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Bi R, Pan LN, Dai H, Sun C, Li C, Lin HJ, Xie LP, Ma HX, Li L, Xie H, Guo K, Hou CH, Yao YG, Chen LN, Zheng P. Epigenetic characterization of adult rhesus monkey spermatogonial stem cells identifies key regulators of stem cell homeostasis. Nucleic Acids Res 2024; 52:13644-13664. [PMID: 39535033 DOI: 10.1093/nar/gkae1013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 09/12/2024] [Accepted: 10/17/2024] [Indexed: 11/16/2024] Open
Abstract
Spermatogonial stem cells (SSCs) play crucial roles in the preservation of male fertility. However, successful ex vivo expansion of authentic human SSCs remains elusive due to the inadequate understanding of SSC homeostasis regulation. Using rhesus monkeys (Macaca mulatta) as a representative model, we characterized SSCs and progenitor subsets through single-cell RNA sequencing using a cell-specific network approach. We also profiled chromatin status and major histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3 and H3K9me3), and subsequently mapped promoters and active enhancers in TSPAN33+ putative SSCs. Comparing the epigenetic changes between fresh TSPAN33+ cells and cultured TSPAN33+ cells (resembling progenitors), we identified the regulatory elements with higher activity in SSCs, and the potential transcription factors and signaling pathways implicated in SSC regulation. Specifically, TGF-β signaling is activated in monkey putative SSCs. We provided evidence supporting its role in promoting self-renewal of monkey SSCs in culture. Overall, this study outlines the epigenetic landscapes of monkey SSCs and provides clues for optimization of the culture condition for primate SSCs expansion.
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Affiliation(s)
- Rui Bi
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Baohua Road, Kunming 650107, China
| | - Lin-Nuo Pan
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, No. 320 Yue Yang Road, Shanghai 200031, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Hao Dai
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, No. 320 Yue Yang Road, Shanghai 200031, China
| | - Chunli Sun
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
| | - Cong Li
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
| | - Hui-Juan Lin
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Baohua Road, Kunming 650107, China
| | - Lan-Ping Xie
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Huai-Xiao Ma
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Baohua Road, Kunming 650107, China
| | - Lin Li
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Heng Xie
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Kun Guo
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
| | - Chun-Hui Hou
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Yong-Gang Yao
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Baohua Road, Kunming 650107, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
| | - Luo-Nan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, No. 320 Yue Yang Road, Shanghai 200031, China
- Key Laboratory of Systems Biology, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, No. 1 Xiangshan Branch Lane, Xihu District, Hangzhou 310024, China
| | - Ping Zheng
- State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Baohua Road, Kunming 650107, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming, Yunnan 650204, China
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Li C, Chen W, Cui Y, Zhang D, Yuan Q, Yu X, He Z. Essential Regulation of YAP1 in Fate Determinations of Spermatogonial Stem Cells and Male Fertility by Interacting with RAD21 and Targeting NEDD4 in Humans and Mice. RESEARCH (WASHINGTON, D.C.) 2024; 7:0544. [PMID: 39659446 PMCID: PMC11628678 DOI: 10.34133/research.0544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 12/12/2024]
Abstract
Spermatogenesis is a sophisticated biological process by which spermatogonial stem cells (SSCs) undergo self-renewal and differentiation into spermatozoa. Molecular mechanisms underlying fate determinations of human SSCs by key genes and signaling pathways remain elusive. Here, we report for the first time that Yes1-associated transcriptional regulator (YAP1) is required for fate determinations of SSCs and male fertility by interacting with RAD21 and targeting NEDD4 in humans and mice. YAP1 was mainly located at cell nuclei of human SSCs. YAP1 silencing resulted in the decreases in proliferation and DNA synthesis as well as an enhancement in apoptosis of human SSCs both in vivo and in vitro. RNA sequencing and real-time polymerase chain reaction assays identified NEDD4 as a target of YAP1, and NEDD4 knockdown inhibited the proliferation of human SSCs and increased their apoptosis. Furthermore, YAP1 interacted with RAD21 to regulate NEDD4 transcription in human SSCs. Importantly, YAP1 abnormalities were found to be associated with non-obstructive azoospermia (NOA) as manifested as lower expression level of YAP1 in testicular tissues of NOA patients and YAP1 single-nucleotide variants (SNVs) in 777 NOA patients. Finally, Yap1 germline conditional knockout (cKO) mice assumed mitotic arrest, low sperm count, and motility. Collectively, these results highlight a critical role of YAP1 in determining the fate determinations of human SSCs and male infertility through the YAP1/RAD21/NEDD4 pathway. This study provides new insights into the genetic regulatory mechanisms underlying human spermatogenesis and the pathogenesis of NOA, and it offers new targets for gene therapy of male infertility.
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Affiliation(s)
- Chunyun Li
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine; Engineering Research Center of Reproduction and Translational Medicine of Hunan Province;
Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha 410013, China
| | - Wei Chen
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine; Engineering Research Center of Reproduction and Translational Medicine of Hunan Province;
Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha 410013, China
| | - Yinghong Cui
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine; Engineering Research Center of Reproduction and Translational Medicine of Hunan Province;
Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha 410013, China
| | - Dong Zhang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine; Engineering Research Center of Reproduction and Translational Medicine of Hunan Province;
Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha 410013, China
| | - Qingqing Yuan
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine,
Shanghai Jiao Tong University, Shanghai 200135, China
| | - Xing Yu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine; Engineering Research Center of Reproduction and Translational Medicine of Hunan Province;
Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha 410013, China
| | - Zuping He
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine; Engineering Research Center of Reproduction and Translational Medicine of Hunan Province;
Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha 410013, China
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Zhang P, Wang C, Liu X, Zhang M, Fu Q, Pan L, Huang Y. Integrated Quantitative Proteomics and Phosphoproteomics Analysis Reveals the Dynamic Process of Buffalo (Bubalus bubalis) Spermatogenesis. Reprod Domest Anim 2024; 59:e14753. [PMID: 39697112 DOI: 10.1111/rda.14753] [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: 07/03/2024] [Revised: 09/22/2024] [Accepted: 11/27/2024] [Indexed: 12/20/2024]
Abstract
Spermatogenesis is a highly complex and tightly regulated cellular differentiation process closely related to the productive performance of male livestock. We do not yet have a clear understanding of the spermatogenesis mechanism of buffalo. In this study, spermatogonia, spermatocytes and spermatids were analysed by flow cytometry. Quantitative proteomic and phosphoproteomic studies were performed on different spermatogenic cells using tandem mass tagging technology and liquid chromatography-tandem mass spectrometry. A total of 219 differentially expressed proteins (involved in focal adhesions and actin cytoskeleton pathways) and 71 phosphoproteins (involved in RNA transport and adhesion junction pathways) were obtained. Through trend analysis, a dynamic profile of protein expression was obtained, enriched to the main biological processes at different stages of spermatogenesis. By immunohistochemical localisation analysis, it was found that MACROH2A2, TOP2A, LMNA, LMNA (pS392), VIM and VIM (pS56) had specific localisation in testis cells. Network analysis of kinase-substrate phosphorylation sites showed that AKT1 is the most active kinase, LMNA is regulated by most kinases and AKT1 can catalyse the phosphorylation of LMNA. This study provides a reference for studying the molecular mechanism of buffalo spermatogenesis and helps clarify the regulatory mechanism of protein translation and post-translational modification during mammalian spermatogenesis.
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Affiliation(s)
- Pengfei Zhang
- Institute of Biological Science and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Chenyang Wang
- Department of Cell and Genetics, College of Basic Medicine, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Xuyang Liu
- Department of Cell and Genetics, College of Basic Medicine, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Ming Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Qiang Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Limei Pan
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yulin Huang
- Department of Cell and Genetics, College of Basic Medicine, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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Zhang T, Zhang X, Wu Z, Ren J, Zhao Z, Zhang H, Wang G, Wang T. VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell-cell communication network. Brief Bioinform 2024; 26:bbae619. [PMID: 39581873 PMCID: PMC11586124 DOI: 10.1093/bib/bbae619] [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: 08/23/2024] [Revised: 10/04/2024] [Accepted: 11/12/2024] [Indexed: 11/26/2024] Open
Abstract
Cell-cell communication plays a critical role in maintaining normal biological functions, regulating development and differentiation, and controlling immune responses. The rapid development of single-cell RNA sequencing and spatial transcriptomics sequencing (ST-seq) technologies provides essential data support for in-depth and comprehensive analysis of cell-cell communication. However, ST-seq data often contain incomplete data and systematic biases, which may reduce the accuracy and reliability of predicting cell-cell communication. Furthermore, other methods for analyzing cell-cell communication mainly focus on individual tissue sections, neglecting cell-cell communication across multiple tissue layers, and fail to comprehensively elucidate cell-cell communication networks within three-dimensional tissues. To address the aforementioned issues, we propose VGAE-CCI, a deep learning framework based on the Variational Graph Autoencoder, capable of identifying cell-cell communication across multiple tissue layers. Additionally, this model can be applied to spatial transcriptomics data with missing or partially incomplete data and can clustered cells at single-cell resolution based on spatial encoding information within complex tissues, thereby enabling more accurate inference of cell-cell communication. Finally, we tested our method on six datasets and compared it with other state of art methods for predicting cell-cell communication. Our method outperformed other methods across multiple metrics, demonstrating its efficiency and reliability in predicting cell-cell communication.
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Affiliation(s)
- Tianjiao Zhang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Xiang Zhang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Zhenao Wu
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Jixiang Ren
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Zhongqian Zhao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Hongfei Zhang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
- Faculty of Computing, Harbin Institute of Technology, Harbin 150001, China
| | - Tao Wang
- School of Computer Science, Northwestern Polytechnical University, Xi'an 710072, China
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Zhou L, Liu H, Chen Y, Hua L, Wu X, Gao X, Mao L. Unveiling Leydig cell heterogeneity and its role in male infertility: A single-cell transcriptomic study of human testicular tissue. Reprod Biol 2024; 25:100972. [PMID: 39566254 DOI: 10.1016/j.repbio.2024.100972] [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: 09/17/2024] [Revised: 11/02/2024] [Accepted: 11/12/2024] [Indexed: 11/22/2024]
Abstract
Male infertility and impaired spermatogenesis are significant concerns in reproductive health, often linked to disruptions in the cellular and molecular processes within the testis. The cellular composition and transcriptional dynamics of human testicular tissue are crucial for understanding these issues. Previous studies have largely relied on bulk tissue analysis, which obscures the distinct roles and interactions of specific cell types. Here, through a comprehensive single-cell transcriptomic analysis of human testes across various developmental stages and pathological conditions, we reveal the intricate cellular heterogeneity and the molecular mechanisms underlying testicular function. Our study identifies significant disruptions in the differentiation trajectories of Germ cells in conditions such as Klinefelter syndrome (KS), AZFa deletion, and Sertoli-cell-only syndrome (SCOS). We further uncover key transcription factors and regulatory networks governing Leydig cell function, particularly those related to steroidogenesis and hormonal regulation. These findings highlight the organized yet complex cellular and molecular landscape of the testis and uncover critical pathways altered in male infertility. Collectively, our data suggest that targeted therapeutic strategies could be developed to address specific disruptions in testicular cell populations and their associated regulatory networks.
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Affiliation(s)
- Liwei Zhou
- Department of Urology, Xinghua People's Hospital Affiliated to Yangzhou University, Taizhou 225700, Jiangsu, China
| | - Hanchao Liu
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Yuming Chen
- Department of Urology, Xinghua People's Hospital Affiliated to Yangzhou University, Taizhou 225700, Jiangsu, China
| | - Lin Hua
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Xiaolong Wu
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Xintao Gao
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China.
| | - Le Mao
- Department of Vascular Surgery, Shanghai Geriatric Medical Center, Shanghai, China; Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Institute of Vascular Surgery, Fudan University, Shanghai, China; National Clinical Research Center for Interventional Medicine, Shanghai, China.
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Wang X, Wang Y, Wang Y, Guo Y, Zong R, Hu S, Yue J, Yao J, Han C, Guo J, Zhao J. Single-cell transcriptomic and cross-species comparison analyses reveal distinct molecular changes of porcine testes during puberty. Commun Biol 2024; 7:1478. [PMID: 39521938 PMCID: PMC11550399 DOI: 10.1038/s42003-024-07163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024] Open
Abstract
The pig is an important model for studying human diseases and is also a significant livestock species, yet its testicular development remains underexplored. Here, we employ single-cell RNA sequencing to characterize the transcriptomic landscapes across multiple developmental stages of Bama pig testes from fetal stage through infancy, puberty to adulthood, and made comparisons with those of humans and mice. We reveal an exceptionally early onset of porcine meiosis shortly after birth, and identify a distinct subtype of porcine spermatogonia resembling transcriptome state 0 spermatogonial stem cells identified in humans, which were previously thought to be primate specific. We also discover the persistent presence of proliferating progenitors for myoid cells in postnatal testes. The regulatory roles of Leydig cell steroidogenesis and estrogen synthesis in supporting cell lineages are also explored, including the potential impact of estrogen on Sertoli cell maturation and spermatogenesis. Overall, this study offers valuable insights into porcine testicular development, paving the way for future research in reproductive biology, advancements in agricultural breeding, and potential applications in translational medicine.
