The accelerating incidence and dismal mortality of hepatocellular carcinoma (HCC) (5-yr survival <12%) highlight the urgent need to improve prediction and prevention of this deadly neoplasm. HCC develops from advanced fibrosis due to hepatitis B virus (HBV), hepatitis C virus (HCV), alcohol, or non-alcoholic fatty liver disease (NAFLD). A 186-gene prognostic signature in stromal cirrhotic liver, previously identified and validated in HCV-related cirrhosis, holds promise to identify patients with highest HCC risk and provide clues to HCC prevention targets. It remains unknown whether this signature is also prognostic for other HCC etiologies. Moreover, the signature has not yet been adapted as a clinically applicable test. Our long-term goal is to develop clinically applicable prognostic biomarkers for the global cirrhosis population caused by variety of etiologies to enable more effective, personalized HCC surveillance and prevention. The objective here is to establish prognostic relevance of the 186-gene signature in the non-HCV etiologies, identify etiology-specific molecular prognostic factors, implement and refine the signature as a clinically applicable assay, and develop genomic database for prognostic biomarker assessment. Our central hypotheses are that the 186-gene signature is universally prognostic irrespective of etiology, and that there are also complementary, etiology-specific prognostic indicators. We will test these hypotheses and address the unmet need by the following interrelated Specific Aims: 1. Establish a gene signature of HCC risk and poor prognosis in patients with non-HCV etiologies of advanced liver disease. We will perform whole-genome expression profiling of stromal cirrhotic liver tissues (905 cirrhosis and 1025 HCC cases affected by HBV, HCV, alcohol, or NAFLD), and validate predictive capability for HCC development as well as cirrhosis progression and death. Etiology-specific prognostic gene signatures will also be identified using the whole-genome datasets. 2. Develop a clinically applicable prognostic test using gene signature that defines HCC risk. We will implement the signature in the digital transcript counting technology specifically designed for clinical lab (nCounter assay, NanoString), and optimize experimental and analytical methods. Transcriptome sequencing-based prediction will also be evaluated as a potential future platform of a clinical test. 3. Develop a web resource for in silico prognostic biomarker assessment for cirrhosis and HCC. Our new and existing datasets, representing a global cirrhosis patient population, will be assembled as a public database that enables quick and easy clinical utility assessment of a user's prognostic molecular signatures.

Public Health Relevance

Liver cirrhosis and cancer are extremely prevalent and lethal diseases, in which key prognostic drivers are still elusive. We propose to establish prognostic biomarkers and generate a panel of genomic datasets comprehensively representing the patient population with liver cirrhosis and cancer worldwide. These data and resources will enable more precise, individualized patient management and contribute to significant improvement in liver cancer's dismal prognosis.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Research Project (R01)
Project #
1R01DK099558-01
Application #
8559992
Study Section
Cancer Biomarkers Study Section (CBSS)
Program Officer
Sherker, Averell H
Project Start
2013-07-15
Project End
2017-06-30
Budget Start
2013-07-15
Budget End
2014-06-30
Support Year
1
Fiscal Year
2013
Total Cost
$490,399
Indirect Cost
$201,078
Name
Icahn School of Medicine at Mount Sinai
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
078861598
City
New York
State
NY
Country
United States
Zip Code
10029
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Chernyavskaya, Yelena; Mudbhary, Raksha; Zhang, Chi et al. (2017) Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling. Development 144:2925-2939
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Ono, Atsushi; Goossens, Nicolas; Finn, Richard S et al. (2017) Persisting risk of hepatocellular carcinoma after hepatitis C virus cure monitored by a liver transcriptome signature. Hepatology 66:1344-1346
Goossens, Nicolas; Singal, Amit G; King, Lindsay Y et al. (2017) Cost-Effectiveness of Risk Score-Stratified Hepatocellular Carcinoma Screening in Patients with Cirrhosis. Clin Transl Gastroenterol 8:e101
Trépo, Eric; Goossens, Nicolas; Fujiwara, Naoto et al. (2017) Combination of Gene Expression Signature and Model for End-stage Liver Disease Score Predicts Survival of Patients With Severe Alcoholic Hepatitis. Gastroenterology :
Van Renne, Nicolaas; Roca Suarez, Armando Andres; Duong, Francois H T et al. (2017) miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis. Gut :
Deshmukh, Manjeet; Nakagawa, Shigeki; Higashi, Takaaki et al. (2017) Cell type-specific pharmacological kinase inhibition for cancer chemoprevention. Nanomedicine 14:317-325
Rodriguez-Bravo, Veronica; Carceles-Cordon, Marc; Hoshida, Yujin et al. (2017) The role of GATA2 in lethal prostate cancer aggressiveness. Nat Rev Urol 14:38-48
Hicks, Daniel F; Goossens, Nicolas; Blas-García, Ana et al. (2017) Transcriptome-based repurposing of apigenin as a potential anti-fibrotic agent targeting hepatic stellate cells. Sci Rep 7:42563

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