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Open Access

Application and prospects of proteomic technology in inflammation: a review

Senye Wanga, Yanhai Chua, Jiajia Yuana, Yiqi Lia, Zhenhua Liua,b,c, Xiaoyu Chena,d(), Wenyi Kanga,b,c,d()
National R & D Center for Edible Fungus Processing Technology, Henan University, Kaifeng 475004, China
Functional Food Engineering Technology Research Center, Kaifeng 475004, China
Joint International Research Laboratory of Food & Medicine Resource Function, Kaifeng 475004, China
College of Agriculture, Henan University, Kaifeng 475004, China

Peer review under responsibility of Tsinghua University Press.

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Abstract

Proteomics is a new technology that has been widely applied in the field of life and health science. It effectively addresses issues related to the impact of dietary structure on organs, tissues, and cells, as well as the changes in proteins in various organs, tissues, and cells under disease conditions. The differential proteins identified through proteomics can serve as disease biomarkers and target proteins affecting health and can be used for disease diagnosis and health regulation. In this paper, the application of proteomics in the field of inflammation in recent years was summarized, especially in the therapeutic target and mechanism of action, which opens up a new way for more effective prevention, diagnosis, and treatment of inflammation, and provides medical protection for human life and health.

Keywords

Proteomics technologyInflammationBiomarkersPotential targetSignaling pathway

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Food Science and Human Wellness
Volume 13 Issue 5,
September 2024
Pages 2373-2385
DOI: 10.26599/FSHW.2022.9250248
Cite this article:
Wang S, Chu Y, Yuan J, et al. Application and prospects of proteomic technology in inflammation: a review. Food Science and Human Wellness, 2024, 13(5): 2373-2385. https://doi.org/10.26599/FSHW.2022.9250248
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Proteomics methods were used to detect potential biomarkers of inflammation.

