1
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Shoaran M, Sabaie H, Mostafavi M, Rezazadeh M. A comprehensive review of the applications of RNA sequencing in celiac disease research. Gene 2024; 927:148681. [PMID: 38871036 DOI: 10.1016/j.gene.2024.148681] [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: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
RNA sequencing (RNA-seq) has undergone substantial advancements in recent decades and has emerged as a vital technique for profiling the transcriptome. The transition from bulk sequencing to single-cell and spatial approaches has facilitated the achievement of higher precision at cell resolution. It provides valuable biological knowledge about individual immune cells and aids in the discovery of the molecular mechanisms that contribute to the development of autoimmune diseases. Celiac disease (CeD) is an autoimmune disorder characterized by a strong immune response to gluten consumption. RNA-seq has led to significantly advanced research in multiple fields, particularly in CeD research. It has been instrumental in studies involving comparative transcriptomics, nutritional genomics and wheat research, cancer research in the context of CeD, genetic and noncoding RNA-mediated epigenetic insights, disease monitoring and biomarker discovery, regulation of mitochondrial functions, therapeutic target identification and drug mechanism of action, dietary factors, immune cell profiling and the immune landscape. This review offers a comprehensive examination of recent RNA-seq technology research in the field of CeD, highlighting future challenges and opportunities for its application.
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Affiliation(s)
- Maryam Shoaran
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehrnaz Mostafavi
- Faculty of Allied Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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2
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Russell SJ, Zhao C, Biondic S, Menezes K, Hagemann-Jensen M, Librach CL, Petropoulos S. An atlas of small non-coding RNAs in human preimplantation development. Nat Commun 2024; 15:8634. [PMID: 39367016 PMCID: PMC11452719 DOI: 10.1038/s41467-024-52943-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: 11/26/2023] [Accepted: 09/26/2024] [Indexed: 10/06/2024] Open
Abstract
Understanding the molecular circuitries that govern early embryogenesis is important, yet our knowledge of these in human preimplantation development remains limited. Small non-coding RNAs (sncRNAs) can regulate gene expression and thus impact blastocyst formation, however, the expression of specific biotypes and their dynamics during preimplantation development remains unknown. Here we identify the abundance of and kinetics of piRNA, rRNA, snoRNA, tRNA, and miRNA from embryonic day (E)3-7 and isolate specific miRNAs and snoRNAs of particular importance in blastocyst formation and pluripotency. These sncRNAs correspond to specific genomic hotspots: an enrichment of the chromosome 19 miRNA cluster (C19MC) in the trophectoderm (TE), and the chromosome 14 miRNA cluster (C14MC) and MEG8-related snoRNAs in the inner cell mass (ICM), which may serve as 'master regulators' of potency and lineage. Additionally, we observe a developmental transition with 21 isomiRs and in tRNA fragment (tRF) codon usage and identify two novel miRNAs. Our analysis provides a comprehensive measure of sncRNA biotypes and their corresponding dynamics throughout human preimplantation development, providing an extensive resource. Better understanding the sncRNA regulatory programmes in human embryogenesis will inform strategies to improve embryo development and outcomes of assisted reproductive technologies. We anticipate broad usage of our data as a resource for studies aimed at understanding embryogenesis, optimising stem cell-based models, assisted reproductive technology, and stem cell biology.
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MESH Headings
- Humans
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- Embryonic Development/genetics
- Blastocyst/metabolism
- Gene Expression Regulation, Developmental
- MicroRNAs/genetics
- MicroRNAs/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Female
- RNA, Small Interfering/metabolism
- RNA, Small Interfering/genetics
- Chromosomes, Human, Pair 19/genetics
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
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Affiliation(s)
| | - Cheng Zhao
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Savana Biondic
- Faculty of Medicine, Molecular Biology Program, Université de Montréal, Montréal, QC, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, Montréal, Canada
| | | | | | - Clifford L Librach
- CReATe Fertility Centre, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
- Sunnybrook Research Institute, Toronto, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Sophie Petropoulos
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden.
- Faculty of Medicine, Molecular Biology Program, Université de Montréal, Montréal, QC, Canada.
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, Montréal, Canada.
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden.
- Faculty of Medicine, Département de Médecine, Université de Montréal, Montréal, QC, Canada.
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3
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Scacchetti A, Shields EJ, Trigg NA, Lee GS, Wilusz JE, Conine CC, Bonasio R. A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini. Mol Cell 2024; 84:3843-3859.e8. [PMID: 39096899 PMCID: PMC11455606 DOI: 10.1016/j.molcel.2024.07.008] [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] [Revised: 12/12/2023] [Accepted: 07/10/2024] [Indexed: 08/05/2024]
Abstract
Despite the numerous sequencing methods available, the diversity in RNA size and chemical modification makes it difficult to capture all RNAs in a cell. We developed a method that combines quasi-random priming with template switching to construct sequencing libraries from RNA molecules of any length and with any type of 3' modifications, allowing for the sequencing of virtually all RNA species. Our ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to identify and quantify all classes of coding and non-coding RNAs. With LIDAR, we comprehensively characterized the transcriptomes of mouse embryonic stem cells, neural progenitor cells, mouse tissues, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared with traditional ligation-dependent sequencing methods and uncovered tDRs with blocked 3' ends that had previously escaped detection. Therefore, LIDAR can capture all RNAs in a sample and uncover RNA species with potential regulatory functions.
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Affiliation(s)
- Alessandro Scacchetti
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emily J Shields
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Urology and Institute of Neuropathology, Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Natalie A Trigg
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Grace S Lee
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Colin C Conine
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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4
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Pedrotti S, Castiglioni I, Perez-Estrada C, Zhao L, Chen JP, Crosetto N, Bienko M. Emerging methods and applications in 3D genomics. Curr Opin Cell Biol 2024; 90:102409. [PMID: 39178735 DOI: 10.1016/j.ceb.2024.102409] [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: 05/13/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 08/26/2024]
Abstract
Since the advent of Hi-C in 2009, a plethora of high-throughput sequencing methods have emerged to profile the three-dimensional (3D) organization of eukaryotic genomes, igniting the era of 3D genomics. In recent years, the genomic resolution achievable by these approaches has dramatically increased and several single-cell versions of Hi-C have been developed. Moreover, a new repertoire of tools not based on proximity ligation of digested chromatin has emerged, enabling the investigation of the higher-order organization of chromatin in the nucleus. In this review, we summarize the expanding portfolio of 3D genomic technologies, highlighting recent developments and applications from the past three years. Lastly, we present an outlook of where this technology-driven field might be headed.
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Affiliation(s)
- Simona Pedrotti
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | | | - Cynthia Perez-Estrada
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden; Science for Life Laboratory, Solna, 17165, Sweden
| | - Linxuan Zhao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden; Science for Life Laboratory, Solna, 17165, Sweden
| | - Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden; Science for Life Laboratory, Solna, 17165, Sweden
| | - Nicola Crosetto
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden; Science for Life Laboratory, Solna, 17165, Sweden.
| | - Magda Bienko
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden; Science for Life Laboratory, Solna, 17165, Sweden.
