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Kamps-Hughes N, McUsic A, Kurihara L, Harkins TT, Pal P, Ray C, Ionescu-Zanetti C. ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data. PLoS One 2018; 13:e0195272. [PMID: 29630678 PMCID: PMC5890993 DOI: 10.1371/journal.pone.0195272] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/19/2018] [Indexed: 12/30/2022] Open
Abstract
The accurate detection of ultralow allele frequency variants in DNA samples is of interest in both research and medical settings, particularly in liquid biopsies where cancer mutational status is monitored from circulating DNA. Next-generation sequencing (NGS) technologies employing molecular barcoding have shown promise but significant sensitivity and specificity improvements are still needed to detect mutations in a majority of patients before the metastatic stage. To address this we present analytical validation data for ERASE-Seq (Elimination of Recurrent Artifacts and Stochastic Errors), a method for accurate and sensitive detection of ultralow frequency DNA variants in NGS data. ERASE-Seq differs from previous methods by creating a robust statistical framework to utilize technical replicates in conjunction with background error modeling, providing a 10 to 100-fold reduction in false positive rates compared to published molecular barcoding methods. ERASE-Seq was tested using spiked human DNA mixtures with clinically realistic DNA input quantities to detect SNVs and indels between 0.05% and 1% allele frequency, the range commonly found in liquid biopsy samples. Variants were detected with greater than 90% sensitivity and a false positive rate below 0.1 calls per 10,000 possible variants. The approach represents a significant performance improvement compared to molecular barcoding methods and does not require changing molecular reagents.
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Affiliation(s)
- Nick Kamps-Hughes
- Fluxion Biosciences Inc., South San Francisco, California, United States of America
| | - Andrew McUsic
- Swift Biosciences Inc., Ann Arbor, Michigan, United States of America
| | - Laurie Kurihara
- Swift Biosciences Inc., Ann Arbor, Michigan, United States of America
| | - Timothy T Harkins
- Swift Biosciences Inc., Ann Arbor, Michigan, United States of America
| | - Prithwish Pal
- Illumina Inc., San Diego, California, United States of America
| | - Claire Ray
- Illumina Inc., San Diego, California, United States of America
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202
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Yoo C, Kang J, Kim D, Kim KP, Ryoo BY, Hong SM, Hwang JJ, Jeong SY, Hwang S, Kim KH, Lee YJ, Hoeflich KP, Schmidt-Kittler O, Miller S, Choi EK. Multiplexed gene expression profiling identifies the FGFR4 pathway as a novel biomarker in intrahepatic cholangiocarcinoma. Oncotarget 2018; 8:38592-38601. [PMID: 28445152 PMCID: PMC5503556 DOI: 10.18632/oncotarget.16951] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/20/2017] [Indexed: 01/07/2023] Open
Abstract
Background The fibroblast growth factor receptor 4 (FGFR4) pathway is an essential regulatory component of bile acid synthesis, and its relationship with hepatocellular carcinoma (HCC) has been reported. We investigated the gene expression and clinical significance of FGFR4 and related pathways in intrahepatic cholangiocarcinoma (iCCA). Results The median age was 56 years (range 30–78) and 34 patients (74%) were male. Six patients (13%) had hepatitis B virus infection, with or without liver cirrhosis. Overall survival was significantly associated with FGFR4 (p = 0.004), FGF19 (p = 0.047), FGF21 (p = 0.04), and KLB (p = 0.03) expression. In the multivariate analysis with potential prognostic factors, high expression of FGF19, FGF21, and FGFR4 was significantly associated with better survival. In the analysis using the TCGA iCCA dataset, mRNA overexpression of at least 1 of the FGFR4-related genes was significantly associated with better disease-free survival (p = 0.02). Materials and Methods We assessed the expression of 98 genes in formalin-fixed paraffin embedded tumor tissue specimens from 46 patients with surgically resected iCCA using a NanoString platform. This included 10 FGF pathway genes (e.g. FGFR1-4, KLB, FGF3, 4, 19, 21, and 23), 19 distal marker genes (e.g. CYP7A1 and CYP17A1), 31 genes relevant to HCC and iCCA (e.g. AFP, TS), 18 copy number variation matched genes, and 20 control genes. Log-transformation of gene expression was performed for normalization and statistical analysis. Overall survival was correlated with gene expression (< median vs. ≥ median) using a log-rank test. The prognostic impact of FGFR4-related genes was validated using the public TCGA dataset for iCCA. Conclusions Our results indicate that mRNA expression of FGFR4-related genes may be a biomarker to define the distinctive molecular phenotype of iCCA. Future preclinical and clinical validation is required to define the role of the FGFR4 pathway in iCCA.
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Affiliation(s)
- Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jihoon Kang
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Deokhoon Kim
- Asan Institute for Life Science, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyu-Pyo Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Baek-Yeol Ryoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Jin Hwang
- Institute for Innovative Cancer Research, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seong-Yun Jeong
- Institute for Innovative Cancer Research, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Shin Hwang
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ki-Hun Kim
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young-Joo Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | | | | | - Stephen Miller
- Blueprint Medicines Corporation, Cambridge, Massachusetts, USA
| | - Eun Kyung Choi
- Institute for Innovative Cancer Research, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Radiation Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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203
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MDM2-p53 Interactions in Human Hepatocellular Carcinoma: What Is the Role of Nutlins and New Therapeutic Options? J Clin Med 2018; 7:jcm7040064. [PMID: 29584707 PMCID: PMC5920438 DOI: 10.3390/jcm7040064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/18/2022] Open
Abstract
Human hepatocellular carcinoma (HCC) is the fifth most common cancer and is associated with poor prognosis worldwide. The molecular mechanisms underlying the pathogenesis of HCC have been an area of continuing interest, and recent studies using next generation sequencing (NGS) have revealed much regarding previously unsettled issues. Molecular studies using HCC samples have been mainly targeted with the aim to identify the fundamental mechanisms contributing to HCC and identify more effective treatments. In response to cellular stresses (e.g., DNA damage or oncogenes), activated p53 elicits appropriate responses that aim at DNA repair, genetic stability, cell cycle arrest, and the deletion of DNA-damaged cells. On the other hand, the murine double minute 2 (MDM2) oncogene protein is an important cellular antagonist of p53. MDM2 negatively regulates p53 activity through the induction of p53 protein degradation. However, current research has shown that the mechanisms underlying MDM2-p53 interactions are more complex than previously thought. Microarray data have added new insight into the transcription changes in HCC. Recently, Nutlin-3 has shown potency against p53-MDM2 binding and the enhancement of p53 stabilization as well as an increment of p53 cellular accumulation with potential therapeutic effects. This review outlines the molecular mechanisms involved in the p53-MDM2 pathways, the biological factors influencing these pathways, and their roles in the pathogenesis of HCC. It also discusses the action of Nutlin-3 treatment in inducing growth arrest in HCC and elaborates on future directions in research in this area. More research on the biology of p53-MDM2 interactions may offer a better understanding of these mechanisms and discover new biomarkers, sensitive prognostic indicators as well as new therapeutic interventions in HCC.
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204
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Ng CKY, Di Costanzo GG, Terracciano LM, Piscuoglio S. Circulating Cell-Free DNA in Hepatocellular Carcinoma: Current Insights and Outlook. Front Med (Lausanne) 2018; 5:78. [PMID: 29632864 PMCID: PMC5880118 DOI: 10.3389/fmed.2018.00078] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 03/08/2018] [Indexed: 12/25/2022] Open
Abstract
Over the past decade, the advancements in massively parallel sequencing have provided a new paradigm in biomedical research to uncover the genetic basis of human diseases. Integration of ‘omics information has begun transforming clinical management of cancer patients in terms of diagnostics and treatment options, giving rise to the era of precision medicine. Currently, nucleic acids for molecular profiling for patients diagnosed with hepatocellular carcinoma (HCC) are typically obtained from resected tumor materials or transplanted neoplastic liver and occasionally from biopsies. Given the intrinsic risks associated with such invasive procedures, circulating cell-free DNA (cfDNA) has been proposed as an alternative source for tumor DNA. Circulating cfDNA is a type of cell-free nucleic acid that derives from apoptotic, necrotic, as well as living eukaryotic cells. Importantly, the detection of abnormal forms of circulating cfDNA that originate from cancer cells provides a new tool for cancer detection, disease monitoring, and molecular profiling. Currently, cfDNA is beginning to be adopted into clinical practice as a non-invasive tool to monitor disease by tracking the evolution of disease-specific genetic alterations in several major cancer types. Moreover, cfDNA is demonstrating potential clinical value as a surrogate to assess the molecular makeup of tumors and to overcome the sampling biases inherent to intra-tumor genetic heterogeneity, especially in the metastatic setting. With the improvements in ‘omics and molecular biology techniques, coupled with the increasing understanding in the molecular pathogenesis of cancer, it can be anticipated that the detection and analysis of cfDNA will become more specific and sensitive and thus enable cfDNA analysis to be used as a diagnostic aid in patients with early-stage disease and perhaps even in a screening setting. In this review, we provide an overview of the latest findings on the role and potential utility of cfDNA analysis in the diagnosis, management, and screening of HCC.
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Affiliation(s)
- Charlotte K Y Ng
- Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, Hepatology Laboratory, University of Basel, Basel, Switzerland
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205
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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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206
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Pan Q, Long X, Song L, Zhao D, Li X, Li D, Li M, Zhou J, Tang X, Ren H, Ding K. Transcriptome sequencing identified hub genes for hepatocellular carcinoma by weighted-gene co-expression analysis. Oncotarget 2018; 7:38487-38499. [PMID: 27220887 PMCID: PMC5122405 DOI: 10.18632/oncotarget.9555] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/05/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and it remains a challenge to understand the genetic mechanisms underlying hepatocarcinogenesis. A global gene network of differential expression profiles in HCC has yet to be fully characterized. In the present study, we performed transcriptome sequencing (mRNA and lncRNA) in liver cancer and cirrhotic tissues of nine HCC patients. We identified differentially expressed genes (DEGs) and constructed a weighted gene co-expression network for the DEGs. In total, 755 DEGs (747 mRNA and eight lncRNA) were identified, and several co-expression modules were significantly associated with HCC clinical traits, including tumor location, tumor grade, and the α-fetoprotein (AFP) level. Of note, we identified 15 hub genes in the module associated with AFP level, and three (SPX, AFP and ADGRE1) of four hub genes were validated in an independent HCC cohort (n=78). Identification of hub genes for HCC clinical traits has implications for further understanding of the molecular genetic basis of HCC.
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Affiliation(s)
- Qi Pan
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Xianli Long
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Liting Song
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xiaoyuan Li
- Department of Medical Oncology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Dewei Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Min Li
- Department of Hepatobiliary Surgery, Suining Central Hospital, Suining, Sichuan Province, P. R. China
| | - Jiahua Zhou
- Department of Hepatobiliary Surgery, Henan Tumor Hospital, Zhenzhou, Henan Province, P.R. China
| | - Xia Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Hong Ren
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Keyue Ding
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
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207
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Kaibori M, Sakai K, Ishizaki M, Matsushima H, De Velasco MA, Matsui K, Iida H, Kitade H, Kwon AH, Nagano H, Wada H, Haji S, Tsukamoto T, Kanazawa A, Takeda Y, Takemura S, Kubo S, Nishio K. Increased FGF19 copy number is frequently detected in hepatocellular carcinoma with a complete response after sorafenib treatment. Oncotarget 2018; 7:49091-49098. [PMID: 27384874 PMCID: PMC5226492 DOI: 10.18632/oncotarget.10077] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 05/17/2016] [Indexed: 12/23/2022] Open
Abstract
The multi-kinase inhibitor sorafenib is clinically approved for the treatment of patients with advanced hepatocellular carcinoma (HCC). We previously reported that fibroblast growth factor 3 and 4 (FGF3/FGF4) amplification is a predictor of a response to sorafenib. This study aims to analyze the relationship between FGF-FGF receptor (FGFR) genetic alterations and the response to sorafenib. Formalin-fixed, paraffin-embedded tissue specimens from HCC patients who had achieved a complete response (CR, N=6) or non-CR (N=39) to sorafenib were collected and were examined for FGF-FGFR gene alterations using next generation sequencing and copy number assay. FGFR mutations were detected in 5 of 45 (11.1%) cases. There was no significant association between FGFR mutation status and the response to sorafenib. We detected no increase in the FGF3/FGF4 copy number in CR cases. An FGF19 copy number gain was detected more frequently among CR cases (2/6, 33.3%) than among non-CR cases (2/39, 5.1%) (P = 0.024, Chi-squared test). In conclusion, a copy number gain for FGF19 may be a predictor of a response to sorafenib, in addition to FGF3/FGF4 amplification.