Cell types Stimulants Time (h) The proteomics approach Potential biomarkers Reference
Note: AARS, aminoacyl-tRNA synthetase; ACC, acetyl-CoA carboxylase; ACL6A, actin-like protein 6A; ALDH, aldehyde dehydrogenase family; APMAP, adipocyte plasma membrane associated protein; ATF3, activating transcription factor 3; BCLF1, Bcl-2-associated transcription factor 1; CBS, cystathionine β-synthase; CDK1, cyclin-dependent kinase 1; CENPF, centromere protein F; CLEC, C-type lectin domain family; CLIC4, chloride intracellular channel 4; COPS5, constitutive photomorphogenic-9 signalosome; CRABP2, cellular retinoic acid-binding protein 2; CREBBP, CREB binding protein; EIF4G1, eukaryotic translation initiation factor 4 gamma 1; GDF15, growth differentiation factor 15; GFI1, growth factor independent 1; GOT1, glutamate oxaloacetate transaminase 1; GTSF1, gametocyte specific factor 1; GYS1, glycogen synthase 1; HSL, hormone-sensitive lipase; IDO1, indoleamine 2,3-dioxygenase 1; IMPDH1, inosine monophosphate dehydrogenase 1; KDM4A, lysine specific demethylase 4A; KYNU, kynureninase; LDHA, lactate dehydrogenase A; LYN, tyrosine-protein kinase Lyn; MCL-1, myeloid Cell Leukemia-1; MEF2D, myocyte enhancer factor 2D; MGMT, O6-methylguanine-DNA methyl-transferase; MRPL3, mitochondrial ribosomal protein L3; MT2A, metallothionein 2A; MTDH, metadherin; MX, myxovirus resistant; MYH11, myosin-11; NCF2, neutrophil cytosolic factor 2; NCOA2, nuclear receptor coactivator 2; NCOR2, nuclear receptor co-repressor 2; NOC2L, nucleolar complex associated 2 homolog; NUCKS1, nuclear casein and cyclin-dependent kinase substrate 1; NUSAP1, nucleolar and spindle associated protein 1; OAS, 2’-5’oligoadenylate synthetase; PDCD4, programmed cell death protein 4; PFKL, phosphofructokinase liver type; PGK1, phosphoglycerate kinase 1; PLAU, urokinase-plasminogen activator; PMA, phorbol-12-myristate-13-acetate; PRKACB, protein kinase A catalytic subunit beta; PRMT, protein arginine methyltransferase; PTPRF, protein tyrosine phosphatase receptor type F; PYCR1, pyrroline-5-carboxylate reductase 1; RET, proto-oncogene tyrosine kinase receptor; SCAM1, secretory carrier-associated membrane protein 1; SCRB1, scavenger receptor class B member 1; SPHK1, sphingosine kinase 1; SRC, steroid receptor