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Sequencing of intraductal biopsies is feasible and potentially impacts clinical management of patients with indeterminate biliary stricture and cholangiocarcinoma. Clin Transl Gastroenterol 2018; 9:151. [PMID: 29712892 PMCID: PMC5928069 DOI: 10.1038/s41424-018-0015-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 02/08/2023] Open
Abstract
Background Definite diagnosis and therapeutic management of cholangiocarcinoma (CCA) remains a challenge. The aim of the current study was to investigate feasibility and potential impact on clinical management of targeted sequencing of intraductal biopsies. Methods Intraductal biopsies with suspicious findings from 16 patients with CCA in later clinical course were analyzed with targeted sequencing including tumor and control benign tissue (n = 55 samples). A CCA-specific sequencing panel containing 41 genes was designed and a dual strand targeted enrichment was applied. Results Sequencing was successfully performed for all samples. In total, 79 mutations were identified and a mean of 1.7 mutations per tumor sample (range 0–4) as well as 2.3 per biopsy (0–6) were detected and potentially therapeutically relevant genes were identified in 6/16 cases. In 14/18 (78%) biopsies with dysplasia or inconclusive findings at least one mutation was detected. The majority of mutations were found in both surgical specimen and biopsy (68%), while 28% were only present in biopsies in contrast to 4% being only present in the surgical tumor specimen. Conclusion Targeted sequencing from intraductal biopsies is feasible and potentially improves the diagnostic yield. A profound genetic heterogeneity in biliary dysplasia needs to be considered in clinical management and warrants further investigation. Translational impact The current study is the first to demonstrate the feasibility of sequencing of intraductal biopsies which holds the potential to impact diagnostic and therapeutical management of patients with biliary dysplasia and neoplasia.
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152
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Shibata T, Arai Y, Totoki Y. Molecular genomic landscapes of hepatobiliary cancer. Cancer Sci 2018; 109:1282-1291. [PMID: 29573058 PMCID: PMC5980207 DOI: 10.1111/cas.13582] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/03/2018] [Accepted: 03/11/2018] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) and biliary tract cancer are more frequent in East Asia including Japan than in Europe or North America. A compilation of 1340 multi‐ethnic HCC genomes, the largest cohort ever reported, identified a comprehensive landscape of HCC driver genes, comprised of three core drivers (TP53,TERT, and WNT signaling) and combinations of infrequent alterations in various cancer pathways. In contrast, five core driver genes (TP53,ARID1A,KRAS,SMAD4, and BAP1) with characteristic molecular alterations including fusion transcripts involving fibroblast growth factor receptor 2 and the protein kinase A pathway, and IDH1/2 mutation constituted the biliary tract cancer genomes. Consistent with their heterogeneous epidemiological backgrounds, mutational signatures and combinations of non‐core driver genes within these cancer genomes were found to be complex. Integrative analyses of multi‐omics data identified molecular classifications of these tumors that are associated with clinical outcome and enrichments of potential therapeutic targets, including immune checkpoint molecules. Translating comprehensive molecular‐genomic analysis together with further basic research and international collaborations are highly anticipated for developing precise and better treatments, diagnosis, and prevention of these tumor types.
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Affiliation(s)
- Tatsuhiro Shibata
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
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153
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Lim HC, Montesion M, Botton T, Collisson EA, Umetsu SE, Behr SC, Gordan JD, Stephens PJ, Kelley RK. Hybrid Capture-Based Tumor Sequencing and Copy Number Analysis to Confirm Origin of Metachronous Metastases in BRCA1-Mutant Cholangiocarcinoma Harboring a Novel YWHAZ-BRAF Fusion. Oncologist 2018; 23:998-1003. [PMID: 29622700 DOI: 10.1634/theoncologist.2017-0645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/12/2018] [Indexed: 01/07/2023] Open
Abstract
Biliary tract cancers such as cholangiocarcinoma represent a heterogeneous group of cancers that can be difficult to diagnose. Recent comprehensive genomic analyses in large cholangiocarcinoma cohorts have defined important molecular subgroups within cholangiocarcinoma that may relate to anatomic location and etiology [1], [2], [3], [4] and may predict responsiveness to targeted therapies in development [5], [6], [7]. These emerging data highlight the potential for tumor genomics to inform diagnosis and treatment options in this challenging tumor type. We report the case of a patient with a germline BRCA1 mutation who presented with a cholangiocarcinoma driven by the novel YWHAZ-BRAF fusion. Hybrid capture-based DNA sequencing and copy number analysis performed as part of clinical care demonstrated that two later-occurring tumors were clonally derived from the primary cholangiocarcinoma rather than distinct new primaries, revealing an unusual pattern of late metachronous metastasis. We discuss the clinical significance of these genetic alterations and their relevance to therapeutic strategies. KEY POINTS Hybrid capture-based next-generation DNA sequencing assays can provide diagnostic clarity in patients with unusual patterns of metastasis and recurrence in which the pathologic diagnosis is ambiguous.To our knowledge, this is the first reported case of a YWHAZ-BRAF fusion in pancreaticobiliary cancer, and a very rare case of cholangiocarcinoma in the setting of a germline BRCA1 mutation.The patient's BRCA1 mutation and YWHAZ-BRAF fusion constitute potential targets for future therapy.
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Affiliation(s)
- Huat C Lim
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Thomas Botton
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Sarah E Umetsu
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Spencer C Behr
- Department of Radiology, University of California, San Francisco, San Francisco, California, USA
| | - John D Gordan
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | | | - Robin K Kelley
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
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154
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Mertens JC, Ilyas SI, Gores GJ. Targeting cholangiocarcinoma. Biochim Biophys Acta Mol Basis Dis 2018; 1864:1454-1460. [PMID: 28844952 PMCID: PMC6013079 DOI: 10.1016/j.bbadis.2017.08.027] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023]
Abstract
Cholangiocarcinoma (CCA) represents a diverse group of epithelial cancers associated with the biliary tract, and can best be stratified anatomically into intrahepatic (iCCA), perihilar (pCCA) and distal (dCCA) subsets. Molecular profiling has identified genetic aberrations associated with these anatomic subsets. For example, IDH catalytic site mutations and constitutively active FGFR2 fusion genes are predominantly identified in iCCA, whereas KRAS mutations and PRKACB fusions genes are identified in pCCA and dCCA. Clinical trials targeting these specific driver mutations are in progress. However, The Tumor Genome Atlas (TCGA) marker analysis of CCA also highlights the tremendous molecular heterogeneity of this cancer rendering comprehensive employment of targeted therapies challenging. CCA also display a rich tumor microenvironment which may be easier to target. For example, targeting cancer associated fibroblasts for apoptosis with BH3-mimetics and/or and reversing T-cell exhaustion with immune check point inhibitors may help aid in the treatment of this otherwise devastating malignancy. Combinatorial therapy attacking the tumor microenvironment plus targeted therapy may help advance treatment for CCA. This article is part of a Special Issue entitled: Cholangiocytes in Health and Disease edited by Jesus Banales, Marco Marzioni, Nicholas LaRusso and Peter Jansen.
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Affiliation(s)
- Joachim C Mertens
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Switzerland.
| | - Sumera I Ilyas
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Gregory J Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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155
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Peng S, Dhruv H, Armstrong B, Salhia B, Legendre C, Kiefer J, Parks J, Virk S, Sloan AE, Ostrom QT, Barnholtz-Sloan JS, Tran NL, Berens ME. Integrated genomic analysis of survival outliers in glioblastoma. Neuro Oncol 2018; 19:833-844. [PMID: 27932423 DOI: 10.1093/neuonc/now269] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background To elucidate molecular features associated with disproportionate survival of glioblastoma (GB) patients, we conducted deep genomic comparative analysis of a cohort of patients receiving standard therapy (surgery plus concurrent radiation and temozolomide); "GB outliers" were identified: long-term survivor of 33 months (LTS; n = 8) versus short-term survivor of 7 months (STS; n = 10). Methods We implemented exome, RNA, whole genome sequencing, and DNA methylation for collection of deep genomic data from STS and LTS GB patients. Results LTS GB showed frequent chromosomal gains in 4q12 (platelet derived growth factor receptor alpha and KIT) and 12q14.1 (cyclin-dependent kinase 4), and deletion in 19q13.33 (BAX, branched chain amino-acid transaminase 2, and cluster of differentiation 33). STS GB showed frequent deletion in 9p11.2 (forkhead box D4-like 2 and aquaporin 7 pseudogene 3) and 22q11.21 (Hypermethylated In Cancer 2). LTS GB showed 2-fold more frequent copy number deletions compared with STS GB. Gene expression differences showed the STS cohort with altered transcriptional regulators: activation of signal transducer and activator of transcription (STAT)5a/b, nuclear factor-kappaB (NF-κB), and interferon-gamma (IFNG), and inhibition of mitogen-activated protein kinase (MAPK1), extracellular signal-regulated kinase (ERK)1/2, and estrogen receptor (ESR)1. Expression-based biological concepts prominent in the STS cohort include metabolic processes, anaphase-promoting complex degradation, and immune processes associated with major histocompatibility complex class I antigen presentation; the LTS cohort features genes related to development, morphogenesis, and the mammalian target of rapamycin signaling pathway. Whole genome methylation analyses showed that a methylation signature of 89 probes distinctly separates LTS from STS GB tumors. Conclusion We posit that genomic instability is associated with longer survival of GB (possibly with vulnerability to standard therapy); conversely, genomic and epigenetic signatures may identify patients where up-front entry into alternative, targeted regimens would be a preferred, more efficacious management.
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Affiliation(s)
- Sen Peng
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA.,Department of Biomedical Informatics, Arizona State University, Scottsdale, Arizona, USA
| | - Harshil Dhruv
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Brock Armstrong
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Bodour Salhia
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Christophe Legendre
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Jeffrey Kiefer
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Julianna Parks
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Selene Virk
- Case Comprehensive Cancer Center, Case Western University, Cleveland, Ohio, USA
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Case Western University, Cleveland, Ohio, USA
| | - Quinn T Ostrom
- Case Comprehensive Cancer Center, Case Western University, Cleveland, Ohio, USA
| | | | - Nhan L Tran
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA.,Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA.,Translational Genomic Research Institute, Phoenix, Arizona, USA
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156
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A phase 2 study of vorinostat in locally advanced, recurrent, or metastatic adenoid cystic carcinoma. Oncotarget 2018; 8:32918-32929. [PMID: 28415633 PMCID: PMC5464838 DOI: 10.18632/oncotarget.16464] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/14/2017] [Indexed: 02/07/2023] Open
Abstract
Purpose Vorinostat is a histone deacetylase inhibitor (HDACi). Based on a confirmed partial response (PR) in an adenoid cystic carcinoma (ACC) patient treated with vorinostat in a prior phase 1 trial, we initiated this phase 2 trial. Methods: Vorinostat was administered orally 400 mg daily, 28 day cycles. The primary objective was to evaluate response rate (RR). Exploratory studies included whole exome sequencing (WES) of selected patients. Results Thirty patients were enrolled. Median age of patients was 53 years (range 21–73). Median number of cycles was 5 (range 1-66). Lymphopenia (n = 5), hypertension (n = 3), oral pain (n = 2), thromboembolic events (n = 2) and fatigue (n = 2) were the only grade 3 adverse events (AEs) that occurred in more than 1 patient. Eleven patients were dose reduced secondary to drug-related AEs. Two patients had a partial response (PR), with response durations of 53 and 7.2 months. One patient had a minor response with a decrease in ascites (for 19 cycles). Stable disease was the best response in 27 patients. Targeted and WES of 8 patients in this trial identified mutations in chromatin remodeling genes highlighting the role of the epigenome in ACC. Conclusion: Vorinostat demonstrated efficacy in patients with ACC supporting the inclusion of HDACi in future studies to treat ACC.
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157
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Gingold JA, Zhu D, Lee DF, Kaseb A, Chen J. Genomic Profiling and Metabolic Homeostasis in Primary Liver Cancers. Trends Mol Med 2018. [PMID: 29530485 DOI: 10.1016/j.molmed.2018.02.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), the two most common primary liver cancers, represent the second most common cancer-related cause of death worldwide, with most cases being diagnosed at an advanced stage. Recent genome-wide studies have helped to elucidate the molecular pathogenesis and genetic heterogeneity of liver cancers. This review of the genetic landscape of HCC and iCCA discusses the most recent findings from genomic profiling and the current understanding of the pathways involved in the initiation and progression of liver cancer. We highlight recent insights gained from metabolic profiling of HCC and iCCA. This knowledge will be key to developing clinically useful diagnostic/prognostic profiles, building targeted molecular and immunologic therapies, and ultimately curing these complex and heterogeneous diseases.
