{"id":"hum0201","version":2,"url":"https://humandbs.dbcls.jp/research/hum0201/v2","datePublished":"2020-10-06","versions":[{"version":1,"datePublished":"2019-12-20"},{"version":2,"datePublished":"2020-10-06"},{"version":3,"datePublished":"2020-11-20"},{"version":4,"datePublished":"2021-11-19"},{"version":5,"datePublished":"2022-06-06"},{"version":6,"datePublished":"2022-08-05"},{"version":7,"datePublished":"2022-12-27"},{"version":8,"datePublished":"2024-08-28"},{"version":9,"datePublished":"2026-04-21"}],"title":{"ja":"ヒト腫瘍試料の収集・分譲とゲノム情報を利用した研究 / 既存試料の分譲とゲノム情報を利用した研究 / 消化器慢性炎症性疾患における遺伝子変異の検索","en":"Collection and transfer of human tumor samples and research using genomic information / Transfer of existing samples and research using genomic information / Reseach of searching gene mutations in gastrointestinal chronic inflammatory diseases"},"summary":{"aims":{"ja":"消化管上皮細胞の、正常組織・炎症組織（消化器炎症性疾患）・腫瘍組織のゲノム解析による形質上の相違の探索","en":"Search for differences in genomics and traits among normal cells, digestive non-tumor cells (inflammatory cells), and tumor cells"},"methods":{"ja":"JGAS000199：腸管上皮細胞の疾患組織（腫瘍・炎症部位）および正常組織から樹立したオルガノイド、末梢血、および、疾患組織から抽出したDNAを用いたWhole Exome sequencing解析\nJGAS000237：腫瘍性疾患の腫瘍組織および非腫瘍組織より樹立したオルガノイドおよび末梢血から抽出したDNA、RNAを用いたWhole Genome sequencing解析、RNA sequencing解析\nJGAS000256：培養液のローテーションによる遺伝子発現変化の検出を目的とした、2D培養した正常十二指腸オルガノイドから抽出したRNAを用いたRNA sequencing解析\nJGAS000378：大腸腫瘍組織および非腫瘍組織由来のオルガノイドならびにBromodomain and extraterminal（BET）ブロモドメイン選択的阻害（(+)-JQ1）を添加した大腸腫瘍組織および非腫瘍組織由来のオルガノイドを用いたRNA sequencing解析、ならびにChIP sequencing解析\nJGAS000350：大腸腫瘍由来のオルガノイドを用いたRNA sequencing解析\nJGAS000550：腫瘍性疾患を有する患者の正常大腸組織を用いたsingle cell RNA sequencing解析および正常大腸オルガノイドを用いたRNA sequencingとWhole Exome sequencing解析\nJGAS000719：膵がん組織周辺の正常膵管オルガノイドを対象とし、CRISPR-Cas9を用いてがん遺伝子を編集した遺伝子改変オルガノイド、および、膵がん腫瘍組織由来のオルガノイドから抽出したDNA、RNAを用いたWhole Exome sequencing解析、RNA sequencing解析、single cell RNA sequencing解析、ATAC sequencing解析、ならびにChIP sequencing解析\nJGAS000881：十二指腸腫瘍、正常十二指腸、正常回腸、正常大腸より樹立したオルガノイド、ならびに、正常回腸、正常大腸より樹立したオルガノイドに遺伝子改変を加えたオルガノイドから抽出したDNA、RNAを用いたWhole Exome sequencing解析、RNA sequencing解析","en":"JGAS000199: The organoids were established from epithelial tissues from patients, and cultured. DNAs were extracted from the organoids and peripheral blood cells. Whole exome sequencing analysis was performed to identify the somatic mutations.\nJGAS000237: Organoids were established from tissue samples (normal and cancer) obtained from any cancer patients. The organoids were cultured, and DNA / RNA was extracted from the organoids for whole genome / RNA sequencing analysis to identify the somatic mutations. Blood samples were substituted when normal tissue samples were not available.\nJGAS000256: RNA was extracted from the 2D-cultured normal duodenal organoids with or without medium rotation. RNA sequencing was performed to identify the changes in gene expression after culture medium rotation.\nJGAS000378: RNA sequencing and Chip-seq analysis for the organoids derived from colon cancer tissues and a normal epithelial tissue from patients\nJGAS000350: RNA sequencing analysis for the organoids derived from colon cancer tissues\nJGAS000550: single cell RNA sequencing analysis for normal colonic tissue and RNA sequencing or Whole Exome sequencing analyses for the organoids derived from healthy normal colonic tissues in the neoplastic disease patient\nJGAS000719: Organoids were derived from surgically resected specimens, endoscopic ultrasound-guided fine needle aspiration samples, brushing samples, pleural effusion, and ascites of patients with pancreatic cancer. Genetically engineered human pancreatic duct organoids were made by introducing cancer gene mutations in duct organoids using CRISPR-Cas9. DNAs/RNAs were extracted from the organoids for whole exome sequencing, RNA sequencing, single cell RNA sequencing, ATAC sequencing, and ChIP sequencing analyses.