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Wang Z, Hu D, Pei G, Zeng R, Yao Y. Identification of driver genes in lupus nephritis based on comprehensive bioinformatics and machine learning. Front Immunol 2023; 14:1288699. [PMID: 38130724 PMCID: PMC10733527 DOI: 10.3389/fimmu.2023.1288699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
Background Lupus nephritis (LN) is a common and severe glomerulonephritis that often occurs as an organ manifestation of systemic lupus erythematosus (SLE). However, the complex pathological mechanisms associated with LN have hindered the progress of targeted therapies. Methods We analyzed glomerular tissues from 133 patients with LN and 51 normal controls using data obtained from the GEO database. Differentially expressed genes (DEGs) were identified and subjected to enrichment analysis. Weighted gene co-expression network analysis (WGCNA) was utilized to identify key gene modules. The least absolute shrinkage and selection operator (LASSO) and random forest were used to identify hub genes. We also analyzed immune cell infiltration using CIBERSORT. Additionally, we investigated the relationships between hub genes and clinicopathological features, as well as examined the distribution and expression of hub genes in the kidney. Results A total of 270 DEGs were identified in LN. Using weighted gene co-expression network analysis (WGCNA), we clustered these DEGs into 14 modules. Among them, the turquoise module displayed a significant correlation with LN (cor=0.88, p<0.0001). Machine learning techniques identified four hub genes, namely CD53 (AUC=0.995), TGFBI (AUC=0.997), MS4A6A (AUC=0.994), and HERC6 (AUC=0.999), which are involved in inflammation response and immune activation. CIBERSORT analysis suggested that these hub genes may contribute to immune cell infiltration. Furthermore, these hub genes exhibited strong correlations with the classification, renal function, and proteinuria of LN. Interestingly, the highest hub gene expression score was observed in macrophages. Conclusion CD53, TGFBI, MS4A6A, and HERC6 have emerged as promising candidate driver genes for LN. These hub genes hold the potential to offer valuable insights into the molecular diagnosis and treatment of LN.
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Affiliation(s)
- Zheng Wang
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danni Hu
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guangchang Pei
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Zeng
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Ying Yao
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Nutrition, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Lee JH, Ahn EH, Kwon MJ, Ryu CS, Ha YH, Ko EJ, Lee JY, Hwang JY, Kim JH, Kim YR, Kim NK. Genetic Correlation of miRNA Polymorphisms and STAT3 Signaling Pathway with Recurrent Implantation Failure in the Korean Population. Int J Mol Sci 2023; 24:16794. [PMID: 38069116 PMCID: PMC10706094 DOI: 10.3390/ijms242316794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The growing prevalence of in vitro fertilization-embryo transfer procedures has resulted in an increased incidence of recurrent implantation failure (RIF), necessitating focused research in this area. STAT3, a key factor in maternal endometrial remodeling and stromal proliferation, is crucial for successful embryo implantation. While the relationship between STAT3 and RIF has been studied, the impact of single nucleotide polymorphisms (SNPs) in miRNAs, well-characterized gene expression modulators, on STAT3 in RIF cases remains uncharacterized. Here, we investigated 161 RIF patients and 268 healthy control subjects in the Korean population, analyzing the statistical association between miRNA genetic variants and RIF risk. We aimed to determine whether SNPs in specific miRNAs, namely miR-218-2 rs11134527 G>A, miR-34a rs2666433 G>A, miR-34a rs6577555 C>A, and miR-130a rs731384 G>A, were significantly associated with RIF risk. We identified a significant association between miR-34a rs6577555 C>A and RIF prevalence (implantation failure [IF] ≥ 2: adjusted odds ratio [AOR] = 2.264, 95% CI = 1.007-5.092, p = 0.048). These findings suggest that miR-34a rs6577555 C>A may contribute to an increased susceptibility to RIF. However, further investigations are necessary to elucidate the precise mechanisms underlying the role of miR-34a rs6577555 C>A in RIF. This study sheds light on the genetic and molecular factors underlying RIF, offering new avenues for research and potential advancements in the diagnosis and treatment of this complex condition.
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Affiliation(s)
- Jung Hun Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Eun Hee Ahn
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam 13496, Republic of Korea; (E.H.A.); (J.H.K.)
| | - Min Jung Kwon
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Chang Su Ryu
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Yong Hyun Ha
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Eun Ju Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Jeong Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Ji Young Hwang
- Department of Obstetrics and Gynecology, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea;
| | - Ji Hyang Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam 13496, Republic of Korea; (E.H.A.); (J.H.K.)
| | - Young Ran Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam 13496, Republic of Korea; (E.H.A.); (J.H.K.)
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
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Wang Y, Ma C, Ma Z, Yang M, Pu J, Ma X, Wu X, Peng L, Huo Z, Dang J. Identification and Clinical Correlation Analysis of IFI44 in Systemic Lupus Erythematosus Combined with Bioinformatics and Immune Infiltration Analysis. J Inflamm Res 2023; 16:3219-3231. [PMID: 37547125 PMCID: PMC10404056 DOI: 10.2147/jir.s419880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023] Open
Abstract
Purpose Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that can cause systemic damage to multiple organs. This study aims to analyze the value and function of IFI44 in the diagnosis and pathology of SLE by bioinformatics and immune infiltration analysis. Patients and Methods GSE49454 and GSE65391 of SLE were obtained from the GEO dataset, and R software was employed to identify DEGs and investigate their functions. The PPI network was utilized to identify hub genes associated with SLE. CIBERSORT was used to assess differences in immune cell infiltration in SLE patients and controls. ROC curve analysis was performed to evaluate the diagnostic value of IFI44 in SLE. The expression of IFI44 in PBMCs was detected by RT-qPCR, and the correlation between IFI44 expression and SLE-related clinical indicators was analyzed. Results A total of 65 DEGs were identified from the GSE49454 and GSE65391 databases. Through PPI analysis, IFI44 and RSAD2 were identified as significantly aberrantly expressed in SLE patients. SLE patients and controls showed a significant difference in the proportion of immune cell infiltration. IFI44 expression was positively correlated with activated DCs, monocytes, PCs, neutrophils, and activated memory CD4+T cells, while negatively correlated with M0 and CD8+T cells. The expression of IFI44 was significantly higher in SLE patients (P<0.01), especially in male patients (P=0.0376). ROC curve analysis demonstrated that IFI44 had a high diagnostic value for SLE. Correlation analysis indicated that IFI44 expression was correlated with levels of RBC, HGB, HCT, IgA, ESR, UPRO, C3, C4, and ENA in SLE patients. Conclusion IFI44 may play a role in the pathogenesis of SLE by influencing the immune microenvironment of SLE patients, and thus has the potential to serve as a diagnostic marker and therapeutic target for SLE.
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Affiliation(s)
- Yuan Wang
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Department of Dermatology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Chengfeng Ma
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Zhanbing Ma
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Mengyi Yang
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Jing Pu
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Xiuhui Ma
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Xi Wu
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Liang Peng
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Zhenghao Huo
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | - Jie Dang
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
- Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
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