and low expression levels represented by scale bars (log2 conversion scale).
  • Fig. 2 shows the prognostic relevance of LNC6 subtypes
  • Figure 2b shows a phylogenetic tree in the predictive model, and the patients were classified into subtypes with high predictability.
  • OS overall survival
  • RFS recurrence-free survival
  • RFS recurrence-free survival period
  • Fig. 4 relates to a subset of L6C anticancer drug resistance and epithelial phenotype
  • This analysis included AJCC stage II, III, or IV patients without primary metastasis.
  • CTX relapse-free survival
  • Figure 5a shows the responsiveness to pembrolizumab according to the LNC6 subtype, and
  • Figures 5b and 5c show the therapeutic responsiveness
  • the predictability of L6C subtypes and L6F subtypes is shown in those who show and those who show non-reactivity.
  • Figure 5d shows the normalized enrichment score (NES) of the up-regulated lncRNA in the L6E subtype in the treatment-responsive and non-responsive subjects.
  • CR means complete response
  • PR means partial response
  • SD stable disease
  • PD means progressive disease.
  • Figure 6 shows the cell type components in each LNC6 subtype
  • Figures 6a and 6b are the averaged xCell scores of TCGA cohort samples in each LNC6 subtype
  • Figure 6a shows the 5 cell type family components in each LNC6 subtype.
  • Figure 6b shows the components of 64 cell types in each LNC6 subtype.
  • FIG. 7 shows in vitro demonstration of the relationship between lncRNA and stem-like features
  • Figure 7b is the result of analyzing the ZNF667-AS1 knockdown efficiency by qRT-PCR after siRNA transformation in the EMT subtype gastric cancer cell line
  • Figure 7f shows the results of Western blot analysis using the EMT marker protein shown in the siRNA-transformed EMT subtype gastric cancer cell line
  • Figure 7g shows the MTS assay of oxaliplatin or 5FU in the siRNA-transformed EMT subtype gastric cancer cell line. shows the half maximal inhibitory concentration (IC 50 ) from
  • X-axis is LNC6 subtype
  • Y-axis is arranged in hierarchical clustering.
  • the 725 gastric developmental TFs identified at the level of mRNA abundance the 723 TFs whose expression levels were available in the TCGA cohort were shown. included in the analysis. TFs highly expressed in the early embryonic stage were classified into Group 1, and TFs highly expressed in the late embryonic stage or maturation stage were classified into Group 2, and the Y-axis was arranged from top to bottom according to the standard deviation in the TF groups and samples.
  • FIG. 11 shows specific gene mutations and copy number changes associated with the LNC6 subtype
  • FIG. 12 relates to the differential methylation of miRNA and protein expression and DNA in the TCGA STAD cohort
  • Figures 12a to 12c are multiple 2 to confirm the subtype-specific methylation of miRNA and protein expression and DNA in the TCGA data set -
  • Rho Spearman correlation coefficients
  • ZNF667-AS1 ZNF667 Antisense RNA 1 (Head To Head)
  • RP11-572C15.6 FENDRR (FOXF1 Adjacent Non-Coding Developmental Regulatory RNA)
  • ACTA2-AS1 ACTA2 Antisense RNA 1
  • a pharmaceutical composition for preventing or treating cancer comprising an expression inhibitor specific to at least one of them as an active ingredient.
  • ZNF667-AS1, RP11-572C15.6, FENDRR and comprising an expression inhibitor specific to at least one of ACTA2-AS1 as an active ingredient, a pharmaceutical composition for inhibiting invasiveness or metastasis of cancer it's about
  • a pharmaceutical composition for overcoming resistance of resistant cancer comprising an expression inhibitor specific to at least one of ZNF667-AS1, RP11-572C15.6, FENDRR and ACTA2-AS1 as an active ingredient it's about
  • ZNF667-AS1, RP11-572C15.6, FENDRR, and containing an expression inhibitor specific for at least one of ACTA2-AS1 as an active ingredient, resistant or metastatic cancer prevention or treatment It relates to a pharmaceutical composition.