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5
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Long S, Zheng Y, Deng X, Guo J, Xu Z, Scharffetter-Kochanek K, Dou Y, Jiang M. Maintaining mitochondrial DNA copy number mitigates ROS-induced oocyte decline and female reproductive aging. Commun Biol 2024; 7:1229. [PMID: 39354016 PMCID: PMC11445474 DOI: 10.1038/s42003-024-06888-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: 02/21/2024] [Accepted: 09/12/2024] [Indexed: 10/03/2024] Open
Abstract
Oocytes play a crucial role in transmitting maternal mitochondrial DNA (mtDNA), essential for the continuation of species. However, the effects of mitochondrial reactive oxygen species (ROS) on mammalian oocyte maturation and mtDNA maintenance remain unclear. We investigated this by conditionally knocking out the Sod2 gene in primordial follicles, elevating mitochondrial matrix ROS levels from early oocyte stages. Our data indicates that reproductive aging in Sod2 conditional knockout females begins at 6 months, with oxidative stress impairing oocyte quality, particularly affecting OXPHOS complex II and mtDNA-encoded mRNA levels. Despite unchanged mtDNA mutation load, mtDNA copy numbers exhibited significant variations. Strikingly, reducing mtDNA copy numbers by reducing mtSSB protein, crucial for mtDNA replication, accelerated reproductive aging onset to three months, underscoring the critical role of mtDNA copy number maintenance under oxidative stress conditions. This research provides new insights into the relationship among mitochondrial ROS, mtDNA, and reproductive aging, offering potential strategies for delaying aging-related fertility decline.
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Affiliation(s)
- Shiyun Long
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yunchao Zheng
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xiaoling Deng
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Fudan University, Shanghai, China
| | - Jing Guo
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Zhe Xu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Karin Scharffetter-Kochanek
- Klinik für Dermatologie und Allergologie, Universitätsklinikum Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Deutschland
| | - Yanmei Dou
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Min Jiang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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6
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Walker CR, Li X, Chakravarthy M, Lounsbery-Scaife W, Choi YA, Singh R, Gürsoy G. Private information leakage from single-cell count matrices. Cell 2024:S0092-8674(24)01030-4. [PMID: 39362221 DOI: 10.1016/j.cell.2024.09.012] [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: 05/24/2024] [Revised: 08/11/2024] [Accepted: 09/05/2024] [Indexed: 10/05/2024]
Abstract
The increase in publicly available human single-cell datasets, encompassing millions of cells from many donors, has significantly enhanced our understanding of complex biological processes. However, the accessibility of these datasets raises significant privacy concerns. Due to the inherent noise in single-cell measurements and the scarcity of population-scale single-cell datasets, recent private information quantification studies have focused on bulk gene expression data sharing. To address this gap, we demonstrate that individuals in single-cell gene expression datasets are vulnerable to linking attacks, where attackers can infer their sensitive phenotypic information using publicly available tissue or cell-type-specific expression quantitative trait loci (eQTLs) information. We further develop a method for genotype prediction and genotype-phenotype linking that remains effective without relying on eQTL information. We show that variants from one study can be exploited to uncover private information about individuals in another study.
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Affiliation(s)
- Conor R Walker
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA; New York Genome Center, New York, NY 10013, USA
| | - Xiaoting Li
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA; New York Genome Center, New York, NY 10013, USA
| | - Manav Chakravarthy
- Department of Computer Science, Brown University, Providence, RI 02912, USA
| | - William Lounsbery-Scaife
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA; New York Genome Center, New York, NY 10013, USA
| | - Yoolim A Choi
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA; New York Genome Center, New York, NY 10013, USA
| | - Ritambhara Singh
- Department of Computer Science, Brown University, Providence, RI 02912, USA
| | - Gamze Gürsoy
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA; New York Genome Center, New York, NY 10013, USA; Department of Computer Science, Columbia University, New York, NY 10032, USA.
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7
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Hu J, Yuan J, Shi Q, Guo X, Liu L, Esteban MA, Lv Y. Single-cell profiling identifies LIN28A mRNA targets in the mouse pluripotent-to-2C-like transition and somatic cell reprogramming. J Biol Chem 2024:107824. [PMID: 39343008 DOI: 10.1016/j.jbc.2024.107824] [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: 05/30/2024] [Revised: 08/26/2024] [Accepted: 09/20/2024] [Indexed: 10/01/2024] Open
Abstract
RNA-binding proteins (RBPs) regulate totipotency, pluripotency maintenance, and induction. The intricacies of how they modulate these processes through their interaction with RNAs remain to be elucidated. Here we employed Targets of RBPs Identified By Editing (TRIBE) with single-cell resolution (scTRIBE) to profile the mRNA targets of the key pluripotency regulator LIN28A in mouse embryonic stem cells (ESCs), 2-cell embryo-like cells (2CLCs) and somatic cell reprogramming. LIN28A is known to act by controlling the maturation of the let-7 microRNA but, in addition, it binds to multiple mRNAs and influences their stability and translation efficiency. However, the mRNA targets of LIN28A in 2CLCs and reprogramming are unclear. Through quantitative single-cell analysis of the scTRIBE dataset, we observed a marked increase in the binding of LIN28A to mRNAs of ribosome biogenesis factors and a selected group of totipotency factors in 2CLCs within ESC cultures. Our results suggest that LIN28A extends the half-life of at least some of these mRNAs, providing new insights into its role in the totipotent state. We also uncovered the distinct trajectory-specific LIN28A-mRNA networks in reprogramming, helping explain how LIN28A facilitates the mesenchymal-to-epithelial transition and pluripotency acquisition. Our study not only clarifies the multifunctional role of LIN28A in these processes but also highlights the importance of decoding RNA-protein interactions at the single-cell level.
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Affiliation(s)
- Jieyi Hu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianwen Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518103, China
| | - Quan Shi
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Xiangpeng Guo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Longqi Liu
- BGI Research, Hangzhou 310030, China; Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; BGI Research, Shenzhen 518103, China.
| | - Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; BGI Research, Hangzhou 310030, China.
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8
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Noble JC, Lentini A, Hagemann-Jensen M, Sandberg R, Reinius B. Introducing synthetic thermostable RNase inhibitors to single-cell RNA-seq. Nat Commun 2024; 15:8373. [PMID: 39333520 PMCID: PMC11437267 DOI: 10.1038/s41467-024-52717-4] [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: 03/28/2024] [Accepted: 09/19/2024] [Indexed: 09/29/2024] Open
Abstract
Single-cell RNA-sequencing (scRNAseq) is revolutionizing biomedicine, propelled by advances in methodology, ease of use, and cost reduction of library preparation. Over the past decade, there have been remarkable technical improvements in most aspects of single-cell transcriptomics. Yet, little to no progress has been made in advancing RNase inhibition despite maintained RNA integrity being critical during cell collection, storage, and cDNA library generation. Here, we demonstrate that a synthetic thermostable RNase inhibitor (SEQURNA) yields single-cell libraries of equal or superior quality compared to ubiquitously used protein-based recombinant RNase inhibitors (RRIs). Importantly, the synthetic RNase inhibitor provides additional unique improvements in reproducibility and throughput, enables new experimental workflows including retained RNase inhibition throughout heat cycles, and can reduce the need for dry-ice transports. In summary, replacing RRIs represents a substantial advancement in the field of single-cell transcriptomics.