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Affiliation(s)
- Masaki Kaibori
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kinki University Faculty of Medicine, Osakasayama, Osaka, 589-8511, Japan
| | - Morihiko Ishizaki
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Hideyuki Matsushima
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Marco A De Velasco
- Department of Genome Biology, Kinki University Faculty of Medicine, Osakasayama, Osaka, 589-8511, Japan
| | - Kosuke Matsui
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Hiroya Iida
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Hiroaki Kitade
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - A-Hon Kwon
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Hiroaki Nagano
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Hiroshi Wada
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Seiji Haji
- Department of Surgery, Kinki University Faculty of Medicine, Osakasayama, Osaka, 589-8511, Japan
| | - Tadashi Tsukamoto
- Department of Hepato-Biliary-Pancreatic Surgery, Osaka City General Hospital, Miyakojima, Osaka, 534-0024, Japan
| | - Akishige Kanazawa
- Department of Hepato-Biliary-Pancreatic Surgery, Osaka City General Hospital, Miyakojima, Osaka, 534-0024, Japan
| | - Yutaka Takeda
- Department of Surgery, Kansai Rosai Hospital, Amagasaki, Hyogo, 660-8511, Japan
| | - Shigekazu Takemura
- Department of Hepato-Biliary-Pancreatic Surgery, Osaka City University Graduate School of Medicine, Osaka, 558-8585, Japan
| | - Shoji Kubo
- Department of Hepato-Biliary-Pancreatic Surgery, Osaka City University Graduate School of Medicine, Osaka, 558-8585, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kinki University Faculty of Medicine, Osakasayama, Osaka, 589-8511, Japan
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208
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Kancherla V, Abdullazade S, Matter MS, Lanzafame M, Quagliata L, Roma G, Hoshida Y, Terracciano LM, Ng CKY, Piscuoglio S. Genomic Analysis Revealed New Oncogenic Signatures in TP53-Mutant Hepatocellular Carcinoma. Front Genet 2018; 9:2. [PMID: 29456550 PMCID: PMC5801302 DOI: 10.3389/fgene.2018.00002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/03/2018] [Indexed: 01/04/2023] Open
Abstract
The TP53 gene is the most commonly mutated gene in human cancers and mutations in TP53 have been shown to have either gain-of-function or loss-of-function effects. Using the data generated by The Cancer Genome Atlas, we sought to define the spectrum of TP53 mutations in hepatocellular carcinomas (HCCs) and their association with clinicopathologic features, and to determine the oncogenic and mutational signatures in TP53-mutant HCCs. Compared to other cancer types, HCCs harbored distinctive mutation hotspots at V157 and R249, whereas common mutation hotspots in other cancer types, R175 and R273, were extremely rare in HCCs. In terms of clinicopathologic features, in addition to the associations with chronic viral infection and high Edmondson grade, we found that TP53 somatic mutations were less frequent in HCCs with cholestasis or tumor infiltrating lymphocytes, but were more frequent in HCCs displaying necrotic areas. An analysis of the oncogenic signatures based on the genetic alterations found in genes recurrently altered in HCCs identified four distinct TP53-mutant subsets, three of which were defined by CTNNB1 mutations, 1q amplifications or 8q24 amplifications, respectively, that co-occurred with TP53 mutations. We also found that mutational signature 12, a liver cancer-specific signature characterized by T>C substitutions, was prevalent in HCCs with wild-type TP53 or with missense TP53 mutations, but not in HCCs with deleterious TP53 mutations. Finally, whereas patients with HCCs harboring deleterious TP53 mutations had worse overall and disease-free survival than patients with TP53-wild-type HCCs, patients with HCCs harboring missense TP53 mutations did not have worse prognosis. In conclusion, our results highlight the importance to consider the genetic heterogeneity among TP53-mutant HCCs in studies of biomarkers and molecular characterization of HCCs.
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Affiliation(s)
| | - Samir Abdullazade
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Matthias S Matter
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Manuela Lanzafame
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Luca Quagliata
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Guglielmo Roma
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Charlotte K Y Ng
- Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
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209
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Differences in somatic mutation landscape of hepatocellular carcinoma in Asian American and European American populations. Oncotarget 2018; 7:40491-40499. [PMID: 27246981 PMCID: PMC5130022 DOI: 10.18632/oncotarget.9636] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 05/09/2016] [Indexed: 02/06/2023] Open
Abstract
The incidence rate of hepatocellular carcinoma (HCC) is higher in populations of Asian ancestry than European ancestry (EA). We sought to investigate HCC mutational differences between the two populations, which may reflect differences in the prevalence of etiological factors. We compared HCC somatic mutations in patients of self-reported Asian American and EA from The Cancer Genome Atlas (TCGA), and assessed associations of tumor mutations with established HCC risk factors. Although the average mutation burden was similar, TP53 and RB1 were mutated at a much higher frequency in Asian Americans than in EAs (TP53: 43% vs. 21%; RB1: 19% vs. 2%). Three putative oncogenic genes, including TRPM3, SAGE1, and ADAMTS7, were mutated exclusively in Asians. In addition, VEGF binding pathway, a druggable target by tyrosine kinase inhibitors such as sorafenib, was mutated at a higher frequency among Asians (13% vs. 2%); while the negative regulation of IL17 production, involved in inflammation and autoimmunity, was mutated only in EAs (12% vs. 0). Accounting for HCC risk factors had little impact on any of the mutational differences. In conclusion, we demonstrated here mutational differences in important cancer genes and pathways between Asian and European ancestries. These differences may have implications for the prevention and treatment of HCC.
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210
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Duan M, Hao J, Cui S, Worthley DL, Zhang S, Wang Z, Shi J, Liu L, Wang X, Ke A, Cao Y, Xi R, Zhang X, Zhou J, Fan J, Li C, Gao Q. Diverse modes of clonal evolution in HBV-related hepatocellular carcinoma revealed by single-cell genome sequencing. Cell Res 2018; 28:359-373. [PMID: 29327728 DOI: 10.1038/cr.2018.11] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/13/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a cancer of substantial morphologic, genetic and phenotypic diversity. Yet we do not understand the relationship between intratumor heterogeneity and the associated morphologic/histological characteristics of the tumor. Using single-cell whole-genome sequencing to profile 96 tumor cells (30-36 each) and 15 normal liver cells (5 each), collected from three male patients with HBV-associated HCC, we confirmed that copy number variations occur early in hepatocarcinogenesis but thereafter remain relatively stable throughout tumor progression. Importantly, we showed that specific HCCs can be of monoclonal or polyclonal origins. Tumors with confluent multinodular morphology are the typical polyclonal tumors and display the highest intratumor heterogeneity. In addition to mutational and copy number profiles, we dissected the clonal origins of HCC using HBV-derived foreign genomic markers. In monoclonal HCC, all the tumor single cells exhibit the same HBV integrations, indicating that HBV integration is an early driver event and remains extremely stable during tumor progression. In addition, our results indicated that both models of metastasis, late dissemination and early seeding, have a role in HCC progression. Notably, early intrahepatic spreading of the initiating clone leads to the formation of synchronous multifocal tumors. Meanwhile, we identified a potential driver gene ZNF717 in HCC, which exhibits a high frequency of mutation at both single-cell and population levels, as a tumor suppressor acting through regulating the IL-6/STAT3 pathway. These findings highlight multiple distinct tumor evolutionary mechanisms in HCC, which suggests the need for specific treatment strategies.
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Affiliation(s)
- Meng Duan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Junfeng Hao
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sijia Cui
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, Zhejiang 310002, China
| | - Daniel L Worthley
- Cancer Theme, South Australian Health and Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Zhichao Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Jieyi Shi
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Longzi Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Xiaoying Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Aiwu Ke
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Xiaoming Zhang
- Key Laboratory of Molecular Virology & Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Chong Li
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China
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211
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Milewska M, Cremona M, Morgan C, O'Shea J, Carr A, Vellanki SH, Hopkins AM, Toomey S, Madden SF, Hennessy BT, Eustace AJ. Development of a personalized therapeutic strategy for ERBB-gene-mutated cancers. Ther Adv Med Oncol 2018; 10:1758834017746040. [PMID: 29383036 PMCID: PMC5784557 DOI: 10.1177/1758834017746040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/12/2017] [Indexed: 01/21/2023] Open
Abstract
Background: The application of genomic technologies to patient tumor samples identified groups of signaling pathways which acquire activating mutations. Some cancers are dependent on these mutations and the aberrant proteins resulting from these mutations can be targeted by novel drugs which can eradicate the cancer. Methods: We used www.cbioportal.org to determine the frequency of ERBB mutations in solid tumors. We then determined the sensitivity of a panel of cell lines to clinically available PI3K inhibitors. Using proliferation and apoptosis assays as well as functional interrogation with reverse phase protein arrays we demonstrated the impact of targeting ERBB-mutant cancers with the combination of a PI3K inhibitor and the pan-HER family inhibitor afatinib. Results: In over 14,000 patients we found that 12% of their tumors have an ERBB family gene mutation (EGFR, ERBB2, ERBB3 and ERBB4). In cancers not commonly associated with HER family protein overexpression, such as ovarian, endometrial, melanoma and head and neck cancers (n = 2116), we found that ERBB family mutations are enriched, occurring at rates from 14% to 34% and commonly co-occur with PIK3CA mutations. Importantly, we demonstrate that ERBB family mutant cancers are sensitive to treatment with PI3K inhibitors. Finally we show that the combination of afatinib and copanlisib represents a novel therapeutic strategy for patients whose cancers harbor both ERBB family and PIK3CA mutation. Conclusions: We demonstrate that ERBB family mutations are common in cancers not associated with overexpression or amplification of HER family proteins. These ERBB family mutant cancers are sensitive to treatment with PI3K inhibitors, and when combined with pan-HER inhibitors have synergistic antiproliferative effects.
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Affiliation(s)
- Malgorzata Milewska
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin 9 Ireland
| | - Mattia Cremona
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin 9 Ireland
| | - Clare Morgan
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin 9 Ireland
| | - John O'Shea
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin 9 Ireland
| | - Aoife Carr
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin 9 Ireland
| | - Sri H Vellanki
- Department of Surgery, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin 9 Ireland
| | - Ann M Hopkins
- Department of Surgery, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin 9 Ireland
| | - Sinead Toomey
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin 9 Ireland
| | - Stephen F Madden
- Data Science Centre Royal College of Surgeons in Ireland, Ireland
| | - Bryan T Hennessy
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Ireland
| | - Alex J Eustace
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, ERC Smurfit Building, Dublin, 9, Ireland
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212
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Tornesello ML, Buonaguro L, Izzo F, Buonaguro FM. Molecular alterations in hepatocellular carcinoma associated with hepatitis B and hepatitis C infections. Oncotarget 2018; 7:25087-102. [PMID: 26943571 PMCID: PMC5041890 DOI: 10.18632/oncotarget.7837] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/20/2016] [Indexed: 02/07/2023] Open
Abstract
Chronic infections with hepatitis B (HBV) and hepatitis C viruses (HCV) are the leading cause of cirrhosis and hepatocellular carcinoma (HCC) worldwide. Both viruses encode multifunctional regulatory proteins activating several oncogenic pathways, which induce accumulation of multiple genetic alterations in the infected hepatocytes. Gene mutations in HBV- and HCV-induced HCCs frequently impair the TP53, Wnt/b-catenin, RAS/RAF/MAPK kinase and AKT/mTOR pathways, which represent important anti-cancer targets. In this review, we highlight the molecular mechanisms underlying the pathogenesis of primary liver cancer, with particular emphasis on the host genetic variations identified by high-throughput technologies. In addition, we discuss the importance of genetic alterations, such as mutations in the telomerase reverse transcriptase (TERT) promoter, for the diagnosis, prognosis, and tumor stratification for development of more effective treatment approaches.
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Affiliation(s)
- Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Luigi Buonaguro
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Francesco Izzo
- Hepato-Biliary Surgery Department, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Franco M Buonaguro
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
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213
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Su WH, Jou YS, Zhang JH, Ho CM, Tai DI. Mutations in NOTCH1 and nucleotide excision repair genes are correlated with prognosis of hepatitis B virus-associated hepatocellular carcinoma. J Cancer 2018; 9:2678-2686. [PMID: 30087708 PMCID: PMC6072809 DOI: 10.7150/jca.25438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/08/2018] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer and the second leading cause of cancer-related mortality because of its poor prognosis. Therefore, identifying targetable genetic mutations and mutational signatures associated with prognosis and treatment strategies are needed. Ultra-deep sequencing of 409 cancer genes using formalin-fixed paraffin-embedded tissue from 33 male patients with hepatitis B virus-associated HCC was performed to identify mutational signatures associated with the prognosis of HCC. A total of 47 genes were found to be mutated in more than 10% of patients. Chromatin remodeling genes were overrepresented in the mutation profile. We found patient survival was associated with mutations in NOTCH1 and the nucleotide excision repair genes which have not been described previously in HCC. From the mutation profile, six patients were eligible for Sorafenib treatment. Among the remaining patients, 7 patients had mutations in genes that are targets for other cancer drugs and 16 patients had mutations in potentially targetable genes. Only one patient carried no potential drug target. We identified mutational signatures associated with the patient survival of HCC. The findings may facilitate identifying subgroups of patients with a poor prognosis as well as potential drug targets for use in personalized strategies for HCC treatment.
