{"id":"hum0268","version":2,"url":"https://humandbs.dbcls.jp/research/hum0268/v2","datePublished":"2025-08-29","versions":[{"version":1,"datePublished":"2021-04-09"},{"version":2,"datePublished":"2025-08-29"}],"title":{"ja":"がん組織を用いたネオアンチゲンスクリーニング","en":"Direct and comprehensive identification of neoantigens using cancer tissues"},"summary":{"aims":{"ja":"がん組織のプロテオゲノミクスHLAリガンドーム解析による新規タイプがん抗原の探索","en":"Proteogenomic discovery of a novel class of cancer antigens by HLA ligandome analysis of colon cancer tissues"},"methods":{"ja":"【ヒト大腸がん細胞株および大腸がん】 RNA-seq、CAGE-seq、ならびにIso-seq解析を実施し、組織解析で同定済みの非コード領域由来新規がん抗原をコードする転写産物バリアントを探索した。\n【子宮体がん】 腫瘍組織を対象としたバルクRNA-seqにより各組織サンプル中で発現する遺伝子群を網羅的解析した。また、腫瘍組織および末梢血のWESにより、症例ごとの体細胞遺伝子変異を検出し、HLAリガンドーム解析と組み合わせてネオ抗原を同定した。さらに、腫瘍浸潤T細胞のシングルセルRNA-seq/TCR-seqから腫瘍反応性の細胞傷害性CD4+T細胞を特定し、これらに特徴的な遺伝子発現パターンを解析した。","en":"[Human colon cancer cell line, colon cancer] RNA-seq, CAGE-seq and Iso-seq data were used to analyze the transcript variants coding an identified non-coding RNA-derived antigen.\n[Endometrial cancer] Bulk RNA-seq of tumor tissues was used to comprehensively analyze the set of genes expressed in each tissue sample. WES of tumor tissue and peripheral blood detected somatic mutations in each case and was combined with HLA ligandome analysis using mass spectrometry to identify neoantigens. Single-cell RNA-seq/TCR-seq of tumor-infiltrating T cells was used to identify tumor-reactive cytotoxic CD4+ T cells and marker genes."},"targets":{"ja":"ヒト大腸がん細胞株：1種類、大腸がん6症例、子宮体がん：5症例","en":"Human colon cancer cell line: 1, colon cancer: 6 cases, endometrial cancer: 5 cases"},"url":{"ja":null,"en":null}},"listingSummary":{"methods":{"ja":"配列\n発現","en":"Sequencing, Expression profiling"},"targets":{"ja":"ヒト大腸癌細胞株：1検体\n（セルライン）\n大腸癌：6症例\n子宮体癌：5症例\n（日本人）","en":"Human colon cancer cell line: 1 sample\n(Cell-line)\nColon cancer: 6 patients\nEndometrial cancer: 5 patients\n(Japanese)"},"typeOfData":{"ja":"NGS\n（Iso-seq、CAGE-seq、RNA-seq、scRNA-seq、scTCR-seq、Exome）","en":"NGS\n(Iso-seq, CAGE-seq, RNA-seq, scRNA-seq, scTCR-seq, Exome)"}},"releaseNote":{"ja":"子宮体がん5症例の腫瘍組織5検体および末梢血5検体から抽出したDNAを用いたWES解析、ならびに、5症例の腫瘍組織5検体を用いたbulkRNA-seq解析データ、ならびに、1症例の腫瘍組織に含まれる腫瘍浸潤T細胞1検体から抽出したRNAを用いたscRNA-seqおよびscTCR-seq解析データをfastqファイルにて提供する。","en":"DNAs extracted from tumor tissues and non-tumor tissues from endometrial cancer patients were used for WES analysis. RNAs extracted from tumor tissues were used for bulk RNA-seq. RNAs extracted from tumor-infiltrating T cells were used for single-cell RNA-seq/TCR-seq analyses. Fastq files are provided."},"dataProviders":[{"name":{"ja":"金関 貴幸","en":"Takayuki Kanaseki"},"organization":{"name":{"ja":"札幌医科大学 病理学第一講座/新潟大学医学部 分子病理学分野","en":"Department of Pathology, Sapporo Medical University/Division of Molecular Pathology, Niigata University School of Medicine"}}}],"researchProjects":[],"grants":[{"title":{"ja":"プロテオゲノミクスによるlncRNAがん抗原を標的とした革新的免疫治療の開発","en":"Proteogenomic discovery of HLA presented tumor antigens that arise from non-coding RNAs"},"agency":{"ja":"日本医療研究開発機構（AMED） 次世代がん医療創生研究事業（P-CREATE）","en":"Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP20cm0106352"]},{"title":{"ja":"NAPプロテオゲノミクス解析基盤によるT細胞腫瘍抗原オミクス研究","en":"Multiomics study of tumor-specific antigens and reactive T cells based on NAP proteogenomics"},"agency":{"ja":"日本医療研究開発機構（AMED） 次世代がん医療加速化研究事業（P-PROMOTE）","en":"Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP24ama221315"]},{"title":{"ja":"新しいネオ抗原検出技術による腫瘍特異的CD4+T細胞の機能解析とがん治療応用","en":"Functional Analysis of Tumor-Specific CD4+ T Cells Using a Novel Neoantigen Detection Technology"},"agency":{"ja":"科学研究費助成事業 基盤研究（B）","en":"KAKENHI Grant-in-Aid for Scientific Research (B)"},"grantIds":["24K02252"]}],"relatedPublications":[{"title":"CD8+ T-cell Immune Surveillance against a Tumor Antigen Encoded by the Oncogenic Long Noncoding RNA PVT1","doi":"https://doi.org/10.1158/2326-6066.CIR-20-0964","datasets":["JGAD000386"]},{"title":"Identification and Phenotypic Characterization of Neoantigen-Specific Cytotoxic CD4+ T Cells in Endometrial Cancer","doi":"https://doi.org/10.1158/2326-6066.CIR-24-0514","datasets":["JGAD000907"]}],"datasets":["JGAD000386","JGAD000907"],"controlledAccessUsers":[{"principalInvestigator":{"ja":"浜田 道昭","en":"Michiaki Hamada"},"affiliation":{"ja":"浜田研究室, 理工学術院, 早稲田大学","en":"Hamada Laboratory, Faculty of Science and Engineering, Waseda University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"RNA標的創薬データベースの構築","en":"Construction of RNA-targeted Drug Discovery Database"},"periodStart":"2023-01-05","periodEnd":"2027-10-31","datasets":["JGAD000386"]}]}