Mutation profiling in cholangiocarcinoma: Prognostic and therapeutic implications

Chaitanya R. Churi, Rachna Shroff, Ying Wang, Asif Rashid, Hyun Seon C. Kang, Jacqueline Weatherly, Mingxin Zuo, Ralph Zinner, David Hong, Funda Meric-Bernstam, Filip Janku, Christopher H. Crane, Lopa Mishra, Jean Nicholas Vauthey, Robert A. Wolff, Gordon Mills, Milind Javle, Chad Creighton

Research output: Contribution to journalArticle

155 Citations (Scopus)

Abstract

Background: Cholangiocarcinoma (CCA) is clinically heterogeneous; intra and extrahepatic CCA have diverse clinical presentations. Next generation sequencing (NGS) technology may identify the genetic differences between these entities and identify molecular subgroups for targeted therapeutics.

Methods: We describe successful NGS-based testing of 75 CCA patients along with the prognostic and therapeutic implications of findings. Mutation profiling was performed using either a) NGS panel of hotspot regions in 46 cancer-related genes using a 318-chip on Ion PGM Sequencer or b) Illumina HiSeq 2000 sequencing platform for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes to an average depth of 1000X. Clinical data was abstracted and correlated with clinical outcome. Patients with targetable mutations were referred to appropriate clinical trials.

Results: There were significant differences between intrahepatic (n555) and extrahepatic CCA (n520) in regard to the nature and frequency of the genetic aberrations (GAs). IDH1 and DNA repair gene alterations occurred more frequently in intrahepatic CCA, while ERBB2 GAs occurred in the extrahepatic group. Commonly occurring GAs in intrahepatic CCA were TP53 (35%), KRAS (24%), ARID1A (20%), IDH1 (18%), MCL1 (16%) and PBRM1 (11%). Most frequent GAs in extrahepatic CCA (n520) were TP53 (45%), KRAS (40%), ERBB2 (25%), SMAD4 (25%), FBXW7 (15%) and CDKN2A (15%). In intrahepatic CCA, KRAS, TP53 or MAPK/mTOR GAs were significantly associated with a worse prognosis while FGFR GAs correlated with a relatively indolent disease course. IDH1 GAs did not have any prognostic significance. GAs in the chromatin modulating genes, BAP1 and PBRM1 were associated with bone metastases and worse survival in extrahepatic CCA. Radiologic responses and clinical benefit was noted with EGFR, FGFR, C-met, B-RAF and MEK inhibitors.

Conclusion: There are significant genetic differences between intra and extrahepatic CCA. NGS can potentially identify disease subsets with distinct prognostic and therapeutic implications.

Original languageEnglish (US)
Article numbere115383
JournalPLoS One
Volume9
Issue number12
DOIs
StatePublished - Dec 23 2014
Externally publishedYes

Fingerprint

Cholangiocarcinoma
Aberrations
mutation
therapeutics
Mutation
Genes
Therapeutics
Neoplasm Genes
genes
Mitogen-Activated Protein Kinase Kinases
neoplasms
Introns
Chromatin
Exons
Bone
DNA repair
Repair
disease course
metastasis
prognosis

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Churi, C. R., Shroff, R., Wang, Y., Rashid, A., Kang, H. S. C., Weatherly, J., ... Creighton, C. (2014). Mutation profiling in cholangiocarcinoma: Prognostic and therapeutic implications. PLoS One, 9(12), [e115383]. https://doi.org/10.1371/journal.pone.0115383

Mutation profiling in cholangiocarcinoma : Prognostic and therapeutic implications. / Churi, Chaitanya R.; Shroff, Rachna; Wang, Ying; Rashid, Asif; Kang, Hyun Seon C.; Weatherly, Jacqueline; Zuo, Mingxin; Zinner, Ralph; Hong, David; Meric-Bernstam, Funda; Janku, Filip; Crane, Christopher H.; Mishra, Lopa; Vauthey, Jean Nicholas; Wolff, Robert A.; Mills, Gordon; Javle, Milind; Creighton, Chad.

In: PLoS One, Vol. 9, No. 12, e115383, 23.12.2014.

Research output: Contribution to journalArticle

Churi, CR, Shroff, R, Wang, Y, Rashid, A, Kang, HSC, Weatherly, J, Zuo, M, Zinner, R, Hong, D, Meric-Bernstam, F, Janku, F, Crane, CH, Mishra, L, Vauthey, JN, Wolff, RA, Mills, G, Javle, M & Creighton, C 2014, 'Mutation profiling in cholangiocarcinoma: Prognostic and therapeutic implications', PLoS One, vol. 9, no. 12, e115383. https://doi.org/10.1371/journal.pone.0115383
Churi CR, Shroff R, Wang Y, Rashid A, Kang HSC, Weatherly J et al. Mutation profiling in cholangiocarcinoma: Prognostic and therapeutic implications. PLoS One. 2014 Dec 23;9(12). e115383. https://doi.org/10.1371/journal.pone.0115383
Churi, Chaitanya R. ; Shroff, Rachna ; Wang, Ying ; Rashid, Asif ; Kang, Hyun Seon C. ; Weatherly, Jacqueline ; Zuo, Mingxin ; Zinner, Ralph ; Hong, David ; Meric-Bernstam, Funda ; Janku, Filip ; Crane, Christopher H. ; Mishra, Lopa ; Vauthey, Jean Nicholas ; Wolff, Robert A. ; Mills, Gordon ; Javle, Milind ; Creighton, Chad. / Mutation profiling in cholangiocarcinoma : Prognostic and therapeutic implications. In: PLoS One. 2014 ; Vol. 9, No. 12.
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T2 - Prognostic and therapeutic implications

AU - Churi, Chaitanya R.