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Affiliation(s)
- Wen-Hui Su
- Department of Biomedical Sciences, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung Molecular Medicine Research Center, Chang Gung University, 259 Wen-Hua 1st Road, Kweishan, Taoyuan 333, Taiwan
- Department of Otolaryngology, Chang Gung Memorial Hospital, Linkou, 5 Fu-Hsing Street, Kweishan, Taoyuan 333, Taiwan
- ✉ Corresponding authors: Prof. Wen-Hui Su, Department of Biomedical Sciences, Chang Gung University, 259 Wen-Hua 1st Road, Kweishan, Taoyuan 333, Taiwan. Tel: +886-3-2118800 ext. 3564; Fax: +886-3-2118700; E-mail: and Prof. Dar-In Tai, Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, 5 Fu-Hsing Street, Kweishan, Taoyuan 333, Taiwan. Tel: +886-3-3281200 ext. 8101; Fax: +886-3-3272236; E-mail:
| | - Yuh-Shan Jou
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Jia-Hao Zhang
- Department of Biomedical Sciences, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung Molecular Medicine Research Center, Chang Gung University, 259 Wen-Hua 1st Road, Kweishan, Taoyuan 333, Taiwan
| | - Chun-Ming Ho
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan
| | - Dar-In Tai
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, 5 Fu-Hsing Street, Kweishan, Taoyuan 333, Taiwan
- ✉ Corresponding authors: Prof. Wen-Hui Su, Department of Biomedical Sciences, Chang Gung University, 259 Wen-Hua 1st Road, Kweishan, Taoyuan 333, Taiwan. Tel: +886-3-2118800 ext. 3564; Fax: +886-3-2118700; E-mail: and Prof. Dar-In Tai, Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, 5 Fu-Hsing Street, Kweishan, Taoyuan 333, Taiwan. Tel: +886-3-3281200 ext. 8101; Fax: +886-3-3272236; E-mail:
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214
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Zhu S, Jin J, Gokhale S, Lu AM, Shan H, Feng J, Xie P. Genetic Alterations of TRAF Proteins in Human Cancers. Front Immunol 2018. [PMID: 30294322 DOI: 10.3389/fimmu.2018.02111/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of cytoplasmic adaptor proteins regulate the signal transduction pathways of a variety of receptors, including the TNF-R superfamily, Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs), and cytokine receptors. TRAF-dependent signaling pathways participate in a diverse array of important cellular processes, including the survival, proliferation, differentiation, and activation of different cell types. Many of these TRAF-dependent signaling pathways have been implicated in cancer pathogenesis. Here we analyze the current evidence of genetic alterations of TRAF molecules available from The Cancer Genome Atlas (TCGA) and the Catalog of Somatic Mutations in Cancer (COSMIC) as well as the published literature, including copy number variations and mutation landscape of TRAFs in various human cancers. Such analyses reveal that both gain- and loss-of-function genetic alterations of different TRAF proteins are commonly present in a number of human cancers. These include pancreatic cancer, meningioma, breast cancer, prostate cancer, lung cancer, liver cancer, head and neck cancer, stomach cancer, colon cancer, bladder cancer, uterine cancer, melanoma, sarcoma, and B cell malignancies, among others. Furthermore, we summarize the key in vivo and in vitro evidence that demonstrates the causal roles of genetic alterations of TRAF proteins in tumorigenesis within different cell types and organs. Taken together, the information presented in this review provides a rationale for the development of therapeutic strategies to manipulate TRAF proteins or TRAF-dependent signaling pathways in different human cancers by precision medicine.
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Affiliation(s)
- Sining Zhu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, United States
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ, United States
| | - Juan Jin
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, United States
- Department of Pharmacology, Anhui Medical University, Hefei, China
| | - Samantha Gokhale
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, United States
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ, United States
| | - Angeli M Lu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, United States
| | - Haiyan Shan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, United States
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jianjun Feng
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, United States
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education of the People's Republic of China, Fisheries College of Jimei University, Xiamen, China
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, United States
- Member, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
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215
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Ding Z, Shi C, Jiang L, Tolstykh T, Cao H, Bangari DS, Ryan S, Levit M, Jin T, Mamaat K, Yu Q, Qu H, Hopke J, Cindhuchao M, Hoffmann D, Sun F, Helms MW, Jahn-Hofmann K, Scheidler S, Schweizer L, Fang DD, Pollard J, Winter C, Wiederschain D. Oncogenic dependency on β-catenin in liver cancer cell lines correlates with pathway activation. Oncotarget 2017; 8:114526-114539. [PMID: 29383099 PMCID: PMC5777711 DOI: 10.18632/oncotarget.21298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022] Open
Abstract
Hepatocellular carcinoma (HCC) represents a serious public health challenge with few therapeutic options available to cancer patients.Wnt/β-catenin pathway is thought to play a significant role in HCC pathogenesis. In this study, we confirmed high frequency of CTNNB1 (β-catenin) mutations in two independent cohorts of HCC patients and demonstrated significant upregulation of β-catenin protein in the overwhelming majority of HCC patient samples, patient-derived xenografts (PDX) and established cell lines. Using genetic tools validated for target specificity through phenotypic rescue experiments, we went on to investigate oncogenic dependency on β-catenin in an extensive collection of human HCC cells lines. Our results demonstrate that dependency on β-catenin generally tracks with its activation status. HCC cell lines that harbored activating mutations in CTNNB1 or displayed elevated levels of non-phosphorylated (active) β-catenin were significantly more sensitive to β-catenin siRNA treatment than cell lines with wild-type CTNNB1 and lower active β-catenin. Finally, significant therapeutic benefit of β-catenin knock-down was demonstrated in established HCC tumor xenografts using doxycycline-inducible shRNA system. β-catenin downregulation and tumor growth inhibition was associated with reduction in AXIN2, direct transcriptional target of β-catenin, and decreased cancer cell proliferation as measured by Ki67 staining. Taken together, our data highlight fundamental importance of aberrant β-catenin signaling in the maintenance of oncogenic phenotype in HCC.
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Affiliation(s)
- Zhihu Ding
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
| | - Chaomei Shi
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
| | - Lan Jiang
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
| | | | - Hui Cao
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
| | | | - Susan Ryan
- Sanofi Translational In Vivo Models, Framingham, MA, USA
| | | | - Taiguang Jin
- Sanofi Asia Pacific R&D Hub, Shanghai, People’s Republic of China
| | - Karl Mamaat
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
- Current address: Leica Biosystems, Boston, MA
| | - Qunyan Yu
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
| | - Hui Qu
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
| | - Joern Hopke
- Sanofi Biologics Research/Molecular Screening Technology, Cambridge, MA, USA
| | - May Cindhuchao
- Sanofi Biologics Research/Molecular Screening Technology, Cambridge, MA, USA
| | - Dietmar Hoffmann
- Sanofi Biologics Research/Molecular Screening Technology, Cambridge, MA, USA
| | - Fangxian Sun
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
| | - Mike W. Helms
- Sanofi Biologics Research/Nucleic Acid Therapeutics, Frankfurt am Main, Germany
| | | | - Sabine Scheidler
- Sanofi Biologics Research/Nucleic Acid Therapeutics, Frankfurt am Main, Germany
| | - Liang Schweizer
- Sanofi Asia Pacific R&D Hub, Shanghai, People’s Republic of China
- Current address: Harbour BioMed, Shanghai, People’s Republic of China
| | - Douglas D. Fang
- Discovery Services, WuXi AppTec Co., Shanghai, China
- Current address: Ascentage Pharma Group, Ltd., Suzhou, People’s Republic of China
| | - Jack Pollard
- Sanofi Oncology Therapeutic Area, Cambridge, MA, USA
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216
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Zhu X, Kong Q, Xie L, Chen Z, Li H, Zhu Z, Huang Y, Lan F, Luo H, Zhan J, Ding H, Lei J, Xiao Q, Fu W, Fan W, Zhang J, Luo H. The single-nucleotide polymorphisms in CHD5 affect the prognosis of patients with hepatocellular carcinoma. Oncotarget 2017; 9:13222-13230. [PMID: 29568352 PMCID: PMC5862573 DOI: 10.18632/oncotarget.23812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 11/19/2017] [Indexed: 12/20/2022] Open
Abstract
Previous studies showed that the low expressions of chromodomain-helicase-DNA-binding protein 5 (CHD5) were intensively associated with deteriorative biologic and clinical characteristics as well as outcomes in many tumors. The aim of this study is to determine whether CHD5 single nucleotide polymorphisms (SNPs) contribute to the prognosis of hepatocellular carcima (HCC). The SNPs were selected according to their linkage disequilibrium (LD) in the targeted next-generation sequencing (NGS) and then genotyped with TaqMan probers. We revealed a rare haplotype AG in CHD5 (SNPs: rs12564469-rs9434711) was markedly associated with HCC prognosis. The univariate and multivariate regression analyses revealed the patients with worse overall survival time were those with tumor metastasis and haplotype AG, as well as cirrhosis, poor differentiation and IV-TNM stage. Based on the available public databases, we discovered the significant association between haplotype AG and CHD5 mRNA expressions only existed in Chinese. These data proposed that the potentially genetic haplotype might functionally contribute to HCC prognosis and CHD5 mRNA expressions.
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Affiliation(s)
- Xiao Zhu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Cancer Center, Medical College of Georgia, Georgia Health Sciences University, Augusta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Qingming Kong
- Immunity and Biochemical Research Lab, Zhejiang Academy of Medical Sciences, Hangzhou, China
| | - Liwei Xie
- Guangdong Institute of Microbiology, Guangzhou, China
| | - Zhihong Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Hongmei Li
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Zhu Zhu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Yongmei Huang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Feifei Lan
- Forensic Identification Institute, Guangdong Women and Children Hospital, Guangzhou, China
| | - Haiqing Luo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,The Affiliated Hospital Cancer Center, Guangdong Medical University, Zhanjiang, China
| | - Jingting Zhan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Hongrong Ding
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Jinli Lei
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Qin Xiao
- Department of Blood Transfusion, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weiming Fu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Wenguo Fan
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jinfang Zhang
- Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hui Luo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
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217
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Zhao H, Lv F, Liang G, Huang X, Wu G, Zhang W, Yu L, Shi L, Teng Y. FGF19 promotes epithelial-mesenchymal transition in hepatocellular carcinoma cells by modulating the GSK3β/β- catenin signaling cascade via FGFR4 activation. Oncotarget 2017; 7:13575-86. [PMID: 26498355 PMCID: PMC4924662 DOI: 10.18632/oncotarget.6185] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 10/04/2015] [Indexed: 12/12/2022] Open
Abstract
Compelling evidence suggests that the epithelial-mesenchymal transition (EMT) correlates with aggressiveness of tumors and poor survival. FGF19 has been shown to be involved in EMT in cholangiocarcinoma and colorectal cancer, however, molecular mechanisms underlying FGF19-induced EMT process in hepatocellular carcinoma (HCC) remain largely unknown. Here, we show the expression of FGF19 is significantly elevated and negatively associated with the expression of E-cadherin in HCC tissues and cell lines. Ectopic FGF19 expression promotes EMT and invasion in epithelial-like HCC cells through repression of E-cadherin expression, whereas FGF19 knockdown enhances E-cadherin expression and hence diminishes EMT traits in mesenchymal-like HCC cells, suggesting FGF19 exerts its tumor progressing functions as an EMT inducer. Interestingly, depletion of FGF19 cannot abrogate EMT traits in the presence of GSK3β inhibitors. Furthermore, FGF19-induced EMT can be markedly attenuated when FGFR4 is knocked out. These observations clearly indicate that FGFR4/GSK3β/β-catenin axis may play a pivotal role in FGF19-induced EMT in HCC cells. As FGF19 and its specific receptor FGFR4 are frequently amplified in HCC cells, selective targeting this signaling node may lend insights into a potential effective therapeutic approach for blocking metastasis of HCC.
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Affiliation(s)
- Huakan Zhao
- School of Life Sciences and School of Bioengineering, Chongqing University, Chongqing, PR China
| | - Fenglin Lv
- School of Life Sciences and School of Bioengineering, Chongqing University, Chongqing, PR China
| | - Guizhao Liang
- School of Life Sciences and School of Bioengineering, Chongqing University, Chongqing, PR China
| | - Xiaobin Huang
- School of Life Sciences and School of Bioengineering, Chongqing University, Chongqing, PR China
| | - Gang Wu
- Third Affiliated Hospital, Third Military Medical University, Chongqing, PR China
| | - Wenfa Zhang
- School of Life Sciences and School of Bioengineering, Chongqing University, Chongqing, PR China
| | - Le Yu
- School of Life Sciences and School of Bioengineering, Chongqing University, Chongqing, PR China
| | - Lei Shi
- School of Life Sciences and School of Bioengineering, Chongqing University, Chongqing, PR China
| | - Yong Teng
- School of Life Sciences and School of Bioengineering, Chongqing University, Chongqing, PR China
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218
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Abstract
The vitamin D receptor (VDR) binds the secosteroid hormone 1,25(OH)2D3 with high affinity and regulates gene programs that control a serum calcium levels, as well as cell proliferation and differentiation. A significant focus has been to exploit the VDR in cancer settings. Although preclinical studies have been strongly encouraging, to date clinical trials have delivered equivocal findings that have paused the clinical translation of these compounds. However, it is entirely possible that mining of genomic data will help to refine precisely what are the key anticancer actions of vitamin D compounds and where these can be used most effectively.
