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Chen SD, Chu CY, Wang CB, Yang Y, Xu ZY, Qu YL, Man Y. Integrated-omics profiling unveils the disparities of host defense to ECM scaffolds during wound healing in aged individuals. Biomaterials 2024; 311:122685. [PMID: 38944969 DOI: 10.1016/j.biomaterials.2024.122685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/11/2024] [Accepted: 06/23/2024] [Indexed: 07/02/2024]
Abstract
Extracellular matrix (ECM) scaffold membranes have exhibited promising potential to better the outcomes of wound healing by creating a regenerative microenvironment around. However, when compared to the application in younger individuals, the performance of the same scaffold membrane in promoting re-epithelialization and collagen deposition was observed dissatisfying in aged mice. To comprehensively explore the mechanisms underlying this age-related disparity, we conducted the integrated analysis, combing single-cell RNA sequencing (scRNA-Seq) with spatial transcriptomics, and elucidated six functionally and spatially distinctive macrophage groups and lymphocytes surrounding the ECM scaffolds. Through intergroup comparative analysis and cell-cell communication, we characterized the dysfunction of Spp1+ macrophages in aged mice impeded the activation of the type Ⅱ immune response, thus inhibiting the repair ability of epidermal cells and fibroblasts around the ECM scaffolds. These findings contribute to a deeper understanding of biomaterial applications in varied physiological contexts, thereby paving the way for the development of precision-based biomaterials tailored specifically for aged individuals in future therapeutic strategies.
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Affiliation(s)
- Shuai-Dong Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chen-Yu Chu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chen-Bing Wang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China
| | - Yang Yang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zhao-Yu Xu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yi-Li Qu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yi Man
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
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2
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Li Y, Dong T, Wan S, Xiong R, Jin S, Dai Y, Guan C. Application of multi-omics techniques to androgenetic alopecia: Current status and perspectives. Comput Struct Biotechnol J 2024; 23:2623-2636. [PMID: 39021583 PMCID: PMC11253216 DOI: 10.1016/j.csbj.2024.06.026] [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: 03/10/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
The rapid advancement of sequencing technologies has enabled the generation of vast datasets, allowing for the in-depth analysis of sequencing data. This analysis has facilitated the validation of novel pathogenesis hypotheses for understanding and treating diseases through ex vivo and in vivo experiments. Androgenetic alopecia (AGA), a common hair loss disorder, has been a key focus of investigators attempting to uncover its underlying mechanisms. Abnormal changes in mRNA, proteins, and metabolites have been identified in individuals with AGA, and future developments in sequencing technologies may reveal new biomarkers for AGA. By integrating multiple omics analysis datasets such as genomics, transcriptomics, proteomics, and metabolomics-along with clinical phenotype data-we can achieve a comprehensive understanding of the molecular underpinnings of AGA. This review summarizes the data-mining studies conducted on various omics analysis datasets as related to AGA that have been adopted to interpret the biological data obtained from different omics layers. We herein discuss the challenges of integrative omics analyses, and suggest that collaborative multi-omics studies can enhance the understanding of the complete pathomechanism(s) of AGA by focusing on the interaction networks comprising DNA, RNA, proteins, and metabolites.
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Affiliation(s)
- Yujie Li
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Tingru Dong
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Sheng Wan
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Renxue Xiong
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Shiyu Jin
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Yeqin Dai
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Cuiping Guan
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
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3
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Zhu X, Xu Z, Liu Y, Yang J, Bai L, Li X, Sun Q, Li H, Chen G. Unveiling microglia heterogeneity in intracerebral hemorrhage. Neuroscience 2024; 555:167-177. [PMID: 39067680 DOI: 10.1016/j.neuroscience.2024.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Microglia are important innate immune cells in the brain, and a rich diversity of subtypes has recently been discovered that expand beyond the traditional classification of traditional M1 (pro-inflammatory) and M2 (anti-inflammatory) classifications. Intracerebral hemorrhage (ICH) is a devastating form of stroke, and the understanding of its later-stage pathological mechanisms remains incomplete. In this study, through the analysis of single-cell transcripts from mice brains 14 days post-ICH, three disease-associated expression patterns of microglia were identified. These include a lipid metabolism and phagocytosis phenotype reminiscent of Disease-Associated Microglia (DAM) initially discovered in Alzheimer's disease models, a phenotype associated with angiogenesis, and a relatively independent phenotype similar to the pro-inflammatory M1 state. These findings were further validated through immunofluorescence in both mouse and human specimens. In addition, analysis of single-cell transcripts from mice brains 3 days post-ICH suggested that microglia involved in lipid metabolism and phagocytosis likely emerge from early proliferating populations. Given the distinct origins and phenotypic characteristics of pro-inflammatory and reparative microglia, interventions targeting these cells hold the potential to modulate the delicate balance between injury and repair during the pathophysiological process of ICH, highlighting a pivotal direction for future therapeutic strategies.
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Affiliation(s)
- Xunan Zhu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Zhongmou Xu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Yangyang Liu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Jian Yang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Lei Bai
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Qing Sun
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China.
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
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Sun RX, Liu YF, Sun YS, Zhou M, Wang Y, Shi BZ, Jiang H, Li ZH. GPC3-targeted CAR-T cells expressing GLUT1 or AGK exhibit enhanced antitumor activity against hepatocellular carcinoma. Acta Pharmacol Sin 2024; 45:1937-1950. [PMID: 38750075 PMCID: PMC11336244 DOI: 10.1038/s41401-024-01287-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 04/08/2024] [Indexed: 08/22/2024] Open
Abstract
Chimeric antigen receptor-expressing T (CAR-T) cells induce robust antitumor responses in patients with hematologic malignancies. However, CAR-T cells exhibit only limited efficacy against solid tumors such as hepatocellular carcinoma (HCC), partially due to their limited expansion and persistence. CD8+ T cells, as key components of the adaptive immune response, play a central role in antitumor immunity. Aerobic glycolysis is the main metabolic feature of activated CD8+ T cells. In the tumor microenvironment, however, the uptake of large amounts of glucose by tumor cells and other immunosuppressive cells can impair the activation of T cells. Only when tumor-infiltrating lymphocytes (TILs) in the tumor microenvironment have a glycolytic advantage might the effector function of T cells be activated. Glucose transporter type 1 (GLUT1) and acylglycerol kinase (AGK) can boost glycolytic metabolism and activate the effector function of CD8+ T cells, respectively. In this study, we generated GPC3-targeted CAR-T cells overexpressing GLUT1 or AGK for the treatment of HCC. GPC3-targeted CAR-T cells overexpressing GLUT1 or AGK specifically and effectively lysed GPC3-positive tumor cells in vitro in an antigen-dependent manner. Furthermore, GLUT1 or AGK overexpression protected CAR-T cells from apoptosis during repeated exposures to tumor cells. Compared with second-generation CAR-T cells, GPC3-targeted CAR-T cells overexpressing GLUT1 or AGK exhibited greater CD8+ T-cell persistence in vivo and better antitumor effects in HCC allograft mouse models. Finally, we revealed that GLUT1 or AGK maintained anti-apoptosis ability in CD8+ T cells via activation of the PI3K/Akt pathway. This finding might identify a therapeutic strategy for advanced HCC.
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Affiliation(s)
- Rui-Xin Sun
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Yi-Fan Liu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Yan-Sha Sun
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Min Zhou
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Yi Wang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
- CARsgen Therapeutics, Shanghai, 200032, China
| | - Bi-Zhi Shi
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
- CARsgen Therapeutics, Shanghai, 200032, China
| | - Hua Jiang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China.
- CARsgen Therapeutics, Shanghai, 200032, China.
| | - Zong-Hai Li
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China.
- CARsgen Therapeutics, Shanghai, 200032, China.
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5
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Li X, An T, Yang Y, Xu Z, Chen S, Yi Z, Deng C, Zhou F, Man Y, Hu C. TLR9 activation in large wound induces tissue repair and hair follicle regeneration via γδT cells. Cell Death Dis 2024; 15:598. [PMID: 39153998 PMCID: PMC11330466 DOI: 10.1038/s41419-024-06994-y] [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: 05/03/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024]
Abstract
The mechanisms underlying tissue repair in response to damage have been one of main subjects of investigation. Here we leverage the wound-induced hair neogenesis (WIHN) models in adult mice to explore the correlation between degree of damage and the healing process and outcome. The multimodal analysis, in combination with single-cell RNA sequencing help to explore the difference in wounds of gentle and heavy damage degrees, identifying the potential role of toll-like receptor 9 (TLR9) in sensing the injury and regulating the immune reaction by promoting the migration of γδT cells. The TLR9 deficient mice or wounds injected with TLR9 antagonist have greatly impaired healing and lower WIHN levels. Inhibiting the migration of γδT cells or knockout of γδT cells also suppress the wound healing and regeneration, which can't be rescued by TLR9agonist. Finally, the amphiregulin (AREG) is shown as one of most important effectors secreted by γδT cells and keratinocytes both in silicon or in the laboratory, whose expression influences WIHN levels and the expression of stem cell markers. In total, our findings reveal a previously unrecognized role for TLR9 in sensing skin injury and influencing the tissue repair and regeneration by modulation of the migration of γδT cells, and identify the TLR9-γδT cells-areg axis as new potential targets for enhancing tissue regeneration.
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Affiliation(s)
- Xinhui Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tiantian An
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yang Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zhaoyu Xu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Shuaidong Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zumu Yi
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chen Deng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Feng Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yi Man
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Chen Hu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
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6
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Lee H, Kim SY, Kwon NJ, Jo SJ, Kwon O, Kim JI. Single-Cell and Spatial Transcriptome Analysis of Dermal Fibroblast Development in Perinatal Mouse Skin: Dynamic Lineage Differentiation and Key Driver Genes. J Invest Dermatol 2024; 144:1238-1250.e11. [PMID: 38072389 DOI: 10.1016/j.jid.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/21/2024]
Abstract
Several single-cell RNA studies of developing mouse skin have elucidated the molecular and cellular processes involved in skin development. However, they have primarily focused on either the fetal or early postnatal period, leaving a gap in our understanding of skin development. In this study, we conducted a comprehensive time-series analysis by combining single-cell RNA-sequencing datasets collected at different stages of development (embryonic days 13.5, 14.5, and 16.5 and postnatal days 0, 2, and 4) and validated our findings through multipanel in situ spatial transcriptomics. Our analysis indicated that embryonic fibroblasts exhibit heterogeneity from a very early stage and that the rapid determination of each lineage occurs within days after birth. The expression of putative key driver genes, including Hey1, Ebf1, Runx3, and Sox11 for the dermal papilla trajectory; Lrrc15 for the dermal sheath trajectory; Zfp536 and Nrn1 for the papillary fibroblast trajectory; and Lrrn4cl and Mfap5 for the fascia fibroblast trajectory, was detected in the corresponding, spatially identified cell types. Finally, cell-to-cell interaction analysis indicated that the dermal papilla lineage is the primary source of the noncanonical Wnt pathway during skin development. Together, our study provides a transcriptomic reference for future research in the field of skin development and regeneration.
