Skip to main content
SpringerLink
Log in

Proteomic Profiles and Protein Network Analysis of Primary Human Leukocytes Revealed Possible Clearance Biomarkers for Staphylococcus aureus Infection

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Staphylococcus aureus is a serious pathogen that can survive within host cells after a typical course of treatment completion, leading to chronic infection. Knowledge of host proteomic patterns after clearance of this pathogen from cells is limited. Here, we looked for S. aureus clearance biomarkers produced by in vitro-infected leukocytes. Extracellular proteins from primary human leukocytes infected with S. aureus ATCC 25923 were investigated as possible treatment-monitoring clearance biomarkers by applying a proteomics approach combining liquid chromatography with tandem mass spectrometry (LC-MS/MS) and protein interaction network analysis. It was found that the expression patterns of proteins secreted by S. aureus-infected leukocytes differed among stages of infection. Proteomic profiles showed that an ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2 (ATP8A2) was expressed in the clearance stage and was not detected at any earlier stage or in uninfected controls. Protein network analysis showed that TERF2 (telomeric repeat-binding factor 2), ZNF440 (zinc finger protein 440), and PPP1R14A (phosphatase 1 regulatory subunit 14A) were up-regulated, while GLE1, an essential RNA-export mediator, was suppressed in both infection and clearance stages, suggesting their potential roles in S. aureus infection and clearance. These findings are the first to report that the ATP8A2 has potential as a clearance biomarker for S. aureus infection.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Data Availability

The datasets used and/or analyzed during the current study available from the corresponding author on reasonable request. The LC-MS/MS raw data have been deposited in the MassIVE database with accession number MSV000089903.

Code Availability

Not applicable.

References

  1. Laux C, Peschel A, Krismer B, Fischetti VA, Novick RP, Ferretti JJ, Portnoy DA, Braunstein M, Rood JI (2019) Staphylococcus aureus colonization of the human nose and interaction with other microbiome members. Microbiol Spectr 7(2):7.2.34. https://doi.org/10.1128/microbiolspec.GPP3-0029-2018

    Article  Google Scholar 

  2. Tong SYC, Davis JS, Eichenberger E, Holland TL, Fowler VG Jr (2015) Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management. Clin Microbiol Rev 28(3):603–661. https://doi.org/10.1128/CMR.00134-14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Hiramatsu K, Katayama Y, Matsuo M, Sasaki T, Morimoto Y, Sekiguchi A, Baba T (2014) Multi-drug-resistant Staphylococcus aureus and future chemotherapy. J Infect Chemother 20(10):593–601. https://doi.org/10.1016/j.jiac.2014.08.001

    Article  CAS  PubMed  Google Scholar 

  4. Bravo-Santano N, Ellis JK, Mateos LM, Calle Y, Keun HC, Behrends V, Letek M (2018) Intracellular Staphylococcus aureus modulates host central carbon metabolism to activate autophagy. mSphere. https://doi.org/10.1128/mSphere.00374-18

    Article  PubMed  PubMed Central  Google Scholar 

  5. Deplanche M, Mouhali N, Nguyen M-T, Cauty C, Ezan F, Diot A, Raulin L, Dutertre S, Langouet S, Legembre P, Taieb F, Otto M, Laurent F, Götz F, Le Loir Y, Berkova N (2019) Staphylococcus aureus induces DNA damage in host cell. Sci Rep 9(1):7694. https://doi.org/10.1038/s41598-019-44213-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Francois P, Scherl A, Hochstrasser D, Schrenzel J (2010) Proteomic approaches to study Staphylococcus aureus pathogenesis. J Proteomics 73(4):701–708. https://doi.org/10.1016/j.jprot.2009.10.007

    Article  CAS  PubMed  Google Scholar 

  7. Otto A, van Dijl JM, Hecker M, Becher D (2014) The Staphylococcus aureus proteome. Int J Med Microbiol 304(2):110–120. https://doi.org/10.1016/j.ijmm.2013.11.007

    Article  CAS  PubMed  Google Scholar 

  8. Basell K, Otto A, Junker S, Zuhlke D, Rappen GM, Schmidt S, Hentschker C, Macek B, Ohlsen K, Hecker M, Becher D (2014) The phosphoproteome and its physiological dynamics in Staphylococcus aureus. Int J Med Microbiol 304(2):121–132. https://doi.org/10.1016/j.ijmm.2013.11.020