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Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, 536 Parks Hall, Columbus, OH 43210, USA.
| | - Donald L Trump
- Department of Medicine, Inova Schar Cancer Institute, Virginia Commonwealth University, 3221 Gallows Road, Fairfax, VA 22031, USA
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219
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Soh KP, Szczurek E, Sakoparnig T, Beerenwinkel N. Predicting cancer type from tumour DNA signatures. Genome Med 2017; 9:104. [PMID: 29183400 PMCID: PMC5706302 DOI: 10.1186/s13073-017-0493-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/10/2017] [Indexed: 12/13/2022] Open
Abstract
Background Establishing the cancer type and site of origin is important in determining the most appropriate course of treatment for cancer patients. Patients with cancer of unknown primary, where the site of origin cannot be established from an examination of the metastatic cancer cells, typically have poor survival. Here, we evaluate the potential and limitations of utilising gene alteration data from tumour DNA to identify cancer types. Methods Using sequenced tumour DNA downloaded via the cBioPortal for Cancer Genomics, we collected the presence or absence of calls for gene alterations for 6640 tumour samples spanning 28 cancer types, as predictive features. We employed three machine-learning techniques, namely linear support vector machines with recursive feature selection, L1-regularised logistic regression and random forest, to select a small subset of gene alterations that are most informative for cancer-type prediction. We then evaluated the predictive performance of the models in a comparative manner. Results We found the linear support vector machine to be the most predictive model of cancer type from gene alterations. Using only 100 somatic point-mutated genes for prediction, we achieved an overall accuracy of 49.4±0.4 % (95 % confidence interval). We observed a marked increase in the accuracy when copy number alterations are included as predictors. With a combination of somatic point mutations and copy number alterations, a mere 50 genes are enough to yield an overall accuracy of 77.7±0.3 %. Conclusions A general cancer diagnostic tool that utilises either only somatic point mutations or only copy number alterations is not sufficient for distinguishing a broad range of cancer types. The combination of both gene alteration types can dramatically improve the performance. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0493-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kee Pang Soh
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland.,Saw Swee Hock School of Public Health, National University of Singapore, Tahir Foundation Building, 12 Science Drive 2 MD1, Singapore, 117549, Singapore
| | - Ewa Szczurek
- Institute of Informatics, University of Warsaw, Banacha 2, Warsaw, 02-097, Poland
| | - Thomas Sakoparnig
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel, 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland.
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Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis. Nat Commun 2017; 8:1315. [PMID: 29101368 PMCID: PMC5670220 DOI: 10.1038/s41467-017-01358-x] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/12/2017] [Indexed: 12/11/2022] Open
Abstract
Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogenous cellular processes. With a diversity of risk factors, liver cancer is an ideal model to study these interactions. Here, we analyze the whole genomes of 44 new and 264 published liver cancers and we identify 10 mutational and 6 structural rearrangement signatures showing distinct relationships with environmental exposures, replication, transcription, and driver genes. The liver cancer-specific signature 16, associated with alcohol, displays a unique feature of transcription-coupled damage and is the main source of CTNNB1 mutations. Flood of insertions/deletions (indels) are identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture reveals mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin B1 signature in African migrants. Finally, chromosome duplications occur late and may represent rate-limiting events in tumorigenesis. These findings shed new light on the natural history of liver cancers. Tumorigenesis is a complex process driven by numerous risk factors. Here, genomic analysis of liver cancer reveals the evolution of mutational signatures during tumor development, highlighting mutational and structural signatures linked to environmental exposures and endogenous cellular processes.
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221
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Swamy SG, Kameshwar VH, Shubha PB, Looi CY, Shanmugam MK, Arfuso F, Dharmarajan A, Sethi G, Shivananju NS, Bishayee A. Targeting multiple oncogenic pathways for the treatment of hepatocellular carcinoma. Target Oncol 2017; 12:1-10. [PMID: 27510230 DOI: 10.1007/s11523-016-0452-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common forms of liver cancer diagnosed worldwide. HCC occurs due to chronic liver disease and is often diagnosed at advanced stages. Chemotherapeutic agents such as doxorubicin are currently used as first-line agents for HCC therapy, but these are non-selective cytotoxic molecules with significant side effects. Sorafenib, a multi-targeted tyrosine kinase inhibitor, is the only approved targeted drug for HCC patients. However, due to adverse side effects and limited efficacy, there is a need for the identification of novel pharmacological drugs beyond sorafenib. Several agents that target and inhibit various signaling pathways involved in HCC are currently being assessed for HCC treatment. In the present review article, we summarize the diverse signal transduction pathways responsible for initiation as well as progression of HCC and also the potential anticancer effects of selected targeted therapies that can be employed for HCC therapy.
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Affiliation(s)
- Supritha G Swamy
- Department of Biotechnology, JSS Science and Technology University, JSS Technical Institutions Campus, Mysore, Karnataka, 570006, India
| | - Vivek H Kameshwar
- Department of Biotechnology, JSS Science and Technology University, JSS Technical Institutions Campus, Mysore, Karnataka, 570006, India
| | - Priya B Shubha
- Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore, 570 006, Karnataka, India
| | - Chung Yeng Looi
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Frank Arfuso
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Biosciences Research Precinct, Curtin University, Bentley, Western Australia, 6009, Australia
| | - Arunasalam Dharmarajan
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Biosciences Research Precinct, Curtin University, Bentley, Western Australia, 6009, Australia
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Biosciences Research Precinct, Curtin University, Bentley, Western Australia, 6009, Australia
| | - Nanjunda Swamy Shivananju
- Department of Biotechnology, JSS Science and Technology University, JSS Technical Institutions Campus, Mysore, Karnataka, 570006, India.
| | - Anupam Bishayee
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin Health Sciences Institute, 18301 N. Miami Avenue, Miami, FL, 33169, USA.
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Calderaro J, Couchy G, Imbeaud S, Amaddeo G, Letouzé E, Blanc JF, Laurent C, Hajji Y, Azoulay D, Bioulac-Sage P, Nault JC, Zucman-Rossi J. Histological subtypes of hepatocellular carcinoma are related to gene mutations and molecular tumour classification. J Hepatol 2017; 67:727-738. [PMID: 28532995 DOI: 10.1016/j.jhep.2017.05.014] [Citation(s) in RCA: 459] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/10/2017] [Accepted: 05/15/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Our increasing understanding of hepatocellular carcinoma (HCC) biology holds promise for personalized care, however its translation into clinical practice requires a precise knowledge of its relationship to tumour phenotype. METHODS We aimed at investigating molecular-phenotypic correlations in a large series of HCC. To this purpose, 343 surgically resected HCC samples were investigated by pathological review, immunohistochemistry, gene expression profiling and sequencing. RESULTS CTNNB1 (40%) and TP53 (21%) mutations were mutually exclusive and defined two major groups of HCC characterized by distinct phenotypes. CTNNB1 mutated tumours were large (p=0.002), well-differentiated (p<0.001), cholestatic (p<0.001), with microtrabecular (p<0.001) and pseudoglandular (p<0.001) patterns and without inflammatory infiltrates (p<0.001). TP53 mutated tumours were poorly differentiated (p<0.001) with a compact pattern (p=0.02), multinucleated (p=0.01) and pleomorphic (p=0.02) cells and frequent vascular invasion (p=0.02). World Health Organization (WHO) classification of histological subtypes were also strongly related to molecular features. The scirrhous subtype was associated with TSC1/TSC2 mutations (p=0.005), epithelial-to-mesenchymal transition and a progenitor expression profile. The steatohepatitic subtype showed frequent IL-6/JAK/STAT activation without CTNNB1, TERT and TP53 pathway alterations (p=0.01). Pathological review identified a novel subtype, designated as "macrotrabecular-massive" associated with poor survival (p<0.001), high alpha-fetoprotein serum level (p=0.02), vascular invasion (p<0.001), TP53 mutations (p<0.001) and FGF19 amplifications (p=0.02), features also validated in The Cancer Genome Atlas (TCGA) data. Finally, integration of HCC pathological characteristics with its transcriptomic classification showed phenotypically distinct tumour subclasses closely related to G1-G6 subgroups. CONCLUSION HCC phenotypes are tightly associated with gene mutations and transcriptomic classification. These findings may help in translating our knowledge of HCC biology into clinical practice. Lay summary: HCC is a very heterogenous tumour, both at the pathological and molecular levels. We show here that HCC phenotype is tightly associated to its molecular alterations and underlying oncogenic pathways.
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Affiliation(s)
- Julien Calderaro
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe Labellisée Ligue Contre le Cancer, Université Paris Descartes, Université Paris Diderot, Université Paris 13, F-75010, France; Assistance Publique-Hôpitaux de Paris, Department of Pathology, CHU Henri Mondor, Créteil, France; Université Paris Est Créteil, Faculté de Médecine, Créteil, France
| | - Gabrielle Couchy
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe Labellisée Ligue Contre le Cancer, Université Paris Descartes, Université Paris Diderot, Université Paris 13, F-75010, France
| | - Sandrine Imbeaud
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe Labellisée Ligue Contre le Cancer, Université Paris Descartes, Université Paris Diderot, Université Paris 13, F-75010, France
| | - Giuliana Amaddeo
- Université Paris Est Créteil, Faculté de Médecine, Créteil, France; Assistance Publique-Hôpitaux de Paris, Department of Hepatology, CHU Henri Mondor, Créteil, France; Inserm U955, Team 18, Créteil, France
| | - Eric Letouzé
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe Labellisée Ligue Contre le Cancer, Université Paris Descartes, Université Paris Diderot, Université Paris 13, F-75010, France
| | - Jean-Frédéric Blanc
- Department of Hepatogastroenterology and Digestive Oncology, CHU Bordeaux, Hôpital Haut-Lévêque, 33600 Pessac, France; Inserm UMR 1053, Université de Bordeaux, 33076 Bordeaux, France
| | - Christophe Laurent
- Department of Digestive and Endocrine Surgery, CHU-Hôpitaux de Bordeaux, France
| | - Yacine Hajji
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe Labellisée Ligue Contre le Cancer, Université Paris Descartes, Université Paris Diderot, Université Paris 13, F-75010, France
| | - Daniel Azoulay
- Université Paris Est Créteil, Faculté de Médecine, Créteil, France; Department of Digestive and Hepatobiliary Surgery, Assistance Publique-Hôpitaux de Paris, Centre Hospitalier Universitaire Henri Mondor, 94000 Créteil, France
| | - Paulette Bioulac-Sage
- Inserm UMR 1053, Université de Bordeaux, 33076 Bordeaux, France; Department of Pathology, Pellegrin Hospital, CHU Bordeaux, Bordeaux 33076, France
| | - Jean-Charles Nault
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe Labellisée Ligue Contre le Cancer, Université Paris Descartes, Université Paris Diderot, Université Paris 13, F-75010, France; Liver Unit, Hôpital Jean Verdier, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bondy, France
| | - Jessica Zucman-Rossi
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe Labellisée Ligue Contre le Cancer, Université Paris Descartes, Université Paris Diderot, Université Paris 13, F-75010, France; Assistance Publique-Hôpitaux de Paris, Department of Oncology, Hôpital Européen Georges Pompidou, Paris, France.
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Prognostic significance of XRCC4 expression in hepatocellular carcinoma. Oncotarget 2017; 8:87955-87970. [PMID: 29152133 PMCID: PMC5675685 DOI: 10.18632/oncotarget.21360] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/29/2017] [Indexed: 12/26/2022] Open
Abstract
Background Our previous investigations have shown that the variants of X-ray repair complementing 4 (XRCC4) may be involved in hepatocellular carcinoma (hepatocarcinoma) tumorigenesis. This study aimed to investigate the possible prognostic significance of XRCC4 expression for hepatocarcinoma patients and possible value for the selection of transarterial chemoembolization (TACE) treatment. Materials and Methods We conducted a hospital-based retrospective analysis (including 421 hepatocarcinoma cases) to analyze the effects of XRCC4 on hepatocarcinoma prognosis and TACE. The levels of XRCC4 expression were tested using immunohistochemistry. The sensitivity of cancer cells to anti-cancer drug doxorubicin was evaluated using the half-maximal inhibitory concentration (IC50). Results XRCC4 expression was significantly correlated with pathological features including tumor stage, liver cirrhosis, and micro-vessel density. XRCC4 expression was an independent prognostic factor of hepatocarcinoma, and TACE treatments had no effects on prognosis of hepatocarcinoma patients with high XRCC4 expression. More intriguingly, TACE improved the prognosis of hepatocarcinoma patients with low XRCC4 expression. Functionally, XRCC4 overexpression increased while XRCC4 knockdown reduced the IC50 of cancer cells to doxorubicin. Conclusions These results suggest that XRCC4 may be an independent prognostic factor for hepatocarcinoma patients, and that decreasing XRCC4 expression may be beneficial for post-operative adjuvant TACE treatment in hepatocarcinoma.
