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2000
Volume 21, Issue 6
  • ISSN: 1570-1646
  • E-ISSN: 1875-6247

Abstract

Background

Post-Translational Modifications (PTMs) are covalent modifications of amino acids added to proteins that can significantly affect proteins’ structures and functions. PTMS are, therefore, important biomarkers due to their regulation of various bioactivities. Protein array is a robust tool for detecting and quantifying proteins with high throughput, small sample requirement, and high sensitivity.

Objectives

On the basis of a high-density array, we developed a new platform to detect the PTM level, such as phosphorylation and acetylation, and changes in larger scales using an anti-PTM antibody.

Methods

THP-1 cells treated with phorbol 12-myristate 13-acetate (PMA) and lipopolysaccharide (LPS) were used for testing the new system and quantifying the phosphorylation and acetylation level change. The proteins whose phosphorylation and acetylation levels changed significantly were screened and compared with reported phenotypic change.

Results

By using antibodies against phosphorylation and acetylation, the PTM change for the same protein can be detected. Based on the proteins whose PTM is significantly different before and after treatment, it was found that the enriched pathways and biological progress agreed with the stimulation of PMA and LPS.

Conclusion

Our results supported the idea that this platform can be used to effectively compare the phosphorylation and acetylation level changes among samples and screen for biomarkers on the proteomic scale.

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2025-10-30
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References

