Generic placeholder image

Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Research Article

Identification of Mitophagy-Related Genes in Sepsis

Author(s): Xiao-Yan Zeng, Min Zhang, Si-Jing Liao, Yong Wang, Ying-Bo Ren, Run Li, Tian-Mei Li, An-Qiong Mao*, Guang-Zhen Li* and Ying Zhang*

Volume 19, Issue 8, 2024

Published on: 03 January, 2024

Page: [704 - 713] Pages: 10

DOI: 10.2174/0115748936266722231116050255

Price: $65

Abstract

Background: Numerous studies have shown that mitochondrial damage induces inflammation and activates inflammatory cells, leading to sepsis, while sepsis, a systemic inflammatory response syndrome, also exacerbates mitochondrial damage and hyperactivation. Mitochondrial autophagy eliminates aged, abnormal or damaged mitochondria to reduce intracellular mitochondrial stress and the release of mitochondria-associated molecules, thereby reducing the inflammatory response and cellular damage caused by sepsis. In addition, mitochondrial autophagy may also influence the onset and progression of sepsis, but the exact mechanisms are unclear.

Methods: In this study, we mined the available publicly available microarray data in the GEO database (Home - GEO - NCBI (nih.gov)) with the aim of identifying key genes associated with mitochondrial autophagy in sepsis.

Results: We identified four mitophagy-related genes in sepsis, TOMM20, TOMM22, TOMM40, and MFN1.

Conclusion: This study provides preliminary evidence for the treatment of sepsis and may provide a solid foundation for subsequent biological studies.