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Affiliation(s)
- Joyce Carol Noble
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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9
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Stöber MC, Chamorro González R, Brückner L, Conrad T, Wittstruck N, Szymansky A, Eggert A, Schulte JH, Koche RP, Henssen AG, Schwarz RF, Haase K. Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity. Cell Rep 2024; 43:114711. [PMID: 39255063 DOI: 10.1016/j.celrep.2024.114711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 05/20/2024] [Accepted: 08/20/2024] [Indexed: 09/12/2024] Open
Abstract
Neuroblastoma exhibits significant inter- and intra-tumor genetic heterogeneity and varying clinical outcomes. Extrachromosomal DNAs (ecDNAs) may drive this heterogeneity by independently segregating during cell division, leading to rapid oncogene amplification. While ecDNA-mediated oncogene amplification is linked to poor prognosis in various cancers, the effects of ecDNA copy-number heterogeneity on intermediate phenotypes are poorly understood. Here, we leverage DNA and RNA sequencing from the same single cells in cell lines and neuroblastoma patients to investigate these effects. By analyzing ecDNA amplicon structures, we reveal extensive intercellular ecDNA copy-number heterogeneity. We also provide direct evidence of how this heterogeneity influences the expression of cargo genes, including MYCN and its downstream targets, and the overall transcriptional state of neuroblastoma cells. Our findings highlight the role of ecDNA copy number in promoting rapid adaptability of cellular states within tumors, underscoring the need for ecDNA-specific treatment strategies to address tumor formation and adaptation.
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Affiliation(s)
- Maja C Stöber
- Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; Humboldt-Universität zu Berlin, Faculty of Life Science, 10099 Berlin, Germany
| | - Rocío Chamorro González
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany
| | - Lotte Brückner
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany
| | - Thomas Conrad
- Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany
| | - Nadine Wittstruck
- Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anton G Henssen
- Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Berlin Institute of Health, 10178 Berlin, Germany; Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, 13125 Berlin, Germany.
| | - Roland F Schwarz
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; BIFOLD - Berlin Institute for the Foundations of Learning and Data, 10587 Berlin, Germany; Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany.
| | - Kerstin Haase
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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10
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Al-Refaie N, Padovani F, Hornung J, Pudelko L, Binando F, Del Carmen Fabregat A, Zhao Q, Towbin BD, Cenik ES, Stroustrup N, Padeken J, Schmoller KM, Cabianca DS. Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis. Nat Cell Biol 2024:10.1038/s41556-024-01512-w. [PMID: 39300311 DOI: 10.1038/s41556-024-01512-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/19/2024] [Indexed: 09/22/2024]
Abstract
Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom, yet how it impacts three-dimensional (3D) genome organization is unknown. Here we show that fasting induces an intestine-specific, reversible and large-scale spatial reorganization of chromatin in Caenorhabditis elegans. This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, acting through the regulation of RNA Pol I, but not Pol II nor Pol III, and is accompanied by remodelling of the nucleolus. By uncoupling the 3D genome configuration from the animal's nutritional status, we find that the expression of metabolic and stress-related genes increases when the spatial reorganization of chromatin occurs, showing that the 3D genome might support the transcriptional response in fasted animals. Our work documents a large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients.
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Affiliation(s)
- Nada Al-Refaie
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Medicine, Ludwig-Maximilians Universität München, Munich, Germany
| | - Francesco Padovani
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Johanna Hornung
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lorenz Pudelko
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Medicine, Ludwig-Maximilians Universität München, Munich, Germany
| | - Francesca Binando
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Andrea Del Carmen Fabregat
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | | | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Nicholas Stroustrup
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jan Padeken
- Institute of Molecular Biology, Mainz, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Daphne S Cabianca
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
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11
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Xiong X, Wang X, Liu CC, Shao ZM, Yu KD. Deciphering breast cancer dynamics: insights from single-cell and spatial profiling in the multi-omics era. Biomark Res 2024; 12:107. [PMID: 39294728 PMCID: PMC11411917 DOI: 10.1186/s40364-024-00654-1] [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: 06/28/2024] [Accepted: 09/10/2024] [Indexed: 09/21/2024] Open
Abstract
As one of the most common tumors in women, the pathogenesis and tumor heterogeneity of breast cancer have long been the focal point of research, with the emergence of tumor metastasis and drug resistance posing persistent clinical challenges. The emergence of single-cell sequencing (SCS) technology has introduced novel approaches for gaining comprehensive insights into the biological behavior of malignant tumors. SCS is a high-throughput technology that has rapidly developed in the past decade, providing high-throughput molecular insights at the individual cell level. Furthermore, the advent of multitemporal point sampling and spatial omics also greatly enhances our understanding of cellular dynamics at both temporal and spatial levels. The paper provides a comprehensive overview of the historical development of SCS, and highlights the most recent advancements in utilizing SCS and spatial omics for breast cancer research. The findings from these studies will serve as valuable references for future advancements in basic research, clinical diagnosis, and treatment of breast cancer.
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Affiliation(s)
- Xin Xiong
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xin Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cui-Cui Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ke-Da Yu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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12
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Mantas I, Flais I, Masarapu Y, Ionescu T, Frapard S, Jung F, Le Merre P, Saarinen M, Tiklova K, Salmani BY, Gillberg L, Zhang X, Chergui K, Carlén M, Giacomello S, Hengerer B, Perlmann T, Svenningsson P. Claustrum and dorsal endopiriform cortex complex cell-identity is determined by Nurr1 and regulates hallucinogenic-like states in mice. Nat Commun 2024; 15:8176. [PMID: 39289358 PMCID: PMC11408527 DOI: 10.1038/s41467-024-52429-9] [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: 04/10/2023] [Accepted: 09/04/2024] [Indexed: 09/19/2024] Open
Abstract
The Claustrum/dorsal endopiriform cortex complex (CLA) is an enigmatic brain region with extensive glutamatergic projections to multiple cortical areas. The transcription factor Nurr1 is highly expressed in the CLA, but its role in this region is not understood. By using conditional gene-targeted mice, we show that Nurr1 is a crucial regulator of CLA neuron identity. Although CLA neurons remain intact in the absence of Nurr1, the distinctive gene expression pattern in the CLA is abolished. CLA has been hypothesized to control hallucinations, but little is known of how the CLA responds to hallucinogens. After the deletion of Nurr1 in the CLA, both hallucinogen receptor expression and signaling are lost. Furthermore, functional ultrasound and Neuropixel electrophysiological recordings revealed that the hallucinogenic-receptor agonists' effects on functional connectivity between prefrontal and sensorimotor cortices are altered in Nurr1-ablated mice. Our findings suggest that Nurr1-targeted strategies provide additional avenues for functional studies of the CLA.