  1. MacekB. ForchhammerK. HardouinJ. Weber-BanE. GrangeasseC. MijakovicI. Protein post-translational modifications in bacteria.Nat. Rev. Microbiol.2019171165166410.1038/s41579‑019‑0243‑0 31485032
    [Google Scholar]
  2. DuttaH. JainN. Post-translational modifications and their implications in cancer.Front. Oncol.202313124011510.3389/fonc.2023.1240115 37795435
    [Google Scholar]
  3. ConsortiumU. The universal protein resource (UniProt) 2009.Nucleic Acids Res.200937Suppl. 1D169D17410.1093/nar/gkn664 18836194
    [Google Scholar]
  4. KhouryG.A. BalibanR.C. FloudasC.A. Proteome-wide post-translational modification statistics: Frequency analysis and curation of the swiss-prot database.Sci. Rep.2011119010.1038/srep00090 22034591
    [Google Scholar]
  5. GarciaB.A. Post-translational Modifications That Modulate Enzyme Activity.Academic Press2019626
    [Google Scholar]
  6. EllgaardL. McCaulN. ChatsisviliA. BraakmanI. Co‐and post‐translational protein folding in the ER.Traffic201617661563810.1111/tra.12392 26947578
    [Google Scholar]
  7. WardenS.M. RichardsonC. O’DonnellJ. StapletonD. KempB.E. WittersL.A. Post-translational modifications of the β-1 subunit of AMP-activated protein kinase affect enzyme activity and cellular localization.Biochem. J.2001354227528310.1042/bj3540275 11171104
    [Google Scholar]
  8. LeckerS.H. GoldbergA.L. MitchW.E. Protein degradation by the ubiquitin-proteasome pathway in normal and disease states.J. Am. Soc. Nephrol.20061771807181910.1681/ASN.2006010083 16738015
    [Google Scholar]
  9. CruickshankM.N. BesantP. UlgiatiD. The impact of histone post-translational modifications on developmental gene regulation.Amino Acids20103951087110510.1007/s00726‑010‑0530‑6 20204433
    [Google Scholar]
  10. Méndez-AcuñaL. Di TomasoM.V. PalittiF. Martínez-LópezW. Histone post-translational modifications in DNA damage response.Cytogenet. Genome Res.20101281-3283610.1159/000296275 20407219
    [Google Scholar]
  11. DeribeY.L. PawsonT. DikicI. Post-translational modifications in signal integration.Nat. Struct. Mol. Biol.201017666667210.1038/nsmb.1842 20495563
    [Google Scholar]
  12. ChenL. LiuS. TaoY. Regulating tumor suppressor genes: Post-translational modifications.Signal Transduct. Target. Ther.2020519010.1038/s41392‑020‑0196‑9 32532965
    [Google Scholar]
  13. RussellC.L. KoncarevicS. WardM.A. Post-translational modifications in Alzheimer’s disease and the potential for new biomarkers.J. Alzheimers Dis.201441234536410.3233/JAD‑132312 24662105
    [Google Scholar]
  14. ZhangX. MaityT. KashyapM.K. BansalM. VenugopalanA. SinghS. AwasthiS. MarimuthuA. Charles JacobH.K. BelkinaN. PittsS. CultraroC.M. GaoS. KirkaliG. BiswasR. ChaerkadyR. CalifanoA. PandeyA. GuhaU. Quantitative tyrosine phosphoproteomics of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor-treated lung adenocarcinoma cells reveals potential novel biomarkers of therapeutic response.Mol. Cell. Proteomics201716589191010.1074/mcp.M117.067439 28331001
    [Google Scholar]
  15. GuhaU. ChaerkadyR. MarimuthuA. PattersonA.S. KashyapM.K. HarshaH.C. SatoM. BaderJ.S. LashA.E. MinnaJ.D. PandeyA. VarmusH.E. Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS.Proc. Natl. Acad. Sci. USA200810537141121411710.1073/pnas.0806158105 18776048
    [Google Scholar]
  16. LiZ. LiS. LuoM. JhongJ.H. LiW. YaoL. PangY. WangZ. WangR. MaR. YuJ. HuangY. ZhuX. ChengQ. FengH. ZhangJ. WangC. HsuJ.B.K. ChangW.C. WeiF.X. HuangH.D. LeeT.Y. dbPTM in 2022: An updated database for exploring regulatory networks and functional associations of protein post-translational modifications.Nucleic Acids Res.202250D1D471D47910.1093/nar/gkab1017 34788852
    [Google Scholar]
  17. KitamuraN. GalliganJ.J. A global view of the human post-translational modification landscape.Biochem. J.2023480161241126510.1042/BCJ20220251 37610048
    [Google Scholar]
  18. RamaziS. ZahiriJ. Post-translational modifications in proteins: Resources, tools and prediction methods.Database (Oxford)20212021baab01210.1093/database/baab012 33826699
    [Google Scholar]