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Berretta M, Cavaliere C, Alessandrini L, Stanzione B, Facchini G, Balestreri L, Perin T, Canzonieri V. Serum and tissue markers in hepatocellular carcinoma and cholangiocarcinoma: clinical and prognostic implications. Oncotarget 2017; 8:14192-14220. [PMID: 28077782 PMCID: PMC5355172 DOI: 10.18632/oncotarget.13929] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 10/28/2016] [Indexed: 12/12/2022] Open
Abstract
HCC represents the sixth most common cancer worldwide and the second leading cause of cancer-related death. Despite the high incidence, treatment options for advanced HCC remain limited and unsuccessful, resulting in a poor prognosis. Despite the major advances achieved in the diagnostic management of HCC, only one third of the newly diagnosed patients are presently eligible for curative treatments. Advances in technology and an increased understanding of HCC biology have led to the discovery of novel biomarkers. Improving our knowledge about serum and tissutal markers could ultimately lead to an early diagnosis and better and early treatment strategies for this deadly disease. Serum biomarkers are striking potential tools for surveillance and early diagnosis of HCC thanks to the non-invasive, objective, and reproducible assessments they potentially enable. To date, many biomarkers have been proposed in the diagnosis of HCC. Cholangiocarcinoma (CCA) is an aggressive malignancy, characterized by early lymph node involvement and distant metastasis, with 5-year survival rates of 5%-10%. The identification of new biomarkers with diagnostic, prognostic or predictive value is especially important as resection (by surgery or combined with a liver transplant) has shown promising results and novel therapies are emerging. However, the relatively low incidence of CCA, high frequency of co-existing cholestasis or cholangitis (primary sclerosing cholangitis –PSC- above all), and difficulties with obtaining adequate samples, despite advances in sampling techniques and in endoscopic visualization of the bile ducts, have complicated the search for accurate biomarkers. In this review, we attempt to analyze the existing literature on this argument.
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Affiliation(s)
| | - Carla Cavaliere
- Department of Onco-Ematology Medical Oncology, S.G. Moscati Hospital of Taranto Taranto, Italy
| | - Lara Alessandrini
- Division of Pathology, National Cancer Institute, Aviano (PN), Italy
| | - Brigida Stanzione
- Department of Medical Oncology, National Cancer Institute, Aviano (PN), Italy
| | - Gaetano Facchini
- Department of Medical Oncology, National Cancer Institute, "G. Pascale" Foundation, Naples, Italy
| | - Luca Balestreri
- Department of Radiology, National Cancer Institute, Aviano (PN), Italy
| | - Tiziana Perin
- Division of Pathology, National Cancer Institute, Aviano (PN), Italy
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225
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Campbell MJ. Bioinformatic approaches to interrogating vitamin D receptor signaling. Mol Cell Endocrinol 2017; 453:3-13. [PMID: 28288905 DOI: 10.1016/j.mce.2017.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022]
Abstract
Bioinformatics applies unbiased approaches to develop statistically-robust insight into health and disease. At the global, or "20,000 foot" view bioinformatic analyses of vitamin D receptor (NR1I1/VDR) signaling can measure where the VDR gene or protein exerts a genome-wide significant impact on biology; VDR is significantly implicated in bone biology and immune systems, but not in cancer. With a more VDR-centric, or "2000 foot" view, bioinformatic approaches can interrogate events downstream of VDR activity. Integrative approaches can combine VDR ChIP-Seq in cell systems where significant volumes of publically available data are available. For example, VDR ChIP-Seq studies can be combined with genome-wide association studies to reveal significant associations to immune phenotypes. Similarly, VDR ChIP-Seq can be combined with data from Cancer Genome Atlas (TCGA) to infer the impact of VDR target genes in cancer progression. Therefore, bioinformatic approaches can reveal what aspects of VDR downstream networks are significantly related to disease or phenotype.
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Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, 536 Parks Hall, The Ohio State University, Columbus, OH 43210, USA.
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226
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Khemlina G, Ikeda S, Kurzrock R. The biology of Hepatocellular carcinoma: implications for genomic and immune therapies. Mol Cancer 2017; 16:149. [PMID: 28854942 PMCID: PMC5577674 DOI: 10.1186/s12943-017-0712-x] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/15/2017] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, is a leading cause of cancer-related death worldwide. It is highly refractory to most systemic therapies. Recently, significant progress has been made in uncovering genomic alterations in HCC, including potentially targetable aberrations. The most common molecular anomalies in this malignancy are mutations in the TERT promoter, TP53, CTNNB1, AXIN1, ARID1A, CDKN2A and CCND1 genes. PTEN loss at the protein level is also frequent. Genomic portfolios stratify by risk factors as follows: (i) CTNNB1 with alcoholic cirrhosis; and (ii) TP53 with hepatitis B virus-induced cirrhosis. Activating mutations in CTNNB1 and inactivating mutations in AXIN1 both activate WNT signaling. Alterations in this pathway, as well as in TP53 and the cell cycle machinery, and in the PI3K/Akt/mTor axis (the latter activated in the presence of PTEN loss), as well as aberrant angiogenesis and epigenetic anomalies, appear to be major events in HCC. Many of these abnormalities may be pharmacologically tractable. Immunotherapy with checkpoint inhibitors is also emerging as an important treatment option. Indeed, 82% of patients express PD-L1 (immunohistochemistry) and response rates to anti-PD-1 treatment are about 19%, and include about 5% complete remissions as well as durable benefit in some patients. Biomarker-matched trials are still limited in this disease, and many of the genomic alterations in HCC remain challenging to target. Future studies may require combination regimens that include both immunotherapies and molecularly matched targeted treatments.
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Affiliation(s)
- Galina Khemlina
- Department of Geriatrics, University of California, UC San Diego, 9500 Gilman Drive, #9111, La Jolla, CA, 92093-9111, USA. .,Kaiser Permanente Southern California, San Diego, USA.
| | - Sadakatsu Ikeda
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, San Diego, USA.,Tokyo Medical and Dental University, Tokyo, Japan
| | - Razelle Kurzrock
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, San Diego, USA
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227
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Huang A, Zhao X, Yang XR, Li FQ, Zhou XL, Wu K, Zhang X, Sun QM, Cao Y, Zhu HM, Wang XD, Yang HM, Wang J, Tang ZY, Hou Y, Fan J, Zhou J. Circumventing intratumoral heterogeneity to identify potential therapeutic targets in hepatocellular carcinoma. J Hepatol 2017; 67:293-301. [PMID: 28323123 DOI: 10.1016/j.jhep.2017.03.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/07/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Identifying target genetic mutations in hepatocellular carcinoma (HCC) for therapy is made challenging by intratumoral heterogeneity. Circulating cell-free DNAs (cfDNA) may contain a more complete mutational spectrum compared to a single tumor sample. This study aimed to identify the most efficient strategy to identify all the mutations within heterogeneous HCCs. METHODS Whole exome sequencing (WES) and targeted deep sequencing (TDS) were carried out in 32 multi-regional tumor samples from five patients. Matched preoperative cfDNAs were sequenced accordingly. Intratumoral heterogeneity was measured using the average percentage of non-ubiquitous mutations (present in parts of tumor regions). Profiling efficiencies of single tumor specimen and cfDNA were compared. The strategy with the highest performance was used to screen for actionable mutations. RESULTS Variable levels of heterogeneity with branched and parallel evolution patterns were observed. The heterogeneity decreased at higher sequencing depth of TDS compared to measurements by WES (28.1% vs. 34.9%, p<0.01) but remained unchanged when additional samples were analyzed. TDS of single tumor specimen identified an average of 70% of the total mutations from multi-regional tissues. Although genome profiling efficiency of cfDNA increased with sequencing depth, an average of 47.2% total mutations were identified using TDS, suggesting that tissue samples outperformed it. TDS of single tumor specimen in 66 patients and cfDNAs in four unresectable HCCs showed that 38.6% (26/66 and 1/4) of patients carried mutations that were potential therapeutic targets. CONCLUSIONS TDS of single tumor specimen could identify actionable mutations targets for therapy in HCC. cfDNA may serve as secondary alternative in profiling HCC genome. LAY SUMMARY Targeted deep sequencing of single tumor specimen is a more efficient method to identify mutations in hepatocellular carcinoma made from mixed subtypes compared to circulating cell-free DNA in blood. cfDNA may serve as secondary alternative in profiling HCC genome. Identifying mutations may help clinicians choose targeted therapy for better individual treatments.
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Affiliation(s)
- Ao Huang
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Xin Zhao
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin-Rong Yang
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Fu-Qiang Li
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin-Lan Zhou
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Zhang
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Qi-Man Sun
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Ya Cao
- Cancer Research Institute, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha 410078, China
| | - Hong-Mei Zhu
- BGI-Shenzhen, Shenzhen 518083, China; BGI-Tianjin, Tianjin 300308, China
| | - Xiang-Dong Wang
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
| | - Huan-Ming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Zhao-You Tang
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
| | - Jia Fan
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
| | - Jian Zhou
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
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228
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Lewin SM, Mehta N, Kelley RK, Roberts JP, Yao FY, Brandman D. Liver transplantation recipients with nonalcoholic steatohepatitis have lower risk hepatocellular carcinoma. Liver Transpl 2017; 23:1015-1022. [PMID: 28340509 DOI: 10.1002/lt.24764] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 02/06/2017] [Accepted: 03/02/2017] [Indexed: 12/15/2022]
Abstract
Liver transplantation (LT) is a well-established treatment for hepatocellular carcinoma (HCC) in carefully selected patients. Risk factors for tumors with poor prognostic features on explant have not been well described in a national cohort. We performed a retrospective cohort study of adult LT recipients with HCC transplanted from April 8, 2012 (when explant pathology in United Network for Organ Sharing [UNOS] became available) until September 30, 2014. We evaluated the association between listing diagnosis and other demographic factors with tumor features on explant using logistic regression. High-risk tumor features included the following: > 3 tumors, largest tumor > 5 cm, presence of vascular invasion, presence of metastases, and poor differentiation of tumor. In total, 3733 LT recipients with HCC who had complete explant data in UNOS were included. The median age was 60 years; 78% were male; and 68% were white. Of the primary non-HCC listing diagnoses, 2608 (70%) had hepatitis C virus (HCV); 271 (7%) had nonalcoholic steatohepatitis (NASH); 246 (7%) had alcoholic cirrhosis; and 189 (5%) had hepatitis B virus. Also, 1140 (31%) had evidence of ≥ 1 high-risk explant feature(s). The presence of ≥ 1 high-risk explant feature(s) was associated with HCC recurrence after transplant (odds ratio [OR], 5.00; P < 0.001). Compared with HCV-associated HCC transplant recipients, individuals with NASH had lower likelihood of high-risk explant features (OR, 0.71; P = 0.02) after adjusting for covariables. Women were more likely to have high-risk explant features (OR, 1.23; P = 0.04). Diabetes mellitus (DM) was not associated with high-risk explant features. In conclusion, LT recipients with NASH-associated HCC had fewer high-risk tumor features on explant compared with HCV-associated HCC, despite having higher rates of DM and other potential risk factors for the development of HCC. Women had a higher likelihood of high-risk tumor features. Further study is warranted whether these differences are due to disease-specific or sex-specific influences on tumor biology or due to selection criteria for transplant. Liver Transplantation 23 1015-1022 2017 AASLD.