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Affiliation(s)
- Xiaoyan Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yang Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yu Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yifei Guo
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruojun Zong
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuaitao Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingwei Yue
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jing Yao
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunsheng Han
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jingtao Guo
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jianguo Zhao
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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7
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Marshall KL, Stadtmauer DJ, Maziarz J, Wagner GP, Lesch BJ. Evolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum. Dev Cell 2024:S1534-5807(24)00632-4. [PMID: 39536760 DOI: 10.1016/j.devcel.2024.10.013] [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: 11/10/2023] [Revised: 05/26/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024]
Abstract
Mammalian spermatogenesis is a highly stereotyped and conserved developmental process that is essential for fitness. At the same time, gene expression in spermatogenic cells is rapidly evolving. This combination of features has been suggested to drive rapid fixation of new gene expression patterns. Using a high-resolution dataset comprising bulk and single-cell data from juvenile and adult testes of the opossum Monodelphis domestica, a model marsupial, we define the developmental timing of the spermatogenic first wave in opossum and delineate conserved and divergent gene expression programs across the placental-marsupial split by comparison to equivalent data from mouse, a model placental mammal. Epigenomic data confirmed divergent regulation at the level of transcription, and comparison to data from four additional amniote species identified hundreds of genes with evidence of rapid fixation of expression. This gene set encompasses known and previously undescribed regulators of spermatogenic development.
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Affiliation(s)
- Kira L Marshall
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Daniel J Stadtmauer
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, USA; Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jamie Maziarz
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, USA; Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, USA; Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA
| | - Bluma J Lesch
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA.
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8
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Chen G, Wang W, Wei X, Chen Y, Peng L, Qu R, Luo Y, He S, Liu Y, Du J, Lu R, Li S, Fan C, Chen S, Dai Y, Yang L. Single-cell transcriptomic analysis reveals that the APP-CD74 axis promotes immunosuppression and progression of testicular tumors. J Pathol 2024; 264:250-269. [PMID: 39161125 DOI: 10.1002/path.6343] [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: 01/24/2024] [Revised: 06/09/2024] [Accepted: 07/16/2024] [Indexed: 08/21/2024]
Abstract
Testicular tumors represent the most common malignancy among young men. Nevertheless, the pathogenesis and molecular underpinning of testicular tumors remain largely elusive. We aimed to delineate the intricate intra-tumoral heterogeneity and the network of intercellular communication within the tumor microenvironment. A total of 40,760 single-cell transcriptomes were analyzed, encompassing samples from six individuals with seminomas, two patients with mixed germ cell tumors, one patient with a Leydig cell tumor, and three healthy donors. Five distinct malignant subclusters were identified in the constructed landscape. Among them, malignant 1 and 3 subclusters were associated with a more immunosuppressive state and displayed worse disease-free survival. Further analysis identified that APP-CD74 interactions were significantly strengthened between malignant 1 and 3 subclusters and 14 types of immune subpopulations. In addition, we established an aberrant spermatogenesis trajectory and delineated the global gene alterations of somatic cells in seminoma testes. Sertoli cells were identified as the somatic cell type that differed the most from healthy donors to seminoma testes. Cellular communication between spermatogonial stem cells and Sertoli cells is disturbed in seminoma testes. Our study delineates the intra-tumoral heterogeneity and the tumor immune microenvironment in testicular tumors, offering novel insights for targeted therapy. © 2024 The Author(s). 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)
- Guo Chen
- Department of Urology/Pelvic Floor and Andrology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
| | - Wei Wang
- Laboratory of Reconstructive Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Xin Wei
- Laboratory of Reconstructive Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Yulin Chen
- Laboratory of Stem Cell Biology, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, PR China
| | - Liao Peng
- Laboratory of Reconstructive Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Rui Qu
- Department of Urology/Pelvic Floor and Andrology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
| | - Yi Luo
- Laboratory of Reconstructive Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Shengyin He
- Department of Urology/Pelvic Floor and Andrology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
| | - Yugao Liu
- Department of Urology/Pelvic Floor and Andrology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
| | - Jie Du
- Department of Urology/Pelvic Floor and Andrology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
| | - Ran Lu
- Laboratory of Stem Cell Biology, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, PR China
| | - Siying Li
- Laboratory of Stem Cell Biology, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, PR China
| | - Chuangwen Fan
- Laboratory of Stem Cell Biology, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, PR China
- Department of Gastrointestinal, Bariatric and Metabolic Surgery, Research Center for Nutrition, Metabolism & Food Safety, West China-PUMC C.C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sujun Chen
- Department of Urology/Pelvic Floor and Andrology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
| | - Yi Dai
- Department of Urology/Pelvic Floor and Andrology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
| | - Luo Yang
- Department of Urology/Pelvic Floor and Andrology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, PR China
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9
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Ding D, Pang MH, Deng M, Nguyen T, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T. Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA-histone interactions. Nucleic Acids Res 2024; 52:11612-11625. [PMID: 39329259 PMCID: PMC11514470 DOI: 10.1093/nar/gkae825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 09/02/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Multiple testis-specific histone variants are involved in the dynamic chromatin transitions during spermatogenesis. H2B.W1 (previously called H2BFWT) is an H2B variant specific to primate testis with hitherto unclear functions, although its single-nucleotide polymorphisms (SNPs) are closely associated with male non-obstructive infertility. Here, we found that H2B.W1 is only expressed in the mid-late spermatogonia stages, and H2B.W1 nucleosomes are defined by a more flexible structure originating from weakened interactions between histones and DNA. Furthermore, one of its SNPs, H2B.W1-H100R, which is associated with infertility, further destabilizes the nucleosomes and increases the nucleosome unwrapping rate by interfering with the R100 and H4 K91/R92 interaction. Our results suggest that destabilizing H2B.W1 containing nucleosomes might change the chromatin structure of spermatogonia, and that H2B.W1-H100R enhances the nucleosome-destabilizing effects, leading to infertility.
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Affiliation(s)
- Dongbo Ding
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
| | - Matthew Y H Pang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
| | - Mingxi Deng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
| | - Thi Thuy Nguyen
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
| | - Yue Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
| | - Xulun Sun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
| | - Zhichun Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, HKSAR, China
| | - Yingyi Zhang
- Biological Cryo-EM Center, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, HKSAR, China
| | - Yan Yan
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
- Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, HKSAR, China
- The Hong Kong University of Science and Technology Fok Ying Tung Research Institute, Nansha, Guangzhou, China
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10
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Konstantinidou P, Loubalova Z, Ahrend F, Friman A, Almeida MV, Poulet A, Horvat F, Wang Y, Losert W, Lorenzi H, Svoboda P, Miska EA, van Wolfswinkel JC, Haase AD. A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals. Cell Rep 2024; 43:114777. [PMID: 39302833 PMCID: PMC11615739 DOI: 10.1016/j.celrep.2024.114777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/09/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs) play a crucial role in safeguarding genome integrity by silencing mobile genetic elements. From flies to humans, piRNAs originate from long single-stranded precursors encoded by genomic piRNA clusters. How piRNA clusters form to adapt to genomic invaders and evolve to maintain protection remain key outstanding questions. Here, we generate a roadmap of piRNA clusters across seven species that highlights both similarities and variations. In mammals, we identify transcriptional readthrough as a mechanism to generate piRNAs from transposon insertions (piCs) downstream of genes (DoG). Together with the well-known stress-dependent DoG transcripts, our findings suggest a molecular mechanism for the formation of piRNA clusters in response to retroviral invasion. Finally, we identify a class of dynamic piRNA clusters in humans, underscoring unique features of human germ cell biology. Our results advance the understanding of conserved principles and species-specific variations in piRNA biology and provide tools for future studies.
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Affiliation(s)
- Parthena Konstantinidou
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zuzana Loubalova
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Franziska Ahrend
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; Oak Ridge Institute for Science and Education, US Department of Energy, Oak Ridge, TN, USA
| | - Aleksandr Friman
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; Biophysics Graduate Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Axel Poulet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA; Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Filip Horvat
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Yuejun Wang
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; Oak Ridge Institute for Science and Education, US Department of Energy, Oak Ridge, TN, USA; TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wolfgang Losert
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Hernan Lorenzi
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eric A Miska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Josien C van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA; Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Astrid D Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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11
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Luo J, Yang C, Xu S, Ji Z, Zhang Y, Bai H, Deng Z, Liang J, Huang Y, Zhi E, Tian R, Li P, Zhao F, Zhou Z, Li Z, Yao C. RNA-binding protein IGF2BP1 is required for spermatogenesis in an age-dependent manner. Commun Biol 2024; 7:1362. [PMID: 39433965 PMCID: PMC11493986 DOI: 10.1038/s42003-024-07055-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: 02/22/2024] [Accepted: 10/11/2024] [Indexed: 10/23/2024] Open
Abstract
Post-transcriptional regulation mediated by RNA binding proteins is crucial for male germline development. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), an RNA binding protein, is specifically expressed in human and mouse male gonads and is involved in manifold biological processes and tumorigenesis. However, the function of IGF2BP1 in mammalian spermatogenesis remains poorly understood. Herein, we generated an Igf2bp1 conditional knockout mouse model using Nanos3-Cre. Germ cell deficiency of Igf2bp1 in mice caused spermatogenic defects in an age-dependent manner, resulting in decreased numbers of undifferentiated spermatogonia and increased germ cell apoptosis. Immunoprecipitation-mass spectrometry analysis revealed that ELAV-like RNA binding protein 1, a well-recognized mRNA stabilizer, interacted with IGF2BP1. Single cell RNA-sequencing showed distinct mRNA profiles in spermatogonia from conditional knockout versus wide type mice. Further research showed that IGF2BP1 plays a vital role in the modulation of spermatogenesis by regulating Lin28a mRNA, which is essential for clonal expansion of undifferentiated spermatogonia. Thus, our results highlight the crucial effects of IGF2BP1 on spermatogonia for the long-term maintenance of spermatogenesis.
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Affiliation(s)
- Jiaqiang Luo
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chao Yang
- Department of Urology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Shuai Xu
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhiyong Ji
- Center for Reproductive Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Yuxiang Zhang
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Haowei Bai
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Zhiwen Deng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiayi Liang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yuhua Huang
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Erlei Zhi
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Ruhui Tian
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Peng Li
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Fujun Zhao
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Zhi Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Zheng Li
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| | - Chencheng Yao
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
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12
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Damyanova KB, Nixon B, Johnston SD, Gambini A, Benitez PP, Lord T. Spermatogonial stem cell technologies: applications from human medicine to wildlife conservation†. Biol Reprod 2024; 111:757-779. [PMID: 38993049 PMCID: PMC11473898 DOI: 10.1093/biolre/ioae109] [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: 05/01/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/13/2024] Open
Abstract
Spermatogonial stem cell (SSC) technologies that are currently under clinical development to reverse human infertility hold the potential to be adapted and applied for the conservation of endangered and vulnerable wildlife species. The biobanking of testis tissue containing SSCs from wildlife species, aligned with that occurring in pediatric human patients, could facilitate strategies to improve the genetic diversity and fitness of endangered populations. Approaches to utilize these SSCs could include spermatogonial transplantation or testis tissue grafting into a donor animal of the same or a closely related species, or in vitro spermatogenesis paired with assisted reproduction approaches. The primary roadblock to progress in this field is a lack of fundamental knowledge of SSC biology in non-model species. Herein, we review the current understanding of molecular mechanisms controlling SSC function in laboratory rodents and humans, and given our particular interest in the conservation of Australian marsupials, use a subset of these species as a case-study to demonstrate gaps-in-knowledge that are common to wildlife. Additionally, we review progress in the development and application of SSC technologies in fertility clinics and consider the translation potential of these techniques for species conservation pipelines.
