ArticleRNA biology2022
Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.
Article in RNA biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 14 citations in OpenAlex.
- LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Perplexity as a Metric for Isoform Diversity in the Human Transcriptome.bioRxiv : the preprint server for biology · 2025Article
- Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.Genome research · 2025Article
- Integrated transcriptomic and proteomic analyses identify the TLR2-CXCR4 axis as a regulator of endothelial cell migration under simulated microgravity.Frontiers in physiology · 2025Article
- IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.Journal of the American Society for Mass Spectrometry · 2024Article
- IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.bioRxiv : the preprint server for biology · 2024Article
- Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.bioRxiv : the preprint server for biology · 2024Article
- A proteogenomic atlas of the human neural retina.Frontiers in genetics · 2024Article
- SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation.BMC genomics · 2023Article
- Transcription factors and splice factors - interconnected regulators of stem cell differentiation.Current stem cell reports · 2023Article
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
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 alternative splicing of RNA to produce distinct protein isoforms. To characterize the RNA and protein isoform landscape within ECs, we applied a long read proteogenomics approach to analyse human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream mass-spectrometry (MS) analysis to infer protein isoform expression. We detected 53,863 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 signalling pathways. Finally, we identified novel protein isoforms arising from a diversity of RNA 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.[Figure: see text].
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.