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Zhang W, Cai Z, Liang D, Han J, Wu P, Shan J, Meng G, Zeng H. Immune Cell-Related Genes in Juvenile Idiopathic Arthritis Identified Using Transcriptomic and Single-Cell Sequencing Data. Int J Mol Sci 2023; 24:10619. [PMID: 37445800 DOI: 10.3390/ijms241310619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/07/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease in children. The heterogeneity of the disease can be investigated via single-cell RNA sequencing (scRNA-seq) for its gap in the literature. Firstly, five types of immune cells (plasma cells, naive CD4 T cells, memory-activated CD4 T cells, eosinophils, and neutrophils) were significantly different between normal control (NC) and JIA samples. WGCNA was performed to identify genes that exhibited the highest correlation to differential immune cells. Then, 168 differentially expressed immune cell-related genes (DE-ICRGs) were identified by overlapping 13,706 genes identified by WGCNA and 286 differentially expressed genes (DEGs) between JIA and NC specimens. Next, four key genes, namely SOCS3, JUN, CLEC4C, and NFKBIA, were identified by a protein-protein interaction (PPI) network and three machine learning algorithms. The results of functional enrichment revealed that SOCS3, JUN, and NFKBIA were all associated with hallmark TNF-α signaling via NF-κB. In addition, cells in JIA samples were clustered into four groups (B cell, monocyte, NK cell, and T cell groups) by single-cell data analysis. CLEC4C and JUN exhibited the highest level of expression in B cells; NFKBIA and SOCS3 exhibited the highest level of expression in monocytes. Finally, real-time quantitative PCR (RT-qPCR) revealed that the expression of three key genes was consistent with that determined by differential analysis. Our study revealed four key genes with prognostic value for JIA. Our findings could have potential implications for JIA treatment and investigation.
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Affiliation(s)
- Wenbo Zhang
- The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou 510623, China
- The Joint Center for Infection and Immunity, CAS Key Laboratory of Molecular Virology & Immunology, Chinese Academy of Sciences, Shanghai 200031, China
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Zhe Cai
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou 510623, China
| | - Dandan Liang
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jiaochan Han
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Ping Wu
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jiayi Shan
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Guangxun Meng
- The Joint Center for Infection and Immunity, CAS Key Laboratory of Molecular Virology & Immunology, Chinese Academy of Sciences, Shanghai 200031, China
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huasong Zeng
- The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou 510623, China
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
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Zhang Y, Wei H, Fan L, Fang M, He X, Lu B, Pang Z. CLEC4s as Potential Therapeutic Targets in Hepatocellular Carcinoma Microenvironment. Front Cell Dev Biol 2021; 9:681372. [PMID: 34409028 PMCID: PMC8367378 DOI: 10.3389/fcell.2021.681372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022] Open
Abstract
Immunosuppressive tumor microenvironment in hepatocellular carcinoma (HCC) is critical in tumor development. C-type (Ca2+ -dependent) lectin (CLEC) receptors, essential in innate pattern recognition, have potential regulatory effects on immune cell trafficking and modulatory effects on cancer cell activity. However, information on the expression and prognostic value of CLECs in HCC is scanty. Herein, we explored the potential role of CLECs in HCC based on TCGA, ONCOMINE, GEPIA, UALCAN, cBioPortal, Metascape, TRRUST, and TIMER databases. Results demonstrated a significantly higher mRNA level of CLEC4A and CLEC4L in HCC tissues than normal liver tissues. Contrarily, we found significantly low CLEC4G/H1/H2/M expression in HCC tissues. The IHC analysis revealed the following: Absence of CLEC4A/J/K/M in normal and liver cancer tissues; high CLEC4C expression in HCC tissues; low expression and zero detection of CLEC4D/E/H1/H2/L in HCC tissues and normal tissues, respectively. And the HepG2 and LX-2 were used to verify the expression level of CLEC4s via qRT-PCR in vitro. Furthermore, the expression of CLEC4H1 (ASGR1) and CLEC4H2 (ASGR2) exhibited a significant relation to clinical stages. However, the expression of CLEC4A, CLEC4D, CLEC4E, CLEC4J (FCER2), CLEC4K (CD207), CLEC4G, CLEC4H1, CLEC4M, and CLEC4H2 decreased with tumor progression. Patients expressing higher CLEC4H1/H2 levels had longer overall survival than patients exhibiting lower expression. Moreover, CLEC4A/D/E/J/K/G/H1/M/H2 had significant down-regulated levels of promoter methylation. The expression level of CLEC4s was correlated with the infiltration of B cells, CD8 + T cells, CD4 + T cells, macrophage cells, neutrophil cells, and dendritic cells. Functional analysis revealed the potential role of CLECL4s in virus infection, including COVID-19. Also, hsa-miR-4278 and hsa-miR-324-5p, two potential miRNA targets of CLEC4s, were uncovered. This article demonstrates that CLEC4 is crucial for the development of HCC and is associated with infiltration of various immune cells, providing evidence for new immunotherapy targets in HCC.
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Affiliation(s)
- Yinjiang Zhang
- School of Pharmacy, Minzu University of China, Beijing, China.,Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, China.,Morning Star Academic Cooperation, Shanghai, China
| | - Hongyun Wei
- Morning Star Academic Cooperation, Shanghai, China.,Department of Gastroenterology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lu Fan
- School of Pharmacy, Minzu University of China, Beijing, China.,Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, China
| | - Mingyan Fang
- School of Pharmacy, Minzu University of China, Beijing, China.,Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, China
| | - Xu He
- School of Pharmacy, Minzu University of China, Beijing, China.,Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, China
| | - Binan Lu
- School of Pharmacy, Minzu University of China, Beijing, China.,Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, China
| | - Zongran Pang
- School of Pharmacy, Minzu University of China, Beijing, China.,Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, China
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