[1]
Evans L, Rhodes A, Alhazzani W, et al. Surviving sepsis campaign: International guidelines for management of sepsis and septic shock 2021. Intensive Care Med 2021; 47(11): 1181-247.
[http://dx.doi.org/10.1007/s00134-021-06506-y] [PMID: 34599691]
[2]
Heming N, Lamothe L, Ambrosi X, Annane D. Emerging drugs for the treatment of sepsis. Expert Opin Emerg Drugs 2016; 21(1): 27-37.
[http://dx.doi.org/10.1517/14728214.2016.1132700] [PMID: 26751198]
[3]
Rello J, Valenzuela-Sánchez F, Ruiz-Rodriguez M, Moyano S. Sepsis: A review of advances in management. Adv Ther 2017; 34(11): 2393-411.
[http://dx.doi.org/10.1007/s12325-017-0622-8] [PMID: 29022217]
[4]
Kellum JA, Formeck CL, Kernan KF, Gómez H, Carcillo JA. Subtypes and mimics of sepsis. Crit Care Clin 2022; 38(2): 195-211.
[http://dx.doi.org/10.1016/j.ccc.2021.11.013] [PMID: 35369943]
[5]
Evans T. Diagnosis and management of sepsis. Clin Med 2018; 18(2): 146-9.
[http://dx.doi.org/10.7861/clinmedicine.18-2-146] [PMID: 29626019]
[6]
Fleischmann-Struzek C, Mellhammar L, Rose N, et al. Incidence and mortality of hospital- and ICU-treated sepsis: results from an updated and expanded systematic review and meta-analysis. Intensive Care Med 2020; 46(8): 1552-62.
[http://dx.doi.org/10.1007/s00134-020-06151-x] [PMID: 32572531]
[7]
Bravo-San Pedro JM, Kroemer G, Galluzzi L. Autophagy and mitophagy in cardiovascular disease. Circ Res 2017; 120(11): 1812-24.
[http://dx.doi.org/10.1161/CIRCRESAHA.117.311082] [PMID: 28546358]
[8]
Kerr JS, Adriaanse BA, Greig NH, et al. Mitophagy and Alzheimer’s Disease: Cellular and molecular mechanisms. Trends Neurosci 2017; 40(3): 151-66.
[http://dx.doi.org/10.1016/j.tins.2017.01.002] [PMID: 28190529]
[9]
Kuma A, Komatsu M, Mizushima N. Autophagy-monitoring and autophagy-deficient mice. Autophagy 2017; 13(10): 1619-28.
[http://dx.doi.org/10.1080/15548627.2017.1343770] [PMID: 28820286]
[10]
Senft D, Ronai ZA. UPR, autophagy, and mitochondria crosstalk underlies the ER stress response. Trends Biochem Sci 2015; 40(3): 141-8.
[http://dx.doi.org/10.1016/j.tibs.2015.01.002] [PMID: 25656104]
[11]
Onishi M, Yamano K, Sato M, Matsuda N, Okamoto K. Molecular mechanisms and physiological functions of mitophagy. EMBO J 2021; 40(3): e104705.
[http://dx.doi.org/10.15252/embj.2020104705] [PMID: 33438778]
[12]
Pickles S, Vigié P, Youle RJ. Mitophagy and quality control mechanisms in mitochondrial maintenance. Curr Biol 2018; 28(4): R170-85.
[http://dx.doi.org/10.1016/j.cub.2018.01.004] [PMID: 29462587]
[13]
Zhang T, Liu Q, Gao W, Sehgal SA, Wu H. The multifaceted regulation of mitophagy by endogenous metabolites. Autophagy 2022; 18(6): 1216-39.
[http://dx.doi.org/10.1080/15548627.2021.1975914] [PMID: 34583624]
[14]
Mohsin M, Tabassum G, Ahmad S, Ali S, Ali Syed M. The role of mitophagy in pulmonary sepsis. Mitochondrion 2021; 59: 63-75.
[http://dx.doi.org/10.1016/j.mito.2021.04.009] [PMID: 33894359]
[15]
Chen H, Lin H, Dong B, Wang Y, Yu Y, Xie K. Hydrogen alleviates cell damage and acute lung injury in sepsis via PINK1/Parkin-mediated mitophagy. Inflamm Res 2021; 70(8): 915-30.
[http://dx.doi.org/10.1007/s00011-021-01481-y] [PMID: 34244821]
[16]
Kim MJ, Bae SH, Ryu JC, et al. SESN2/sestrin2 suppresses sepsis by inducing mitophagy and inhibiting NLRP3 activation in macrophages. Autophagy 2016; 12(8): 1272-91.
[http://dx.doi.org/10.1080/15548627.2016.1183081] [PMID: 27337507]
[17]
Biasizzo M, Kopitar-Jerala N. Interplay between NLRP3 inflammasome and autophagy. Front Immunol 2020; 11: 591803.
[http://dx.doi.org/10.3389/fimmu.2020.591803] [PMID: 33163006]
[18]
Zhu C, Yao R, Li L, et al. Mechanism of mitophagy and its role in sepsis induced organ dysfunction: A review. Front Cell Dev Biol 2021; 9: 664896.
[http://dx.doi.org/10.3389/fcell.2021.664896] [PMID: 34164394]
[19]