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Affiliation(s)
- Katerina B Damyanova
- Discipline of Biological Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
- Infertility and Reproduction Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Brett Nixon
- Discipline of Biological Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
- Infertility and Reproduction Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Stephen D Johnston
- School of Environment, The University of Queensland, Gatton, QLD 4343, Australia
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Andrés Gambini
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
- School of Agriculture and Food Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Patricio P Benitez
- School of Agriculture and Food Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Tessa Lord
- Discipline of Biological Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
- Infertility and Reproduction Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
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13
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Conti Nibali S, Battiato G, Pappalardo XG, De Pinto V. Voltage-Dependent Anion Channels in Male Reproductive Cells: Players in Healthy Fertility? Biomolecules 2024; 14:1290. [PMID: 39456223 PMCID: PMC11506323 DOI: 10.3390/biom14101290] [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: 09/09/2024] [Revised: 10/07/2024] [Accepted: 10/10/2024] [Indexed: 10/28/2024] Open
Abstract
Male infertility affects nearly 50% of infertile couples, with various underlying causes, including endocrine disorders, testicular defects, and environmental factors. Spermatozoa rely on mitochondrial oxidative metabolism for motility and fertilization, with mitochondria playing a crucial role in sperm energy production, calcium regulation, and redox balance. Voltage-dependent anion channels (VDACs), located on the outer mitochondrial membrane, regulate energy and metabolite exchange, which are essential for sperm function. This review offers an updated analysis of VDACs in the male reproductive system, summarizing recent advances in understanding their expression patterns, molecular functions, and regulatory mechanisms. Although VDACs have been widely studied in other tissues, their specific roles in male reproductive physiology still remain underexplored. Special attention is given to the involvement of VDAC2/3 isoforms, which may influence mitochondrial function in sperm cells and could be implicated in male fertility disorders. This update provides a comprehensive framework for future research in reproductive biology, underscoring the significance of VDACs as a molecular link between mitochondrial function and male fertility.
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Affiliation(s)
| | | | | | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy; (S.C.N.); (G.B.); (X.G.P.)
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14
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Zhi M, Gao D, Yao Y, Zhao Z, Wang Y, He P, Feng Z, Zhang J, Huang Z, Gu W, Zhao J, Zhang H, Wang S, Li X, Zhang Q, Zhao Z, Chen X, Zhang X, Qin L, Liu J, Liu C, Cao S, Gao S, Yu W, Ma Z, Han J. Elucidation of the pluripotent potential of bovine embryonic lineages facilitates the establishment of formative stem cell lines. Cell Mol Life Sci 2024; 81:427. [PMID: 39377807 PMCID: PMC11461730 DOI: 10.1007/s00018-024-05457-z] [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: 06/27/2024] [Revised: 06/27/2024] [Accepted: 09/19/2024] [Indexed: 10/09/2024]
Abstract
The establishment of epiblast-derived pluripotent stem cells (PSCs) from cattle, which are important domestic animals that provide humans with milk and meat while also serving as bioreactors for producing valuable proteins, poses a challenge due to the unclear molecular signaling required for embryonic epiblast development and maintenance of PSC self-renewal. Here, we selected six key stages of bovine embryo development (E5, E6, E7, E10, E12, and E14) to track changes in pluripotency and the dependence on signaling pathways via modified single-cell transcription sequencing technology. The remarkable similarity of the gene expression patterns between cattle and pigs during embryonic lineage development contributed to the successful establishment of bovine epiblast stem cells (bEpiSCs) using 3i/LAF (WNTi, GSK3βi, SRCi, LIF, Activin A, and FGF2) culture system. The generated bEpiSCs exhibited consistent expression patterns of formative epiblast pluripotency genes and maintained clonal morphology, normal karyotypes, and proliferative capacity for more than 112 passages. Moreover, these cells exhibited high-efficiency teratoma formation as well as the ability to differentiate into various cell lineages. The potential of bEpiSCs for myogenic differentiation, primordial germ cell like cells (PGCLCs) induction, and as donor cells for cell nuclear transfer was also assessed, indicating their promise in advancing cell-cultured meat production, gene editing, and animal breeding.
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Affiliation(s)
- Minglei Zhi
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Dengfeng Gao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yixuan Yao
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zimo Zhao
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yingjie Wang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Pengcheng He
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhiqiang Feng
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jinying Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ziqi Huang
- Department of Histology and Embryology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Wenyuan Gu
- Shijiazhuang Tianquan Elite Dairy Co., Ltd. Shijiazhuang, Hebei, 050200, People's Republic of China
| | - Jianglin Zhao
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi, 712100, People's Republic of China
| | - He Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shunxin Wang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xin Li
- Shijiazhuang Tianquan Elite Dairy Co., Ltd. Shijiazhuang, Hebei, 050200, People's Republic of China
| | - Qiang Zhang
- Key Laboratory of Animal Genetics, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zengyuan Zhao
- Shijiazhuang Tianquan Elite Dairy Co., Ltd. Shijiazhuang, Hebei, 050200, People's Republic of China
| | - Xinze Chen
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lun Qin
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Jun Liu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chengjun Liu
- Beijing Dairy Cattle Center, Beijing, 100192, People's Republic of China
| | - Suying Cao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Shuai Gao
- Key Laboratory of Animal Genetics, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Wenli Yu
- Shijiazhuang Tianquan Elite Dairy Co., Ltd. Shijiazhuang, Hebei, 050200, People's Republic of China.
| | - Zhu Ma
- Beijing Dairy Cattle Center, Beijing, 100192, People's Republic of China.
| | - Jianyong Han
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, People's Republic of China.
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15
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Chen Z, Liu C, Qu W, Han Y, Zhu X, Li Z, Ma D, Huang M, Gong W, Sun Q, Lei J, Guo R, Luo M. PWWP3A deficiency accelerates testicular senescence in aged mice. Andrology 2024. [PMID: 39363403 DOI: 10.1111/andr.13774] [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: 03/13/2024] [Revised: 09/15/2024] [Accepted: 09/17/2024] [Indexed: 10/05/2024]
Abstract
BACKGROUND The PWWP domain-containing proteins are involved in chromatin-associated biological processes, including transcriptional regulation and DNA repair, and most of them are significant for gametogenesis and early embryonic development in mammals. PWWP3A, one of the PWWP domain proteins, is a reader of H3K36me2/H3K36me3 and a response factor to DNA damage. However, the physiological role of PWWP3A in spermatogenesis and fertility remains unclear. OBJECTIVE The goal of this study was to explore the function and mechanism of PWWP3A in the process of spermatogenesis. MATERIALS AND METHODS We generated V5-Pwwp3a KI mice and PWWP3A polyclonal antibody to observe the localization of PWWP3A in vivo. Meanwhile, Pwwp3a KO mice was used to explore the function in spermatogenesis. RESULTS We reported that PWWP3A is a predominant expression in the testis of mice. During spermatogenesis, PWWP3A exhibits the temporal expression from early-pachytene to the round spermatids. The results of spermatocyte spreading and immunostaining showed that PWWP3A aggregated on the XY body, which then diffused as the XY chromosome separated at late-diplotene. Although the depletion of PWWP3A had no obvious reproductive defects in young male mice, there were observed morphological abnormalities in sperm heads. Immunoprecipitation demonstrated the interaction of PWWP3A with DNA repair proteins SMC5/6; however, PWWP3A deficiency did not result in any meiotic defects. Notably, the testes of aged male Pwwp3a KO mice displayed pronounced degeneration, and were characterized by the presence of vacuolated seminiferous tubules. Furthermore, RNA-seq analysis revealed an upregulation in the expression of genes which may be involving in immunoregulatory and inflammatory response pathways in aged Pwwp3a KO mice with testicular degeneration. CONCLUSIONS Our study showed that PWWP3A was highly enriched in the mouse testis, and the Pwwp3a KO mice were fertile. However, the aged Pwwp3a KO male mice displayed testicular atrophy that may be due to changes in the immune micro-environment or abnormal repair of DNA damage.
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Affiliation(s)
- Zhen Chen
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Cong Liu
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wei Qu
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yan Han
- The Assisted Reproduction Department, Yichun Maternal and Child Health Hospital, Yichun, China
| | - Xiaoyu Zhu
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zejia Li
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Dupeng Ma
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Mengya Huang
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Weihao Gong
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Qi Sun
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Junhao Lei
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rui Guo
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mengcheng Luo
- Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Center for Life and Medical Sciences, School of Basic Medical Sciences, Wuhan University, Wuhan, China
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16
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Herrboldt MA, Wright CNC, Bonett RM. Seasonal heterochrony of reproductive development and gene expression in a polymorphic salamander. Dev Dyn 2024. [PMID: 39360498 DOI: 10.1002/dvdy.744] [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: 03/04/2024] [Revised: 07/24/2024] [Accepted: 08/21/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Life cycle evolution includes ecological transitions and shifts in the timing of somatic and reproductive development (heterochrony). However, heterochronic changes can be tissue-specific, ultimately leading to the differential diversification of traits. Salamanders exhibit alternative life cycle polymorphisms involving either an aquatic to terrestrial metamorphosis (biphasic) or retention of aquatic larval traits into adulthood (paedomorphic). In this study, we used gene expression and histology to evaluate how life cycle evolution impacts temporal reproductive patterns in males of a polymorphic salamander. RESULTS We found that heterochrony shifts the distribution of androgen signaling in the integument, which is correlated with significant differences in seasonal reproductive gland development and pheromone gene expression. In the testes, androgen receptor (ar) expression does not significantly vary between morphs or across seasons. We found significant differences in the onset of spermatogenesis, but by peak breeding season the testes were the same with respect to both histology and gene expression. CONCLUSION This study provides an example of how seasonal heterochronic shifts in tissue-specific ar gene expression can disparately impact seasonal development and expression patterns across tissues, providing a potential mechanism for differential diversification of reproductive traits.
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Affiliation(s)
| | - Claire N C Wright
- Department of Biological Science, University of Tulsa, Tulsa, Oklahoma, USA
| | - Ronald M Bonett
- Department of Biological Science, University of Tulsa, Tulsa, Oklahoma, USA
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Jin J, Yim HCH, Chang HME, Wang Y, Choy KHK, Chan SY, Alqawasmeh OAM, Liao J, Jiang XT, Chan DYL, Fok EKL. DEFB119 stratifies dysbiosis with distorted networks in the seminal microbiome associated with male infertility. PNAS NEXUS 2024; 3:pgae419. [PMID: 39359400 PMCID: PMC11443970 DOI: 10.1093/pnasnexus/pgae419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 09/06/2024] [Indexed: 10/04/2024]
Abstract
Infertility is associated with the alteration of the seminal microbiome. However, the onset of dysbiosis remains controversial and the involvement of host factors remains elusive. This study investigates the alterations of the seminal microbiome in male infertility and examines the association and function of DEFB119, a reproductive-tract-specific host antimicrobial peptide, on the seminal microbiome and male fertility. While we observed comparable genera, diversity and evenness of bacterial communities, a marked decrease in the modularity of the metacommunities was observed in patients with abnormal spermiogram (n = 57) as compared to the control (n = 30). A marked elevation of DEFB119 was observed in a subpopulation of male infertile patients (n = 5). Elevated seminal DEFB119 was associated with a decrease in the observed genera, diversity and evenness of bacterial communities, and further distortion of the metacommunities. Mediation analysis suggests the involvement of elevated DEFB119 and dysbiosis of the seminal microbiome in mediating the abnormalities in the spermiogram. Functional experiments showed that recombinant DEFB119 significantly decrease the progressive motility of sperm in patients with abnormal spermiogram. Moreover, DEFB119 demonstrated species-specific antimicrobial activity against common seminal and nonseminal species. Our work identifies an important host factor that mediates the host-microbiome interaction and stratifies the seminal microbiome associated with male infertility. These results may lead to a new diagnostic method for male infertility and regimens for formulating the microbiome in the reproductive tract and other organ systems.
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Affiliation(s)
- Jing Jin
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Howard Chi Ho Yim
- Faculty of Medicine and Health, Microbiome Research Centre, St George and Sutherland Campus, School of Clinical Medicine, The University of New South Wales, Sydney 2217, Australia
| | - Hsiao Mei Ellie Chang
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Yiwei Wang
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Kathleen Hoi Kei Choy
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Sze Yan Chan
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Odai A M Alqawasmeh
- Department of Obstetrics and Gynecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR
| | - Jinyue Liao
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Xiao-Tao Jiang
- Faculty of Medicine and Health, Microbiome Research Centre, St George and Sutherland Campus, School of Clinical Medicine, The University of New South Wales, Sydney 2217, Australia
| | - David Yiu Leung Chan
- Department of Obstetrics and Gynecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR
| | - Ellis Kin Lam Fok
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR
- School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, PR China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Chengdu, PR China
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18
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Yu Z, Liu W, Wang Z, Chen Y, Yan J, Benet LZ, Zhai S. Is there a possibility that P-glycoprotein reduces reproductive toxicity in males but breast cancer resistance protein does not? Clin Transl Sci 2024; 17:e70027. [PMID: 39356462 PMCID: PMC11446187 DOI: 10.1111/cts.70027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 10/03/2024] Open
Abstract
In traditional understanding, P-glycoprotein (P-gp) and Breast Cancer Resistance Protein (BCRP) are regarded as efflux transporters that can decrease the concentration of their substrates in the testis, thereby reducing reproductive toxicity in males (RTM) and protecting spermatogenesis. However, there is currently no direct pharmacological evidence demonstrating that P-gp and BCRP can reduce the occurrence of drug-induced RTM. In this study, we chose small molecule targeted anti-tumor agents as model drugs and systematically retrieved and collected information on the transporters and RTM for these drugs, followed by correlation analysis. The results showed a lower incidence of RTM for P-gp substrate drugs, which aligns with previous knowledge. Surprisingly, BCRP substrate drugs exhibited higher rates of RTM in various dimensions, contradicting previous notions. This discrepancy may be attributed to the differential distribution and transport directions of P-gp and BCRP on the blood-testis barrier (BTB). For the first time, this study may provide clues that BCRP may facilitate the passage of exogenous compounds across the BTB, increasing the occurrence of RTM, rather than protecting spermatogenesis as traditionally believed. Furthermore, this study provides the first direct verification of the role of P-gp in reducing RTM and protecting spermatogenesis.
