Analysis of Tissue and Circulating Tumor DNA by Next-Generation Sequencing of Hepatocellular Carcinoma: Implications for Targeted Therapeutics

Abstract

Hepatocellular carcinoma (HCC) has limited treatment options. Molecular analysis of its mutational landscape may enable the identification of novel therapies. However, biopsy is not routinely performed in HCC. The utility of analyzing cell-free circulating tumor DNA (ctDNA) by next-generation sequencing (NGS) is not established. We performed 32 ctDNA NGS analyses on 26 patients; 10 of these patients had tissue NGS (236 to 626 genes). ctDNA was evaluated using an assay that detects single nucleotide variants, amplifications, fusions, and specific insertion/deletion alterations in 54 to 70 genes. The ctDNA demonstrated that 23 of 26 patients (88.5%) had ≥1 characterized alteration, and all these individuals had ≥1 potentially actionable alteration. The most frequently mutated gene was (16 of 26 patients, 61.5%). There were 47 unique characterized molecular alterations among 18 total gene alterations [variants of unknown significance (VUS) excluded)]. ctDNA and tissue NGS frequently showed different profiles, perhaps due to length of time between tissue and blood samples [median = 370 days (range, 29 to 876 days)]. Serial ctDNA evaluation in an illustrative patient treated with capecitabine demonstrated emergence of a new alteration after progression. In conclusion, ctDNA profiling is feasible in advanced HCC, and serial assessment using ctDNA NGS can reveal genomic changes with time. NGS of ctDNA provides a minimally invasive alternative for identifying potentially actionable gene alterations and potential molecular targeted therapies. Dynamic changes in molecular portfolio associated with therapeutic pressure in difficult-to-biopsy patients can be observed. .

Liver-derived cell-free nucleic acids in plasma: Biology and applications in liquid biopsies

“…[74][75][76] The mutational profile of cfDNA was further shown to reflect the status in the corresponding tumour tissues. 77 Currently, mutational analysis in patients with HCC is not routinely used to guide treatment decisions for 2 reasons. First, there are only 6 approved systemic therapies for HCC, including sorafenib and lenvatinib as first-line treatments for advanced HCC and regorafenib, cabozantinib, nivolumab and pembrolizumab as second-line treatments for patients who were previously treated with sorafenib or lenvatinib.…”

Circulating tumor DNAs and non-coding RNAs as potential biomarkers for hepatocellular carcinoma diagnosis, prognosis and response to therapy

“…Confirming tumor heterogeneity in HCC, a recent study analysed plasma cfDNA from 26 HCC patients for the presence of mutations in a large set of genes. Authors found tumor heterogeneity and evolution over time by tracking circulating mutation pattern in a patient who developed progression after capecitabine treatment [29] .…”

Liquid Biopsy to Characterize Cell-Free DNA in Cancer Detection and Monitoring

“…Another study in advanced liver cancer demonstrated that serial assessment of alterations in cancer-related driver genes using cfDNA NGS can reveal genomic changes with time. The concordance levels between genomic alterations found in plasma and tissue were high for the three most commonly altered genes, TP53, CTNNB1, and ARID1A, indicating that liquid biopsy is relatively accurate compared to traditional biopsy in monitoring of advanced liver cancer patients [32]. Cai et al demonstrated that both single nucleotide variants (SNVs) and copy number variants (CNVs) of cfDNA found in plasma samples can quantifiably reflect the tumor size of liver cancer patients and may be prognostic [33].…”