AU - Shroff, Rachna

AU - Wang, Ying

AU - Rashid, Asif

AU - Kang, Hyun Seon C.

AU - Weatherly, Jacqueline

AU - Zuo, Mingxin

AU - Zinner, Ralph

AU - Hong, David

AU - Meric-Bernstam, Funda

AU - Janku, Filip

AU - Crane, Christopher H.

AU - Mishra, Lopa

AU - Vauthey, Jean Nicholas

AU - Wolff, Robert A.

AU - Mills, Gordon

AU - Javle, Milind

AU - Creighton, Chad

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N2 - Background: Cholangiocarcinoma (CCA) is clinically heterogeneous; intra and extrahepatic CCA have diverse clinical presentations. Next generation sequencing (NGS) technology may identify the genetic differences between these entities and identify molecular subgroups for targeted therapeutics.Methods: We describe successful NGS-based testing of 75 CCA patients along with the prognostic and therapeutic implications of findings. Mutation profiling was performed using either a) NGS panel of hotspot regions in 46 cancer-related genes using a 318-chip on Ion PGM Sequencer or b) Illumina HiSeq 2000 sequencing platform for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes to an average depth of 1000X. Clinical data was abstracted and correlated with clinical outcome. Patients with targetable mutations were referred to appropriate clinical trials.Results: There were significant differences between intrahepatic (n555) and extrahepatic CCA (n520) in regard to the nature and frequency of the genetic aberrations (GAs). IDH1 and DNA repair gene alterations occurred more frequently in intrahepatic CCA, while ERBB2 GAs occurred in the extrahepatic group. Commonly occurring GAs in intrahepatic CCA were TP53 (35%), KRAS (24%), ARID1A (20%), IDH1 (18%), MCL1 (16%) and PBRM1 (11%). Most frequent GAs in extrahepatic CCA (n520) were TP53 (45%), KRAS (40%), ERBB2 (25%), SMAD4 (25%), FBXW7 (15%) and CDKN2A (15%). In intrahepatic CCA, KRAS, TP53 or MAPK/mTOR GAs were significantly associated with a worse prognosis while FGFR GAs correlated with a relatively indolent disease course. IDH1 GAs did not have any prognostic significance. GAs in the chromatin modulating genes, BAP1 and PBRM1 were associated with bone metastases and worse survival in extrahepatic CCA. Radiologic responses and clinical benefit was noted with EGFR, FGFR, C-met, B-RAF and MEK inhibitors.Conclusion: There are significant genetic differences between intra and extrahepatic CCA. NGS can potentially identify disease subsets with distinct prognostic and therapeutic implications.

AB - Background: Cholangiocarcinoma (CCA) is clinically heterogeneous; intra and extrahepatic CCA have diverse clinical presentations. Next generation sequencing (NGS) technology may identify the genetic differences between these entities and identify molecular subgroups for targeted therapeutics.Methods: We describe successful NGS-based testing of 75 CCA patients along with the prognostic and therapeutic implications of findings. Mutation profiling was performed using either a) NGS panel of hotspot regions in 46 cancer-related genes using a 318-chip on Ion PGM Sequencer or b) Illumina HiSeq 2000 sequencing platform for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes to an average depth of 1000X. Clinical data was abstracted and correlated with clinical outcome. Patients with targetable mutations were referred to appropriate clinical trials.Results: There were significant differences between intrahepatic (n555) and extrahepatic CCA (n520) in regard to the nature and frequency of the genetic aberrations (GAs). IDH1 and DNA repair gene alterations occurred more frequently in intrahepatic CCA, while ERBB2 GAs occurred in the extrahepatic group. Commonly occurring GAs in intrahepatic CCA were TP53 (35%), KRAS (24%), ARID1A (20%), IDH1 (18%), MCL1 (16%) and PBRM1 (11%). Most frequent GAs in extrahepatic CCA (n520) were TP53 (45%), KRAS (40%), ERBB2 (25%), SMAD4 (25%), FBXW7 (15%) and CDKN2A (15%). In intrahepatic CCA, KRAS, TP53 or MAPK/mTOR GAs were significantly associated with a worse prognosis while FGFR GAs correlated with a relatively indolent disease course. IDH1 GAs did not have any prognostic significance. GAs in the chromatin modulating genes, BAP1 and PBRM1 were associated with bone metastases and worse survival in extrahepatic CCA. Radiologic responses and clinical benefit was noted with EGFR, FGFR, C-met, B-RAF and MEK inhibitors.Conclusion: There are significant genetic differences between intra and extrahepatic CCA. NGS can potentially identify disease subsets with distinct prognostic and therapeutic implications.

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