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Affiliation(s)
- Julian A Gingold
- Women's Health Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Dandan Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Ahmed Kaseb
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Chen
- Department of Gastroenterology, Hepatology, and Nutrition, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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158
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Bryce AH, Egan JB, Borad MJ, Stewart AK, Nowakowski GS, Chanan-Khan A, Patnaik MM, Ansell SM, Banck MS, Robinson SI, Mansfield AS, Klee EW, Oliver GR, McCormick JB, Huneke NE, Tagtow CM, Jenkins RB, Rumilla KM, Kerr SE, Kocher JPA, Beck SA, Fernandez-Zapico ME, Farrugia G, Lazaridis KN, McWilliams RR. Experience with precision genomics and tumor board, indicates frequent target identification, but barriers to delivery. Oncotarget 2018; 8:27145-27154. [PMID: 28423702 PMCID: PMC5432324 DOI: 10.18632/oncotarget.16057] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/15/2017] [Indexed: 01/16/2023] Open
Abstract
Background The ability to analyze the genomics of malignancies has opened up new possibilities for off-label targeted therapy in cancers that are refractory to standard therapy. At Mayo Clinic these efforts are organized through the Center for Individualized Medicine (CIM). Results Prior to GTB, datasets were analyzed and integrated by a team of bioinformaticians and cancer biologists. Therapeutically actionable mutations were identified in 65% (92/141) of the patients tested with 32% (29/92) receiving genomically targeted therapy with FDA approved drugs or in an independent clinical trial with 45% (13/29) responding. Standard of care (SOC) options were continued by 15% (14/92) of patients tested before exhausting SOC options, with 71% (10/14) responding to treatment. Over 35% (34/92) of patients with actionable targets were not treated with 65% (22/34) choosing comfort measures or passing away. Materials and Methods Patients (N = 165) were referred to the CIM Clinic between October 2012 and December 2015. All patients received clinical genomic panel testing with selected subsets receiving array comparative genomic hybridization and clinical whole exome sequencing to complement and validate panel findings. A genomic tumor board (GTB) reviewed results and, when possible, developed treatment recommendations. Conclusions Treatment decisions driven by tumor genomic analysis can lead to significant clinical benefit in a minority of patients. The success of genomically driven therapy depends both on access to drugs and robustness of bioinformatics analysis. While novel clinical trial designs are increasing the utility of genomic testing, robust data sharing of outcomes is needed to optimize clinical benefit for all patients.
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Affiliation(s)
- Alan H Bryce
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Jan B Egan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Mitesh J Borad
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - A Keith Stewart
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Grzegorz S Nowakowski
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Asher Chanan-Khan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology/Oncology, Mayo Clinic, Jacksonville, FL, U.S.A
| | - Mrinal M Patnaik
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Stephen M Ansell
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Michaela S Banck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Steven I Robinson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Aaron S Mansfield
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Norine E Huneke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Colleen M Tagtow
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Robert B Jenkins
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Sarah E Kerr
- Anatomic Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | - Jean-Pierre A Kocher
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | - Scott A Beck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Martin E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Gianrico Farrugia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Gastroenterology, Mayo Clinic, Rochester, MN, U.S.A
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Gastroenterology, Mayo Clinic, Rochester, MN, U.S.A
| | - Robert R McWilliams
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A.,Mayo Clinic Cancer Center, Rochester, MN, U.S.A
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159
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Pu XH, Ye Q, Yang J, Wu HY, Ding XW, Shi J, Mao L, Fan XS, Chen J, Qiu YD, Huang Q. Low-level clonal FGFR2 amplification defines a unique molecular subtype of intrahepatic cholangiocarcinoma in a Chinese population. Hum Pathol 2018. [PMID: 29514108 DOI: 10.1016/j.humpath.2017.12.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a subtype of primary liver cancer rarely curable by surgery that is increasing rapidly in incidence. Chromosomal translocations and amplifications of the fibroblast growth factor receptor 2 (FGFR2) locus are present in several kinds of tumors including ICC, but their incidence has not been assessed in Chinese patients. Using break-apart probes and by determining the ratios of FGFR2/chromosome enumeration probe (CEP) 10 double-color probes, we evaluated 122 ICCs for the presence of FGFR2 translocations and amplifications, respectively, by fluorescence in situ hybridization. We further determined FGFR2 protein expression by immunohistochemistry and analyzed the clinicopathologic records of the patients. Eight tumors (6.6%) had FGFR2 translocations, whereas 15 (12.3%) had low-level FGFR2 amplification. Interestingly, the tumors that showed both translocation and low-level amplification frequently were of the mass-forming type. Compared with the ICCs with normal FGFR2s, tumors with amplifications secreted less mucus (P = .017) and typically were accompanied by hepatitis B virus infection (P = .004). Tumors with low-level amplification generally were of lower stage (P = .013) and associated with better overall survival (P = .017). As tumors with FGFR2 amplification exhibit different biology from lesions with a normal gene, low-level amplification of FGFR2 may play an important role in tumor progression and may be a marker for targeted therapy.
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Affiliation(s)
- Xiao-Hong Pu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu Province, China
| | - Qing Ye
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu Province, China
| | - Jun Yang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu Province, China
| | - Hong-Yan Wu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu Province, China
| | - Xi-Wei Ding
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Jiong Shi
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu Province, China
| | - Liang Mao
- Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Xiang-Shan Fan
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu Province, China
| | - Jun Chen
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu Province, China.
| | - Yu-Dong Qiu
- Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School.
| | - Qin Huang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu Province, China; Department of Pathology and Laboratory Medicine, Veterans Affairs Boston Healthcare System and Harvard Medical School, West Roxbury, MA 02132, USA
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160
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Lampis A, Carotenuto P, Vlachogiannis G, Cascione L, Hedayat S, Burke R, Clarke P, Bosma E, Simbolo M, Scarpa A, Yu S, Cole R, Smyth E, Mateos JF, Begum R, Hezelova B, Eltahir Z, Wotherspoon A, Fotiadis N, Bali MA, Nepal C, Khan K, Stubbs M, Hahne JC, Gasparini P, Guzzardo V, Croce CM, Eccles S, Fassan M, Cunningham D, Andersen JB, Workman P, Valeri N, Braconi C. MIR21 Drives Resistance to Heat Shock Protein 90 Inhibition in Cholangiocarcinoma. Gastroenterology 2018; 154:1066-1079.e5. [PMID: 29113809 PMCID: PMC5863695 DOI: 10.1053/j.gastro.2017.10.043] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/12/2017] [Accepted: 10/27/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Cholangiocarcinomas (CCA) are resistant to chemotherapy, so new therapeutic agents are needed. We performed a screen to identify small-molecule compounds that are active against CCAs. Levels of microRNA 21 (MIR21 or miRNA21) are increased in CCAs. We investigated whether miRNA21 mediates resistance of CCA cells and organoids to HSP90 inhibitors. METHODS We performed a high-throughput screen of 484 small-molecule compounds to identify those that reduced viability of 6 human CCA cell lines. We tested the effects of HSP90 inhibitors on cells with disruption of the MIR21 gene, cells incubated with MIR21 inhibitors, and stable cell lines with inducible expression of MIR21. We obtained CCA biopsies from patients, cultured them as organoids (patient-derived organoids). We assessed their architecture, mutation and gene expression patterns, response to compounds in culture, and when grown as subcutaneous xenograft tumors in mice. RESULTS Cells with IDH1 and PBRM1 mutations had the highest level of sensitivity to histone deacetylase inhibitors. HSP90 inhibitors were effective in all cell lines, irrespective of mutations. Sensitivity of cells to HSP90 inhibitors correlated inversely with baseline level of MIR21. Disruption of MIR21 increased cell sensitivity to HSP90 inhibitors. CCA cells that expressed transgenic MIR21 were more resistant to HSP90 inhibitors than cells transfected with control vectors; inactivation of MIR21 in these cells restored sensitivity to these agents. MIR21 was shown to target the DnaJ heat shock protein family (Hsp40) member B5 (DNAJB5). Transgenic expression of DNAJB5 in CCA cells that overexpressed MIR21 re-sensitized them to HSP90 inhibitors. Sensitivity of patient-derived organoids to HSP90 inhibitors, in culture and when grown as xenograft tumors in mice, depended on expression of miRNA21. CONCLUSIONS miRNA21 appears to mediate resistance of CCA cells to HSP90 inhibitors by reducing levels of DNAJB5. HSP90 inhibitors might be developed for the treatment of CCA and miRNA21 might be a marker of sensitivity to these agents.
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Affiliation(s)
| | | | | | - Luciano Cascione
- Bioinformatics Core Unit, Institute of Oncology Research, Bellinzona, Switzerland
| | | | | | - Paul Clarke
- The Institute of Cancer Research, London, UK
| | - Else Bosma
- The Institute of Cancer Research, London, UK
| | - Michele Simbolo
- ARC-Net Research Centre and Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Research Centre and Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Sijia Yu
- The Institute of Cancer Research, London, UK
| | | | | | | | | | | | | | | | | | | | - Chirag Nepal
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Khurum Khan
- The Royal Marsden NHS Trust, London and Surrey, UK
| | - Mark Stubbs
- The Institute of Cancer Research, London, UK
| | | | | | | | | | | | - Matteo Fassan
- ARC-Net Research Centre and Department of Pathology and Diagnostics, University of Verona, Verona, Italy; Department of Medicine, University of Padua, Padua, Italy
| | | | - Jesper B Andersen
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Nicola Valeri
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Trust, London and Surrey, UK
| | - Chiara Braconi
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Trust, London and Surrey, UK.
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161
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Lombardi P, Marino D, Fenocchio E, Chilà G, Aglietta M, Leone F. Emerging molecular target antagonists for the treatment of biliary tract cancer. Expert Opin Emerg Drugs 2018; 23:63-75. [PMID: 29468924 DOI: 10.1080/14728214.2018.1444749] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Biliary tract cancers (BTCs) are a heterogeneous group of cancers, characterized by low incidence but poor prognosis. Even after complete surgical resection for early stage, relapse is frequent and the lack of effective treatments contributes to the dismal prognosis. To date, the only standard treatment in first-line is cisplatin/gemcitabine combination, whereas no standard in 2nd-line has been defined. Hence, the current goal is to better understand the biology of BTCs, discovering new treatment methods and improving clinical outcomes. Areas covered: The development of next-generation-sequencing has unveiled the picture of the molecular signatures characterizing BTCs, leading to the identification of actionable mutations in biomarker-driven clinical trials. In this review we will cover the genetic landscape of BTC, focusing on the efficacy of existing treatments. Furthermore, we will discuss emerging molecular targets and evaluate the findings of pre-clinical studies. Finally, the encouraging results of clinical trials involving targeted therapies or immunotherapy will be reviewed. Expert opinion: FGFR fusion rearrangements and IDH1 or IDH2 mutations are the most promising targeted treatments under evaluation. In addition, innovative trial design will allow to offer a chance for tailored medicine to infrequent subgroups of BTCs patients based on their molecular features rather than their histology.
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Affiliation(s)
- Pasquale Lombardi
- a Department of Oncology , University of Turin Medical School , Turin , Italy
| | - Donatella Marino
- b Medical Oncology , Candiolo Cancer Institute - FPO- IRCCS , Candiolo , Italy
| | | | - Giovanna Chilà
- a Department of Oncology , University of Turin Medical School , Turin , Italy
| | - Massimo Aglietta
- a Department of Oncology , University of Turin Medical School , Turin , Italy.,b Medical Oncology , Candiolo Cancer Institute - FPO- IRCCS , Candiolo , Italy
| | - Francesco Leone
- a Department of Oncology , University of Turin Medical School , Turin , Italy
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DeLeon TT, Ahn DH, Bogenberger JM, Anastasiadis PZ, Arora M, Ramanathan RK, Aqel BA, Vasmatzis G, Truty MJ, Oklu R, Bekaii-Saab TS, Borad MJ. Novel targeted therapy strategies for biliary tract cancers and hepatocellular carcinoma. Future Oncol 2018; 14:553-566. [PMID: 29460642 DOI: 10.2217/fon-2017-0451] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Worldwide hepatobiliary cancers are the second leading cause of cancer related death. Despite their relevance, hepatobiliary cancers have a paucity of approved systemic therapy options. However, there are a number of emerging therapeutic biomarkers and therapeutic concepts that show promise. In hepatocellular carcinoma, nivolumab appears particularly promising and recently received US FDA approval. In intrahepatic cholangiocarcinoma, therapies targeting FGFR2 and IDH1 and immune checkpoint inhibitors are the furthest along and generating the most excitement. There are additional biomarkers that merit further exploration in hepatobiliary cancers including FGF19, ERRFI1, TERT, BAP1, BRAF, CDKN2A, tumor mutational burden and ERBB2 (HER2/neu). Development of new and innovative therapies would help address the unmet need for effective systemic therapies in advanced and metastatic hepatobiliary cancers.
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Affiliation(s)
- Thomas T DeLeon
- Division of Hematology Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Daniel H Ahn
- Division of Hematology Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - James M Bogenberger
- Division of Hematology Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | | | - Mansi Arora
- Division of Hematology Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Ramesh K Ramanathan
- Division of Hematology Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Bashar A Aqel
- Division of Gastroenterology & Hepatology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Mark J Truty
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN 55902, USA
| | - Rahmi Oklu
- Division of Interventional Radiology, Department of Radiology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Tanios S Bekaii-Saab
- Division of Hematology Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Mitesh J Borad
- Division of Hematology Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
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163
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Kieler M, Müllauer L, Koperek O, Bianconi D, Unseld M, Raderer M, Prager GW. Analysis of 10 Adrenocortical Carcinoma Patients in the Cohort of the Precision Medicine Platform MONDTI. Oncology 2018; 94:306-310. [PMID: 29444511 DOI: 10.1159/000486678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/22/2017] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Adrenocortical carcinoma (ACC) is a rare disease with a dismal prognosis. We aimed to evaluate if a personalized medicine approach may be useful for matching patients with ACC to targeted therapies. METHODS This is an analysis of 10 molecularly profiled ACCs that were progressing under standard of care treatment. The profile consisted of a 50-gene next-generation sequencing panel, immunohistochemistry (IHC), and fluorescence in situ hybridization for several proteins or chromosomal aberrations. RESULTS In 6 (60%) tumor samples, no somatic mutation was detected, while in 3 (30%) tumors 1 mutation was detected and in 1 (10%) tumor 2 mutations were detected. These mutations were CTNNB1 (2 samples), TP53 (1 sample), RB1 (1 sample) and APC (1 sample). Expression of phospho-mTOR and of EGFR was commonly detected by IHC (87.5 and 62.5%). In 4 (50%) samples, IHC revealed a weak expression of progesterone receptor. Less frequent alterations were expression of PDGFR-α, c-KIT, and estrogen receptor, each in 1 case. CONCLUSIONS Based on the molecular profile, no recommendation for targeted therapy was made by the multi-disciplinary team. Currently, ACC might not be suitable for a precision medicine approach according to our tests.
