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A high-stringency blueprint of the human proteome.

ABSTRACT: The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.

SUBMITTER: Adhikari S

PROVIDER: S-EPMC7568584 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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A high-stringency blueprint of the human proteome.

Adhikari Subash S Nice Edouard C EC Deutsch Eric W EW Lane Lydie L Omenn Gilbert S GS Pennington Stephen R SR Paik Young-Ki YK Overall Christopher M CM Corrales Fernando J FJ Cristea Ileana M IM Van Eyk Jennifer E JE Uhlén Mathias M Lindskog Cecilia C Chan Daniel W DW Bairoch Amos A Waddington James C JC Justice Joshua L JL LaBaer Joshua J Rodriguez Henry H He Fuchu F Kostrzewa Markus M Ping Peipei P Gundry Rebekah L RL Stewart Peter P Srivastava Sanjeeva S Srivastava Sudhir S Nogueira Fabio C S FCS Domont Gilberto B GB Vandenbrouck Yves Y Lam Maggie P Y MPY Wennersten Sara S Vizcaino Juan Antonio JA Wilkins Marc M Schwenk Jochen M JM Lundberg Emma E Bandeira Nuno N Marko-Varga Gyorgy G Weintraub Susan T ST Pineau Charles C Kusebauch Ulrike U Moritz Robert L RL Ahn Seong Beom SB Palmblad Magnus M Snyder Michael P MP Aebersold Ruedi R Baker Mark S MS

Nature communications 20201016 1

The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HP ...[more]

PMID: 33067450

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Project description:BACKGROUND: A large variety of proteins involved in inflammation, coagulation, lipid-oxidation and lipid metabolism have been associated with high-density lipoprotein (HDL) and it is anticipated that changes in the HDL proteome have implications for the multiple functions of HDL. Here, SELDI-TOF mass spectrometry (MS) was used to study the dynamic changes of HDL protein composition in a human experimental low-dose endotoxemia model. Ten healthy men with low HDL cholesterol (0.7+/-0.1 mmol/L) and 10 men with high HDL cholesterol levels (1.9+/-0.4 mmol/L) were challenged with endotoxin (LPS) intravenously (1 ng/kg bodyweight). We previously showed that subjects with low HDL cholesterol are more susceptible to an inflammatory challenge. The current study tested the hypothesis that this discrepancy may be related to differences in the HDL proteome. RESULTS: Plasma drawn at 7 time-points over a 24 hour time period after LPS challenge was used for direct capture of HDL using antibodies against apolipoprotein A-I followed by subsequent SELDI-TOF MS profiling. Upon LPS administration, profound changes in 21 markers (adjusted p-value < 0.05) were observed in the proteome in both study groups. These changes were observed 1 hour after LPS infusion and sustained up to 24 hours, but unexpectedly were not different between the 2 study groups. Hierarchical clustering of the protein spectra at all time points of all individuals revealed 3 distinct clusters, which were largely independent of baseline HDL cholesterol levels but correlated with paraoxonase 1 activity. The acute phase protein serum amyloid A-1/2 (SAA-1/2) was clearly upregulated after LPS infusion in both groups and comprised both native and N-terminal truncated variants that were identified by two-dimensional gel electrophoresis and mass spectrometry. Individuals of one of the clusters were distinguished by a lower SAA-1/2 response after LPS challenge and a delayed time-response of the truncated variants. CONCLUSIONS: This study shows that the semi-quantitative differences in the HDL proteome as assessed by SELDI-TOF MS cannot explain why subjects with low HDL cholesterol are more susceptible to a challenge with LPS than those with high HDL cholesterol. Instead the results indicate that hierarchical clustering could be useful to predict HDL functionality in acute phase responses towards LPS.

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A high-stringency blueprint of the human proteome.

Publications

A high-stringency blueprint of the human proteome.

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