  • each of the ZNF667-AS1, RP11-572C15.6, FENDRR and ACTA2-AS1 is a long non-coding RNA gene (lncRNA), and the ZNF667-AS1 may be represented by SEQ ID NO: 1
  • the RP11-572C15.6 may be represented by SEQ ID NO: 2
  • the FENDRR may be represented by SEQ ID NO: 3
  • the ACTA2-AS1 may be represented by SEQ ID NO: 4, but is not limited thereto.
  • a total of 12,727 lncRNA expression profiles and mRNA expression profiles were downloaded from the TCGA gastric adenocarcinoma (STAD) cohort consisting of 258 tumors, and then converted to a log2 base. Somatic mutations, copy-number alteration (CNA) and clinical data of TCGA STAD were downloaded from cBioPortal for Cancer Genomics. DNA methylation, miRNA expression and protein expression data from reverse phase protein array (RPPA) were downloaded from the UCSC Xena platform.
  • STAD gastric adenocarcinoma
  • Cluster analysis and visualization of lncRNA data were performed through Gene Cluster 3.0 and Java TreeView.
  • 258 TCGA STAD patients were classified into 6 clusters: 25 as L6A, 66 as L6B, 51 as L6C, 51 as L6D, 14 as L6E, and 51 as L6F.
  • multiple two-class t tests were performed on all possible combinations of the six subtypes.
  • five 2-sample t-tests were performed (L6A vs. L6B, L6A vs. L6C, L6A vs. L6D, L6A vs.
  • L6E, and L6A vs. L6A vs. L6A. L6F comparison) (P ⁇ 0.05).
  • lncRNAs with significant differences in expression in the 5 possible comparisons corresponded to the following 262 subtype-specific lncRNAs: 24 L6A, 67 L6B, 20 L6C, 55 L6D , 30 were classified as L6E, and 66 as L6F.
  • the lncRNA subtype signature was converted into an mRNA subtype signature by identifying the mRNA whose expression is specific to the LNC6 subtype, and the mRNA signature was independently verified using the mRNA expression data. applied to the cohort. Subtype-specific mRNA expression signatures were confirmed by multiple two-class t tests. For subtype L6A selection, five two-sample t-tests were performed (L6A vs. L6B, L6A vs. L6C, L6A vs. L6D, L6A vs. L6E, and L6A vs. L6F comparisons) (P ⁇ 0.001). .
  • the top 200 mRNAs were selected for each subtype according to the log ratio. Genes with significant differences in 4 comparisons were considered subtype-specific if the number of genes with significantly different expression in 5 possible comparisons was less than 200.
  • BCCP Bayesian compound covariate predictor
  • BCCP model was constructed based on lncRNA expression data in TCGA cohort for LNC6 subtype prediction in immunotherapy cohort and cancer cell line. Due to differences in the reference genome annotation version in the dataset, only 241 of the 262 subtype-specific lncRNAs were used.
  • lncRNA expression was analyzed from raw RNA sequencing data.
  • Pembrolizumab and 29 DNA-fingerprint GC cell lines were performed on 45 samples obtained from patients with metastatic GC who participated in Phase 2 clinical trials. Reads were aligned with the reference human genome GRCh38 according to the methods of the International Cancer Genome Consortium using STAR 2.6.0c.
  • Uniquely mapped reads for each non-coding RNA were calculated using the Rsubread package (ver. 1.34.0) with Gencode annotation (Release 22). Fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated according to its definition using R ( https://www.r-project.org/).
  • TCGA subtypes and microsatellite instability (MSI) status were defined.
  • the BCCP model was applied to predict the benefits of different molecular subtypes and immunotherapy.
  • GIST gastrointestinal stromal tumor
  • ACRG Asian Cancer Research Group
  • ssGSEA Single-sample GSEA
  • GSEA Gene Set Enrichment Analysis
  • IPA Ingenuity Pathway Analysis
  • TCGA cohort transcripts by a gene signature-based method (xCell).
  • the 64 cell types were grouped into 5 cell type families, and the score of each cell type family was calculated as the sum of the cell type scores it contained.
  • Stem cell ability for each subtype was evaluated from the expression level of transcription factors that are expressed differently in the developmental stage of the mouse stomach.