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Affiliation(s)
- Ioannis Mantas
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Ivana Flais
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- CNSDR, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
- Department of Neuroimaging King's College London, London, UK
| | - Yuvarani Masarapu
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tudor Ionescu
- CNSDR, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Solène Frapard
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Felix Jung
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Pierre Le Merre
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Saarinen
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Katarina Tiklova
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Linda Gillberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xiaoqun Zhang
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Karima Chergui
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Marie Carlén
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Bastian Hengerer
- CNSDR, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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13
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Tomizawa SI, Fellows R, Ono M, Kuroha K, Dočkal I, Kobayashi Y, Minamizawa K, Natsume K, Nakajima K, Hoshi I, Matsuda S, Seki M, Suzuki Y, Aoto K, Saitsu H, Ohbo K. The non-canonical bivalent gene Wfdc15a controls spermatogenic protease and immune homeostasis. Development 2024; 151:dev202834. [PMID: 39222051 DOI: 10.1242/dev.202834] [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: 02/26/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Male infertility can be caused by chromosomal abnormalities, mutations and epigenetic defects. Epigenetic modifiers pre-program hundreds of spermatogenic genes in spermatogonial stem cells (SSCs) for expression later in spermatids, but it remains mostly unclear whether and how those genes are involved in fertility. Here, we report that Wfdc15a, a WFDC family protease inhibitor pre-programmed by KMT2B, is essential for spermatogenesis. We found that Wfdc15a is a non-canonical bivalent gene carrying both H3K4me3 and facultative H3K9me3 in SSCs, but is later activated along with the loss of H3K9me3 and acquisition of H3K27ac during meiosis. We show that WFDC15A deficiency causes defective spermiogenesis at the beginning of spermatid elongation. Notably, depletion of WFDC15A causes substantial disturbance of the testicular protease-antiprotease network and leads to an orchitis-like inflammatory response associated with TNFα expression in round spermatids. Together, our results reveal a unique epigenetic program regulating innate immunity crucial for fertility.
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Affiliation(s)
- Shin-Ichi Tomizawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Rachel Fellows
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Michio Ono
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Kazushige Kuroha
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Ivana Dočkal
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Yuki Kobayashi
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Keisuke Minamizawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Koji Natsume
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Kuniko Nakajima
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Ikue Hoshi
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Shion Matsuda
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Kazushi Aoto
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
- Central Laboratory, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kazuyuki Ohbo
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
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14
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Penning A, Snoeck S, Garritsen O, Tosoni G, Hof A, de Boer F, van Hasenbroek J, Zhang L, Thrupp N, Craessaerts K, Fiers M, Salta E. NACC2, a molecular effector of miR-132 regulation at the interface between adult neurogenesis and Alzheimer's disease. Sci Rep 2024; 14:21163. [PMID: 39256511 PMCID: PMC11387632 DOI: 10.1038/s41598-024-72096-6] [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: 05/03/2024] [Accepted: 09/03/2024] [Indexed: 09/12/2024] Open
Abstract
The generation of new neurons at the hippocampal neurogenic niche, known as adult hippocampal neurogenesis (AHN), and its impairment, have been implicated in Alzheimer's disease (AD). MicroRNA-132 (miR-132), the most consistently downregulated microRNA (miRNA) in AD, was recently identified as a potent regulator of AHN, exerting multilayered proneurogenic effects in adult neural stem cells (NSCs) and their progeny. Supplementing miR-132 in AD mouse brain restores AHN and relevant memory deficits, yet the exact mechanisms involved are still unknown. Here, we identify NACC2 as a novel miR-132 target implicated in both AHN and AD. miR-132 deficiency in mouse hippocampus induces Nacc2 expression and inflammatory signaling in adult NSCs. We show that miR-132-dependent regulation of NACC2 is involved in the initial stages of human NSC differentiation towards astrocytes and neurons. Later, NACC2 function in astrocytic maturation becomes uncoupled from miR-132. We demonstrate that NACC2 is present in reactive astrocytes surrounding amyloid plaques in mouse and human AD hippocampus, and that there is an anticorrelation between miR-132 and NACC2 levels in AD and upon induction of inflammation. Unraveling the molecular mechanisms by which miR-132 regulates neurogenesis and cellular reactivity in AD, will provide valuable insights towards its possible application as a therapeutic target.
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Affiliation(s)
- Amber Penning
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Sarah Snoeck
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Oxana Garritsen
- UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Giorgia Tosoni
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Amber Hof
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Fleur de Boer
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | | | - Lin Zhang
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Nicky Thrupp
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
| | | | - Mark Fiers
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
| | - Evgenia Salta
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
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15
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Swaminath S, Mendes M, Zhang Y, Remick KA, Mejia I, Güereca M, te Velthuis AJ, Russell AB. Efficient genome replication in influenza A virus requires NS2 and sequence beyond the canonical promoter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.612348. [PMID: 39314307 PMCID: PMC11419028 DOI: 10.1101/2024.09.10.612348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Influenza A virus encodes promoters in both the sense and antisense orientations. These support the generation of new genomes, antigenomes, and mRNA transcripts. Using minimal replication assays-transfections with viral polymerase, nucleoprotein, and a genomic template-the influenza promoter sequences were identified as 13nt at the 5' end of the viral genomic RNA (U13) and 12nt at the 3' end (U12). Other than the fourth 3' nucleotide, the U12 and U13 sequences are identical between all eight RNA molecules that comprise the segmented influenza genome. Despite possessing identical promoters, individual segments can exhibit different transcriptional dynamics during infection. However flu promoter sequences were defined in experiments without influenza NS2, a protein which modulates transcription and replication differentially between genomic segments. This suggests that the identity of the "complete" promoter may depend on NS2. Here we assess how internal sequences of two genomic segments, HA and PB1, may contribute to NS2-dependent replication as well as map such interactions down to individual nucleotides in PB1. We find that the expression of NS2 significantly alters sequence requirements for efficient replication beyond the identical U12 and U13 sequence, providing a mechanism for the divergent replication and transcription dynamics across the influenza A virus genome.
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Affiliation(s)
- Sharmada Swaminath
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Marisa Mendes
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yipeng Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kaleigh A. Remick
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Isabel Mejia
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Melissa Güereca
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Aartjan J.W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alistair B. Russell
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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16
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Thowfeequ S, Fiorentino J, Hu D, Solovey M, Ruane S, Whitehead M, Zhou F, Godwin J, Mateo-Otero Y, Vanhaesebroeck B, Scialdone A, Srinivas S. An integrated approach identifies the molecular underpinnings of murine anterior visceral endoderm migration. Dev Cell 2024; 59:2347-2363.e9. [PMID: 38843837 DOI: 10.1016/j.devcel.2024.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/09/2023] [Accepted: 05/14/2024] [Indexed: 09/12/2024]
Abstract
The anterior visceral endoderm (AVE) differs from the surrounding visceral endoderm (VE) in its migratory behavior and ability to restrict primitive streak formation to the opposite side of the mouse embryo. To characterize the molecular bases for the unique properties of the AVE, we combined single-cell RNA sequencing of the VE prior to and during AVE migration with phosphoproteomics, high-resolution live-imaging, and short-term lineage labeling and intervention. This identified the transient nature of the AVE with attenuation of "anteriorizing" gene expression as cells migrate and the emergence of heterogeneities in transcriptional states relative to the AVE's position. Using cell communication analysis, we identified the requirement of semaphorin signaling for normal AVE migration. Lattice light-sheet microscopy showed that Sema6D mutants have abnormalities in basal projections and migration speed. These findings point to a tight coupling between transcriptional state and position of the AVE and identify molecular controllers of AVE migration.
