Identification of sepsis-associated mitochondrial genes through RNA and single-cell sequencing approaches.
Mitochondria-associated genes(MiAGs)
Prognosis
Sepsis
scRNA-seq
Journal
BMC medical genomics
ISSN: 1755-8794
Titre abrégé: BMC Med Genomics
Pays: England
ID NLM: 101319628
Informations de publication
Date de publication:
03 May 2024
03 May 2024
Historique:
received:
07
03
2024
accepted:
25
04
2024
medline:
4
5
2024
pubmed:
4
5
2024
entrez:
3
5
2024
Statut:
epublish
Résumé
Sepsis ranks among the most formidable clinical challenges, characterized by exorbitant treatment costs and substantial demands on healthcare resources. Mitochondrial dysfunction emerges as a pivotal risk factor in the pathogenesis of sepsis, underscoring the imperative to identify mitochondrial-related biomarkers. Such biomarkers are crucial for enhancing the accuracy of sepsis diagnostics and prognostication. In this study, adhering to the SEPSIS 3.0 criteria, we collected peripheral blood within 24 h of admission from 20 sepsis patients at the ICU of the Southwest Medical University Affiliated Hospital and 10 healthy volunteers as a control group for RNA-seq. The RNA-seq data were utilized to identify differentially expressed RNAs. Concurrently, mitochondrial-associated genes (MiAGs) were retrieved from the MitoCarta3.0 database. The differentially expressed genes were intersected with MiAGs. The intersected genes were then subjected to GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses and core genes were filtered using the PPI (Protein-Protein Interaction) network. Subsequently, relevant sepsis datasets (GSE65682, GSE28750, GSE54514, GSE67652, GSE69528, GSE95233) were downloaded from the GEO (Gene Expression Omnibus) database to perform bioinformatic validation of these core genes. Survival analysis was conducted to assess the prognostic value of the core genes, while ROC (Receiver Operating Characteristic) curves determined their diagnostic value, and a meta-analysis confirmed the accuracy of the RNA-seq data. Finally, we collected 5 blood samples (2 normal controls (NC); 2 sepsis; 1 SIRS (Systemic Inflammatory Response Syndrome), and used single-cell sequencing to assess the expression levels of the core genes in the different blood cell types. Integrating high-throughput sequencing with bioinformatics, this study identified two mitochondrial genes (COX7B, NDUFA4) closely linked with sepsis prognosis. Survival analysis demonstrated that patients with lower expression levels of COX7B and NDUFA4 exhibited a higher day survival rate over 28 days, inversely correlating with sepsis mortality. ROC curves highlighted the significant sensitivity and specificity of both genes, with AUC values of 0.985 for COX7B and 0.988 for NDUFA4, respectively. Meta-analysis indicated significant overexpression of COX7B and NDUFA4 in the sepsis group in contrast to the normal group (P < 0.01). Additionally, single-cell RNA sequencing revealed predominant expression of these core genes in monocytes-macrophages, T cells, and B cells. The mitochondrial-associated genes (MiAGs) COX7B and NDUFA4 are intimately linked with the prognosis of sepsis, offering potential guidance for research into the mechanisms underlying sepsis.
Sections du résumé
BACKGROUND
BACKGROUND
Sepsis ranks among the most formidable clinical challenges, characterized by exorbitant treatment costs and substantial demands on healthcare resources. Mitochondrial dysfunction emerges as a pivotal risk factor in the pathogenesis of sepsis, underscoring the imperative to identify mitochondrial-related biomarkers. Such biomarkers are crucial for enhancing the accuracy of sepsis diagnostics and prognostication.
