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Yang K, Gao L, Hao H, Yu L. Identification of a novel gene signature for the prognosis of sepsis. Comput Biol Med 2023; 159:106958. [PMID: 37087781 DOI: 10.1016/j.compbiomed.2023.106958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/03/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023]
Abstract
Sepsis is a life-threatening organ dysfunction caused by the host's dysfunctional response to infection, and its pathogenesis is still unclear. In view of the complex pathological process of sepsis, finding suitable biomarkers is helpful for the research and treatment of sepsis. This study determined the potential prognostic markers of sepsis by analyzing the molecular characteristics of patients with sepsis. During this study, bioinformatics analysis was conducted on the RNA sequencing data and DNA methylation sites from the public database to determine the prognostic genes related to sepsis, and a 9-gene prognostic signature for sepsis was constructed. According to the risk score, all sepsis samples were divided into two groups. Then, the prediction effect of the 9-gene signature was verified in two cohorts, and the association between these genes and sepsis was further revealed through immune infiltration analysis, gene set enrichment analysis and the relationship between clinical phenotype and survival rate. Our study provided a reliable prognostic signature for sepsis. The signature could predict the survival of patients with sepsis and serve as a predictor.
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Affiliation(s)
- Kai Yang
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
| | - HongXia Hao
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China.
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China.
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Sharif FA, Abuwarda HN. Autoimmunity and re-expression of cancer/testis antigens: Numerous disorders one mechanism hypothesis. Med Hypotheses 2023. [DOI: 10.1016/j.mehy.2023.111019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Li YP, Liu CR, Deng HL, Wang MQ, Tian Y, Chen Y, Zhang YF, Dang SS, Zhai S. DNA methylation and single-nucleotide polymorphisms in DDX58 are associated with hand, foot and mouth disease caused by enterovirus 71. PLoS Negl Trop Dis 2022; 16:e0010090. [PMID: 35041675 PMCID: PMC8765647 DOI: 10.1371/journal.pntd.0010090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/14/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND This research aimed to explore the association between the RIG-I-like receptor (RIG-I and MDA5 encoded by DDX58 and IFIH1, respectively) pathways and the risk or severity of hand, foot, and mouth disease caused by enterovirus 71 (EV71-HFMD). In this context, we explored the influence of gene methylation and polymorphism on EV71-HFMD. METHODOLOGY/PRINCIPAL FINDINGS 60 healthy controls and 120 EV71-HFMD patients, including 60 mild EV71-HFMD and 60 severe EV71-HFMD patients, were enrolled. First, MiSeq was performed to explore the methylation of CpG islands in the DDX58 and IFIH1 promoter regions. Then, DDX58 and IFIH1 expression were detected in PBMCs using RT-qPCR. Finally, imLDR was used to detect DDX58 and IFIH1 single-nucleotide polymorphism (SNP) genotypes. Severe EV71-HFMD patients exhibited higher DDX58 promoter methylation levels than healthy controls and mild EV71-HFMD patients. DDX58 promoter methylation was significantly associated with severe HFMD, sex, vomiting, high fever, neutrophil abundance, and lymphocyte abundance. DDX58 expression levels were significantly lower in mild patients than in healthy controls and lower in severe patients than in mild patients. Binary logistic regression analysis revealed statistically significant differences in the genotype frequencies of DDX58 rs3739674 between the mild and severe groups. GeneMANIA revealed that 19 proteins displayed correlations with DDX58, including DHX58, HERC5, MAVS, RAI14, WRNIP1 and ISG15, and 19 proteins displayed correlations with IFIH1, including TKFC, IDE, MAVS, DHX58, NLRC5, TSPAN6, USP3 and DDX58. CONCLUSIONS/SIGNIFICANCE DDX58 expression and promoter methylation were associated with EV71 infection progression, especially in severe EV71-HFMD patients. The effect of DDX58 in EV71-HFMD is worth further attention.