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Affiliation(s)
- Shifaan Thowfeequ
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK
| | - Jonathan Fiorentino
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 81377, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome 00161, Italy
| | - Di Hu
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK
| | - Maria Solovey
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 81377, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Sharon Ruane
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK
| | - Maria Whitehead
- UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Felix Zhou
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathan Godwin
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK
| | - Yentel Mateo-Otero
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK; Unit of Cell Biology, Department of Biology, University of Girona, Girona 17004, Spain
| | | | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 81377, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany.
| | - Shankar Srinivas
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK.
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17
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Zeng X, Yang X, Zhong Z, Lin X, Chen Q, Jiang S, Mo M, Lin S, Zhang H, Zhu Z, Li J, Song J, Yang C. AMAR-seq: Automated Multimodal Sequencing of DNA Methylation, Chromatin Accessibility, and RNA Expression with Single-Cell Resolution. Anal Chem 2024. [PMID: 39250680 DOI: 10.1021/acs.analchem.4c02765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Parallel single-cell multimodal sequencing is the most intuitive and precise tool for cellular status research. In this study, we propose AMAR-seq to automate methylation, chromatin accessibility, and RNA expression coanalysis with single-cell precision. We validated the accuracy and robustness of AMAR-seq in comparison with standard single-omics methods. The high gene detection rate and genome coverage of AMAR-seq enabled us to establish a genome-wide gene expression regulatory atlas and triple-omics landscape with single base resolution and implement single-cell copy number variation analysis. Applying AMAR-seq to investigate the process of mouse embryonic stem cell differentiation, we revealed the dynamic coupling of the epigenome and transcriptome, which may contribute to unraveling the molecular mechanisms of early embryonic development. Collectively, we propose AMAR-seq for the in-depth and accurate establishment of single-cell multiomics regulatory patterns in a cost-effective, efficient, and automated manner, paving the way for insightful dissection of complex life processes.
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Affiliation(s)
- Xi Zeng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical of Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering and Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
| | - Xiaoping Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical of Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering and Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
| | - Zhixing Zhong
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical of Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering and Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
| | - Xin Lin
- Chemistry and Materials Science College, Shanghai Normal University, Shanghai 200234, China
| | - Qiuyue Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical of Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering and Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
| | - Shaowei Jiang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical of Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering and Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
| | - Mengwu Mo
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical of Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering and Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
| | - Shichao Lin
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Xiamen 361005, China
| | - Huimin Zhang
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Xiamen 361005, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical of Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering and Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
| | - Jin Li
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jia Song
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical of Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering and Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
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18
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Montaño J, Garnica J, Yamanouchi J, Moro J, Solé P, Mondal D, Serra P, Yang Y, Santamaria P. Transcriptional re-programming of liver-resident iNKT cells into T-regulatory type-1-like liver iNKT cells involves extensive gene de-methylation. Front Immunol 2024; 15:1454314. [PMID: 39315110 PMCID: PMC11416961 DOI: 10.3389/fimmu.2024.1454314] [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: 06/24/2024] [Accepted: 08/13/2024] [Indexed: 09/25/2024] Open
Abstract
Unlike conventional CD4+ T cells, which are phenotypically and functionally plastic, invariant NKT (iNKT) cells generally exist in a terminally differentiated state. Naïve CD4+ T cells can acquire alternative epigenetic states in response to different cues, but it remains unclear whether peripheral iNKT cells are epigenetically stable or malleable. Repetitive encounters of liver-resident iNKT cells (LiNKTs) with alpha-galactosylceramide (αGalCer)/CD1d-coated nanoparticles (NPs) can trigger their differentiation into a LiNKT cell subset expressing a T regulatory type 1 (TR1)-like (LiNKTR1) transcriptional signature. Here we dissect the epigenetic underpinnings of the LiNKT-LiNKTR1 conversion as compared to those underlying the peptide-major histocompatibility complex (pMHC)-NP-induced T-follicular helper (TFH)-to-TR1 transdifferentiation process. We show that gene upregulation during the LINKT-to-LiNKTR1 cell conversion is associated with demethylation of gene bodies, inter-genic regions, promoters and distal gene regulatory elements, in the absence of major changes in chromatin exposure or deposition of expression-promoting histone marks. In contrast, the naïve CD4+ T cell-to-TFH differentiation process involves extensive remodeling of the chromatin and the acquisition of a broad repertoire of epigenetic modifications that are then largely inherited by TFH cell-derived TR1 cell progeny. These observations indicate that LiNKT cells are epigenetically malleable and particularly susceptible to gene de-methylation.
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Affiliation(s)
- Javier Montaño
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Josep Garnica
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Jun Yamanouchi
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Joel Moro
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Patricia Solé
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Debajyoti Mondal
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Yang Yang
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pere Santamaria
- Institut D’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Basso V, Döbrössy MD, Thompson LH, Kirik D, Fuller HR, Gates MA. State of the Art in Sub-Phenotyping Midbrain Dopamine Neurons. BIOLOGY 2024; 13:690. [PMID: 39336117 PMCID: PMC11428604 DOI: 10.3390/biology13090690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024]
Abstract
Dopaminergic neurons in the ventral tegmental area (VTA) and the substantia nigra pars compacta (SNpc) comprise around 75% of all dopaminergic neurons in the human brain. While both groups of dopaminergic neurons are in close proximity in the midbrain and partially overlap, development, function, and impairments in these two classes of neurons are highly diverse. The molecular and cellular mechanisms underlying these differences are not yet fully understood, but research over the past decade has highlighted the need to differentiate between these two classes of dopaminergic neurons during their development and in the mature brain. This differentiation is crucial not only for understanding fundamental circuitry formation in the brain but also for developing therapies targeted to specific dopaminergic neuron classes without affecting others. In this review, we summarize the state of the art in our understanding of the differences between the dopaminergic neurons of the VTA and the SNpc, such as anatomy, structure, morphology, output and input, electrophysiology, development, and disorders, and discuss the current technologies and methods available for studying these two classes of dopaminergic neurons, highlighting their advantages, limitations, and the necessary improvements required to achieve more-precise therapeutic interventions.
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Affiliation(s)
- Valentina Basso
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Máté D Döbrössy
- Laboratory of Stereotaxy and Interventional Neurosciences, Department of Stereotactic and Functional, Neurosurgery, Medical Center, University of Freiburg, 79106 Freiburg im Breisgau, Germany
- Department of Stereotactic and Functional Neurosurgery, Medical Center, University of Freiburg, 79106 Freiburg im Breisgau, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Lachlan H Thompson
- Charles Perkins Centre, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Deniz Kirik
- Brain Repair and Imaging in Neural Systems (B.R.A.I.N.S) Unit, Department of Experimental Medical Science, Lund University, BMC D11, 22184 Lund, Sweden
| | - Heidi R Fuller
- School of Pharmacy and Bioengineering, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, TORCH Building, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Monte A Gates
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
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20
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Li X, Zou Y, Geng B, Liu P, Cao L, Zhang Z, Hu S, Wang C, Zhao Y, Wu Q, Tan J. Transcriptome analysis reveals that defects in cell cycle regulation contribute to preimplantation embryo arrest. Genomics 2024; 116:110946. [PMID: 39326642 DOI: 10.1016/j.ygeno.2024.110946] [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: 06/18/2024] [Revised: 09/09/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Patients with preimplantation embryo arrest (PREMBA) often experience assisted reproductive failure primarily due to the lack of transferable embryos, and the molecular mechanisms underlying PREMBA remain unclear. In our study, the embryos from five women with recurrent preimplantation embryo arrest and three women with tubal factor infertility were used for single-embryo transcriptome sequencing. Meanwhile, the transcriptomes of normal human preimplantation embryos obtained from GSE36552 were utilized to perform a comparative analysis with the transcriptomes of PREMBA embryos. Our results showed dysregulation of the cell cycle phase transition might be a potential pathogenic factor contributing to PREMBA. Through integrated analysis of the differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA), we identified a number of hub genes using the protein-protein interaction network. The top 5 hub genes were as follows: CCNB2, BUB1B, CDC25A, CCNB3, and PLK3. The expression of hub genes was validated in PREMBA embryos and donated embryos using RT-qPCR. The knockdown of Ccnb2 in mouse zygotes led to an increase in embryo fragmentation, a rise in apoptosis, and a reduction in blastocyst formation. Furthermore, silencing the expression of CDC25A in HEK293T cells resulted in a decrease in cell proliferation and an increase in apoptosis, providing further support for our findings. Our findings could predict the development outcomes of preimplantation embryos and be used as potential therapeutic targets to prevent recurrent failures of IVF/ICSI attempts.