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Affiliation(s)
- Hanjae Lee
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - So Young Kim
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | | | - Seong Jin Jo
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Laboratory of Cutaneous Aging and Hair Research, Clinical Research Institute, Seoul National University Hospital, Seoul, Korea; Institute of Human-Environment Interface Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Ohsang Kwon
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Laboratory of Cutaneous Aging and Hair Research, Clinical Research Institute, Seoul National University Hospital, Seoul, Korea; Institute of Human-Environment Interface Biology, Seoul National University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea; Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University, Seoul, Korea
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7
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Lin Y, Li X, Fang J, Zeng Q, Cheng D, Wang G, Shi R, Luo Y, Ma Y, Li M, Tang X, Wang X, Tian R. Single-cell transcriptome profiling reveals cell type-specific variation and development in HLA expression of human skin. Int Immunopharmacol 2024; 133:112070. [PMID: 38640716 DOI: 10.1016/j.intimp.2024.112070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Skin, the largest organ of body, is a highly immunogenic tissue with a diverse collection of immune cells. Highly polymorphic human leukocyte antigen (HLA) molecules have a central role in coordinating immune responses as recognition molecules. Nevertheless, HLA gene expression patterns among diverse cell types within a specific organ, like the skin, have yet to be thoroughly investigated, with stromal cells attracting much less attention than immune cells. To illustrate HLA expression profiles across different cell types in the skin, we performed single-cell RNA sequencing (scRNA-seq) analyses on skin datasets, covering adult and fetal skin, and hair follicles as the skin appendages. We revealed the variation in HLA expression between different skin populations by examining normal adult skin datasets. Moreover, we evaluated the potential immunogenicity of multiple skin populations based on the expression of classical HLA class I genes, which were well represented in all cell types. Furthermore, we generated scRNA-seq data of developing skin from fetuses of 15 post conception weeks (PCW), 17 PCW, and 22 PCW, delineating the dynamic expression of HLA genes with cell type-dependent variation among various cell types during development. Notably, the pseudotime trajectory analysis unraveled the significant variance in HLA genes during the evolution of vascular endothelial cells. Moreover, we uncovered the immune-privileged properties of hair follicles at single-cell resolution. Our study presents a comprehensive single-cell transcriptomic landscape of HLA genes in the skin, which provides new insights into variation in HLA molecules and offers a clue for allogeneic skin transplantation.
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Affiliation(s)
- Yumiao Lin
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Xinxin Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jingxian Fang
- Department of Pediatric Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - Qinglan Zeng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Danling Cheng
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen 518172, China
| | - Gaofeng Wang
- Department of Pastic and Aesthetic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China
| | - Runlu Shi
- Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Yilin Luo
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Yihe Ma
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Miaomiao Li
- Department of Hemangioma and Vascular Malformation Surgery, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Xiang Tang
- Department of Minimal Invasive Gynecology, Guangzhou Women and Children's Hospital, Guangzhou Medical University, Guangzhou 510000, China.
| | - Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
| | - Ruiyun Tian
- The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China; GuangDong Engineering Technology Research Center of Stem Cell and Cell therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China.
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8
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Tan GH, Liu SJ, Dou ML, Zhao DF, Zhang A, Li HK, Luo FN, Shi T, Wang HP, Lei JY, Zhang Y, Jiang Y, Zheng Y, Wang F. Spatially resolved transcriptomic profiling of placental development in dairy cow. Zool Res 2024; 45:586-600. [PMID: 38766743 PMCID: PMC11188604 DOI: 10.24272/j.issn.2095-8137.2023.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/05/2023] [Indexed: 05/22/2024] Open
Abstract
The placenta plays a crucial role in successful mammalian reproduction. Ruminant animals possess a semi-invasive placenta characterized by a highly vascularized structure formed by maternal endometrial caruncles and fetal placental cotyledons, essential for full-term fetal development. The cow placenta harbors at least two trophoblast cell populations: uninucleate (UNC) and binucleate (BNC) cells. However, the limited capacity to elucidate the transcriptomic dynamics of the placental natural environment has resulted in a poor understanding of both the molecular and cellular interactions between trophoblast cells and niches, and the molecular mechanisms governing trophoblast differentiation and functionalization. To fill this knowledge gap, we employed Stereo-seq to map spatial gene expression patterns at near single-cell resolution in the cow placenta at 90 and 130 days of gestation, attaining high-resolution, spatially resolved gene expression profiles. Based on clustering and cell marker gene expression analyses, key transcription factors, including YBX1 and NPAS2, were shown to regulate the heterogeneity of trophoblast cell subpopulations. Cell communication and trajectory analysis provided a framework for understanding cell-cell interactions and the differentiation of trophoblasts into BNCs in the placental microenvironment. Differential analysis of cell trajectories identified a set of genes involved in regulation of trophoblast differentiation. Additionally, spatial modules and co-variant genes that help shape specific tissue structures were identified. Together, these findings provide foundational insights into important biological pathways critical to the placental development and function in cows.
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Affiliation(s)
- Guang-Hui Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Shi-Jie Liu
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Ming-Le Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - De-Feng Zhao
- College of Information Engineering, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Ao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Heng-Kuan Li
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Fu-Nong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Tao Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Hao-Ping Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Jing-Yuan Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yong Zhang
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yi Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China. E-mail:
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China. E-mail:
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9
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Wang Y, Jiang Y, Ni G, Li S, Balderson B, Zou Q, Liu H, Jiang Y, Sun J, Ding X. Integrating Single-Cell and Spatial Transcriptomics Reveals Heterogeneity of Early Pig Skin Development and a Subpopulation with Hair Placode Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306703. [PMID: 38561967 PMCID: PMC11132071 DOI: 10.1002/advs.202306703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/08/2024] [Indexed: 04/04/2024]
Abstract
The dermis and epidermis, crucial structural layers of the skin, encompass appendages, hair follicles (HFs), and intricate cellular heterogeneity. However, an integrated spatiotemporal transcriptomic atlas of embryonic skin has not yet been described and would be invaluable for studying skin-related diseases in humans. Here, single-cell and spatial transcriptomic analyses are performed on skin samples of normal and hairless fetal pigs across four developmental periods. The cross-species comparison of skin cells illustrated that the pig epidermis is more representative of the human epidermis than mice epidermis. Moreover, Phenome-wide association study analysis revealed that the conserved genes between pigs and humans are strongly associated with human skin-related diseases. In the epidermis, two lineage differentiation trajectories describe hair follicle (HF) morphogenesis and epidermal development. By comparing normal and hairless fetal pigs, it is found that the hair placode (Pc), the most characteristic initial structure in HFs, arises from progenitor-like OGN+/UCHL1+ cells. These progenitors appear earlier in development than the previously described early Pc cells and exhibit abnormal proliferation and migration during differentiation in hairless pigs. The study provides a valuable resource for in-depth insights into HF development, which may serve as a key reference atlas for studying human skin disease etiology using porcine models.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Yao Jiang
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Guiyan Ni
- Division of Genetics and GenomicsInstitute for Molecular BioscienceThe University of QueenslandBrisbane4072Australia
| | - Shujuan Li
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Brad Balderson
- School of Chemistry & Molecular BiosciencesThe University of QueenslandBrisbane4067Australia
| | - Quan Zou
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Huatao Liu
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Yifan Jiang
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Jingchun Sun
- Key Laboratory of Animal GeneticsBreeding and Reproduction of Shaanxi ProvinceLaboratory of Animal Fat Deposition & Muscle DevelopmentCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China
| | - Xiangdong Ding
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
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10
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Kovale L, Lee S, Song M, Lee J, Son HJ, Sung YK, Kwack MH, Choe W, Kang I, Kim SS, Ha J. Gynostemma pentaphyllum Hydrodistillate and Its Major Component Damulin B Promote Hair Growth-Inducing Properties In Vivo and In Vitro via the Wnt/β-Catenin Pathway in Dermal Papilla Cells. Nutrients 2024; 16:985. [PMID: 38613018 PMCID: PMC11013310 DOI: 10.3390/nu16070985] [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: 02/16/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Alopecia, a prevalent yet challenging condition with limited FDA-approved treatments which is accompanied by notable side effects, necessitates the exploration of natural alternatives. This study elucidated the hair growth properties of Gynostemma pentaphyllum leaf hydrodistillate (GPHD) both in vitro and in vivo. Furthermore, damulin B, a major component of GPHD, demonstrated hair growth-promoting properties in vitro. Beyond its established anti-diabetic, anti-obesity, and anti-inflammatory attributes, GPHD exhibited hair growth induction in mice parallel to minoxidil. Moreover, it upregulated the expression of autocrine factors associated with hair growth, including VEGF, IGF-1, KGF, and HGF. Biochemical assays revealed that minoxidil, GPHD, and damulin B induced hair growth via the Wnt/β-catenin pathway through AKT signaling, aligning with in vivo experiments demonstrating improved expression of growth factors. These findings suggest that GPHD and damulin B contribute to the hair growth-inducing properties of dermal papilla cells through the AKT/β-catenin signaling pathway.
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Affiliation(s)
- Lochana Kovale
- Department of Biochemistry and Molecular Biology, Graduate School, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (L.K.); (S.L.); (M.S.); (H.J.S.); (W.C.); (I.K.); (S.S.K.)
| | - Seoyeon Lee
- Department of Biochemistry and Molecular Biology, Graduate School, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (L.K.); (S.L.); (M.S.); (H.J.S.); (W.C.); (I.K.); (S.S.K.)
| | - Minhyeok Song
- Department of Biochemistry and Molecular Biology, Graduate School, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (L.K.); (S.L.); (M.S.); (H.J.S.); (W.C.); (I.K.); (S.S.K.)
| | - Jihyun Lee
- Easy Hydrogen Corporation, Jeju City 63196, Republic of Korea;
| | - Hyeong Jig Son
- Department of Biochemistry and Molecular Biology, Graduate School, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (L.K.); (S.L.); (M.S.); (H.J.S.); (W.C.); (I.K.); (S.S.K.)
| | - Young Kwan Sung
- Department of Immunology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (Y.K.S.); (M.H.K.)
| | - Mi Hee Kwack
- Department of Immunology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (Y.K.S.); (M.H.K.)
| | - Wonchae Choe
- Department of Biochemistry and Molecular Biology, Graduate School, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (L.K.); (S.L.); (M.S.); (H.J.S.); (W.C.); (I.K.); (S.S.K.)
| | - Insug Kang
- Department of Biochemistry and Molecular Biology, Graduate School, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (L.K.); (S.L.); (M.S.); (H.J.S.); (W.C.); (I.K.); (S.S.K.)
| | - Sung Soo Kim
- Department of Biochemistry and Molecular Biology, Graduate School, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (L.K.); (S.L.); (M.S.); (H.J.S.); (W.C.); (I.K.); (S.S.K.)
| | - Joohun Ha
- Department of Biochemistry and Molecular Biology, Graduate School, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (L.K.); (S.L.); (M.S.); (H.J.S.); (W.C.); (I.K.); (S.S.K.)