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Affiliation(s)
- Zhiheng Yu
- Pharmacy DepartmentPeking University Third HospitalBeijingChina
- Department of Obstetrics and GynecologyPeking University Third HospitalBeijingChina
| | - Wei Liu
- Pharmacy DepartmentPeking University Third HospitalBeijingChina
| | - Ziyu Wang
- Pharmacy DepartmentPeking University Third HospitalBeijingChina
| | - Yidong Chen
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, National Clinical Research Center for Obstetrics and Gynecology, Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyPeking University Third HospitalBeijingChina
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyBeijingChina
| | - Jie Yan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, National Clinical Research Center for Obstetrics and Gynecology, Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyPeking University Third HospitalBeijingChina
- State Key Laboratory of Female Fertility PromotionBeijingChina
| | - Leslie Z. Benet
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Suodi Zhai
- Pharmacy DepartmentPeking University Third HospitalBeijingChina
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19
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Zhao J, Tang K, Jiang G, Yang X, Cui M, Wan C, Ouyang Z, Zheng Y, Liu Z, Wang M, Zhao XY, Chang G. Dynamic transcriptomic and regulatory networks underpinning the transition from fetal primordial germ cells to spermatogonia in mice. Cell Prolif 2024:e13755. [PMID: 39329203 DOI: 10.1111/cpr.13755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/24/2024] [Accepted: 09/14/2024] [Indexed: 09/28/2024] Open
Abstract
The transition from fetal primordial germ cells (PGCs) to spermatogonia (SPG) is critical for male germ cell development; however, the detailed transcriptomic dynamics and regulation underlying this transition remain poorly understood. Here by interrogating the comprehensive transcriptome atlas dataset of mouse male germ cells and gonadal cells development, we elucidated the regulatory networks underlying this transition. Our single-cell transcriptome analysis revealed that the transition from PGCs to SPG was characterized by global hypertranscription. A total of 315 highly active regulators were identified to be potentially involved in this transition, among which a non-transcription factor (TF) regulator TAGLN2 was validated to be essential for spermatogonial stem cells (SSCs) maintenance and differentiation. Metabolism profiling analysis also revealed dynamic changes in metabolism-related gene expression during PGC to SPG transition. Furthermore, we uncovered that intricate cell-cell communication exerted potential functions in the regulation of hypertranscription in germ cells by collaborating with stage-specific active regulators. Collectively, our work extends the understanding of molecular mechanisms underlying male germ cell development, offering insights into the recapitulation of germ cell generation in vitro.
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Affiliation(s)
- Jiexiang Zhao
- The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, Guangdong, PR China
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Kang Tang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Gurong Jiang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Xinyan Yang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Manman Cui
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Cong Wan
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
- Maoming People's Hospital, Maoming, Guangdong, PR China
| | - Zhaoxiang Ouyang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yi Zheng
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Zhaoting Liu
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Mei Wang
- The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, Guangdong, PR China
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Xiao-Yang Zhao
- The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, Guangdong, PR China
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong, PR China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders
- Department of Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Gang Chang
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, Guangdong, PR China
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20
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Yu T, Wang C, Fan J, Chen R, Liu G, Xu X, Ning J, Lu X. Single-cell RNA sequencing revealed the roles of macromolecule epidermal growth factor receptor (EGFR) in the hybrid sterility of hermaphroditic Argopecten scallops. Int J Biol Macromol 2024; 280:136062. [PMID: 39341320 DOI: 10.1016/j.ijbiomac.2024.136062] [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: 08/09/2024] [Revised: 09/24/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024]
Abstract
The macromolecule epidermal growth factor receptor (EGFR) is a transmembrane glycoprotein that belongs to the protein kinase superfamily, which plays versatile functions in cell proliferation, development and fertility regulation. Almost all F1 hybrids obtained from the hermaphroditic bay scallops and Peruvian scallops exhibit infertility, and the genetic mechanism remains unclear. In this study, the comprehensive scRNA-seq was first conducted in the gonads of hybrid scallops, deducing the developmental sequence of germ cells and identifying the critical regulators in hybrid sterility: epidermal growth factor receptor. During the development from oogenesis phase germ cells to oocytes, the expression of the EGFR gene gradually decreased in sterile hybrids but increased in fertile hybrids. The significantly lower EGFR expression and ATP content, but higher ROS production rate was detected in the gonad of sterile hybrids than that in fertile hybrids, which might cause slow development of oocytes, stagnation of cell cycle, insufficient energy supply, high level of apoptosis and final sterility. Specific knock-down of EGFR gene led to decreased ATP content, increased ROS production rate, and inhibited oocyte maturation and gonadal development. These findings provide new insights into the roles of EGFR in hybrid infertility of bivalves and the healthy development of scallop breeding.
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Affiliation(s)
- Tieying Yu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunde Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China; College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Jiawei Fan
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongjie Chen
- Laizhou Marine Development and Fishery Service Center, Laizhou 261400, China
| | - Guilong Liu
- Yantai Spring-Sea AquaSeed, Ltd., Yantai 264006, China
| | - Xin Xu
- Yantai Spring-Sea AquaSeed, Ltd., Yantai 264006, China
| | - Junhao Ning
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China.
| | - Xia Lu
- School of Ocean, Yantai University, Yantai, Shandong 264005, China.
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21
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Zhao X, Zhao F, Yan L, Wu J, Fang Y, Wang C, Xin Z, Yang X. Long non-coding ribonucleic acid SNHG18 induced human granulosa cell apoptosis via disruption of glycolysis in ovarian aging. J Ovarian Res 2024; 17:185. [PMID: 39272131 PMCID: PMC11395969 DOI: 10.1186/s13048-024-01510-4] [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: 03/13/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND In-depth understanding of dynamic expression profiles of human granulosa cells (GCs) during follicular development will contribute to the diagnostic and targeted interventions for female infertility. However, genome-scale analysis of long non-coding ribonucleic acid (lncRNA) in GCs across diverse developmental stages is challenging. Meanwhile, further research is needed to determine how aberrant lncRNA expression participates in ovarian diseases. METHODS Granulosa cell-related lncRNAs data spanning five follicular development stages were retrieved and filtered from the NCBI dataset (GSE107746). Stage-specific lncRNA expression patterns and mRNA-lncRNA co-expression networks were identified with bioinformatic approaches. Subsequently, the expression pattern of SNHG18 was detected in GCs during ovarian aging. And SNHG18 siRNA or overexpression plasmids were transfected to SVOG cells in examining the regulatory roles of SNHG18 in GC proliferation and apoptosis. Moreover, whether PKCɛ/SNHG18 signaling take part in GC glycolysis via ENO1 were verified in SVOG cells. RESULTS We demonstrated that GC-related lncRNAs were specifically expressed across different developmental stages, and coordinated crucial biological functions like mitotic cell cycle and metabolic processes in the folliculogenesis. Thereafter, we noticed a strong correlation of PRKCE and SNHG18 expression in our analysis. With downregulated SNHG18 of GCs identified in the context of ovarian aging, SNHG18 knockdown could further induce cell apoptosis, retard cell proliferation and exacerbate DNA damage in SVOG cell. Moreover, downregulated PKCɛ/SNHG18 pathway interrupted the SVOG cell glycolysis by lowering the ENO1 expression. CONCLUSIONS Altogether, our results revealed that folliculogenesis-related lncRNA SNHG18 participated in the pathogenesis of ovarian aging, which may provide novel biomarkers for ovarian function and new insights for the infertility treatment.
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Affiliation(s)
- Xuehan Zhao
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feiyan Zhao
- Department of Obstetrics and Gynecology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Long Yan
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Jiaqi Wu
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Fang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Cong Wang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Zhimin Xin
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China.
| | - Xiaokui Yang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China.
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Liu Z, Yuan Z, Guo Y, Wang R, Guan Y, Wang Z, Chen Y, Wang T, Jiang M, Bian S. SMARTdb: An Integrated Database for Exploring Single-cell Multi-omics Data of Reproductive Medicine. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae005. [PMID: 39380204 DOI: 10.1093/gpbjnl/qzae005] [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: 09/04/2023] [Revised: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 10/10/2024]
Abstract
Single-cell multi-omics sequencing has greatly accelerated reproductive research in recent years, and the data are continually growing. However, utilizing these data resources is challenging for wet-lab researchers. A comprehensive platform for exploring single-cell multi-omics data related to reproduction is urgently needed. Here, we introduce the single-cell multi-omics atlas of reproduction (SMARTdb), an integrative and user-friendly platform for exploring molecular dynamics of reproductive development, aging, and disease, which covers multi-omics, multi-species, and multi-stage data. We curated and analyzed single-cell transcriptomic and epigenomic data of over 2.0 million cells from 6 species across the entire lifespan. A series of powerful functionalities are provided, such as "Query gene expression", "DIY expression plot", "DNA methylation plot", and "Epigenome browser". With SMARTdb, we found that the male germ cell-specific expression pattern of RPL39L and RPL10L is conserved between human and other model animals. Moreover, DNA hypomethylation and open chromatin may collectively regulate the specific expression pattern of RPL39L in both male and female germ cells. In summary, SMARTdb is a powerful platform for convenient data mining and gaining novel insights into reproductive development, aging, and disease. SMARTdb is publicly available at https://smart-db.cn.
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Affiliation(s)
- Zekai Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhen Yuan
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yunlei Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ruilin Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yusheng Guan
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhanglian Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yunan Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Tianlu Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Meining Jiang
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Shuhui Bian
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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Jia H, Wang W, Zhou Z, Chen Z, Lan Z, Bo H, Fan L. Single-cell RNA sequencing technology in human spermatogenesis: Progresses and perspectives. Mol Cell Biochem 2024; 479:2017-2033. [PMID: 37659974 DOI: 10.1007/s11010-023-04840-x] [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: 06/09/2023] [Accepted: 08/14/2023] [Indexed: 09/04/2023]
Abstract
Spermatogenesis, a key part of the spermiation process, is regulated by a combination of key cells, such as primordial germ cells, spermatogonial stem cells, and somatic cells, such as Sertoli cells. Abnormal spermatogenesis can lead to azoospermia, testicular tumors, and other diseases related to male infertility. The application of single-cell RNA sequencing (scRNA-seq) technology in male reproduction is gradually increasing with its unique insight into deep mining and analysis. The data cover different periods of neonatal, prepubertal, pubertal, and adult stages. Different types of male infertility diseases including obstructive and non-obstructive azoospermia (NOA), Klinefelter Syndrome (KS), Sertoli Cell Only Syndrome (SCOS), and testicular tumors are also covered. We briefly review the principles and application of scRNA-seq and summarize the research results and application directions in spermatogenesis in different periods and pathological states. Moreover, we discuss the challenges of applying this technology in male reproduction and the prospects of combining it with other technologies.
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Affiliation(s)
- Hanbo Jia
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Wei Wang
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zhaowen Zhou
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zhiyi Chen
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zijun Lan
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Hao Bo
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.
| | - Liqing Fan
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.
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24
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Ou N, Wang Y, Xu S, Luo J, Zhang C, Zhang Y, Shi X, Xiong M, Zhao L, Ji Z, Zhang Y, Zhao J, Bai H, Tian R, Li P, Zhi E, Huang Y, Chen W, Wang R, Jin Y, Wang D, Li Z, Chen H, Yao C. Primate-Specific DAZ Regulates Translation of Cell Proliferation-Related mRNAs and is Essential for Maintenance of Spermatogonia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400692. [PMID: 38783578 PMCID: PMC11304246 DOI: 10.1002/advs.202400692] [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: 01/19/2024] [Revised: 05/05/2024] [Indexed: 05/25/2024]
Abstract
Primate-specific DAZ (deleted in azoospermia) has evolved in the azoospermia factor c (AZFc) locus on the Y chromosome. Loss of DAZ is associated with azoospermia in patients with deletion of the AZFc region (AZFc_del). However, the molecular mechanisms of DAZ in spermatogenesis remain uncertain. In this study, the molecular mechanism of DAZ is identified, which is unknown since it is identified 40 years ago because of the lack of a suitable model. Using clinical samples and cell models, it is shown that DAZ plays an important role in spermatogenesis and that loss of DAZ is associated with defective proliferation of c-KIT-positive spermatogonia in patients with AZFc_del. Mechanistically, it is shown that knockdown of DAZ significantly downregulated global translation and subsequently decreased cell proliferation. Furthermore, DAZ interacted with PABPC1 via the DAZ repeat domain to regulate global translation. DAZ targeted mRNAs that are involved in cell proliferation and cell cycle phase transition. These findings indicate that DAZ is a master translational regulator and essential for the maintenance of spermatogonia. Loss of DAZ may result in defective proliferation of c-KIT-positive spermatogonia and spermatogenic failure.