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Affiliation(s)
- Xin Li
- Reproductive Medicine Center, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China; JXHC Key Laboratory of Fertility Preservation, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China
| | - Yang Zou
- Central Laboratory, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China
| | - Baobao Geng
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, SuZhou, Jiangsu Province, China
| | - Peipei Liu
- Reproductive Medicine Center, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China; JXHC Key Laboratory of Fertility Preservation, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China
| | - Liyun Cao
- Reproductive Medicine Center, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China; JXHC Key Laboratory of Fertility Preservation, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China
| | - Zhiqin Zhang
- Reproductive Medicine Center, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China
| | - Shaofeng Hu
- JXHC Key Laboratory of Fertility Preservation, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China
| | - Changhua Wang
- JXHC Key Laboratory of Fertility Preservation, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China
| | - Yan Zhao
- Reproductive Medicine Center, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China.
| | - Qiongfang Wu
- Reproductive Medicine Center, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China.
| | - Jun Tan
- Reproductive Medicine Center, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China; JXHC Key Laboratory of Fertility Preservation, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi Province, China.
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21
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Liu M, Chen J, Cui G, Dai Y, Song M, Zhou C, Hu Q, Chen Q, Wang H, Chen W, Han JJ, Peng G, Jing N, Shen Y. Germline loss in C. elegans enhances longevity by disrupting adhesion between niche and stem cells. EMBO J 2024; 43:4000-4019. [PMID: 39060516 PMCID: PMC11405865 DOI: 10.1038/s44318-024-00185-3] [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] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Ageing and fertility are intertwined. Germline loss extends the lifespan in various organisms, termed gonadal longevity. However, the original longevity signal from the somatic gonad remains poorly understood. Here, we focused on the interaction between germline stem cells (GSCs) and their niche, the distal tip cells (DTCs), to explore the barely known longevity signal from the somatic gonad in C. elegans. We found that removing germline disrupts the cell adhesions between GSC and DTC, causing a significant transcriptomic change in DTC through hmp-2/β-catenin and two GATA transcription factors, elt-3 and pqm-1 in this niche cell. Inhibiting elt-3 and pqm-1 in DTC suppresses gonadal longevity. Moreover, we further identified the TGF-β ligand, tig-2, as the cytokine from DTC upon the loss of germline, which evokes the downstream gonadal longevity signalling throughout the body. Our findings thus reveal the source of the longevity signalling in response to germline removal, highlighting the stem cell niche as a critical signalling hub in ageing.
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Affiliation(s)
- Meng Liu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jiehui Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Guizhong Cui
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- Guangzhou Laboratory, 510005, Guangzhou, China
| | - Yumin Dai
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Mengjiao Song
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Chunyu Zhou
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, 102213, Beijing, China
| | - Qingyuan Hu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qingxia Chen
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Institute of Early Life Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China
| | - Hongwei Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wanli Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jingdong Jackie Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, 102213, Beijing, China
| | - Guangdun Peng
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Guangzhou Laboratory, 510005, Guangzhou, China
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Guangzhou Laboratory, 510005, Guangzhou, China
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Yidong Shen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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22
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Wang J, Liang Y, Xu C, Gao J, Tong J, Shi L. The heterogeneity of erythroid cells: insight at the single-cell transcriptome level. Cell Tissue Res 2024; 397:179-192. [PMID: 38953986 DOI: 10.1007/s00441-024-03903-9] [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: 12/11/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Erythroid cells, the most prevalent cell type in blood, are one of the earliest products and permeate through the entire process of hematopoietic development in the human body, the oxygen-transporting function of which is crucial for maintaining overall health and life support. Previous investigations into erythrocyte differentiation and development have primarily focused on population-level analyses, lacking the single-cell perspective essential for comprehending the intricate pathways of erythroid maturation, differentiation, and the encompassing cellular heterogeneity. The continuous optimization of single-cell transcriptome sequencing technology, or single-cell RNA sequencing (scRNA-seq), provides a powerful tool for life sciences research, which has a particular superiority in the identification of unprecedented cell subgroups, the analyzing of cellular heterogeneity, and the transcriptomic characteristics of individual cells. Over the past decade, remarkable strides have been taken in the realm of single-cell RNA sequencing technology, profoundly enhancing our understanding of erythroid cells. In this review, we systematically summarize the recent developments in single-cell transcriptome sequencing technology and emphasize their substantial impact on the study of erythroid cells, highlighting their contributions, including the exploration of functional heterogeneity within erythroid populations, the identification of novel erythrocyte subgroups, the tracking of different erythroid lineages, and the unveiling of mechanisms governing erythroid fate decisions. These findings not only invigorate erythroid cell research but also offer new perspectives on the management of diseases related to erythroid cells.
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Affiliation(s)
- Jingwei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yipeng Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Changlu Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin, 300020, China.
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23
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Xiang L, Rao J, Yuan J, Xie T, Yan H. Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research. Int J Mol Sci 2024; 25:9482. [PMID: 39273429 PMCID: PMC11395021 DOI: 10.3390/ijms25179482] [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: 07/31/2024] [Revised: 08/25/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Breast cancer is the most prevalent malignant tumor among women with high heterogeneity. Traditional techniques frequently struggle to comprehensively capture the intricacy and variety of cellular states and interactions within breast cancer. As global precision medicine rapidly advances, single-cell RNA sequencing (scRNA-seq) has become a highly effective technique, revolutionizing breast cancer research by offering unprecedented insights into the cellular heterogeneity and complexity of breast cancer. This cutting-edge technology facilitates the analysis of gene expression profiles at the single-cell level, uncovering diverse cell types and states within the tumor microenvironment. By dissecting the cellular composition and transcriptional signatures of breast cancer cells, scRNA-seq provides new perspectives for understanding the mechanisms behind tumor therapy, drug resistance and metastasis in breast cancer. In this review, we summarized the working principle and workflow of scRNA-seq and emphasized the major applications and discoveries of scRNA-seq in breast cancer research, highlighting its impact on our comprehension of breast cancer biology and its potential for guiding personalized treatment strategies.