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11
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Liu Y, Zhang Y, Chang X, Liu X. MDIC3: Matrix decomposition to infer cell-cell communication. PATTERNS (NEW YORK, N.Y.) 2024; 5:100911. [PMID: 38370122 PMCID: PMC10873161 DOI: 10.1016/j.patter.2023.100911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/31/2023] [Accepted: 12/08/2023] [Indexed: 02/20/2024]
Abstract
Crosstalk among cells is vital for maintaining the biological function and intactness of systems. Most existing methods for investigating cell-cell communications are based on ligand-receptor (L-R) expression, and they focus on the study between two cells. Thus, the final communication inference results are particularly sensitive to the completeness and accuracy of the prior biological knowledge. Because existing L-R research focuses mainly on humans, most existing methods can only examine cell-cell communication for humans. As far as we know, there is currently no effective method to overcome this species limitation. Here, we propose MDIC3 (matrix decomposition to infer cell-cell communication), an unsupervised tool to investigate cell-cell communication in any species, and the results are not limited by specific L-R pairs or signaling pathways. By comparing it with existing methods for the inference of cell-cell communication, MDIC3 obtained better performance in both humans and mice.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- School of Mathematics and Statistics, Shandong University, Weihai 364209, China
| | - Yuelei Zhang
- School of Mathematics and Statistics, Shandong University, Weihai 364209, China
| | - Xiao Chang
- Institute of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu 233030, China
| | - Xiaoping Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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12
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Li C, He X, Wu Y, Li J, Zhang R, An X, Yue Y. Single-Cell Transcriptome Sequence Profiling on the Morphogenesis of Secondary Hair Follicles in Ordos Fine-Wool Sheep. Int J Mol Sci 2024; 25:584. [PMID: 38203755 PMCID: PMC10779399 DOI: 10.3390/ijms25010584] [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: 11/20/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The Ordos fine-wool sheep is a high-quality breed in China that produces superior natural textiles and raw materials such as wool and lamb meat. However, compared to the Australian Merino sheep, there is still a gap in terms of the wool fiber fineness and wool yield. The hair follicle is the main organ that controls the type of wool fiber, and the morphological changes in the secondary hair follicle are crucial in determining wool quality. However, the process and molecular mechanisms of hair follicle morphogenesis in Ordos fine-wool sheep are not yet clear. Therefore, analyzing the molecular mechanisms underlying the process of follicle formation is of great significance for improving the fiber diameter and wool production of Ordos fine-wool sheep. The differential expressed genes, APOD, POSTN, KRT5, and KRT15, which related to primary hair follicles and secondary hair follicles, were extracted from the dermal papillae. Based on pseudo-time analysis, the differentiation trajectories of dermal lineage cells and epidermal lineage cells in the Ordos fine-wool sheep were successfully constructed, providing a theoretical basis for breeding research in Ordos fine-wool sheep.
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Affiliation(s)
- Chenglan Li
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xue He
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yi Wu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianye Li
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Rui Zhang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xuejiao An
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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13
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Wang Q, Zhang YF, Li CL, Wang Y, Wu L, Wang XR, Huang T, Liu GL, Chen X, Yu Q, He PF. Integrating scRNA-seq and bulk RNA-seq to characterize infiltrating cells in the colorectal cancer tumor microenvironment and construct molecular risk models. Aging (Albany NY) 2023; 15:13799-13821. [PMID: 38054820 PMCID: PMC10756133 DOI: 10.18632/aging.205263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023]
Abstract
Colorectal cancer (CRC) is a malignancy that is both highly lethal and heterogeneous. Although the correlation between intra-tumoral genetic and functional heterogeneity and cancer clinical prognosis is well-established, the underlying mechanism in CRC remains inadequately understood. Utilizing scRNA-seq data from GEO database, we re-isolated distinct subsets of cells, constructed a CRC tumor-related cell differentiation trajectory, and conducted cell-cell communication analysis to investigate potential interactions across cell clusters. A prognostic model was built by integrating scRNA-seq results with TCGA bulk RNA-seq data through univariate, LASSO, and multivariate Cox regression analyses. Eleven distinct cell types were identified, with Epithelial cells, Fibroblasts, and Mast cells exhibiting significant differences between CRC and healthy controls. T cells were observed to engage in extensive interactions with other cell types. Utilizing the 741 signature genes, prognostic risk score model was constructed. Patients with high-risk scores exhibited a significant correlation with unfavorable survival outcomes, high-stage tumors, metastasis, and low responsiveness to chemotherapy. The model demonstrated a strong predictive performance across five validation cohorts. Our investigation involved an analysis of the cellular composition and interactions of infiltrates within the microenvironment, and we developed a prognostic model. This model provides valuable insights into the prognosis and therapeutic evaluation of CRC.
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Affiliation(s)
- Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Yi-Fan Zhang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
- The First clinical Medical College, Shanxi medical University, Taiyuan, China
| | - Chen-Long Li
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Yang Wang
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Li Wu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Xing-Ru Wang
- The Fifth Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Tai Huang
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Ge-Liang Liu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Xing Chen
- Department of Gastroenterology, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Qi Yu
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Pei-Feng He
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
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14
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Cai W, Xu Y, Bai Z, Lin G, Wang L, Dou X, Han D, Wang Z, Wang J, Zhang X, Zhang Y, Qin Y, Gu M, Sun Y, Wu Y, Chen R, Wang Z. Association analysis for SNPs of BAAT and COL1A1 genes with cashmere production performance and other production traits in Liaoning cashmere goats. Anim Biotechnol 2023; 34:2324-2335. [PMID: 35749728 DOI: 10.1080/10495398.2022.2088550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
This study aimed to investigate the relationship between the polymorphism of bile acid-CoA: amino acid N-acyltransferase (BAAT) and collagen type I alpha 1 chain (COL1A1) genes and the production performance of Liaoning Cashmere goat (LCG). The potential single nucleotide polymorphisms (SNPs) of LCG were detected by sequence comparison of BAAT and COL1A1 genes and PCR-Seq polymorphism, and the effect of SNPs on production performance was analyzed by SPSS software. The results showed that three SNPs loci were detected in BAAT gene: G7900A, T7967C, C7998T, and one SNP locus T6716C was detected in COL1AL gene. At G7900A locus, the dominant genotype for cashmere performance was GG, and the dominant genotype for body measurement traits and milk production traits was AG. At T7967C locus, the dominant genotype for cashmere performance was TT, and the dominant genotype for body measurement traits and milk production traits was CC. At C7998T locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. At the T6716C locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. H1H1: AACC is the dominant haplotype combination. Therefore, this study will provide a reliable reference for future research on cashmere production performance, body measurement traits, and milk production traits of LCG.
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Affiliation(s)
- Weidong Cai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Guangyu Lin
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Lingling Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Zhanhong Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Jiaming Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuting Qin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yinggang Sun
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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15
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Zhang G, Xie XX, Zhang SE, Zhang FL, Li CX, Qiao T, Dyce PW, Feng XL, Lin WB, Sun QC, Shen W, Cheng SF. Induced differentiation of primordial germ cell like cells from SOX9 + porcine skin derived stem cells. Theriogenology 2023; 212:129-139. [PMID: 37717516 DOI: 10.1016/j.theriogenology.2023.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Understanding the mechanisms behind porcine primordial germ cell like cells (pPGCLCs) development, differentiation, and gametogenesis is crucial in the treatment of infertility. In this study, SOX9+ skin derived stem cells (SOX9+ SDSCs) were isolated from fetal porcine skin and a high-purity SOX9+ SDSCs population was obtained. The SOX9+ SDSCs were induced to transdifferentiate into PGCLCs during 8 days of cultured. The results of RNA-seq, western blot and immunofluorescence staining verified SDSCs have the potential to transdifferentiate into PGCLCs from aspects of transcription factor activation, germ layer differentiation, energy metabolism, and epigenetic changes. Both adherent and suspended cells were collected. The adherent cells were found to be very similar to early porcine primordial germ cells (pPGCs). The suspended cells resembled late stage pPGCs and had a potential to enter meiotic process. This SDSCs culture-induced in vitro model is expected to provide suitable donor cells for stem cell transplantation in the future.
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Affiliation(s)
- Geng Zhang
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin-Xiang Xie
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shu-Er Zhang
- Animal Husbandry General Station of Shandong Province, Jinan, 250010, China
| | - Fa-Li Zhang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Chun-Xiao Li
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Tian Qiao
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Paul W Dyce
- Department of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xin-Lei Feng
- Shandong Animal Products Quality and Safety Center, Jinan, 250010, China
| | - Wei-Bo Lin
- Animal Husbandry Development Center of Changyi City, Weifang, 261300, China
| | - Qi-Cheng Sun
- School of Finance, Southwestern University of Finance and Economics, Chengdu, 611130, China
| | - Wei Shen
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Shun-Feng Cheng
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
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16
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Jacob T, Annusver K, Czarnewski P, Dalessandri T, Kalk C, Levra Levron C, Campamà Sanz N, Kastriti ME, Mikkola ML, Rendl M, Lichtenberger BM, Donati G, Björklund ÅK, Kasper M. Molecular and spatial landmarks of early mouse skin development. Dev Cell 2023; 58:2140-2162.e5. [PMID: 37591247 PMCID: PMC11088744 DOI: 10.1016/j.devcel.2023.07.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 05/05/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023]
Abstract
A wealth of specialized cell populations within the skin facilitates its hair-producing, protective, sensory, and thermoregulatory functions. How the vast cell-type diversity and tissue architecture develops is largely unexplored. Here, with single-cell transcriptomics, spatial cell-type assignment, and cell-lineage tracing, we deconstruct early embryonic mouse skin during the key transitions from seemingly uniform developmental precursor states to a multilayered, multilineage epithelium, and complex dermal identity. We identify the spatiotemporal emergence of hair-follicle-inducing, muscle-supportive, and fascia-forming fibroblasts. We also demonstrate the formation of the panniculus carnosus muscle (PCM), sprouting blood vessels without pericyte coverage, and the earliest residence of mast and dendritic immune cells in skin. Finally, we identify an unexpected epithelial heterogeneity within the early single-layered epidermis and a signaling-rich periderm layer. Overall, this cellular and molecular blueprint of early skin development-which can be explored at https://kasperlab.org/tools-establishes histological landmarks and highlights unprecedented dynamic interactions among skin cells.
