Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells

Anil K. Madugundu, Chan Hyun Na, Raja Sekhar Nirujogi, Santosh Renuse, Kwang Pyo Kim, Kathleen H. Burns, Christopher Wilks, Ben Langmead, Shannon E. Ellis, Leonardo Collado-Torres, Marc K. Halushka, Min Sik Kim, Akhilesh Pandey

Research output: Contribution to journalArticle

Abstract

Understanding the molecular profile of every human cell type is essential for understanding its role in normal physiology and disease. Technological advancements in DNA sequencing, mass spectrometry, and computational methods allow us to carry out multiomics analyses although such approaches are not routine yet. Human umbilical vein endothelial cells (HUVECs) are a widely used model system to study pathological and physiological processes associated with the cardiovascular system. In this study, next-generation sequencing and high-resolution mass spectrometry to profile the transcriptome and proteome of primary HUVECs is employed. Analysis of 145 million paired-end reads from next-generation sequencing confirmed expression of 12 186 protein-coding genes (FPKM ≥0.1), 439 novel long non-coding RNAs, and revealed 6089 novel isoforms that were not annotated in GENCODE. Proteomics analysis identifies 6477 proteins including confirmation of N-termini for 1091 proteins, isoforms for 149 proteins, and 1034 phosphosites. A database search to specifically identify other post-translational modifications provide evidence for a number of modification sites on 117 proteins which include ubiquitylation, lysine acetylation, and mono-, di- and tri-methylation events. Evidence for 11 “missing proteins,” which are proteins for which there was insufficient or no protein level evidence, is provided. Peptides supporting missing protein and novel events are validated by comparison of MS/MS fragmentation patterns with synthetic peptides. Finally, 245 variant peptides derived from 207 expressed proteins in addition to alternate translational start sites for seven proteins and evidence for novel proteoforms for five proteins resulting from alternative splicing are identified. Overall, it is believed that the integrated approach employed in this study is widely applicable to study any primary cell type for deeper molecular characterization.

Original languageEnglish (US)
Article number1800315
JournalProteomics
Volume19
Issue number15
DOIs
StatePublished - Jan 1 2019

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Endothelial cells
Human Umbilical Vein Endothelial Cells
Proteomics
Proteins
Methylation
Peptides
Mass spectrometry
Mass Spectrometry
Protein Isoforms
Long Noncoding RNA
Physiological Phenomena
Cardiovascular system
Acetylation
Ubiquitination
Physiology
Alternative Splicing
Pathologic Processes
Proteome
Post Translational Protein Processing
Cardiovascular System

Keywords

  • allelic expression
  • coding SNP
  • mass-spectrometry
  • proteoform
  • proteogenomics
  • RNA-seq
  • splice variants
  • transcriptome

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Madugundu, A. K., Na, C. H., Nirujogi, R. S., Renuse, S., Kim, K. P., Burns, K. H., ... Pandey, A. (2019). Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. Proteomics, 19(15), [1800315]. https://doi.org/10.1002/pmic.201800315

Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. / Madugundu, Anil K.; Na, Chan Hyun; Nirujogi, Raja Sekhar; Renuse, Santosh; Kim, Kwang Pyo; Burns, Kathleen H.; Wilks, Christopher; Langmead, Ben; Ellis, Shannon E.; Collado-Torres, Leonardo; Halushka, Marc K.; Kim, Min Sik; Pandey, Akhilesh.

In: Proteomics, Vol. 19, No. 15, 1800315, 01.01.2019.

Research output: Contribution to journalArticle

Madugundu, AK, Na, CH, Nirujogi, RS, Renuse, S, Kim, KP, Burns, KH, Wilks, C, Langmead, B, Ellis, SE, Collado-Torres, L, Halushka, MK, Kim, MS & Pandey, A 2019, 'Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells', Proteomics, vol. 19, no. 15, 1800315. https://doi.org/10.1002/pmic.201800315
Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH et al. Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. Proteomics. 2019 Jan 1;19(15). 1800315. https://doi.org/10.1002/pmic.201800315
Madugundu, Anil K. ; Na, Chan Hyun ; Nirujogi, Raja Sekhar ; Renuse, Santosh ; Kim, Kwang Pyo ; Burns, Kathleen H. ; Wilks, Christopher ; Langmead, Ben ; Ellis, Shannon E. ; Collado-Torres, Leonardo ; Halushka, Marc K. ; Kim, Min Sik ; Pandey, Akhilesh. / Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. In: Proteomics. 2019 ; Vol. 19, No. 15.
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