Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination

Liu, Yu Chen; Ishikawa, Masakazu; Sakakibara, Shuhei; Al Kadi, Mohamad; Motooka, Daisuke; Naito, Yoko; Ito, Shingo; Imamura, Yuko; Matsumoto, Hisatake; Sugihara, Fuminori; Hirata, Haruhiko; Ogura, Hiroshi; Okuzaki, Daisuke

doi:https://doi.org/10.1016/j.gene.2024.148971

Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination

Liu, Yu Chen; Ishikawa, Masakazu; Sakakibara, Shuhei et al.

Gene, 2025, 933, 148971

Number of Access:2,263（2025-08-16 04:45 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/98596

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Title	Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination
Creator	NRID 1000050894698 1000050894698 ORCID 0000-0002-2750-0182 0000-0002-2750-0182 researchmap permalink liuyuchen liuyuchen CreatorName Liu, Yu Chen
	CreatorName Ishikawa, Masakazu
	NRID 1000010618838 1000010618838 ORCID 0000-0003-3157-5870 0000-0003-3157-5870 researchmap permalink SSakakibara SSakakibara CreatorName Sakakibara, Shuhei
	NRID 1000070963883 1000070963883 researchmap permalink malkadi malkadi CreatorName Al Kadi, Mohamad
	NRID 1000010636830 1000010636830 researchmap permalink daisukem daisukem Scopus Author ID 35315737900 35315737900 CreatorName Motooka, Daisuke
	NRID 1000010553026 1000010553026 researchmap permalink nyoko nyoko CreatorName Naito, Yoko
	CreatorName Ito, Shingo
	NRID 1000050610937 1000050610937 researchmap permalink yimamura78 yimamura78 Scopus Author ID 22937335400 22937335400 CreatorName Imamura, Yuko
	NRID 1000070644003 1000070644003 researchmap permalink 38283828 38283828 Scopus Author ID 36632584800 36632584800 CreatorName Matsumoto, Hisatake
	NRID 1000050381645 1000050381645 researchmap permalink sugiharaf sugiharaf CreatorName Sugihara, Fuminori
	NRID 1000030546867 1000030546867 researchmap permalink hh_resmed hh_resmed Scopus Author ID 7202342767 7202342767 CreatorName Hirata, Haruhiko
	NRID 1000070301265 1000070301265 researchmap permalink read0054647 read0054647 Scopus Author ID 7202495132 7202495132 CreatorName Ogura, Hiroshi
	NRID 1000000346131 1000000346131 ORCID 0000-0002-4552-783X 0000-0002-4552-783X researchmap permalink read0092307 read0092307 Scopus Author ID 6506703054 6506703054 CreatorName Okuzaki, Daisuke
Subject	Blood sample
	BNT162b2
	circRNA
	mRNA vaccine
	SARS-CoV-2
Description	Liu Y.C., Ishikawa M., Sakakibara S., et al. Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination. Gene 933, 148971 (2025); https://doi.org/10.1016/j.gene.2024.148971.
Abstract	Circular RNAs (circRNA) lack 5′ or 3′ ends; their unique covalently closed structures prevent RNA degradation by exonucleases. These characteristics provide circRNAs with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNAs. CircRNA levels are reportedly associated with certain human diseases, making them novel disease biomarkers and a noncanonical class of therapeutic targets. In this study, the endogenous circRNAs underlying the response to BNT162b2 mRNA vaccination were evaluated. To this end, peripheral blood samples were subjected to full-length sequencing of circRNAs via nanopore sequencing and transcriptome sequencing. Fifteen samples, comprising pre-, first, and second vaccination cohorts, were obtained from five healthcare workers with no history of SARS-CoV-2 infection or previous vaccination. A total of 4706 circRNAs were detected; following full-length sequencing, 4217 novel circRNAs were identified as being specifically expressed during vaccination. These circRNAs were enriched in the binding motifs of stress granule assemblies and SARS-CoV-2 RNA binding proteins, namely poly(A) binding protein cytoplasmic 1 (PABPC1), pumilio RNA binding family member 1 (PUM1), and Y box binding protein 1 (YBX1). Moreover, 489 circRNAs were identified as previously reported miRNA sponges. The differentially expressed circRNAs putatively originated from plasma B cells compared to circRNAs reported in human blood single-cell RNA sequencing datasets. The pre- and post-vaccination differences observed in the circRNA expression landscape in response to the SARS-CoV-2 BNT162b2 mRNA vaccine.
Publisher	Elsevier B.V.
Source Title	Gene
Volume (Issue)	933
Page	148971
Date of Issued	2025-01-15
Language	English
Handle URL	https://hdl.handle.net/11094/98596
PISSN	03781119
eISSN	18790038
Relation.isIdenticalTo	DOI (Publisher Version) https://doi.org/10.1016/j.gene.2024.148971
Access Rights	open access
CopyRight	This article is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
oaire:version	Version of Record
Category	学術雑誌論文 Journal Article

Resource Type	journal article
Local Type	Journal Article
DCTERMS.bibliographicCitation	Gene. 2025, 933, p. 148971
DC.title	Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination
DC.creator	Liu, Yu Chen
	Ishikawa, Masakazu
	Sakakibara, Shuhei
	Al Kadi, Mohamad
	Motooka, Daisuke
	Naito, Yoko
	Ito, Shingo
	Imamura, Yuko
	Matsumoto, Hisatake
	Sugihara, Fuminori
	Hirata, Haruhiko
	Ogura, Hiroshi
	Okuzaki, Daisuke
DC.publisher	Elsevier B.V.
DC.language' scheme='DCTERMS.RFC1766	English
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2025-01-15
DC.identifier	https://doi.org/10.1016/j.gene.2024.148971
DC.subject	Blood sample
	BNT162b2
	circRNA
	mRNA vaccine
	SARS-CoV-2
DC.description	Liu Y.C., Ishikawa M., Sakakibara S., et al. Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination. Gene 933, 148971 (2025); https://doi.org/10.1016/j.gene.2024.148971.
DCTERMS.abstract	Circular RNAs (circRNA) lack 5′ or 3′ ends; their unique covalently closed structures prevent RNA degradation by exonucleases. These characteristics provide circRNAs with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNAs. CircRNA levels are reportedly associated with certain human diseases, making them novel disease biomarkers and a noncanonical class of therapeutic targets. In this study, the endogenous circRNAs underlying the response to BNT162b2 mRNA vaccination were evaluated. To this end, peripheral blood samples were subjected to full-length sequencing of circRNAs via nanopore sequencing and transcriptome sequencing. Fifteen samples, comprising pre-, first, and second vaccination cohorts, were obtained from five healthcare workers with no history of SARS-CoV-2 infection or previous vaccination. A total of 4706 circRNAs were detected; following full-length sequencing, 4217 novel circRNAs were identified as being specifically expressed during vaccination. These circRNAs were enriched in the binding motifs of stress granule assemblies and SARS-CoV-2 RNA binding proteins, namely poly(A) binding protein cytoplasmic 1 (PABPC1), pumilio RNA binding family member 1 (PUM1), and Y box binding protein 1 (YBX1). Moreover, 489 circRNAs were identified as previously reported miRNA sponges. The differentially expressed circRNAs putatively originated from plasma B cells compared to circRNAs reported in human blood single-cell RNA sequencing datasets. The pre- and post-vaccination differences observed in the circRNA expression landscape in response to the SARS-CoV-2 BNT162b2 mRNA vaccine.
DC.rights	This article is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
DC.format	98596
citation_title	Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination
citation_author	Liu, Yu Chen
	Ishikawa, Masakazu
	Sakakibara, Shuhei
	Al Kadi, Mohamad
	Motooka, Daisuke
	Naito, Yoko
	Ito, Shingo
	Imamura, Yuko
	Matsumoto, Hisatake
	Sugihara, Fuminori
	Hirata, Haruhiko
	Ogura, Hiroshi
	Okuzaki, Daisuke
citation_publisher	Elsevier B.V.
citation_language	English
citation_date	2025-01-15
citation_journal_title	Gene
citation_volume	933
citation_firstpage	148971
citation_doi	https://doi.org/10.1016/j.gene.2024.148971
citation_public_url	https://hdl.handle.net/11094/98596

Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination

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