The Full-Length Transcriptomic Atlas of Human Colorectal Cancer from Single-Cell Isoform Sequencing 

Colorectal cancer (CRC) is the second leading cause of cancer death worldwide. In recent years, short-read single-cell RNA sequencing (scRNA-seq) has been instrumental in deciphering tumor cell heterogeneities. However, these studies only enable gene-level expression quantification but neglect alterations in transcript structures, which arise from alternative end processing or splicing, and are frequently observed in cancer.

In this study, we integrated short- and long-read scRNA-seq of CRC patient samples to build the first isoform-resolution CRC transcriptomic atlas. We identified 394 dysregulated transcript structures in tumor epithelial cells, including 299 resulting from various combinations of multiple splicing events. Secondly, we characterized genes and isoforms associated with different epithelial lineages and subpopulations. Finally, we built an algorithm that integrated novel peptides derived from predicted ORFs of recurrent tumor-specific transcripts with mass spectrometry data and identified a panel of recurring neoepitopes that may aid the development of neoantigen-based cancer vaccines.

In this webinar Zhongxiao Li will discuss:

  • Building the first isoform-resolution colorectal cancer (CRC) transcriptomic atlas
  • Characterizing genes and isoforms associated with different epithelial lineages and subpopulations
  • An algorithm to identify recurring neoepitopes that may aid development of neoantigen-based cancer vaccines

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Zhongxiao Li
PhD student in Computer Science, Structural and Functional Bioinformatics Group (SFB)
King Abdullah University of Science and Technology (KAUST)

Wilson Cheng

Sr. Bioinformatics Scientist, Field Application, Asia Pacific

Host & Moderator

Minning Chin
Staff Scientist, FAS, Asia Pacific

Jonathan Bibliowicz, PhD

Associate Director
Oncology and Cancer Research

Xingliang Liu, PhD
Bioinformatics Scientist II, Field Application, Asia Pacific