    Article  CAS  PubMed  Google Scholar 

  9. Hecker M, Becher D, Fuchs S, Engelmann S (2010) A proteomic view of cell physiology and virulence of Staphylococcus aureus. Int J Med Microbiol 300(2–3):76–87. https://doi.org/10.1016/j.ijmm.2009.10.006

    Article  CAS  PubMed  Google Scholar 

  10. Resch A, Leicht S, Saric M, Pasztor L, Jakob A, Gotz F, Nordheim A (2006) Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling. Proteomics 6(6):1867–1877. https://doi.org/10.1002/pmic.200500531

    Article  PubMed  Google Scholar 

  11. Becher D, Hempel K, Sievers S, Zuhlke D, Pane-Farre J, Otto A, Fuchs S, Albrecht D, Bernhardt J, Engelmann S, Volker U, van Dijl JM, Hecker M (2009) A proteomic view of an important human pathogen–towards the quantification of the entire Staphylococcus aureus proteome. PLoS ONE 4(12):e8176. https://doi.org/10.1371/journal.pone.0008176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Fischer A, Yang SJ, Bayer AS, Vaezzadeh AR, Herzig S, Stenz L, Girard M, Sakoulas G, Scherl A, Yeaman MR, Proctor RA, Schrenzel J, Francois P (2011) Daptomycin resistance mechanisms in clinically derived Staphylococcus aureus strains assessed by a combined transcriptomics and proteomics approach. J Antimicrob Chemother 66(8):1696–1711. https://doi.org/10.1093/jac/dkr195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Sirichoat A, Lulitanond A, Kanlaya R, Tavichakorntrakool R, Chanawong A, Wongthong S, Thongboonkerd V (2016) Phenotypic characteristics and comparative proteomics of Staphylococcus aureus strains with different vancomycin-resistance levels. Diagn Microbiol Infect Dis 86(4):340–344. https://doi.org/10.1016/j.diagmicrobio.2016.09.011

    Article  CAS  PubMed  Google Scholar 

  14. Broker BM, van Belkum A (2011) Immune proteomics of Staphylococcus aureus. Proteomics 11(15):3221–3231. https://doi.org/10.1002/pmic.201100010

    Article  CAS  PubMed  Google Scholar 

  15. Dryla A, Prustomersky S, Gelbmann D, Hanner M, Bettinger E, Kocsis B, Kustos T, Henics T, Meinke A, Nagy E (2005) Comparison of antibody repertoires against Staphylococcus aureus in healthy individuals and in acutely infected patients. Clin Diagn Lab Immunol 12(3):387–398. https://doi.org/10.1128/CDLI.12.3.387-398.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Jacobsson G, Colque-Navarro P, Gustafsson E, Andersson R, Mollby R (2010) Antibody responses in patients with invasive Staphylococcus aureus infections. Eur J Clin Microbiol Infect Dis 29(6):715–725. https://doi.org/10.1007/s10096-010-0919-x

    Article  CAS  PubMed  Google Scholar 

  17. Kolata J, Bode LG, Holtfreter S, Steil L, Kusch H, Holtfreter B, Albrecht D, Hecker M, Engelmann S, van Belkum A, Volker U, Broker BM (2011) Distinctive patterns in the human antibody response to Staphylococcus aureus bacteremia in carriers and non-carriers. Proteomics 11(19):3914–3927. https://doi.org/10.1002/pmic.201000760

    Article  CAS  PubMed  Google Scholar 

  18. Kaewseekhao B, Roytrakul S, Yingchutrakul Y, Laohaviroj M, Salao K, Faksri K (2021) Characterisation of secretome-based immune responses of human leukocytes infected with various Mycobacterium tuberculosis lineages. PeerJ 9:e11565. https://doi.org/10.7717/peerj.11565

    Article  PubMed  PubMed Central  Google Scholar 

  19. Xia J, Benner MJ, Hancock REW (2014) NetworkAnalyst-integrative approaches for protein-protein interaction network analysis and visual exploration. Nucleic Acids Res. https://doi.org/10.1093/nar/gku443