Kimura T, Isaka Y, Yoshimori T. Autophagy and kidney inflammation. Autophagy 2017; 13(6): 997-1003.
[http://dx.doi.org/10.1080/15548627.2017.1309485] [PMID: 28441075]
[20]
Yang H, Zhang Z. Sepsis-induced myocardial dysfunction: The role of mitochondrial dysfunction. Inflamm Res 2021; 70(4): 379-87.
[http://dx.doi.org/10.1007/s00011-021-01447-0] [PMID: 33683374]
[21]
Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: Archive for functional genomics data sets--update. Nucleic Acids Res 2013; 41(Database issue): D991-5.
[PMID: 23193258]
[22]
Kolde R, Laur S, Adler P, Vilo J. Robust rank aggregation for gene list integration and meta-analysis. Bioinformatics 2012; 28(4): 573-80.
[http://dx.doi.org/10.1093/bioinformatics/btr709] [PMID: 22247279]
[23]
Szklarczyk D, Gable AL, Nastou KC, et al. The STRING database in 2021: Customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res 2021; 49(D1): D605-12.
[http://dx.doi.org/10.1093/nar/gkaa1074] [PMID: 33237311]
[24]
Liu AC, Patel K, Vunikili RD, et al. Sepsis in the era of data-driven medicine: Personalizing risks, diagnoses, treatments and prognoses. Brief Bioinform 2020; 21(4): 1182-95.
[http://dx.doi.org/10.1093/bib/bbz059] [PMID: 31190075]
[25]
O’Brien JM Jr, Ali NA, Aberegg SK, Abraham E. Sepsis. Am J Med 2007; 120(12): 1012-22.
[http://dx.doi.org/10.1016/j.amjmed.2007.01.035] [PMID: 18060918]
[26]
Gullo A, Iscra F, Di Capua G, et al. Sepsis and organ dysfunction: An ongoing challenge. Minerva Anestesiol 2005; 71(11): 671-99. [J].
[PMID: 16278628]
[27]
Chen P, Stanojcic M, Jeschke MG. Differences between murine and human sepsis. Surg Clin North Am 2014; 94(6): 1135-49.
[http://dx.doi.org/10.1016/j.suc.2014.08.001] [PMID: 25440115]
[28]
Sessler CN, Shepherd W. New concepts in sepsis. Curr Opin Crit Care 2002; 8(5): 465-72.
[http://dx.doi.org/10.1097/00075198-200210000-00016] [PMID: 12357117]
[29]
Ingels C, Gunst J, Van den Berghe G. Endocrine and metabolic alterations in sepsis and implications for treatment. Crit Care Clin 2018; 34(1): 81-96.
[http://dx.doi.org/10.1016/j.ccc.2017.08.006] [PMID: 29149943]
[30]
Patoli D, Mignotte F, Deckert V, et al. Inhibition of mitophagy drives macrophage activation and antibacterial defense during sepsis. J Clin Invest 2020; 130(11): 5858-74.
[http://dx.doi.org/10.1172/JCI130996] [PMID: 32759503]
[31]
Liu Q, Wu J, Zhang X, et al. Circulating mitochondrial DNA-triggered autophagy dysfunction via STING underlies sepsis-related acute lung injury. Cell Death Dis 2021; 12(7): 673.
[http://dx.doi.org/10.1038/s41419-021-03961-9] [PMID: 34218252]
[32]
Sun Y, Cai Y, Zang QS. Cardiac autophagy in sepsis. Cells 2019; 8(2): 141.
[http://dx.doi.org/10.3390/cells8020141] [PMID: 30744190]
[33]
Sun J, Zhang J, Tian J, et al. Mitochondria in sepsis-induced AKI. J Am Soc Nephrol 2019; 30(7): 1151-61.
[http://dx.doi.org/10.1681/ASN.2018111126] [PMID: 31076465]
[34]
Wang Y, Zhu J, Liu Z, et al. The PINK1/PARK2/optineurin pathway of mitophagy is activated for protection in septic acute kidney injury. Redox Biol 2021; 38: 101767.
[http://dx.doi.org/10.1016/j.redox.2020.101767] [PMID: 33137712]
[35]
Wang Y, Jasper H, Toan S, Muid D, Chang X, Zhou H. Mitophagy coordinates the mitochondrial unfolded protein response to attenuate inflammation-mediated myocardial injury. Redox Biol 2021; 45: 102049.
[http://dx.doi.org/10.1016/j.redox.2021.102049] [PMID: 34174558]
[36]
Hampton HR, Chtanova T. Lymphatic migration of immune cells. Front Immunol 2019; 10: 1168.
[http://dx.doi.org/10.3389/fimmu.2019.01168] [PMID: 31191539]
[37]
König T, Nolte H, Aaltonen MJ, et al. MIROs and DRP1 drive mitochondrial-derived vesicle biogenesis and promote quality control. Nat Cell Biol 2021; 23(12): 1271-86.
[http://dx.doi.org/10.1038/s41556-021-00798-4] [PMID: 34873283]
[38]