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MESH Headings
- Child
- Child, Preschool
- CpG Islands/genetics
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/metabolism
- DNA Methylation/genetics
- Enterovirus A, Human
- Female
- Genetic Predisposition to Disease/genetics
- Hand, Foot and Mouth Disease/pathology
- Hand, Foot and Mouth Disease/virology
- Humans
- Infant
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/metabolism
- Male
- Polymorphism, Single Nucleotide/genetics
- Promoter Regions, Genetic/genetics
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Severity of Illness Index
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Affiliation(s)
- Ya-Ping Li
- Department of Infectious Diseases, Xi’an Jiaotong University Second Affiliated Hospital, Xi’an, China
| | - Chen-Rui Liu
- Department of Infectious Diseases, Xi’an Jiaotong University Second Affiliated Hospital, Xi’an, China
| | - Hui-Ling Deng
- Department of Infectious Diseases, Xi’an Children’s Hospital, Xi’an, China
- Department of Pediatric, Xi’an Central Hospital, Xi’an, China
| | - Mu-Qi Wang
- Department of Infectious Diseases, Xi’an Jiaotong University Second Affiliated Hospital, Xi’an, China
| | - Yan Tian
- Department of Infectious Diseases, Xi’an Jiaotong University Second Affiliated Hospital, Xi’an, China
| | - Yuan Chen
- Department of Infectious Diseases, Xi’an Children’s Hospital, Xi’an, China
| | - Yu-Feng Zhang
- Department of Infectious Diseases, Xi’an Children’s Hospital, Xi’an, China
| | - Shuang-Suo Dang
- Department of Infectious Diseases, Xi’an Jiaotong University Second Affiliated Hospital, Xi’an, China
| | - Song Zhai
- Department of Infectious Diseases, Xi’an Jiaotong University Second Affiliated Hospital, Xi’an, China
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Li M, Li YP, Deng HL, Wang MQ, Chen Y, Zhang YF, Wang J, Dang SS. DNA methylation and SNP in IFITM3 are correlated with hand, foot and mouth disease caused by enterovirus 71. Int J Infect Dis 2021; 105:199-208. [PMID: 33596480 DOI: 10.1016/j.ijid.2021.02.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES To explore the mechanisms of interferon-induced transmembrane protein 3 (IFITM3) in response to enterovirus-71-associated hand, foot and mouth disease (EV71-HFMD), in terms of DNA methylation, single-nucleotide polymorphism (SNP) genotype and gene expression. METHODS In total, 120 patients with EV71-HFMD (60 with mild EV71-HFMD and 60 with severe EV71-HFMD) and 60 healthy controls were enrolled in this study. SNP genotype, IFITM3 promoter methylation and mRNA expression of peripheral blood mononuclear cells were examined using the improved multi-temperature ligase detection reaction, quantitative reverse transcriptase polymerase chain reaction and MiSeq, respectively. RESULTS The distribution of methylation in patients with EV71-HFMD was significantly lower compared with healthy controls, and the severe EV71-HFMD group showed the lowest frequency of IFITM3 promoter methylation. The average level of IFITM3 promoter CpG methylation was negatively correlated with IFITM3 mRNA expression, and hypermethylation of several specific CpG units contributed to IFITM3 downregulation. IFITM3 expression and promoter methylation correlated with EV71 infection progression, especially in the severe EV71-HFMD group. Compared with mild cases, genotype GG and the G allele of rs12252 were over-represented in patients with severe EV71-HFMD. CONCLUSIONS IFITM3 methylation status and SNP genotyping may help clinicians to choose the correct treatment strategy for patients with EV71-HFMD.
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Affiliation(s)
- Mei Li
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Ya-Ping Li
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China.
| | - Hui-Ling Deng
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China; Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China; Department of Paediatrics, Xi'an Central Hospital, Xi'an, China
| | - Mu-Qi Wang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Yuan Chen
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Yu-Feng Zhang
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Jun Wang
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Shuang-Suo Dang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
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Li YP, Deng HL, Wang WJ, Wang MQ, Li M, Zhang YF, Wang J, Dang SS. Vitamin D receptor gene methylation in patients with hand, foot, and mouth disease caused by enterovirus 71. Arch Virol 2020; 165:1979-1985. [PMID: 32556549 DOI: 10.1007/s00705-020-04701-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/07/2023]
Abstract
To evaluate the epigenetic regulation of the VDR gene in enterovirus 71 (EV71)-associated severe hand, foot, and mouth disease (HFMD), a total of 116 patients with EV71-HFMD, including 58 with mild EV71-HFMD and 58 with severe EV71-HFMD, as well as 60 healthy controls, were enrolled in this study. Quantitative real-time PCR was used to measure the relative levels of VDR mRNA expression, and the methylation status of the VDR promoter was assessed using a MethylTarget™ assay. The DNA methylation levels of the VDR promoter in children with EV71-associated severe HFMD were lower than those in the healthy controls and in children with mild HFMD (P < 0.05). Hypomethylation at CpG site 133 and hypermethylation at the CpG 42 sites and 68 downregulated VDR expression. Moreover, the methylation level of VDR could be used for differential diagnosis of mild and severe EV71-associated HFMD (AUC56, 0.73; AUC68, 0.699; AUC42, 0.694; AUC66, 0.693). VDR expression and promoter methylation were associated with the progression of EV71 infection. Determining the VDR promoter status might help clinicians initiate the appropriate strategy for treatment of EV71-associated HFMD.
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Affiliation(s)
- Ya-Ping Li
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Hui-Ling Deng
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China.,Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, 710003, China
| | - Wen-Jun Wang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Mu-Qi Wang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Mei Li
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Yu-Feng Zhang
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, 710003, China
| | - Jun Wang
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, 710003, China
| | - Shuang-Suo Dang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China.
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