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Affiliation(s)
- Sara M Lewin
- Department of Medicine, Divisions of Gastroenterology, University of California, San Francisco, San Francisco, CA
| | - Neil Mehta
- Department of Medicine, Divisions of Gastroenterology, University of California, San Francisco, San Francisco, CA
| | - R Kate Kelley
- Hematology/Oncology, University of California, San Francisco, San Francisco, CA
| | - John P Roberts
- Department of Surgery, University of California, San Francisco, San Francisco, CA
| | - Francis Y Yao
- Department of Medicine, Divisions of Gastroenterology, University of California, San Francisco, San Francisco, CA
| | - Danielle Brandman
- Department of Medicine, Divisions of Gastroenterology, University of California, San Francisco, San Francisco, CA
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Ziogas DE, Lykoudis EG, Roukos DH, Glantzounis GK. Genomic heterogeneity: next-generation sequencing enables biomarker identification for hepatocellular carcinoma. Biomark Med 2017; 11:515-518. [PMID: 28699774 DOI: 10.2217/bmm-2017-0121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Demosthenes E Ziogas
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, 'G. Hatzikosta' General Hospital, Ioannina, Greece
| | | | - Dimitrios H Roukos
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, Ioannina University Hospital, Ioannina, Greece.,Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
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Jansen PL. Fibroblast growth factor 19, a double-edged sword. Hepat Oncol 2017; 4:1-4. [PMID: 30191047 DOI: 10.2217/hep-2017-0008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/12/2017] [Indexed: 01/26/2023] Open
Affiliation(s)
- Peter Lm Jansen
- Department of Gastroenterology & Hepatology, Academic Medical Center, Amsterdam, The Netherlands
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231
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Ally A, Balasundaram M, Carlsen R, Chuah E, Clarke A, Dhalla N, Holt RA, Jones SJ, Lee D, Ma Y, Marra MA, Mayo M, Moore RA, Mungall AJ, Schein JE, Sipahimalani P, Tam A, Thiessen N, Cheung D, Wong T, Brooks D, Robertson AG, Bowlby R, Mungall K, Sadeghi S, Xi L, Covington K, Shinbrot E, Wheeler DA, Gibbs RA, Donehower LA, Wang L, Bowen J, Gastier-Foster JM, Gerken M, Helsel C, Leraas KM, Lichtenberg TM, Ramirez NC, Wise L, Zmuda E, Gabriel SB, Meyerson M, Cibulskis C, Murray BA, Shih J, Beroukhim R, Cherniack AD, Schumacher SE, Saksena G, Pedamallu CS, Chin L, Getz G, Noble M, Zhang H, Heiman D, Cho J, Gehlenborg N, Saksena G, Voet D, Lin P, Frazer S, Defreitas T, Meier S, Lawrence M, Kim J, Creighton CJ, Muzny D, Doddapaneni H, Hu J, Wang M, Morton D, Korchina V, Han Y, Dinh H, Lewis L, Bellair M, Liu X, Santibanez J, Glenn R, Lee S, Hale W, Parker JS, Wilkerson MD, Hayes DN, Reynolds SM, Shmulevich I, Zhang W, Liu Y, Iype L, Makhlouf H, Torbenson MS, Kakar S, Yeh MM, Jain D, Kleiner DE, Jain D, Dhanasekaran R, El-Serag HB, Yim SY, Weinstein JN, Mishra L, Zhang J, Akbani R, Ling S, Ju Z, Su X, Hegde AM, Mills GB, Lu Y, Chen J, Lee JS, Sohn BH, Shim JJ, Tong P, Aburatani H, Yamamoto S, Tatsuno K, Li W, Xia Z, Stransky N, Seiser E, Innocenti F, Gao J, Kundra R, Zhang H, Heins Z, Ochoa A, Sander C, Ladanyi M, Shen R, Arora A, Sanchez-Vega F, Schultz N, Kasaian K, Radenbaugh A, Bissig KD, Moore DD, Totoki Y, Nakamura H, Shibata T, Yau C, Graim K, Stuart J, Haussler D, Slagle BL, Ojesina AI, Katsonis P, Koire A, Lichtarge O, Hsu TK, Ferguson ML, Demchok JA, Felau I, Sheth M, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Hutter CM, Sofia HJ, Verhaak RG, Zheng S, Lang F, Chudamani S, Liu J, Lolla L, Wu Y, Naresh R, Pihl T, Sun C, Wan Y, Benz C, Perou AH, Thorne LB, Boice L, Huang M, Rathmell WK, Noushmehr H, Saggioro FP, Tirapelli DPDC, Junior CGC, Mente ED, Silva ODC, Trevisan FA, Kang KJ, Ahn KS, Giama NH, Moser CD, Giordano TJ, Vinco M, Welling TH, Crain D, Curley E, Gardner J, Mallery D, Morris S, Paulauskis J, Penny R, Shelton C, Shelton T, Kelley R, Park JW, Chandan VS, Roberts LR, Bathe OF, Hagedorn CH, Auman JT, O'Brien DR, Kocher JPA, Jones CD, Mieczkowski PA, Perou CM, Skelly T, Tan D, Veluvolu U, Balu S, Bodenheimer T, Hoyle AP, Jefferys SR, Meng S, Mose LE, Shi Y, Simons JV, Soloway MG, Roach J, Hoadley KA, Baylin SB, Shen H, Hinoue T, Bootwalla MS, Van Den Berg DJ, Weisenberger DJ, Lai PH, Holbrook A, Berrios M, Laird PW. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell 2017; 169:1327-1341.e23. [PMID: 28622513 PMCID: PMC5680778 DOI: 10.1016/j.cell.2017.05.046] [Citation(s) in RCA: 1683] [Impact Index Per Article: 240.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/02/2017] [Accepted: 05/26/2017] [Indexed: 12/12/2022]
Abstract
Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also. DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or downregulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed. Integrative molecular HCC subtyping incorporating unsupervised clustering of five data platforms identified three subtypes, one of which was associated with poorer prognosis in three HCC cohorts. Integrated analyses enabled development of a p53 target gene expression signature correlating with poor survival. Potential therapeutic targets for which inhibitors exist include WNT signaling, MDM4, MET, VEGFA, MCL1, IDH1, TERT, and immune checkpoint proteins CTLA-4, PD-1, and PD-L1.
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232
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Kyrochristos ID, Ziogas DE, Roukos DH. Regorafenib: a newly approved drug for advanced hepatocellular carcinoma. Future Oncol 2017; 13:1665-1668. [PMID: 28613123 DOI: 10.2217/fon-2017-0237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Ioannis D Kyrochristos
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, Ioannina University Hospital, Ioannina, Greece
| | - Demosthenes E Ziogas
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, 'G. Hatzikosta' General Hospital, Ioannina, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, Ioannina University Hospital, Ioannina, Greece.,Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
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233
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Novel SF3B1 in-frame deletions result in aberrant RNA splicing in CLL patients. Blood Adv 2017; 1:995-1000. [PMID: 29296742 DOI: 10.1182/bloodadvances.2017007062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022] Open
Abstract
We identify and characterize novel SF3B1 in-frame deletions in chronic lymphocytic leukemia.These deletions are functionally similar to well-known SF3B1 hotspot mutations and are sensitive to splicing modulation.
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234
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Yin X, Yi H, Wang L, Wu W, Wu X, Yu L. R-spondin 2 promotes proliferation and migration via the Wnt/β-catenin pathway in human hepatocellular carcinoma. Oncol Lett 2017; 14:1757-1765. [PMID: 28789406 DOI: 10.3892/ol.2017.6339] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 02/13/2017] [Indexed: 12/21/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of malignant disease-associated mortality, particularly in China. The RSPO2 (R-spondin 2) gene is evolutionarily conserved in vertebrates and is involved in developmental and physiological processes. Importantly, RSPO2 has been reported to be associated with colon cancer and potentiate the Wnt/β-catenin signaling pathway. In the present study, enhanced expression of RSPO2 in HCC was observed using tissue microarray. Similarly, the expression level of RSPO2 was higher in HepG2, Huh7 and Hep3B cells but lower in Bel7404 and QGY7703 cells compared with human normal QSG7701 liver cells. Subsequently, gain-of-function studies indicated that RSPO2 promotes the proliferation and migration of QGY7703 cells based on lentivirus-based gene delivery. Furthermore, it was revealed that p21 and leptin, rather than vascular endothelial growth factor-A, are involved in the function of RSPO2 in QGY7703 cells. Particularly, the signal transducer and activator of transcription 3 (STAT3) and Wnt/β-catenin signaling pathways are involved in this process. Overexpression of RSPO2 resulted in the elevated expression of phosphorylated STAT3, β-catenin and c-Myc. Therefore, the present study is beneficial to the understanding of RSPO2-involved liver cancer transformation and drug discovery.
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Affiliation(s)
- Xinguang Yin
- Centre for Gastroenterology and Hepatology, The First Affiliated Hospital of Jiaxing College, Jiaxing, Zhejiang 314001, P.R. China.,Centre for Gastroenterology and Hepatology, The Maternity and Child Health Care Hospital Affiliated to Jiaxing College, Jiaxing, Zhejiang 314001, P.R. China
| | - Huixing Yi
- Intensive Care Unit, The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Linlin Wang
- Department of Basic Medicine Sciences, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Wanxin Wu
- Deparment of Pathology, The First Affiliated Hospital of Jiaxing College, Jiaxing, Zhejiang 314001, P.R. China
| | - Xiaojun Wu
- Centre for Gastroenterology and Hepatology, The First Affiliated Hospital of Jiaxing College, Jiaxing, Zhejiang 314001, P.R. China
| | - Linghua Yu
- Centre for Gastroenterology and Hepatology, The First Affiliated Hospital of Jiaxing College, Jiaxing, Zhejiang 314001, P.R. China
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235
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Precision medicine for hepatocellular carcinoma: driver mutations and targeted therapy. Oncotarget 2017; 8:55715-55730. [PMID: 28903454 PMCID: PMC5589693 DOI: 10.18632/oncotarget.18382] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the third most frequent cause of tumor-related mortality and there are an estimated approximately 850,000 new cases annually. Most HCC patients are diagnosed at middle or advanced stage, losing the opportunity of surgery. The development of HCC is promoted by accumulated diverse genetic mutations, which confer selective growth advantages to tumor cells and are called "driver mutations". The discovery of driver mutations provides a novel precision medicine strategy for late stage HCC, called targeted therapy. In this review, we summarized currently discovered driver mutations and corresponding signaling pathways, made an overview of identification methods of driver mutations and genes, and classified targeted drugs for HCC. The knowledge of mutational landscape deepen our understanding of carcinogenesis and promise future precision medicine for HCC patients.
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236
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Xu W, Yu J, Wong VWS. Mechanism and prediction of HCC development in HBV infection. Best Pract Res Clin Gastroenterol 2017; 31:291-298. [PMID: 28774411 DOI: 10.1016/j.bpg.2017.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/28/2017] [Indexed: 02/07/2023]
Abstract
Chronic hepatitis B virus (HBV) infection remains one of the leading causes of hepatocellular carcinoma (HCC) globally. Over the past few decades, the risk factors of HCC in patients with chronic hepatitis B have been well characterized, and can be divided into host and viral factors. A few groups have also derived and validated HCC prediction scores based on these risk factors. In general, the scores have high negative predictive value in identifying a low risk group who may not need HCC surveillance in the next 3-5 years. The scores have been tested originally in Asian patients, and results on their performance in the Caucasian population are conflicting. Furthermore, new research has identified genetic factors and new virological markers (e.g. hepatitis B surface antigen and core-related antigen levels) for HCC, but they are yet to be applied in routine clinical practice.
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Affiliation(s)
- Weiqi Xu
- State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Vincent Wai-Sun Wong
- State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong.