  • 725 gastric developmental transcription factors identified at the mRNA abundance level 723 of the available expression level values in the TCGA cohort were used for analysis.
  • Each subtype cell cycle phase was evaluated from the expression level of S-phase abundant lncRNA identified by initial RNA capture sequencing.
  • lncRNA-mediated transcriptional network changes identified in LncRNA Modulator Atlas in Pan-cancer LncMAP
  • altered lncRNA-transcription factor gene triplets for each cancer type were identified by integrating paired lncRNA and gene expression profiles with genome-wide transcriptional regulation. Thereafter, only triplets containing immune-related genes obtained from the ImmPort project were used for analysis (17,572 triplets in STAD). The degree of immune regulation was defined as the number of triplets composed of each lncRNA.
  • CNA genes from TCGA cohort data were filtered by Q-value ( ⁇ 0.25) and frequency (>5%).
  • DNA methylation data were filtered to standard deviation >0.15, and if there was a significant difference in ⁇ -values in all five possible comparisons (P ⁇ 0.01), it was considered subtype specific, and a total of 38,476 subtype specific probes were identified.
  • L6A was 451, L6B 773, L6C 84, L6D 10, L6E 28,803, and L6F 8,355.
  • miRNA data were filtered for missing values ( ⁇ 20% of cohorts) and were considered subtype-specific if there was a significant difference (P ⁇ 0.05) in all five possible comparisons, and 143 subtype-specific miRNAs were identified: 17 L6A, 4 L6B, 0 L6C, 4 L6D, 8 L6E, and 110 L6F.
  • Proteins with a significant difference (P ⁇ 0.05) in all five possible comparisons were considered subtype-specific, resulting in a total of 40 subtype-specific proteins: 3 for L6A, 1 for L6B, 0 for L6C, 1 L6D, 10 L6E, and 25 L6F.
  • HM450 probes were annotated to lncRNA genes. Gene fusion cases were downloaded from the TCGA cohort, and data on gene fusion among 258 patients were available for 183 patients.
  • the gastric cancer cell line was cultured in RPMI-1640 medium containing 10% fetal bovine serum and penicillin/streptomycin (100ug/L each), wherein the culture was performed in a humidified incubator containing 5% CO 2 37 It was carried out under temperature conditions of °C.
  • ZNF667-AS1 knockdown by siRNA (Thermofisher Scientific) shown in Table 1 was performed using mirus transformation reagent (Mirus bio).
  • Cancer cells transformed with si-non-target or si-ZNF667-AS1 were inoculated into 96-well plates at an amount of 2X10 3 cells/well and cultured overnight before drug treatment, and 20uL CellTiter 96 AQueous One solution per well (MTS, Promega ) was maintained in the presence of drug for 72 h before addition. After incubating the plate for 3 hours, absorbance was measured at 490 nm using an ELISA reader (Bio tek).
  • a 24-well plate containing an 8-um-pore size chamber insert (Corning Costar) was used. did 2 X 10 5 cells in 200uL FBS-free culture medium were loaded into each filter insert (upper chamber), 700uL of culture medium containing 10% FBS was added to each lower chamber, and cultured at 37°C for 16 hours. did After harvesting, the bottom of the insert was fixed and dyed with crystal violet. The number of migrating or infiltrating cells was measured using an EVOS M7000 imaging system (Thermofisher Scientific).
  • the primary antibodies used were: ZNF667 (1:2000, Abcam, ab106432), N-Cadherin (1:1000, Cell signaling, 4061S), E-Cadherin (1:1000, Cell signaling, 14472S), Vimentin (1:1000, Cell signaling, 5741) and GAPDH (1:1000, Sigma, G9545). After washing 5 times with TBS-T, the blots were incubated with mustard radish hydrogen peroxide-conjugated secondary antibody and visualized with enhanced chemi-luminescence detection (ECL plus kit, Pierce).
  • lncRNA genes with unique expression for each subtype were identified: a total of 262 lncRNAs with distinct expression in the six subtypes corresponded to a total of 262 (Fig. 1b; Table 3).
  • LNC6 subtypes in the TCGA cohort represent sex, ethnicity, tumor location and stage of cancer, histological grade, and Loren subtype (Table 4).