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Affiliation(s)
- Lingyan Xiang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jie Rao
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ting Xie
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Honglin Yan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
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24
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Xie D, An B, Yang M, Wang L, Guo M, Luo H, Huang S, Sun F. Application and research progress of single cell sequencing technology in leukemia. Front Oncol 2024; 14:1389468. [PMID: 39267837 PMCID: PMC11390353 DOI: 10.3389/fonc.2024.1389468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 08/08/2024] [Indexed: 09/15/2024] Open
Abstract
Leukemia is a malignant tumor with high heterogeneity and a complex evolutionary process. It is difficult to resolve the heterogeneity and clonal evolution of leukemia cells by applying traditional bulk sequencing techniques, thus preventing a deep understanding of the mechanisms of leukemia development and the identification of potential therapeutic targets. However, with the development and application of single-cell sequencing technology, it is now possible to investigate the gene expression profile, mutations, and epigenetic features of leukemia at the single-cell level, thus providing a new perspective for leukemia research. In this article, we review the recent applications and advances of single-cell sequencing technology in leukemia research, discuss its potential for enhancing our understanding of the mechanisms of leukemia development, discovering therapeutic targets and personalized treatment, and provide reference guidelines for the significance of this technology in clinical research.
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Affiliation(s)
- Dan Xie
- Medical College, Guizhou University, Guiyang, China
| | - Bangquan An
- Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Mingyue Yang
- Medical College, Guizhou University, Guiyang, China
| | - Lei Wang
- Medical College, Guizhou University, Guiyang, China
| | - Min Guo
- Medical College, Guizhou University, Guiyang, China
| | - Heng Luo
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou, China
- Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang, Guizhou, China
| | - Shengwen Huang
- Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Fa Sun
- Medical College, Guizhou University, Guiyang, China
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25
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Wai AWY, Lui VCH, Tang CSM, Wang B, Tam PKH, Wong KKY, Chung PHY. Human Liver Organoids to Predict the Outcome of Kasai Portoenterostomy. J Pediatr Surg 2024:161686. [PMID: 39271308 DOI: 10.1016/j.jpedsurg.2024.161686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/11/2024] [Accepted: 08/08/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND Kasai portoenterostomy (KPE) remains the primary intervention for biliary atresia (BA), but its outcomes are highly variable. Reliable prognostic biomarkers remain elusive, complicating the management and prediction of postoperative progression. METHOD Liver biopsies from BA patients taken at and after KPE (post-KPE) were used to generate organoids for RNA-sequencing analysis. Control organoids were derived from non-BA livers. Differential gene expression and enrichment analyses were performed to assess post-KPE transcriptomic changes between native liver survivors (NLS) and patients who eventually became liver transplant recipients (LTR). RESULTS Organoid datasets: 70 from liver biopsies at KPE (10 patients), 112 from post-KPE livers (13 livers; 12 patients), and 47 from control livers (9 patients). At KPE, BA organoids displayed mainly hepatocyte expression, a trait notably reduced in control organoids. Similarly, post-KPE organoids from NLS revealed a significant decrease in hepatocyte expression features and an overall increase in cholangiocyte expression features. A similar hepatocyte-to-cholangiocyte expression transition was evidenced in paired liver organoids (at- and post-KPE) generated from an NLS. In contrast, post-KPE organoids from LTR maintained a high level of hepatocyte expression features. CONCLUSION Our study demonstrated that an elevated expression of hepatocyte features in KPE organoids may indicate aberrant cholangiocyte development in BA livers. In contrast, a post-KPE hepatocyte-to-cholangiocyte expression transition in NLS may imply effective biliary recovery. The lack of this transition in LTR organoids indicates ongoing disease progression, highlighting the potential for organoid-based transcriptomic profiling to inform KPE success and guide BA management. LEVEL OF EVIDENCE Level III.
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Affiliation(s)
- Amy Wing Yi Wai
- Department of Surgery, School of Clinical Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Vincent Chi Hang Lui
- Department of Surgery, School of Clinical Medicine, The University of Hong Kong, Hong Kong SAR, China; Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China
| | - Clara Sze Man Tang
- Department of Surgery, School of Clinical Medicine, The University of Hong Kong, Hong Kong SAR, China; Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Paul Kwong Hang Tam
- Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China
| | - Kenneth Kak Yuen Wong
- Department of Surgery, School of Clinical Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Patrick Ho Yu Chung
- Department of Surgery, School of Clinical Medicine, The University of Hong Kong, Hong Kong SAR, China.
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Töhönen V, Antonson P, Boggavarapu NR, Ali H, Motaholi LA, Gustafsson JÅ, Varshney M, Rodriguez-Wallberg KA, Katayama S, Nalvarte I, Inzunza J. Transcriptomic profiling of the oocyte-cumulus-granulosa cell complex from estrogen receptor β knockout mice. F&S SCIENCE 2024:S2666-335X(24)00056-9. [PMID: 39168303 DOI: 10.1016/j.xfss.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024]
Abstract
OBJECTIVE To study the role of estrogen receptor β in follicle development and maturation and the response to gonadotropin stimulation aiming at superovulation. DESIGN Experimental study and transcriptomic analysis. SETTING Karolinka Institutet, medical university. ANIMAL(S) Healthy wild-type (WT) and estrogen receptor β knockout (Esr2-KO) female mice undergoing superovulation at 4 weeks, 7 weeks, and 6 months of age. INTERVENTION(S) Not applicable. MAIN OUTCOME MEASURE(S) Oocyte yield after superovulation, transcriptomic profiling of cumulus-granulosa cell complexes and oocytes, and immunohistochemical analyses. RESULT(S) Superovulation of estrogen receptor β (ERβ) knockout mice resulted in reduced oocyte yield at 6 months of age compared with WT mice, but younger mice had similar yields. RNA-seq analysis of cumulus cells from superovulated WT and Esr2-KO mice identified genes and pathways associated with among others adhesion, proliferation, Wnt-signaling, and placed ERβ in bipotential granulosa cell cluster. Loss of ERβ increased expression of the other estrogen receptors Esr1 and Gper1. CONCLUSION(S) Our results show that ERβ has an important role in regulating ovulation in response to exogenous gonadotropins in 6-month-old mice, but not in younger mice. Our transcriptomic and immunohistochemical observations suggest a dysregulation of the granulosa cell communication and lack of tight coordination between granulosa cell replication and antrum expansion. A significant upregulation of other estrogen receptors may support a compensatory mechanism sustaining fertility during younger age in Esr2-KO mice.
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Affiliation(s)
- Virpi Töhönen
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Per Antonson
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | | | - Heba Ali
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Visionsgatan, Solna, Sweden; Department of Biochemistry, Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
| | | | - Jan-Åke Gustafsson
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden; Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas
| | - Mukesh Varshney
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Kenny A Rodriguez-Wallberg
- Department of Oncology-Pathology, Laboratory of Translational Fertility Preservation, Karolinska Institutet, Stockholm, Sweden; Division of Gynecology and Reproduction, Department of Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Shintaro Katayama
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden; Folkhälsan Research Center, Helsinki, Finland; Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Ivan Nalvarte
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Visionsgatan, Solna, Sweden
| | - Jose Inzunza
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden.