coactivator; SRSF2, serine/arginine-rich splicing factor 2; ST14, suppressor of tumorigenicity 14; TAP1, transporters associated with antigen processing 1; THBS1, thrombospondin 1; TMOD1, tropomodulin 1; TP53BP1, tumor protein p53 binding protein 1; TPX2, targeting protein for xenopus kinesin-like protein 2; USP18, ubiquitin specific peptidase 18; VEGFA, vascular endothelial growth aactor A; VLDLR, very low-density lipoprotein receptor; YAP1, yes-associated protein 1.
THP-1 LPS 2 TMT, LC-MS/MS IL-1β [19]
LPS 4 IL-1β, IFIT2, IFIT3, CXCL10
LPS 6 IL-1β, IFIT2, IFIT3, IFIH1, CXCL10, SP100, CMPK2, RSAD2, MX1, Sequestosome 1, EPSTI1, MT2A, PARP9, PARP14, PDCD4, KDM4A, CLEC11A
LPS 12 IL-1β, IFIT1, IFIT2, IFIT3, IFIH1, IFI16, CXCL10, CMPK2, ISG20, GBP3, EPSTL1, MMP9, MX1, PDCD4, CLEC11A, IRF8, RET, VLDLR, PTPRF, CETN3
LPS 24 IL-1β, IFIT2, IFIT3, IFIT5, CMPK2, ISG15, EPSTL1, MMP9, MX2, SRC, GBP2, GBP3, PDCD4, CLEC11A, RET, TMOD1, PTPRF, TPX2, MEF2D, GTSF1, CENPF, GFI1, CD37, ST14, CD37, Cyclin-B2, NUSAP1, ST14
Monocytes TNF 48 LC-MS/MS IDO1, SIG10, MYH11, SRSF2, Ladinin-1, CD82, CLIC4, KYNU, AIM1 [24]
TiO2, LC-MS/MS GSK3
RAW264.7 LPS 4 LFQ, LC-MS/MS PFKL, PGK1, GYS1, ACC, HSL, LDHA, RAB14, PRKAA1, IKKs, NF-κB, IRAK, IKB, PI3K, AKT, MCL-1, BID, Sequestosome 1 [25]
THP-1 IFN-γ/LPS - LFQ, LC-MS/MS IRF1, IFIT1, IFIT2, IFIT3 [28]
THP-1 IFN-γ, LPS 48 LFQ, LC-MS/MS CMPK2, RSAD2, CD14, CXCL10, USP18, CD274, RSAD2, IDO1, GBP1, TAP1 [30]
THP-1 IL-4, IL-13 72 TiO2, LC-MS/MS CMPK2, RSAD2, TGM2, Glypican 4, LPL, SCAM1, Drebrin 1
THP-1 PMA 16 LC-MS/MS CD36, CD11b, MAPK1, CDK1, PRKACB [35]
48 TBK1, IRF3, IL-1β, SCRB1, ISG15, LYN, COPS5, MRPL3, GTPase KRas
72 GOT1, PSAT1, AARS, CBS, IMPDH1
THP-1 LPS 24 TMT, LC-MS/MS APMAP [36]
RAW264.7 LPS 28 iTRAQ, LC-MS/MS PRMT [37]
THP-1 IFN-α 48 LFQ, LC-MS/MS IFIT1, IFI22, IFI44L, IFIT3, IFI16, MX1/2, OAS2/3, ISG15 [38]
THP-1 IL-33 4 TMT, TiO2, LC-MS/MS NOC2L (S49, S56), NCOA2 (S736), NUCKS1 (S19), NCOR2 (S149, S152), TP53BP1 (S366), MTDH (S308), YAP1 (T110), EIF4G1 (S1147), BCLF1 (S531), ACL6A (S233) [39]
THP-1 IL-4 24 LFQ, LC-MS/MS TGM2, ALDH1A2, FABP4, CREBBP, CRABP2 [40]
LPS and IgG-OVA SPHK1, CXCL1, SCRB1, MMP9, THBS1, Cathepsin D, Plasminogen, CCR1
IL-10 MSR1, Dysferlin, PYCR1, CXCL8, NCF2, GGA2, Presenilin-1
NECA and LPS VEGFA, MMP1, GDF15, ATF3, PLAU, MGMT