METHODS
METHODS
In this study, adhering to the SEPSIS 3.0 criteria, we collected peripheral blood within 24 h of admission from 20 sepsis patients at the ICU of the Southwest Medical University Affiliated Hospital and 10 healthy volunteers as a control group for RNA-seq. The RNA-seq data were utilized to identify differentially expressed RNAs. Concurrently, mitochondrial-associated genes (MiAGs) were retrieved from the MitoCarta3.0 database. The differentially expressed genes were intersected with MiAGs. The intersected genes were then subjected to GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses and core genes were filtered using the PPI (Protein-Protein Interaction) network. Subsequently, relevant sepsis datasets (GSE65682, GSE28750, GSE54514, GSE67652, GSE69528, GSE95233) were downloaded from the GEO (Gene Expression Omnibus) database to perform bioinformatic validation of these core genes. Survival analysis was conducted to assess the prognostic value of the core genes, while ROC (Receiver Operating Characteristic) curves determined their diagnostic value, and a meta-analysis confirmed the accuracy of the RNA-seq data. Finally, we collected 5 blood samples (2 normal controls (NC); 2 sepsis; 1 SIRS (Systemic Inflammatory Response Syndrome), and used single-cell sequencing to assess the expression levels of the core genes in the different blood cell types.
RESULTS
RESULTS
Integrating high-throughput sequencing with bioinformatics, this study identified two mitochondrial genes (COX7B, NDUFA4) closely linked with sepsis prognosis. Survival analysis demonstrated that patients with lower expression levels of COX7B and NDUFA4 exhibited a higher day survival rate over 28 days, inversely correlating with sepsis mortality. ROC curves highlighted the significant sensitivity and specificity of both genes, with AUC values of 0.985 for COX7B and 0.988 for NDUFA4, respectively. Meta-analysis indicated significant overexpression of COX7B and NDUFA4 in the sepsis group in contrast to the normal group (P < 0.01). Additionally, single-cell RNA sequencing revealed predominant expression of these core genes in monocytes-macrophages, T cells, and B cells.
CONCLUSION
CONCLUSIONS
The mitochondrial-associated genes (MiAGs) COX7B and NDUFA4 are intimately linked with the prognosis of sepsis, offering potential guidance for research into the mechanisms underlying sepsis.
Identifiants
pubmed: 38702721
doi: 10.1186/s12920-024-01891-x
pii: 10.1186/s12920-024-01891-x
doi:
Substances chimiques
Biomarkers
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
120Subventions
Organisme : Sichuan Provincial Health and Health Committee Science and Technology Project
ID : 23LCYJ001
Organisme : Sichuan Provincial Health and Health Committee Science and Technology Project
ID : 23LCYJ001
Organisme : Sichuan Provincial Health and Health Committee Science and Technology Project
ID : 23LCYJ001
Informations de copyright
© 2024. The Author(s).
Références
Paterson CW, Ford ML, Coopersmith CM. Breaking the bond between tetranectin and HMGB1 in sepsis. Sci Transl Med 2020, 12(539).
Yan J, Mitra A, Hu J, Cutrera JJ, Xia X, Doetschman T, Gagea M, Mishra L, Li S. Interleukin-30 (IL27p28) alleviates experimental sepsis by modulating cytokine profile in NKT cells. J Hepatol. 2016;64(5):1128–36.
doi: 10.1016/j.jhep.2015.12.020
pubmed: 26767500
pmcid: 4834232
Garrabou G, Morén C, López S, Tobías E, Cardellach F, Miró O, Casademont J. The effects of sepsis on mitochondria. J Infect Dis. 2012;205(3):392–400.
doi: 10.1093/infdis/jir764
pubmed: 22180620
Yu L, Zhao Z, Yao G. [Research of progress of mitochondria in the pathogenesis of sepsis]. Zhonghua Wei Zhong Bing Ji jiu Yi Xue. 2023;35(6):669–72.
pubmed: 37366138
Nagar H, Piao S, Kim CS. Role of mitochondrial oxidative stress in Sepsis. Acute Crit care. 2018;33(2):65–72.
doi: 10.4266/acc.2018.00157
pubmed: 31723865
pmcid: 6849061
Montero-Jodra A, de la Fuente M, Gobelli D, Martín-Fernández M, Villar J, Tamayo E, Simarro M. The mitochondrial signature of cultured endothelial cells in sepsis: identifying potential targets for treatment. Biochim et Biophys acta Mol Basis Disease. 2024;1870(2):166946.