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27
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Su Y, Shea J, Destephanis D, Su Z. Transcriptomic analysis of the spatiotemporal axis of oogenesis and fertilization in C. elegans. Front Cell Dev Biol 2024; 12:1436975. [PMID: 39224437 PMCID: PMC11366716 DOI: 10.3389/fcell.2024.1436975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Caenorhabditis elegans hermaphrodite presents a unique model to study the formation of oocytes. However, the size of the model animal and difficulties in retrieval of specific stages of the germline have obviated closer systematic studies of this process throughout the years. Here, we present a transcriptomic level analysis into the oogenesis of C. elegans hermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene region, the diplotene region, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq (scRNA-seq) protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the gonad and provided novel insights into underlying mechanisms of the oogenesis process. Furthermore, through careful review of relevant research literature coupled with patterns observed in our analysis, we delineate transcripts that may serve functions in the interactions between the germline and cells of the somatic gonad. These results expand our knowledge of the transcriptomic space of the C. elegans germline and lay a foundation on which future studies of the germline can be based upon.
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Affiliation(s)
| | | | | | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, United States
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Gu LJ, Li L, Li QN, Xu K, Yue W, Qiao JY, Meng TG, Dong MZ, Lei WL, Guo JN, Wang ZB, Sun QY. The transgenerational effects of maternal low-protein diet during lactation on offspring. J Genet Genomics 2024; 51:824-835. [PMID: 38657948 DOI: 10.1016/j.jgg.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
Environmental factors such as diet and lifestyle can influence the health of both mothers and offspring. However, its transgenerational transmission and underlying mechanisms remain largely unknown. Here, using a maternal lactation-period low-protein diet (LPD) mouse model, we show that maternal LPD during lactation causes decreased survival and stunted growth, significantly reduces ovulation and litter size, and alters the gut microbiome in the female LPD-F1 offspring. The transcriptome of LPD-F1 metaphase II (MII) oocytes shows that differentially expressed genes are enriched in female pregnancy and multiple metabolic processes. Moreover, maternal LPD causes early stunted growth and impairs metabolic health, which is transmitted over two generations. The methylome alteration of LPD-F1 oocytes can be partly transmitted to the F2 oocytes. Together, our results reveal that LPD during lactation transgenerationally affects offspring health, probably via oocyte epigenetic changes.
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Affiliation(s)
- Lin-Jian Gu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Li
- Institute of Laboratory Animal Sciences, CAMS & PUMC, Beijing 100021, China
| | - Qian-Nan Li
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China
| | - Ke Xu
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China
| | - Wei Yue
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing-Yi Qiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tie-Gang Meng
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China
| | - Ming-Zhe Dong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Long Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia-Ni Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing-Yuan Sun
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China.
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Cai C, Keoshkerian E, Wing K, Samir J, Effenberger M, Schober K, Bull RA, Lloyd AR, Busch DH, Luciani F. Discovery of a monoclonal, high-affinity CD8 + T-cell clone following natural hepatitis C virus infection. Immunol Cell Biol 2024; 102:630-641. [PMID: 38855806 DOI: 10.1111/imcb.12791] [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: 02/26/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024]
Abstract
CD8+ T cells recognizing their cognate antigen are typically recruited as a polyclonal population consisting of multiple clonotypes with varying T-cell receptor (TCR) affinity to the target peptide-major histocompatibility complex (pMHC) complex. Advances in single-cell sequencing have increased accessibility toward identifying TCRs with matched antigens. Here we present the discovery of a monoclonal CD8+ T-cell population with specificity for a hepatitis C virus (HCV)-derived human leukocyte antigen (HLA) class I epitope (HLA-B*07:02 GPRLGVRAT) which was isolated directly ex vivo from an individual with an episode of acutely resolved HCV infection. This population was absent before infection and underwent expansion and stable maintenance for at least 2 years after infection as measured by HLA-multimer staining. Furthermore, the monoclonal clonotype was characterized by an unusually long dissociation time (half-life = 794 s and koff = 5.73 × 10-4) for its target antigen when compared with previously published results. A comparison with related populations of HCV-specific populations derived from the same individual and a second individual suggested that high-affinity TCR-pMHC interactions may be inherent to epitope identity and shape the phenotype of responses which has implications for rational TCR selection and design in the age of personalized immunotherapies.
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Affiliation(s)
- Curtis Cai
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Elizabeth Keoshkerian
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Kristof Wing
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Jerome Samir
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Manuel Effenberger
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Kilian Schober
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rowena A Bull
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew R Lloyd
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Dirk H Busch
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (Deutsches Zentrum für Infektionsforschung), Partner Site Munich, Munich, Germany
| | - Fabio Luciani
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- Cellular Genomics Future Institute, UNSW Sydney, Sydney, NSW, Australia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
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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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31
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Gordon MG, Kathail P, Choy B, Kim MC, Mazumder T, Gearing M, Ye CJ. Population Diversity at the Single-Cell Level. Annu Rev Genomics Hum Genet 2024; 25:27-49. [PMID: 38382493 DOI: 10.1146/annurev-genom-021623-083207] [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] [Indexed: 02/23/2024]
Abstract
Population-scale single-cell genomics is a transformative approach for unraveling the intricate links between genetic and cellular variation. This approach is facilitated by cutting-edge experimental methodologies, including the development of high-throughput single-cell multiomics and advances in multiplexed environmental and genetic perturbations. Examining the effects of natural or synthetic genetic variants across cellular contexts provides insights into the mutual influence of genetics and the environment in shaping cellular heterogeneity. The development of computational methodologies further enables detailed quantitative analysis of molecular variation, offering an opportunity to examine the respective roles of stochastic, intercellular, and interindividual variation. Future opportunities lie in leveraging long-read sequencing, refining disease-relevant cellular models, and embracing predictive and generative machine learning models. These advancements hold the potential for a deeper understanding of the genetic architecture of human molecular traits, which in turn has important implications for understanding the genetic causes of human disease.
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Affiliation(s)
| | - Pooja Kathail
- Center for Computational Biology, University of California, Berkeley, California, USA
| | - Bryson Choy
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Min Cheol Kim
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Thomas Mazumder
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Chun Jimmie Ye
- Arc Institute, Palo Alto, California, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
- Bakar Computational Health Sciences Institute, Gladstone-UCSF Institute of Genomic Immunology, Parker Institute for Cancer Immunotherapy, Department of Epidemiology and Biostatistics, Department of Microbiology and Immunology, and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA;
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Dong P, Zhang S, Gandin V, Xie L, Wang L, Lemire AL, Li W, Otsuna H, Kawase T, Lander AD, Chang HY, Liu ZJ. Cohesin prevents cross-domain gene coactivation. Nat Genet 2024; 56:1654-1664. [PMID: 39048795 PMCID: PMC11319207 DOI: 10.1038/s41588-024-01852-1] [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: 02/08/2023] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The contrast between the disruption of genome topology after cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic coexpression tendencies of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene coactivation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks spatial mixing of transcriptional hubs. Single-molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene coexpression in single cells.
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Affiliation(s)
- Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Shu Zhang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Valentina Gandin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Cancer Biology and Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Wenhong Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Hideo Otsuna
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Takashi Kawase
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Zhe J Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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Jiang C, Gu S, Pan T, Wang X, Qin W, Wang G, Gao X, Zhang J, Chen K, Warren A, Xiong J, