1
|
Wang Y, Lin X, Wang C, Liu X, Wu X, Qiu Y, Chen Y, Zhou Q, Zhao H, Chen J, Huang H. Identification of PDCD1 as a potential biomarker in acute rejection after kidney transplantation via comprehensive bioinformatic analysis. Front Immunol 2023; 13:1076546. [PMID: 36776400 PMCID: PMC9911868 DOI: 10.3389/fimmu.2022.1076546] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/22/2022] [Indexed: 01/28/2023] Open
Abstract
Background Acute rejection is a determinant of prognosis following kidney transplantation. It is essential to search for novel noninvasive biomarkers for early diagnosis and prompt treatment. Methods Gene microarray data was downloaded from the Gene Expression Omnibus (GEO) expression profile database and the intersected differentially expressed genes (DEGs) was calculated. We conducted the DEGs with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Distribution of immune cell infiltration was calculated by CIBERSORT. A hub gene marker was identified by intersecting the rejection-related genes from WGCNA and a selected KEGG pathway-T cell receptor signaling pathway (hsa04660), and building a protein-protein interaction network using the STRING database and Cytoscape software. We performed flow-cytometry analysis to validate the hub gene. Results A total of 1450 integrated DEGs were obtained from five datasets (GSE1563, GSE174020, GSE98320, GSE36059, GSE25902). The GO, KEGG and immune infiltration analysis results showed that AR was mainly associated with T cell activation and various T-cell related pathways. Other immune cells, such as B cells, Macrophage and Dendritic cells were also associated with the progress. After utilizing the WGCNA and PPI network, PDCD1 was identified as the hub gene. The flow-cytometry analysis demonstrated that both in CD4+ and CD8+ T cells, PD1+CD57-, an exhausted T cell phenotype, were downregulated in the acute rejection whole blood samples. Conclusions Our study illustrated that PDCD1 may be a candidate diagnostic biomarker for acute kidney transplant rejection via integrative bioinformatic analysis.
Collapse
Affiliation(s)
- Yucheng Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Xiaoli Lin
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Cuili Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Xinyu Liu
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Xiaoying Wu
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Yingying Qiu
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Ying Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Qin Zhou
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Haige Zhao
- Department of Cardiothoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China
| | - Hongfeng Huang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Zhejiang, China,*Correspondence: Hongfeng Huang,
| |
Collapse
|
3
|
Chen YM, Zhu Q, Cai J, Zhao ZJ, Yao BB, Zhou LM, Ji LD, Xu J. Upregulation of T Cell Receptor Signaling Pathway Components in Gestational Diabetes Mellitus Patients: Joint Analysis of mRNA and circRNA Expression Profiles. Front Endocrinol (Lausanne) 2021; 12:774608. [PMID: 35046894 PMCID: PMC8763273 DOI: 10.3389/fendo.2021.774608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/01/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Gestational diabetes mellitus (GDM) is one of the most common complications of pregnancy, and its pathogenesis is still unclear. Studies have shown that circular RNAs (circRNAs) can regulate blood glucose levels by targeting mRNAs, but the role of circRNAs in GDM is still unknown. Therefore, a joint microarray analysis of circRNAs and their target mRNAs in GDM patients and healthy pregnant women was carried out. METHODS In this study, microarray analyses of mRNA and circRNA in 6 GDM patients and 6 healthy controls were conducted to identify the differentially expressed mRNA and circRNA in GDM patients, and some of the discovered mRNAs and circRNAs were further validated in additional 56 samples by quantitative realtime PCR (qRT-PCR) and droplet digital PCR (ddPCR). RESULTS Gene ontology and pathway analyses showed that the differentially expressed genes were significantly enriched in T cell immune-related pathways. Cross matching of the differentially expressed mRNAs and circRNAs in the top 10 KEGG pathways identified 4 genes (CBLB, ITPR3, NFKBIA, and ICAM1) and 4 corresponding circRNAs (circ-CBLB, circ-ITPR3, circ-NFKBIA, and circ-ICAM1), and these candidates were subsequently verified in larger samples. These differentially expressed circRNAs and their linear transcript mRNAs were all related to the T cell receptor signaling pathway, and PCR results confirmed the initial microarray results. Moreover, circRNA/miRNA/mRNA interactions and circRNA-binding proteins were predicted, and circ-CBLB, circ-ITPR3, and circ-ICAM1 may serve as GDM-related miRNA sponges and regulate the expression of CBLB, ITPR3, NFKBIA, and ICAM1 in cellular immune pathways. CONCLUSION Upregulation of T cell receptor signaling pathway components may represent the major pathological mechanism underlying GDM, thus providing a potential approach for the prevention and treatment of GDM.
Collapse
Affiliation(s)
- Yan-ming Chen
- Department of Science and Education, Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Qiong Zhu
- Department of Pediatrics, Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Jie Cai
- Department of Reproductive Medicine, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Zhi-jia Zhao
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Bin-bin Yao
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Li-ming Zhou
- Department of Reproductive Medicine, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Lin-dan Ji
- Department of Science and Education, Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Department of Biochemistry, School of Medicine, Ningbo University, Ningbo, China
- Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
- *Correspondence: Lin-dan Ji, ; Jin Xu,
| | - Jin Xu
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
- Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
- *Correspondence: Lin-dan Ji, ; Jin Xu,
| |
Collapse
|
4
|
Abstract
BACKGROUND Overall survival (OS) is a key endpoint measure in the management of patients with cancer. Immunotherapy has become a dominant strategy in cancer therapy. To investigate the relationship between OS and the immune system, we assessed the role of immune genes in OS in 8648 patients across 22 cancer types. METHODS Gene expression data and clinical information were collected from The Cancer Genome Atlas (TCGA) and cBioPortal. Survival analysis was performed with a Cox proportional hazards regression model. RESULTS (1) The number of prognostic genes, prognostic immune genes (PIGs) and the hazard ratio (HR) of PIGs in different cancer types all varied greatly; (2) KEGG pathway enrichment analyses indicated that the prognostic genes of 6 cancer types were significantly enriched in multiple (≥5) immune system-related pathways. Of the PIGs in these 6 cancer types, we screened 48 common PIGs in at least 5 cancer types. Eleven out of the 48 PIGs were found to participate in the T cell receptor (TCR) signaling pathway according to the STRING database. Among these genes, ZAP70, CD3E, CD3G, CD3D, and CD247 were part of the TCR 'signal-triggering module'; (3) High expression of the PIGs involved in the TCR signaling pathway was associated with improved OS in 5 cancer types (breast invasive carcinoma (BRCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), head and neck squamous cell carcinoma (HNSC), lung adenocarcinoma (LUAD), and sarcoma (SARC)), but was associated with decreased OS in brain lower-grade glioma (LGG). CONCLUSIONS The TCR signaling pathway played a distinct role in the OS of these 6 cancer types.
Collapse
Affiliation(s)
- Qian Wang
- Center for Public Health Informatics, School of Public Health, Xinxiang Medical University, Xinxiang, Henan, People's Republic of China
| | - Pan Li
- Center for Public Health Informatics, School of Public Health, Xinxiang Medical University, Xinxiang, Henan, People's Republic of China.
| | - Weidong Wu
- Center for Public Health Informatics, School of Public Health, Xinxiang Medical University, Xinxiang, Henan, People's Republic of China.
| |
Collapse
|