doi: 10.1016/j.bbadis.2023.166946
Alamili M, Bendtzen K, Lykkesfeldt J, Rosenberg J, Gögenur I. Melatonin suppresses markers of inflammation and oxidative damage in a human daytime endotoxemia model. J Crit Care. 2014;29(1):e184189–184113.
doi: 10.1016/j.jcrc.2013.09.006
Srivastava A, McGinniss J, Wong Y, Shinn AS, Lam TT, Lee PJ, Mannam P. MKK3 deletion improves mitochondrial quality. Free Radic Biol Med. 2015;87:373–84.
doi: 10.1016/j.freeradbiomed.2015.06.024
pubmed: 26119780
Skierka AS, Michels KB. Ethical principles and placebo-controlled trials - interpretation and implementation of the declaration of Helsinki’s placebo paragraph in medical research. BMC Med Ethics. 2018;19(1):24.
doi: 10.1186/s12910-018-0262-9
pubmed: 29544543
pmcid: 5856313
Chai V, Vassilakos A, Lee Y, Wright JA, Young AH. Optimization of the PAXgene blood RNA extraction system for gene expression analysis of clinical samples. J Clin Lab Anal. 2005;19(5):182–8.
doi: 10.1002/jcla.20075
pubmed: 16170815
pmcid: 6807908
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinf (Oxford England). 2008;24(5):713–4.
Ge SX, Son EW, Yao R. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics. 2018;19(1):534.
doi: 10.1186/s12859-018-2486-6
pubmed: 30567491
pmcid: 6299935
Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, Goodman RP, Grabarek Z, Haas ME, Hung WHW, et al. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res. 2021;49(D1):D1541–7.
doi: 10.1093/nar/gkaa1011
pubmed: 33174596
Qiao Y, Zhang B, Liu Y. Identification of potential diagnostic gene targets for Pediatric Sepsis based on Bioinformatics and Machine Learning. Front Pead. 2021;9:576585.
doi: 10.3389/fped.2021.576585
Shi C, Li Y, Wan E, Zhang E, Sun L. Construction of an lncRNA model for prognostic prediction of bladder cancer. BMC Med Genom. 2022;15(1):257.
doi: 10.1186/s12920-022-01414-6
Ma H, He Z, Chen J, Zhang X, Song P. Identifying of biomarkers associated with gastric cancer based on 11 topological analysis methods of CytoHubba. Sci Rep. 2021;11(1):1331.
doi: 10.1038/s41598-020-79235-9
pubmed: 33446695
pmcid: 7809423
Carnero-Alcázar M, Montero-Cruces L, Cobiella-Carnicer J, Pérez-Camargo D, Maroto Castellanos L. Advanced considerations in survival analysis. Eur J cardio-thoracic Surgery: Official J Eur Association Cardio-thoracic Surg 2024, 65(2).
Xu JH, Chang WH, Fu HW, Yuan T, Chen P. The mRNA, miRNA and lncRNA networks in hepatocellular carcinoma: an integrative transcriptomic analysis from Gene expression Omnibus. Mol Med Rep. 2018;17(5):6472–82.
pubmed: 29512731
pmcid: 5928629
Xiang L, Ren H, Wang Y, Zhang J, Qian J, Li B, An K, Fu L. Clinical value of pediatric sepsis-induced coagulopathy score in diagnosis of sepsis-induced coagulopathy and prognosis in children. J Thromb Haemostasis: JTH. 2021;19(12):2930–7.
doi: 10.1111/jth.15500
Zhang Q, Wang C, Li S, Li Y, Chen M, Hu Y. Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network. BMC Med Genom. 2023;16(1):37.
doi: 10.1186/s12920-023-01460-8
Tian Y, Wang C, Lu Q, Zhang C, Hu L, Ling J, Chen M, Hu Y. Screening of potential immune-related genes expressed during sepsis using gene sequencing technology. Sci Rep. 2023;13(1):4258.