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Affiliation(s)
- Tina Jacob
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Karl Annusver
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Paulo Czarnewski
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, 17165 Stockholm, Sweden
| | - Tim Dalessandri
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Christina Kalk
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Chiara Levra Levron
- Department of Life Sciences and Systems Biology, Molecular Biotechnology Center, University of Turin, 10126 Turin, Italy
| | - Nil Campamà Sanz
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Maria Eleni Kastriti
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Marja L Mikkola
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Michael Rendl
- Institute for Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Beate M Lichtenberger
- Skin and Endothelium Research Division, Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, Molecular Biotechnology Center, University of Turin, 10126 Turin, Italy
| | - Åsa K Björklund
- Department of Life Science, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, 41296 Göteborg, Sweden
| | - Maria Kasper
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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17
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Guo J, Mei H, Zhang Y, Che C, Guo L, Zhang Y, Li H, Sun S. Glutamate-aspartate transporter dysfunction enhances aminoglycoside-induced cochlear hair cell death via NMDA receptor activation. Neurochem Int 2023; 169:105587. [PMID: 37495172 DOI: 10.1016/j.neuint.2023.105587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/02/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Glutamate is a crucial neurotransmitter for hearing transduction in the cochlea, but excess glutamate is detrimental to the survival of cochlear sensory cells. Glutamate-aspartate transporter (GLAST) is the major transporter for glutamate removal; however, its role in aminoglycoside-induced hair cell loss is not well studied. In the present study, we first investigated the localization and expression of GLAST over the course of development of the mouse cochlea, and we found that inhibition of GLAST increased hair cell death. However, when the glutamate receptor NMDAR was inhibited by D-AP5, hair cell death was no longer increased by the GLAST inhibitor. Our results indicate that GLAST inhibition aggravates damage to cochlear hair cells, which may occur via NMDAR, and this suggests new clinical strategies for ameliorating the ototoxicity associated with the dysfunction of glutamate metabolism.
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Affiliation(s)
- Jin Guo
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Honglin Mei
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Yanping Zhang
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Chenhao Che
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Luo Guo
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Yunzhong Zhang
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Huawei Li
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; The Institutes of Brain Science and the Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, 200032, China.
| | - Shan Sun
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China.
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18
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Deng Z, Rong S, Gan L, Wang F, Bao L, Cai F, Liao Z, Jin Y, Feng S, Feng Z, Wei Y, Chen R, Jin Y, Zhou Y, Zheng X, Huang L, Zhao L. Temporal transcriptome features identify early skeletal commitment during human epiphysis development at single-cell resolution. iScience 2023; 26:107200. [PMID: 37554462 PMCID: PMC10405011 DOI: 10.1016/j.isci.2023.107200] [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: 12/15/2022] [Revised: 05/18/2023] [Accepted: 06/20/2023] [Indexed: 08/10/2023] Open
Abstract
Human epiphyseal development has been mainly investigated through radiological and histological approaches, uncovering few details of cellular temporal genetic alternations. Using single-cell RNA sequencing, we investigated the dynamic transcriptome changes during post-conception weeks (PCWs) 15-25 of human distal femoral epiphysis cells. We find epiphyseal cells contain multiple subtypes distinguished by specific markers, gene signatures, Gene Ontology (GO) enrichment analysis, and gene set variation analysis (GSVA). We identify the populations committed to cartilage or ossification at this time, although the secondary ossification centers (SOCs) have not formed. We describe the temporal alternation in transcriptional expression utilizing trajectories, transcriptional regulatory networks, and intercellular communication analyses. Moreover, we find the emergence of the ossification-committed population is correlated with the COL2A1-(ITGA2/11+ITGB1) signaling. NOTCH signaling may contribute to the formation of cartilage canals and ossification via NOTCH signaling. Our findings will advance the understanding of single-cell genetic changes underlying fetal epiphysis development.
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Affiliation(s)
- Zhonghao Deng
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Shengwei Rong
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Lu Gan
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Fuhua Wang
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Liangxiao Bao
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Fang Cai
- Department of Obstetrics and Gynecology, Southern Medical University Nanfang Hospital Taihe Branch, Guangzhou, Guangdong 510515, China
| | - Zheting Liao
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yu Jin
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Shuhao Feng
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zihang Feng
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yiran Wei
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Ruge Chen
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yangchen Jin
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yanli Zhou
- Department of Obstetrics and Gynecology, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong 510515, China
| | - Xiaoyong Zheng
- Orthopaedic Department, The 8th medical center of Chinese PLA General Hospital, Beijing 100091, China
| | - Liping Huang
- Department of Obstetrics and Gynecology, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong 510515, China
| | - Liang Zhao
- Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
- Department of Orthopaedic Surgery, Shunde First People Hospital, Foshan, Guangdong 528300, China
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19
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Bensa T, Tekkela S, Rognoni E. Skin fibroblast functional heterogeneity in health and disease. J Pathol 2023; 260:609-620. [PMID: 37553730 DOI: 10.1002/path.6159] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 08/10/2023]
Abstract
Fibroblasts are the major cell population of connective tissue, including the skin dermis, and are best known for their function in depositing and remodelling the extracellular matrix. Besides their role in extracellular matrix homeostasis, fibroblasts have emerged as key players in many biological processes ranging from tissue immunity and wound healing to hair follicle development. Recent advances in single-cell RNA-sequencing technologies have revealed an astonishing transcriptional fibroblast heterogeneity in the skin and other organs. A key challenge in the field is to understand the functional relevance and significance of the identified new cell clusters in health and disease. Here, we discuss the functionally distinct fibroblast subtypes identified in skin homeostasis and repair and how they evolve in fibrotic disease conditions, in particular keloid scars and cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Tjaša Bensa
- Centre for Cell Biology & Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Stavroula Tekkela
- Centre for Cell Biology & Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Emanuel Rognoni
- Centre for Cell Biology & Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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20
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Zou Q, Yuan R, Zhang Y, Wang Y, Zheng T, Shi R, Zhang M, Li Y, Fei K, Feng R, Pan B, Zhang X, Gong Z, Zhu L, Tang G, Li M, Li X, Jiang Y. A single-cell transcriptome atlas of pig skin characterizes anatomical positional heterogeneity. eLife 2023; 12:86504. [PMID: 37276016 DOI: 10.7554/elife.86504] [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: 01/29/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
Different anatomical locations of the body skin show differences in their gene expression patterns depending on different origins, and the inherent heterogeneous information can be maintained in adults. However, highly resolvable cellular specialization is less well characterized in different anatomical regions of the skin. Pig is regarded as an excellent model animal for human skin research in view of its similar physiology to human. In this study, single-cell RNA sequencing was performed on pig skin tissues from six different anatomical regions of Chenghua (CH) pigs, with a superior skin thickness trait, and the back site of large white (LW) pigs. We obtained 233,715 cells, representing seven cell types, among which we primarily characterized the heterogeneity of the top three cell types, including smooth muscle cells (SMCs), endothelial cells (ECs), and fibroblasts (FBs). Then, we further identified several subtypes of SMCs, ECs, and FBs, and discovered the expression patterns of site-specific genes involved in some important pathways such as the immune response and extracellular matrix (ECM) synthesis in different anatomical regions. By comparing differentially expressed genes of skin FBs among different anatomical regions, we considered TNN, COL11A1, and INHBA as candidate genes for facilitating ECM accumulation. These findings of heterogeneity in the main skin cell types from different anatomical sites will contribute to a better understanding of inherent skin information and place the potential focus on skin generation, transmission, and transplantation, paving the foundation for human skin priming.
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Affiliation(s)
- Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, China
| | - Yu Zhang
- BGI Beijing Genome Institute, Beijing, China
| | - Yifei Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Ting Zheng
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Mei Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Kaixin Fei
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Ran Feng
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Binyun Pan
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Xinyue Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Zhengyin Gong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
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21
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Du L, Gan Y, Zheng B, Huang J, Hu Z, Miao Y. An optimized force-triggered density gradient sedimentation method for isolation of pelage follicle dermal papilla cells from neonatal mouse skin. Stem Cell Res Ther 2023; 14:140. [PMID: 37226186 PMCID: PMC10210473 DOI: 10.1186/s13287-023-03343-2] [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: 05/16/2022] [Accepted: 04/12/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The dermal papilla cells are a specialized population of mesenchymal cells located at the base of the hair follicle (HF), which possess the capacity to regulate HF morphogenesis and regeneration. However, lack of cell-type specific surface markers restricts the isolation of DP cells and application for tissue engineering purposes. METHODS We describe a novel force-triggered density gradient sedimentation (FDGS) method to efficiently obtain purified follicular DP-spheres cells from neonatal mouse back skin, utilizing only centrifugation and optimized density gradients. RESULTS Expression of characteristic DP cell markers, alkaline phosphatase, β-catenin, versican, and neural cell adhesion molecules, were confirmed by immunofluorescence. Further, the patch assays demonstrated that DP cells maintained their hair regenerative capacity in vivo. Compared with current methods, including microdissection and fluorescence-activated cell sorting, the FDGS technique is simpler and more efficient for isolating DP cells from neonatal mouse skin. CONCLUSIONS The FDGS method will improve the research potential of neonatal mouse pelage-derived DP cells for tissue engineering purposes.
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Affiliation(s)
- Lijuan Du
- Department of Plastic and Aesthetic Surgery, Nan Fang Hospital of Southern Medical University, 1838 North Guangzhou AV, Guangzhou, Guangdong, China
| | - Yuyang Gan
- Department of Plastic and Aesthetic Surgery, Nan Fang Hospital of Southern Medical University, 1838 North Guangzhou AV, Guangzhou, Guangdong, China
| | - Bowen Zheng
- Department of Plastic and Aesthetic Surgery, Nan Fang Hospital of Southern Medical University, 1838 North Guangzhou AV, Guangzhou, Guangdong, China
| | - Junfei Huang
- Department of Plastic and Aesthetic Surgery, Nan Fang Hospital of Southern Medical University, 1838 North Guangzhou AV, Guangzhou, Guangdong, China
| | - Zhiqi Hu
- Department of Plastic and Aesthetic Surgery, Nan Fang Hospital of Southern Medical University, 1838 North Guangzhou AV, Guangzhou, Guangdong, China.
| | - Yong Miao
- Department of Plastic and Aesthetic Surgery, Nan Fang Hospital of Southern Medical University, 1838 North Guangzhou AV, Guangzhou, Guangdong, China.