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Affiliation(s)
- Ningjing Ou
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
- Department of UrologyDepartment of Interventional MedicineGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated HospitalSun Yat‐sen UniversityZhuhaiGuangdong519000China
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Yuci Wang
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Shuai Xu
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Jiaqiang Luo
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Chenwang Zhang
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Yangyi Zhang
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Xiaoyan Shi
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Minggang Xiong
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Liangyu Zhao
- Department of UrologyDepartment of Interventional MedicineGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated HospitalSun Yat‐sen UniversityZhuhaiGuangdong519000China
| | - Zhiyong Ji
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Yuxiang Zhang
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Jingpeng Zhao
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Haowei Bai
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Ruhui Tian
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Peng Li
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Erlei Zhi
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Yuhua Huang
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Wei Chen
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Ruiqi Wang
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Yuxuan Jin
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Dian Wang
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Zheng Li
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
| | - Hao Chen
- Department of Human Cell Biology and GeneticsJoint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and DiseasesSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518000China
| | - Chencheng Yao
- Department of AndrologyCenter for Men's HealthUrologic Medical CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
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25
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AbuMadighem A, Cohen O, Huleihel M. Elucidating the Transcriptional States of Spermatogenesis-Joint Analysis of Germline and Supporting Cell, Mice and Human, Normal and Perturbed, Bulk and Single-Cell RNA-Seq. Biomolecules 2024; 14:840. [PMID: 39062554 PMCID: PMC11274546 DOI: 10.3390/biom14070840] [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: 06/11/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
In studying the molecular underpinning of spermatogenesis, we expect to understand the fundamental biological processes better and potentially identify genes that may lead to novel diagnostic and therapeutic strategies toward precision medicine in male infertility. In this review, we emphasized our perspective that the path forward necessitates integrative studies that rely on complementary approaches and types of data. To comprehensively analyze spermatogenesis, this review proposes four axes of integration. First, spanning the analysis of spermatogenesis in the healthy state alongside pathologies. Second, the experimental analysis of model systems (in which we can deploy treatments and perturbations) alongside human data. Third, the phenotype is measured alongside its underlying molecular profiles using known markers augmented with unbiased profiles. Finally, the testicular cells are studied as ecosystems, analyzing the germ cells alongside the states observed in the supporting somatic cells. Recently, the study of spermatogenesis has been advancing using single-cell RNA sequencing, where scientists have uncovered the unique stages of germ cell development in mice, revealing new regulators of spermatogenesis and previously unknown cell subtypes in the testis. An in-depth analysis of meiotic and postmeiotic stages led to the discovery of marker genes for spermatogonia, Sertoli and Leydig cells and further elucidated all the other germline and somatic cells in the testis microenvironment in normal and pathogenic conditions. The outcome of an integrative analysis of spermatogenesis using advanced molecular profiling technologies such as scRNA-seq has already propelled our biological understanding, with additional studies expected to have clinical implications for the study of male fertility. By uncovering new genes and pathways involved in abnormal spermatogenesis, we may gain insights into subfertility or sterility.
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Affiliation(s)
- Ali AbuMadighem
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;
- The Center of Advanced Research and Education in Reproduction (CARER), Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Ofir Cohen
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;
| | - Mahmoud Huleihel
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;
- The Center of Advanced Research and Education in Reproduction (CARER), Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
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26
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Tirumalasetty MB, Bhattacharya I, Mohiuddin MS, Baki VB, Choubey M. Understanding testicular single cell transcriptional atlas: from developmental complications to male infertility. Front Endocrinol (Lausanne) 2024; 15:1394812. [PMID: 39055054 PMCID: PMC11269108 DOI: 10.3389/fendo.2024.1394812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024] Open
Abstract
Spermatogenesis is a multi-step biological process where mitotically active diploid (2n) spermatogonia differentiate into haploid (n) spermatozoa via regulated meiotic programming. The alarming rise in male infertility has become a global concern during the past decade thereby demanding an extensive profiling of testicular gene expression. Advancements in Next-Generation Sequencing (NGS) technologies have revolutionized our empathy towards complex biological events including spermatogenesis. However, despite multiple attempts made in the past to reveal the testicular transcriptional signature(s) either with bulk tissues or at the single-cell, level, comprehensive reviews on testicular transcriptomics and associated disorders are limited. Notably, technologies explicating the genome-wide gene expression patterns during various stages of spermatogenic progression provide the dynamic molecular landscape of testicular transcription. Our review discusses the advantages of single-cell RNA-sequencing (Sc-RNA-seq) over bulk RNA-seq concerning testicular tissues. Additionally, we highlight the cellular heterogeneity, spatial transcriptomics, dynamic gene expression and cell-to-cell interactions with distinct cell populations within the testes including germ cells (Gc), Sertoli cells (Sc), Peritubular cells (PTc), Leydig cells (Lc), etc. Furthermore, we provide a summary of key finding of single-cell transcriptomic studies that have shed light on developmental mechanisms implicated in testicular disorders and male infertility. These insights emphasize the pivotal roles of Sc-RNA-seq in advancing our knowledge regarding testicular transcriptional landscape and may serve as a potential resource to formulate future clinical interventions for male reproductive health.
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Affiliation(s)
| | - Indrashis Bhattacharya
- Department of Zoology, School of Biological Sciences, Central University of Kerala, Kasargod, Kerala, India
| | - Mohammad Sarif Mohiuddin
- Department of Foundations of Medicine, NYU Grossman Long Island School of Medicine, Mineola, NY, United States
| | - Vijaya Bhaskar Baki
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Mayank Choubey
- Department of Foundations of Medicine, NYU Grossman Long Island School of Medicine, Mineola, NY, United States
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27
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Zhang Y, Yang Y, Ren L, Zhan M, Sun T, Zou Q, Zhang Y. Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb. BMC Biol 2024; 22:152. [PMID: 38978014 PMCID: PMC11232326 DOI: 10.1186/s12915-024-01950-w] [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: 03/16/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Metabolite-associated cell communications play critical roles in maintaining human biological function. However, most existing tools and resources focus only on ligand-receptor interaction pairs where both partners are proteinaceous, neglecting other non-protein molecules. To address this gap, we introduce the MRCLinkdb database and algorithm, which aggregates and organizes data related to non-protein L-R interactions in cell-cell communication, providing a valuable resource for predicting intercellular communication based on metabolite-related ligand-receptor interactions. RESULTS Here, we manually curated the metabolite-ligand-receptor (ML-R) interactions from the literature and known databases, ultimately collecting over 790 human and 670 mouse ML-R interactions. Additionally, we compiled information on over 1900 enzymes and 260 transporter entries associated with these metabolites. We developed Metabolite-Receptor based Cell Link Database (MRCLinkdb) to store these ML-R interactions data. Meanwhile, the platform also offers extensive information for presenting ML-R interactions, including fundamental metabolite information and the overall expression landscape of metabolite-associated gene sets (such as receptor, enzymes, and transporter proteins) based on single-cell transcriptomics sequencing (covering 35 human and 26 mouse tissues, 52 human and 44 mouse cell types) and bulk RNA-seq/microarray data (encompassing 62 human and 39 mouse tissues). Furthermore, MRCLinkdb introduces a web server dedicated to the analysis of intercellular communication based on ML-R interactions. MRCLinkdb is freely available at https://www.cellknowledge.com.cn/mrclinkdb/ . CONCLUSIONS In addition to supplementing ligand-receptor databases, MRCLinkdb may provide new perspectives for decoding the intercellular communication and advancing related prediction tools based on ML-R interactions.
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Affiliation(s)
- Yuncong Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Yu Yang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Meixiao Zhan
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Taoping Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
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28
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Zou D, Li K, Su L, Liu J, Lu Y, Huang R, Li M, Mang X, Geng Q, Li P, Tang J, Yu Z, Zhang Z, Chen D, Miao S, Yu J, Yan W, Song W. DDX20 is required for cell-cycle reentry of prospermatogonia and establishment of spermatogonial stem cell pool during testicular development in mice. Dev Cell 2024; 59:1707-1723.e8. [PMID: 38657611 DOI: 10.1016/j.devcel.2024.04.002] [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: 05/11/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
RNA-binding proteins (RBPs), as key regulators of mRNA fate, are abundantly expressed in the testis. However, RBPs associated with human male infertility remain largely unknown. Through bioinformatic analyses, we identified 62 such RBPs, including an evolutionarily conserved RBP, DEAD-box helicase 20 (DDX20). Male germ-cell-specific inactivation of Ddx20 at E15.5 caused T1-propsermatogonia (T1-ProSG) to fail to reenter cell cycle during the first week of testicular development in mice. Consequently, neither the foundational spermatogonial stem cell (SSC) pool nor progenitor spermatogonia were ever formed in the knockout testes. Mechanistically, DDX20 functions to control the translation of its target mRNAs, many of which encode cell-cycle-related regulators, by interacting with key components of the translational machinery in prospermatogonia. Our data demonstrate a previously unreported function of DDX20 as a translational regulator of critical cell-cycle-related genes, which is essential for cell-cycle reentry of T1-ProSG and formation of the SSC pool.
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Affiliation(s)
- Dingfeng Zou
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Kai Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Luying Su
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Jun Liu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Yan Lu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Rong Huang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Mengzhen Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Xinyu Mang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Qi Geng
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Pengyu Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Jielin Tang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Zhixin Yu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Zexuan Zhang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Dingyao Chen
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Shiying Miao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Jia Yu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China; The Institute of Blood Transfusion, Chinese Academy of Medical Sciences, and Peking Union Medical College, Chengdu 610052, China.
| | - Wei Yan
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China.
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29
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Li G, Che K, Wu J, Yang B. Construction of m6A-Related Gene Prediction Model and Subtype Analysis in Non-Obstructive Azoospermia Based on Bioinformatics. Am J Reprod Immunol 2024; 92:e13892. [PMID: 38958252 DOI: 10.1111/aji.13892] [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: 05/01/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024] Open
Abstract
PURPOSE Non-obstructive azoospermia (NOA) is a severe and common cause of male infertility. Currently, the most reliable predictor of sperm retrieval success in NOA is histopathology, but preoperative testicular biopsy often increases the difficulty of sperm retrieval surgery. This study aims to explore the characteristics of N6-methyladenosine (m6A) modification in NOA patients and investigate the potential biomarkers and molecular mechanisms for pathological diagnosis and treatment of NOA using m6A-related genes. METHODS NOA-related datasets were downloaded from the GEO database. Based on the results of LASSO regression analysis, a prediction model was established from differentially expressed m6A-related genes, and the predictive performance of the model was evaluated using ROC curves. Cluster analysis was performed based on differentially expressed m6A-related genes to evaluate the differences in different m6A modification patterns in terms of differentially expressed genes (DEGs), biological features, and immune features. RESULTS There were significant differences in eight m6A-related genes between NOA samples and healthy controls. The ROC curves showed excellent predictive performance for the diagnostic models constructed with ALKBH5 and FTO. DEGs of two m6A modification subtypes indicated the influence of m6A-related genes in the biological processes of mitosis and meiosis in NOA patients, and there were significant immune differences between the two subtypes. CONCLUSION The NOA pathological diagnostic models constructed with FTO and ALKBH5 have good predictive ability. We have identified two different m6A modification subtypes, which may help predict sperm retrieval success rate and treatment selection in NOA patients.
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Affiliation(s)
- Guikang Li
- Department of Urology, The Affiliated Hospital of Qingdao University, Qing Dao, China
| | - Kai Che
- Department of Urology, The Affiliated Hospital of Qingdao University, Qing Dao, China
| | - Jie Wu
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qing Dao, China
| | - Bin Yang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qing Dao, China
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30
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Guo X, Zhao Y, You F. MOI is a comprehensive database collecting processed multi-omics data associated with viral infection. Sci Rep 2024; 14:14725. [PMID: 38926513 PMCID: PMC11208532 DOI: 10.1038/s41598-024-65629-6] [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: 01/26/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
Viral infections pose significant public health challenges, exemplified by the global impact of COVID-19 caused by SARS-CoV-2. Understanding the intricate molecular mechanisms governing virus-host interactions is pivotal for effective intervention strategies. Despite the burgeoning multi-omics data on viral infections, a centralized database elucidating host responses to viruses remains lacking. In response, we have developed a comprehensive database named 'MOI' (available at http://www.fynn-guo.cn/ ), specifically designed to aggregate processed Multi-Omics data related to viral Infections. This meticulously curated database serves as a valuable resource for conducting detailed investigations into virus-host interactions. Leveraging high-throughput sequencing data and metadata from PubMed and Gene Expression Omnibus (GEO), MOI comprises over 3200 viral-infected samples, encompassing human and murine infections. Standardized processing pipelines ensure data integrity, including bulk RNA sequencing (RNA-seq), single-cell RNA-seq (scRNA-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). MOI offers user-friendly interfaces presenting comprehensive cell marker tables, gene expression data, and epigenetic landscape charts. Analytical tools for DNA sequence conversion, FPKM calculation, differential gene expression, and Gene Ontology (GO)/ Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment enhance data interpretation. Additionally, MOI provides 16 visualization plots for intuitive data exploration. In summary, MOI serves as a valuable repository for researchers investigating virus-host interactions. By centralizing and facilitating access to multi-omics data, MOI aims to advance our understanding of viral pathogenesis and expedite the development of therapeutic interventions.