\nJGAS000881: Organoids were established from the tumor and normal counterpart of patients with duodenal tumor. Also, organoids were established from healthy ileum, colon or duodenum of patients with colon cancer, stomach cancer or a healthy individual and were further genetically engineered with CRISPR-Cas9. DNAs/RNAs were extracted from the organoids for whole exome sequencing and RNA sequencing analyses."},"targets":{"ja":"JGAS000199：潰瘍性大腸炎29症例、腫瘍を併発する潰瘍性大腸炎26症例、下部消化管内視鏡検査を受けた健常者16名\nJGAS000237：腫瘍性疾患23症例\nJGAS000256：腫瘍性疾患1症例1検体の正常十二指腸組織\nJGAS000378：腫瘍性疾患4症例の腫瘍組織4検体および非腫瘍組織 （正常大腸上皮）1検体\nJGAS000350：腫瘍性疾患2症例11検体（1症例から2検体、もう1症例から9検体）\nJGAS000550：腫瘍性疾患3症例17検体の正常大腸組織\nJGAS000719：膵がん50症例\nJGAS000881：大腸がん3症例、十二指腸腺腫3症例、胃がん1症例、健常者1名","en":"JGAS000199: Controls who underwent colonoscopy, gastrointestinal inflammatory disease patients, and neoplastic disease patients\nJGAS000237: Neoplastic disease patients\nJGAS000256: Normal duodenum tissue from a neoplastic disease patient\nJGAS000378: Colon cancer tissues and a normal epithelial tissue from neoplastic disease patients\nJGAS000350: Neoplastic disease patient\nJGAS000550: Neoplastic disease patient\nJGAS000719: Pancreatic cancer patients\nJGAS000881: Colon cancer patients, duodenal adenoma patients, a stomach cancer patient and a healthy individual"},"url":{"ja":null,"en":null}},"listingSummary":{},"releaseNote":{"ja":"腫瘍性疾患の腫瘍組織および非腫瘍組織より樹立したオルガノイドおよび末梢血から抽出したDNA、RNAを用いたWhole Genome sequecing解析、RNA sequecing解析結果をfastqファイルにて提供する。","en":"DNAs and RNAs extracted from peripheral blood cells and organoids established from normal and cancer tissues of the patients were used for the whole genome and RNA sequencing analysis. Fastq files are provided."},"dataProviders":[{"name":{"ja":"佐藤 俊朗","en":"Toshiro Sato"},"organization":{"name":{"ja":"慶應義塾大学医学部 坂口光洋記念講座（オルガノイド医学）","en":"Department of Organoid Medicine, Keio University School of Medicine"}}}],"researchProjects":[],"grants":[{"title":{"ja":"消化器疾患発症制御を目指した加齢形質変化の理解","en":"Understanding changes in aging traits aimed at controlling the onset of gastrointestinal diseases"},"agency":{"ja":"日本医療研究開発機構（AMED） 老化メカニズムの解明・制御プロジェクト","en":"Project for Elucidating and Controlling Mechanisms of Aging and Longevity, Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP19gm5010002"]},{"title":{"ja":"がん多階層フェノタイプの理解に基づいた先端的創薬システムの開発","en":"Development of advanced drug discovery system based on understanding of cancer multi-level phenotype"},"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":["JP19cm0106206"]},{"title":{"ja":"新しい4次元モデルシステムを用いた腸管線維化疾患の病態解明","en":"Dissecting intestinal fibrogenic diseases by a newly developed 4D disease model system"},"agency":{"ja":"日本医療研究開発機構 革新的先端研究開発支援事業（AMED-CREST）","en":"Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST)"},"grantIds":["JP19gm1210001"]},{"title":{"ja":"オルガノドライブラリーの構築による消化器疾患形質の統合的理解","en":"Gaining Integrative Understanding of Gastrointestinal Disease Phenotypes through Establishment of an Organoid Library"},"agency":{"ja":"科学研究費助成事業 基盤研究（S）","en":"KAKENHI Grant-in-Aid for Scientific Research (S)"},"grantIds":["17H06176"]},{"title":{"ja":"小腸上皮オルガノイドにより創出した移植グラフトの機能解析","en":"Functional analysis of small intestinal epithelial organoid-based transplant graft"},"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":["20H03746"]},{"title":{"ja":"ニッチ構築によるヒト消化器疾患の発症・進展のメカニズムを解き明かす","en":"Elucidating a role of niche construction in pathophysiological mechanism of human digestive diseases"},"agency":{"ja":"科学研究費助成事業 