Park SH, Lee AR, Choi K, Joung S, Yoon JB, Kim S. TOMM20 as a potential therapeutic target of colorectal cancer. BMB Rep 2019; 52(12): 712-7.
[http://dx.doi.org/10.5483/BMBRep.2019.52.12.249] [PMID: 31818360]
[39]
Fu ZJ, Wang ZY, Xu L, et al. HIF-1α-BNIP3-mediated mitophagy in tubular cells protects against renal ischemia/reperfusion injury. Redox Biol 2020; 36: 101671.
[http://dx.doi.org/10.1016/j.redox.2020.101671] [PMID: 32829253]
[40]
Choong CJ, Okuno T, Ikenaka K, et al. Alternative mitochondrial quality control mediated by extracellular release. Autophagy 2021; 17(10): 2962-74.
[http://dx.doi.org/10.1080/15548627.2020.1848130] [PMID: 33218272]
[41]
Zhou B, Zhang J, Liu X, et al. Tom20 senses iron-activated ROS signaling to promote melanoma cell pyroptosis. Cell Res 2018; 28(12): 1171-85.
[http://dx.doi.org/10.1038/s41422-018-0090-y] [PMID: 30287942]
[42]
Beyer AM, Norwood Toro LE, Hughes WE, et al. Autophagy, TERT, and mitochondrial dysfunction in hyperoxia. Am J Physiol Heart Circ Physiol 2021; 321(5): H985-H1003.
[http://dx.doi.org/10.1152/ajpheart.00166.2021] [PMID: 34559580]
[43]
Curado S, Ober EA, Walsh S, et al. The mitochondrial import gene tomm22 is specifically required for hepatocyte survival and provides a liver regeneration model. Dis Model Mech 2010; 3(7-8): 486-95.
[http://dx.doi.org/10.1242/dmm.004390] [PMID: 20483998]
[44]
Kravic B, Harbauer AB, Romanello V, et al. In mammalian skeletal muscle, phosphorylation of TOMM22 by protein kinase CSNK2/CK2 controls mitophagy. Autophagy 2018; 14(2): 311-35.
[http://dx.doi.org/10.1080/15548627.2017.1403716] [PMID: 29165030]
[45]
Dou Y, Tan Y. Presequence protease reverses mitochondria‐specific amyloid‐β‐induced mitophagy to protect mitochondria. FASEB J 2023; 37(5): e22890.
[http://dx.doi.org/10.1096/fj.202200216RRRR] [PMID: 37002885]
[46]
Bertolin G, Ferrando-Miguel R, Jacoupy M, et al. The TOMM machinery is a molecular switch in PINK1 and PARK2/PARKIN-dependent mitochondrial clearance. Autophagy 2013; 9(11): 1801-17.
[http://dx.doi.org/10.4161/auto.25884] [PMID: 24149440]
[47]
Chiba-Falek O, Gottschalk WK, Lutz MW. The effects of the TOMM40 poly‐T alleles on Alzheimer’s disease phenotypes. Alzheimers Dement 2018; 14(5): 692-8.
[http://dx.doi.org/10.1016/j.jalz.2018.01.015] [PMID: 29524426]
[48]
Li T, Pappas C, Le ST, et al. APOE, TOMM40, and sex interactions on neural network connectivity. Neurobiol Aging 2022; 109: 158-65.
[http://dx.doi.org/10.1016/j.neurobiolaging.2021.09.020] [PMID: 34740077]
[49]
Chen S, Sarasua SM, Davis NJ, et al. TOMM40 genetic variants associated with healthy aging and longevity: A systematic review. BMC Geriatr 2022; 22(1): 667.
[http://dx.doi.org/10.1186/s12877-022-03337-4] [PMID: 35964003]
[50]
Lee EG, Chen S, Leong L, Tulloch J, Yu CE. TOMM40 RNA transcription in Alzheimer’s Disease brain and its implication in mitochondrial dysfunction. Genes 2021; 12(6): 871.
[http://dx.doi.org/10.3390/genes12060871] [PMID: 34204109]
[51]
Li C, Liu J, Hou W, Kang R, Tang D. STING1 promotes ferroptosis through mfn1/2-dependent mitochondrial fusion. Front Cell Dev Biol 2021; 9: 698679.
[http://dx.doi.org/10.3389/fcell.2021.698679] [PMID: 34195205]
[52]
Li S, Han S, Zhang Q, et al. FUNDC2 promotes liver tumorigenesis by inhibiting MFN1-mediated mitochondrial fusion. Nat Commun 2022; 13(1): 3486.
[http://dx.doi.org/10.1038/s41467-022-31187-6] [PMID: 35710796]
[53]
Sun K, Jing X, Guo J, Yao X, Guo F. Mitophagy in degenerative joint diseases. Autophagy 2021; 17(9): 2082-92.
[http://dx.doi.org/10.1080/15548627.2020.1822097] [PMID: 32967533]
[54]
Hu S, Kuwabara R, de Haan BJ, Smink AM, de Vos P. Acetate and butyrate improve β-cell metabolism and mitochondrial respiration under oxidative stress. Int J Mol Sci 2020; 21(4): 1542.
[http://dx.doi.org/10.3390/ijms21041542] [PMID: 32102422]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy