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An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing.
Li, Zhongxiao; Zhang, Bin; Chan, Jia Jia; Tabatabaeian, Hossein; Tong, Qing Yun; Chew, Xiao Hong; Fan, Xiaonan; Driguez, Patrick; Chan, Charlene; Cheong, Faith; Wang, Shi; Siew, Bei En; Tan, Ian Jse-Wei; Lee, Kai-Yin; Lieske, Bettina; Cheong, Wai-Kit; Kappei, Dennis; Tan, Ker-Kan; Gao, Xin; Tay, Yvonne.
Afiliación
  • Li Z; Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology
  • Zhang B; Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology
  • Chan JJ; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
  • Tabatabaeian H; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
  • Tong QY; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
  • Chew XH; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
  • Fan X; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
  • Driguez P; Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
  • Chan C; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
  • Cheong F; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
  • Wang S; Department of Pathology, National University Health System, Singapore 119228, Singapore.
  • Siew BE; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
  • Tan IJ; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore.
  • Lee KY; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore.
  • Lieske B; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore.
  • Cheong WK; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore.
  • Kappei D; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National
  • Tan KK; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Singapore.
  • Gao X; Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology
  • Tay Y; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National
Cell Genom ; 4(9): 100641, 2024 Sep 11.
Article en En | MEDLINE | ID: mdl-39216476
ABSTRACT
Colorectal cancer (CRC) ranks as the second leading cause of cancer deaths globally. In recent years, short-read single-cell RNA sequencing (scRNA-seq) has been instrumental in deciphering tumor heterogeneities. However, these studies only enable gene-level quantification but neglect alterations in transcript structures arising from alternative end processing or splicing. In this study, we integrated short- and long-read scRNA-seq of CRC samples to build an isoform-resolution CRC transcriptomic atlas. We identified 394 dysregulated transcript structures in tumor epithelial cells, including 299 resulting from various combinations of splicing events. Second, we characterized genes and isoforms associated with epithelial lineages and subpopulations exhibiting distinct prognoses. Among 31,935 isoforms with novel junctions, 330 were supported by The Cancer Genome Atlas RNA-seq and mass spectrometry data. Finally, we built an algorithm that integrated novel peptides derived from open reading frames of recurrent tumor-specific transcripts with mass spectrometry data and identified recurring neoepitopes that may aid the development of cancer vaccines.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias Colorrectales / Análisis de la Célula Individual / Transcriptoma Límite: Humans Idioma: En Revista: Cell Genom Año: 2024 Tipo del documento: Article Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias Colorrectales / Análisis de la Célula Individual / Transcriptoma Límite: Humans Idioma: En Revista: Cell Genom Año: 2024 Tipo del documento: Article Pais de publicación: Estados Unidos