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Affiliation(s)
- Markus Kieler
- Division of Oncology, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Leonhard Müllauer
- Clinical Institute of Pathology, Medical University Vienna, Vienna, Austria
| | - Oskar Koperek
- Clinical Institute of Pathology, Medical University Vienna, Vienna, Austria
| | - Daniela Bianconi
- Division of Oncology, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Matthias Unseld
- Division of Oncology, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Markus Raderer
- Division of Oncology, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Gerald W Prager
- Division of Oncology, Department of Medicine I, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
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The landscape of targeted therapies for cholangiocarcinoma: current status and emerging targets. Oncotarget 2018; 7:46750-46767. [PMID: 27102149 PMCID: PMC5216834 DOI: 10.18632/oncotarget.8775] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 04/10/2016] [Indexed: 01/07/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a relatively rare malignancy that arises from the epithelial cells of the intrahepatic, perihilar and distal biliary tree. Intrahepatic CCA (ICC) represents the second most common primary liver cancer, after hepatocellular cancer. Two-thirds of the patients with ICC present with locally advanced or metastatic disease. Despite standard treatment with gemcitabine and cisplatin, prognosis remains dismal with a median survival of less than one year. Several biological plausibilities can account for its poor clinical outcomes. First, despite the advent of next generation and whole exome sequencing, no oncogenic addiction loops have been validated as clinically actionable targets. Second, the anatomical, pathological and molecular heterogeneity, and rarity of CCA confer an ongoing challenge of instituting adequately powered clinical trials. Last, most of the studies were not biomarker-driven, which may undermine the potential benefit of targeted therapy in distinct subpopulations carrying the unique molecular signature. Recent whole genome sequencing efforts have identified known mutations in genes such as epidermal growth factor receptor (EGFR), Kirsten rat sarcoma viral oncogene homolog (KRAS), v-raf murine sarcoma viral oncogene homolog (BRAF) and tumor protein p53 (TP53), novel mutations in isocitrate dehydrogenase (IDH), BRCA1-Associated Protein 1 (BAP1) and AT-rich interactive domain-containing protein 1A (ARID1A), and novel fusions such as fibroblast growth factor receptor 2 (FGFR2) and ROS proto-oncogene 1 (ROS1). In this review, we will discuss the evolving genetic landscape of CCA, with an in depth focus on novel fusions (e.g. FGFR2 and ROS1) and somatic mutations (e.g. IDH1/2), which are promising actionable molecular targets.
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165
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Ilyas SI, Khan SA, Hallemeier CL, Kelley RK, Gores GJ. Cholangiocarcinoma - evolving concepts and therapeutic strategies. Nat Rev Clin Oncol 2018; 15:95-111. [PMID: 28994423 PMCID: PMC5819599 DOI: 10.1038/nrclinonc.2017.157] [Citation(s) in RCA: 946] [Impact Index Per Article: 157.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cholangiocarcinoma is a disease entity comprising diverse epithelial tumours with features of cholangiocyte differentiation: cholangiocarcinomas are categorized according to anatomical location as intrahepatic (iCCA), perihilar (pCCA), or distal (dCCA). Each subtype has a distinct epidemiology, biology, prognosis, and strategy for clinical management. The incidence of cholangiocarcinoma, particularly iCCA, has increased globally over the past few decades. Surgical resection remains the mainstay of potentially curative treatment for all three disease subtypes, whereas liver transplantation after neoadjuvant chemoradiation is restricted to a subset of patients with early stage pCCA. For patients with advanced-stage or unresectable disease, locoregional and systemic chemotherapeutics are the primary treatment options. Improvements in external-beam radiation therapy have facilitated the treatment of cholangiocarcinoma. Moreover, advances in comprehensive whole-exome and transcriptome sequencing have defined the genetic landscape of each cholangiocarcinoma subtype. Accordingly, promising molecular targets for precision medicine have been identified, and are being evaluated in clinical trials, including those exploring immunotherapy. Biomarker-driven trials, in which patients are stratified according to anatomical cholangiocarcinoma subtype and genetic aberrations, will be essential in the development of targeted therapies. Targeting the rich tumour stroma of cholangiocarcinoma in conjunction with targeted therapies might also be useful. Herein, we review the evolving developments in the epidemiology, pathogenesis, and management of cholangiocarcinoma.
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Affiliation(s)
- Sumera I Ilyas
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, USA
| | - Shahid A Khan
- Department of Hepatology, St Mary's Hospital, Imperial College London, Praed Street, London W2 1NY, UK
- Department of Hepatology, Hammersmith Hospital, Imperial College London, Ducane Road, London W12 0HS, UK
| | - Christopher L Hallemeier
- Department of Radiation Oncology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, USA
| | - Robin K Kelley
- The University of California, San Francisco Medical Center, 505 Parnassus Avenue, San Francisco, California 94143, USA
| | - Gregory J Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, USA
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166
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Shiao MS, Chiablaem K, Charoensawan V, Ngamphaiboon N, Jinawath N. Emergence of Intrahepatic Cholangiocarcinoma: How High-Throughput Technologies Expedite the Solutions for a Rare Cancer Type. Front Genet 2018; 9:309. [PMID: 30158952 PMCID: PMC6104394 DOI: 10.3389/fgene.2018.00309] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 07/23/2018] [Indexed: 12/16/2022] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is the cancer of the intrahepatic bile ducts, and together with hepatocellular carcinoma (HCC), constitute the majority of primary liver cancers. ICC is a rare disorder as its overall incidence is < 1/100,000 in the United States and Europe. However, it shows much higher incidence in particular geographical regions, such as northeastern Thailand, where liver fluke infection is the most common risk factor of ICC. Since the early stages of ICC are often asymptomatic, the patients are usually diagnosed at advanced stages with no effective treatments available, leading to the high mortality rate. In addition, unclear genetic mechanisms, heterogeneous nature, and various etiologies complicate the development of new efficient treatments. Recently, a number of studies have employed high-throughput approaches, including next-generation sequencing and mass spectrometry, in order to understand ICC in different biological aspects. In general, the majority of recurrent genetic alterations identified in ICC are enriched in known tumor suppressor genes and oncogenes, such as mutations in TP53, KRAS, BAP1, ARID1A, IDH1, IDH2, and novel FGFR2 fusion genes. Yet, there are no major driver genes with immediate clinical solutions characterized. Interestingly, recent studies utilized multi-omics data to classify ICC into two main subgroups, one with immune response genes as the main driving factor, while another is enriched with driver mutations in the genes associated with epigenetic regulations, such as IDH1 and IDH2. The two subgroups also show different hypermethylation patterns in the promoter regions. Additionally, the immune response induced by host-pathogen interactions, i.e., liver fluke infection, may further stimulate tumor growth through alterations of the tumor microenvironment. For in-depth functional studies, although many ICC cell lines have been globally established, these homogeneous cell lines may not fully explain the highly heterogeneous genetic contents of this disorder. Therefore, the advent of patient-derived xenograft and 3D patient-derived organoids as new disease models together with the understanding of evolution and genetic alterations of tumor cells at the single-cell resolution will likely become the main focus to fill the current translational research gaps of ICC in the future.
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Affiliation(s)
- Meng-Shin Shiao
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Khajeelak Chiablaem
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
- Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Nuttapong Ngamphaiboon
- Medical Oncology Unit, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
- *Correspondence: Natini Jinawath ;
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167
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Basturk O, Berger MF, Yamaguchi H, Adsay V, Askan G, Bhanot UK, Zehir A, Carneiro F, Hong SM, Zamboni G, Dikoglu E, Jobanputra V, Wrzeszczynski KO, Balci S, Allen P, Ikari N, Takeuchi S, Akagawa H, Kanno A, Shimosegawa T, Morikawa T, Motoi F, Unno M, Higuchi R, Yamamoto M, Shimizu K, Furukawa T, Klimstra DS. Pancreatic intraductal tubulopapillary neoplasm is genetically distinct from intraductal papillary mucinous neoplasm and ductal adenocarcinoma. Mod Pathol 2017; 30:1760-1772. [PMID: 28776573 DOI: 10.1038/modpathol.2017.60] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 12/14/2022]
Abstract
Intraductal tubulopapillary neoplasm is a relatively recently described member of the pancreatic intraductal neoplasm family. The more common member of this family, intraductal papillary mucinous neoplasm, often carries genetic alterations typical of pancreatic infiltrating ductal adenocarcinoma (KRAS, TP53, and CDKN2A) but additionally has mutations in GNAS and RNF43 genes. However, the genetic characteristics of intraductal tubulopapillary neoplasm have not been well characterized. Twenty-two intraductal tubulopapillary neoplasms were analyzed by either targeted next-generation sequencing, which enabled the identification of sequence mutations, copy number alterations, and selected structural rearrangements involving all targeted (≥300) genes, or whole-exome sequencing. Three of these intraductal tubulopapillary neoplasms were also subjected to whole-genome sequencing. All intraductal tubulopapillary neoplasms revealed the characteristic histologic (cellular intraductal nodules of back-to-back tubular glands lined by predominantly cuboidal cells with atypical nuclei and no obvious intracellular mucin) and immunohistochemical (immunolabeled with MUC1 and MUC6 but were negative for MUC2 and MUC5AC) features. By genomic analyses, there was loss of CDKN2A in 5/20 (25%) of these cases. However, the majority of the previously reported intraductal papillary mucinous neoplasm-related alterations were absent. Moreover, in contrast to most ductal neoplasms of the pancreas, MAP-kinase pathway was not involved. In fact, 2/22 (9%) of intraductal tubulopapillary neoplasms did not reveal any mutations in the tested genes. However, certain chromatin remodeling genes (MLL1, MLL2, MLL3, BAP1, PBRM1, EED, and ATRX) were found to be mutated in 7/22 (32%) of intraductal tubulopapillary neoplasms and 27% harbored phosphatidylinositol 3-kinase (PI3K) pathway (PIK3CA, PIK3CB, INPP4A, and PTEN) mutations. In addition, 4/18 (18%) of intraductal tubulopapillary neoplasms had FGFR2 fusions (FGFR2-CEP55, FGFR2-SASS6, DISP1-FGFR2, FGFR2-TXLNA, and FGFR2-VCL) and 1/18 (5.5%) had STRN-ALK fusion. Intraductal tubulopapillary neoplasm is a distinct clinicopathologic entity in the pancreas. Although its intraductal nature and some clinicopathologic features resemble those of intraductal papillary mucinous neoplasm, our results suggest that intraductal tubulopapillary neoplasm has distinguishing genetic characteristics. Some of these mutated genes are potentially targetable. Future functional studies will be needed to determine the consequences of these gene alterations.
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Affiliation(s)
- Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Volkan Adsay
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - Gokce Askan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umesh K Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatima Carneiro
- Department of Pathology, Centro Hospitalar São João/Faculty of Medicine of Porto University and Institute for Research and Innovation in Health/Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Giuseppe Zamboni
- Department of Pathology, University of Verona, Ospedale S.C.-Don Calabria-Negrar, Verona, Italy
| | - Esra Dikoglu
- New York Genome Center, Molecular Diagnostics, New York, NY, USA
| | - Vaidehi Jobanputra
- New York Genome Center, Molecular Diagnostics, New York, NY, USA.,Department of Pathology, Colombia University Medical Center, New York, NY, USA
| | | | - Serdar Balci
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - Peter Allen
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Naoki Ikari
- Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Shoko Takeuchi
- Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Akagawa
- Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Atsushi Kanno
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tooru Shimosegawa
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takanori Morikawa
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fuyuhiko Motoi
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryota Higuchi
- Department of Surgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Masakazu Yamamoto
- Department of Surgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Kyoko Shimizu
- Department of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Toru Furukawa
- Department of Pathology, Tokyo Women's Medical University, Tokyo, Japan
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Bragazzi MC, Ridola L, Safarikia S, Matteo SD, Costantini D, Nevi L, Cardinale V. New insights into cholangiocarcinoma: multiple stems and related cell lineages of origin. Ann Gastroenterol 2017; 31:42-55. [PMID: 29333066 PMCID: PMC5759612 DOI: 10.20524/aog.2017.0209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a heterogeneous group of malignancies that may develop at any level of the biliary tree. CCA is currently classified into intrahepatic (iCCA), perihilar (pCCA) and distal (dCCA) on the basis of its anatomical location. Notably, although these three CCA subtypes have common features, they also have important inter- and intra-tumor differences that can affect their pathogenesis and outcome. A unique feature of CCA is that it manifests in the hepatic parenchyma or large intrahepatic and extrahepatic bile ducts, furnished by two distinct stem cell niches: the canals of Hering and the peribiliary glands, respectively. The complexity of CCA pathogenesis highlights the need for a multidisciplinary, translational, and systemic approach to this malignancy. This review focuses on advances in the knowledge of CCA histomorphology, risk factors, molecular pathogenesis, and subsets of CCA.
