Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma

We performed the first proteogenomic characterization of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) using paired tumor and adjacent liver tissues from 159 patients. Integrated proteogenomic analyses revealed consistency and discordance among multi-omics, activation status of key signaling pathways, and liver-specific metabolic reprogramming in HBV-related HCC. Proteomic profiling identified three subgroups associated with clinical and molecular attributes including patient survival, tumor thrombus, genetic profile, and the liver-specific proteome. These proteomic subgroups have distinct features in metabolic reprogramming, microenvironment dysregulation, cell proliferation, and potential therapeutics. Two prognostic biomarkers, PYCR2 and ADH1A, related to proteomic subgrouping and involved in HCC metabolic reprogramming, were identified. CTNNB1 and TP53 mutation-associated signaling and metabolic profiles were revealed, among which mutated CTNNB1-associated ALDOA phosphorylation was validated to promote glycolysis and cell proliferation. Our study provides a valuable resource that significantly expands the knowledge of HBV-related HCC and may eventually benefit clinical practice.

[1]  Y. Pomyen,et al.  Common Molecular Subtypes Among Asian Hepatocellular Carcinoma and Cholangiocarcinoma. , 2017, Cancer cell.

[2]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[3]  S. Dooley,et al.  TGF-beta enhances alcohol dependent hepatocyte damage via down-regulation of alcohol dehydrogenase I. , 2009, Journal of hepatology.

[4]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[5]  Ronald J. Moore,et al.  Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer , 2016, Cell.

[6]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer genes , 2014 .

[7]  Michael E. Coulter,et al.  Mutations in PYCR2, Encoding Pyrroline-5-Carboxylate Reductase 2, Cause Microcephaly and Hypomyelination. , 2015, American journal of human genetics.

[8]  D. Russell.  The enzymes, regulation, and genetics of bile acid synthesis. , 2003, Annual review of biochemistry.

[9]  Wenhui Li,et al.  Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus , 2012, eLife.

[10]  S. Alavian,et al.  Global prevalence, treatment, and prevention of hepatitis B virus infection in 2016: a modelling study. , 2018, The lancet. Gastroenterology & hepatology.

[11]  Benjamin Schubert,et al.  OptiType: precision HLA typing from next-generation sequencing data , 2014, Bioinform..

[12]  S. Morganella,et al.  A Compendium of Mutational Signatures of Environmental Agents , 2019, Cell.

[13]  Xianghuo He,et al.  CXCR6 upregulation contributes to a proinflammatory tumor microenvironment that drives metastasis and poor patient outcomes in hepatocellular carcinoma. , 2012, Cancer research.

[14]  D. Nelson,et al.  Oral Direct-Acting Agent Therapy for Hepatitis C Virus Infection: A Systematic Review. , 2017, Annals of internal medicine.

[15]  G. Getz,et al.  GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers , 2011, Genome Biology.

[16]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[17]  Derek Y. Chiang,et al.  Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma. , 2009, Cancer research.

[18]  Jüergen Cox,et al.  The MaxQuant computational platform for mass spectrometry-based shotgun proteomics , 2016, Nature Protocols.

[19]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[20]  Jessica Zucman-Rossi,et al.  Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets , 2015, Nature Genetics.

[21]  Hiromi Nakamura,et al.  Trans-ancestry mutational landscape of hepatocellular carcinoma genomes , 2014, Nature Genetics.

[22]  G. Giannelli,et al.  Transforming growth factor-β as a therapeutic target in hepatocellular carcinoma. , 2014, Cancer research.

[23]  P. Meier,et al.  Molecular cloning, chromosomal localization, and functional characterization of a human liver Na+/bile acid cotransporter. , 1994, The Journal of clinical investigation.

[24]  W. Hahn,et al.  Transformation of Human and Murine Fibroblasts without Viral Oncoproteins , 2005, Molecular and Cellular Biology.

[25]  Daniel C. Liebler,et al.  Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction* , 2016, Molecular & Cellular Proteomics.