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237
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Zhou M, Luo J, Chen M, Yang H, Learned RM, DePaoli AM, Tian H, Ling L. Mouse species-specific control of hepatocarcinogenesis and metabolism by FGF19/FGF15. J Hepatol 2017; 66:1182-1192. [PMID: 28189755 DOI: 10.1016/j.jhep.2017.01.027] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND & AIMS Bile acid nuclear receptor farnesoid X receptor (FXR) is a key molecular mediator of many metabolic processes, including the regulation of bile acid, lipid and glucose homeostasis. A significant component of FXR-mediated events essential to its biological activity is attributed to induction of the enteric endocrine hormone fibroblast growth factor (FGF)19 or its rodent ortholog, FGF15. In this report, we compared the properties of human FGF19 and murine FGF15 in the regulation of hepatocarcinogenesis and metabolism in various mouse models of disease. METHODS Tumorigenicity was assessed in three mouse models (db/db, diet-induced obese, and multi-drug resistance 2 [Mdr2]-deficient) following continuous exposure to FGF19 or FGF15 via adeno-associated viral-mediated gene delivery. Glucose, hemoglobin A1c and β-cell mass were characterized in db/db mice. Oxygen consumption, energy expenditure, and body composition were evaluated in diet-induced obese mice. Serum levels of alkaline phosphatase, alanine aminotransferase, and aspartate aminotransferase were assessed in Mdr2-deficient mice. Expression profiles of genes encoding key proteins involved in bile acid synthesis and hepatocarcinogenesis were also determined. RESULTS Both FGF15 and FGF19 hormones repressed bile acid synthesis (p<0.001 for both). However, murine FGF15 lacked the protective effects characteristic of human FGF19 in db/db mice with overt diabetes, such as weight-independent HbA1c-lowering and β-cell-protection. Unlike FGF19, FGF15 did not induce hepatocellular carcinomas (HCC) in three mouse models of metabolic diseases (db/db, diet-induced obese, and multi-drug resistance 2 [Mdr2]-deficient mice), even at supra-pharmacological exposure levels. CONCLUSIONS Fundamental species-associated differences between FGF19 and FGF15 may restrict the relevance of mouse models for the study of the FXR/FGF19 pathway, and underscore the importance of clinical assessment of this pathway, with respect to both safety and efficacy in humans. LAY SUMMARY Activation of the nuclear receptor, FXR, leads to the production of a hormone called fibroblast growth factor 19 (FGF19) and subsequently regulation of multiple metabolic processes. Synthetic activators of FXR have been recently approved or are currently in clinical development for treatment of chronic liver diseases, including primary biliary cholangitis (PBC) and non-alcoholic steatohepatitis (NASH). The safety of these activators was partly assessed in mice exposed for prolonged periods of time. However, the results of this study show that mouse FGF15 and human FGF19 exhibit fundamentally different biological activities in mice. This could raise the concern of relying on rodent models for safety assessment of FXR activators. The potential risk of HCC development in patients treated with FXR agonists may need to be monitored.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B/deficiency
- ATP Binding Cassette Transporter, Subfamily B/genetics
- Animals
- Bile Acids and Salts/biosynthesis
- Carcinogenesis/metabolism
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/pathology
- Fibroblast Growth Factors/genetics
- Fibroblast Growth Factors/metabolism
- Glycated Hemoglobin/metabolism
- Humans
- Hyperglycemia/metabolism
- Insulin-Secreting Cells/metabolism
- Insulin-Secreting Cells/pathology
- Liver Neoplasms, Experimental/etiology
- Liver Neoplasms, Experimental/metabolism
- Male
- Metabolic Networks and Pathways
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Mutant Strains
- Obesity/metabolism
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, Leptin/genetics
- STAT3 Transcription Factor/metabolism
- Species Specificity
- ATP-Binding Cassette Sub-Family B Member 4
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Affiliation(s)
- Mei Zhou
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Jian Luo
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Michael Chen
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Hong Yang
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - R Marc Learned
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Alex M DePaoli
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Hui Tian
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Lei Ling
- NGM Biopharmaceuticals, Inc., 333 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
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238
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EZH2 in Cancer Progression and Potential Application in Cancer Therapy: A Friend or Foe? Int J Mol Sci 2017; 18:ijms18061172. [PMID: 28561778 PMCID: PMC5485996 DOI: 10.3390/ijms18061172] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 05/24/2017] [Accepted: 05/27/2017] [Indexed: 01/26/2023] Open
Abstract
Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase, catalyzes tri-methylation of histone H3 at Lys 27 (H3K27me3) to regulate gene expression through epigenetic machinery. EZH2 functions as a double-facet molecule in regulation of gene expression via repression or activation mechanisms, depending on the different cellular contexts. EZH2 interacts with both histone and non-histone proteins to modulate diverse physiological functions including cancer progression and malignancy. In this review article, we focused on the updated information regarding microRNAs (miRNAs) and long non coding RNAs (lncRNAs) in regulation of EZH2, the oncogenic and tumor suppressive roles of EZH2 in cancer progression and malignancy, as well as current pre-clinical and clinical trials of EZH2 inhibitors.
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239
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Yang S, Wang XQ. XLF-mediated NHEJ activity in hepatocellular carcinoma therapy resistance. BMC Cancer 2017; 17:344. [PMID: 28526069 PMCID: PMC5437682 DOI: 10.1186/s12885-017-3345-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 05/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background DNA repair pathways are used by cancer cells to overcome many standard anticancer treatments, causing therapy resistance. Here, we investigated the role of XRCC4-like factor (XLF), a core member of the non-homologous end joining (NHEJ) repair pathway, in chemoresistance in hepatocellular carcinoma (HCC). Methods qRT-PCR analysis and western blotting were performed to detect expression levels of genes and proteins related to NHEJ. NHEJ repair capacity was assessed in vitro (cell-free) and in vivo by monitoring the activity of the NHEJ pathway. Cell viability and IC50 assays were used to measure sensitivity to drug therapy. A xenograft HCC model was used to develop methods of targeting XLF-induced chemosensitization. Clinicopathological analysis was conducted on patients with HCC treated with transarterial chemoembolization (TACE). Results Many conventional cancer chemotherapeutics induce DNA double-strand breaks (DSBs). HCC cells respond to these breaks by increasing their NHEJ activity, resulting in resistance. XLF-knockdown cells show an inhibition of NHEJ activity in both cell-free and live-cell assays as well as a high level of unrepaired cellular DSBs. These results indicate that XLF facilitates DNA end-joining and therefore promotes NHEJ activity in cancer cells. Consequently, knockdown of XLF significantly chemosensitized resistant cells both in vitro and in xenograft tumors. A low rate of XLF genomic alteration was found in patients with primary HCC, but XLF expression was induced after drug treatment. Clinically, a high level of XLF expression is significantly associated with advanced HCC and shorter overall survival. Conclusion Chemotherapy-induced overexpression of XLF and XLF-mediated enhancements in NHEJ activity contribute to chemoresistance in HCC cells and patients with HCC. Targeting XLF to modulate DSB repair could enhance drug sensitivity and may be a therapeutically useful addition to conventional therapy. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3345-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sitian Yang
- Department of Surgery, The University of Hong Kong, 21 Sassoon Road, Hong Kong, China
| | - Xiao Qi Wang
- Department of Surgery, The University of Hong Kong, 21 Sassoon Road, Hong Kong, China. .,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
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240
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Non-cell-autonomous activation of IL-6/STAT3 signaling mediates FGF19-driven hepatocarcinogenesis. Nat Commun 2017; 8:15433. [PMID: 28508871 PMCID: PMC5440856 DOI: 10.1038/ncomms15433] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/29/2017] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC), a primary malignancy of the liver, is the second leading cause of cancer mortality worldwide. Fibroblast Growth Factor 19 (FGF19) is one of the most frequently amplified genes in HCC patients. Moreover, mice expressing an FGF19 transgene have been shown to develop HCC. However, the downstream signalling pathways that mediate FGF19-dependent tumorigenesis remain to be deciphered. Here we show that FGF19 triggers a previously unsuspected, non-cell-autonomous program to activate STAT3 signalling in hepatocytes through IL-6 produced in the liver microenvironment. We show that the hepatocyte-specific deletion of Stat3, genetic ablation of Il6, treatment with a neutralizing anti-IL-6 antibody or administration of a small-molecule JAK inhibitor, abolishes FGF19-induced tumorigenesis, while the regulatory functions of FGF19 in bile acid, glucose and energy metabolism remain intact. Collectively, these data reveal a key role for the IL-6/STAT3 axis in potentiating FGF19-driven HCC in mice, a finding which may have translational relevance in HCC pathogenesis. Fibroblast Growth Factor 19 (FGF19) neutralizing antibodies inhibit hepatocellular carcinoma (HCC) growth but have safety issues. Here, the authors show that FGF19 promotes HCC by activating STAT3 signalling via IL-6 production and that targeting IL-6 pathway abolishes FGF19-induced HCC without side effects.
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241
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Cress WD, Yu P, Wu J. Expression and alternative splicing of the cyclin-dependent kinase inhibitor-3 gene in human cancer. Int J Biochem Cell Biol 2017; 91:98-101. [PMID: 28504190 DOI: 10.1016/j.biocel.2017.05.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 01/04/2023]
Abstract
The cyclin-dependent kinase inhibitor-3 (CDKN3) gene encodes a dual-specificity protein tyrosine phosphatase that dephosphorylates CDK1/CDK2 and other proteins. CDKN3 is often overexpressed in human cancer, and this overexpression correlates with reduced survival in several types of cancer. CDKN3 transcript variants and mutations have also been reported. The mechanism of CDKN3 overexpression and the role of CDKN3 transcript variants in human cancer are not entirely clear. Here, we review the literature and provide additional data to assess the correlation of CDKN3 expression with patient survival. Besides the full-length CDKN3 encoding transcript and a major transcript that skips exon 2 express in normal and cancer cells, minor aberrant transcript variants have been reported. Aberrant CDKN3 transcripts were postulated to encode dominant-negative inhibitors of CDKN3 as an explanation for overexpression of the perceived tumor suppressor gene in human cancer. However, while CDKN3 is often overexpressed in human cancer, aberrant CDKN3 transcripts occur infrequently and at lower levels. CDKN3 mutations and copy number alternation are rare in human cancer, implying that neither loss of CDKN3 activity nor constitutive gain of CDKN3 expression offer an advantage to tumorigenesis. Recently, it was found that CDKN3 transcript and protein levels fluctuate during the cell cycle, peaking in mitosis. Given that rapidly growing tumors have more mitotic cells, the high level of mitotic CDKN3 expression is the most plausible mechanism of frequent CDKN3 overexpression in human cancer. This finding clarifies the mechanism of CDKN3 overexpression in human cancer and questions the view of CDKN3 as a tumor suppressor.
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Affiliation(s)
- W Douglas Cress
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Peng Yu
- Department of Electrical and Computer Engineering, and TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, Texas, USA
| | - Jie Wu
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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242
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Lin DC, Mayakonda A, Dinh HQ, Huang P, Lin L, Liu X, Ding LW, Wang J, Berman BP, Song EW, Yin D, Koeffler HP. Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma. Cancer Res 2017; 77:2255-2265. [PMID: 28302680 PMCID: PMC5413372 DOI: 10.1158/0008-5472.can-16-2822] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/14/2016] [Accepted: 02/04/2017] [Indexed: 02/06/2023]
Abstract
Understanding the intratumoral heterogeneity of hepatocellular carcinoma is instructive for developing personalized therapy and identifying molecular biomarkers. Here we applied whole-exome sequencing to 69 samples from 11 patients to resolve the genetic architecture of subclonal diversification. Spatial genomic diversity was found in all 11 hepatocellular carcinoma cases, with 29% of driver mutations being heterogeneous, including TERT, ARID1A, NOTCH2, and STAG2. Similar with other cancer types, TP53 mutations were always shared between all tumor regions, that is, located on the "trunk" of the evolutionary tree. In addition, we found that variants within several drug targets such as KIT, SYK, and PIK3CA were mutated in a fully clonal manner, indicating their therapeutic potentials for hepatocellular carcinoma. Temporal dissection of mutational signatures suggested that mutagenic processes associated with exposure to aristolochic acid and aflatoxin might play a more important role in early, as opposed to late, stages of hepatocellular carcinoma development. Moreover, we observed extensive intratumoral epigenetic heterogeneity in hepatocellular carcinoma based on multiple independent analytical methods and showed that intratumoral methylation heterogeneity might play important roles in the biology of hepatocellular carcinoma cells. Our results also demonstrated prominent heterogeneity of intratumoral methylation even in a stable hepatocellular carcinoma genome. Together, these findings highlight widespread intratumoral heterogeneity at both the genomic and epigenomic levels in hepatocellular carcinoma and provide an important molecular foundation for better understanding the pathogenesis of this malignancy. Cancer Res; 77(9); 2255-65. ©2017 AACR.
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Affiliation(s)
- De-Chen Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Huy Q Dinh
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California
| | - Pinbo Huang
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Hepatobiliary Surgery, Sun-Yat-Sen Memorial Hospital, Sun-Yat-Sen University, Guangzhou, China
| | - Lehang Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoping Liu
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jie Wang
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Hepatobiliary Surgery, Sun-Yat-Sen Memorial Hospital, Sun-Yat-Sen University, Guangzhou, China
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California.
| | - Er-Wei Song
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Dong Yin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - H Phillip Koeffler
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- National University Cancer Institute, National University Hospital Singapore, Singapore
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243
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Lee JH, Shin DH, Park WY, Shin N, Kim A, Lee HJ, Kim YK, Choi KU, Kim JY, Yang YI, Lee CH, Sol MY. IDH1 R132C mutation is detected in clear cell hepatocellular carcinoma by pyrosequencing. World J Surg Oncol 2017; 15:82. [PMID: 28403884 PMCID: PMC5389153 DOI: 10.1186/s12957-017-1144-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/02/2017] [Indexed: 12/21/2022] Open
Abstract
Background Isocitrate dehydrogenase 1 (IDH1) mutation is common in low-grade glioma (approximately 80%) and acute myeloid leukemia (approximately 10%). Other than brain tumor or hematologic malignancies, intrahepatic cholangiocarcinoma (iCC) is a well-known solid tumor with IDH1 mutation (6.8–20%). Histologically, poor differentiation and clear cell change are associated with IDH1 mutation in iCC. Since hepatocellular carcinoma (HCC) shares histologic features with iCC, some specific subtypes of HCC might show a higher IDH1 mutation rate than reported before (0.5–1.5%). Methods Forty-six cases of iCC and 48 cases of HCC (including 20 cases of clear cell type and 13 cases of pseudoglandular pattern) were tested for IDH1 mutation by pyrosequencing. Results Three cases in iCC (6.5%) and five cases in HCC (10.4%) had IDH1 mutation, all of which were Arg132Cys. IDH1 mutant HCCs were all clear cell type. Although the IDH1 mutation rate between iCC and HCC demonstrated no significant difference, clear cell HCC revealed statistically increased mutation rate compared to that of HCC without clear cell change (P = 0.009). Presence of IDH1 mutation was related with poor survival in clear cell HCC patients (P = 0.004). Conclusions Clear cell HCC showed higher frequency of IDH1 mutation rate than other variants of HCC. This result consolidates the assumption that morphological features of tumors reflect molecular alterations.