doi: 10.1038/s41598-022-23062-7
pubmed: 36918563
pmcid: 10014830
Sweeney TE, Perumal TM, Henao R, Nichols M, Howrylak JA, Choi AM, Bermejo-Martin JF, Almansa R, Tamayo E, Davenport EE, et al. A community approach to mortality prediction in sepsis via gene expression analysis. Nat Commun. 2018;9(1):694.
doi: 10.1038/s41467-018-03078-2
pubmed: 29449546
pmcid: 5814463
Joshi MS, Julian MW, Huff JE, Bauer JA, Xia Y, Crouser ED. Calcineurin regulates myocardial function during acute endotoxemia. Am J Respir Crit Care Med. 2006;173(9):999–1007.
doi: 10.1164/rccm.200411-1507OC
pubmed: 16424445
pmcid: 2662919
Ballance WC, Qin EC, Chung HJ, Gillette MU, Kong H. Reactive oxygen species-responsive drug delivery systems for the treatment of neurodegenerative diseases. Biomaterials. 2019;217:119292.
doi: 10.1016/j.biomaterials.2019.119292
pubmed: 31279098
pmcid: 7081518
Arulkumaran N, Routledge M, Schlebusch S, Lipman J, Conway Morris A. Antimicrobial-associated harm in critical care: a narrative review. Intensive Care Med. 2020;46(2):225–35.
doi: 10.1007/s00134-020-05929-3
pubmed: 31996961
pmcid: 7046486
Pitceathly RDS, Taanman JW. NDUFA4 (renamed COXFA4) is a Cytochrome-c oxidase subunit. Trends Endocrinol Metab. 2018;29(7):452–4.
doi: 10.1016/j.tem.2018.03.009
pubmed: 29636225
Song Y, Gao N, Yang Z, Zhang S, Fan T, Zhang B. COX7B Is a New Prognostic Biomarker and Correlates with Tumor Immunity in Esophageal Carcinoma. Mediators of inflammation 2023, 2023:6831695.
Blackman M, Capeloa T, Rondeau JD, Zampieri LX, Benyahia Z, Van de Velde JA, Fransolet M, Daskalopoulos EP, Michiels C, Beauloye C et al. Mitochondrial Protein Cox7b Is a Metabolic Sensor Driving Brain-Specific Metastasis of Human Breast Cancer Cells. Cancers 2022, 14(18).
Lee I, Hüttemann M. Energy crisis: the role of oxidative phosphorylation in acute inflammation and sepsis. Biochim Biophys Acta. 2014;1842(9):1579–86.
doi: 10.1016/j.bbadis.2014.05.031
pubmed: 24905734
pmcid: 4147665
Shu Q, Du Y, She H, Mo J, Zhu Z, Zhong L, He F, Fan J, Zhu J. Construction and validation of a mitochondria-associated genes prognostic signature and immune microenvironment characteristic of sepsis. Int Immunopharmacol. 2024;126:111275.
doi: 10.1016/j.intimp.2023.111275
pubmed: 37995567
Wang Z, Tao E, Chen Y, Wang Q, Liu M, Wei L, Xu S, Chen W, Zhong C. NDUFA4 promotes the progression of head and neck paraganglioma by inhibiting ferroptosis. Biochem cell Biology = Biochimie et Biol cellulaire. 2023;101(6):523–30.
doi: 10.1139/bcb-2023-0018
Wu H, Chen H, Wang J, Yin S, Huang J, Wang Z, Zhang X, Wang M. Identification of key genes associated with sepsis patients infected by staphylococcus aureus through weighted gene co-expression network analysis. Am J Translational Res. 2021;13(12):13579–89.
Chen D, Hou Y, Cai X. MiR-210-3p enhances Cardiomyocyte apoptosis and mitochondrial dysfunction by targeting the NDUFA4 gene in Sepsis-Induced Myocardial Dysfunction. Int Heart J. 2021;62(3):636–46.
doi: 10.1536/ihj.20-512
pubmed: 33994501