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22
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Ge W, Sun YC, Qiao T, Liu HX, He TR, Wang JJ, Chen CL, Cheng SF, Dyce PW, De Felici M, Shen W. Murine skin-derived multipotent papillary dermal fibroblast progenitors show germline potential in vitro. Stem Cell Res Ther 2023; 14:17. [PMID: 36737797 PMCID: PMC9898921 DOI: 10.1186/s13287-023-03243-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Many laboratories have described the in vitro isolation of multipotent cells with stem cell properties from the skin of various species termed skin-derived stem cells (SDSCs). However, the cellular origin of these cells and their capability to give rise, among various cell types, to male germ cells, remain largely unexplored. METHODS SDSCs were isolated from newborn mice skin, and then differentiated into primordial germ cell-like cells (PGCLCs) in vitro. Single-cell RNA sequencing (scRNA-seq) was then applied to dissect the cellular origin of SDSCs using cells isolated from newborn mouse skin and SDSC colonies. Based on an optimized culture strategy, we successfully generated spermatogonial stem cell-like cells (SSCLCs) in vitro. RESULTS Here, using scRNA-seq and analyzing the profile of 7543 single-cell transcriptomes from newborn mouse skin and SDSCs, we discovered that they mainly consist of multipotent papillary dermal fibroblast progenitors (pDFPs) residing in the dermal layer. Moreover, we found that epidermal growth factor (EGF) signaling is pivotal for the capability of these progenitors to proliferate and form large colonies in vitro. Finally, we optimized the protocol to efficiently generate PGCLCs from SDSCs. Furthermore, PGCLCs were induced into SSCLCs and these SSCLCs showed meiotic potential when cultured with testicular organoids. CONCLUSIONS Our findings here identify pDFPs as SDSCs derived from newborn skin and show for the first time that such precursors can be induced to generate cells of the male germline.
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Affiliation(s)
- Wei Ge
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuan-Chao Sun
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Tian Qiao
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hai-Xia Liu
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Tao-Ran He
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jun-Jie Wang
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chun-Lei Chen
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shun-Feng Cheng
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Paul W Dyce
- Department of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Massimo De Felici
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Wei Shen
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China.
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23
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Liu C, Hong T, Yu L, Chen Y, Wang S, Ren Z. Single-nucleus RNA and ATAC sequencing uncovers the molecular and cellular characteristics in the musk gland of Chinese forest musk deer (Moschus berezovskii). FASEB J 2023; 37:e22742. [PMID: 36583723 DOI: 10.1096/fj.202201372r] [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: 08/20/2022] [Revised: 11/21/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022]
Abstract
The Chinese forest musk deer (FMD; Moschus berezovskii) is an endangered artiodactyl mammal. Musk secreted by the musk gland of male has extremely high economic and medicinal value. However, the molecular and cellular characteristics of the musk gland have not been studied. Here, we investigated the diversity and transcriptional composition of musk gland cell types and the effect of cell type-specific chromatin accessibility on gene expression using single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq) association analysis. Based on uniform manifold approximation and projection (UMAP) analysis, we identified 13 cell types from the musk gland, which included two different acinar cells (cluster 0 and cluster 10). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that many pathways related to musk secretion were enriched in acinar cells. Our analysis also revealed acinar cell core transcription factors and core target genes, and further constructed acinar cell-specific regulatory networks. In cluster 0, 11 core target genes (Nedd4l, Adcy9, Akr1c1, Vapb, Me1, Acsl1, Acss3, Srd5a1, Scnn1a, Acadm, and Nceh1) possibly related to musk secretion were regulated by 24 core transcription factors (SP3, NFIC, NR6A1, EHF, RUNX1, TFAP2A, RREB1, GRHL2, NFIB, ELF1, MAX, KLF5, REL, HES1, POU2F3, TFDP1, NR2C1, ATF7, MEIS1, NR4A2, NFIA, PBX1, ZNF652, and NFKB1). In cluster 10, four core target genes (Akr1c1, Pcca, Atp1b1, and Sgk1) possibly related to musk secretion were regulated by 10 core transcription factors (BARX2, EHF, PBX1, RUNX1, NFIB, FOXP1, KLF3, KLF6, ETV6, and NR3C2). Moreover, the credibility of snRNA-seq and snATAC-seq data was verified by fluorescence in situ hybridization and immunohistochemistry. Finally, cell communication analysis demonstrated that the two types of acinar cells mainly have communications in musk secretion-related processes. In conclusion, we provided important insights and invaluable resources for the molecular and cellular characteristics of the musk gland, which will lay a foundation for the study of musk secretion mechanism in the future.
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Affiliation(s)
- Chenmiao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Tingting Hong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lin Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuan Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhanjun Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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24
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Comparative Analysis of mRNA and miRNA Expression between Dermal Papilla Cells and Hair Matrix Cells of Hair Follicles in Yak. Cells 2022; 11:cells11243985. [PMID: 36552749 PMCID: PMC9776824 DOI: 10.3390/cells11243985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
The interaction between the dermal papilla cells (DPCs) and epidermal hair matrix cells (HMCs) of hair follicles (HFs) is crucial for the growth and development of HFs, but the molecular mechanism is complex and remains unclear. MicroRNAs (miRNAs) are the key signaling molecules for cellular communication. In this study, the DPCs and HMCs of yak were isolated and cultured, and the differentially expressed mRNA and miRNA were characterized to analyze the molecular basis of the interaction between DPCs and HMCs during hair follicle (HF) development in yak. The mRNA differential expression and functional enrichment analysis revealed that there were significant differences between DPCs and HMCs, and they showed the molecular functional characteristics of dermal cells and epidermal cells, respectively. Multiple KEGG pathways related to HF development were enriched in the highly expressed genes in DPCs, while the pathways associated with microbiota and immunity were significantly enriched in the highly expressed genes in HMCs. By combining analysis with our previous 10× genomics single-cell transcriptome data, 39 marker genes of DPCs of yak were identified. A total of 123 relatively specifically expressed miRNAs were screened; among these, the miRNAs associated with HF development such as miR-143, miR-214, miR-125b, miR-31, and miR-200 were presented. In conclusion, the large changes in yak DPCs and HMCs for both mRNA and miRNA expression were revealed, and numerous specifically expressed mRNAs and miRNAs in DPCs or HMCs were identified, which may contribute to the interaction and cellular communication between DPCs and HMCs during HF development in yak.
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25
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Construction of transcriptome atlas of white yak hair follicle during anagen and catagen using single-cell RNA sequencing. BMC Genomics 2022; 23:813. [PMID: 36482306 PMCID: PMC9730603 DOI: 10.1186/s12864-022-09003-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND As the direct organ of villus, hair follicles have obvious seasonal cycles. The hair follicle cycle is orchestrated by multiple cell types that together direct cell renewal and differentiation. But the regulation property of hair follicle cells from anagen to catagen in yak is still unknown. RESULTS In this study, single-cell RNA sequencing was performed on 24,124 single cells of the scapular skin from white yak. Based on tSNE cluster analysis, the cell types of IFE-DC, epidermal cell lines, fibroblasts, keratinocytes, IRS, DS, INFU, and other cells in yak hair follicles during anagen and catagen were successfully identified, and the gene expression profiles were described. The GO enrichment analysis indicated the different cells characteristic genes to be mainly enriched in the epidermal development, epithelial cell differentiation and wound healing pathways. The pseudotime trajectory analysis described the differentiation trajectory of the epidermal lineage and dermal lineage of the hair follicle during anagen and catagen. Moreover, the dynamic changes of the genes like LHX2, KRT25, and KRT71 were found to be highly expressed in HS and IRS, but not in the IFE-DC, INFU, and keratinocyte during differentiation. CONCLUSIONS Our results analyzed the time-varying process of gene expression in the dermal cell lineage and epidermal cell lineage of hair follicles during anagen and catagen during fate differentiation was expounded at the single cell level, revealing the law of fate specialization of different types of cells. In addition, based on the enrichment analysis, the transcriptional regulatory factors involved in the different cell fates were also revealed. These results will help to enhance our understanding of yak hair follicle cycle and promote the development and utilization of yak villus.
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Single-cell chromatin landscapes of mouse skin development. Sci Data 2022; 9:741. [PMID: 36460683 PMCID: PMC9718782 DOI: 10.1038/s41597-022-01839-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
The coat of mammals is produced by hair follicles, and hair follicle is an important and complex accessory organ of skin. As a complex physiological regulation process, hair follicle morphogenesis is regulated by a series of signal pathway factors, involves the interaction of multiple cell types and begins in the early embryonic stage. However, its transcriptional regulatory mechanism is unclear. We have therefore utilized single-cell ATAC sequencing to obtain the chromatin accessibility landscapes of 6,928, 6,961 and 7,374 high-quality cells from the dorsal skins of E13.5, E16.5 and P0 mice (Mus musculus), respectively. Based on marker gene activity clustering, we defined 6, 8 and 5 distinct cell types in E13.5, E16.5 and P0 stages, respectively. Furtherly, we integrated the fibroblasts and keratinocytes clusters, performed further analysis and re-clustered. The single cell map of the chromatin open area was drawn from each cell type and the mechanism of cell transcription regulation was explored. Collectively, our data provide a reference for deeply exploring the epigenetic regulation mechanism of mouse hair follicles development.
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Zhou Y, Huang Z, Wang C, Su J, Jiang P, Li L, Qin J, Xie Z. Investigation of hub genes and immune infiltration in androgenetic alopecia using bioinformatics analysis. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1226. [PMID: 36544676 PMCID: PMC9761178 DOI: 10.21037/atm-22-4634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022]
Abstract
Background Androgenetic alopecia (AGA) is a type of non-scarring hair loss. Current drugs for AGA are accompanied by adverse reactions and a high recurrence rate. Thus, the discovery of diagnostic biomarkers and therapeutic targets for AGA remains imperatively warranted. Methods The GSE90594 dataset, which contained scalp skin biopsies from 14 male AGA cases and healthy volunteers, was used to identify the differentially expressed genes (DEGs). Functional enrichment analysis was subsequently performed. Next, the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database combined with the cytoHubba plugin of Cytoscape were used to obtain the key genes of AGA. Thereafter, the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was performed to evaluate the relative abundance of immune cells between male AGA patients and healthy controls. The correlation between key genes and infiltrating immune cells was analyzed to obtain the significant immune-cell related genes (IRGs), then intersected with the DEGs between immortalized balding and non-balding human dermal papilla cells (DPCs) of the GSE93766 dataset as well as the DEGs obtained by the GSE90594 dataset, thus obtaining the hub genes of AGA. Finally, the hub genes were validated using GSE36169, which contained expression profiling of tissues biopsied from haired and bald scalps of five individuals with AGA. Results A total of 234 DEGs were obtained from the GSE90594 dataset, which were mainly enriched in the extracellular matrix (ECM)-related pathways and immune-related activities. The STRING database and ten algorithms in the cytoHubba plugin of Cytoscape disclosed 21 key DEGs. The results of the CIBERSORT algorithm revealed the relative abundances of 20 kinds of immune cells between diseased and healthy individuals, and yielded 15 IRGs involved in the pathogenesis of AGA. Next, the intersection analysis identified four hub genes of AGA, comprising COL1A2, PCOLCE, ITGAX, and LOX. The GSE36169 dataset validated the expression pattern of hub genes in the haired scalp of AGA patients. Conclusions We discovered that the hub genes identified are closely linked with the causative factors of AGA, which could be used as the viable diagnostic and therapeutic target in the clinical applications.