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Affiliation(s)
- Jung Hee Lee
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea.,Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, 50612, South Korea
| | - Dong Hoon Shin
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea.,Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, 50612, South Korea
| | - Won Young Park
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea
| | - Nari Shin
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea
| | - Ahrong Kim
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea
| | - Hyun Jung Lee
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea
| | - Young Keum Kim
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea
| | - Kyung Un Choi
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea
| | - Jee Yeon Kim
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea
| | - Young Il Yang
- Paik Institute for Clinical Research, Inje University College of Medicine, Busan, 47392, South Korea
| | - Chang Hun Lee
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea
| | - Mee Young Sol
- Department of Pathology, School of Medicine, Pusan National University, Yangsan, 50612, South Korea.
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244
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Suresh S, Durakoglugil D, Zhou X, Zhu B, Comerford SA, Xing C, Xie XJ, York B, O’Donnell KA. SRC-2-mediated coactivation of anti-tumorigenic target genes suppresses MYC-induced liver cancer. PLoS Genet 2017; 13:e1006650. [PMID: 28273073 PMCID: PMC5362238 DOI: 10.1371/journal.pgen.1006650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 03/22/2017] [Accepted: 02/23/2017] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common solid tumor in the world and the third leading cause of cancer-associated deaths. A Sleeping Beauty-mediated transposon mutagenesis screen previously identified mutations that cooperate with MYC to accelerate liver tumorigenesis. This revealed a tumor suppressor role for Steroid Receptor Coactivator 2/Nuclear Receptor Coactivator 2 (Src-2/Ncoa2) in liver cancer. In contrast, SRC-2 promotes survival and metastasis in prostate cancer cells, suggesting a tissue-specific and context-dependent role for SRC-2 in tumorigenesis. To determine if genetic loss of SRC-2 is sufficient to accelerate MYC-mediated liver tumorigenesis, we bred Src-2-/- mice with a MYC-induced liver tumor model and observed a significant increase in liver tumor burden. RNA sequencing of liver tumors and in vivo chromatin immunoprecipitation assays revealed a set of direct target genes that are bound by SRC-2 and exhibit downregulated expression in Src-2-/- liver tumors. We demonstrate that activation of SHP (Small Heterodimer Partner), DKK4 (Dickkopf-4), and CADM4 (Cell Adhesion Molecule 4) by SRC-2 suppresses tumorigenesis in vitro and in vivo. These studies suggest that SRC-2 may exhibit oncogenic or tumor suppressor activity depending on the target genes and nuclear receptors that are expressed in distinct tissues and illuminate the mechanisms of tumor suppression by SRC-2 in liver.
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Affiliation(s)
- Shruthy Suresh
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Deniz Durakoglugil
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Xiaorong Zhou
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, United States of America
- Department of Immunology, Nantong University School of Medicine, Nantong, China
| | - Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Sarah A. Comerford
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Chao Xing
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, United States of America
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Xian-Jin Xie
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, United States of America
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States of America
| | - Kathryn A. O’Donnell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, United States of America
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, United States of America
- * E-mail:
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245
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Fu S, Liu X, Luo M, Xie K, Nice EC, Zhang H, Huang C. Proteogenomic studies on cancer drug resistance: towards biomarker discovery and target identification. Expert Rev Proteomics 2017; 14:351-362. [PMID: 28276747 DOI: 10.1080/14789450.2017.1299006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment. Areas covered: In this review, we will present recent advances in proteogenomic investigations of cancer drug resistance with an emphasis on integrative proteogenomic pipelines and the biomarker discovery which contributes to achieving the goal of using precision/personalized medicine for cancer treatment. Expert commentary: The discovery and comprehensive understanding of potential biomarkers help identify the cohort of patients who may benefit from particular treatments, and will assist real-time clinical decision-making to maximize therapeutic efficacy and minimize adverse effects. With the development of MS-based proteomics and NGS-based sequencing, a growing number of proteogenomic tools are being developed specifically to investigate cancer drug resistance.
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Affiliation(s)
- Shuyue Fu
- a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Xiang Liu
- b Department of Pathology , Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital , Chengdu , P.R. China
| | - Maochao Luo
- c West China School of Public Health, Sichuan University , Chengdu , P.R.China
| | - Ke Xie
- d Department of Oncology , Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital , Chengdu , P.R. China
| | - Edouard C Nice
- e Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- f School of Medicine , Yangtze University , P. R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
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246
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The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma. Nat Commun 2017; 8:4565. [PMID: 28240289 PMCID: PMC5333358 DOI: 10.1038/ncomms14565] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/12/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy.
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247
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Tan Q, Li F, Wang G, Xia W, Li Z, Niu X, Ji W, Yuan H, Xu Q, Luo Q, Zhang J, Lu S. Identification of FGF19 as a prognostic marker and potential driver gene of lung squamous cell carcinomas in Chinese smoking patients. Oncotarget 2017; 7:18394-402. [PMID: 26943773 PMCID: PMC4951296 DOI: 10.18632/oncotarget.7817] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/24/2016] [Indexed: 11/25/2022] Open
Abstract
Comprehensive genomic characterizations of lung squamous cell carcinoma (LSCC) have been performed, but the differences between smokers (S-LSCC) and never smokers (NS-LSCC) are not clear, as NS-LSCC could be considered as a different disease from S-LSCC. In this study we delineated genomic alterations in a cohort of 21 NS-LSCC and 16 S-LSCC patients, and identified common gene mutations and amplifications as previously reported. Inclusion of more NS-LSCC patients enabled us to identify unreported S-LSCC- or NS-LSCC-specific alterations. Importantly, an amplification region containing FGF19, FGF3, FGF4 and CCND1 was found five-times more frequent in S-LSCC than in NS-LSCC. Amplification of FGF19 was validated in independent LSCC samples. Furthermore, FGF19 stimulated LSCC cell growth in vitro. These data implicate FGF19 as a potential driver gene in LSCC with clinic characteristics as smoking.
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Affiliation(s)
- Qiang Tan
- Shanghai Lung Cancer Center, Lung Cancer Research Laboratory, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200030, China
| | - Fan Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Guan Wang
- Genomics Center, WuXi AppTec Co., Ltd., Shanghai 200131, China
| | - Weiliang Xia
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ziming Li
- Shanghai Lung Cancer Center, Lung Cancer Research Laboratory, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaomin Niu
- Shanghai Lung Cancer Center, Lung Cancer Research Laboratory, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200030, China
| | - Wenxiang Ji
- Shanghai Lung Cancer Center, Lung Cancer Research Laboratory, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200030, China.,State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hong Yuan
- Shanghai Lung Cancer Center, Lung Cancer Research Laboratory, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200030, China.,State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qiang Xu
- Jiahui International Hospital, Shanghai 200120, China
| | - Qingquan Luo
- Shanghai Lung Cancer Center, Lung Cancer Research Laboratory, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jie Zhang
- Shanghai Lung Cancer Center, Lung Cancer Research Laboratory, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shun Lu
- Shanghai Lung Cancer Center, Lung Cancer Research Laboratory, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200030, China
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248
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Chen J, Herlong FH, Stroehlein JR, Mishra L. Mutations of Chromatin Structure Regulating Genes in Human Malignancies. Curr Protein Pept Sci 2017; 17:411-37. [PMID: 26796307 PMCID: PMC5403969 DOI: 10.2174/1389203717666160122120008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 12/25/2015] [Accepted: 12/30/2015] [Indexed: 02/08/2023]
Abstract
Chromatin structure regulating processes mediated by the adenosine triphosphate (ATP) –dependent chromatin remodeling complex and the covalent histone-modifying complexes are critical to gene transcriptional control and normal cellular processes, including cell stemness, differentiation, and proliferation. Gene mutations, structural abnormalities, and epigenetic modifications that lead to aberrant expression of chromatin structure regulating members have been observed in most of human malignancies. Advances in next-generation sequencing (NGS) technologies in recent years have allowed in-depth study of somatic mutations in human cancer samples. The Cancer Genome Atlas (TCGA) is the largest effort to date to characterize cancer genome using NGS technology. In this review, we summarize somatic mutations of chromatin-structure regulating genes from TCGA publications and other cancer genome studies, providing an overview of genomic alterations of chromatin regulating genes in human malignancies.
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Affiliation(s)
- Jian Chen
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.
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249
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Kyrochristos ID, Glantzounis GK, Ziogas DE, Gizas I, Schizas D, Lykoudis EG, Felekouras E, Machairas A, Katsios C, Liakakos T, Cho WC, Roukos DH. From Clinical Standards to Translating Next-Generation Sequencing Research into Patient Care Improvement for Hepatobiliary and Pancreatic Cancers. Int J Mol Sci 2017; 18:E180. [PMID: 28106782 PMCID: PMC5297812 DOI: 10.3390/ijms18010180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 12/19/2016] [Accepted: 12/27/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatobiliary and pancreatic (HBP) cancers are associated with high cancer-related death rates. Surgery aiming for complete tumor resection (R0) remains the cornerstone of the treatment for HBP cancers. The current progress in the adjuvant treatment is quite slow, with gemcitabine chemotherapy available only for pancreatic ductal adenocarcinoma (PDA). In the advanced and metastatic setting, only two targeted drugs have been approved by the Food & Drug Administration (FDA), which are sorafenib for hepatocellular carcinoma and erlotinib for PDA. It is a pity that multiple Phase III randomized control trials testing the efficacy of targeted agents have negative results. Failure in the development of effective drugs probably reflects the poor understanding of genome-wide alterations and molecular mechanisms orchestrating therapeutic resistance and recurrence. In the post-ENCODE (Encyclopedia of DNA Elements) era, cancer is referred to as a highly heterogeneous and systemic disease of the genome. The unprecedented potential of next-generation sequencing (NGS) technologies to accurately identify genetic and genomic variations has attracted major research and clinical interest. The applications of NGS include targeted NGS with potential clinical implications, while whole-exome and whole-genome sequencing focus on the discovery of both novel cancer driver genes and therapeutic targets. These advances dictate new designs for clinical trials to validate biomarkers and drugs. This review discusses the findings of available NGS studies on HBP cancers and the limitations of genome sequencing analysis to translate genome-based biomarkers and drugs into patient care in the clinic.
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Affiliation(s)
- Ioannis D Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
| | | | - Demosthenes E Ziogas
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, 'G. Hatzikosta' General Hospital, 45001 Ioannina, Greece.
| | | | - Dimitrios Schizas
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Efstathios G Lykoudis
- Department of Plastic Surgery, Ioannina University School of Medicine, 45110 Ioannina, Greece.
| | - Evangelos Felekouras
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Anastasios Machairas
- Third Department of Surgery, Attikon General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece.
| | - Christos Katsios
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
| | - Theodoros Liakakos
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China.
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece.
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250
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Panera N, Crudele A, Romito I, Gnani D, Alisi A. Focal Adhesion Kinase: Insight into Molecular Roles and Functions in Hepatocellular Carcinoma. Int J Mol Sci 2017; 18:ijms18010099. [PMID: 28067792 PMCID: PMC5297733 DOI: 10.3390/ijms18010099] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Due to the high incidence of post-operative recurrence after current treatments, the identification of new and more effective drugs is required. In previous years, new targetable genes/pathways involved in HCC pathogenesis have been discovered through the help of high-throughput sequencing technologies. Mutations in TP53 and β-catenin genes are the most frequent aberrations in HCC. However, approaches able to reverse the effect of these mutations might be unpredictable. In fact, if the reactivation of proteins, such as p53 in tumours, holds great promise as anticancer therapy, there are studies arguing that chronic activation of these types of molecules may be deleterious. Thus, recently the efforts on potential targets have focused on actionable mutations, such as those occurring in the gene encoding for focal adhesion kinase (FAK). This tyrosine kinase, localized to cellular focal contacts, is over-expressed in a variety of human tumours, including HCC. Moreover, several lines of evidence demonstrated that FAK depletion or inhibition impair in vitro and in vivo HCC growth and metastasis. Here, we provide an overview of FAK expression and activity in the context of tumour biology, discussing the current evidence of its connection with HCC development and progression.
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Affiliation(s)
- Nadia Panera
- Liver Research Unit, Bambino Gesù Children's Hospital, IRCCS, Via S. Paolo, 15, 00146 Rome, Italy.
| | - Annalisa Crudele
- Liver Research Unit, Bambino Gesù Children's Hospital, IRCCS, Via S. Paolo, 15, 00146 Rome, Italy.
| | - Ilaria Romito
- Liver Research Unit, Bambino Gesù Children's Hospital, IRCCS, Via S. Paolo, 15, 00146 Rome, Italy.
| | - Daniela Gnani
- Liver Research Unit, Bambino Gesù Children's Hospital, IRCCS, Via S. Paolo, 15, 00146 Rome, Italy.
| | - Anna Alisi
- Liver Research Unit, Bambino Gesù Children's Hospital, IRCCS, Via S. Paolo, 15, 00146 Rome, Italy.
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