Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma.

Autor: Santiago JC; University of Washington, Department of Microbiology, Seattle, Washington, United States of America., Goldman JD; University of Washington, Department of Medicine Seattle, Washington, United States of America.; Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America., Zhao H; University of Washington, Department of Microbiology, Seattle, Washington, United States of America., Pankow AP; University of Washington, Department of Microbiology, Seattle, Washington, United States of America., Okuku F; Uganda Cancer Institute, Kampala, Uganda., Schmitt MW; University of Washington, Department of Medicine Seattle, Washington, United States of America., Chen LH; University of Washington, Department of Microbiology, Seattle, Washington, United States of America., Hill CA; University of Washington, Department of Microbiology, Seattle, Washington, United States of America., Casper C; University of Washington, Department of Medicine Seattle, Washington, United States of America.; Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America., Phipps WT; University of Washington, Department of Medicine Seattle, Washington, United States of America.; Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America., Mullins JI; University of Washington, Department of Microbiology, Seattle, Washington, United States of America.; University of Washington, Department of Medicine Seattle, Washington, United States of America.; University of Washington, Department of Global Health, Seattle, Washington, United States of America.; University of Washington, Department of Laboratory Medicine, Seattle, Washington, United States of America.
Jazyk: angličtina
Zdroj: PLoS pathogens [PLoS Pathog] 2021 Jan 19; Vol. 17 (1), pp. e1008594. Date of Electronic Publication: 2021 Jan 19 (Print Publication: 2021).
DOI: 10.1371/journal.ppat.1008594
Abstrakt: Intra-host tumor virus variants may influence the pathogenesis and treatment responses of some virally-associated cancers. However, the intra-host variability of Kaposi sarcoma-associated herpesvirus (KSHV), the etiologic agent of Kaposi sarcoma (KS), has to date been explored with sequencing technologies that possibly introduce more errors than that which occurs in the viral population, and these studies have only studied variable regions. Here, full-length KSHV genomes in tumors and/or oral swabs from 9 Ugandan adults with HIV-associated KS were characterized. Furthermore, we used deep, short-read sequencing using duplex unique molecular identifiers (dUMI)-random double-stranded oligonucleotides that barcode individual DNA molecules before library amplification. This allowed suppression of PCR and sequencing errors to ~10-9/base as well as afforded accurate determination of KSHV genome numbers sequenced in each sample. KSHV genomes were assembled de novo, and rearrangements observed were confirmed by PCR and Sanger sequencing. 131-kb KSHV genome sequences, excluding major repeat regions, were successfully obtained from 23 clinical specimens, averaging 2.3x104 reads/base. Strikingly, KSHV genomes were virtually identical within individuals at the point mutational level. The intra-host heterogeneity that was observed was confined to tumor-associated KSHV mutations and genome rearrangements, all impacting protein-coding sequences. Although it is unclear whether these changes were important to tumorigenesis or occurred as a result of genomic instability in tumors, similar changes were observed across individuals. These included inactivation of the K8.1 gene in tumors of 3 individuals and retention of a region around the first major internal repeat (IR1) in all instances of genomic deletions and rearrangements. Notably, the same breakpoint junctions were found in distinct tumors within single individuals, suggesting metastatic spread of rearranged KSHV genomes. These findings define KSHV intra-host heterogeneity in vivo with greater precision than has been possible in the past and suggest the possibility that aberrant KSHV genomes may contribute to aspects of KS tumorigenesis. Furthermore, study of KSHV with use of dUMI provides a proof of concept for utilizing this technique for detailed study of other virus populations in vivo.
Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: MWS is a founder and equity holder at TwinStrand Biosciences, Inc., which is commercializing Duplex Sequencing technology.
Databáze: MEDLINE
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