Integrative Analyses of Mitophagy-Related Genes and Mechanisms Associated with Type 2 Diabetes in Muscle Tissue

Overview

Journal Curr Issues Mol Biol

Publisher MDPI

Specialty Molecular Biology

Date 2024 Sep 27

PMID 39329971

Authors

Wangjia Mao

Guannan Zong

Yuan Gao

Shen Qu

Xiaoyun Cheng

Affiliations

Soon will be listed here.

Abstract

Type 2 diabetes (T2D) represents the most prevalent metabolic condition that is primarily distinguished by a range of metabolic imbalances, including hyperglycemia, hyperlipidemia, and insulin resistance (IR). Currently, mitophagy has become increasingly recognized as an important process involved in the pathogenesis and progression of T2D. Therefore, it is very important to explore the role of mitochondrial damage and autophagy-related genes in T2D. This study investigated the role of mitophagy in the development of T2D, and 12 MRHGs associated with T2D were identified using bioinformatic analysis and machine learning methods. Our findings provide the first insight into mitophagy-related genes and their mechanisms in T2D. This study aimed to investigate possible molecular targets for therapy and the underlying mechanisms involved in T2D. This information might be useful to further elucidate the pathogenesis of T2D-related diseases and identify more optimal therapeutic approaches.

References

Karam B, Chavez-Moreno A, Koh W, Akar J, Akar F . Oxidative stress and inflammation as central mediators of atrial fibrillation in obesity and diabetes. Cardiovasc Diabetol. 2017; 16(1):120. PMC: 5622555. DOI: 10.1186/s12933-017-0604-9. View

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

Debril M, Renaud J, Fajas L, Auwerx J . The pleiotropic functions of peroxisome proliferator-activated receptor gamma. J Mol Med (Berl). 2001; 79(1):30-47. DOI: 10.1007/s001090000145. View

Kintscher U, Law R . PPARgamma-mediated insulin sensitization: the importance of fat versus muscle. Am J Physiol Endocrinol Metab. 2005; 288(2):E287-91. DOI: 10.1152/ajpendo.00440.2004. View

Zhang H, Meltzer P, Davis S . RCircos: an R package for Circos 2D track plots. BMC Bioinformatics. 2013; 14:244. PMC: 3765848. DOI: 10.1186/1471-2105-14-244. View

Yu G, Wang L, Han Y, He Q . clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16(5):284-7. PMC: 3339379. DOI: 10.1089/omi.2011.0118. View

Newman A, Liu C, Green M, Gentles A, Feng W, Xu Y . Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015; 12(5):453-7. PMC: 4739640. DOI: 10.1038/nmeth.3337. View

Cheignon C, Tomas M, Bonnefont-Rousselot D, Faller P, Hureau C, Collin F . Oxidative stress and the amyloid beta peptide in Alzheimer's disease. Redox Biol. 2017; 14:450-464. PMC: 5680523. DOI: 10.1016/j.redox.2017.10.014. View

Bai B, Wu F, Ying K, Xu Y, Shan L, Lv Y . Therapeutic effects of dihydroartemisinin in multiple stages of colitis-associated colorectal cancer. Theranostics. 2021; 11(13):6225-6239. PMC: 8120200. DOI: 10.7150/thno.55939. View

10.

Van Calster B, Wynants L, Verbeek J, Verbakel J, Christodoulou E, Vickers A . Reporting and Interpreting Decision Curve Analysis: A Guide for Investigators. Eur Urol. 2018; 74(6):796-804. PMC: 6261531. DOI: 10.1016/j.eururo.2018.08.038. View

11.

Hanzelmann S, Castelo R, Guinney J . GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013; 14:7. PMC: 3618321. DOI: 10.1186/1471-2105-14-7. View

12.

Davegardh C, Sall J, Benrick A, Broholm C, Volkov P, Perfilyev A . VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics. Nat Commun. 2021; 12(1):2431. PMC: 8065135. DOI: 10.1038/s41467-021-22068-5. View

13.

Kanehisa M, Goto S . KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999; 28(1):27-30. PMC: 102409. DOI: 10.1093/nar/28.1.27. View

14.

Leek J, Johnson W, Parker H, Jaffe A, Storey J . The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012; 28(6):882-3. PMC: 3307112. DOI: 10.1093/bioinformatics/bts034. View

15.

Yeo H, Shin M, Yoo K, Jung B, Eum W, Choi S . Tat-CIAPIN1 Prevents Pancreatic β-Cell Death in hIAPP-Induced RINm5F Cells and T2DM Animal Model. Int J Mol Sci. 2023; 24(13). PMC: 10342139. DOI: 10.3390/ijms241310478. View

16.

Sheng N, Zhang Z, Zheng H, Ma C, Li M, Wang Z . Scutellarin Rescued Mitochondrial Damage through Ameliorating Mitochondrial Glucose Oxidation via the Pdk-Pdc Axis. Adv Sci (Weinh). 2023; 10(32):e2303584. PMC: 10646256. DOI: 10.1002/advs.202303584. View

17.

Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S . The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses. Curr Protoc Bioinformatics. 2016; 54:1.30.1-1.30.33. DOI: 10.1002/cpbi.5. View

18.

Grey A . Skeletal consequences of thiazolidinedione therapy. Osteoporos Int. 2007; 19(2):129-37. DOI: 10.1007/s00198-007-0477-y. View

19.

Wu X, Yu T, Ji N, Huang Y, Gao L, Shi W . IL6R inhibits viability and apoptosis of pancreatic beta-cells in type 2 diabetes mellitus via regulation by miR-22 of the JAK/STAT signaling pathway. Diabetes Metab Syndr Obes. 2019; 12:1645-1657. PMC: 6718245. DOI: 10.2147/DMSO.S211700. View

20.

Gerber P, Rutter G . The Role of Oxidative Stress and Hypoxia in Pancreatic Beta-Cell Dysfunction in Diabetes Mellitus. Antioxid Redox Signal. 2016; 26(10):501-518. PMC: 5372767. DOI: 10.1089/ars.2016.6755. View