Skip to main content

Advertisement

SpringerLink
Log in

Single-Cell RNA Sequencing Reveals RAC1 Involvement in Macrophages Efferocytosis in Diabetic Kidney Disease

  • RESEARCH
  • Published:
Inflammation Aims and scope Submit manuscript

Abstract

Macrophage-mediated inflammation plays a significant role in the development and progression of diabetic kidney disease (DKD). Studies have suggested that impaired macrophage efferocytosis aggravates the inflammatory response. However, its contribution to DKD progression remains unknown. Using single-cell RNA sequencing (scRNA-seq) data obtained from the GSE131882, GSE195460, GSE151302, GSE195460, and GSE131685 datasets, we successfully clustered 13 cell types. Through analysis of the ligand-receptor network, it was discovered that macrophages interact with other cells. Additionally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that macrophages exhibit a heightened presence of phagocytosis signaling. We discovered that RAC1 was closely related to macrophage efferocytosis through a Venn diagram and protein-protein interaction (PPI) analysis, which predicted the correlation with the clinical features of DKD using the NephroseqV5 tool. Furthermore, we verified that RAC1 exhibited decreased expression in macrophages cultured with lipopolysaccharide (LPS) and high glucose. Nevertheless, the overexpression of RAC1 promoted macrophage efferocytosis and inhibited the inflammatory response. In summary, our study focused on examining the presence and importance of efferocytosis-related molecules in DKD macrophages. Through a comprehensive analysis using scRNA-seq, we discovered that RAC1 plays a crucial role as an efferocytosis molecule in DKD. These findings enhance our current knowledge of the molecular mechanisms involved in the development of DKD and aid the exploration of new treatments.

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
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

DATA AVAILABILITY

Data are available from authors upon reasonable request.

REFERENCES

  1. Jung, C.-Y., and T.-H. Yoo. 2022. Pathophysiologic mechanisms and potential biomarkers in diabetic kidney disease. Diabetes and Metabolism Journal 46: 181–197.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Hu, Q., Y. Chen, X. Deng, Y. Li, X. Ma, J. Zeng, and Y. Zhao. 2023. Diabetic nephropathy: Focusing on pathological signals, clinical treatment, and dietary regulation. Biomedicine & Pharmacotherapy 159: 114252.

    Article  Google Scholar 

  3. Liu, Y., A. Uruno, R. Saito, N. Matsukawa, E. Hishinuma, D. Saigusa, H. Liu, and M. Yamamoto. 2022. Nrf2 deficiency deteriorates diabetic kidney disease in Akita model mice. Redox Biology 58: 102525.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Boada-Romero, E., J. Martinez, B.L. Heckmann, and D.R. Green. 2020. The clearance of dead cells by efferocytosis. Nature Reviews Molecular Cell Biology 21: 398–414.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Doddapattar, P., R. Dev, M. Ghatge, R.B. Patel, M. Jain, N. Dhanesha, S.R. Lentz, and A.K. Chauhan. 2022. Myeloid cell PKM2 deletion enhances efferocytosis and reduces atherosclerosis. Circulation Research 130: 1289–1305.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Cai, W., X. Dai, J. Chen, J. Zhao, M. Xu, L. Zhang, B. Yang, W. Zhang, M. Rocha, T. Nakao, J. Kofler, Y. Shi, R.A. Stetler, X. Hu, and J. Chen. 2019. STAT6/Arg1 promotes microglia/macrophage efferocytosis and inflammation resolution in stroke mice. JCI Insight 4: e131355.

