Prospective Genotyping of Hepatocellular Carcinoma: Clinical Implications of Next-Generation Sequencing for Matching Patients to Targeted and Immune Therapies

Abstract

Purpose: Prior molecular profiling of hepatocellular carcinoma (HCC) has identified actionable findings that may have a role in guiding therapeutic decision-making and clinical trial enrollment. We implemented prospective next-generation sequencing (NGS) in the clinic to determine whether such analyses provide predictive and/or prognostic information for HCC patients treated with contemporary systemic therapies.

Experimental design: Matched tumor/normal DNA from patients with HCC (N = 127) were analyzed using a hybridization capture-based NGS assay designed to target 341 or more cancer-associated genes. Demographic and treatment data were prospectively collected with the goal of correlating treatment outcomes and drug response with molecular profiles.

Results: WNT/β-catenin pathway (45%) and TP53 (33%) alterations were frequent and represented mutually exclusive molecular subsets. In sorafenib-treated patients (n = 81), oncogenic PI3K-mTOR pathway alterations were associated with lower disease control rates (DCR, 8.3% vs. 40.2%), shorter median progression-free survival (PFS; 1.9 vs. 5.3 months), and shorter median overall survival (OS; 10.4 vs. 17.9 months). For patients treated with immune checkpoint inhibitors (n = 31), activating alteration WNT/β-catenin signaling were associated with lower DCR (0% vs. 53%), shorter median PFS (2.0 vs. 7.4 months), and shorter median OS (9.1 vs. 15.2 months). Twenty-four percent of patients harbored potentially actionable alterations including TSC1/2 (8.5%) inactivating/truncating mutations, FGF19 (6.3%) and MET (1.5%) amplifications, and IDH1 missense mutations (<1%). Six percent of patients treated with systemic therapy were matched to targeted therapeutics.

Conclusions: Linking NGS to routine clinical care has the potential to identify those patients with HCC likely to benefit from standard systemic therapies and can be used in an investigational context to match patients to genome-directed targeted therapies.See related commentary by Pinyol et al., p. 2021.

Figure 1.

Landscape of genomic alterations in HCC. A, Comparison of the clinical characteristics of the MSK HCC (N = 127) and the TCGA HCC cohorts (N = 196). B, The most common genomic alterations in liver cancer listed in order of frequency. C, Oncoprint of commonly altered genes. Tumors are split into three groups (WNT/β-catenin pathway altered, TP53 altered, and other). Genes were grouped by pathway/function, and select clinicopathologic parameters are shown for all tumors. Clinicopathologic features and mutations were color coded by type. VUS, variant of unknown significance.

Figure 2.

Genomic determinants of response to sorafenib in patients with advanced HCC. A, Months of treatment (y-axis) for each patient annotated with gene alteration and objective response. B, Kaplan-Meier PFS on sorafenib therapy for patients with PI3K-mTOR-activated tumors (N = 12) versus non-PI3K-mTOR tumors (N = 67), demonstrating shorter PFS in PI3K-mTOR activated HCCs. C, Kaplan-Meier OS on first-line sorafenib therapy for patients with PI3K-mTOR- activated tumors (N = 12) versus non-PI3K-mTOR tumors (N = 67), demonstrating a shorter OS in PI3K-mTOR-activated HCCs.

Figure 3.

Genomic determinants of response to immune checkpoint blockade in patients with advanced HCC. A, Waterfall plot for 27 evaluable patients treated with immune checkpoint blockade showing best change in target lesions for each patient, annotated with response and most frequent genomic alterations. B, Kaplan-Meier PFS on immune oncology agent (IO) for patients with WNT- activated tumors versus non-WNT- activated tumors, demonstrating shorter PFS in WNT-activated HCCs. C, Kaplan-Meier PFS on sorafenib therapy for patients with WNT-activated tumors versus non- WNT-activated tumors, demonstrating equivalent PFS in WNT-activated HCCs.

Figure 4.

Prospective genotyping of HCC and matching to genome-driven therapy. A, Highest level ofclinical actionability across thecohort, as defined by OncoKB. Standard therapeutic implications include FDA-recognized or National Comprehensive Cancer Network (NCCN) guideline listed biomarkers that are predictive of response to an FDA-approved drug in a specific indication (level 1). Investigational therapeutic implications include FDA-approved biomarkers predictive of response to an FDA-approved drug detected in an off-label indication (level 2B), FDA- or non-FDA-recognized biomarkers that are predictive of response to novel targeted agents that haveshown promising results in clinical trials (level 3B),and non-FDA-recognized biomarkersthatare predictive of responseto novel targeted agentson the basisof compelling preclinical data (level 4). B, Duration of treatment for 4 patients with TSC-mutant HCC treated with sorafenib and mTOR inhibitors. C, A patient with autoimmune hepatitis with Child-Pugh A hepatic function and a TSC2 E95*-mutant HCC who had rapid progression on prior sorafenib with stabilization ofdisease with minor tumoral shrinkage on everolimus.