Frequent mutation of isocitrate dehydrogenase (IDH)1 and IDH2 in cholangiocarcinoma identified through broad-based tumor genotyping

Abstract

Cancers of origin in the gallbladder and bile ducts are rarely curable with current modalities of cancer treatment. Our clinical application of broad-based mutational profiling for patients diagnosed with a gastrointestinal malignancy has led to the novel discovery of mutations in the gene encoding isocitrate dehydrogenase 1 (IDH1) in tumors from a subset of patients with cholangiocarcinoma. A total of 287 tumors from gastrointestinal cancer patients (biliary tract, colorectal, gastroesophageal, liver, pancreatic, and small intestine carcinoma) were tested during routine clinical evaluation for 130 site-specific mutations within 15 cancer genes. Mutations were identified within a number of genes, including KRAS (35%), TP53 (22%), PIK3CA (10%), BRAF (7%), APC (6%), NRAS (3%), AKT1 (1%), CTNNB1 (1%), and PTEN (1%). Although mutations in the metabolic enzyme IDH1 were rare in the other common gastrointestinal malignancies in this series (2%), they were found in three tumors (25%) of an initial series of 12 biliary tract carcinomas. To better define IDH1 and IDH2 mutational status, an additional 75 gallbladder and bile duct cancers were examined. Combining these cohorts of biliary cancers, mutations in IDH1 and IDH2 were found only in cholangiocarcinomas of intrahepatic origin (nine of 40, 23%) and in none of the 22 extrahepatic cholangiocarcinomas and none of the 25 gallbladder carcinomas. In an analysis of frozen tissue specimens, IDH1 mutation was associated with highly elevated tissue levels of the enzymatic product 2-hydroxyglutarate. Thus, IDH1 mutation is a molecular feature of cholangiocarcinomas of intrahepatic origin. These findings define a specific metabolic abnormality in this largely incurable type of gastrointestinal cancer and present a potentially new target for therapy.

Conflict of interest statement

Disclosures: Darrell R. Borger: Bio-Reference Laboratories, Inc. (C/A); Kenneth K. Tanabe: None; Kenneth C. Fan: None; Hector U. Lopez: None; Valeria R. Fantin: Agios Pharmaceuticals (E); Coinventor of discovery of neoactivity of IDH1 and IDH2 mutations (IP); Kimberly S. Straley: Agios Pharmaceuticals (E, OI); David P. Schenkein: Agios Pharmaceuticals (E, OI); Aram F. Hezel: Amgen, (H, RF), Bayer (H); Marek Ancukiewicz: None; Hannah M. Liebman: None; Eunice L. Kwak: None; Jeffrey W. Clark: None; David P. Ryan: None; Vikram Deshpande: None; Dora Dias-Santagata: SNaPshot Genotyping Assay (IP); Bio-Reference Laboratories, Inc. (C/A); Leif W. Ellisen: Bio-Reference Laboratories, Inc. (C/A); Andrew X. Zhu: Onyx, ImClone, Novartis, Pfizer, Sanofi (C/A); Bayer (RF); A. John Iafrate: SNaPshot Genotyping Assay (IP); Bio-Reference Laboratories, Inc. (C/A).

Figures

Figure 1.

Mutational profile in biliary tract carcinomas. The frequency of cancer genes mutated in cholangiocarcinoma (blue bars; n = 62) versus gallbladder carcinoma (green bars; n = 25) is shown. Nucleic acids were extracted from formalin-fixed, paraffin-embedded tumor tissue and were tested for mutations using a single-base extension approach.

Figure 2.

The distribution and frequency of profiled mutations across cholangiocarcinoma subtypes. Patient cholangiocarcinoma samples were designated as either intrahepatic (dark-blue bars; n = 40) or extrahepatic (light-blue bars; n = 22) based on surgical record and/or pathological review. Extrahepatic cholangiocarcinomas included tumors arising in the perihilar duct (n = 11), common bile duct (n = 4), or distal bile duct (n = 7) region. Abbreviations: IDH, isocitrate dehydrogenase; KRAS, Kirsten-ras; PTEN, phosphatase and tensin homologue deleted on chromosome ten; TP53, p53 tumor suppressor.

Figure 3.

Mutations in the genes encoding isocitrate dehydrogenase (IDH1 and IDH2) in cholangiocarcinoma are associated with 2-hydroxyglutarate metabolite accumulation. 2-Hydroxyglutarate levels were measured in frozen cholangiocarcinoma specimens using liquid chromatography mass spectrometry analysis. Three tumor samples were wild-type (WT) IDH1 and IDH2, one was IDH1 p.R132C mutation positive, and one was IDH2 p.R172W mutation positive. SNaPshot genotyping electropherograms are shown in the boxes with the mutation peak filled.