    Article  PubMed  PubMed Central  Google Scholar 

  7. Birge, R.B., S. Boeltz, S. Kumar, J. Carlson, J. Wanderley, D. Calianese, M. Barcinski, R.A. Brekken, X. Huang, J.T. Hutchins, B. Freimark, C. Empig, J. Mercer, A.J. Schroit, G. Schett, and M. Herrmann. 2016. Phosphatidylserine is a global immunosuppressive signal in efferocytosis, infectious disease, and cancer. Cell Death and Differentiation 23: 962–978.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Stuart, T., A. Butler, P. Hoffman, C. Hafemeister, E. Papalexi, W.M. Mauck, Y. Hao, M. Stoeckius, P. Smibert, and R. Satija. 2019. Comprehensive integration of single-cell data. Cell 177: 1888–1902.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Fu, J., K.M. Akat, Z. Sun, W. Zhang, D. Schlondorff, Z. Liu, T. Tuschl, K. Lee, and J.C. He. 2019. Single-cell RNA profiling of glomerular cells shows dynamic changes in experimental diabetic kidney disease. Journal of the American Society of Nephrology 30: 533–545.

    Article  CAS  PubMed  Google Scholar 

  10. Wilson, P.C., H. Wu, Y. Kirita, K. Uchimura, N. Ledru, H.G. Rennke, P.A. Welling, S.S. Waikar, and B.D. Humphreys. 2019. The single-cell transcriptomic landscape of early human diabetic nephropathy. Proceedings of the National Academy of Sciences 116: 19619–19625.

    Article  CAS  Google Scholar 

  11. Wei, Y., X. Gao, A. Li, M. Liang, and Z. Jiang. 2021. Single-nucleus transcriptomic analysis reveals important cell cross-talk in diabetic kidney disease. Frontiers in Medicine 8: 657956.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Lu, X., L. Li, L. Suo, P. Huang, H. Wang, S. Han, and M. Cao. 2022. Single-cell RNA sequencing profiles identify important pathophysiologic factors in the progression of diabetic nephropathy. Frontiers in Cell and Developmental Biology 10: 798316.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Cai, X.-Y., Z.-F. Wang, S.-W. Ge, and G. Xu. 2022. Identification of hub genes and immune-related pathways for membranous nephropathy by bioinformatics analysis. Frontiers in Physiology 13: 914382.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Aran, D., A.P. Looney, L. Liu, E. Wu, V. Fong, A. Hsu, S. Chak, R.P. Naikawadi, P.J. Wolters, A.R. Abate, A.J. Butte, and M. Bhattacharya. 2019. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nature Immunology 20: 163–172.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Efremova, M., M. Vento-Tormo, S.A. Teichmann, and R. Vento-Tormo. 2020. Cell PhoneDB: Inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nature Protocols 15: 1484–1506.

    Article  CAS  PubMed  Google Scholar 

  16. Shannon, P., A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13: 2498–2504.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Szklarczyk, D., A.L. Gable, K.C. Nastou, D. Lyon, R. Kirsch, S. Pyysalo, N.T. Doncheva, M. Legeay, T. Fang, P. Bork, L.J. Jensen, and C. von Mering. 2021. The STRING database in 2021: Customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research 49: D605–D612.

    Article  CAS  PubMed  Google Scholar 

  18. Muto, Y., E.E. Dixon, Y. Yoshimura, H. Wu, K. Omachi, N. Ledru, P.C. Wilson, A.J. King, N. Eric Olson, M.G. Gunawan, J.J. Kuo, J.H. Cox, J.H. Miner, S.L. Seliger, O.M. Woodward, P.A. Welling, T.J. Watnick, and B.D. Humphreys. 2022. Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis. Nature Communications 13: 6497.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Muto, Y., P.C. Wilson, N. Ledru, H. Wu, H. Dimke, S.S. Waikar, and B.D. Humphreys. 2021. Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney. Nature Communications 12: 2190.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Doran, A.C., A. Yurdagul, and I. Tabas. 2020. Efferocytosis in health and disease. Nature Reviews Immunology 20: 254–267.

    Article  CAS  PubMed  Google Scholar 

  21. Fabregat, A., S. Jupe, L. Matthews, K. Sidiropoulos, M. Gillespie, P. Garapati, R. Haw, B. Jassal, F. Korninger, B. May, M. Milacic, C.D. Roca, K. Rothfels, C. Sevilla, V. Shamovsky, S. Shorser, T. Varusai, G. Viteri, J. Weiser, G. Wu, L. Stein, H. Hermjakob, and P. D’Eustachio. 2018. The reactome pathway knowledgebase. Nucleic Acids Research 46: D649–D655.