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Affiliation(s)
- Xuefei Guo
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China.
| | - Yang Zhao
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Fuping You
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
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31
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Kwaspen L, Kanbar M, Wyns C. Mapping the Development of Human Spermatogenesis Using Transcriptomics-Based Data: A Scoping Review. Int J Mol Sci 2024; 25:6925. [PMID: 39000031 PMCID: PMC11241379 DOI: 10.3390/ijms25136925] [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: 05/19/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
In vitro maturation (IVM) is a promising fertility restoration strategy for patients with nonobstructive azoospermia or for prepubertal boys to obtain fertilizing-competent spermatozoa. However, in vitro spermatogenesis is still not achieved with human immature testicular tissue. Knowledge of various human testicular transcriptional profiles from different developmental periods helps us to better understand the testis development. This scoping review aims to describe the testis development and maturation from the fetal period towards adulthood and to find information to optimize IVM. Research papers related to native and in vitro cultured human testicular cells and single-cell RNA-sequencing (scRNA-seq) were identified and critically reviewed. Special focus was given to gene ontology terms to facilitate the interpretation of the biological function of related genes. The different consecutive maturation states of both the germ and somatic cell lineages were described. ScRNA-seq regularly showed major modifications around 11 years of age to eventually reach the adult state. Different spermatogonial stem cell (SSC) substates were described and scRNA-seq analyses are in favor of a paradigm shift, as the Adark and Apale spermatogonia populations could not distinctly be identified among the different SSC states. Data on the somatic cell lineage are limited, especially for Sertoli cells due technical issues related to cell size. During cell culture, scRNA-seq data showed that undifferentiated SSCs were favored in the presence of an AKT-signaling pathway inhibitor. The involvement of the oxidative phosphorylation pathway depended on the maturational state of the cells. Commonly identified cell signaling pathways during the testis development and maturation highlight factors that can be essential during specific maturation stages in IVM.
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Affiliation(s)
- Lena Kwaspen
- Laboratoire d’Andrologie, Pôle de Recherche en Physiologie de la Reproduction, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, 1200 Brussels, Belgium; (L.K.); (M.K.)
| | - Marc Kanbar
- Laboratoire d’Andrologie, Pôle de Recherche en Physiologie de la Reproduction, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, 1200 Brussels, Belgium; (L.K.); (M.K.)
- Department of Gynecology-Andrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Christine Wyns
- Laboratoire d’Andrologie, Pôle de Recherche en Physiologie de la Reproduction, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, 1200 Brussels, Belgium; (L.K.); (M.K.)
- Department of Gynecology-Andrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
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32
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Cheng K, Seita Y, Whelan EC, Yokomizo R, Hwang YS, Rotolo A, Krantz ID, Ginsberg JP, Kolon TF, Lal P, Luo X, Pierorazio PM, Linn RL, Ryeom S, Sasaki K. Defining the cellular origin of seminoma by transcriptional and epigenetic mapping to the normal human germline. Cell Rep 2024; 43:114323. [PMID: 38861385 DOI: 10.1016/j.celrep.2024.114323] [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: 03/11/2024] [Revised: 04/26/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Aberrant male germline development can lead to the formation of seminoma, a testicular germ cell tumor. Seminomas are biologically similar to primordial germ cells (PGCs) and many bear an isochromosome 12p [i(12p)] with two additional copies of the short arm of chromosome 12. By mapping seminoma transcriptomes and open chromatin landscape onto a normal human male germline trajectory, we find that seminoma resembles premigratory/migratory PGCs; however, it exhibits enhanced germline and pluripotency programs and upregulation of genes involved in apoptosis, angiogenesis, and MAPK/ERK pathways. Using pluripotent stem cell-derived PGCs from Pallister-Killian syndrome patients mosaic for i(12p), we model seminoma and identify gene dosage effects that may contribute to transformation. As murine seminoma models do not exist, our analyses provide critical insights into genetic, cellular, and signaling programs driving seminoma transformation, and the in vitro platform developed herein permits evaluation of additional signals required for seminoma tumorigenesis.
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Affiliation(s)
- Keren Cheng
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Yasunari Seita
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Eoin C Whelan
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Ryo Yokomizo
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Young Sun Hwang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Antonia Rotolo
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Ian D Krantz
- Division of Human Genetics, The Roberts Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Jill P Ginsberg
- Department of Pediatrics, The Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Thomas F Kolon
- Division of Urology, The Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Priti Lal
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Xunda Luo
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Presbyterian Medical Center, 51 North 39th Street, Philadelphia, PA 19104, USA
| | - Phillip M Pierorazio
- Division of Urology, University of Pennsylvania Presbyterian Medical Center, 3737 Market St. 4th Floor, Philadelphia, PA 19104, USA
| | - Rebecca L Linn
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, Philadelphia, PA 19104, USA; Department of Pathology, The Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Sandra Ryeom
- Department of Surgery, Columbia University Irving Medical Center, 630 W. 168th Street, P&S 17-409, New York, NY 10032, USA
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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33
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Al-Madhagi H, Tarabishi AA. Nutritional aphrodisiacs: Biochemistry and Pharmacology. Curr Res Food Sci 2024; 9:100783. [PMID: 38974844 PMCID: PMC11225857 DOI: 10.1016/j.crfs.2024.100783] [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: 03/11/2024] [Revised: 04/08/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024] Open
Abstract
In 2022, the global prevalence of erectile dysfunction (ED) was estimated to be at least 150 million cases. This number is greatly suspected to be underestimate as most men withhold information about ED. Also, about 15% of world population have infertility troubles, and male factors are responsible for almost half of these cases. Studies have shown that the quality of semen has decreased in the past several decades owing to various health factors and environmental toxicants. The current medical interventions involve the inhibition of phosphodiesterase 5 which suffer from serious side effects and costly. One of the popular and most sought interventions are the natural and nutritional remedies as they are foods in essence and potentially with no harm to the body. Therefore, the goal of this paper is to provide a review of the most common nutritional aphrodisiacs with increasing libido and fertility highlighting the potential active constituents as well as the underlying mechanisms.
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Wang H, Iida-Norita R, Mashiko D, Pham AH, Miyata H, Ikawa M. Golgi associated RAB2 interactor protein family contributes to murine male fertility to various extents by assuring correct morphogenesis of sperm heads. PLoS Genet 2024; 20:e1011337. [PMID: 38935810 PMCID: PMC11236154 DOI: 10.1371/journal.pgen.1011337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/10/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Sperm heads contain not only the nucleus but also the acrosome which is a distinctive cap-like structure located anterior to the nucleus and is derived from the Golgi apparatus. The Golgi Associated RAB2 Interactors (GARINs; also known as FAM71) protein family shows predominant expression in the testis and all possess a RAB2-binding domain which confers binding affinity to RAB2, a small GTPase that is responsible for membrane transport and vesicle trafficking. Our previous study showed that GARIN1A and GARIN1B are important for acrosome biogenesis and that GARIN1B is indispensable for male fertility in mice. Here, we generated KO mice of other Garins, namely Garin2, Garin3, Garin4, Garin5a, and Garin5b (Garin2-5b). Using computer-assisted morphological analysis, we found that the loss of each Garin2-5b resulted in aberrant sperm head morphogenesis. While the fertilities of Garin2-/- and Garin4-/- males are normal, Garin5a-/- and Garin5b-/- males are subfertile, and Garin3-/- males are infertile. Further analysis revealed that Garin3-/- males exhibited abnormal acrosomal morphology, but not as severely as Garin1b-/- males; instead, the amounts of membrane proteins, particularly ADAM family proteins, decreased in Garin3 KO spermatozoa. Moreover, only Garin4 KO mice exhibit vacuoles in the sperm head. These results indicate that GARINs assure correct head morphogenesis and some members of the GARIN family function distinctively in male fertility.
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Affiliation(s)
- Haoting Wang
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Rie Iida-Norita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Daisuke Mashiko
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Anh Hoang Pham
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Haruhiko Miyata
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masahito Ikawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
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Liu T, Qiao H, Wang Z, Yang X, Pan X, Yang Y, Ye X, Sakurai T, Lin H, Zhang Y. CodLncScape Provides a Self-Enriching Framework for the Systematic Collection and Exploration of Coding LncRNAs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400009. [PMID: 38602457 PMCID: PMC11165466 DOI: 10.1002/advs.202400009] [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: 01/01/2024] [Revised: 03/19/2024] [Indexed: 04/12/2024]
Abstract
Recent studies have revealed that numerous lncRNAs can translate proteins under specific conditions, performing diverse biological functions, thus termed coding lncRNAs. Their comprehensive landscape, however, remains elusive due to this field's preliminary and dispersed nature. This study introduces codLncScape, a framework for coding lncRNA exploration consisting of codLncDB, codLncFlow, codLncWeb, and codLncNLP. Specifically, it contains a manually compiled knowledge base, codLncDB, encompassing 353 coding lncRNA entries validated by experiments. Building upon codLncDB, codLncFlow investigates the expression characteristics of these lncRNAs and their diagnostic potential in the pan-cancer context, alongside their association with spermatogenesis. Furthermore, codLncWeb emerges as a platform for storing, browsing, and accessing knowledge concerning coding lncRNAs within various programming environments. Finally, codLncNLP serves as a knowledge-mining tool to enhance the timely content inclusion and updates within codLncDB. In summary, this study offers a well-functioning, content-rich ecosystem for coding lncRNA research, aiming to accelerate systematic studies in this field.
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Affiliation(s)
- Tianyuan Liu
- Tsukuba Life Science Innovation ProgramUniversity of TsukubaTsukuba3058577Japan
| | - Huiyuan Qiao
- Innovative Institute of Chinese Medicine and PharmacyAcademy for InterdisciplineChengdu University of Traditional Chinese MedicineChengdu611137China
| | - Zixu Wang
- Department of Computer ScienceUniversity of TsukubaTsukuba3058577Japan
| | - Xinyan Yang
- Department of Developmental BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Xianrun Pan
- Innovative Institute of Chinese Medicine and PharmacyAcademy for InterdisciplineChengdu University of Traditional Chinese MedicineChengdu611137China
| | - Yu Yang
- School of Healthcare TechnologyChengdu Neusoft UniversityChengdu611844China
| | - Xiucai Ye
- Tsukuba Life Science Innovation ProgramUniversity of TsukubaTsukuba3058577Japan
- Department of Computer ScienceUniversity of TsukubaTsukuba3058577Japan
| | - Tetsuya Sakurai
- Tsukuba Life Science Innovation ProgramUniversity of TsukubaTsukuba3058577Japan
- Department of Computer ScienceUniversity of TsukubaTsukuba3058577Japan
| | - Hao Lin
- School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengdu611731China
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and PharmacyAcademy for InterdisciplineChengdu University of Traditional Chinese MedicineChengdu611137China
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36
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An K, Yao B, Tan Y, Kang Y, Wang Z, Su J. Spermatocytes are the terminals of germ cell differentiation in plateau zokor (Eospalax baileyi) during the non-breeding season. Integr Zool 2024. [PMID: 38816925 DOI: 10.1111/1749-4877.12849] [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] [Indexed: 06/01/2024]
Abstract
Plateau zokor (Eospalax baileyi) is a subterranean rodent and seasonal breeder. During the non-breeding season, the testicles regress, leading to the arrest of spermatogenesis and loss of fertility. The identification of the specific germ cell type at which spermatogenesis is arrested, as well as potential regulatory factors during the non-breeding season, is important for understanding seasonal spermatogenesis in subterranean species. This study analyzed genes in spermatocytes of plateau zokor by referring to single-cell RNA results in mice. We discovered that spermatogenesis is arrested at the spermatocyte during the non-breeding season, which was corroborated via immunofluorescence staining results. The analysis of gene expression during different stages of meiotic prophase I has revealed that germ cell development may be arrested, starting from zygonema, during the non-breeding season. Meanwhile, we discovered that the apoptosis genes were up-regulated, leading to apoptosis in spermatocytes. To confirm that the germ cell differentiation was blocked during the non-breeding season due to a decrease in the androgen level, we used androgen receptor antagonist (flutamide) to intervene in the breeding season and found that the inner diameter of the seminiferous tubules was significantly reduced, spermatogenesis was arrested, and spermatocytes underwent apoptosis. This study revealed that spermatocytes are the terminal of germ cell differentiation in plateau zokor during the non-breeding season and that the arrest of differentiation is attributed to a decline in androgen levels. Our results complement the theoretical basis of seasonal reproduction in plateau zokor.