    Article  PubMed  PubMed Central  Google Scholar 

  20. Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman F, Cesareni G, Chatr-Aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock R, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H (2012) Protein interaction data curation: the international molecular exchange (IMEx) consortium. Nat Methods 9:345–350. https://doi.org/10.1038/nmeth.1931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Coleman JA, Quazi F (1831) Molday RS (2013) Mammalian P4-ATPases and ABC transporters and their role in phospholipid transport. Biochim Biophys Acta 3:555–574. https://doi.org/10.1016/j.bbalip.2012.10.006

    Article  CAS  Google Scholar 

  22. de Lange T (2002) Protection of mammalian telomeres. Oncogene 21(4):532–540. https://doi.org/10.1038/sj.onc.1205080

    Article  PubMed  Google Scholar 

  23. Palm W, de Lange T (2008) How shelterin protects mammalian telomeres. Annu Rev Genet 42:301–334. https://doi.org/10.1146/annurev.genet.41.110306.130350

    Article  CAS  PubMed  Google Scholar 

  24. Smogorzewska A, de Lange T (2004) Regulation of telomerase by telomeric proteins. Annu Rev Biochem 73:177–208. https://doi.org/10.1146/annurev.biochem.73.071403.160049

    Article  CAS  PubMed  Google Scholar 

  25. Matsutani N, Yokozaki H, Tahara E, Tahara H, Kuniyasu H, Haruma K, Chayama K, Yasui W, Tahara E (2001) Expression of telomeric repeat binding factor 1 and 2 and TRF1-interacting nuclear protein 2 in human gastric carcinomas. Int J Oncol 19(3):507–512. https://doi.org/10.3892/ijo.19.3.507

    Article  CAS  PubMed  Google Scholar 

  26. Pal D, Sharma U, Singh SK, Kakkar N, Prasad R (2015) Over-expression of telomere binding factors (TRF1 & TRF2) in renal cell carcinoma and their inhibition by using SiRNA induce apoptosis, reduce cell proliferation and migration invitro. PLoS ONE 10(3):e0115651. https://doi.org/10.1371/journal.pone.0115651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Hu H, Zhang Y, Zou M, Yang S, Liang XQ (2010) Expression of TRF1, TRF2, TIN2, TERT, KU70, and BRCA1 proteins is associated with telomere shortening and may contribute to multistage carcinogenesis of gastric cancer. J Cancer Res Clin Oncol 136(9):1407–1414. https://doi.org/10.1007/s00432-010-0795-x

    Article  CAS  PubMed  Google Scholar 

  28. Kumar R, Khan R, Gupta N, Seth T, Sharma A, Kalaivani M, Sharma A (2018) Identifying the biomarker potential of telomerase activity and shelterin complex molecule, telomeric repeat binding factor 2 (TERF2), in multiple myeloma. Leuk Lymphoma 59(7):1677–1689. https://doi.org/10.1080/10428194.2017.1387915

    Article  CAS  PubMed  Google Scholar 

  29. Klug A (2010) The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation. Q Rev Biophys 43(1):1–21. https://doi.org/10.1017/S0033583510000089

    Article  CAS  PubMed  Google Scholar 

  30. Mesuraca M, Galasso O, Guido L, Chiarella E, Scicchitano S, Vatrinet R, Morrone G, Bond HM, Gasparini G (2014) Expression profiling and functional implications of a set of zinc finger proteins, ZNF423, ZNF470, ZNF521, and ZNF780B, in primary osteoarthritic articular chondrocytes. Mediators Inflamm 2014:318793. https://doi.org/10.1155/2014/318793

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Nakamura A, Rampersaud YR, Sundararajan K, Nakamura S, Wu B, Matip E, Haroon N, Krawetz RJ, Rossomacha E, Gandhi R, Kotlyar M, Rockel JS, Jurisica I, Kapoor M (2021) Zinc finger protein-440 promotes cartilage degenerative mechanisms in human facet and knee osteoarthritis chondrocytes. Osteoarthr Cartil 29(3):372–379. https://doi.org/10.1016/j.joca.2020.12.004