    Article  CAS  PubMed  Google Scholar 

  22. Chin, C.-H., S.-H. Chen, H.-H. Wu, C.-W. Ho, M.-T. Ko, and C.-Y. Lin. 2014. cytoHubba: Identifying hub objects and sub-networks from complex interactome. BMC Systems Biology 8 (Suppl 4): S11.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Tang, S.C.W., and W.H. Yiu. 2020. Innate immunity in diabetic kidney disease. Nature Reviews. Nephrology 16: 206–222.

    Article  CAS  PubMed  Google Scholar 

  24. Ma, T., X. Li, Y. Zhu, S. Yu, T. Liu, X. Zhang, D. Chen, S. Du, T. Chen, S. Chen, Y. Xu, and Q. Fan. 2022. Excessive activation of notch signaling in macrophages promote kidney inflammation, fibrosis, and necroptosis. Frontiers in Immunology 13: 835879.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Li, Q., J. Liao, W. Chen, K. Zhang, H. Li, F. Ma, H. Zhang, Q. Han, J. Guo, Y. Li, L. Hu, J. Pan, and Z. Tang. 2022. NAC alleviative ferroptosis in diabetic nephropathy via maintaining mitochondrial redox homeostasis through activating SIRT3-SOD2/Gpx4 pathway. Free Radical Biology & Medicine 187: 158–170.

    Article  CAS  Google Scholar 

  26. Dias, C.G., L. Venkataswamy, and S. Balakrishna. 2022. Diabetic nephropathy patients show hyper-responsiveness to N6-carboxymethyllysine. Brazilian Journal of Medical and Biological Research 55: e11984.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Song, Y., F. Guo, Y.-Y. Zhao, X.-J. Ma, L.-N. Wu, J.-F. Yu, H.-F. Ji, M.-W. Shao, F.-J. Huang, L. Zhao, X.-J. Fan, Y.-N. Xu, Q.-Z. Wang, and G.-J. Qin. 2023. Novel lncRNA-prader willi/angelman region RNA, SNRPN neighbour (PWARSN) aggravates tubular epithelial cell pyroptosis by regulating TXNIP via dual way in diabetic kidney disease. Cell Proliferation 56: e13349.

    Article  CAS  PubMed  Google Scholar 

  28. Barutta, F., S. Bellini, S. Kimura, K. Hase, B. Corbetta, A. Corbelli, F. Fiordaliso, S. Bruno, L. Biancone, A. Barreca, M.G. Papotti, E. Hirsh, M. Martini, R. Gambino, M. Durazzo, H. Ohno, and G. Gruden. 2023. Protective effect of the tunneling nanotube-TNFAIP2/M-sec system on podocyte autophagy in diabetic nephropathy. Autophagy 19: 505–524.

    Article  CAS  PubMed  Google Scholar 

  29. Maschalidi, S., P. Mehrotra, B.N. Keçeli, H.K.L. De Cleene, K. Lecomte, R. Van der Cruyssen, P. Janssen, J. Pinney, G. van Loo, D. Elewaut, A. Massie, E. Hoste, and K.S. Ravichandran. 2022. Targeting SLC7A11 improves efferocytosis by dendritic cells and wound healing in diabetes. Nature 606: 776–784.

    Article  CAS  PubMed  Google Scholar 

  30. Geng, L., J. Zhao, Y. Deng, I. Molano, X. Xu, L. Xu, P. Ruiz, Q. Li, X. Feng, M. Zhang, W. Tan, D.L. Kamen, S.-C. Bae, G.S. Gilkeson, L. Sun, and B.P. Tsao. 2022. Human SLE variant NCF1-R90H promotes kidney damage and murine lupus through enhanced Tfh2 responses induced by defective efferocytosis of macrophages. Annals of the Rheumatic Diseases 81: 255–267.