基盤研究（S）","en":"KAKENHI Grant-in-Aid for Scientific Research (S)"},"grantIds":["22H04995"]}],"relatedPublications":[{"title":"Somatic inflammatory gene mutations in human ulcerative colitis epithelium","doi":"https://doi.org/10.1038/s41586-019-1844-5","datasets":["JGAD000284"]},{"title":"An Organoid Biobank of Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping","doi":"https://doi.org/10.1016/j.cell.2020.10.023","datasets":["JGAD000335","JGAD000336"]},{"title":"An organoid-based organ repurposing approach to treat short bowel syndrome","doi":"https://doi.org/10.1038/s41586-021-03247-2","datasets":["JGAD000359"]},{"title":"Organoid screening reveals epigenetic vulnerabilities in human colorectal cancer","doi":"https://doi.org/10.1038/s41589-022-00984-x","datasets":["JGAD000492"]}],"datasets":["JGAD000284","JGAD000335","JGAD000336"],"controlledAccessUsers":[{"principalInvestigator":{"en":"Klaus Kaestner"},"affiliation":{"en":"Institue for Diabetes, Obesity & Metabolism at Unversity of Pennsylvania"},"country":{"ja":"アメリカ合衆国 (ペンシルベニア州)","en":"Pennsylvania, United States"},"researchTitle":{"ja":"Somatic mutation analysis of the pancreas in type 1 diabetes","en":"Somatic mutation analysis of the pancreas in type 1 diabetes"},"periodStart":"2020-04-13","periodEnd":"2021-09-08","datasets":["JGAD000284"]},{"principalInvestigator":{"en":"Ulf Leser"},"affiliation":{"en":"Department of Mathematics and Computer Science, Humboldt-Universitaet zu Berlin"},"country":{"ja":"ドイツ","en":"Germany"},"researchTitle":{"en":"MAPTor-NET: MAPK-mTOR network model driven individualized therapies of pancreatic neuro-endocrine tumors (pNETs)"},"periodStart":"2021-06-08","periodEnd":"2023-06-05","datasets":["JGAD000336"]},{"principalInvestigator":{"ja":"有田 正規","en":"Masanori Arita"},"affiliation":{"ja":"生命情報・DDBJ センター, 国立遺伝学研究所","en":"Bioinformation and DDBJ Center, National Institute of Genetics"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"DDBJ センターと NBDC による JGA 解析データの提供","en":"Provision of processed JGA data analyzed by DDBJ Center and NBDC"},"periodStart":"2021-10-07","periodEnd":"2030-03-31","datasets":["JGAD000284","JGAD000335","JGAD000336","JGAD000359"]},{"principalInvestigator":{"ja":"田沼 延公","en":"Nobuhiro Tanuma"},"affiliation":{"ja":"研究所, 宮城県立がんセンター","en":"Research Institute, Miyagi Cancer Center"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"患者由来オルガノイドを用いた、膵・消化管神経内分泌腫瘍の生物学的特性の解明","en":"Study on biological characters of pancreatic and gastrointestinal neuroendocrine tumors using patient-derived organoids."},"periodStart":"2022-09-22","periodEnd":"2024-11-25","datasets":["JGAD000336"]},{"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":["JGAD000284","JGAD000335","JGAD000336","JGAD000359","JGAD000464","JGAD000492","JGAD000669","JGAD000687","JGAD000852"]},{"principalInvestigator":{"ja":"吉田 健一","en":"Kenichi Yoshida"},"affiliation":{"ja":"がん進展研究分野, 国立がん研究センター","en":"Division of Cancer Evolution, National Cancer Center Research Institute"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"固形腫瘍のゲノム解析に関する多施設共同研究","en":"A multicenter study on genomic analysis of solid tumors"},"periodStart":"2024-08-01","periodEnd":"2028-03-31","datasets":["JGAD000852"]},{"principalInvestigator":{"ja":"山本 拓也","en":"Takuya Yamamoto"},"affiliation":{"ja":"プレシジョン免疫プロジェクト, 国立研究開発法人 医薬基盤・健康・栄養研究所","en":"Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"新規がん抗原の同定に基づく消化器がんおよび悪性黒色腫（メラノーマ）に対するワクチン開発基盤研究\r\n","en":"Basic research for vaccine development against gastrointestinal cancer and malignant melanoma based on the identification of novel cancer antigens\r\n"},"periodStart":"2024-11-12","periodEnd":"2026-03-31","datasets":["JGAD000852"]}]}