[26]  Hugo Y. K. Lam,et al.  Performance comparison of exome DNA sequencing technologies , 2011, Nature Biotechnology.

[27]  Justin Guinney,et al.  GSVA: gene set variation analysis for microarray and RNA-Seq data , 2013, BMC Bioinformatics.

[28]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[29]  Q. Gao,et al.  Critical appraisal of Chinese 2017 guideline on the management of hepatocellular carcinoma. , 2017, Hepatobiliary surgery and nutrition.

[30]  P. A. Futreal,et al.  Genome-Wide Mutational Signatures of Aristolochic Acid and Its Application as a Screening Tool , 2013, Science Translational Medicine.

[31]  J. Marin,et al.  Wnt–β-catenin signalling in liver development, health and disease , 2018, Nature Reviews Gastroenterology & Hepatology.

[32]  M. Mann,et al.  Universal sample preparation method for proteome analysis , 2009, Nature Methods.

[33]  Steven J. M. Jones,et al.  Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma , 2017, Cell.

[34]  Lijun Xue,et al.  Human mitochondrial pyrroline-5-carboxylate reductase 1 promotes invasiveness and impacts survival in breast cancers , 2017, Carcinogenesis.

[35]  C. Eyers.  Universal sample preparation method for proteome analysis , 2009 .

[36]  Michael L. Gatza,et al.  Proteogenomics connects somatic mutations to signaling in breast cancer , 2016, Nature.

[37]  B. Sartorius,et al.  Global and country underestimation of hepatocellular carcinoma (HCC) in 2012 and its implications. , 2015, Cancer epidemiology.

[38]  S. Imbeaud,et al.  Tissue metabolomics of hepatocellular carcinoma: Tumor energy metabolism and the role of transcriptomic classification , 2013, Hepatology.

[39]  Yan Zhu,et al.  Prognostic Biomarker Identification Through Integrating the Gene Signatures of Hepatocellular Carcinoma Properties , 2017, EBioMedicine.

[40]  P. Meier,et al.  Chlorambucil-taurocholate is transported by bile acid carriers expressed in human hepatocellular carcinomas. , 1997, Gastroenterology.

[41]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[42]  Robert Tibshirani,et al.  Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data , 2013, Statistical methods in medical research.

[43]  Clinical Proteomic Tumor Analysis Consortium , 2020, Definitions.

[44]  M. Mann,et al.  Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation* , 2011, Molecular & Cellular Proteomics.

[45]  S. Thorgeirsson,et al.  Transforming growth factor‐β gene expression signature in mouse hepatocytes predicts clinical outcome in human cancer , 2008, Hepatology.

[46]  K. Kinzler,et al.  Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing , 2013, Science Translational Medicine.

[47]  Shicai Wang,et al.  COSMIC: the Catalogue Of Somatic Mutations In Cancer , 2018, Nucleic Acids Res..

[48]  C. Brennan,et al.  Tumor mutational load predicts survival after immunotherapy across multiple cancer types , 2019, Nature Genetics.

[49]  Non-communicable Disease Control.  [Strategies of primary prevention of liver cancer in China: Expert Consensus (2018)]. , 2019, Zhonghua zhong liu za zhi [Chinese journal of oncology].

[50]  Manal M. Hassan,et al.  Inactivation of Hippo Pathway Is Significantly Associated with Poor Prognosis in Hepatocellular Carcinoma , 2015, Clinical Cancer Research.

[51]  H. Bonkovsky,et al.  Contemporary clinical research of traditional Chinese medicines for chronic hepatitis B in China: An analytical review , 2010, Hepatology.

[52]  Marcos Díaz-Gay,et al.  Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples , 2018, BMC Bioinformatics.

[53]  Derek Y. Chiang,et al.  Focal gains of VEGFA and molecular classification of hepatocellular carcinoma. , 2008, Cancer research.