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Affiliation(s)
- Kang An
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, China
| | - Baohui Yao
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, China
| | - Yuchen Tan
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, China
| | - Yukun Kang
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, China
| | - Zhicheng Wang
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, China
| | - Junhu Su
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, China
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, China
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37
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Zong W, Wang Y, Zhang L, Lu W, Li W, Wang F, Cheng J. DNA Methylation Mediates Sperm Quality via piwil1 and piwil2 Regulation in Japanese Flounder ( Paralichthys olivaceus). Int J Mol Sci 2024; 25:5935. [PMID: 38892123 PMCID: PMC11172970 DOI: 10.3390/ijms25115935] [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: 04/11/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
DNA methylation is an important way to regulate gene expression in eukaryotes. In order to reveal the role of DNA methylation in the regulation of germ cell-specific piwi gene expression during spermatogenesis of Japanese flounder (Paralichthys olivaceus), the expression profiles of piwil1 (piwi-like 1) and piwil2 (piwi-like 2) genes in the gonads of female, male, and sex-reversed pseudo-male P. olivaceus were analyzed, and the dynamic of DNA methylation was investigated. As a result, piwil1 and piwil2 genes were highly expressed in the testis of both male and pseudo-male P. olivaceus, with significant variation among male individuals. The DNA methylation levels in the promoter regions of both piwil1 and piwil2 were negatively correlated with their expression levels, which may contribute to the transcriptional regulation of piwi genes during spermatogenesis. There was also sperm quality variation among male P. olivaceus, and the sperm curvilinear velocity was positively correlated with the expression of both piwil1 and piwil2 genes. These results indicated that the DNA methylation in piwil1 and piwil2 promoter regions may affect the initiation of piwi gene transcription, thereby regulating gene expression and further affecting the spermatogenesis process and gamete quality in P. olivaceus.
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Affiliation(s)
- Wenyu Zong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yapeng Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lingqun Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Wei Lu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Weigang Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Fengchi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jie Cheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao 266237, China
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38
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An J, Wang J, Kong S, Song S, Chen W, Yuan P, He Q, Chen Y, Li Y, Yang Y, Wang W, Li R, Yan L, Yan Z, Qiao J. GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad004. [PMID: 38862425 DOI: 10.1093/gpbjnl/qzad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been uniformed and integrated, which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and spermatogenesis. Here, we develop GametesOmics, a comprehensive database that integrates the data of gene expression, DNA methylation, and chromatin accessibility during oogenesis and spermatogenesis in humans and mice. GametesOmics provides a user-friendly website and various tools, including Search and Advanced Search for querying the expression and epigenetic modification(s) of each gene; Tools with Differentially expressed gene (DEG) analysis for identifying DEGs, Correlation analysis for demonstrating the genetic and epigenetic changes, Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors (TFs), and MethylView for studying the genomic distribution of epigenetic modifications. GametesOmics also provides Genome Browser and Ortholog for tracking and comparing gene expression, DNA methylation, and chromatin accessibility between humans and mice. GametesOmics offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development, and can be accessed at http://gametesomics.cn/.
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Affiliation(s)
- Jianting An
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jing Wang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Siming Kong
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shi Song
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Wei Chen
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Peng Yuan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Qilong He
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yidong Chen
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ye Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yi Yang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Wei Wang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rong Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Liying Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Zhiqiang Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100191, China
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Robinson M, Zhou K, Kung SHY, Karaoğlanoğlu F, Golin A, Safa A, Cai C, Witherspoon L, Hach F, Flannigan R. A novel sorting method for the enrichment of early human spermatocytes from clinical biopsies. F&S SCIENCE 2024; 5:130-140. [PMID: 38369016 DOI: 10.1016/j.xfss.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE To determine if early spermatocytes can be enriched from a human testis biopsy using fluorescence-activated cell sorting (FACS). DESIGN Potential surface markers for early spermatocytes were identified using bioinformatics analysis of single-cell RNA-sequenced human testis tissue. Testicular sperm extraction samples from three participants with normal spermatogenesis were digested into single-cell suspensions and cryopreserved. Two to four million cells were obtained from each and sorted by FACS as separate biologic replicates using antibodies for the identified surface markers. A portion from each biopsy remained unsorted to serve as controls. The sorted cells were then characterized for enrichment of early spermatocytes. SETTING A laboratory study. PATIENTS Three men with a diagnosis of obstructive azoospermia (age range, 30-40 years). INTERVENTION None. MAIN OUTCOME MEASURES Sorted cells were characterized for RNA expression of markers encompassing the stages of spermatogenesis. Sorting markers were validated by their reactivity on human testis formalin-fixed paraffin-embedded tissue. RESULTS Serine protease 50 (TSP50) and SWI5-dependent homologous recombination repair protein 1 were identified as potential surface proteins specific for early spermatocytes. After FACS sorting, the TSP50-sorted populations accounted for 1.6%-8.9% of total populations and exhibited the greatest average-fold increases in RNA expression for the premeiotic marker stimulated by retinoic acid (STRA8), by 23-fold. Immunohistochemistry showed the staining pattern for TSP50 to be strong in premeiotic undifferentiated embryonic cell transcription factor 1-/doublesex and Mab-3 related transcription factor 1-/STRA8+ spermatogonia as well as SYCP3+/protamine 2- spermatocytes. CONCLUSION This work shows that TSP50 can be used to enrich early STRA8-expressing spermatocytes from human testicular biopsies, providing a means for targeted single-cell RNA sequencing analysis and in vitro functional interrogation of germ cells during the onset of meiosis. This could enable investigation into details of the regulatory pathways underlying this critical stage of spermatogenesis, previously difficult to enrich from whole tissue samples.
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Affiliation(s)
- Meghan Robinson
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Kevin Zhou
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sonia H Y Kung
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Fatih Karaoğlanoğlu
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; School of Computing Science, Department of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Andrew Golin
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Armita Safa
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charley Cai
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke Witherspoon
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Department of Urology, the Ottawa Hospital, Ottawa, Ontario, Canada
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan Flannigan
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Department of Urology, Weill Cornell Medicine, New York, New York.
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40
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Fu L, Wu Q, Fu J. Exploring the biological roles of DHX36, a DNA/RNA G-quadruplex helicase, highlights functions in male infertility: A comprehensive review. Int J Biol Macromol 2024; 268:131811. [PMID: 38677694 DOI: 10.1016/j.ijbiomac.2024.131811] [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: 01/04/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/29/2024]
Abstract
It is estimated that 15 % of couples at reproductive age worldwide suffer from infertility, approximately 50 % of cases are caused by male factors. Significant progress has been made in the diagnosis and treatment of male infertility through assisted reproductive technology and molecular genetics methods. However, there is still inadequate research on the underlying mechanisms of gene regulation in the process of spermatogenesis. Guanine-quadruplexes (G4s) are a class of non-canonical secondary structures of nucleic acid commonly found in genomes and RNAs that play important roles in various biological processes. Interestingly, the DEAH-box helicase 36 (DHX36) displays high specificity for the G4s which can unwind both DNA G4s and RNA G4s enzymatically and is highly expressed in testis, thereby regulating multiple cellular functions including transcription, pre-mRNA splicing, translation, telomere maintenance, genomic stability, and RNA metabolism in development and male infertility. This review provides an overview of the roles of G4s and DHX36 in reproduction and development. We mainly focus on the potential role of DHX36 in male infertility. We also discuss possible future research directions regarding the mechanism of spermatogenesis mediated by DHX36 through G4s in spermatogenesis-related genes and provide new targets for gene therapy of male infertility.
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Affiliation(s)
- Li Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; Department of Reproductive Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China; Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Junjiang Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China.
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Bush SJ, Nikola R, Han S, Suzuki S, Yoshida S, Simons BD, Goriely A. Adult Human, but Not Rodent, Spermatogonial Stem Cells Retain States with a Foetal-like Signature. Cells 2024; 13:742. [PMID: 38727278 PMCID: PMC11083513 DOI: 10.3390/cells13090742] [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: 03/19/2024] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
Spermatogenesis involves a complex process of cellular differentiation maintained by spermatogonial stem cells (SSCs). Being critical to male reproduction, it is generally assumed that spermatogenesis starts and ends in equivalent transcriptional states in related species. Based on single-cell gene expression profiling, it has been proposed that undifferentiated human spermatogonia can be subclassified into four heterogenous subtypes, termed states 0, 0A, 0B, and 1. To increase the resolution of the undifferentiated compartment and trace the origin of the spermatogenic trajectory, we re-analysed the single-cell (sc) RNA-sequencing libraries of 34 post-pubescent human testes to generate an integrated atlas of germ cell differentiation. We then used this atlas to perform comparative analyses of the putative SSC transcriptome both across human development (using 28 foetal and pre-pubertal scRNA-seq libraries) and across species (including data from sheep, pig, buffalo, rhesus and cynomolgus macaque, rat, and mouse). Alongside its detailed characterisation, we show that the transcriptional heterogeneity of the undifferentiated spermatogonial cell compartment varies not only between species but across development. Our findings associate 'state 0B' with a suppressive transcriptomic programme that, in adult humans, acts to functionally oppose proliferation and maintain cells in a ready-to-react state. Consistent with this conclusion, we show that human foetal germ cells-which are mitotically arrested-can be characterised solely as state 0B. While germ cells with a state 0B signature are also present in foetal mice (and are likely conserved at this stage throughout mammals), they are not maintained into adulthood. We conjecture that in rodents, the foetal-like state 0B differentiates at birth into the renewing SSC population, whereas in humans it is maintained as a reserve population, supporting testicular homeostasis over a longer reproductive lifespan while reducing mutagenic load. Together, these results suggest that SSCs adopt differing evolutionary strategies across species to ensure fertility and genome integrity over vastly differing life histories and reproductive timeframes.
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Affiliation(s)
- Stephen J. Bush
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Rafail Nikola
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Seungmin Han
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Shinnosuke Suzuki
- Division of Germ Cell Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Shosei Yoshida
- Division of Germ Cell Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Benjamin D. Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Wellcome—MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Science, University of Cambridge, Cambridge CB3 0WA, UK
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
- NIHR Biomedical Research Centre, Oxford OX3 7JX, UK
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Wei X, Wang X, Yang C, Gao Y, Zhang Y, Xiao Y, Ju Z, Jiang Q, Wang J, Liu W, Li Y, Gao Y, Huang J. CFAP58 is involved in the sperm head shaping and flagellogenesis of cattle and mice. Development 2024; 151:dev202608. [PMID: 38602507 DOI: 10.1242/dev.202608] [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: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 04/12/2024]
Abstract
CFAP58 is a testis-enriched gene that plays an important role in the sperm flagellogenesis of humans and mice. However, the effect of CFAP58 on bull semen quality and the underlying molecular mechanisms involved in spermatogenesis remain unknown. Here, we identified two single-nucleotide polymorphisms (rs110610797, A>G and rs133760846, G>T) and one indel (g.-1811_ g.-1810 ins147bp) in the promoter of CFAP58 that were significantly associated with semen quality of bulls, including sperm deformity rate and ejaculate volume. Moreover, by generating gene knockout mice, we found for the first time that the loss of Cfap58 not only causes severe defects in the sperm tail, but also affects the manchette structure, resulting in abnormal sperm head shaping. Cfap58 deficiency causes an increase in spermatozoa apoptosis. Further experiments confirmed that CFAP58 interacts with IFT88 and CCDC42. Moreover, it may be a transported cargo protein that plays a role in stabilizing other cargo proteins, such as CCDC42, in the intra-manchette transport/intra-flagellar transport pathway. Collectively, our findings reveal that CFAP58 is required for spermatogenesis and provide genetic markers for evaluating semen quality in cattle.
