Characterization of protein isoform diversity in human umbilical vein endothelial cells (HUVECs) via long-read proteogenomics

Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by protein isoforms. To characterize the isoform landscape within ECs, we applied a long read proteogenomics approach to analy...

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Bibliographic Details
Published inbioRxiv
Main Authors Mehlferber, Madison M, Jordan, Ben T, Jeffery, Erin D, Sheynkman, Leon, Saquing, Jamie, Acharya, Bipul R, Hirschi, Karen K, Sheynkman, Gloria M
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 18.05.2022
Subjects
Blood vessels
Cardiovascular system
Endothelial cells
Isoforms
Peptides
Phenotypes
Proteins
Umbilical vein
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Summary:Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by protein isoforms. To characterize the isoform landscape within ECs, we applied a long read proteogenomics approach to analyze human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream MS analysis to infer protein isoform expression. We detected 53,836 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted reference isoform 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related gene CDH5, suggesting potential changes in its associated signaling pathways. Finally, we identified novel protein isoforms arising from a diversity of splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://zenodo.org/record/6484865 * https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR18959149 * https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=4320a3159ee647a1a956faab4be41ba5
DOI:10.1101/2022.05.17.490813