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Affiliation(s)
- Yuan Zhou
- Department of Dermatology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zhongbo Huang
- Department of Laboratory Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Chen Wang
- Department of Dermatology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jinping Su
- Department of Dermatology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Ping Jiang
- Department of Dermatology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lili Li
- Department of Dermatology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jinglin Qin
- Department of Dermatology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zhi Xie
- Department of Dermatology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Talbott HE, Mascharak S, Griffin M, Wan DC, Longaker MT. Wound healing, fibroblast heterogeneity, and fibrosis. Cell Stem Cell 2022; 29:1161-1180. [PMID: 35931028 PMCID: PMC9357250 DOI: 10.1016/j.stem.2022.07.006] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fibroblasts are highly dynamic cells that play a central role in tissue repair and fibrosis. However, the mechanisms by which they contribute to both physiologic and pathologic states of extracellular matrix deposition and remodeling are just starting to be understood. In this review article, we discuss the current state of knowledge in fibroblast biology and heterogeneity, with a primary focus on the role of fibroblasts in skin wound repair. We also consider emerging techniques in the field, which enable an increasingly nuanced and contextualized understanding of these complex systems, and evaluate limitations of existing methodologies and knowledge. Collectively, this review spotlights a diverse body of research examining an often-overlooked cell type-the fibroblast-and its critical functions in wound repair and beyond.
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Affiliation(s)
- Heather E Talbott
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shamik Mascharak
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michelle Griffin
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Derrick C Wan
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Michael T Longaker
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Liu Y, Guerrero-Juarez CF, Xiao F, Shettigar NU, Ramos R, Kuan CH, Lin YC, de Jesus Martinez Lomeli L, Park JM, Oh JW, Liu R, Lin SJ, Tartaglia M, Yang RB, Yu Z, Nie Q, Li J, Plikus MV. Hedgehog signaling reprograms hair follicle niche fibroblasts to a hyper-activated state. Dev Cell 2022; 57:1758-1775.e7. [PMID: 35777353 PMCID: PMC9344965 DOI: 10.1016/j.devcel.2022.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 03/10/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023]
Abstract
Hair follicle stem cells are regulated by dermal papilla fibroblasts, their principal signaling niche. Overactivation of Hedgehog signaling in the niche dramatically accelerates hair growth and induces follicle multiplication in mice. On single-cell RNA sequencing, dermal papilla fibroblasts increase heterogeneity to include new Wnt5ahigh states. Transcriptionally, mutant fibroblasts activate regulatory networks for Gli1, Alx3, Ebf1, Hoxc8, Sox18, and Zfp239. These networks jointly upregulate secreted factors for multiple hair morphogenesis and hair-growth-related pathways. Among these is non-conventional TGF-β ligand Scube3. We show that in normal mouse skin, Scube3 is expressed only in dermal papillae of growing, but not in resting follicles. SCUBE3 protein microinjection is sufficient to induce new hair growth, and pharmacological TGF-β inhibition rescues mutant hair hyper-activation phenotype. Moreover, dermal-papilla-enriched expression of SCUBE3 and its growth-activating effect are partially conserved in human scalp hair follicles. Thus, Hedgehog regulates mesenchymal niche function in the hair follicle via SCUBE3/TGF-β mechanism.
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Affiliation(s)
- Yingzi Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Christian F Guerrero-Juarez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA; Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Fei Xiao
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Nitish Udupi Shettigar
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA; Amplifica Holdings Group, Inc., San Diego, CA 92128, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Chen-Hsiang Kuan
- Division of Plastic Surgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yuh-Charn Lin
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Jung Min Park
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Korea; Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji Won Oh
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Korea; Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Korea; Hair Transplantation Center, Kyungpook National University Hospital, Daegu, Korea
| | - Ruiqi Liu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Sung-Jan Lin
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan; Institute of Biomedical Engineering and Department of Dermatology, National Taiwan University, Taipei, Taiwan
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA.
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Kang MS, Kwon M, Lee SH, Kim WH, Lee GW, Jo HJ, Kim B, Yang SY, Kim KS, Han DW. 3D printing of skin equivalents with hair follicle structures and epidermal-papillary-dermal layers using gelatin/hyaluronic acid hydrogels. Chem Asian J 2022; 17:e202200620. [PMID: 35866189 DOI: 10.1002/asia.202200620] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/18/2022] [Indexed: 11/10/2022]
Abstract
Recent advances in three-dimensional (3D) bioprinting technologies enabled the fabrication of sophisticated live 3D tissue analogs. Although various hydrogel-based bioink has been reported, the development of advanced bioink materials that can reproduce the composition of native extracellular matrix (ECM) accurately and mimic the intrinsic property of laden cells is still challenging. In this work, 3D printed skin equivalents incorporating hair follicle structures and epidermal-papillary-dermal layers are fabricated with gelatin methacryloyl (GelMA)/hyaluronic acid (HA) MA (HAMA) hydrogel (GelMA/HAMA) bioink. The composition of collagen and glycosaminoglycan (GAG) of native skin was recapitulated by adjusting the combination of GelMA and HAMA. The GelMA/HAMA bioink was proven to have excellent viscoelastic and physicochemical properties, 3D printability, cytocompatibility, and functionality to maintain the hair inductive potency and facilitated spontaneous hair pore development. Overall, we suggest that the GelMA/HAMA hydrogels can be promising candidates as bioinks for the 3D printing of skin equivalents with epidermal-papillary-dermal multi-layers and hair follicle structures, and they might serve as a useful model in skin tissue engineering and regeneration.
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Affiliation(s)
- Moon Sung Kang
- Pusan National University, Cogno-Mechatronics Engineering, KOREA, REPUBLIC OF
| | - Mina Kwon
- Pusan National University, School of Chemical Engineering, KOREA, REPUBLIC OF
| | - Seok Hyun Lee
- Pusan National University, Cogno-Mechatronics Engineering, KOREA, REPUBLIC OF
| | - Won-Hyeon Kim
- Seoul National University Dental Hospital, Dental Life Science Research Institute, KOREA, REPUBLIC OF
| | - Gyeong Won Lee
- Pusan National University - Milyang Campus, Biomaterials Science, KOREA, REPUBLIC OF
| | - Hyo Jung Jo
- Pusan National University, Cogno-Mechatronics Engineering, KOREA, REPUBLIC OF
| | - Bongju Kim
- Seoul National University Dental Hospital, Dental Life Science Research Institute, KOREA, REPUBLIC OF
| | - Seung Yun Yang
- Pusan National University - Milyang Campus, Biomaterials Science, KOREA, REPUBLIC OF
| | - Ki Su Kim
- Pusan National University, School of Chemical Engineering, KOREA, REPUBLIC OF
| | - Dong-Wook Han
- Pusan National University, Cogno-Mechatronics Engineering, Department of Cogno-Mechatronics Engineering, College of Nanoscience & Nanotechnology, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea, 46241, Busan, KOREA, REPUBLIC OF
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31
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Cellular Heterogeneity Facilitates the Functional Differences Between Hair Follicle Dermal Sheath Cells and Dermal Papilla Cells: A New Classification System for Mesenchymal Cells within the Hair Follicle Niche. Stem Cell Rev Rep 2022; 18:2016-2027. [PMID: 35849252 DOI: 10.1007/s12015-022-10411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2022] [Indexed: 10/17/2022]
Abstract
Mesenchymal stem cells (MSCs) are known for their self-renewal and multi-lineage differentiation potential, with these cells often being evaluated in the regulation and maintenance of specific cellular niches including those of the hair follicle. Most mesenchymal stem cells in the hair follicles are housed in the dermal papilla (DP) and dermal sheath (DS), with both niches characterized by a broad variety of cellular subsets. However, while most previous studies describing the hair follicle mesenchymal niche treated all DP and DS cells as Hair Follicle Mesenchymal Stem Cells (HF-MSCs), the high number of cellular subsets would suggest that these cells are actually too heterogenous for such a broad definition. Given this we designed this study to evaluate the differentiation processes in these cells and used this data to create a new set of classifications for DP and DS cells, dividing them into "hair follicle mesenchymal stem cells (HF-MSCs)", "hair follicle mesenchymal progenitor cells (HF-MPCs)", and "hair follicle mesenchymal functional cells (HF-MFCs)". In addition, those cells that possess self-renewal and differentiation were re-named hair follicle derived mesenchymal multipotent cells (HF-MMCs). This new classification may help to further our understanding of the heterogeneity of hair follicle dermal cells and provide new insights into their evaluation.
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32
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He J, Zhao B, Huang X, Fu X, Liu G, Tian Y, Wu C, Mao J, Liu J, Gun S, Tian K. Gene network analysis reveals candidate genes related with the hair follicle development in sheep. BMC Genomics 2022; 23:428. [PMID: 35672687 PMCID: PMC9175362 DOI: 10.1186/s12864-022-08552-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
Background Merino sheep are the most famous fine wool sheep in the world. They have high wool production and excellent wool quality and have attracted worldwide attention. The fleece of the Merino sheep is composed predominantly of wool fibers grown from secondary wool follicles. Therefore, it is necessary to study the development of hair follicles to understand the mechanism of wool production. The hair follicle is a complex biological system involved in a dynamic process governed by gene regulation. The hair follicle development process is very complex and poorly understood. The purpose of our research is to identify candidate genes related to hair follicle development, provide a theoretical molecular breeding basis for the cultivation of fine wool sheep, and provide a reference for the problems of hair loss and alopecia areata that affect human beings. Results We analyzed mRNAs data in skin tissues of 18 Merino sheep at four embryonic days (E65, E85, E105 and E135) and two postnatal days (P7 and P30). G1 to G6 represent hair follicles developmental at six stages (i.e. E65 to P30). We identified 7879 differentially expressed genes (DEGs) and 12623 novel DEGs, revealed different expression patterns of these DEGs at six stages of hair follicle development, and demonstrated their complex interactions. DEGs with stage-specific expression were significantly enriched in epidermal differentiation and development, hair follicle development and hair follicle morphogenesis and were enriched in many pathways related to hair follicle development. The key genes (LAMA5, WNT10A, KRT25, SOSTDC1, ZDHHC21, FZD1, BMP7, LRP4, TGFβ2, TMEM79, SOX10, ITGB4, KRT14, ITGA6, and GLI2) affecting hair follicle morphogenesis were identified by network analysis. Conclusion This study provides a new reference for the molecular basis of hair follicle development and lays a foundation for further improving sheep hair follicle breeding. Candidate genes related to hair follicular development were found, which provided a theoretical basis for molecular breeding for the culture of fine wool sheep. These results are a valuable resource for biological investigations of fleece evolution in animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08552-2.