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Affiliation(s)
- Maria Consiglia Bragazzi
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Ridola
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Samira Safarikia
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Sabina Di Matteo
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Daniele Costantini
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Nevi
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Vincenzo Cardinale
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
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169
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Borad MJ, LoRusso PM. Twenty-First Century Precision Medicine in Oncology: Genomic Profiling in Patients With Cancer. Mayo Clin Proc 2017; 92:1583-1591. [PMID: 28982488 DOI: 10.1016/j.mayocp.2017.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/27/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022]
Abstract
The advent of next-generation sequencing has accelerated the implementation of genomic profiling in the care and management of patients with cancer. Initial efforts have focused on target identification in patients with advanced cancer. Prognostication, resistance detection, disease monitoring, and early detection efforts are also underway. This review highlights some of the challenges in this evolving space. This includes choosing between gene-panel and comprehensive approaches, DNA and transcriptome data integration, reduction of false-positive variants, addressing tumor heterogeneity, establishment of workflows to address unsolicited findings, and data sharing and privacy concerns.
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Affiliation(s)
- Mitesh J Borad
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, AZ; Mayo Clinic Comprehensive Cancer Center, Scottsdale, AZ; Department of Molecular Medicine, Mayo Clinic, Rochester, MN; Center for Individualized Medicine, Mayo Clinic, Rochester, MN.
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170
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Ilyas SI, Gores GJ. Emerging molecular therapeutic targets for cholangiocarcinoma. J Hepatol 2017; 67:632-644. [PMID: 28389139 PMCID: PMC5563275 DOI: 10.1016/j.jhep.2017.03.026] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/06/2017] [Accepted: 03/24/2017] [Indexed: 02/06/2023]
Abstract
Cholangiocarcinomas (CCAs) are diverse epithelial tumors arising from the liver or large bile ducts with features of cholangiocyte differentiation. CCAs are classified anatomically into intrahepatic (iCCA), perihilar (pCCA), and distal CCA (dCCA). Each subtype has distinct risk factors, molecular pathogenesis, therapeutic options, and prognosis. CCA is an aggressive malignancy with a poor overall prognosis and median survival of less than 2years in patients with advanced disease. Potentially curative surgical treatment options are limited to the subset of patients with early-stage disease. Presently, the available systemic medical therapies for advanced or metastatic CCA have limited therapeutic efficacy. Molecular alterations define the differences in biological behavior of each CCA subtype. Recent comprehensive genetic analysis has better characterized the genomic and transcriptomic landscape of each CCA subtype. Promising candidates for targeted, personalized therapy have emerged, including potential driver fibroblast growth factor receptor (FGFR) gene fusions and somatic mutations in isocitrate dehydrogenase (IDH)1/2 in iCCA, protein kinase cAMP-activated catalytic subunit alpha (PRKACA) or beta (PRKACB) gene fusions in pCCA, and ELF3 mutations in dCCA/ampullary carcinoma. A precision genomic medicine approach is dependent on an enhanced understanding of driver mutations in each subtype and stratification of patients according to their genetic drivers. We review the current genomic landscape of CCA, the potentially actionable molecular aberrations in each CCA subtype, and the role of immunotherapy in CCA.
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Affiliation(s)
- Sumera I Ilyas
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Gregory J Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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Valle JW, Lamarca A, Goyal L, Barriuso J, Zhu AX, Knittel G, Leeser U, van Oers J, Edelmann W, Heukamp LC, Reinhardt HC. New Horizons for Precision Medicine in Biliary Tract Cancers. Cancer Discov 2017. [PMID: 28818953 DOI: 10.1158/2159-8290] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biliary tract cancers (BTC), including cholangiocarcinoma and gallbladder cancer, are poor-prognosis and low-incidence cancers, although the incidence of intrahepatic cholangiocarcinoma is rising. A minority of patients present with resectable disease but relapse rates are high; benefit from adjuvant capecitabine chemotherapy has been demonstrated. Cisplatin/gemcitabine combination chemotherapy has emerged as the reference first-line treatment regimen; there is no standard second-line therapy. Selected patients may be suitable for liver-directed therapy (e.g., radioembolization or external beam radiation), pending confirmation of benefit in randomized studies. Initial trials targeting the epithelial growth factor receptor and angiogenesis pathways have failed to deliver new treatments. Emerging data from next-generation sequencing analyses have identified actionable mutations (e.g., FGFR fusion rearrangements and IDH1 and IDH2 mutations), with several targeted drugs entering clinical development with encouraging results. The role of systemic therapies, including targeted therapies and immunotherapy for BTC, is rapidly evolving and is the subject of this review.Significance: The authors address genetic drivers and molecular biology from a translational perspective, in an intent to offer a clear view of the recent past, present, and future of BTC. The review describes a state-of-the-art update of the current status and future directions of research and therapy in advanced BTC. Cancer Discov; 7(9); 943-62. ©2017 AACR.
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Affiliation(s)
- Juan W Valle
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK. .,Institute of Cancer Sciences, University of Manchester, Wilmslow Road, Manchester, UK
| | - Angela Lamarca
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK
| | - Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jorge Barriuso
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK.,Faculty of Medical, Biological and Human Sciences, University of Manchester, Rumford Street, Manchester, UK
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
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172
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Valle JW, Lamarca A, Goyal L, Barriuso J, Zhu AX. New Horizons for Precision Medicine in Biliary Tract Cancers. Cancer Discov 2017; 7:943-962. [PMID: 28818953 DOI: 10.1158/2159-8290.cd-17-0245] [Citation(s) in RCA: 386] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/24/2017] [Accepted: 07/10/2017] [Indexed: 02/06/2023]
Abstract
Biliary tract cancers (BTC), including cholangiocarcinoma and gallbladder cancer, are poor-prognosis and low-incidence cancers, although the incidence of intrahepatic cholangiocarcinoma is rising. A minority of patients present with resectable disease but relapse rates are high; benefit from adjuvant capecitabine chemotherapy has been demonstrated. Cisplatin/gemcitabine combination chemotherapy has emerged as the reference first-line treatment regimen; there is no standard second-line therapy. Selected patients may be suitable for liver-directed therapy (e.g., radioembolization or external beam radiation), pending confirmation of benefit in randomized studies. Initial trials targeting the epithelial growth factor receptor and angiogenesis pathways have failed to deliver new treatments. Emerging data from next-generation sequencing analyses have identified actionable mutations (e.g., FGFR fusion rearrangements and IDH1 and IDH2 mutations), with several targeted drugs entering clinical development with encouraging results. The role of systemic therapies, including targeted therapies and immunotherapy for BTC, is rapidly evolving and is the subject of this review.Significance: The authors address genetic drivers and molecular biology from a translational perspective, in an intent to offer a clear view of the recent past, present, and future of BTC. The review describes a state-of-the-art update of the current status and future directions of research and therapy in advanced BTC. Cancer Discov; 7(9); 943-62. ©2017 AACR.
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Affiliation(s)
- Juan W Valle
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK. .,Institute of Cancer Sciences, University of Manchester, Wilmslow Road, Manchester, UK
| | - Angela Lamarca
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK
| | - Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jorge Barriuso
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK.,Faculty of Medical, Biological and Human Sciences, University of Manchester, Rumford Street, Manchester, UK
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
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173
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Jain A, Kwong LN, Javle M. Genomic Profiling of Biliary Tract Cancers and Implications for Clinical Practice. Curr Treat Options Oncol 2017; 17:58. [PMID: 27658789 DOI: 10.1007/s11864-016-0432-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OPINION STATEMENT Biliary tract cancers are relatively uncommon, have an aggressive disease course and a dismal clinical outcome. Until recently, there have been very few clinical advances in the management of these patients and gemcitabine-based chemotherapy has been the only widely accepted systemic therapy. The advent of next generation sequencing technologies can potentially change the treatment paradigm of this disease. Targeted therapy directed against actionable mutations and identification of molecular subsets with distinct prognostic significance is now feasible in clinical practice. Mutation profiling has highlighted the genomic differences between the intra, extrahepatic cholangiocarcinoma, and gallbladder cancer. The mutational spectrum of intrahepatic cholangiocarcinoma differs according to geographic location and ethnicity. There is a higher incidence of chromatin modulating gene mutations in Western patients as compared with Asian patients with liver fluke-associated cholangiocarcinoma. KRAS and p53 mutations are associated with an aggressive disease prognosis while FGFR mutations may signify a relatively indolent disease course of intrahepatic cholangiocarcinoma. FGFR and IDH mutations have promising agents in clinical trials at this time. An estimated 15 % of gallbladder cancers have Her2/neu amplification and can be targeted by trastuzumab. On the other hand, an estimated 10-15 % of cholangiocarcinomas have DNA repair mutations and may be candidates for immune therapies with checkpoint inhibitors. The promise of targeted therapies for biliary tract cancers can be fulfilled with well-designed, prospective, and multi-center clinical trials.
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Affiliation(s)
- Apurva Jain
- Department of Gastrointestinal Medical Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 426, Houston, TX, 77030, USA
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 426, Houston, TX, 77030, USA.
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174
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Macias RIR, Banales JM, Sangro B, Muntané J, Avila MA, Lozano E, Perugorria MJ, Padillo FJ, Bujanda L, Marin JJG. The search for novel diagnostic and prognostic biomarkers in cholangiocarcinoma. Biochim Biophys Acta Mol Basis Dis 2017; 1864:1468-1477. [PMID: 28782657 DOI: 10.1016/j.bbadis.2017.08.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023]
Abstract
The poor prognosis of cholangiocarcinoma (CCA) is in part due to late diagnosis, which is currently achieved by a combination of clinical, radiological and histological approaches. Available biomarkers determined in serum and biopsy samples to assist in CCA diagnosis are not sufficiently sensitive and specific. Therefore, the identification of new biomarkers, preferably those obtained by minimally invasive methods, such as liquid biopsy, is important. The development of innovative technologies has permitted to identify a significant number of genetic, epigenetic, proteomic and metabolomic CCA features with potential clinical usefulness in early diagnosis, prognosis or prediction of treatment response. Potential new candidates must be rigorously evaluated prior to entering routine clinical application. Unfortunately, to date, no such biomarker has achieved validation for these purposes. This review is an up-to-date of currently used biomarkers and the candidates with promising characteristics that could be included in the clinical practice in the next future. This article is part of a Special Issue entitled: Cholangiocytes in Health and Disease edited by Jesus Banales, Marco Marzioni, Nicholas LaRusso and Peter Jansen.
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Affiliation(s)
- Rocio I R Macias
- Experimental Hepatology and Drug Targeting (HEVEFARM), University of Salamanca, IBSAL, Salamanca, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain.
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Bruno Sangro
- Liver Unit, Clínica Universidad de Navarra, IDISNA, Pamplona, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Jordi Muntané
- Department of General Surgery, "Virgen del Rocío" University Hospital, IBiS/CSIC/University of Sevilla, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Matias A Avila
- Division of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Pamplona, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Elisa Lozano
- Experimental Hepatology and Drug Targeting (HEVEFARM), University of Salamanca, IBSAL, Salamanca, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Francisco J Padillo
- Department of General Surgery, "Virgen del Rocío" University Hospital, IBiS/CSIC/University of Sevilla, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Jose J G Marin
- Experimental Hepatology and Drug Targeting (HEVEFARM), University of Salamanca, IBSAL, Salamanca, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
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175
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Verlingue L, Hollebecque A, Boige V, Ducreux M, Malka D, Ferté C. Matching genomic molecular aberrations with molecular targeted agents: Are biliary tract cancers an ideal playground? Eur J Cancer 2017. [DOI: 10.1016/j.ejca.2017.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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176
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Kayhanian H, Smyth EC, Braconi C. Emerging molecular targets and therapy for cholangiocarcinoma. World J Gastrointest Oncol 2017; 9:268-280. [PMID: 28808500 PMCID: PMC5534395 DOI: 10.4251/wjgo.v9.i7.268] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/05/2017] [Accepted: 03/24/2017] [Indexed: 02/05/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a rare cancer arising from the biliary tree with a poor prognosis and limited therapeutic options. Recent large scale molecular characterisation studies have identified recurrent genetic alterations in CCA which may be amenable to therapeutic targeting. In this review we explore the genomic landscape of CCA and examine results from trials of molecularly targeted agents and immunotherapy in this disease. Challenges in CCA diagnosis, treatment and trial design are discussed and we reflect on future directions which may lead to improved outcomes for CCA patients.
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177
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Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson M, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep 2017; 19:2878-2880. [PMID: 28658632 PMCID: PMC6141445 DOI: 10.1016/j.celrep.2017.06.008] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas, of a set of predominantly intrahepatic CCA cases, and propose a molecular classification scheme. We identified an IDH -mutant enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH -mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.
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Affiliation(s)
- Farshad Farshidfar
- Departments of Surgery and Oncology, Arnie Charbonneau
Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Siyuan Zheng
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
| | - Yulia Newton
- University of California Santa Cruz, Santa Cruz, CA 95064,
USA
| | - Juliann Shih
- The Eli and Edythe L. Broad Institute of Massachusetts
Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
| | - A. Gordon Robertson
- Canada’s Michael Smith Genome Sciences Centre, BC
Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Toshinori Hinoue
- Center for Epigenetics, Van Andel Research Institute, Grand
Rapids, MI 49503
| | - Katherine A. Hoadley
- Departments of Genetics and Pathology and Laboratory
Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599,
USA
- Lineberger Comprehensive Cancer Center, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ewan A. Gibb
- Canada’s Michael Smith Genome Sciences Centre, BC
Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Jason Roszik
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Kyle R. Covington
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
| | - Chia-Chin Wu
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
| | | | - Apurva Hegde
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Ju Dong Yang
- Divisions of Gastroenterology and Hepatology and
Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
55905, USA
| | - Ed Reznik
- Memorial Sloan Kettering Cancer Center, New York, NY
10005, USA
| | - Sara Sadeghi
- Canada’s Michael Smith Genome Sciences Centre, BC
Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Chandra Sekhar Pedamallu
- The Eli and Edythe L. Broad Institute of Massachusetts
Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
| | - Akinyemi I. Ojesina
- University of Alabama at Birmingham, Birmingham, AL
35294, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
35806, USA
| | - Julian M. Hess
- The Eli and Edythe L. Broad Institute of Massachusetts
Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - J. Todd Auman
- Departments of Genetics and Pathology and Laboratory
Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599,
USA
| | - Suhn K. Rhie
- University of Southern California, USC/Norris
Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Reanne Bowlby
- Canada’s Michael Smith Genome Sciences Centre, BC
Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Mitesh J. Borad
- Division of Hematology and Oncology, Mayo Clinic,
Scottsdale, AZ 85054, USA
| | | | - Andrew X Zhu
- Departments of Hematology and Oncology, Massachusetts
General Hospital, Boston, MA 02114, USA
| | - Josh M. Stuart
- University of California Santa Cruz, Santa Cruz, CA 95064,
USA
| | - Chris Sander
- Memorial Sloan Kettering Cancer Center, New York, NY
10005, USA
| | - Rehan Akbani
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Andrew D. Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts
Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
| | - Vikram Deshpande
- Departments of Pathology and Oncology, Massachusetts
General Hospital, Boston, MA 02114, USA
| | - Taofic Mounajjed
- Divisions of Gastroenterology and Hepatology and
Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
55905, USA
| | - Wai Chin Foo
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Michael Torbenson
- Divisions of Gastroenterology and Hepatology and
Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
55905, USA
| | | | - Peter W. Laird
- Center for Epigenetics, Van Andel Research Institute, Grand
Rapids, MI 49503
| | - David A. Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
| | - Autumn J. McRee
- Lineberger Comprehensive Cancer Center, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oliver F. Bathe
- Departments of Surgery and Oncology, Arnie Charbonneau
Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jesper B. Andersen
- Biotech Research and Innovation Centre, University of
Copenhagen, DK-2200, Denmark
| | - Nabeel Bardeesy
- Departments of Pathology and Oncology, Massachusetts
General Hospital, Boston, MA 02114, USA
| | - Lewis R. Roberts
- Divisions of Gastroenterology and Hepatology and
Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
55905, USA
| | - Lawrence N. Kwong
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
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178
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Schuierer S, Carbone W, Knehr J, Petitjean V, Fernandez A, Sultan M, Roma G. A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples. BMC Genomics 2017; 18:442. [PMID: 28583074 PMCID: PMC5460543 DOI: 10.1186/s12864-017-3827-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/29/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND RNA-sequencing (RNA-seq) has emerged as one of the most sensitive tool for gene expression analysis. Among the library preparation methods available, the standard poly(A) + enrichment provides a comprehensive, detailed, and accurate view of polyadenylated RNAs. However, on samples of suboptimal quality ribosomal RNA depletion and exon capture methods have recently been reported as better alternatives. METHODS We compared for the first time three commercial Illumina library preparation kits (TruSeq Stranded mRNA, TruSeq Ribo-Zero rRNA Removal, and TruSeq RNA Access) as representatives of these three different approaches using well-established human reference RNA samples from the MAQC/SEQC consortium on a wide range of input amounts (from 100 ng down to 1 ng) and degradation levels (intact, degraded, and highly degraded). RESULTS We assessed the accuracy of the generated expression values by comparison to gold standard TaqMan qPCR measurements and gained unprecedented insight into the limits of applicability in terms of input quantity and sample quality of each protocol. We found that each protocol generates highly reproducible results (R 2 > 0.92) on intact RNA samples down to input amounts of 10 ng. For degraded RNA samples, Ribo-Zero showed clear performance advantages over the other two protocols as it generated more accurate and better reproducible gene expression results even at very low input amounts such as 1 ng and 2 ng. For highly degraded RNA samples, RNA Access performed best generating reliable data down to 5 ng input. CONCLUSIONS We found that the ribosomal RNA depletion protocol from Illumina works very well at amounts far below recommendation and over a good range of intact and degraded material. We also infer that the exome-capture protocol (RNA Access, Illumina) performs better than other methods on highly degraded and low amount samples.
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Affiliation(s)
- Sven Schuierer
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Walter Carbone
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Virginie Petitjean
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Anita Fernandez
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Marc Sultan
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
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179
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Zhao DY, Lim KH. Current biologics for treatment of biliary tract cancers. J Gastrointest Oncol 2017; 8:430-440. [PMID: 28736630 PMCID: PMC5506280 DOI: 10.21037/jgo.2017.05.04] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/26/2017] [Indexed: 12/16/2022] Open
Abstract
Biliary tract cancers (BTC) is a group of malignancies that arise from the epithelial cells of the biliary tree. These cancers are typically classified by anatomic site of origin: intrahepatic cholangiocarcinoma (IHCC) and extrahepatic cholangiocarcinoma (EHCC), and gallbladder cancer (GBC). To date, complete surgical resection remains the mainstay of treatment especially for earlier stage disease. Unfortunately, most patients present with advanced or metastatic disease, when systemic chemotherapy is the only treatment option. Due to the paucity of effective treatments, BTCs have a dismal prognosis. There is a tremendous need to better understand the disease biology, discover new therapies, and improve clinical outcomes for this challenging disease. Next-generation sequencing has produced a more accurate and detailed picture of the molecular signatures in BTCs. The three BTC histologic subtypes are, in fact, quite molecularly distinct. IHCC commonly contain FGFR2 fusions and IDH 1 and 2 mutations, whereas EHCC and GBC tend to carry mutations in EGFR, HER2, and MAPK pathway. In light of this emerging knowledge, clinical trials have become more biomarker-driven, which allows capturing of subsets of patients that are most likely to respond to certain therapies. Many new and promising targeted therapeutics are currently in the pipeline. Here we review the genetic landscape of BTCs while focusing on new molecular targets and targeted therapeutics currently being investigated in biomarker-driven clinical trials.
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Affiliation(s)
- Diana Y. Zhao
- Medical Scientist Training Program, Department of Internal Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Kian-Huat Lim
- Division of Oncology, Department of Internal Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
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180
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Au TH, Wang K, Stenehjem D, Garrido-Laguna I. Personalized and precision medicine: integrating genomics into treatment decisions in gastrointestinal malignancies. J Gastrointest Oncol 2017; 8:387-404. [PMID: 28736627 PMCID: PMC5506274 DOI: 10.21037/jgo.2017.01.04] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/21/2016] [Indexed: 12/19/2022] Open
Abstract
The advent of next generation sequencing (NGS) technologies has advanced our understanding of the intrinsic biology of different gastrointestinal (GI) tumor types. The use of novel, more efficient sequencing platforms has improved turnaround times of sequencing results. This is providing real time opportunities to put precision medicine to the test. A number of early phase clinical trials are testing targeted therapies in unique molecularly characterized subsets of patients (baskets). While basket studies are gaining momentum, treatment failures serve to remind us that shifting from a histology-driven to a histology-agnostic approach is unlikely to be a failure-free strategy for a number of tumor types as recently learnt from vemurafenib failure in BRAF mutated metastatic colorectal cancer (mCRC). GI malignancies are clinically and molecularly heterogeneous. Unfortunately, development of biomarkers of response to therapy as well as targeted therapies for GI adenocarcinomas has fallen behind compared to other malignancies. Trastuzumab is the only FDA approved targeted therapy for GI adenocarcinomas for which a biomarker of response (HER2 amplifications) is available. In addition, RAS mutations are known to predict lack of response to epidermal growth factor receptor (EGFR) inhibitors in advanced colorectal cancer (CRC) patients. However, NGS has recently revealed that a number of actionable genetic aberrations are present at low prevalence across different GI malignancies. Prospective randomized clinical trials will determine whether matching actionable aberration with targeted therapy will contribute to improve survival in patients with GI malignancies. Here, we review current evidence for targeted therapies in GI malignancies, as well as application and pitfalls of NGS including tissue testing and liquid biopsies.
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Affiliation(s)
- Trang H. Au
- Department of Pharmacotherapy, University of Utah College of Pharmacy, Salt Lake City, Utah, USA
| | - Kai Wang
- OrigiMed, Shanghai 200000, China
| | - David Stenehjem
- Department of Pharmacotherapy, University of Utah College of Pharmacy, Salt Lake City, Utah, USA
- Center for Investigational Therapeutics, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Ignacio Garrido-Laguna
- Center for Investigational Therapeutics, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Division of Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
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181
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Du L, Che Z, Wang-Gillam A. Promising therapeutics of gastrointestinal cancers in clinical trials. J Gastrointest Oncol 2017; 8:524-533. [PMID: 28736639 DOI: 10.21037/jgo.2017.01.08] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Many novel therapeutics are being developed for patients with cancers along the gastrointestinal (GI) tract. These emerging agents are frequently classified by their biological targets such as tumor growth pathways, tumor metabolism, microenvironment, etc. Some agents targeting cancer growth pathways are based on existing clinically validated therapeutic targets, such as regorafenib for hepatocellular carcinoma (HCC), while other agents focus on newly identified targets, such as FGFR fusions in cholangiocarcinoma. Drugs modifying the immunosuppressive tumor microenvironment have emerged as an attractive area of clinical investigation. Moreover, drugs targeting the stem-cell like qualities of cancer and the tight junction protein claudin 18.2 have generated quite a lot of excitement in the field. In this paper, we will systemically review the recent promising agents and therapeutic strategies in GI cancers.
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Affiliation(s)
- Lingling Du
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | | | - Andrea Wang-Gillam
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
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182
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Dalton WB, Forde PM, Kang H, Connolly RM, Stearns V, Gocke CD, Eshleman JR, Axilbund J, Petry D, Geoghegan C, Wolff AC, Loeb DM, Pratilas CA, Meyer CF, Christenson ES, Slater SA, Ensminger J, Parsons HA, Park BH, Lauring J. Personalized Medicine in the Oncology Clinic: Implementation and Outcomes of the Johns Hopkins Molecular Tumor Board. JCO Precis Oncol 2017; 2017. [PMID: 30003184 DOI: 10.1200/po.16.00046] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Purpose Tumor genomic profiling for personalized oncology therapy is being widely applied in clinical practice even as it is being evaluated more formally in clinical trials. Given the complexities of genomic data and its application to clinical use, molecular tumor boards with diverse expertise can provide guidance to oncologists and patients seeking to implement personalized genetically targeted therapy in practice. Methods A multidisciplinary molecular tumor board reviewed tumor molecular profiling reports from consecutive referrals at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins over a 3-year period. The tumor board weighed evidence for actionability of genomic alterations identified by molecular profiling and provided recommendations including US Food and Drug Administration-approved drug therapy, clinical trials of matched targeted therapy, off-label use of such therapy, and additional tumor or germline genetic testing. Results One hundred fifty-five patients were reviewed. Actionable genomic alterations were identified in 132 patients (85%). Off-label therapies were recommended in 37 patients (24%). Eleven patients were treated off-label, and 13 patients were enrolled onto clinical trials of matched targeted therapies. Median progression-free survival of patients treated with matched therapies was 5 months (95% CI, 2.9 months to not reached), and the progression-free survival probability at 6 months was 43%(95% CI, 26% to 71%). Lack of locally available clinical trials was the major limitation on clinical actionability of tumor profiling reports. Conclusion The molecular tumor board recommended off-label targeted therapies for a quarter of all patients reviewed. Outcomes were heterogeneous, although 43% of patients receiving genomically matched therapy derived clinical benefit lasting at least 6 months. Until more data become available from precision oncology trials, molecular tumor boards can help guide appropriate use of tumor molecular testing to direct therapy.
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Affiliation(s)
- W Brian Dalton
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Patrick M Forde
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Hyunseok Kang
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Roisin M Connolly
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Vered Stearns
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Christopher D Gocke
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - James R Eshleman
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Dana Petry
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Antonio C Wolff
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - David M Loeb
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Christian F Meyer
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Shannon A Slater
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Jennifer Ensminger
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Heather A Parsons
- Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ben H Park
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Josh Lauring
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
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183
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Rahnemai-Azar AA, Weisbrod AB, Dillhoff M, Schmidt C, Pawlik TM. Intrahepatic cholangiocarcinoma: current management and emerging therapies. Expert Rev Gastroenterol Hepatol 2017; 11:439-449. [PMID: 28317403 DOI: 10.1080/17474124.2017.1309290] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a malignancy with an increasing incidence and a high-case fatality. While surgery offers the best hope at long-term survival, only one-third of tumors are amenable to surgical resection at the time of the diagnosis. Unfortunately, conventional chemotherapy offers limited survival benefit in the management of unresectable or metastatic disease. Recent advances in understanding the molecular pathogenesis of iCCA and the use of next-generation sequencing techniques have provided a chance to identify 'target-able' molecular aberrations. These novel molecular therapies offer the promise to personalize therapy for patients with iCCA and, in turn, improve the outcomes of patients. Area covered: We herein review the current management options for iCCA with a focus on defining both established and emerging therapies. Expert commentary: Surgical resection remains as an only hope for cure in iCCA patients. However, frequently the diagnosis is delayed till advanced stages when surgery cannot be offered; signifying the urge for specific diagnostic tumor biomarkers and targeted therapies. New advances in genomic profiling have contributed to a better understanding of the landscape of molecular alterations in iCCA and offer hope for the development of novel diagnostic biomarkers and targeted therapies.
