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

C. Peraldo-Neia, P. Ostano, G. Cavalloni, Y. Pignochino, D. Sangiolo, L. De Cecco, E. Marchesi, D. Ribero, A. Scarpa, A. M. De Rose, A. Giuliani, F. Calise, C. Raggi, P. Invernizzi, M. Aglietta, G. Chiorino, F. Leone

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: Effective target therapies for intrahepatic cholangiocarcinoma (ICC) have not been identified so far. One of the reasons may be the genetic evolution from primary (PR) to recurrent (REC) tumors. We aim to identify peculiar characteristics and to select potential targets specific for recurrent tumors. Eighteen ICC paired PR and REC tumors were collected from 5 Italian Centers. Eleven pairs were analyzed for gene expression profiling and 16 for mutational status of IDH1. For one pair, 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 in an independent cohort; FANCG is statistically associated with survival in the chol-TCGA dataset. IDH1 was mutated in the RECs of five patients; 4 of them displayed the mutation only in RECs. Deep sequencing performed in one patient confirmed the IDH1 mutation in REC. Conclusions: RECs are enriched for genes involved in EMT, resistance to apoptosis, and cytoskeleton remodeling. Key players of these pathways might be considered druggable targets in RECs. IDH1 is mutated in 30% of RECs, becoming both a marker of progression and a target for therapy.

Original languageEnglish
Article number440
JournalBMC Genomics
Volume19
Issue number1
DOIs
Publication statusPublished - Jun 5 2018

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Cholangiocarcinoma
Epithelial-Mesenchymal Transition
Genes
Cytoskeleton
Neoplasms
Apoptosis
Matched-Pair Analysis
High-Throughput Nucleotide Sequencing
Mutation
Molecular Evolution
Gene Expression Profiling
Proteolysis
Cell Differentiation
Cell Cycle
Epithelial Cells
RNA
Survival
DNA
Therapeutics

Keywords

  • IDH1 mutation
  • Intrahepatic cholangiocarcinoma
  • Microarray
  • Prognostic marker
  • Recurrence

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma. / Peraldo-Neia, C.; Ostano, P.; Cavalloni, G.; Pignochino, Y.; Sangiolo, D.; De Cecco, L.; Marchesi, E.; Ribero, D.; Scarpa, A.; De Rose, A. M.; Giuliani, A.; Calise, F.; Raggi, C.; Invernizzi, P.; Aglietta, M.; Chiorino, G.; Leone, F.

In: BMC Genomics, Vol. 19, No. 1, 440, 05.06.2018.

Research output: Contribution to journalArticle

Peraldo-Neia, C, Ostano, P, Cavalloni, G, Pignochino, Y, Sangiolo, D, De Cecco, L, Marchesi, E, Ribero, D, Scarpa, A, De Rose, AM, Giuliani, A, Calise, F, Raggi, C, Invernizzi, P, Aglietta, M, Chiorino, G & Leone, F 2018, 'Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma', BMC Genomics, vol. 19, no. 1, 440. https://doi.org/10.1186/s12864-018-4829-0
Peraldo-Neia, C. ; Ostano, P. ; Cavalloni, G. ; Pignochino, Y. ; Sangiolo, D. ; De Cecco, L. ; Marchesi, E. ; Ribero, D. ; Scarpa, A. ; De Rose, A. M. ; Giuliani, A. ; Calise, F. ; Raggi, C. ; Invernizzi, P. ; Aglietta, M. ; Chiorino, G. ; Leone, F. / Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma. In: BMC Genomics. 2018 ; Vol. 19, No. 1.
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abstract = "Background: Effective target therapies for intrahepatic cholangiocarcinoma (ICC) have not been identified so far. One of the reasons may be the genetic evolution from primary (PR) to recurrent (REC) tumors. We aim to identify peculiar characteristics and to select potential targets specific for recurrent tumors. Eighteen ICC paired PR and REC tumors were collected from 5 Italian Centers. Eleven pairs were analyzed for gene expression profiling and 16 for mutational status of IDH1. For one pair, 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 in an independent cohort; FANCG is statistically associated with survival in the chol-TCGA dataset. IDH1 was mutated in the RECs of five patients; 4 of them displayed the mutation only in RECs. Deep sequencing performed in one patient confirmed the IDH1 mutation in REC. Conclusions: RECs are enriched for genes involved in EMT, resistance to apoptosis, and cytoskeleton remodeling. Key players of these pathways might be considered druggable targets in RECs. IDH1 is mutated in 30{\%} of RECs, becoming both a marker of progression and a target for therapy.",
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AU - Peraldo-Neia, C.

AU - Ostano, P.

AU - Cavalloni, G.

AU - Pignochino, Y.

AU - Sangiolo, D.

AU - De Cecco, L.

AU - Marchesi, E.

AU - Ribero, D.

AU - Scarpa, A.

AU - De Rose, A. M.

AU - Giuliani, A.

AU - Calise, F.

AU - Raggi, C.

AU - Invernizzi, P.

AU - Aglietta, M.

AU - Chiorino, G.

AU - Leone, F.

PY - 2018/6/5

Y1 - 2018/6/5

N2 - Background: Effective target therapies for intrahepatic cholangiocarcinoma (ICC) have not been identified so far. One of the reasons may be the genetic evolution from primary (PR) to recurrent (REC) tumors. We aim to identify peculiar characteristics and to select potential targets specific for recurrent tumors. Eighteen ICC paired PR and REC tumors were collected from 5 Italian Centers. Eleven pairs were analyzed for gene expression profiling and 16 for mutational status of IDH1. For one pair, 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 in an independent cohort; FANCG is statistically associated with survival in the chol-TCGA dataset. IDH1 was mutated in the RECs of five patients; 4 of them displayed the mutation only in RECs. Deep sequencing performed in one patient confirmed the IDH1 mutation in REC. Conclusions: RECs are enriched for genes involved in EMT, resistance to apoptosis, and cytoskeleton remodeling. Key players of these pathways might be considered druggable targets in RECs. IDH1 is mutated in 30% of RECs, becoming both a marker of progression and a target for therapy.

AB - Background: Effective target therapies for intrahepatic cholangiocarcinoma (ICC) have not been identified so far. One of the reasons may be the genetic evolution from primary (PR) to recurrent (REC) tumors. We aim to identify peculiar characteristics and to select potential targets specific for recurrent tumors. Eighteen ICC paired PR and REC tumors were collected from 5 Italian Centers. Eleven pairs were analyzed for gene expression profiling and 16 for mutational status of IDH1. For one pair, 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 in an independent cohort; FANCG is statistically associated with survival in the chol-TCGA dataset. IDH1 was mutated in the RECs of five patients; 4 of them displayed the mutation only in RECs. Deep sequencing performed in one patient confirmed the IDH1 mutation in REC. Conclusions: RECs are enriched for genes involved in EMT, resistance to apoptosis, and cytoskeleton remodeling. Key players of these pathways might be considered druggable targets in RECs. IDH1 is mutated in 30% of RECs, becoming both a marker of progression and a target for therapy.

KW - IDH1 mutation

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KW - Microarray

KW - Prognostic marker

KW - Recurrence

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