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Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

ABSTRACT: Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

PROVIDER: PRJNA418989 | ENA |

REPOSITORIES: ENA

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Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma [Agilent]

Project description:Purpose: Effective target therapies for intrahepatic cholangiocarcinoma have not been identified so far. One of the reasons may be the molecular and genomic alteration difference between paired primary (PR) and recurrent (REC) tumors. We aim to identify peculiar characteristics and to select potential targets specific for recurrent tumors. Experimental design: Thirteen ICC pairs from Italian patients were collected and analyzed for gene expression profiling and mutational status of IDH1. For two pairs, deep mutational analysis by Next Generation Sequencing was also carried out. An independent cohort of patients was used for validation. Results: Two class paired comparison yielded 315 differentially expressed genes between REC and PR tumors. Up-regulated genes in RECs are involved in RNA/DNA processing, cell cycle, epithelial to mesenchymal transition (EMT), resistance to apoptosis, and cytoskeleton remodeling. Down-regulated genes participate to epithelial cell differentiation, proteolysis, apoptotic, immune response, and inflammatory processes. A 24 gene signature is able to discriminate RECs from PRs, and 9 genes predict recurrence in an independent cohort; FANCG is statistically associated with survival in the chol-TCGA dataset. IDH1 was mutated in the RECs of three patients. In the independent cohort, 2 out of 5 patients displayed the IDH1 mutation only in RECs. Deep sequencing revealed TP53, ASXL1, PTEN and DICER1 novel mutations. Conclusions: RECs displayed more aggressive phenotype; EMT, resistance to apoptosis, and cytoskeleton remodeling were key players and druggable pathways in REC. IDH1 is mutated in about 30% of patients, becoming a marker of progression and a target for therapy.

2018-04-28 | GSE107101 | GEO

Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma [Illumina]

2018-04-28 | GSE107100 | GEO

Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma [Illumina]

Project description:Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma [Illumina]

| PRJNA418992 | ENA

Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma [Agilent]

Project description:Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma [Agilent]

| PRJNA418993 | ENA

Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma.

Project description: Not available

| S-EPMC5989353 | biostudies-literature

Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-04-28 | GSE107102 | GEO

Intrahepatic Cholangiocarcinoma MSKCC

Project description:Cohort of primary tumor and tumor-adjacent non-malignant tissue from 142 intrahepatic cholangiocarcinoma patients and patient-derived xenografts.

2024-07-15 | MSV000095336 | MassIVE

Homo sapiens strain:Intrahepatic cholangiocarcinoma

Project description:Homo sapiens strain:Intrahepatic cholangiocarcinoma Exome

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Mutant IDH1 activates JOSD2-YAP/TAZ in a non-classical manner to sustain intrahepatic cholangiocarcinoma cell growth

Project description:Gain of function mutations in isocitrate dehydrogenase 1 are one of the most common genetic lesions in intrahepatic cholangiocarcinoma (ICC). The mutant IDH1 (mIDH1) causes aberrant metabolic, epigenetic and differentiation process by converting α-ketoglutarate (α-KG) to onco-metabolite 2-hydroxyglutarate (2-HG). However, mIDH1 inhibitor ivosidenib appears much more effective in acute myeloid leukemia than that in ICC, suggesting that in addition to these common mechanisms, other pathways may be also involved. Our results indicated that mIDH1 exhibited high correlation of transcription profiles with JOSD2, a deubiquitinating enzyme reported to stabilize YAP/TAZ by our previous work. Further exploration suggested that mIDH1 up-regulated JOSD2 protein stability independent of 2-HG and couldn’t be intervened by ivosidenib. The targeted silence of JOSD2 exhibited more potent anti-tumor effect in cells with mIDH1 than wild type cells. Together, this study may provide novel insights for understanding the tumor-promoting effects of mIDH1 to derive new therapeutic strategies.

2025-04-30 | GSE231839 | GEO

Mutations in IDH1 and IDH2 are associated with DNA hypermethylation in intrahepatic cholangiocarcinomas

Project description:We compared the DNA methylation profiles of 12 intrahepatic cholangiocarcinomas harboring mutations in the genes encoding isocitrate dehydrogenase, IDH1 and IDH2, with 28 intrahepatic cholangiocarcinomas without these mutations. We profiled these samples with the Illumina HumanMethylation450 BeadChip, and characterized over 2,000 genes that were hypermethylated in tumors with mutations in IDH1 or IDH2. Genomic DNA from fresh frozen tumors was bisulfite converted with the Zymo Research EZ DNA Methylation kit, then hybridized to the Illumina HumanMethylation450 Beadchip.

2012-06-10 | E-GEOD-32079 | biostudies-arrayexpress

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