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Affiliation(s)
- Amir A Rahnemai-Azar
- a Department of Surgery , University of Washington Medical Center , Seattle , WA , USA
| | - Allison B Weisbrod
- b Department of Surgery , The Ohio State University Wexner Medical Center , Columbus , OH , USA
| | - Mary Dillhoff
- b Department of Surgery , The Ohio State University Wexner Medical Center , Columbus , OH , USA
| | - Carl Schmidt
- b Department of Surgery , The Ohio State University Wexner Medical Center , Columbus , OH , USA
| | - Timothy M Pawlik
- b Department of Surgery , The Ohio State University Wexner Medical Center , Columbus , OH , USA
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184
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Lasorella A, Sanson M, Iavarone A. FGFR-TACC gene fusions in human glioma. Neuro Oncol 2017; 19:475-483. [PMID: 27852792 PMCID: PMC5464372 DOI: 10.1093/neuonc/now240] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/12/2016] [Indexed: 12/30/2022] Open
Abstract
Chromosomal translocations joining in-frame members of the fibroblast growth factor receptor-transforming acidic coiled-coil gene families (the FGFR-TACC gene fusions) were first discovered in human glioblastoma multiforme (GBM) and later in many other cancer types. Here, we review this rapidly expanding field of research and discuss the unique biological and clinical features conferred to isocitrate dehydrogenase wild-type glioma cells by FGFR-TACC fusions. FGFR-TACC fusions generate powerful oncogenes that combine growth-promoting effects with aneuploidy through the activation of as yet unclear intracellular signaling mechanisms. FGFR-TACC fusions appear to be clonal tumor-initiating events that confer strong sensitivity to FGFR tyrosine kinase inhibitors. Screening assays have recently been reported for the accurate identification of FGFR-TACC fusion variants in human cancer, and early clinical data have shown promising effects in cancer patients harboring FGFR-TACC fusions and treated with FGFR inhibitors. Thus, FGFR-TACC gene fusions provide a "low-hanging fruit" model for the validation of precision medicine paradigms in human GBM.
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Affiliation(s)
- Anna Lasorella
- Institute for Cancer Genetics, Department of Pediatrics and Pathology, Columbia University Medical Center, New York, New York, USA
| | - Marc Sanson
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013,Groupe Hospitalier Pitié-Salpêtrière, Service de Neurologie 2, Paris, France
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology and Pathology, Columbia University Medical Center, New York, New York, USA
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185
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Oliveira DVNP, Zhang S, Chen X, Calvisi DF, Andersen JB. Molecular profiling of intrahepatic cholangiocarcinoma: the search for new therapeutic targets. Expert Rev Gastroenterol Hepatol 2017; 11:349-356. [PMID: 28162004 DOI: 10.1080/17474124.2017.1292127] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is the second most frequent primary tumor of the liver and a highly lethal disease. Therapeutic options for advanced iCCA are limited and ineffective due to the largely incomplete understanding of the molecular pathogenesis of this deadly tumor. Areas covered: The present review article outlines the main studies and resulting discoveries on the molecular profiling of iCCA, with a special emphasis on the different techniques used for this purpose, the diagnostic and prognostic markers identified, as well as the genes and pathways that could be potentially targeted with innovative therapies. Expert commentary: Molecular profiling has led to the identification of distinct iCCA subtypes, characterized by peculiar genetic alterations and transcriptomic features. Targeted therapies against some of the identified genes are ongoing and hold great promise to improve the prognosis of iCCA patients.
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Affiliation(s)
- Douglas V N P Oliveira
- a Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences , University of Copenhagen , Copenhagen N , Denmark
| | - Shanshan Zhang
- b Department of Bioengineering and Therapeutic Sciences and Liver Center , University of California , San Francisco , CA , USA
| | - Xin Chen
- b Department of Bioengineering and Therapeutic Sciences and Liver Center , University of California , San Francisco , CA , USA
| | - Diego F Calvisi
- c Institute of Pathology, University Medicine of Greifswald , Greifswald , Germany
| | - Jesper B Andersen
- a Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences , University of Copenhagen , Copenhagen N , Denmark
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186
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Ahn DH, Bekaii-Saab T. Biliary cancer: intrahepatic cholangiocarcinoma vs. extrahepatic cholangiocarcinoma vs. gallbladder cancers: classification and therapeutic implications. J Gastrointest Oncol 2017; 8:293-301. [PMID: 28480068 DOI: 10.21037/jgo.2016.10.01] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Biliary cancers (BCs) are a diverse group of tumors that arise from the bile duct epithelium and are divided into cholangiocarcinomas of the intrahepatic and extrahepatic cholangiocarcinoma (EHCC) and cancer of the gallbladder. Despite improvements in treatment and diagnosis, BCs are often diagnosed at an advanced stage and associated with poor prognosis and limited treatment options. Recent discoveries have allowed us to have a better understanding of the genomic diversity in BC, and identify genes that are likely contributing to its pathogenesis, proliferation and treatment resistance. Additionally, these advances have allowed us to reason that each anatomic group within BC behave as distinct diseases, with differences in prognosis and outcomes. Based on this knowledge, recent advances have allowed us to identify actionable mutations that form rational therapeutic targets with novel agents, where their relevance will be better understood through the completion of prospective clinical trials.
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Affiliation(s)
- Daniel H Ahn
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
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187
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Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep 2017; 18:2780-2794. [PMID: 28297679 PMCID: PMC5493145 DOI: 10.1016/j.celrep.2017.02.033] [Citation(s) in RCA: 333] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 01/04/2017] [Accepted: 02/09/2017] [Indexed: 02/07/2023] Open
Abstract
Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.
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Affiliation(s)
- Farshad Farshidfar
- Departments of Surgery and Oncology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Siyuan Zheng
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yulia Newton
- University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Juliann Shih
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Toshinori Hinoue
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Katherine A Hoadley
- Departments of Genetics and Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ewan A Gibb
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Jason Roszik
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kyle R Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chia-Chin Wu
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Apurva Hegde
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ju Dong Yang
- Divisions of Gastroenterology and Hepatology and Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Ed Reznik
- Memorial Sloan Kettering Cancer Center, New York, NY 10005, USA
| | - Sara Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Chandra Sekhar Pedamallu
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Akinyemi I Ojesina
- University of Alabama at Birmingham, Birmingham, AL 35294, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Julian M Hess
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - J Todd Auman
- Departments of Genetics and Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Suhn K Rhie
- USC/Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Mitesh J Borad
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, AZ 85054, USA
| | - Andrew X Zhu
- Departments of Hematology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Josh M Stuart
- University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chris Sander
- Memorial Sloan Kettering Cancer Center, New York, NY 10005, USA
| | - Rehan Akbani
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Vikram Deshpande
- Departments of Pathology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Taofic Mounajjed
- Divisions of Gastroenterology and Hepatology and Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Wai Chin Foo
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael S Torbenson
- Divisions of Gastroenterology and Hepatology and Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Autumn J McRee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oliver F Bathe
- Departments of Surgery and Oncology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jesper B Andersen
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
| | - Nabeel Bardeesy
- Departments of Pathology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Lewis R Roberts
- Divisions of Gastroenterology and Hepatology and Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Lawrence N Kwong
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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188
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Goyal L, Saha SK, Liu LY, Siravegna G, Leshchiner I, Ahronian LG, Lennerz JK, Vu P, Deshpande V, Kambadakone A, Mussolin B, Reyes S, Henderson L, Sun JE, Van Seventer EE, Gurski JM, Baltschukat S, Schacher-Engstler B, Barys L, Stamm C, Furet P, Ryan DP, Stone JR, Iafrate AJ, Getz G, Porta DG, Tiedt R, Bardelli A, Juric D, Corcoran RB, Bardeesy N, Zhu AX. Polyclonal Secondary FGFR2 Mutations Drive Acquired Resistance to FGFR Inhibition in Patients with FGFR2 Fusion-Positive Cholangiocarcinoma. Cancer Discov 2017; 7:252-263. [PMID: 28034880 PMCID: PMC5433349 DOI: 10.1158/2159-8290.cd-16-1000] [Citation(s) in RCA: 355] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/21/2016] [Accepted: 12/27/2016] [Indexed: 12/16/2022]
Abstract
Genetic alterations in the fibroblast growth factor receptor (FGFR) pathway are promising therapeutic targets in many cancers, including intrahepatic cholangiocarcinoma (ICC). The FGFR inhibitor BGJ398 displayed encouraging efficacy in patients with FGFR2 fusion-positive ICC in a phase II trial, but the durability of response was limited in some patients. Here, we report the molecular basis for acquired resistance to BGJ398 in three patients via integrative genomic characterization of cell-free circulating tumor DNA (cfDNA), primary tumors, and metastases. Serial analysis of cfDNA demonstrated multiple recurrent point mutations in the FGFR2 kinase domain at progression. Accordingly, biopsy of post-progression lesions and rapid autopsy revealed marked inter- and intralesional heterogeneity, with different FGFR2 mutations in individual resistant clones. Molecular modeling and in vitro studies indicated that each mutation led to BGJ398 resistance and was surmountable by structurally distinct FGFR inhibitors. Thus, polyclonal secondary FGFR2 mutations represent an important clinical resistance mechanism that may guide the development of future therapeutic strategies.Significance: We report the first genetic mechanisms of clinical acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive ICC. Our findings can inform future strategies for detecting resistance mechanisms and inducing more durable remissions in ICC and in the wide variety of cancers where the FGFR pathway is being explored as a therapeutic target. Cancer Discov; 7(3); 252-63. ©2016 AACR.See related commentary by Smyth et al., p. 248This article is highlighted in the In This Issue feature, p. 235.
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MESH Headings
- Adult
- Antineoplastic Agents/therapeutic use
- Bile Duct Neoplasms/drug therapy
- Bile Duct Neoplasms/genetics
- Bile Duct Neoplasms/pathology
- Cell Cycle Proteins
- Cholangiocarcinoma/drug therapy
- Cholangiocarcinoma/genetics
- Cholangiocarcinoma/pathology
- Circulating Tumor DNA/genetics
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Fusion
- Humans
- Male
- Membrane Transport Proteins
- Middle Aged
- Mutation
- Phenylurea Compounds/therapeutic use
- Pyrimidines/therapeutic use
- Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 2/chemistry
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 3/chemistry
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Transcription Factor TFIIIA/genetics
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Affiliation(s)
- Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Supriya K Saha
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Leah Y Liu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Giulia Siravegna
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Torino, Italy
- Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology (IFOM), Milano, Italy
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Leanne G Ahronian
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Phuong Vu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Avinash Kambadakone
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Stephanie Reyes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Laura Henderson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jiaoyuan Elisabeth Sun
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Emily E Van Seventer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Joseph M Gurski
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Sabrina Baltschukat
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | | | - Louise Barys
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Christelle Stamm
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Basel, Switzerland
| | - David P Ryan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Diana Graus Porta
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Ralph Tiedt
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Alberto Bardelli
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Torino, Italy
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
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189
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Sia D, Villanueva A, Friedman SL, Llovet JM. Liver Cancer Cell of Origin, Molecular Class, and Effects on Patient Prognosis. Gastroenterology 2017; 152:745-761. [PMID: 28043904 DOI: 10.1053/j.gastro.2016.11.048] [Citation(s) in RCA: 727] [Impact Index Per Article: 103.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/09/2016] [Accepted: 11/26/2016] [Indexed: 12/11/2022]
Abstract
Primary liver cancer is the second leading cause of cancer-related death worldwide and therefore a major public health challenge. We review hypotheses of the cell of origin of liver tumorigenesis and clarify the classes of liver cancer based on molecular features and how they affect patient prognosis. Primary liver cancer comprises hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (iCCA), and other rare tumors, notably fibrolamellar carcinoma and hepatoblastoma. The molecular and clinical features of HCC versus iCCA are distinct, but these conditions have overlapping risk factors and pathways of oncogenesis. A better understanding of the cell types originating liver cancer can aid in exploring molecular mechanisms of carcinogenesis and therapeutic options. Molecular studies have identified adult hepatocytes as the cell of origin. These cells have been proposed to transform directly into HCC cells (via a sequence of genetic alterations), to dedifferentiate into hepatocyte precursor cells (which then become HCC cells that express progenitor cell markers), or to transdifferentiate into biliary-like cells (which give rise to iCCA). Alternatively, progenitor cells also give rise to HCCs and iCCAs with markers of progenitor cells. Advances in genome profiling and next-generation sequencing have led to the classification of HCCs based on molecular features and assigned them to categories such as proliferation-progenitor, proliferation-transforming growth factor β, and Wnt-catenin β1. iCCAs have been assigned to categories of proliferation and inflammation. Overall, proliferation subclasses are associated with a more aggressive phenotype and poor outcome of patients, although more specific signatures have refined our prognostic abilities. Analyses of genetic alterations have identified those that might be targeted therapeutically, such as fusions in the FGFR2 gene and mutations in genes encoding isocitrate dehydrogenases (in approximately 60% of iCCAs) or amplifications at 11q13 and 6p21 (in approximately 15% of HCCs). Further studies of these alterations are needed before they can be used as biomarkers in clinical decision making.
