Molecular Profiling of Hepatocellular Carcinoma Using Circulating Cell-Free DNA

Abstract

Purpose: Molecular profiling has been used to select patients for targeted therapy and determine prognosis. Noninvasive strategies are critical to hepatocellular carcinoma (HCC) given the challenge of obtaining liver tissue biopsies.Experimental Design: We analyzed blood samples from 206 patients with HCC using comprehensive genomic testing (Guardant Health) of circulating tumor DNA (ctDNA).Results: A total of 153/206 (74.3%) were men; median age, 62 years (range, 18-91 years). A total of 181/206 patients had 1 alteration. The total number of alterations was 680 (nonunique); median number of alterations/ patient was three (range, 1-13); median mutant allele frequency (% cfDNA), 0.49% (range, 0.06%-55.03%). TP53 was the common altered gene [>120 alterations (non-unique)] followed by EGFR, MET, ARID1A, MYC, NF1, BRAF, and ERBB2 [20-38 alterations (nonunique)/gene]. Of the patients with alterations, 56.9% (103/181) had 1 actionable alterations, most commonly in MYC, EGFR, ERBB2, BRAF, CCNE1, MET, PIK3CA, ARID1A, CDK6, and KRAS. In these genes, amplifications occurred more frequently than mutations. Hepatitis B (HBV)-positive patients were more likely to have ERBB2 alterations, 35.7% (5/14) versus 8.8% HBV-negative (P ¼ 0.04).Conclusions: This study represents the first large-scale analysis of blood-derived ctDNA in HCC in United States. The genomic distinction based on HCC risk factors and the high percentage of potentially actionable genomic alterations suggests potential clinical utility for this technology.Recent technological advances in molecular diagnostics have allowed for the study of solid malignancies through noninvasive blood sampling. Importantly, intact circulating tumor cells (CTCs) and cell-free DNA (cfDNA) [leukocyte-derived and tumor-derived (circulating tumor DNA; ctDNA)] can now be interrogated through advanced sequencing methods in order to identify somatic mutations that may be druggable targets for future therapies (1, 2). Although cfDNA and ctDNA are similar in that they both derive from cell lysis and apoptosis (3), ctDNA is the fraction of cfDNA, which can range from <0.1% to >10% (4), specifically derived from primary or metastatic tumors (5). Therefore, profiling the mutational landscape of ctDNA from solid tumors may represent a particularly attractive method for identifying tumor-associated somatic mutations. Applications that can be envisioned to be of clinical utility for hepatocellular carcinoma (HCC) include detection of genomic changes, mutational analysis, prognostication, oncogenic

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“…The prognosis of Stage I/II is not only associated with tumor size and number, vascular invasion and/or lymph node metastasis but also might be influenced by circulating tumor cells. Perioperative circulating tumor cells have been associated with survival in HCC 28‐30 …”

<p>Dynamic Changes in Serum Markers and Their Utility in the Early Diagnosis of All Stages of Hepatitis B-Associated Hepatocellular Carcinoma</p>

“…Thus, specificity is affected to some extent. Therefore, nucleic acid markers are now largely developed towards based on their biology, such as methylation 35,36 and mutation, [37][38][39] to provide insight into treatment choice or potential drug resistance. As complete cells, CTCs can provide all the same information as nucleic acids.…”

Liquid Biopsies in Hepatocellular Carcinoma: Are We Winning?

“…TP53 mutations are the most commonly found mutations in HCC tissue and cfDNA, with more than 120 non-unique alterations [108,109]. Using digital droplet PCR targeting, the TP53 c.747G > T (p.R249S) mutation, as well as CTNNB1 c.121A > G (p.T41A), CTNNB1 c.133T > C (p.S45A), and TERT c.-124C > T mutations, were identified in at least one mutation in 56.3% (27/48) of the cfDNAs obtained from patients with HCC.…”