Protein Interactome Analysis of ATP1B1 in Alveolar Epithelial Cells Using Co-Immunoprecipitation Mass Spectrometry and Parallel Reaction Monitoring Assay

Overview

Journal Heliyon

Specialty Social Sciences

Date 2024 Jun 24

PMID 38912441

Authors

Yu Zheng

Weiting Peng

Xupeng Wen

Qiquan Wan

Affiliations

Soon will be listed here.

Abstract

Aims: Alveolar epithelial barrier integrity is essential for lung homeostasis. Na, K-ATPase β1 subunit (ATP1B1) involves alveolar edema fluid clearance and alveolar epithelial barrier stability. However, the underlying molecular mechanism of ATP1B1 in alveolar epithelial cells still needs to be understood.

Main Methods: We utilized Co-Immunoprecipitation mass spectrometry proteomic analysis, protein-protein interaction (PPI) analysis, enrichment analysis, and parallel reaction monitoring (PRM) analysis to investigate proteins interacting with ATP1B1 in A549 cells.

Key Findings: A total of 159 proteins were identified as significant proteins interacting with ATP1B1 in A549 cells. Ribosomal and heat shock proteins were major constituents of the two main functional modules based on the PPI network. Enrichment analysis showed that significant proteins were involved in protein translation, posttranslational processing, and function regulation. Moreover, 10 proteins of interest were verified by PRM, and fold changes in 6 proteins were consistent with proteomics results. Finally, HSP90AB1, EIF4A1, TUBB4B, HSPA8, STAT1, and PLEC were considered candidates for binding to ATP1B1 to function in alveolar epithelial cells.

Significance: Our study provides new insights into the role of ATP1B1 in alveolar epithelial cells and indicates that six proteins, in particular HSP90AB1, may be key proteins interacting with and regulating ATP1B1, which might be potential targets for the treatment of acute respiratory distress syndrome.

References

Vagin O, Dada L, Tokhtaeva E, Sachs G . The Na-K-ATPase α₁β₁ heterodimer as a cell adhesion molecule in epithelia. Am J Physiol Cell Physiol. 2012; 302(9):C1271-81. PMC: 3361946. DOI: 10.1152/ajpcell.00456.2011. View

Lamouille S, Xu J, Derynck R . Molecular mechanisms of epithelial-mesenchymal transition. Nat Rev Mol Cell Biol. 2014; 15(3):178-96. PMC: 4240281. DOI: 10.1038/nrm3758. View

Clausen M, Hilbers F, Poulsen H . The Structure and Function of the Na,K-ATPase Isoforms in Health and Disease. Front Physiol. 2017; 8:371. PMC: 5459889. DOI: 10.3389/fphys.2017.00371. View

Wang Y, Zhang Y, Guo X, Zheng Y, Zhang X, Feng S . CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis. BMC Biol. 2023; 21(1):124. PMC: 10210458. DOI: 10.1186/s12915-023-01622-1. View

Factor P, Saldias F, Ridge K, Dumasius V, Zabner J, Jaffe H . Augmentation of lung liquid clearance via adenovirus-mediated transfer of a Na,K-ATPase beta1 subunit gene. J Clin Invest. 1998; 102(7):1421-30. PMC: 508990. DOI: 10.1172/JCI3214. View

Pino L, Searle B, Bollinger J, Nunn B, MacLean B, MacCoss M . The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrom Rev. 2017; 39(3):229-244. PMC: 5799042. DOI: 10.1002/mas.21540. View

Bader G, Hogue C . An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003; 4:2. PMC: 149346. DOI: 10.1186/1471-2105-4-2. View

Bozaykut P, Ozer N, Karademir B . Regulation of protein turnover by heat shock proteins. Free Radic Biol Med. 2014; 77:195-209. DOI: 10.1016/j.freeradbiomed.2014.08.012. View

Wen X, Long G, Zhang Y, Huang H, Liu T, Wan Q . Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis. Proteome Sci. 2022; 20(1):10. PMC: 9178877. DOI: 10.1186/s12953-022-00193-3. View

10.

Mirzapoiazova T, Kolosova I, Moreno L, Sammani S, Garcia J, Verin A . Suppression of endotoxin-induced inflammation by taxol. Eur Respir J. 2007; 30(3):429-35. DOI: 10.1183/09031936.00154206. View

11.

Meyer N, Gattinoni L, Calfee C . Acute respiratory distress syndrome. Lancet. 2021; 398(10300):622-637. PMC: 8248927. DOI: 10.1016/S0140-6736(21)00439-6. View

12.

Rauniyar N . Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry. Int J Mol Sci. 2015; 16(12):28566-81. PMC: 4691067. DOI: 10.3390/ijms161226120. View

13.

Matos A, Dominguez-Perez D, Almeida D, Aguero-Chapin G, Campos A, Osorio H . Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host-Microbe Interactions by Revealing Diverse Antimicrobial Peptides. Mar Drugs. 2020; 18(7). PMC: 7401272. DOI: 10.3390/md18070362. View

14.

Tokhtaeva E, Sachs G, Souda P, Bassilian S, Whitelegge J, Shoshani L . Epithelial junctions depend on intercellular trans-interactions between the Na,K-ATPase β₁ subunits. J Biol Chem. 2011; 286(29):25801-12. PMC: 3138299. DOI: 10.1074/jbc.M111.252247. View

15.

Wang X, Fei A . Identification of Genes as Potential Biomarkers for Sepsis-related ARDS using Weighted Gene Co-expression Network Analysis. Comb Chem High Throughput Screen. 2022; 26(4):789-800. DOI: 10.2174/1386207325666220509180737. View

16.

Xu R, He S, Ma D, Liang R, Luo Q, Song G . Plectin Downregulation Inhibits Migration and Suppresses Epithelial Mesenchymal Transformation of Hepatocellular Carcinoma Cells via ERK1/2 Signaling. Int J Mol Sci. 2023; 24(1). PMC: 9820339. DOI: 10.3390/ijms24010073. View

17.

Ware L, Matthay M . Alveolar fluid clearance is impaired in the majority of patients with acute lung injury and the acute respiratory distress syndrome. Am J Respir Crit Care Med. 2001; 163(6):1376-83. DOI: 10.1164/ajrccm.163.6.2004035. View

18.

Kiritsi D, Tsakiris L, Schauer F . Plectin in Skin Fragility Disorders. Cells. 2021; 10(10). PMC: 8534787. DOI: 10.3390/cells10102738. View

19.

Kryvenko V, Vagin O, Dada L, Sznajder J, Vadasz I . Maturation of the Na,K-ATPase in the Endoplasmic Reticulum in Health and Disease. J Membr Biol. 2021; 254(5-6):447-457. PMC: 8192048. DOI: 10.1007/s00232-021-00184-z. View

20.

. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2022; 51(D1):D523-D531. PMC: 9825514. DOI: 10.1093/nar/gkac1052. View