    Article  CAS  Google Scholar 

  32. Ferreira M, Beullens M, Bollen M, Van Eynde A (2019) Functions and therapeutic potential of protein phosphatase 1: insights from mouse genetics. Biochim Biophys Acta Mol Cell Res 1866(1):16–30. https://doi.org/10.1016/j.bbamcr.2018.07.019

    Article  CAS  PubMed  Google Scholar 

  33. Hamaguchi T, Ito M, Feng J, Seko T, Koyama M, Machida H, Takase K, Amano M, Kaibuchi K, Hartshorne DJ, Nakano T (2000) Phosphorylation of CPI-17, an inhibitor of myosin phosphatase, by protein kinase N. Biochem Biophys Res Commun 274(3):825–830. https://doi.org/10.1006/bbrc.2000.3225

    Article  CAS  PubMed  Google Scholar 

  34. Li Z, Yu L, Zhang Y, Gao J, Zhang P, Wan B, Chen C, Zhao S (2001) Identification of human, mouse and rat PPP1R14A, protein phosphatase-1 inhibitor subunit 14A, & mapping human PPP1R14A to chromosome 19q13.13-q13.2. Mol Biol Rep 28(2):91–101. https://doi.org/10.1023/a:1017998029053

    Article  CAS  PubMed  Google Scholar 

  35. Yang Q, Fujii W, Kaji N, Kakuta S, Kada K, Kuwahara M, Tsubone H, Ozaki H, Hori M (2018) The essential role of phospho-T38 CPI-17 in the maintenance of physiological blood pressure using genetically modified mice. FASEB J 32(4):2095–2109. https://doi.org/10.1096/fj.201700794R

    Article  CAS  PubMed  Google Scholar 

  36. Gómez MI, Lee A, Reddy B, Muir A, Soong G, Pitt A, Cheung A, Prince A (2004) Staphylococcus aureus protein A induces airway epithelial inflammatory responses by activating TNFR1. Nat Med 10(8):842–848. https://doi.org/10.1038/nm1079

    Article  CAS  PubMed  Google Scholar 

  37. Prince LR, Graham KJ, Connolly J, Anwar S, Ridley R, Sabroe I, Foster SJ, Whyte MKB (2012) Staphylococcus aureus induces eosinophil cell death mediated by α-hemolysin. PLoS ONE 7(2):e31506. https://doi.org/10.1371/journal.pone.0031506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Ozaki H, Yasuda K, Kim YS, Egawa M, Kanzaki H, Nakazawa H, Hori M, Seto M, Karaki H (2003) Possible role of the protein kinase C/CPI-17 pathway in the augmented contraction of human myometrium after gestation. Br J Pharmacol 140(7):1303–1312. https://doi.org/10.1038/sj.bjp.0705552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Sakai H, Chiba Y, Hirano T, Misawa M (2005) Possible involvement of CPI-17 in augmented bronchial smooth muscle contraction in antigen-induced airway hyper-responsive rats. Mol Pharmacol 68(1):145–151. https://doi.org/10.1124/mol.104.004325

    Article  CAS  PubMed  Google Scholar 

  40. Hagel C, Dornblut C, Schulz A, Wiehl U, Friedrich RE, Huckhagel T, Mautner V-F, Morrison H (2016) The putative oncogene CPI-17 is up-regulated in schwannoma. Neuropathol Appl Neurobiol 42(7):664–668. https://doi.org/10.1111/nan.12330

    Article  CAS  PubMed  Google Scholar 

  41. Xu J, Zhang Y, Shi Y, Yin D, Dai P, Zhao W, Zhang T (2020) CPI-17 overexpression and its correlation with the NF2 mutation spectrum in sporadic vestibular schwannomas. Otol Neurotol 41(1):e94–e102. https://doi.org/10.1097/MAO.0000000000002430

    Article  PubMed  Google Scholar 

  42. Bolger TA, Folkmann AW, Tran EJ, Wente SR (2008) The mRNA export factor Gle1 and inositol hexakisphosphate regulate distinct stages of translation. Cell 134(4):624–633. https://doi.org/10.1016/j.cell.2008.06.027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Murphy R, Wente SR (1996) An RNA-export mediator with an essential nuclear export signal. Nature 383(6598):357–360. https://doi.org/10.1038/383357a0