  19. WilsonJ.J. BurgessR. MaoY.Q. LuoS. TangH. JonesV.S. WeishengB. HuangR.Y. ChenX. HuangR.P. Antibody arrays in biomarker discovery.Adv. Clin. Chem.20156925532410.1016/bs.acc.2015.01.002 25934364
    [Google Scholar]
  20. HermannJ. SchurgersL. JankowskiV. Identification and characterization of post-translational modifications: Clinical implications.Mol. Aspects Med.20228610106610.1016/j.mam.2022.101066 35033366
    [Google Scholar]
  21. VillafañezF. GottifrediV. SoriaG. Development and optimization of a miniaturized western blot-based screening platform to identify regulators of post-translational modifications.High Throughput2019821510.3390/ht8020015 31163614
    [Google Scholar]
  22. DaiB. DahmaniF. CichockiJ.A. SwansonL.C. RasmussenT.P. Detection of post-translational modifications on native intact nucleosomes by ELISA.J. Vis. Exp.2011502593 21540828
    [Google Scholar]
  23. HuangR. JiangW. YangJ. MaoY.Q. ZhangY. YangW. YangD. BurkholderB. HuangR.F. HuangR.P. A biotin label-based antibody array for high-content profiling of protein expression.Cancer Genomics Proteomics201073129141 20551245
    [Google Scholar]
  24. LockhartD.J. WinzelerE.A. Genomics, gene expression and DNA arrays.Nature2000405678882783610.1038/35015701 10866209
    [Google Scholar]
  25. ShalonD. SmithS.J. BrownP.O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.Genome Res.19966763964510.1101/gr.6.7.639 8796352
    [Google Scholar]
  26. SchröderC. AlhamdaniM.S. FellenbergK. BauerA. JacobA. HoheiselJ.D. Robust protein profiling with complex antibody microarrays in a dual-colour mode. In: Protein Microarrays. KorfU. Humana Press201120322110.1007/978‑1‑61779‑286‑1_14
    [Google Scholar]
  27. SchröderC. JacobA. TonackS. RadonT.P. SillM. ZucknickM. RüfferS. CostelloE. NeoptolemosJ.P. Crnogorac-JurcevicT. BauerA. FellenbergK. HoheiselJ.D. Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies.Mol. Cell. Proteomics2010961271128010.1074/mcp.M900419‑MCP200 20164060
    [Google Scholar]
  28. R: A language and environment for statistical computing.2013Available from: https://www.scirp.org/reference/referencespapers? referenceid=1061517
  29. YuG. WangL.G. HanY. HeQ.Y. clusterProfiler: An R package for comparing biological themes among gene clusters.OMICS201216528428710.1089/omi.2011.0118 22455463
    [Google Scholar]
  30. TsuchiyaS. YamabeM. YamaguchiY. KobayashiY. KonnoT. TadaK. Establishment and characterization of a human acute monocytic leukemia cell line (THP‐1).Int. J. Cancer198026217117610.1002/ijc.2910260208 6970727
    [Google Scholar]
  31. AbrahamR.T. WeissA. Jurkat T cells and development of the T-cell receptor signalling paradigm.Nat. Rev. Immunol.20044430130810.1038/nri1330 15057788
    [Google Scholar]
  32. PshenichnikovS. OmelyanchikA. EfremovaM. LunovaM. GazatovaN. MalashchenkoV. KhaziakhmatovaO. LitvinovaL. PerovN. PaninaL. PeddisD. LunovO. RodionovaV. LevadaK. Control of oxidative stress in Jurkat cells as a model of leukemia treatment.J. Magn. Magn. Mater.202152316762310.1016/j.jmmm.2020.167623
    [Google Scholar]
  33. Soto-MercadoV. Mendivil-PerezM. Jimenez-Del-RioM. FoxJ.E. Velez-PardoC. Cannabinoid CP55940 selectively induces apoptosis in Jurkat cells and in ex vivo T-cell acute lymphoblastic leukemia through H2O2 signaling mechanism.Leuk. Res.20209510638910.1016/j.leukres.2020.106389 32540572
    [Google Scholar]
  34. JinguD. IinoM. KawasakiJ. UranoE. KusakariS. HayashiY. MatozakiT. OhnishiH. Protein tyrosine phosphatase Shp2 positively regulates cold stress-induced tyrosine phosphorylation of SIRPα in neurons.Biochem. Biophys. Res. Commun.2021569727810.1016/j.bbrc.2021.06.084 34237430
    [Google Scholar]
  35. SharmaK. D’SouzaR.C.J. TyanovaS. SchaabC. WiśniewskiJ.R. CoxJ. MannM. Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling.Cell Rep.2014851583159410.1016/j.celrep.2014.07.036 25159151
    [Google Scholar]
  36. ChanputW. MesJ.J. WichersH.J. THP-1 cell line: An in vitro cell model for immune modulation approach.Int. Immunopharmacol.2014231374510.1016/j.intimp.2014.08.002 25130606
    [Google Scholar]