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Affiliation(s)
- Daniela Sia
- Mount Sinai Liver Cancer Program, Divisions of Liver Diseases, Hematology, and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Augusto Villanueva
- Mount Sinai Liver Cancer Program, Divisions of Liver Diseases, Hematology, and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Scott L Friedman
- Mount Sinai Liver Cancer Program, Divisions of Liver Diseases, Hematology, and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Josep M Llovet
- Mount Sinai Liver Cancer Program, Divisions of Liver Diseases, Hematology, and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Liver Cancer Translational Research Laboratory, BCLC, Liver Unit, CIBEREHD, IDIBAPS, Hospital Clinic, University of Barcelona, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain.
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190
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Walter D, Döring C, Feldhahn M, Battke F, Hartmann S, Winkelmann R, Schneider M, Bankov K, Schnitzbauer A, Zeuzem S, Hansmann ML, Peveling-Oberhag J. Intratumoral heterogeneity of intrahepatic cholangiocarcinoma. Oncotarget 2017; 8:14957-14968. [PMID: 28146430 PMCID: PMC5362457 DOI: 10.18632/oncotarget.14844] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/16/2017] [Indexed: 02/06/2023] Open
Abstract
No personalized therapy regimens could demonstrate a benefit in survival of intrahepatic cholangiocarcinoma (iCCA). Since genetic heterogeneity might influence single biopsy based targeted therapy or the outcome of clinical trials, aim of the present study was to investigate intratumoral heterogeneity of iCCA by whole exome sequencing. Therefore, samples from tumor center and tumor periphery of large iCCA lesions as well as a control from healthy liver tissue were obtained from four patients and whole exome sequencing was performed. Mutations that occurred only in the tumor center or periphery were defined as private, whereas mutations present in both samples were regarded as common. A mean of 3 non-synonymous private mutations (range 0-14) per sample compared to 33,3 common mutations per sample (range 24-41) was identified. Mean percentage of non-synonymous private mutations per sample was 12% (range 0-58). In all samples of patient 1-3 as well as the central sample of patient 4 ≤ 10% private mutations were found, whereas 58% of private mutations were identified in the peripheral sample of patient 4. In this sample a private mutation in the DNA mismatch repair protein MSH6 could be identified most likely causing the high amount of private mutations. No substantial intratumoral heterogeneity was found in copy number variation analysis. In conclusion, iCCA show a small but distinct intratumoral heterogeneity. Somatic mutations in mismatch repair proteins might contribute significantly to increased spatial tumor burden and thereby may influence clinical management.
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Affiliation(s)
- Dirk Walter
- Department of Internal Medicine I, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | | | | | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Markus Schneider
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Katrin Bankov
- Department of Internal Medicine I, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Andreas Schnitzbauer
- Department of General and Visceral Surgery, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine I, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Martin Leo Hansmann
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
| | - Jan Peveling-Oberhag
- Department of Internal Medicine I, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University Hospital, 60590 Frankfurt, Germany
- Department for Gastroenterology, Hepatology and Endocrinology, Robert-Bosch Hospital, 70376 Stuttgart, Germany
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191
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Rahnemai-Azar AA, Weisbrod A, Dillhoff M, Schmidt C, Pawlik TM. Intrahepatic cholangiocarcinoma: Molecular markers for diagnosis and prognosis. Surg Oncol 2017; 26:125-137. [PMID: 28577718 DOI: 10.1016/j.suronc.2016.12.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/24/2016] [Accepted: 12/29/2016] [Indexed: 02/08/2023]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver tumor with increasing incidence worldwide. The outcome of patients with iCCA is dismal owing to tumor's aggressiveness, late diagnosis and lack of effective treatment options. Detection of the tumor at early stages may make surgical resection, as only potential curative treatment, more feasible. Unfortunately, despite recent developments in imaging modalities and laboratory tests, the diagnosis of iCCA remains challenging and patients often present in advanced stages when surgery cannot be offered. Moreover, accurate assessment of disease burden is critical to optimize management strategy, including the use of adjuvant therapies and clinical trials. Identifying iCCA specific diagnostic and prognostic biomarkers has been a focus of interest among many investigators with a progressive increase in data on iCCA related to advances in "omics" technologies. We herein summarize iCCA biomarkers and define the molecular mechanisms underlying iCCA carcinogenesis, as well as highlight potential diagnostic and prognostic application of molecular biomarkers.
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Affiliation(s)
- Amir A Rahnemai-Azar
- Department of Surgery, University of Washington Medical Center, Seattle, WA, USA
| | - Allison Weisbrod
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Mary Dillhoff
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Carl Schmidt
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Timothy M Pawlik
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
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192
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Ahn DH, Ozer HG, Hancioglu B, Lesinski GB, Timmers C, Bekaii-Saab T. Whole-exome tumor sequencing study in biliary cancer patients with a response to MEK inhibitors. Oncotarget 2017; 7:5306-12. [PMID: 26683364 PMCID: PMC4868687 DOI: 10.18632/oncotarget.6632] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/12/2015] [Indexed: 12/13/2022] Open
Abstract
We previously conducted a phase-II study with selumetinib (AZD6244), a small molecule inhibitor of MEK1/2, in advanced biliary tract cancers (BTC), where the primary endpoint was response rate. Several patients experienced objective response. These findings were confirmed with MEK162 in a similar patient population. To assess for tumor-specific genetic variants that mediate sensitivity to MEK inhibition in BTC, we performed whole-exome sequencing in patients with an objective response to selumetinib. Normal and tumor DNA from FFPE tissue from two patients who experienced an objective response underwent whole-exome sequencing. Raw sequence reads were processed with GATK workflow and tumor specific variants were identified using MuTect and VarScan2. Ensemble Variant Effect Predictor was used to determine functional consequences of these variants. Copy number changes and potential gene fusion events were also screened. Findings were compared to assess for any commonality between the two tumor samples, and whether the identified variants were intrinsic to the MAPK pathway. 1169 and 628 tumor-specific variants were identified in the two samples. Further analysis demonstrated 60 and 53 functional and novel variants, respectively. Of the identified tumor-specific variants, fusion events or copy number changes, no commonality was seen. Several variants in genes associated with ERK signaling were present in each tumor sample. Although there were no common tumor-specific variants in the two patients who exhibited an objective response to selumetinib, several genes associated with ERK signaling were identified. Confirmatory studies investigating the role of the identified genes and other potential tumor independent factors need further investigation.
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Affiliation(s)
- Daniel H Ahn
- Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Hatice Gulcin Ozer
- Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - Baris Hancioglu
- Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - Gregory B Lesinski
- Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Cynthia Timmers
- Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Tanios Bekaii-Saab
- Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
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193
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Sicklick JK, Fanta PT, Shimabukuro K, Kurzrock R. Genomics of gallbladder cancer: the case for biomarker-driven clinical trial design. Cancer Metastasis Rev 2017; 35:263-75. [PMID: 26857926 DOI: 10.1007/s10555-016-9602-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Gallbladder carcinoma is a rare, aggressive malignancy of the biliary tract associated with a poor prognosis. Despite the deployment of targeted therapies that have demonstrated marked survival benefits in many tumor types, traditional cytotoxic chemotherapy has remained the mainstay of treatment for unresectable and metastatic gallbladder cancer. METHODS Systematic review of ongoing and prior clinical studies shows a paucity of biomarker-driven therapeutic trials using targeted agents in gallbladder cancer. In fact, over the past 6 years, of the 38 therapeutic biliary tract protocols listed on clinicaltrials.gov, only 6 (21 %) utilized targeted therapies based upon tumor biomarkers or genomics. Now that we have entered the era of next-generation sequencing and precision medicine, we are beginning to identify common and specific genetic alterations in gallbladder carcinomas. RESULTS A review of the literature reveals alterations in ARID1A, BRAF, CDKN2A/B, EGFR, ERBB2-4, HKN-RAS, PIK3CA, PBRM1, and TP53. Given the widespread use of tumor genomic profiling and the fact that most of the aforementioned alterations are pharmacologically tractable, these observations suggest the potential for new therapeutic strategies in this aggressive malignancy. CONCLUSIONS Taken together, further understanding of the genomic landscape of gallbladder cancer coupled with biomarker-driven clinical trials that match therapies to targets are urgently needed.
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Affiliation(s)
- Jason K Sicklick
- Center for Personalized Cancer Therapy, San Diego, CA, USA. .,Division of Surgical Oncology, Department of Surgery, University of California, San Diego Moores Cancer Center, 3855 Health Sciences Drive, MC 0987, La Jolla, CA, 92093-0987, USA.
| | - Paul T Fanta
- Center for Personalized Cancer Therapy, San Diego, CA, USA.,Division of Hematology and Oncology, University of California, San Diego Moores Cancer Center, 3855 Health Sciences Drive, MC 0987, La Jolla, 92093-0987, CA, USA
| | - Kelly Shimabukuro
- Center for Personalized Cancer Therapy, San Diego, CA, USA.,Division of Hematology and Oncology, University of California, San Diego Moores Cancer Center, 3855 Health Sciences Drive, MC 0987, La Jolla, 92093-0987, CA, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, San Diego, CA, USA.,Division of Hematology and Oncology, University of California, San Diego Moores Cancer Center, 3855 Health Sciences Drive, MC 0987, La Jolla, 92093-0987, CA, USA
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194
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Borad MJ, Egan JB, Condjella RM, Liang WS, Fonseca R, Ritacca NR, McCullough AE, Barrett MT, Hunt KS, Champion MD, Patel MD, Young SW, Silva AC, Ho TH, Halfdanarson TR, McWilliams RR, Lazaridis KN, Ramanathan RK, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Cuyugan L, McDonald J, Adkins J, Mastrian SD, Valdez R, Jaroszewski DE, Von Hoff DD, Craig DW, Stewart AK, Carpten JD, Bryce AH. Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers. Sci Rep 2016; 6:25. [PMID: 28003660 PMCID: PMC5431338 DOI: 10.1038/s41598-016-0021-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/02/2016] [Indexed: 12/20/2022] Open
Abstract
DNA focused panel sequencing has been rapidly adopted to assess therapeutic targets in advanced/refractory cancer. Integrated Genomic Profiling (IGP) utilising DNA/RNA with tumour/normal comparisons in a Clinical Laboratory Improvement Amendments (CLIA) compliant setting enables a single assay to provide: therapeutic target prioritisation, novel target discovery/application and comprehensive germline assessment. A prospective study in 35 advanced/refractory cancer patients was conducted using CLIA-compliant IGP. Feasibility was assessed by estimating time to results (TTR), prioritising/assigning putative therapeutic targets, assessing drug access, ascertaining germline alterations, and assessing patient preferences/perspectives on data use/reporting. Therapeutic targets were identified using biointelligence/pathway analyses and interpreted by a Genomic Tumour Board. Seventy-five percent of cases harboured 1–3 therapeutically targetable mutations/case (median 79 mutations of potential functional significance/case). Median time to CLIA-validated results was 116 days with CLIA-validation of targets achieved in 21/22 patients. IGP directed treatment was instituted in 13 patients utilising on/off label FDA approved drugs (n = 9), clinical trials (n = 3) and single patient IND (n = 1). Preliminary clinical efficacy was noted in five patients (two partial response, three stable disease). Although barriers to broader application exist, including the need for wider availability of therapies, IGP in a CLIA-framework is feasible and valuable in selection/prioritisation of anti-cancer therapeutic targets.
