Systematic characterization of full-length RNA isoforms in human colorectal cancer at single-cell resolution.

Ping LU; Yu ZHANG; Yueli CUI; Yuhan LIAO; Zhenyu LIU; Zhi-Jie CAO; Jun-E LIU; Lu WEN; Xin ZHOU; Wei FU; Fuchou TANG

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Systematic characterization of full-length RNA isoforms in human colorectal cancer at single-cell resolution.

Author: Ping LU ¹ ; Yu ZHANG ¹ ; Yueli CUI ¹ ; Yuhan LIAO ¹ ; Zhenyu LIU ¹ ; Zhi-Jie CAO ¹ ; Jun-E LIU ¹ ; Lu WEN ¹ ; Xin ZHOU ¹ ; Wei FU ¹ ; Fuchou TANG ¹
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1. Biomedical Pioneering Innovative Center, School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing 100871, China.
Publication Type:Journal Article
Keywords: RNA splicing; colorectal cancer; differential transcript usage; full-length RNA isoforms; long-read scRNA-seq
MeSH: Humans; Colorectal Neoplasms/metabolism*; RNA Isoforms/metabolism*; Single-Cell Analysis; RNA Splicing; Gene Expression Regulation, Neoplastic; RNA, Neoplasm/metabolism*; Transcriptome
From: Protein & Cell 2025;16(10):873-895
CountryChina
Language:English
Abstract: Dysregulated RNA splicing is a well-recognized characteristic of colorectal cancer (CRC); however, its intricacies remain obscure, partly due to challenges in profiling full-length transcript variants at the single-cell level. Here, we employ high-depth long-read scRNA-seq to define the full-length transcriptome of colorectal epithelial cells in 12 CRC patients, revealing extensive isoform diversities and splicing alterations. Cancer cells exhibited increased transcript complexity, with widespread 3'-UTR shortening and reduced intron retention. Distinct splicing regulation patterns were observed between intrinsic-consensus molecular subtypes (iCMS), with iCMS3 displaying even higher splicing factor activities and more pronounced 3'-UTR shortening. Furthermore, we revealed substantial shifts in isoform usage that result in alterations of protein sequences from the same gene with distinct carcinogenic effects during tumorigenesis of CRC. Allele-specific expression analysis revealed dominant mutant allele expression in key oncogenes and tumor suppressors. Moreover, mutated PPIG was linked to widespread splicing dysregulation, and functional validation experiments confirmed its critical role in modulating RNA splicing and tumor-associated processes. Our findings highlight the transcriptomic plasticity in CRC and suggest novel candidate targets for splicing-based therapeutic strategies.