  37. BosshartH. HeinzelmannM. THP-1 cells as a model for human monocytes.Ann. Transl. Med.201642143810.21037/atm.2016.08.53 27942529
    [Google Scholar]
  38. DaigneaultM. PrestonJ.A. MarriottH.M. WhyteM.K.B. DockrellD.H. The identification of markers of macrophage differentiation in PMA-stimulated THP-1 cells and monocyte-derived macrophages.PLoS One201051e866810.1371/journal.pone.0008668 20084270
    [Google Scholar]
  39. WeinsteinS.L. GoldM.R. DeFrancoA.L. Bacterial lipopolysaccharide stimulates protein tyrosine phosphorylation in macrophages.Proc. Natl. Acad. Sci. USA199188104148415210.1073/pnas.88.10.4148 1709735
    [Google Scholar]
  40. RosenA. NairnA.C. GreengardP. CohnZ.A. AderemA. Bacterial lipopolysaccharide regulates the phosphorylation of the 68K protein kinase C substrate in macrophages.J. Biol. Chem.1989264169118912110.1016/S0021‑9258(18)60499‑5 2722820
    [Google Scholar]
  41. NewtonA.C. Protein kinase C: Structure, function, and regulation.J. Biol. Chem.199527048284952849810.1074/jbc.270.48.28495 7499357
    [Google Scholar]
  42. NewtonA.C. Protein kinase C: Perfectly balanced.Crit. Rev. Biochem. Mol. Biol.201853220823010.1080/10409238.2018.1442408 29513138
    [Google Scholar]
  43. SpitalerM. CantrellD.A. Protein kinase C and beyond.Nat. Immunol.20045878579010.1038/ni1097 15282562
    [Google Scholar]
  44. SokolR.J. HudsonG. JamesN.T. FrostI.J. WalesJ. Human macrophage development: A morphometric study.J. Anat.19871512735 3654357
    [Google Scholar]
  45. PhuangbubphaP. TharaS. SriboonaiedP. SaetanP. TumnoiW. CharoenpanichA. Optimizing THP-1 macrophage culture for an immune-responsive human intestinal model.Cells20231210142710.3390/cells12101427 37408263
    [Google Scholar]
  46. KounalakisN.S. CorbettS.A. Lipopolysaccharide transiently activates THP-1 cell adhesion.J. Surg. Res.2006135113714310.1016/j.jss.2005.12.018 16488432
    [Google Scholar]
  47. SchwendeH. FitzkeE. AmbsP. DieterP. Differences in the state of differentiation of THP-1 cells induced by phorbol ester and 1,25-dihydroxyvitamin D3.J. Leukoc. Biol.199659455556110.1002/jlb.59.4.555 8613704
    [Google Scholar]
  48. YangM. TangM. MaX. YangL. HeJ. PengX. GuoG. ZhouL. LuoN. YuanZ. TongA. AP-57/C10orf99 is a new type of mutifunctional antimicrobial peptide.Biochem. Biophys. Res. Commun.2015457334735210.1016/j.bbrc.2014.12.115 25585381
    [Google Scholar]
  49. ChenJ. LuJ. ChenZ. LiuZ. SunY. HeS. MiY. GaoY. ShenD. LinQ. SPINK5 inhibits esophageal squamous cell carcinoma metastasis via immune activity.J. Gene Med.2024263e366710.1002/jgm.3667 38442944
    [Google Scholar]
  50. QiW. EbbertK.V. CraigA.W. GreerP.A. McCaffertyD.M. Absence of Fer protein tyrosine kinase exacerbates endotoxin induced intestinal epithelial barrier dysfunction in vivo.Gut20055481091109710.1136/gut.2004.061887 16009680
    [Google Scholar]
  51. ChamaillardM. HashimotoM. HorieY. MasumotoJ. QiuS. SaabL. OguraY. KawasakiA. FukaseK. KusumotoS. ValvanoM.A. FosterS.J. MakT.W. NuñezG. InoharaN. An essential role for NOD1 in host recognition of bacterial peptidoglycan containing diaminopimelic acid.Nat. Immunol.20034770270710.1038/ni945 12796777
    [Google Scholar]
  52. SunY.V. HuY.J. Integrative analysis of multi-omics data for discovery and functional studies of complex human diseases.Adv. Genet.20169314719010.1016/bs.adgen.2015.11.004 26915271
    [Google Scholar]
  53. HasinY. SeldinM. LusisA. Multi-omics approaches to disease.Genome Biol.20171818310.1186/s13059‑017‑1215‑1 28476144
    [Google Scholar]
  54. ChenC. WangJ. PanD. WangX. XuY. YanJ. WangL. YangX. YangM. LiuG.P. Applications of multi‐omics analysis in human diseases.MedComm202344e31510.1002/mco2.315 37533767
    [Google Scholar]
  55. SharmaJ. BalakrishnanL. KaushikS. KashyapM.K. Editorial: Multi-omics approaches to study signaling pathways.Front. Bioeng. Biotechnol.2020882910.3389/fbioe.2020.00829 33014991
    [Google Scholar]
  56. LeutertM. EntwisleS.W. VillénJ. Decoding post-translational modification crosstalk with proteomics.Mol. Cell. Proteomics20212010012910.1016/j.mcpro.2021.100129 34339852
    [Google Scholar]
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