    Article  CAS  PubMed  Google Scholar 

  31. Chen, Z.Z., L. Johnson, U. Trahtemberg, A. Baker, S. Huq, J. Dufresne, P. Bowden, M. Miao, J.-A. Ho, C.-C. Hsu, C.C. Dos Santos, and J.G. Marshall. 2023. Mitochondria and cytochrome components released into the plasma of severe COVID-19 and ICU acute respiratory distress syndrome patients. Clinical Proteomics 20: 17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Brustovetsky, N.N., Z.G. Amerkhanov, E. Popova, and A.A. Konstantinov. 1990. Reversible inhibition of electron transfer in the ubiquinol: cytochrome c reductase segment of the mitochondrial respiratory chain in hibernating ground squirrels. FEBS Letters 263: 73–76.

    Article  CAS  PubMed  Google Scholar 

  33. Lv, Z., M. Hu, M. Fan, X. Li, J. Lin, J. Zhen, Z. Wang, H. Jin, and R. Wang. 2018. Podocyte-specific Rac1 deficiency ameliorates podocyte damage and proteinuria in STZ-induced diabetic nephropathy in mice. Cell Death & Disease 9: 342.

    Article  Google Scholar 

  34. Ying, C., Z. Zhou, J. Dai, M. Wang, J. Xiang, D. Sun, and X. Zhou. 2022. Activation of the NLRP3 inflammasome by RAC1 mediates a new mechanism in diabetic nephropathy. Inflammation Research 71: 191–204.

    Article  CAS  PubMed  Google Scholar 

  35. Tang, J., Y. Jin, F. Jia, T. Lv, A. Manaenko, L.-F. Zhang, Z. Zhang, X. Qi, Y. Xue, B. Zhao, X. Zhang, J.H. Zhang, J. Lu, and Q. Hu. 2022. Gas6 promotes microglia efferocytosis and suppresses inflammation through activating Axl/Rac1 signaling in subarachnoid hemorrhage mice. Translational Stroke Research 14: 955–969.

    Article  PubMed  Google Scholar 

  36. Proto, J.D., A.C. Doran, G. Gusarova, A. Yurdagul, E. Sozen, M. Subramanian, M.N. Islam, C.C. Rymond, J. Du, J. Hook, G. Kuriakose, J. Bhattacharya, and I. Tabas. 2018. Regulatory T cells promote macrophage efferocytosis during inflammation resolution. Immunity 49 (4): 666–677.

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This work was supported by grants from the National Natural Science Foundation of China (81974110, 82170839) to Qin, from the National Natural Science Foundation of China (82300930) to Song, and Hubei Chen Xiaoping Science and Technology Development Foundation (CXPJJH122012-023) to Song.

Author information

Author notes

  1. Yi Song and Yifan Liu contributed equally to this work.

Authors and Affiliations

  1. Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China

    Yi Song, Feng Guo, Lin Zhao & Guijun Qin

  2. Department of Hepatobiliary Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China

    Yifan Liu

Authors
  1. Yi Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yifan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Feng Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lin Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Guijun Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

YS and YL: conceptualization, methodology, software, investigation, formal analysis, writing – original draft. FG: resources, supervision, data curation, writing – original draft. LZ: visualization, investigation, validation. GQ: conceptualization, funding acquisition, resources, supervision, writing – review and editing.

Corresponding author

Correspondence to Guijun Qin.

Ethics declarations

Competing Interests

The authors declare that they have no competing interests.

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.

Supplementary file1 (DOCX 1438 KB)

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

Song, Y., Liu, Y., Guo, F. et al. Single-Cell RNA Sequencing Reveals RAC1 Involvement in Macrophages Efferocytosis in Diabetic Kidney Disease. Inflammation (2023). https://doi.org/10.1007/s10753-023-01942-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10753-023-01942-y

KEY WORDS

Search

Navigation