Next-generation sequencing (NGS) of serum microRNA in hepatocellular carcinoma (HCC) patients treated with sorafenib and an mTOR inhibitor

LBA204 Background: Noninvasive biomarkers are urgently needed in HCC. MicroRNA (miRNA) are small, noncoding RNA that regulate mRNA expression and are detectable in tumor tissue and extracellular compartments. miRNA signatures in blood specimens show association with HCC diagnosis but have not been explored as pharmacodynamic or predictive biomarkers. We present a pilot study to identify differentially expressed miRNA using NGS on serum from HCC patients at baseline and on targeted therapy, compared to controls. Methods: Serum samples were obtained from HCC patients enrolled on a clinical trial of sorafenib plus temsirolimus. Control sera were obtained from patients with non-malignant liver diseases (NMLD) and healthy volunteers (HV). Total RNA was extracted using RNAzol followed by library construction for each sample. Small RNA were separated by gel purification and sequenced by Illumina HiSeq 2500 at 5M+ reads per sample. Raw sequencing reads were mapped using Novoalign and quantified. Counts were normalized using an exogenous spike-in miRNA. Comparisons between HCC vs. control and baseline vs. on treatment cohorts were performed by linear regression (one-way ANOVA) and multiple-test corrected using Benjamini-Hochberg statistics. Candidate signature miRNA were derived using fold change, p-value, and abundance cutoffs. Results: Cohorts: HCC baseline (n=23) and paired on treatment (n=20), NMLD (n=12), and HV (n=10). HCC cohort: HBV+/dual 40%, HCV+ 32%. NMLD cohort: HCV+ 83%. Median RNA yield/200 µL was 410 ng (range: 69-1066) for HCC, 406 ng (range: 224-1100) for NMLD. The mapping rate ranged from 10-70%. Elevated AFP was associated with up-regulated miRNA identified in TCGA HCC cases, including miR-10a/b. No significant differences were observed for HBV+ vs. HCV+. Multiple oncomiRs appeared downregulated on treatment including Let-7 and miR-17/92 family members. Some miRNA isoforms were differentially regulated in each cohort. Conclusions: Serum miRNA in HCC patients demonstrate changes on treatment and can be characterized by NGS. Certain miRNA implicated in HCC appeared related to clinical covariates and warrant further study as novel biomarkers.