[54]  Jeffrey R. Whiteaker,et al.  Proteogenomic characterization of human colon and rectal cancer , 2014, Nature.

[55]  Wei Liu,et al.  Proline biosynthesis augments tumor cell growth and aerobic glycolysis: involvement of pyridine nucleotides , 2015, Scientific Reports.

[56]  Jeffrey R. Whiteaker,et al.  Clinical potential of mass spectrometry-based proteogenomics , 2018, Nature Reviews Clinical Oncology.

[57]  Emanuel J. V. Gonçalves,et al.  Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer , 2017, Cell systems.

[58]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[59]  Xiaojing Wang,et al.  customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search , 2013, Bioinform..

[60]  Mehdi Mesri,et al.  Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium. , 2013, Cancer discovery.

[61]  C. Ponting,et al.  Sequencing depth and coverage: key considerations in genomic analyses , 2014, Nature Reviews Genetics.

[62]  Eric Talevich,et al.  CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing , 2016, PLoS Comput. Biol..

[63]  G. Duester,et al.  Distinct Retinoid Metabolic Functions for Alcohol Dehydrogenase Genes Adh1 and Adh4 in Protection against Vitamin A Toxicity or Deficiency Revealed in Double Null Mutant Mice* , 2002, The Journal of Biological Chemistry.

[64]  Derek Y. Chiang,et al.  Pivotal role of mTOR signaling in hepatocellular carcinoma. , 2008, Gastroenterology.

[65]  Matthew D. Wilkerson,et al.  ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking , 2010, Bioinform..

[66]  Yaming Li,et al.  Guidelines for Diagnosis and Treatment of Primary Liver Cancer in China (2017 Edition) , 2018, Liver Cancer.

[67]  Subha Madhavan,et al.  Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities , 2019, Cell.

[68]  Peiyuan Yin,et al.  Global Metabolic Profiling Identifies a Pivotal Role of Proline and Hydroxyproline Metabolism in Supporting Hypoxic Response in Hepatocellular Carcinoma , 2017, Clinical Cancer Research.

[69]  A. Butte,et al.  xCell: digitally portraying the tissue cellular heterogeneity landscape , 2017, Genome Biology.

[70]  M. Nielsen,et al.  NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets , 2016, Genome Medicine.

[71]  G. Duester,et al.  Excessive vitamin A toxicity in mice genetically deficient in either alcohol dehydrogenase Adh1 or Adh3. , 2002, European journal of biochemistry.

[72]  See-Tong Pang,et al.  Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia , 2017, Science Translational Medicine.

[73]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[74]  V. Mazzaferro,et al.  Wnt-Pathway Activation in Two Molecular Classes of Hepatocellular Carcinoma and Experimental Modulation by Sorafenib , 2012, Clinical Cancer Research.

[75]  M. Meyerson,et al.  DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors , 2015, BMC Cancer.

[76]  Wenhui Li,et al.  Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus. , 2012, eLife.

[77]  Y. Shaul,et al.  Hepatocyte metabolic signalling pathways and regulation of hepatitis B virus expression , 2011, Liver international : official journal of the International Association for the Study of the Liver.

[78]  Zhou Zhu,et al.  Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma , 2013, Hepatology.

[79]  David S. Wishart,et al.  DrugBank 5.0: a major update to the DrugBank database for 2018 , 2017, Nucleic Acids Res..

[80]  A. Villanueva.  Hepatocellular Carcinoma. , 2019, The New England journal of medicine.

[81]  Yuri A. Mirokhin,et al.  A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline. , 2016, Journal of proteome research.

[82]  S. Imbeaud,et al.  Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma , 2012, Nature Genetics.

[83]  S. Thorgeirsson,et al.  Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling , 2004, Hepatology.

[84]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[85]  Levi Garraway,et al.  Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden , 2017, Genome Medicine.

[86]  Xin Li,et al.  Spatially resolved metabolomics to discover tumor-associated metabolic alterations , 2018, Proceedings of the National Academy of Sciences.