A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer

Swensen, Adam C.; He, Jingtang; Fang, Alexander C.; Ye, Yinyin; Nicora, Carrie D.; Shi, Tujin; Liu, Alvin Y.; Sigdel, Tara K.; Sarwal, Minnie M.; Qian, Wei-Jun

doi:10.3389/fmed.2021.548212

A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer

Journal Article · Tue Apr 13 00:00:00 EDT 2021 · Frontiers in Medicine

DOI:https://doi.org/10.3389/fmed.2021.548212· OSTI ID:1808283

Swensen, Adam C. ^[1]; He, Jingtang ^[1]; Fang, Alexander C. ^[1]; Ye, Yinyin ^[1]; ^[1]; Shi, Tujin ^[1]; Liu, Alvin Y. ^[2]; Sigdel, Tara K. ^[3]; Sarwal, Minnie M. ^[3]; ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Univ. of Washington, Seattle, WA (United States)
Univ. of California, San Francisco, CA (United States)

Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1808283

Report Number(s):: PNNL-SA--152473

Journal Information:: Frontiers in Medicine, Journal Name: Frontiers in Medicine Vol. 8; ISSN 2296-858X

Publisher:: Frontiers Media S.A.Copyright Statement

Country of Publication:: United States

Language:: English

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60 APPLIED LIFE SCIENCES
Kidney disease
LC-MS/MS
Prostate cancer
Proteomics
Urinary biomarkers
Urine proteome

A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer

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