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 vivoand in vitrodatasets. The top 2000 expressed genes from in vitrodatasets and 779 genes from in vivoexperiments 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 vivoand in vitrodatasets, 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, GPD2and 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.

Keywords

human monocytes / proteomics knowledgebase / gene ontology / gene-disease association / network analysis

References

[1] Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z, Galon J (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091–1093

[2] Bindea G, Galon J, Mlecnik B (2013) CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics 29:661–663

[3] Chimma P, Roussilhon C, Sratongno P, Ruangveerayuth R, Pattanapanyasat K, Perignon JL, Roberts DJ, Druilhe P (2009) A distinct peripheral blood monocyte phenotype is associated with parasite inhibitory activity in acute uncomplicated Plasmodium falciparum malaria. PLoS Pathog 5:e1000631

[4] de Boer M, Singh V, Dekker J, Di Rocco M, Goldblatt D, Roos D (2002) Prenatal diagnosis in two families with autosomal, p47 (phox)-deficient chronic granulomatous disease due to a novel point mutation in NCF1. Prenat Diagn 22:235–240

[5] Deng FY, Liu YZ, Li LM, Jiang C, Wu S, Chen Y, Jiang H, Yang F, Xiong JX, Xiao P(2008) Proteomic analysis of circulating monocytes in Chinese premenopausal females with extremely discordant bone mineral density. Proteomics 8:4259–4272

[6] Deng FY, Lei SF, Zhang Y, Zhang YL, Zheng YP, Zhang LS, Pan R, Wang L, Tian Q, Shen H (2011a) Peripheral blood monocyteexpressed ANXA2 gene is involved in pathogenesis of osteoporosis in humans. Mol Cell Proteomics 10(M111):011700

[7] Deng FY, Lei SF, Zhang Y, Zhang YL, Zheng YP, Zhang LS, Pan R, Wang L, Tian Q, Shen H(2011b) Peripheral blood monocyte-expressed ANXA2 geneis involved in pathogenesis of osteoporosis in humans. Mol Cell Proteomics 10:M111–11700

[8] Deng FY, Zhu W, Zeng Y, Zhang JG, Yu N, Liu YZ, Liu YJ, Tian Q, Deng HW (2014) Is GSN significant for hip BMD in female Caucasians? Bone 63:69–75

[9] Dichamp I, Bourgeois A, Dirand C, Herbein G, Wendling D (2007) Increased nuclear factor-kappaB activation in peripheral blood monocytes of patientswith rheumatoid arthritis ismediated primarily by tumor necrosis factor-alpha. J Rheumatol 34:1976–1983

[10] Emanuel VL, Mnuskina MM, Smirnov AV, Panina I, Rumiantsev A, Vasina E, Vasina LB (2013) [Annexin-5 as a biochemical marker of early vascular disorders under chronic disease of kidneys]. Klin Lab Diagn, 9–10

[11] Genetos DC, Wong A, Weber TJ, Karin NJ, Yellowley CE (2014) Impaired osteoblast differentiation in annexin A2- and-A5- deficient cells. PLoS ONE 9:e107482

[12] Grunberg W, Sacchetto R, Wijnberg I, Neijenhuis K, Mascarello F, Damiani E, Drogemuller C (2010) Pseudomyotonia, a muscle function disorder associated with an inherited ATP2A1 (SERCA1) defect in a Dutch improved red and white cross-breed calf. Neuromuscul Disord 20:467–470

[13] Hrecka K, Hao C, Gierszewska M, Swanson SK, Kesik-Brodacka M, Srivastava S, Florens L, Washburn MP, Skowronski J (2011) Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature 474:658–661

[14] Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57

[15] Jin M, Diaz PT, Bourgeois T, Eng C, Marsh CB, Wu HM (2006) Twodimensional gel proteome reference map of blood monocytes. Proteome Sci 4:16

