Targeted long-read sequencing reveals clonally expanded HBV-associated chromosomal translocations in patients with chronic hepatitis B

作者：Nicholas van Buuren, Ricardo Ramírez, Cameron M. Soulette, Vithika Suri, Dong Han, Lindsey May, Scott Turner, P.C. Parvangada, Ross Martin, Henry Lik‐Yuen Chan, Patrick Marcellin, Marı́a Buti, Nam Bui, Neeru Bhardwaj, Anuj Gaggar, Li Li, Hongmei Mo, Becket Feierbach · 发表于：JHEP Reports · 年份：2022 · DOI：10.1016/j.jhepr.2022.100449 · 被引用次数：50 · 研究领域：Hepatitis B Virus Studies、Hepatitis C virus research、Hepatocellular Carcinoma Treatment and Prognosis

Background & Aims: HBV infects over 257 million people worldwide and is associated with the development of hepatocellular carcinoma (HCC). Integration of HBV DNA into the host genome is likely a key driver of HCC oncogenesis. Here, we utilise targeted long-read sequencing to determine the structure of HBV DNA integrations as well as full isoform information of HBV mRNA with more accurate quantification than traditional next generation sequencing platforms. Methods: DNA and RNA were isolated from fresh frozen liver biopsies collected within the GS-US-174-0149 clinical trial. A pan-genotypic panel of biotinylated oligos was developed to enrich for HBV sequences from sheared genomic DNA (∼7 kb) and full-length cDNA libraries from poly-adenylated RNA. Samples were sequenced on the PacBio long-read platform and analysed using a custom bioinformatic pipeline. Results: HBV-targeted long-read DNA sequencing generated high coverage data spanning entire integrations. Strikingly, in 13 of 42 samples (31%) we were able to detect HBV sequences flanked by 2 different chromosomes, indicating a chromosomal translocation associated with HBV integration. Chromosomal translocations were unique to each biopsy sample, suggesting that each originated randomly, and in some cases had evidence of clonal expansion. Using targeted long-read RNA sequencing, we determined that upwards of 95% of all HBV transcripts in patients who are HBeAg-positive originate from cccDNA. In contrast, patients who are HBe...