Proteomics methods were used to detect potential therapeutic targets of inflammation.

Cell types Stimulants The proteomics approach Potential targets Reference
Note: AK1BA, aldo-keto reductase family 1 member B10; AP3B2, adaptor related protein complex 3 beta 2; APOD, apolipoprotein D; CARD9, caspase aecruitment domain family member 9; G-CSF, granulocyte colony stimulating factor; GPR120, G-protein coupled receptor 120; GPS1, COP9 signalosome complex subunit 1; HCCS, holocytochrome c synthase; HMGB, high mobility group box; HMOX1, heme oxygenase 1; hnRNP AB, heterogeneousnuclear ribonucleoprotein AB; ILEU, leukocyte elastase inhibitor; LPL, lipoprotein lipase; MAP2K2, mitogen activated protein kinase kinase 2; MEK, mitogen-activated extracellular signal-regulated kinase; MRPS35, mitochondrial ribosomal protein S35; NDKA, nucleoside diphosphate kinase A; NOX2, NADPH oxidases 2; NQO1, NAD(P)H: quinone oxidoreductase 1; PGM1, phosphoglucomutase 1; PKM, pyruvate kinase M; PPIP1, proline-serine-threonine phosphatase-interacting protein 1; PRDX, peroxiredoxin; PSMB8, proteasome subunit beta 8; RAS, rat sarcoma; RPL22L1, ribosomal protein L22 like 1; SLC11A2, solute carrier family 11 member 2; SPP1, secreted phosphoprotein 1; SRPK1, serine/arginine protein-specific kinases 1; SYK, spleen tyrosine kinase; TNFSF9, TNF superfamily member 9; TP53, tumor antigen p53; TRIM25, tripartite motif containing 25; YES1, YES proto-oncogene 1.
THP-1 Near-infrared LC-MS/MS CS [45]
THP-1 Rickettsia parkeri, Rickettsia africae, Rickettsia massiliae LFQ, LC-MS/MS GBP1, GBP2, GBP4, OAS2, OAS3, OASL, MDA5, DHX58, TRIM25, ISG15 [48]
THP-1 Legionella pneumophila SILAC, LC-MS/MS MX1, Galectin-8, RIG-1, TP53 [49]
THP-1 Candida albicans SILAC, LC-MS/MS MAP2K2, SYK, STK3, MAP3K2, NDKA, SRPK1 [50]
THP-1 EBOV-Makona SILAC, LC-MS/MS SP1, KLF4, HIF1A [51]
RESTV SP1, KLF4
RAW264.7 Burkholderia pseudomallei LC-MS/MS CXCL2, TNFR2, CCR1, G-CSF, TRAF1, complement C3, GPS1, IRAK1, AP3B2, CASP6, CARD9 [52]
RAW264.7 Silica TMT, LC-MS/MS SPP1, HMGB3, hnRNP AB [53]
RAW264.7 MetQ SILAC, LC-MS/MS SRC, CCL9, PPIP1, Neurabin-2 [54]
RAW264.7 Wild-type/Tat-mutant Brucella LFQ, LC-MS/MS IFIH1, IFI202, IFI204, ISG15, PTGS2, TRAF1 [55]
RAW264.7 LPS TMT, Lip-MS HSP60 [56]
RAW264.7 SiO2 iTRAQ, LC-MS/MS CASP8, HSP90, CCL3, CXCL2, CCL4, NOD2 [57]
RAW264.7 Graphene oxide SILAC, LC-MS/MS LPL, Lysozyme 1 [58]
RAW264.7 Docosahexaenoic acid LFQ, LC-MS/MS GPR120, RAS, MEK [59]
RAW264.7 Listeria monocytogenes LC-MS/MS MRPS35, RPL22L1 [60]
RAW264.7 B. pseudomallei TMT, LC-MS/MS PGM1, PKM, PGK1 [61]
RAW264.7 Mycobacterium tuberculosis Rv1987 LC-MS/MS Rv1987 [62]
RAW264.7 trans, trans-2,4-decadienal LFQ, LC-MS/MS HSP90, 14-3-3ζ [63]
Dusp1-knockdRAW264.7 LPS TiO2, LC-MS/MS Protein tyrosine phosphotase 1B, mitogen-activated protein kinase 1 [64]
Macrophages LPS SEC, LC-MS/MS PARP9 [65]
Macrophage IL-4 LC-MS/MS MSR1 [66]
A549 SMAC knocked LC-HR-MS/MS SMAC [67]
MM6 miR-328 knocked TMT, LC-MS/MS HMGB1, S100A9, NOX2, TLR2 [68]
SW620 Shikonin iTRAQ, LC-MS/MS Galectin-1 [46]
ReN TNF-α or IL-1β LC-MS/MS PSMB8, B2MG [69]
HRECs Anti-PlGF antibody TMT, LC-MS/MS PRDX6, HMOX1, NQO1, YES1 [70]
Caco-2 Aflatoxin M1, ochratoxin A iTRAQ, LC-MS/MS APOD, HCCS, SLC11A2 [71]
MEPiC and MCF10A IL-1β, TNF-α, and IL-6 2D-DIGE, Nano LC-ESI-MS/MS ILEU, S100A8, S100A9, SOD2 [72]
Hs578T Overexpression of NOD1 or NOD2 LFQ, LC-MS/MS NOD1, NOD2 [73]
BMECs LPS iTRAQ, LC-MS/MS NLRP3 [74]
LoVo Shikonin Quantitative NEMO/IKKβ [75]
HBEpC O3 Nano LC-QTOF-MS/MS AK1BA [76]
U937 Fusobacterium nucleatum AI-2 TMT, iTRAQ, LC-MS/MS TNFSF9 [77]

Application of proteomics techniques to therapeutic targets on inflammation.

