Molecular signatures of long-term hepatocellular carcinoma risk in nonalcoholic fatty liver disease

Abstract

Prediction of hepatocellular carcinoma (HCC) risk is an urgent unmet need in patients with nonalcoholic fatty liver disease (NAFLD). In cohorts of 409 patients with NAFLD from multiple global regions, we defined and validated hepatic transcriptome and serum secretome signatures predictive of long-term HCC risk in patients with NAFLD. A 133-gene signature, prognostic liver signature (PLS)–NAFLD, predicted incident HCC over up to 15 years of longitudinal observation. High-risk PLS-NAFLD was associated with IDO1 + dendritic cells and dysfunctional CD8 + T cells in fibrotic portal tracts along with impaired metabolic regulators. PLS-NAFLD was validated in independent cohorts of patients with NAFLD who were HCC naïve (HCC incidence rates at 15 years were 22.7 and 0% in high- and low-risk patients, respectively) or HCC experienced (de novo HCC recurrence rates at 5 years were 71.8 and 42.9% in high- and low-risk patients, respectively). PLS-NAFLD was bioinformatically translated into a four-protein secretome signature, PLSec-NAFLD, which was validated in an independent cohort of HCC-naïve patients with NAFLD and cirrhosis (HCC incidence rates at 15 years were 37.6 and 0% in high- and low-risk patients, respectively). Combination of PLSec-NAFLD with our previously defined etiology-agnostic PLSec-AFP yielded improved HCC risk stratification. PLS-NAFLD was modified by bariatric surgery, lipophilic statin, and IDO1 inhibitor, suggesting that the signature can be used for drug discovery and as a surrogate end point in HCC chemoprevention clinical trials. Collectively, PLS/PLSec-NAFLD may enable NAFLD-specific HCC risk prediction and facilitate clinical translation of NAFLD-directed HCC chemoprevention.

Hepatocellular carcinoma surveillance in patients with non-alcoholic fatty liver disease

“…However, in brief, several risk models incorporating clinical risk factors, genetic factors, and molecular factors have been proposed, with most not yet having been sufficiently validated for routine use in clinical practice. (42)(43)(44)(45) If sufficiently validated, these risk models may facilitate a more individualized precision screening approach to targeted HCC surveillance to those at the highest risk. (46,47) While we await validated models to better risk stratify patients with noncirrhotic NAFLD and identify subgroups who may benefit from HCC surveillance, consistently observed risk factors such as male sex, older age, and increasing number of metabolic syndrome components may help identify individuals with non-cirrhotic NAFLD who have higher HCC risk.…”

Hepatocellular Carcinoma Chemoprevention with Generic Agents

“…[29][30][31][32][33][34][35][36] Of note, the PLS can also be induced in simple cell culture models, ex vivo organotypic culture of patient-derived precision-cut liver slice (PCLS), and patient-derived organoids for high-throughput screening and mechanistic assessment of candidate chemoprevention agents. [34][35][36][37][38]…”

“…A relatively large phase III RCT is recruiting participants to assess simvastatin in compensated cirrhosis for HCC development as a part of composite secondary endpoint (SACRED trial; NCT03654053). Atorvastatin is being evaluated in another phase II RCT using modulation of an HCC risk biomarker, Prognostic Liver Secretome signature (PLSec), 38,47 as the primary endpoint (NCT05028829). A nationwide multi-center clinical trial of lipophilic statin is being launched to assess lipophilic statin on adverse outcomes in cirrhotics with support from the NIH/NIDDK Liver Cirrhosis Network.…”

“…In addition, new bioinformatic methods have allowed in silico search of molecular targeted generic agents that likely serve as HCC chemoprevention. 29,35,37,38 Similar informatic approach can also be utilized to infer clinical toxicities and drug-drug interactions in an unbiased manner. [104][105][106] These generic agents may enable HCC chemoprevention selectively directed to molecular targets to achieve satisfactory potency, while limiting toxicity.…”

“…[29][30][31][32][33][34][35][36] Of note, the PLS can also be induced in simple cell culture models, ex vivo organotypic culture of patient-derived pre-cision-cut liver slice, and patient-derived organoids for highthroughput screening and mechanistic assessment of candidate chemoprevention agents. [34][35][36][37][38] New Approaches to Refine Clinical Trial Design Clinical HCC risk-predictive molecular features can also serve as companion biomarkers in chemoprevention clinical trials to monitor pharmacological response, surrogate end points to estimate the agents' effect on future HCC incidence, and/or select patients who are expected to benefit from the therapies (►Fig. 3).…”