[16] Kakazu E, Ueno Y, Kondo Y, Inoue J, Ninomiya M, Kimura O, Wakui Y, Fukushima K, Tamai K, Shimosegawa T (2011) Plasma L-cystine/L-glutamate imbalance increases tumor necrosis factoralpha from CD14+ circulating monocytes in patients with advanced cirrhosis. PLoS ONE 6:e23402

[17] Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S(2014) A draft map of the human proteome. Nature 509:575–581

[18] Koker MY (2010) Novel human pathological mutations. Gene symbol: NCF2. Disease: chronic granulomatous disease. Hum Genet 127:113

[19] Kraft-Terry S, Gerena Y, Wojna V, Plaud-Valentin M, Rodriguez Y, Ciborowski P, Mayo R, Skolasky R, Gendelman HE, Melendez LM (2010) Proteomic analyses of monocytes obtained from Hispanic women with HIV-associated dementia show depressed antioxidants. Proteomics Clin Appl 4:706–714

[20] Liu YZ, Dvornyk V, Lu Y, Shen H, Lappe JM, Recker RR, Deng HW (2005) A novel pathophysiological mechanism for osteoporosis suggested by an in vivo gene expression study of circulating monocytes. J Biol Chem 280:29011–29016

[21] Merindol N, Berthoux L (2015) Restriction factors in HIV-1 disease progression. Curr HIV Res 13:448–461

[22] Nabavizadeh SH, Anushiravani A (2007) The prevalence of G6PD deficiency in blood transfusion recipients. Hematology 12:85–88

[23] Olsson LM, Nerstedt A, Lindqvist AK, Johansson ACM, Medstrand P, Olofsson P, Holmdahl R (2012) Copy number variation of the gene NCF1 Is associated with rheumatoid arthritis. Antioxid Redox Signal 16:71–78

[24] Pandey S, Ranjan R, Pandey S, Mishra RM, Seth T, Saxena R (2012) Effect of ANXA2 gene single nucleotide polymorphism (SNP) on the development of osteonecrosis in Indian sickle cell patient: a PCR-RFLP approach. Indian J Exp Biol 50:455–458

[25] Sherman BT, da Huang W, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA (2007) DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 8:426

[26] Shive CL, Jiang W, Anthony DD, Lederman MM (2015) Soluble CD14 is a nonspecific marker of monocyte activation. AIDS 29:1263–1265

[27] Swa HL, Shaik AA, Lim LH, Gunaratne J (2014) Mass spectrometry based quantitative proteomics and integrative network analysis accentuates modulating roles of annexin-1 in mammary tumorigenesis. Proteomics 15:408–418

[28] Tang J, Jiang C, Xiao X, Fang Z, Li L, Han L, Mei A, Feng Y, Guo Y, Li H (2015) Changes in red blood cell membrane structure in G6PD deficiency: an atomic force microscopy study. Clin Chim Acta 444:264–270

[29] Vasconcelos Dde M, Beitler B, Martinez GA, Pereira J, Amigo Filho JU, Klautau GB, Lian YC, Della Negra M, Duarte AJ (2014) CD18 deficiency evolving to megakaryocytic (M7) acute myeloid leukemia: case report. Blood Cells Mol Dis 53:180–184

[30] Verkman AS, Ratelade J, Rossi A, Zhang H, Tradtrantip L (2011) Aquaporin-4: orthogonal array assembly, CNS functions, and role in neuromyelitis optica. Acta Pharmacol Sin 32:702–710

[31] Walter S, Doering A, Letiembre M, Liu Y, HaoW, Diem R, Bernreuther C, Glatzel M, Engelhardt B, Fassbender K (2006) The LPS receptor, CD14, in experimental autoimmune encephalomyelitis and multiple sclerosis. Cell Physiol Biochem 17:167–172

[32] Zhou Y, Deng HW, Shen H (2015) Circulating monocytes: an appropriate model for bone-related study. Osteoporos Int 26:2561–2572

RIGHTS & PERMISSIONS

The Author(s) 2016. This article is published with open access at Springerlink.com and journal.hep.com.cn