Comprehensive Analysis of Autophagy Status and Its Relationship with Immunity and Inflammation in Ischemic Stroke Through Integrated Transcriptomic and Single-cell Sequencing

Overview

Journal Genes Immun

Date 2025 Jan 18

PMID 39827328

Authors

Xiaole Zhu

Zhongman Zhang

Yi Zhu

Yanlong Chen

Wei Li

Huae Xu

Xufeng Chen

Affiliations

Soon will be listed here.

Abstract

Ischemic stroke (IS) significantly impacts patients' health and quality of life, with the roles of autophagy and autophagy-related genes in IS still not fully understood. In this study, IS datasets were retrieved from the GEO database. Autophagy-related genes(ARGs) were identified and screened for differential expression. A prediction model was constructed using machine learning algorithm. WGCNA was employed to analyze differential regulation modules among different clusters of stroke patients. The analysis results were validated using single-cell sequencing data. Finally, autophagy hub genes were validated in an external cohort and an IS mouse model. We observed suppressed autophagy states in IS patients. A diagnostic model with good clinical efficacy for stroke diagnosis was constructed based on the selected key genes (AUC = 0.87). Consensus clustering identified two IS subtypes with distinct gene expression patterns and immune cell infiltration. scRNA-seq data analysis confirmed downregulation of pexophagy in IS. CellChat analysis identified key signaling pathways and intercellular interactions related to pexophagy. Validation in an external cohort and IS mouse model confirmed differential gene expression, supporting the involvement of pexophagy in IS pathogenesis. The identified key genes, molecular subtypes, and cellular interactions provide a foundation for further research into targeted therapies and precision medicine approaches for IS patients.

References

Herpich F, Rincon F . Management of Acute Ischemic Stroke. Crit Care Med. 2020; 48(11):1654-1663. PMC: 7540624. DOI: 10.1097/CCM.0000000000004597. View

DeLong J, Ohashi S, OConnor K, Sansing L . Inflammatory Responses After Ischemic Stroke. Semin Immunopathol. 2022; 44(5):625-648. DOI: 10.1007/s00281-022-00943-7. View

Paul S, Candelario-Jalil E . Emerging neuroprotective strategies for the treatment of ischemic stroke: An overview of clinical and preclinical studies. Exp Neurol. 2020; 335:113518. PMC: 7869696. DOI: 10.1016/j.expneurol.2020.113518. View

Mizushima N, Komatsu M . Autophagy: renovation of cells and tissues. Cell. 2011; 147(4):728-41. DOI: 10.1016/j.cell.2011.10.026. View

Parzych K, Klionsky D . An overview of autophagy: morphology, mechanism, and regulation. Antioxid Redox Signal. 2013; 20(3):460-73. PMC: 3894687. DOI: 10.1089/ars.2013.5371. View

Ajoolabady A, Wang S, Kroemer G, Penninger J, Uversky V, Pratico D . Targeting autophagy in ischemic stroke: From molecular mechanisms to clinical therapeutics. Pharmacol Ther. 2021; 225:107848. PMC: 8263472. DOI: 10.1016/j.pharmthera.2021.107848. View

Beccari S, Sierra-Torre V, Valero J, Pereira-Iglesias M, Garcia-Zaballa M, Soria F . Microglial phagocytosis dysfunction in stroke is driven by energy depletion and induction of autophagy. Autophagy. 2023; 19(7):1952-1981. PMC: 10283420. DOI: 10.1080/15548627.2023.2165313. View

Guan R, Zou W, Dai X, Yu X, Liu H, Chen Q . Mitophagy, a potential therapeutic target for stroke. J Biomed Sci. 2018; 25(1):87. PMC: 6271612. DOI: 10.1186/s12929-018-0487-4. View

Vargas J, Hamasaki M, Kawabata T, Youle R, Yoshimori T . The mechanisms and roles of selective autophagy in mammals. Nat Rev Mol Cell Biol. 2022; 24(3):167-185. DOI: 10.1038/s41580-022-00542-2. View

10.

Thind A, Monga I, Thakur P, Kumari P, Dindhoria K, Krzak M . Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief Bioinform. 2021; 22(6). DOI: 10.1093/bib/bbab259. View

11.

Wilkerson M, Hayes D . ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010; 26(12):1572-3. PMC: 2881355. DOI: 10.1093/bioinformatics/btq170. View

12.

Liebermeister W, Noor E, Flamholz A, Davidi D, Bernhardt J, Milo R . Visual account of protein investment in cellular functions. Proc Natl Acad Sci U S A. 2014; 111(23):8488-93. PMC: 4060655. DOI: 10.1073/pnas.1314810111. View

13.

Aibar S, Gonzalez-Blas C, Moerman T, Huynh-Thu V, Imrichova H, Hulselmans G . SCENIC: single-cell regulatory network inference and clustering. Nat Methods. 2017; 14(11):1083-1086. PMC: 5937676. DOI: 10.1038/nmeth.4463. View

14.

Nabavi S, Sureda A, Sanches-Silva A, Devi K, Ahmed T, Shahid M . Novel therapeutic strategies for stroke: The role of autophagy. Crit Rev Clin Lab Sci. 2019; 56(3):182-199. DOI: 10.1080/10408363.2019.1575333. View

15.

Malampati S, Song J, Tong B, Nalluri A, Yang C, Wang Z . Targeting Aggrephagy for the Treatment of Alzheimer's Disease. Cells. 2020; 9(2). PMC: 7072705. DOI: 10.3390/cells9020311. View

16.

Cui W, Sathyanarayan A, LoPresti M, Aghajan M, Chen C, Mashek D . Lipophagy-derived fatty acids undergo extracellular efflux via lysosomal exocytosis. Autophagy. 2020; 17(3):690-705. PMC: 8032247. DOI: 10.1080/15548627.2020.1728097. View

17.

Picca A, Faitg J, Auwerx J, Ferrucci L, DAmico D . Mitophagy in human health, ageing and disease. Nat Metab. 2023; 5(12):2047-2061. DOI: 10.1038/s42255-023-00930-8. View

18.

Germain K, Kim P . Pexophagy: A Model for Selective Autophagy. Int J Mol Sci. 2020; 21(2). PMC: 7013971. DOI: 10.3390/ijms21020578. View

19.

Cheng A, Tse K, Chow H, Gan Y, Song X, Ma F . ATM loss disrupts the autophagy-lysosomal pathway. Autophagy. 2020; 17(8):1998-2010. PMC: 8386711. DOI: 10.1080/15548627.2020.1805860. View

20.

Bingol B, Tea J, Phu L, Reichelt M, Bakalarski C, Song Q . The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy. Nature. 2014; 510(7505):370-5. DOI: 10.1038/nature13418. View