Cell types Control group Experimental group Proteomic approach Potential targets Signaling pathways Reference
Note: ADH5, alcohol dehydrogenase 5; CBP, CREB binding protein; CREB1, cAMP responsive element binding protein 1; EEF1G, eukaryotic translation elongation factor 1 gamma; GPX1, glutathione peroxidase 1; HIF, hypoxia inducible factor; ITGA, integrin alpha; MIPEP, mitochondrial intermediate peptidase; NCAPH, non-SMC condensin I complex subunit H; NFAT5, nuclear factor of activated T-cells 5; PEBP1, phosphatidylethanolamine-binding protein 1; PFAS, phosphoribosyl formylglycinamidine synthase; PITRM1, pitrilysin metallopeptidase 1; PMPCA, processing peptidase subunit alpha; PMPCB, mitochondrial-processing peptidase subunit beta; PSMD6, 26S proteasome non-ATPase regulatory subunit 6; PTGES3, prostaglandin E synthase 3; RSK1, ribosomal S6 kinase 1; SNX5, sorting nexin 5; TGFβR1, transforming growth factor-beta receptor 1; TRMT2A, tRNA methyltransferase 2 homolog A; UTP18, U3 small nucleolar RNA-associated protein 18.
RAW264.7 LPS Phillygenin iTRAQ, LC-MS/MS GSK-3β, CBP, NIK, RSK1 RIG-I-like receptor/NF-κB/MAPK signaling pathway [102]
RAW264.7 LPS Tetramethylpyrazine TiO2, LC-MS/MS TRAF6, NF-κB TLR4/NF-κB signaling pathway [110]
RAW264.7 LPS Artemisinin LC-MS/MS HSP90 - [111]
RAW264.7 LPS Sinomenine LFQ, LC-MS/MS RIPK3, PTGES3, PRDX4, ADH5, UTP18, DDX27, SNX5, MYH11, TRMT2A, PSMD6, NCAPH NF-κB signaling pathway [112]
RAW264.7 LPS Carnosic acid LC-MS/MS - NF-κB/MAPK signaling pathway, FOXO signaling pathway [91]
RAW264.7 LPS Arctigenin TMT, LC-MS/MS Keratin 14 NF-κB signaling pathway [113]
RAW264.7 LPS κ/ι-Carrageenan hexaoses LFQ, LC-MS/MS RELA/p65, CREB1, NFAT5 NF-κB/MAPK signaling pathway [114]
RAW264.7 H1N1 ShuFengJieDu capsule iTRAQ, LC-MS/MS - NF-κB/MAPK signaling pathway [97]
RAW264.7 H2O2 SEPS-4 2D-GE, MALDI-TOF MS PRDX2, EEF1G, PEBP1, Enolase 1, PFAS [115]
RAW264.7 LPS Tetramethylpyrazine TiO2, LC-MS/MS ITGA4, HSP90α, TRAF, CASP8, AP-1, PTGS2 TLR4/NF-κB signaling pathways [116]
RAW264.7 LPS GDF11 TMT, Lip-MS TGFβR1 NF-κB/MAPK signaling pathway [117]
THP-1 DMSO Berberine probes LC-MS/MS NIMA-related kinase 7 [118]
THP-1 Dengue virus PLT LC-MS/MS Platelet gactor 4 MAPK signaling pathway, JAK/STAT signaling pathway [119]
THP-1 S protein Perindopril LFQ, Nano-LC-MS/MS ER oxidoreduclin 1α TNF signaling pathway, IFN signaling pathway [120]
THP-1 LPS Cyclohexane-1,2-dicarboxylic acid diisononyl ester TMT, LC-MS/MS - Toll-like receptor pathway/NF-κB signaling pathway [121]
THP-1 LPS 1G244 iTRAQ, LC-MS/MS Dipeptidyl peptidase 8/9 Toll-like receptor/NF-κB signaling pathway [122]
BV-2 DMSO Arone LC-MS/MS ASF1a NF-κB signaling pathway [83]
BV-2 LPS 1,6-O,O-Diacetylbritannilactone LC-MS/MS NLRP3 TLR4/NF-κB/MAPK signaling pathway [123]
BV-2 LPS/IFNγ 1,2,3,4,6-Penta-O-galloyl-β-D-glucose-purity LC-MS/MS Ataxin-2, septin 7, adenylosuccinate synthase NF-κB/MAPK signaling pathway [124]
Macrophage LPS Nicotinamide mononucleotide TMT, LC-MS/MS Cyclooxygenase-2, prostaglandin E2 - [125]
EA.hy926 Tert-butyl hydroperoxide Crude flavonoids of pollen iTRAQ, LC-MS/MS PMPCB, PMPCA, MIPEP, GPX1, PITRM1 NF-κB signaling pathway [126]
bMECs Streptococcus agalactiae Soybean isoflavones TMT, LC-MS/MS ITGA5 HIF-1 signaling pathway [127]