  • the majority of L6A and L6E patients were male (84% and 100%).
  • the majority of L6A and L6D patients were from Western countries (96% and 92%).
  • Such ethnic differences were not found in the molecular subtypes of gastric cancer.
  • L6A patients had the highest proportion of the proximal part of the tumor (36%), whereas L6F patients had the lowest proportion (10%).
  • gastric cancer is usually diagnosed after advanced stage in Western countries, L6A subtype tumors showed a relatively low cancer stage.
  • L6C tumors also showed relatively low cancer stage, but L6E and L6F tumors showed high stage and histological grade.
  • the L6F subtype was rich in the diffuse subtype in the Loren classification.
  • the L6C probability corresponds to a positive predictive marker of response to immunotherapy
  • the L6F probability corresponds to a negative predictive marker of response to immunotherapy.
  • the deviation corresponds to 0 or 1, so that the predicted probability of the L6E subtype does not stratify immunotherapy responders and non-responders, although it is specifically upregulated in the L6E subtype.
  • L6F tumors are predicted to consist of stromal cells, that is, lymphoid epithelial cells, fibroblasts, chondrocytes, pericytes, and adipocytes, suggesting that the immune response is limited in L6F tumors (Fig. 6b). ).
  • L6F subtype showed the most significant association with clinical outcomes such as poor prognosis, early recurrence, and resistance to chemotherapy.
  • L6F-like gastric cancer cell lines were identified by applying BCCP predictors for L6F subtype to lncRNA expression data from 29 gastric cancer cell lines.
  • L6F probability showed a high correlation with epithelial-mesenchymal transition (EMT) subtype (Fig. 7a).
  • EMT epithelial-mesenchymal transition
  • L6A subtype was expressed through activation of metabolic pathways such as glycosylation, oxidative phosphorylation and fatty acid metabolism.
  • Hepatocyte nuclear factor-4 ⁇ (HNF4 ⁇ ) was predicted to be the most important upstream regulator of L6A.
  • the L6C subtype is associated with activation of the G2M checkpoint, E2F target, DNA repair, MYC target and MTORC1 signal, while the L6D subtype is associated with protein release and activation of KRAS signaling.
  • the L6E subtype is associated with the activation of an interferon response that maintains the activated immunity of the L6E subtype.
  • the L6F subtype is associated with activation of Wnt/ ⁇ -catenin signaling, TGF- ⁇ signaling, EMT, and angiogenesis.
  • TGF- ⁇ and Twist1 which are major regulators of EMT, are known as upstream regulators of the L6F subtype.
  • the molecular characteristics of the LNC6 subtype were further investigated using genomic and proteome data from TCGA data.
  • the L6B subtype was defined as a high copy number change, and only some genes were expressed differently among the LNC6 subtypes (Fig. 11a).
  • the L6C subtype is characterized by a high mutation burden, and many genes were mutated differently among the LNC6 subtypes (Fig. 11b).
  • the L6E subtype was characterized by a hypermethylation pattern (Fig. 12a), and the L6F subtype was characterized by the most distinct expression pattern of miRNAs and proteins (Figs. 12b and 12c) and a recurrent (15.4%) CLDN18-ARHGAP fusion.
  • the epigenetic background of subtype-specific lncRNAs and the identified epigenetic regulated lncRNAs were identified ( FIG. 13 ).
  • L6A and L6B subtypes were abundant in chromosomal instability (CIN) and microsatellite stability (MSS) subtypes.
  • the L6C subtype was abundant in the microsatellite instability (MSI) subtype, and the L6D subtype was mixed with a number of other molecular subtypes.
  • the L6E subtype corresponded to 100% Epstein-Barr virus (EBV) subtype, and the L6F subtype was abundant in the genetically stable (GS) subtype, the MP subtype and the EMT subtype.
  • An object of the present invention is to provide a composition capable of preventing or treating gastric cancer among cancers, or inhibiting invasiveness or metastasis of gastric cancer cells.