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Affiliation(s)
- Junmin He
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bingru Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Guifen Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Cuiling Wu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jingyi Mao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jing Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
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Ganier C, Rognoni E, Goss G, Lynch M, Watt FM. Fibroblast Heterogeneity in Healthy and Wounded Skin. Cold Spring Harb Perspect Biol 2022; 14:a041238. [PMID: 35667795 PMCID: PMC9248828 DOI: 10.1101/cshperspect.a041238] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Fibroblasts are the main cell type in the dermis. They are responsible for the synthesis and deposition of structural proteins such as collagen and elastin, which are integrated into the extracellular matrix (ECM). Mouse and human studies using flow cytometry, cell culture, skin reconstitution, and lineage tracing experiments have shown the existence of different subpopulations of fibroblasts, including papillary fibroblasts, reticular fibroblasts, and fibroblasts comprising the dermal papilla at the base of the hair follicle. In recent years, the technological advances in single-cell sequencing have allowed researchers to study the repertoire of cells present in full-thickness skin including the dermis. Multiple groups have confirmed that distinct fibroblast populations can be identified in mouse and human dermis on the basis of differences in the transcriptional profile. Here, we discuss the current state of knowledge regarding dermal fibroblast heterogeneity in healthy mouse and human skin, highlighting the similarities and differences between mouse and human fibroblast subpopulations. We also discuss how fibroblast heterogeneity may provide insights into physiological wound healing and its dysfunction in pathological states such as hypertrophic and keloid scars.
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Affiliation(s)
- Clarisse Ganier
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Emanuel Rognoni
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Georgina Goss
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Magnus Lynch
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, London SE1 9RT, United Kingdom
- St John's Institute of Dermatology, King's College London, London SE1 9RT, United Kingdom
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, London SE1 9RT, United Kingdom
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Lin X, Zhu L, He J. Morphogenesis, Growth Cycle and Molecular Regulation of Hair Follicles. Front Cell Dev Biol 2022; 10:899095. [PMID: 35646909 PMCID: PMC9133560 DOI: 10.3389/fcell.2022.899095] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/18/2022] [Indexed: 12/19/2022] Open
Abstract
As one of the main appendages of skin, hair follicles play an important role in the process of skin regeneration. Hair follicle is a tiny organ formed by the interaction between epidermis and dermis, which has complex and fine structure and periodic growth characteristics. The hair growth cycle is divided into three continuous stages, growth (anagen), apoptosis-driven regression (catagen) and relative quiescence (telogen). And The Morphogenesis and cycle of hair follicles are regulated by a variety of signal pathways. When the signal molecules in the pathways are abnormal, it will affect the development and cycle of hair follicles, which will lead to hair follicle-related diseases.This article will review the structure, development, cycle and molecular regulation of hair follicles, in order to provide new ideas for solving diseases and forming functional hair follicle.
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35
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Mao MQ, Jing J, Miao YJ, Lv ZF. Epithelial-Mesenchymal Interaction in Hair Regeneration and Skin Wound Healing. Front Med (Lausanne) 2022; 9:863786. [PMID: 35492363 PMCID: PMC9048199 DOI: 10.3389/fmed.2022.863786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022] Open
Abstract
Interactions between epithelial and mesenchymal cells influence hair follicles (HFs) during embryonic development and skin regeneration following injury. Exchanging soluble molecules, altering key pathways, and extracellular matrix signal transduction are all part of the interplay between epithelial and mesenchymal cells. In brief, the mesenchyme contains dermal papilla cells, while the hair matrix cells and outer root sheath represent the epithelial cells. This study summarizes typical epithelial–mesenchymal signaling molecules and extracellular components under the control of follicular stem cells, aiming to broaden our current understanding of epithelial–mesenchymal interaction mechanisms in HF regeneration and skin wound healing.
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Wang J, Wu X, Kang Y, Zhang L, Niu H, Qu J, Wang Y, Ji D, Li Y. Integrative analysis of circRNAs from Yangtze River Delta white goat neck skin tissue by high-throughput sequencing (circRNA-seq). Anim Genet 2022; 53:405-415. [PMID: 35383992 DOI: 10.1111/age.13198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/16/2022] [Accepted: 03/22/2022] [Indexed: 01/22/2023]
Abstract
The Yangtze River Delta white goat is a unique goat species that can produce superior-quality brush hair. The formation of this brush hair is controlled by a series of critical genes and related signaling pathways. Circular RNAs (circRNAs), are ubiquitous endogenous non-coding RNAs that regulate many biological and physiological processes in mammals. However, little is known about the potential regulatory role of circRNAs on superior-quality brush hair formation in Yangtze River Delta white goat. In this study, high-throughput sequencing technology was used to only detect circRNAs in the neck skin tissue of normal-quality goats (NHQs) and superior-quality goats (HQs). A total of 61 803 circRNAs were identified and 32 of them were differentially expressed in the NHQ group vs. the HQ group. Functional enrichment analysis showed that the source gene of differentially expressed circRNAs (DE-circRNAs) was enriched mostly in platelet activation and the focal adhesion signal pathway. Action mechanism analysis revealed that DE-circRNAs could sponge to many identified miRNAs, including miR-31, miR-125b, miR-let-7a and miR-149-5p, which have important roles in goat hair follicle stem cell growth, hair follicle development and morphogenesis. Altogether, our findings provide a valuable basis for studying circRNAs involved in superior-quality brush hair traits and meanwhile advance our understanding of circRNA complex regulation mechanisms in Yangtze River Delta white goat skin hair follicle development.
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Affiliation(s)
- Jian Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Xi Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yan Kang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Liuming Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Haoyuan Niu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingwen Qu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yanhu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Dejun Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yongjun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
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37
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Wang S, Wu T, Sun J, Li Y, Yuan Z, Sun W. Single-Cell Transcriptomics Reveals the Molecular Anatomy of Sheep Hair Follicle Heterogeneity and Wool Curvature. Front Cell Dev Biol 2022; 9:800157. [PMID: 34993204 PMCID: PMC8724054 DOI: 10.3389/fcell.2021.800157] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/26/2021] [Indexed: 12/19/2022] Open
Abstract
Wool is the critical textile raw material which is produced by the hair follicle of sheep. Therefore, it has important implications to investigate the molecular mechanism governing hair follicle development. Due to high cellular heterogeneity as well as the insufficient cellular, molecular, and spatial characterization of hair follicles on sheep, the molecular mechanisms involved in hair follicle development and wool curvature of sheep remains largely unknown. Single-cell RNA sequencing (scRNA-seq) technologies have made it possible to comprehensively dissect the cellular composition of complex skin tissues and unveil the differentiation and spatial signatures of epidermal and hair follicle development. However, such studies are lacking so far in sheep. Here, single-cell suspensions from the curly wool and straight wool lambskins were prepared for unbiased scRNA-seq. Based on UAMP dimension reduction analysis, we identified 19 distinct cell populations from 15,830 single-cell transcriptomes and characterized their cellular identity according to specific gene expression profiles. Furthermore, novel marker gene was applied in identifying dermal papilla cells isolated in vitro. By using pseudotime ordering analysis, we constructed the matrix cell lineage differentiation trajectory and revealed the dynamic gene expression profiles of matrix progenitors' commitment to the hair shaft and inner root sheath (IRS) cells. Meanwhile, intercellular communication between mesenchymal and epithelial cells was inferred based on CellChat and the prior knowledge of ligand–receptor pairs. As a result, strong intercellular communication and associated signaling pathways were revealed. Besides, to clarify the molecular mechanism of wool curvature, differentially expressed genes in specific cells between straight wool and curly wool were identified and analyzed. Our findings here provided an unbiased and systematic view of the molecular anatomy of sheep hair follicle comprising 19 clusters; revealed the differentiation, spatial signatures, and intercellular communication underlying sheep hair follicle development; and at the same time revealed the potential molecular mechanism of wool curvature, which will give important new insights into the biology of the sheep hair follicle and has implications for sheep breeding.
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Affiliation(s)
- Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tianyi Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingyi Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yue Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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38
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Hernandez JOR, Wang X, Vazquez-Segoviano M, Lopez-Marfil M, Sobral-Reyes MF, Moran-Horowich A, Sundberg M, Lopez-Cantu DO, Probst CK, Ruiz-Esparza GU, Giannikou K, Abdi R, Henske EP, Kwiatkowski DJ, Sahin M, Lemos DR. A tissue-bioengineering strategy for modeling rare human kidney diseases in vivo. Nat Commun 2021; 12:6496. [PMID: 34764250 PMCID: PMC8586030 DOI: 10.1038/s41467-021-26596-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/13/2021] [Indexed: 01/03/2023] Open
Abstract
The lack of animal models for some human diseases precludes our understanding of disease mechanisms and our ability to test prospective therapies in vivo. Generation of kidney organoids from Tuberous Sclerosis Complex (TSC) patient-derived-hiPSCs allows us to recapitulate a rare kidney tumor called angiomyolipoma (AML). Organoids derived from TSC2-/- hiPSCs but not from isogenic TSC2+/- or TSC2+/+ hiPSCs share a common transcriptional signature and a myomelanocytic cell phenotype with kidney AMLs, and develop epithelial cysts, replicating two major TSC-associated kidney lesions driven by genetic mechanisms that cannot be consistently recapitulated with transgenic mice. Transplantation of multiple TSC2-/- renal organoids into the kidneys of immunodeficient rats allows us to model AML in vivo for the study of tumor mechanisms, and to test the efficacy of rapamycin-loaded nanoparticles as an approach to rapidly ablate AMLs. Collectively, our experimental approaches represent an innovative and scalable tissue-bioengineering strategy for modeling rare kidney disease in vivo.