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Affiliation(s)
- Xiaochao Wei
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Xiuge Wang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Chunhong Yang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Yaping Gao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Yaran Zhang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Yao Xiao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Zhihua Ju
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Qiang Jiang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Jinpeng Wang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Wenhao Liu
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Yanqin Li
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Yundong Gao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Technical Innovation Center of Dairy Cattle Breeding Industry of Shandong Province, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
| | - Jinming Huang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
- Technical Innovation Center of Dairy Cattle Breeding Industry of Shandong Province, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, P. R. China
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Murugesh V, Ritting M, Salem S, Aalam SMM, Garcia J, Chattha AJ, Zhao Y, Knapp DJHF, Kalthur G, Granberg CF, Kannan N. Puberty Blocker and Aging Impact on Testicular Cell States and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.23.586441. [PMID: 38585884 PMCID: PMC10996503 DOI: 10.1101/2024.03.23.586441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Spermatogonial stem cell (SSC) acquisition of meiotogenetic state during puberty to produce genetically diverse gametes is blocked by drugs collectively referred as 'puberty blocker' (PB). Investigating the impact of PB on juvenile SSC state and function is challenging due to limited tissue access and clinical data. Herein, we report largest clinically annotated juvenile testicular biorepository with all children with gender dysphoria on chronic PB treatment highlighting shift in pediatric patient demography in US. At the tissue level, we report mild-to-severe sex gland atrophy in PB treated children. We developed most extensive integrated single-cell RNA dataset to date (>100K single cells; 25 patients), merging both public and novel (52 month PB-treated) datasets, alongside innovative computational approach tailed for germ cells and evaluated the impact of PB and aging on SSC. We report novel constitutional ranges for each testicular cell type across the entire age spectrum, distinct effects of treatments on prepubertal vs adult SSC, presence of spermatogenic epithelial cells exhibiting post-meiotic-state, irrespective of age, puberty status, or PB treatment. Further, we defined distinct effects of PB and aging on testicular cell lineage composition, and SSC meiotogenetic state and function. Using single cell data from prepubertal and young adult, we were able to accurately predict sexual maturity based both on overall cell type proportions, as well as on gene expression patterns within each major cell type. Applying these models to a PB-treated patient that they appeared pre-pubertal across the entire tissue. This combined with the noted gland atrophy and abnormalities from the histology data raise a potential concern regarding the complete 'reversibility' and reproductive fitness of SSC. The biorepository, data, and research approach presented in this study provide unique opportunity to explore the impact of PB on testicular reproductive health.
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Affiliation(s)
- Varshini Murugesh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Megan Ritting
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Salem Salem
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Joaquin Garcia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Asma J Chattha
- Department of Pediatrics, Mayo Clinic, Rochester, MN, USA
| | - Yulian Zhao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
| | - David JHF Knapp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Institut de Recherche en Immunologie et Cancérologie, and Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC, Canada
- Senior authors
| | - Guruprasad Kalthur
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Division of Reproductive Biology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Senior authors
| | | | - Nagarajan Kannan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Center for Regenerative Biotherapeutics, Mayo Clinic, Rochester, MN, USA
- Senior authors
- Lead contact
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Lin S, Feng D, Han X, Li L, Lin Y, Gao H. Microfluidic platform for omics analysis on single cells with diverse morphology and size: A review. Anal Chim Acta 2024; 1294:342217. [PMID: 38336406 DOI: 10.1016/j.aca.2024.342217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Microfluidic techniques have emerged as powerful tools in single-cell research, facilitating the exploration of omics information from individual cells. Cell morphology is crucial for gene expression and physiological processes. However, there is currently a lack of integrated analysis of morphology and single-cell omics information. A critical challenge remains: what platform technologies are the best option to decode omics data of cells that are complex in morphology and size? RESULTS This review highlights achievements in microfluidic-based single-cell omics and isolation of cells based on morphology, along with other cell sorting methods based on physical characteristics. Various microfluidic platforms for single-cell isolation are systematically presented, showcasing their diversity and adaptability. The discussion focuses on microfluidic devices tailored to the distinct single-cell isolation requirements in plants and animals, emphasizing the significance of considering cell morphology and cell size in optimizing single-cell omics strategies. Simultaneously, it explores the application of microfluidic single-cell sorting technologies to single-cell sequencing, aiming to effectively integrate information about cell shape and size. SIGNIFICANCE AND NOVELTY The novelty lies in presenting a comprehensive overview of recent accomplishments in microfluidic-based single-cell omics, emphasizing the integration of different microfluidic platforms and their implications for cell morphology-based isolation. By underscoring the pivotal role of the specialized morphology of different cells in single-cell research, this review provides robust support for delving deeper into the exploration of single-cell omics data.
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Affiliation(s)
- Shujin Lin
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China.
| | - Ling Li
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; The First Clinical Medical College of Fujian Medical University, Fuzhou, 350004, China; Hepatopancreatobiliary Surgery Department, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, China.
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China; Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, China.
| | - Haibing Gao
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China.
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Li R, Du Y, Li K, Xiong X, Zhang L, Guo C, Gao S, Yao Y, Xu Y, Yang J. Single-cell transcriptome profiling implicates the psychological stress-induced disruption of spermatogenesis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102158. [PMID: 38439912 PMCID: PMC10910125 DOI: 10.1016/j.omtn.2024.102158] [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: 09/24/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Male infertility has emerged as a global issue, partly attributed to psychological stress. However, the cellular and molecular mechanisms underlying the adverse effects of psychological stress on male reproductive function remain elusive. We created a psychologically stressed model using terrified-sound and profiled the testes from stressed and control rats using single-cell RNA sequencing. Comparative and comprehensive transcriptome analyses of 11,744 testicular cells depicted the cellular landscape of spermatogenesis and revealed significant molecular alterations of spermatogenesis suffering from psychological stress. At the cellular level, stressed rats exhibited delayed spermatogenesis at the spermatogonia and pachytene phases, resulting in reduced sperm production. Additionally, psychological stress rewired cellular interactions among germ cells, negatively impacting reproductive development. Molecularly, we observed the down-regulation of anti-oxidation-related genes and up-regulation of genes promoting reactive oxygen species (ROS) generation in the stress group. These alterations led to elevated ROS levels in testes, affecting the expression of key regulators such as ATF2 and STAR, which caused reproductive damage through apoptosis or inhibition of testosterone synthesis. Overall, our study aimed to uncover the cellular and molecular mechanisms by which psychological stress disrupts spermatogenesis, offering insights into the mechanisms of psychological stress-induced male infertility in other species and promises in potential therapeutic targets.
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Affiliation(s)
- Rufeng Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Yuefeng Du
- Department of Urology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, P.R. China
| | - Kang Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Xiaofan Xiong
- Center for Tumor and Immunology, the Precision Medical Institute, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, P.R. China
| | - Lingyu Zhang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Chen Guo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Shanfeng Gao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Yufei Yao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Yungang Xu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Juan Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, P.R. China
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Taelman J, Czukiewska SM, Moustakas I, Chang YW, Hillenius S, van der Helm T, van der Meeren LE, Mei H, Fan X, Chuva de Sousa Lopes SM. Characterization of the human fetal gonad and reproductive tract by single-cell transcriptomics. Dev Cell 2024; 59:529-544.e5. [PMID: 38295793 PMCID: PMC10898717 DOI: 10.1016/j.devcel.2024.01.006] [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: 02/12/2022] [Revised: 09/05/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
During human fetal development, sex differentiation occurs not only in the gonads but also in the adjacent developing reproductive tract. However, while the cellular composition of male and female human fetal gonads is well described, that of the adjacent developing reproductive tract remains poorly characterized. Here, we performed single-cell transcriptomics on male and female human fetal gonads together with the adjacent developing reproductive tract from first and second trimesters, highlighting the morphological and molecular changes during sex differentiation. We validated different cell populations of the developing reproductive tract and gonads and compared the molecular signatures between the first and second trimesters, as well as between sexes, to identify conserved and sex-specific features. Together, our study provides insights into human fetal sex-specific gonadogenesis and development of the reproductive tract beyond the gonads.
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Affiliation(s)
- Jasin Taelman
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Sylwia M Czukiewska
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Ioannis Moustakas
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Yolanda W Chang
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Sanne Hillenius
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Talia van der Helm
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Lotte E van der Meeren
- Department of Pathology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Department of Pathology, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Xueying Fan
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
| | - Susana M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Department for Reproductive Medicine, Ghent University Hospital, 9000 Ghent, Belgium.
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47
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Chen W, Cui Y, Li C, He C, Du L, Liu W, He Z. KLF2 controls proliferation and apoptosis of human spermatogonial stem cells via targeting GJA1. iScience 2024; 27:109024. [PMID: 38352225 PMCID: PMC10863320 DOI: 10.1016/j.isci.2024.109024] [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: 07/25/2023] [Revised: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Human spermatogonial stem cells (SSCs) are essential for spermatogenesis and male fertility. However, molecular mechanisms regulating fate determinations of human SSCs remain elusive. In this study, we revealed that KLF2 decreased the proliferation, DNA synthesis, and colonization of human SSCs as well as increased apoptosis of these cells. We identified and demonstrated that GJA1 was a target gene for KLF2 in human SSCs. Notably, KLF2 overexpression rescued the reduction of proliferation of human SSCs caused by GJA1 silencing as well as the enhancement of apoptosis of human SSCs. Abnormalities in the higher level of KLF2 and/or KIF2 mutations might lead to male infertility. Collectively, these results implicate that KLF2 inhibits proliferation of human SSCs and enhances their apoptosis by targeting GJA1. This study thus provides novel genetic mechanisms underlying human spermatogenesis and azoospermia, and it offers new endogenous targets for treating male infertility.
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Affiliation(s)
- Wei Chen
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, China
| | - Yinghong Cui
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, China
| | - Chunyun Li
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, China
| | - Caimei He
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, China
| | - Li Du
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, China
| | - Wei Liu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, China
| | - Zuping He
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Manufacture-Based Learning and Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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48
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Ma JY, Xia TJ, Li S, Yin S, Luo SM, Li G. Germline cell de novo mutations and potential effects of inflammation on germline cell genome stability. Semin Cell Dev Biol 2024; 154:316-327. [PMID: 36376195 DOI: 10.1016/j.semcdb.2022.11.003] [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: 07/14/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
Uncontrolled pathogenic genome mutations in germline cells might impair adult fertility, lead to birth defects or even affect the adaptability of a species. Understanding the sources of DNA damage, as well as the features of damage response in germline cells are the overarching tasks to reduce the mutations in germline cells. With the accumulation of human genome data and genetic reports, genome variants formed in germline cells are being extensively explored. However, the sources of DNA damage, the damage repair mechanisms, and the effects of DNA damage or mutations on the development of germline cells are still unclear. Besides exogenous triggers of DNA damage such as irradiation and genotoxic chemicals, endogenous exposure to inflammation may also contribute to the genome instability of germline cells. In this review, we summarized the features of de novo mutations and the specific DNA damage responses in germline cells and explored the possible roles of inflammation on the genome stability of germline cells.
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Affiliation(s)
- Jun-Yu Ma
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China.
| | - Tian-Jin Xia
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China; College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shuai Li
- Center for Clinical Epidemiology and Methodology, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Shen Yin
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| | - Shi-Ming Luo
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China.
| | - Guowei Li
- Center for Clinical Epidemiology and Methodology, Guangdong Second Provincial General Hospital, Guangzhou, China.
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49
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Chen S, Liu S, Shi S, Yin H, Tang Y, Zhang J, Li W, Liu G, Qu K, Ding X, Wang Y, Liu J, Zhang S, Fang L, Yu Y. Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats. Mol Biol Evol 2024; 41:msae003. [PMID: 38266195 PMCID: PMC10834038 DOI: 10.1093/molbev/msae003] [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: 07/24/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.
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Affiliation(s)
- Siqian Chen
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuli Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Shaolei Shi
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hongwei Yin
- Agriculture Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yongjie Tang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jinning Zhang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenlong Li
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100125, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianfeng Liu
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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50
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Piechka A, Sparanese S, Witherspoon L, Hach F, Flannigan R. Molecular mechanisms of cellular dysfunction in testes from men with non-obstructive azoospermia. Nat Rev Urol 2024; 21:67-90. [PMID: 38110528 DOI: 10.1038/s41585-023-00837-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2023] [Indexed: 12/20/2023]
Abstract
Male factor infertility affects 50% of infertile couples worldwide; the most severe form, non-obstructive azoospermia (NOA), affects 10-15% of infertile males. Treatment for individuals with NOA is limited to microsurgical sperm extraction paired with in vitro fertilization intracytoplasmic sperm injection. Unfortunately, spermatozoa are only retrieved in ~50% of patients, resulting in live birth rates of 21-46%. Regenerative therapies could provide a solution; however, understanding the cell-type-specific mechanisms of cellular dysfunction is a fundamental necessity to develop precision medicine strategies that could overcome these abnormalities and promote regeneration of spermatogenesis. A number of mechanisms of cellular dysfunction have been elucidated in NOA testicular cells. These mechanisms include abnormalities in both somatic cells and germ cells in NOA testes, such as somatic cell immaturity, aberrant growth factor signalling, increased inflammation, increased apoptosis and abnormal extracellular matrix regulation. Future cell-type-specific investigations in identifying modulators of cellular transcription and translation will be key to understanding upstream dysregulation, and these studies will require development of in vitro models to functionally interrogate spermatogenic niche dysfunction in both somatic and germ cells.
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Affiliation(s)
- Arina Piechka
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Sydney Sparanese
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke Witherspoon
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Urology, Department of Surgery, University of Ottawa, Ontario, Canada
| | - Faraz Hach
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Ryan Flannigan
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada.
- Department of Urology, Weill Cornell Medicine, New York, NY, USA.
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