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Abstract

La présente invention se rapporte à une composition qui peut prévenir ou traiter le cancer, en particulier le cancer gastrique, inhiber l'invasion ou la métastase de cellules cancéreuses gastriques, et améliorer la sensibilité aux médicaments anticancéreux.
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Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN113999918A (zh) * 2021-12-31 2022-02-01 北京大学人民医院 结直肠癌远端转移特异性长链非编码rna标记物linc01871及其检测试剂盒
CN114886910A (zh) * 2022-06-21 2022-08-12 上海市同仁医院 Linc00938在神经细胞凋亡中的应用
CN115786513A (zh) * 2022-11-25 2023-03-14 徐州医科大学 Itga8在拉帕替尼耐药的her2阳性胃癌诊断、治疗中的应用

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2024181737A1 (fr) * 2023-02-28 2024-09-06 아주대학교산학협력단 Utilisation de n6-méthyladénosine modifiée rp11-108 m9.4 pour le diagnostic ou le traitement du cancer du foie récurrent

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107213161A (zh) * 2017-05-27 2017-09-29 西南交通大学 长链非编码rna rp11‑224o19.2抑制剂的用途
CN109988765A (zh) * 2019-03-29 2019-07-09 中国医科大学附属盛京医院 一种fendrr基因的靶向抑制剂及其用途

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2019157345A1 (fr) * 2018-02-09 2019-08-15 The Broad Institute, Inc. Compositions et procédés de caractérisation du cancer de la vessie

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107213161A (zh) * 2017-05-27 2017-09-29 西南交通大学 长链非编码rna rp11‑224o19.2抑制剂的用途
CN109988765A (zh) * 2019-03-29 2019-07-09 中国医科大学附属盛京医院 一种fendrr基因的靶向抑制剂及其用途

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DONG ZHIMING, LI SHENGMIAN, WU XUAN, NIU YUNFENG, LIANG XIAOLIANG, YANG LIU, GUO YANLI, SHEN SUPENG, LIANG JIA, GUO WEI: "Aberrant hypermethylation-mediated downregulation of antisense lncRNA ZNF667-AS1 and its sense gene ZNF667 correlate with progression and prognosis of esophageal squamous cell carcinoma", CELL DEATH & DISEASE, vol. 10, no. 12, 1 December 2019 (2019-12-01), pages 930, XP055871273, DOI: 10.1038/s41419-019-2171-3 *
ZHOU RU‑JIAN, LV HUI‑ZENG: "Knockdown of ACTA2‑AS1 promotes liver cancer cell proliferation, migration and invasion", MOLECULAR MEDICINE REPORTS, SPANDIDOS PUBLICATIONS, GR, GR , XP055871275, ISSN: 1791-2997, DOI: 10.3892/mmr.2019.9856 *
ZHU YUNHENG, ZHANG XIAOHUA, WANG LIFENG, ZHU XIUXIANG, XIA ZIYIN, XU LING, XU JUN: "FENDRR suppresses cervical cancer proliferation and invasion by targeting miR-15a/b-5p and regulating TUBA1A expression", CANCER CELL INTERNATIONAL, vol. 20, no. 1, 1 December 2020 (2020-12-01), XP055871274, DOI: 10.1186/s12935-020-01223-w *

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN113999918A (zh) * 2021-12-31 2022-02-01 北京大学人民医院 结直肠癌远端转移特异性长链非编码rna标记物linc01871及其检测试剂盒
CN114886910A (zh) * 2022-06-21 2022-08-12 上海市同仁医院 Linc00938在神经细胞凋亡中的应用
CN114886910B (zh) * 2022-06-21 2023-09-22 上海市同仁医院 Linc00938在神经细胞凋亡中的应用
CN115786513A (zh) * 2022-11-25 2023-03-14 徐州医科大学 Itga8在拉帕替尼耐药的her2阳性胃癌诊断、治疗中的应用
CN115786513B (zh) * 2022-11-25 2023-09-19 徐州医科大学 Itga8在拉帕替尼耐药的her2阳性胃癌诊断、治疗中的应用

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