@article{17a8e838f18641f0b36575cb83eac6e2,
title = "Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor-β Pathway",
abstract = "Background & Aims Development of hepatocellular carcinoma (HCC) is associated with alterations in the transforming growth factor-beta (TGF-β) signaling pathway, which regulates liver inflammation and can have tumor suppressor or promoter activities. Little is known about the roles of specific members of this pathway at specific of HCC development. We took an integrated approach to identify and validate the effects of changes in this pathway in HCC and identify therapeutic targets. Methods We performed transcriptome analyses for a total of 488 HCCs that include data from The Cancer Genome Atlas. We also screened 301 HCCs reported in the Catalogue of Somatic Mutations in Cancer and 202 from Cancer Genome Atlas for mutations in genome sequences. We expressed mutant forms of spectrin beta, non-erythrocytic 1 (SPTBN1) in HepG2, SNU398, and SNU475 cells and measured phosphorylation, nuclear translocation, and transcriptional activity of SMAD family member 3 (SMAD3). Results We found somatic mutations in at least 1 gene whose product is a member of TGF-β signaling pathway in 38% of HCC samples. SPTBN1 was mutated in the largest proportion of samples (12 of 202, 6%). Unsupervised clustering of transcriptome data identified a group of HCCs with activation of the TGF-β signaling pathway (increased transcription of genes in the pathway) and a group of HCCs with inactivation of TGF-β signaling (reduced expression of genes in this pathway). Patients with tumors with inactivation of TGF-β signaling had shorter survival times than patients with tumors with activation of TGF-β signaling (P =.0129). Patterns of TGF-β signaling correlated with activation of the DNA damage response and sirtuin signaling pathways. HepG2, SNU398, and SNU475 cells that expressed the D1089Y mutant or with knockdown of SPTBN1 had increased sensitivity to DNA crosslinking agents and reduced survival compared with cells that expressed normal SPTBN1 (controls). Conclusions In genome and transcriptome analyses of HCC samples, we found mutations in genes in the TGF-β signaling pathway in almost 40% of samples. These correlated with changes in expression of genes in the pathways; up-regulation of genes in this pathway would contribute to inflammation and fibrosis, whereas down-regulation would indicate loss of TGF-β tumor suppressor activity. Our findings indicate that therapeutic agents for HCCs can be effective, based on genetic features of the TGF-β pathway; agents that block TGF-β should be used only in patients with specific types of HCCs.",
keywords = "COSMIC, Gene Regulation, Genetics, Immune Response, Liver Cancer",
author = "Jian Chen and Sobia Zaidi and Shuyun Rao and Chen, {Jiun Sheng} and Liem Phan and Patrizia Farci and Xiaoping Su and Kirti Shetty and Jon White and Fausto Zamboni and Xifeng Wu and Asif Rashid and Nagarajan Pattabiraman and Raja Mazumder and Anelia Horvath and Wu, {Ray Chang} and Shulin Li and Cuiying Xiao and Deng, {Chu Xia} and Wheeler, {David A.} and Bibhuti Mishra and Rehan Akbani and Lopa Mishra",
note = "Funding Information: Funding This work was supported by National Institutes of Health grants R01AA023146 (L.M.), R01 CA106614 (L.M.), R01 CA042857 (L.M.), VA Merit I01BX003732 (L.M.), P01 CA130821 (L.M.), Multidisciplinary Research Program Proposal (L.M.), Science & Technology Acquisition and Retention Funding (STARs) (L.M.), R01CA120895 (S.L.) and R01DK102767-01A1 (S.L.), CA143883 and CA083639 (National Cancer Institute; MD Anderson TCGA Genome Data Analysis Center), and MD Anderson Cancer Center Support Grant P30 CA016672 (the Bioinformatics Shared Resource). Funding Information: Hierarchical clustering was performed in TCGA transcriptome sequencing database of 147 HCC cases. TGF-β signatures were validated with the following cohorts: (1) additional 53 HCC cases from TCGA; (2) cohort GSE 14520 (225 HCC samples and 220 normal liver samples); (3) cohort GSE 14323 (55 HCC samples and 20 normal liver samples) from the National Center for Biotechnology Information{\textquoteright}s Gene Expression Omnibus (GEO); (4) transcriptome sequencing of 4 pairs of matched normal liver tissue and HCC samples obtained from the US National Institute of Allergy and Infectious Diseases (9194-N/T, 9401-N/T, 9195-N/T, and 9128-N/T), and 4 human HCC tumor samples (TP2, TP3, TO301, TP504) obtained from Georgetown University School of Medicine. We screened for mutations in whole-exome/genome sequencing of 202 HCC TCGA cases and 301 HCC cases reported in the Catalogue of Somatic Mutations in Cancer (COSMIC). The study was approved by the Office of Human Subjects Research of the National Institutes of Health, Georgetown University School of Medicine, and MD Anderson Cancer Center, and all samples were de-identified. Whole genome sequencing was performed by Complete Genomics and analyzed at MD Anderson Cancer Center DNA core facility. TCGA liver hepatocellular carcinoma mutation and transcriptome RNA sequencing (bam files) and their related clinical data were obtained from the Cancer Genomics Hub (CGHub, https://cghub.ucsc.edu/ ) and TCGA Data Portal ( https://tcga-data.nci.nih.gov/tcga/ ). The paired-end FASTQ files for each sample were extracted from bam files using bam2fastq ( http://www.hudsonalpha.org/gsl/information/software/bam2fastq ). Detailed methods of whole genome sequencing, characterization of TGF-β signaling in HCC, identification, and functional validation of SPTBN1 mutation is in the Supplementary Material available online. Publisher Copyright: {\textcopyright} 2018 AGA Institute",
year = "2018",
month = jan,
doi = "10.1053/j.gastro.2017.09.007",
language = "English (US)",
volume = "154",
pages = "195--210",
journal = "Gastroenterology",
issn = "0016-5085",
publisher = "W.B. Saunders Ltd",
number = "1",
}