    Article  CAS  PubMed  Google Scholar 

  44. Watkins JL, Murphy R, Emtage JL, Wente SR (1998) The human homologue of Saccharomyces cerevisiae Gle1p is required for poly(A)+ RNA export. Proc Natl Acad Sci U S A 95(12):6779–6784. https://doi.org/10.1073/pnas.95.12.6779

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Mason AC, Wente SR (2020) Functions of Gle1 are governed by two distinct modes of self-association. J Biol Chem 295(49):16813–16825. https://doi.org/10.1074/jbc.RA120.015715

    Article  CAS  PubMed  Google Scholar 

  46. Folkmann AW, Collier SE, Zhan X, Aditi OMD, Wente SR (2013) Gle1 functions during mRNA export in an oligomeric complex that is altered in human disease. Cell 155(3):582–593. https://doi.org/10.1016/j.cell.2013.09.023

    Article  CAS  PubMed  Google Scholar 

  47. Nousiainen HO, Kestila M, Pakkasjarvi N, Honkala H, Kuure S, Tallila J, Vuopala K, Ignatius J, Herva R, Peltonen L (2008) Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease. Nat Genet 40(2):155–157. https://doi.org/10.1038/ng.2007.65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We would like to acknowledge Prof. David Blair for editing the MS via Publication Clinic KKU, Thailand.

Funding

This study was supported by Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Thailand. This study has received scholarship under the Post-Doctoral Training Program (PD2565-05).

Author information

Authors and Affiliations

  1. Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand

    Auttawit Sirichoat, Benjawan Kaewseekhao, Arnone Nithichanon & Kiatichai Faksri

  2. Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand

    Auttawit Sirichoat, Benjawan Kaewseekhao, Arnone Nithichanon & Kiatichai Faksri

  3. Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand

    Sittiruk Roytrakul

Authors
  1. Auttawit Sirichoat
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Benjawan Kaewseekhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Arnone Nithichanon
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sittiruk Roytrakul
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kiatichai Faksri
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

KF conceived the ideas and designed methodology; SR managed LC–MS/MS and provided raw data. AS, BK, and AN curated data and performed experimental work and data analysis. AS, BK, AN, and KF interpreted the results and drafted manuscript. KF and AS performed critical revision of the manuscript. All authors have read and agreed to the published version of manuscript.

Corresponding author

Correspondence to Kiatichai Faksri.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest.

Ethical Approval

This study was conducted in accordance with the Declaration of Helsinki and was approved by the Ethics Committee of Khon Kaen University (project number HE581377).

Consent to Participate

All study participants gave their written informed consent before they participated in the study.

Consent for Publication

The authors approve consent for publication of the above work.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

284_2023_3450_MOESM1_ESM.tif

Supplementary file1 (TIF 138969 KB) The drop plate method on LB agar confirming the in vitro clearance stage. The extracellular proteins secreted by leukocytes infected with S. aureus in cell cultures were harvested during infection (Day 1 and Day 3) and clearance stages (Day 5). The culture cell pellets and supernatant were dropped onto LB plates and these were incubated for five days to ensure the in vitro clearance of S. aureus. S.a. Staphylococcus aureus, P penicillin, LB Luria–Bertani agar. Sample: H2, H3, and H4 are leukocytes isolated from each three participants

284_2023_3450_MOESM2_ESM.xlsx

Supplementary file2 (XLSX 10 KB) Classification of proteins according to qualitative or quantitative differences (up-regulation or down-regulation) among S. aureus-infected leukocytes under the various experimental conditions

284_2023_3450_MOESM3_ESM.xlsx

Supplementary file3 (XLSX 16 KB) List of differentially expressed proteins and their expression levels detected in the S. aureus infection with penicillin treatment at Day 1 and Day 5 experiments

284_2023_3450_MOESM4_ESM.xlsx

Supplementary file4 (XLSX 11 KB) List of top ten pathways associated with proteins over-expressed or suppressed during S. aureus infection

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sirichoat, A., Kaewseekhao, B., Nithichanon, A. et al. Proteomic Profiles and Protein Network Analysis of Primary Human Leukocytes Revealed Possible Clearance Biomarkers for Staphylococcus aureus Infection. Curr Microbiol 80, 335 (2023). https://doi.org/10.1007/s00284-023-03450-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00284-023-03450-6

Search

Navigation