A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP

Abstract Bovine leukemia virus (BLV) is an oncogenic retrovirus which induces malignant lymphoma termed enzootic bovine leukosis (EBL) after a long incubation period. Insertion sites of the BLV proviral genome as well as the associations between disease progression and polymorphisms of the virus and...

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Autores principales:	Nagaki Ohnuki, Tomoko Kobayashi, Misaki Matsuo, Kohei Nishikaku, Kazuya Kusama, Yasushi Torii, Yasuko Inagaki, Masatoshi Hori, Kazuhiko Imakawa, Yorifumi Satou
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/061573a7de70457ba4db65d47273971d
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spelling	oai:doaj.org-article:061573a7de70457ba4db65d47273971d2021-12-02T13:33:51ZA target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP10.1038/s41598-021-83909-32045-2322https://doaj.org/article/061573a7de70457ba4db65d47273971d2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83909-3https://doaj.org/toc/2045-2322Abstract Bovine leukemia virus (BLV) is an oncogenic retrovirus which induces malignant lymphoma termed enzootic bovine leukosis (EBL) after a long incubation period. Insertion sites of the BLV proviral genome as well as the associations between disease progression and polymorphisms of the virus and host genome are not fully understood. To characterize the biological coherence between virus and host, we developed a DNA-capture-seq approach, in which DNA probes were used to efficiently enrich target sequence reads from the next-generation sequencing (NGS) library. In addition, enriched reads can also be analyzed for detection of proviral integration sites and clonal expansion of infected cells since the reads include chimeric reads of the host and proviral genomes. To validate this DNA-capture-seq approach, a persistently BLV-infected fetal lamb kidney cell line (FLK-BLV), four EBL tumor samples and four non-EBL blood samples were analyzed to identify BLV integration sites. The results showed efficient enrichment of target sequence reads and oligoclonal integrations of the BLV proviral genome in the FLK-BLV cell line. Moreover, three out of four EBL tumor samples displayed multiple integration sites of the BLV proviral genome, while one sample displayed a single integration site. In this study, we found the evidence for the first time that the integrated provirus defective at the 5′ end was present in the persistent lymphocytosis cattle. The efficient and sensitive identification of BLV variability, integration sites and clonal expansion described in this study provide support for use of this innovative tool for understanding the detailed mechanisms of BLV infection during the course of disease progression.Nagaki OhnukiTomoko KobayashiMisaki MatsuoKohei NishikakuKazuya KusamaYasushi ToriiYasuko InagakiMasatoshi HoriKazuhiko ImakawaYorifumi SatouNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nagaki Ohnuki Tomoko Kobayashi Misaki Matsuo Kohei Nishikaku Kazuya Kusama Yasushi Torii Yasuko Inagaki Masatoshi Hori Kazuhiko Imakawa Yorifumi Satou A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP
description	Abstract Bovine leukemia virus (BLV) is an oncogenic retrovirus which induces malignant lymphoma termed enzootic bovine leukosis (EBL) after a long incubation period. Insertion sites of the BLV proviral genome as well as the associations between disease progression and polymorphisms of the virus and host genome are not fully understood. To characterize the biological coherence between virus and host, we developed a DNA-capture-seq approach, in which DNA probes were used to efficiently enrich target sequence reads from the next-generation sequencing (NGS) library. In addition, enriched reads can also be analyzed for detection of proviral integration sites and clonal expansion of infected cells since the reads include chimeric reads of the host and proviral genomes. To validate this DNA-capture-seq approach, a persistently BLV-infected fetal lamb kidney cell line (FLK-BLV), four EBL tumor samples and four non-EBL blood samples were analyzed to identify BLV integration sites. The results showed efficient enrichment of target sequence reads and oligoclonal integrations of the BLV proviral genome in the FLK-BLV cell line. Moreover, three out of four EBL tumor samples displayed multiple integration sites of the BLV proviral genome, while one sample displayed a single integration site. In this study, we found the evidence for the first time that the integrated provirus defective at the 5′ end was present in the persistent lymphocytosis cattle. The efficient and sensitive identification of BLV variability, integration sites and clonal expansion described in this study provide support for use of this innovative tool for understanding the detailed mechanisms of BLV infection during the course of disease progression.
format	article
author	Nagaki Ohnuki Tomoko Kobayashi Misaki Matsuo Kohei Nishikaku Kazuya Kusama Yasushi Torii Yasuko Inagaki Masatoshi Hori Kazuhiko Imakawa Yorifumi Satou
author_facet	Nagaki Ohnuki Tomoko Kobayashi Misaki Matsuo Kohei Nishikaku Kazuya Kusama Yasushi Torii Yasuko Inagaki Masatoshi Hori Kazuhiko Imakawa Yorifumi Satou
author_sort	Nagaki Ohnuki
title	A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP
title_short	A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP
title_full	A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP
title_fullStr	A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP
title_full_unstemmed	A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP
title_sort	target enrichment high throughput sequencing system for characterization of blv whole genome sequence, integration sites, clonality and host snp
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/061573a7de70457ba4db65d47273971d
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A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP

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