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Affiliation(s)
- Mitesh J Borad
- Division of Hematology/Oncology Mayo Clinic, Scottsdale, AZ, USA. .,Mayo Clinic Cancer Center, Scottsdale, AZ, USA. .,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Jan B Egan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Rafael Fonseca
- Division of Hematology/Oncology Mayo Clinic, Scottsdale, AZ, USA.,Mayo Clinic Cancer Center, Scottsdale, AZ, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Michael T Barrett
- Mayo Clinic Cancer Center, Scottsdale, AZ, USA.,Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Katherine S Hunt
- Division of Hematology/Oncology Mayo Clinic, Scottsdale, AZ, USA
| | - Mia D Champion
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biomedical Statistics and Informatics, Mayo Clinic, Scottsdale, AZ, USA
| | | | - Scott W Young
- Department of Radiology, Mayo Clinic, Scottsdale, AZ, USA
| | - Alvin C Silva
- Department of Radiology, Mayo Clinic, Scottsdale, AZ, USA
| | - Thai H Ho
- Division of Hematology/Oncology Mayo Clinic, Scottsdale, AZ, USA.,Mayo Clinic Cancer Center, Scottsdale, AZ, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Thorvardur R Halfdanarson
- Division of Hematology/Oncology Mayo Clinic, Scottsdale, AZ, USA.,Mayo Clinic Cancer Center, Scottsdale, AZ, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Robert R McWilliams
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Mayo Clinic Cancer Center, Rochester, MN, USA
| | | | - Ramesh K Ramanathan
- Division of Hematology/Oncology Mayo Clinic, Scottsdale, AZ, USA.,Mayo Clinic Cancer Center, Scottsdale, AZ, USA
| | - Angela Baker
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Ahmet Kurdoglu
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Tyler Izatt
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Irene Cherni
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sara Nasser
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Rebecca Reiman
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Lori Cuyugan
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | | | | | | | | | - David W Craig
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - A Keith Stewart
- Division of Hematology/Oncology Mayo Clinic, Scottsdale, AZ, USA.,Mayo Clinic Cancer Center, Scottsdale, AZ, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - John D Carpten
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Alan H Bryce
- Division of Hematology/Oncology Mayo Clinic, Scottsdale, AZ, USA.,Mayo Clinic Cancer Center, Scottsdale, AZ, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
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195
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Wong JKL, Campbell D, Ngo ND, Yeung F, Cheng G, Tang CSM, Chung PHY, Tran NS, So MT, Cherny SS, Sham PC, Tam PK, Garcia-Barcelo MM. Genetic study of congenital bile-duct dilatation identifies de novo and inherited variants in functionally related genes. BMC Med Genomics 2016; 9:75. [PMID: 27955658 PMCID: PMC5154011 DOI: 10.1186/s12920-016-0236-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/07/2016] [Indexed: 12/18/2022] Open
Abstract
Background Congenital dilatation of the bile-duct (CDD) is a rare, mostly sporadic, disorder that results in bile retention with severe associated complications. CDD affects mainly Asians. To our knowledge, no genetic study has ever been conducted. Methods We aim to identify genetic risk factors by a “trio-based” exome-sequencing approach, whereby 31 CDD probands and their unaffected parents were exome-sequenced. Seven-hundred controls from the local population were used to detect gene-sets significantly enriched with rare variants in CDD patients. Results Twenty-one predicted damaging de novo variants (DNVs; 4 protein truncating and 17 missense) were identified in several evolutionarily constrained genes (p < 0.01). Six genes carrying DNVs were associated with human developmental disorders involving epithelial, connective or bone morphologies (PXDN, RTEL1, ANKRD11, MAP2K1, CYLD, ACAN) and four linked with cholangio- and hepatocellular carcinomas (PIK3CA, TLN1 CYLD, MAP2K1). Importantly, CDD patients have an excess of DNVs in cancer-related genes (p < 0.025). Thirteen genes were recurrently mutated at different sites, forming compound heterozygotes or functionally related complexes within patients. Conclusions Our data supports a strong genetic basis for CDD and show that CDD is not only genetically heterogeneous but also non-monogenic, requiring mutations in more than one genes for the disease to develop. The data is consistent with the rarity and sporadic presentation of CDD. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0236-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John K L Wong
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China
| | - Desmond Campbell
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China
| | | | - Fanny Yeung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Guo Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Patrick H Y Chung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China.,Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Pak C Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China.,Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Paul K Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Maria-Mercè Garcia-Barcelo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China. .,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
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196
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Bryce AH, Borad MJ, Egan JB, Condjella RM, Liang WS, Fonseca R, McCullough AE, Hunt KS, Ritacca NR, Barrett MT, Patel MD, Young SW, Silva AC, Ho TH, Halfdanarson TR, Stanton ML, Cheville J, Swanson S, Schneider DE, McWilliams RR, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Cuyugan L, McDonald J, Adkins J, Mastrian SD, Von Hoff DD, Craig DW, Stewart AK, Carpten JD. Comprehensive Genomic Analysis of Metastatic Mucinous Urethral Adenocarcinoma Guides Precision Oncology Treatment: Targetable EGFR Amplification Leading to Successful Treatment With Erlotinib. Clin Genitourin Cancer 2016; 15:e727-e734. [PMID: 28057415 PMCID: PMC7513310 DOI: 10.1016/j.clgc.2016.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/20/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Alan H Bryce
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ; Mayo Clinic Cancer Center, Phoenix, AZ; Center for Individualized Medicine, Mayo Clinic, Rochester, MN.
| | - Mitesh J Borad
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ; Mayo Clinic Cancer Center, Phoenix, AZ; Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Jan B Egan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Rafael Fonseca
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ; Mayo Clinic Cancer Center, Phoenix, AZ; Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Ann E McCullough
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ
| | | | | | - Michael T Barrett
- Mayo Clinic Cancer Center, Phoenix, AZ; Translational Genomics Research Institute, Phoenix, AZ
| | | | - Scott W Young
- Department of Radiology, Mayo Clinic, Scottsdale, AZ
| | - Alvin C Silva
- Department of Radiology, Mayo Clinic, Scottsdale, AZ
| | - Thai H Ho
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ; Mayo Clinic Cancer Center, Phoenix, AZ; Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Thorvardur R Halfdanarson
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ; Mayo Clinic Cancer Center, Phoenix, AZ; Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Melissa L Stanton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ
| | - John Cheville
- Department of Anatomic and Clinical Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Robert R McWilliams
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Mayo Clinic Cancer Center, Rochester, MN
| | - Angela Baker
- Translational Genomics Research Institute, Phoenix, AZ
| | | | | | - Tyler Izatt
- Translational Genomics Research Institute, Phoenix, AZ
| | | | - Irene Cherni
- Translational Genomics Research Institute, Phoenix, AZ
| | - Sara Nasser
- Translational Genomics Research Institute, Phoenix, AZ
| | | | - Lori Cuyugan
- Translational Genomics Research Institute, Phoenix, AZ
| | | | | | | | | | - David W Craig
- Translational Genomics Research Institute, Phoenix, AZ
| | - A Keith Stewart
- Division of Hematology/Oncology, Mayo Clinic, Phoenix, AZ; Mayo Clinic Cancer Center, Phoenix, AZ; Center for Individualized Medicine, Mayo Clinic, Rochester, MN
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197
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Squadroni M, Tondulli L, Gatta G, Mosconi S, Beretta G, Labianca R. Cholangiocarcinoma. Crit Rev Oncol Hematol 2016; 116:11-31. [PMID: 28693792 DOI: 10.1016/j.critrevonc.2016.11.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 11/07/2016] [Accepted: 11/22/2016] [Indexed: 12/15/2022] Open
Abstract
Biliary tract cancer accounts for <1% of all cancers and affects chiefly an elderly population, with predominance in men. We distinguish cholangiocarcinoma (intrahepatic, hilar and distal) and gallbladder cancer, with different pathogenesis and prognosis. The treatment is based on surgery (whenever possible), radiotherapy in selected cases, and chemotherapy. The standard cytotoxic treatment for advanced/metastatic disease is represented by the combination of gemcitabine and cisplatin, whereas fluoropyrimidines are generally administered in second line setting. At the present time, no biologic drug demonstrated a clear efficacy in this cancer, although the molecular characterisation could provide a promising basis for experimental treatments. A good supportive care and an early palliative care are warranted in most patients and should be delivered as a part of a global approach.
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Affiliation(s)
| | - Luca Tondulli
- Medical Oncology Unit, Borgo Roma Hospital, Verona, Italy
| | - Gemma Gatta
- Italian National Cancer Institute, Milan, Italy
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198
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Haslem DS, Van Norman SB, Fulde G, Knighton AJ, Belnap T, Butler AM, Rhagunath S, Newman D, Gilbert H, Tudor BP, Lin K, Stone GR, Loughmiller DL, Mishra PJ, Srivastava R, Ford JM, Nadauld LD. A Retrospective Analysis of Precision Medicine Outcomes in Patients With Advanced Cancer Reveals Improved Progression-Free Survival Without Increased Health Care Costs. J Oncol Pract 2016; 13:e108-e119. [PMID: 27601506 PMCID: PMC5455156 DOI: 10.1200/jop.2016.011486] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose: The advent of genomic diagnostic technologies such as next-generation sequencing has recently enabled the use of genomic information to guide targeted treatment in patients with cancer, an approach known as precision medicine. However, clinical outcomes, including survival and the cost of health care associated with precision cancer medicine, have been challenging to measure and remain largely unreported. Patients and Methods: We conducted a matched cohort study of 72 patients with metastatic cancer of diverse subtypes in the setting of a large, integrated health care delivery system. We analyzed the outcomes of 36 patients who received genomic testing and targeted therapy (precision cancer medicine) between July 1, 2013, and January 31, 2015, compared with 36 historical control patients who received standard chemotherapy (n = 29) or best supportive care (n = 7). Results: The average progression-free survival was 22.9 weeks for the precision medicine group and 12.0 weeks for the control group (P = .002) with a hazard ratio of 0.47 (95% CI, 0.29 to 0.75) when matching on age, sex, histologic diagnosis, and previous lines of treatment. In a subset analysis of patients who received all care within the Intermountain Healthcare system (n = 44), per patient charges per week were $4,665 in the precision treatment group and $5,000 in the control group (P = .126). Conclusion: These findings suggest that precision cancer medicine may improve survival for patients with refractory cancer without increasing health care costs. Although the results of this study warrant further validation, this precision medicine approach may be a viable option for patients with advanced cancer.
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Affiliation(s)
- Derrick S Haslem
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - S Burke Van Norman
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Gail Fulde
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Andrew J Knighton
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Tom Belnap
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Allison M Butler
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Sharanya Rhagunath
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - David Newman
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Heather Gilbert
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Brian P Tudor
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Karen Lin
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Gary R Stone
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - David L Loughmiller
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Pravin J Mishra
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Rajendu Srivastava
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - James M Ford
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
| | - Lincoln D Nadauld
- Intermountain Healthcare, Saint George and Salt Lake City; University of Utah School of Medicine, Salt Lake City, UT; Duke University School of Medicine, Durham, NC; and Stanford University School of Medicine, Stanford, CA
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199
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Ilyas SI, Borad MJ. The rise of the FGFR inhibitor in advanced biliary cancer: the next cover of time magazine? J Gastrointest Oncol 2016; 7:789-796. [PMID: 27747092 PMCID: PMC5056253 DOI: 10.21037/jgo.2016.08.12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/19/2016] [Indexed: 12/27/2022] Open
Abstract
Cholangiocarcinomas (CCAs) are heterogeneous tumors arising from the biliary tract with features of cholangiocyte differentiation. CCAs are aggressive tumors with limited treatment options and poor overall survival. Only a subset of CCA patients with early stage disease can avail potentially curative treatment options. For advanced biliary tract tumors, currently there are limited effective treatment modalities. Recent advances have provided greater insight into the genomic landscape of CCAs. The fibroblast growth factor receptor (FGFR) pathway is involved in key cellular processes essential to survival and differentiation. Accordingly, aberrant FGFR signaling has significant oncogenic potential. Recent discovery of FGFR2 gene fusions in CCA has heightened interest in FGFR inhibition in advanced biliary tract cancer. These findings have served as a catalyst for ongoing clinical investigation of FGFR inhibition in CCA patients with various FGFR signaling abnormalities. Herein, we review FGFR aberrations in CCA and their prognostic implications, FGFR targeting as a viable therapeutic option in advanced biliary tract malignancies, and future directions for development of combination approaches utilizing FGFR inhibition.
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Affiliation(s)
- Sumera I. Ilyas
- Division of Gastroenterology and Hepatology, Mayo
Clinic, Rochester, Minnesota, USA
| | - Mitesh J. Borad
- Division of Hematology and Oncology, Mayo Clinic,
Scottsdale, Arizona, USA
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200
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Wang Y, Ding X, Wang S, Moser CD, Shaleh HM, Mohamed EA, Chaiteerakij R, Allotey LK, Chen G, Miyabe K, McNulty MS, Ndzengue A, Barr Fritcher EG, Knudson RA, Greipp PT, Clark KJ, Torbenson MS, Kipp BR, Zhou J, Barrett MT, Gustafson MP, Alberts SR, Borad MJ, Roberts LR. Antitumor effect of FGFR inhibitors on a novel cholangiocarcinoma patient derived xenograft mouse model endogenously expressing an FGFR2-CCDC6 fusion protein. Cancer Lett 2016; 380:163-73. [PMID: 27216979 PMCID: PMC5119950 DOI: 10.1016/j.canlet.2016.05.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/15/2022]
Abstract
Cholangiocarcinoma is a highly lethal cancer with limited therapeutic options. Recent genomic analysis of cholangiocarcinoma has revealed the presence of fibroblast growth factor receptor 2 (FGFR2) fusion proteins in up to 13% of intrahepatic cholangiocarcinoma (iCCA). FGFR fusions have been identified as a novel oncogenic and druggable target in a number of cancers. In this study, we established a novel cholangiocarcinoma patient derived xenograft (PDX) mouse model bearing an FGFR2-CCDC6 fusion protein from a metastatic lung nodule of an iCCA patient. Using this PDX model, we confirmed the ability of the FGFR inhibitors, ponatinib, dovitinib and BGJ398, to modulate FGFR signaling, inhibit cell proliferation and induce cell apoptosis in cholangiocarcinoma tumors harboring FGFR2 fusions. In addition, BGJ398 appeared to be superior in potency to ponatinib and dovitinib in this model. Our findings provide a strong rationale for the investigation of FGFR inhibitors, particularly BGJ398, as a therapeutic option for cholangiocarcinoma patients harboring FGFR2 fusions.
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Affiliation(s)
- Yu Wang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China; Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Xiwei Ding
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA; Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shaoqing Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA; Department of Pathology, Qiqihar Medical University, Qiqihar, China
| | - Catherine D Moser
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Hassan M Shaleh
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Essa A Mohamed
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Roongruedee Chaiteerakij
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Loretta K Allotey
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Gang Chen
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Katsuyuki Miyabe
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Melissa S McNulty
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Albert Ndzengue
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Emily G Barr Fritcher
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Ryan A Knudson
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Michael S Torbenson
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jie Zhou
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Michael T Barrett
- Division of Hematology and Medical Oncology, Mayo Clinic College of Medicine, Phoenix, AZ, USA
| | - Michael P Gustafson
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Steven R Alberts
- Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mitesh J Borad
- Division of Hematology and Medical Oncology, Mayo Clinic College of Medicine, Phoenix, AZ, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Mayo Clinic Cancer Center, Rochester, MN, USA.
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