Mass spectrometry based proteomics profiling of human monocytes

Abstract

Human monocyte is an important cell type which is involved in various complex human diseases. To better understand the biology of human monocytes and facilitate further studies, we developed the first comprehensive proteome knowledge base specifically for human monocytes by integrating both in vivo and in vitro datasets. The top 2000 expressed genes from in vitro datasets and 779 genes from in vivo experiments were integrated into this study. Altogether, a total of 2237 unique monocyte-expressed genes were cataloged. Biological functions of these monocyte-expressed genes were annotated and classified via Gene Ontology (GO) analysis. Furthermore, by extracting the overlapped genes from in vivo and in vitro datasets, a core gene list including 541 unique genes was generated. Based on the core gene list, further gene-disease associations, pathway and network analyses were performed. Data analyses based on multiple bioinformatics tools produced a large body of biologically meaningful information, and revealed a number of genes such as SAMHD1, G6PD, GPD2 and ENO1, which have been reported to be related to immune response, blood biology, bone remodeling, and cancer respectively. As a unique resource, this study can serve as a reference map for future in-depth research on monocytes biology and monocyte-involved human diseases.Electronic supplementary materialThe online version of this article (doi:10.1007/s13238-016-0342-x) contains supplementary material, which is available to authorized users.

Quantitative proteomics of small numbers of closely-related cells: Selection of the optimal method for a clinical setting

“…Likewise, Soday et al ( 38 ) defined 593 plasma-membrane annotated proteins in cMo by following an analogous biotinylating-based strategy, of which 347 (contributing to 88% of cMo surface proteome) were detected from 2,500 cells in our report. Interestingly, Zeng et al ( 39 ) claimed to have profiled the monocyte proteome knowledge base; however, monocyte samples only consisted of cMo contaminated with basophils and dendritic cells, and relaxed criteria were used for protein selection (i.e., 4% FDR, 1 peptide/protein). Their results reported 2,237 proteins, but only 1,461 (39%, 1,461/3,737) matched our data from FACS-purified cMo (purity>96.4%; 2 pp/protein, 1% FDR, proteins present in all donors) highlighting the importance of high-quality samples and strict selection criteria to define cell reference maps.…”

“…Despite major monocytic populations and GBM macrophages have been extensively studied by different approaches ( 51 , 59 – 64 ), including MS-based proteomics strategies ( 37 , 39 , 65 – 69 ), none of these analyses has been performed in a quantity-restricted setting. Therefore, a 2.5k-cell number lower limit was set for investigating the cMo, iMo, and ncMo subsets from PB and MAC from GBM samples, together with T cells from both tissues as an internal control.…”

Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques

“…Mass spectrometric analysis of proteins from organisms with sequenced genomes is advantageous as it allows for their routine identification, and modifications in analyzed proteins to be detected simultaneously. Thus, mass spectrometry ( 160 ), in particular tandem mass spectrometry has emerged as a powerful technique for the parallel quantitation and identification of proteins, with quantitation broadly assigned into two categories: label and label-free proteomics. While mass spectrometry is not inherently quantitative, several labeling methods are now available that afford robust quantification ( 161 , 162 ).…”

Postmenopausal osteoporosis: Effect of moderate-intensity treadmill exercise on bone proteomics in ovariectomized rats

“…Proteomics is an important tool for identifying new human disease biomarkers and new targets for drug treatment by analyzing the changes in proteins in target tissues. In recent years, many proteomic studies have been conducted on bone-related cells or tissues, such as mononuclear cells, plasma, and serum, to explore the pathogenesis and monitoring indicators of PMOP (2)(3)(4)(5). In 2017, the first comprehensive human monocyte proteome knowledge base was developed (2).…”

“…In recent years, many proteomic studies have been conducted on bone-related cells or tissues, such as mononuclear cells, plasma, and serum, to explore the pathogenesis and monitoring indicators of PMOP (2)(3)(4)(5). In 2017, the first comprehensive human monocyte proteome knowledge base was developed (2). Bone tissue is the main pathogenesis site of PMOP, and the occurrence of the disease is often accompanied by changes in protein expression.…”