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Affiliation(s)
- J O R Hernandez
- Renal Division, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - X Wang
- Renal Division, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | | | - M Lopez-Marfil
- Renal Division, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - M F Sobral-Reyes
- Renal Division, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - A Moran-Horowich
- Renal Division, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - M Sundberg
- Rosamund Zander Stone Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - D O Lopez-Cantu
- Renal Division, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - C K Probst
- Cancer Genetics Lab, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - G U Ruiz-Esparza
- Renal Division, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - K Giannikou
- Harvard Medical School, Boston, MA, 02115, USA
- Cancer Genetics Lab, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - R Abdi
- Transplantation Research Center, Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - E P Henske
- Harvard Medical School, Boston, MA, 02115, USA
- Cancer Genetics Lab, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - D J Kwiatkowski
- Harvard Medical School, Boston, MA, 02115, USA
- Cancer Genetics Lab, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - M Sahin
- Rosamund Zander Stone Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - D R Lemos
- Renal Division, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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39
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Ge W, Zhang W, Zhang Y, Zheng Y, Li F, Wang S, Liu J, Tan S, Yan Z, Wang L, Shen W, Qu L, Wang X. A Single-cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:437-451. [PMID: 34534715 PMCID: PMC8864196 DOI: 10.1016/j.gpb.2021.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/17/2021] [Accepted: 08/02/2021] [Indexed: 01/06/2023]
Abstract
Cashmere, also known as soft gold, is produced from the secondary hair follicles (SHFs) of cashmere goats. The number of SHFs determines the yield and quality of cashmere; therefore, it is of interest to investigate the transcriptional profiles present during cashmere goat hair follicle development. However, mechanisms underlying this development process remain largely unexplored, and studies regarding hair follicle development mostly use a murine research model. In this study, to provide a comprehensive understanding of cellular heterogeneity and cell fate decisions, single-cell RNA sequencing was performed on 19,705 single cells of the dorsal skin from cashmere goat fetuses at induction (embryonic day 60; E60), organogenesis (E90), and cytodifferentiation (E120) stages. For the first time, unsupervised clustering analysis identified 16 cell clusters, and their corresponding cell types were also characterized. Based on lineage inference, a detailed molecular landscape was revealed along the dermal and epidermal cell lineage developmental pathways. Notably, our current data also confirmed the heterogeneity of dermal papillae from different hair follicle types, which was further validated by immunofluorescence analysis. The current study identifies different biomarkers during cashmere goat hair follicle development and has implications for cashmere goat breeding in the future.
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Affiliation(s)
- Wei Ge
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Weidong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuelang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yujie Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shanhe Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; College of Animal Science & Technology, Yangzhou University, Yangzhou 225000, China
| | - Jinwang Liu
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Shaojing Tan
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Zihui Yan
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Lu Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Lei Qu
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Xin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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40
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Ge W, Yan ZH, Wang L, Tan SJ, Liu J, Reiter RJ, Luo SM, Sun QY, Shen W. A hypothetical role for autophagy during the day/night rhythm-regulated melatonin synthesis in the rat pineal gland. J Pineal Res 2021; 71:e12742. [PMID: 33960014 DOI: 10.1111/jpi.12742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/12/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022]
Abstract
Melatonin is a highly conserved molecule that regulates day/night rhythms; it is associated with sleep improvement, reactive oxygen species (ROS) scavenging, anti-aging effects, and seasonal and circadian rhythms and has been a hot topic of research for decades. Using single-cell RNA sequencing, a recent study describes a single-cell transcriptome atlas for the rat pineal gland. Based on a more comprehensive analysis of the retrieved data (Mays et al., PLoS One, 2018, 13, e0205883), results from the current study unveiled the underappreciated gene regulatory network behind different cell populations in the pineal gland. More importantly, our study here characterized, for the first time, the day/night activation of autophagy flux in the rat pineal gland, indicating a potential role of autophagy in regulating melatonin synthesis in the rat pineal gland. These findings emphasized a hypothetical role of day/night autophagy in linking the biological clock with melatonin synthesis. Furthermore, ultrastructure analysis of pinealocytes provided fascinating insights into differences in their intracellular structure between daytime and nighttime. In addition, we also provide a preliminary description of cell-cell communication in the rat pineal gland. In summary, the current study unveils the day/night regulation of autophagy in the rat pineal gland, raising a potential role of autophagy in day/night-regulated melatonin synthesis.
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Affiliation(s)
- Wei Ge
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Zi-Hui Yan
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lu Wang
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shao-Jing Tan
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jing Liu
- Central Laboratory of Qingdao Agricultural University, Qingdao Agricultural University, Qingdao, China
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, Long School of Medicine, UT Health, San Antonio, TX, USA
| | - Shi-Ming Luo
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Wei Shen
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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41
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Chovatiya G, Ghuwalewala S, Walter LD, Cosgrove BD, Tumbar T. High-resolution single-cell transcriptomics reveals heterogeneity of self-renewing hair follicle stem cells. Exp Dermatol 2021; 30:457-471. [PMID: 33319418 PMCID: PMC8016723 DOI: 10.1111/exd.14262] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/30/2020] [Accepted: 12/09/2020] [Indexed: 12/17/2022]
Abstract
Multipotent bulge stem cells (SCs) fuel the hair follicle (HF) cyclic growth during adult skin homeostasis, but their intrinsic molecular heterogeneity is not well understood. These hair follicle stem cells (HFSCs) engage in bouts of self-renewal, migration and differentiation during the hair cycle. Here, we perform high-resolution single-cell RNA sequencing (scRNA-seq) of HFSCs sorted as CD34+ /K14-H2BGFP+ from mouse skin at mid-anagen, the self-renewal stage. We dissect the transcriptomic profiles and unravel population-specific transcriptional heterogeneity. Unsupervised clustering reveals five major HFSC populations, which distinguished by known markers associated with both the bulge and the outer root sheath (ORS) underneath. These populations include quiescent bulge, ORS cellular states and proliferative cells. Lineage trajectory analysis predicted the prospective differentiation path of these cellular states and their corresponding self-renewing subpopulations. The bulge population itself can be further sub-divided into distinct subpopulations that can be mapped to the upper, mid and lower bulge regions, and present a decreasing quiescence score. Gene set enrichment analysis (GSEA) revealed new markers and suggested potentially distinct functions of the ORS and bulge subpopulations. This included communications between the upper bulge subpopulation and sensory nerves and between the upper ORS and skin vasculature, as well as enrichment of a bulge subset in cell migratory functions. The lower ORS enriched genes may potentially enable nutrients passing from the surrounding fat and vasculature cells towards the proliferating hair matrix cells. Thus, we provide a comprehensive account of HFSC molecular heterogeneity during their self-renewing stage, which enables future HF functional studies.
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Affiliation(s)
- Gopal Chovatiya
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Sangeeta Ghuwalewala
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Lauren D. Walter
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Benjamin D. Cosgrove
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Tudorita Tumbar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
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42
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Han B, Yan Z, Yu S, Ge W, Li Y, Wang Y, Yang B, Shen W, Jiang H, Sun Z. Infertility network and hub genes for nonobstructive azoospermia utilizing integrative analysis. Aging (Albany NY) 2021; 13:7052-7066. [PMID: 33621950 PMCID: PMC7993690 DOI: 10.18632/aging.202559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/29/2020] [Indexed: 11/25/2022]
Abstract
Non-obstructive azoospermia (NOA) is the most severe form of male infertility owing to the absence of sperm during ejaculation as a result of failed spermatogenesis. The molecular mechanisms of NOA have not been well studied. Here, we revealed the dysregulated differentially expressed genes in NOA and related signaling pathways or biological processes. Cluster features of biological processes include spermatogenesis, fertilization, cilium movement, penetration of zona pellucida, sperm chromatin condensation, and being significantly enriched metabolic pathways in proximal tubule bicarbonate reclamation, aldosterone synthesis and secretion, glycolysis and glycogenesis pathways in NOA using Gene Ontology analysis and pathway enrichment analysis. The NOA gene co-expression network was constructed by weighted gene co-expression network analysis to identify the hub genes (CHD5 and SPTBN2). In addition, we used another Gene Expression Omnibus dataset (GSE45887) to validate these hub genes. Furthermore, we used the Seurat package to classify testicular tissue cells from NOA patients and to characterize the differential expression of hub genes in different cell types from different adult males based on the scRNA-seq dataset (GSE106487). These results provide new insights into the pathogenesis of NOA. Of particular note, CHD5 and SPTBN2 may be potential biomarkers for the diagnosis and treatment of NOA.
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Affiliation(s)
- Baoquan Han
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Zihui Yan
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuai Yu
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Wei Ge
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Yaqi Li
- Department of Urology, Zaozhuang Hospital of Zaozhuang Mining Group, Zaozhuang 277100, China
| | - Yan Wang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Bo Yang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China
| | - Wei Shen
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China.,College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Hui Jiang
- Department of Urology, Department of Andrology, Department of Human Sperm Bank, Peking University Third Hospital, Beijing 100191, China
| | - Zhongyi Sun
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
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43
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Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH, Myung P, Plikus MV, Nie Q. Inference and analysis of cell-cell communication using CellChat. Nat Commun 2021; 12:1088. [PMID: 33597522 PMCID: PMC7889871 DOI: 10.1038/s41467-021-21246-9] [Citation(s) in RCA: 2281] [Impact Index Per Article: 760.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer ( http://www.cellchat.org/ ) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues.
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Affiliation(s)
- Suoqin Jin
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Christian F Guerrero-Juarez
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Lihua Zhang
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Ivan Chang
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
- Research Cyberinfrastructure Center, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Chen-Hsiang Kuan
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Plastic Surgery, Department of Surgery, National Taiwan University, Taipei, Taiwan
| | - Peggy Myung
- Department of Dermatology, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Maksim V Plikus
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
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44
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Wang J, Sui J, Mao C, Li X, Chen X, Liang C, Wang X, Wang SH, Jia C. Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats. Genes (Basel) 2021; 12:genes12020180. [PMID: 33513983 PMCID: PMC7911279 DOI: 10.3390/genes12020180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
The development of hair follicle in cashmere goats shows significant periodic change, as with mice and humans. However, for cashmere goat with double-coat, the periodic change may be due to other regulatory molecules and signal pathways. To understand the mechanism of periodic development of hair follicle, we performed a weighted gene coexpression network analysis (WGCNA) to mine key genes and establish an interaction network by utilizing the NCBI public dataset. Ten coexpression modules, including 7689 protein-coding genes, were constructed by WGCNA, six of which are considered to be significantly related to the development of the hair follicle cycle. A functional enrichment analysis for each model showed that they are closely related to ECM- receptor interaction, focal adhesion, PI3K-Akt signaling pathway, estrogen signaling pathway, and so on. Combined with the analysis of differential expressed genes, 12 hub genes from coexpression modules were selected as candidate markers, i.e., COL1A1, C1QTNF6, COL1A2, AQP3, KRTAP3-1, KRTAP11-1, FA2H, NDUFS5, DERL2, MRPL14, ANTKMT and XAB2, which might be applied to improve cashmere production.
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