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Zhou B, Zhou N, Liu Y, Dong E, Peng L, Wang Y, Yang L, Suo H, Tao J. Identification and validation of CCR5 linking keloid with atopic dermatitis through comprehensive bioinformatics analysis and machine learning. Front Immunol 2024; 15:1309992. [PMID: 38476235 PMCID: PMC10927814 DOI: 10.3389/fimmu.2024.1309992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
There is sufficient evidence indicating that keloid is strongly associated with atopic dermatitis (AD) across ethnic groups. However, the molecular mechanism underlying the association is not fully understood. The aim of this study is to discover the underlying mechanism of the association between keloid and AD by integrating comprehensive bioinformatics techniques and machine learning methods. The gene expression profiles of keloid and AD were downloaded from the Gene Expression Omnibus (GEO) database. A total of 449 differentially expressed genes (DEGs) were found to be shared in keloid and AD using the training datasets of GEO (GSE158395 and GSE121212). The hub genes were identified using the protein-protein interaction network and Cytoscape software. 20 of the most significant hub genes were selected, which were mainly involved in the regulation of the inflammatory and immune response. Through two machine learning algorithms of LASSO and SVM-RFE, CCR5 was identified as the most important key gene. Subsequently, upregulated CCR5 gene expression was confirmed in validation GEO datasets (GSE188952 and GSE32924) and clinical samples of keloid and AD. Immune infiltration analysis showed that T helper (Th) 1, 2 and 17 cells were significantly enriched in the microenvironment of both keloid and AD. Positive correlations were found between CCR5 and Th1, Th2 and Th17 cells. Finally, two TFs of CCR5, NR3C2 and YY1, were identified, both of which were downregulated in keloid and AD tissues. Our study firstly reveals that keloid and AD shared common inflammatory and immune pathways. Moreover, CCR5 plays a key role in the pathogenesis association between keloid and AD. The common pathways and key genes may shed light on further mechanism research and targeted therapy, and may provide therapeutic interventions of keloid with AD.
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Affiliation(s)
- Bin Zhou
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Nuoya Zhou
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Yan Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Enzhu Dong
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Lianqi Peng
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Yifei Wang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Liu Yang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Huinan Suo
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Juan Tao
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
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Lv W, Peng Y, Hu J, Zhu M, Mao Y, Wang L, Wang G, Xu Z, Wu W, Zuo B. Functional SNPs in SYISL promoter significantly affect muscle fiber density and muscle traits in pigs. Anim Genet 2024; 55:66-78. [PMID: 37881102 DOI: 10.1111/age.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/06/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
Abstract
Our previous studies showed that SYISL is a negative regulator of muscle growth and regeneration in mice, pigs and humans. SYISL knockout resulted in an increase in the density of muscle fibers and muscle growth. However, it is unclear whether there are natural mutations in pig SYNPO2 intron sense-overlapping lncRNA (pSYISL) that affect the expression of pSYISL and muscle growth traits. In this study, three SNPs in exons and six SNPs within the promoter of pSYISL were identified. Association analysis showed that the two SNPs in exons are significantly associated with loin muscle area (p < 0.05); the six SNPs in the promoter that show complete linkage are significantly associated with live backfat thickness and live loin muscle area in American Large White pigs. Bioinformatics and luciferase reporter assays as well as in vitro binding experiments indicated that the mutation of SNP rs702045770 (g.539G>A) leads to the loss of YY1 binding to the promoter, thus affecting the expression level of pSYISL, and we found that Jiangshan Black pigs with genotype GG have a higher expression level of pSYISL than genotype AA individuals, but the muscle fiber density was significantly lower than in genotype AA individuals. Furthermore, the association analysis showed that the carcass backfat thickness of genotype GG of SNP rs702045770 was significantly higher than that of other genotypes in (Pietrain × Duroc) × (Landrace × Yorkshire) crossbred pigs (p < 0.05). The glycolytic potential of genotype GG was significantly higher than that of other genotypes (p < 0.05). These results provide novel insight into the identification of functional SNPs in non-coding genomic regions.
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Affiliation(s)
- Wei Lv
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yaxin Peng
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Hu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Mingfei Zhu
- The Tianpeng Group Co. Ltd, Jiangshan, China
| | | | - Litong Wang
- The Tianpeng Group Co. Ltd, Jiangshan, China
| | | | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Hamzehlou S, Glass DA. Down expressed in keloid (DEIK): a new player in the pathogenesis of keloids. Br J Dermatol 2023; 188:7. [PMID: 36689528 DOI: 10.1093/bjd/ljac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 10/05/2022] [Indexed: 01/22/2023]
Affiliation(s)
- Sepideh Hamzehlou
- Department of Dermatology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Donald Alexander Glass
- Department of Dermatology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
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Zhou S, Xie M, Su J, Cai B, Li J, Zhang K. New insights into balancing wound healing and scarless skin repair. J Tissue Eng 2023; 14:20417314231185848. [PMID: 37529248 PMCID: PMC10388637 DOI: 10.1177/20417314231185848] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023] Open
Abstract
Scars caused by skin injuries after burns, wounds, abrasions and operations have serious physical and psychological effects on patients. In recent years, the research of scar free wound repair has been greatly expanded. However, understanding the complex mechanisms of wound healing, in which various cells, cytokines and mechanical force interact, is critical to developing a treatment that can achieve scarless wound healing. Therefore, this paper reviews the types of wounds, the mechanism of scar formation in the healing process, and the current research progress on the dual consideration of wound healing and scar prevention, and some strategies for the treatment of scar free wound repair.
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Affiliation(s)
- Shengxi Zhou
- School of Life Science, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Mengbo Xie
- School of Life Science, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Jingjing Su
- School of Life Science, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Bingjie Cai
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Jingan Li
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Kun Zhang
- School of Life Science, Zhengzhou University, Zhengzhou, Henan, P. R. China
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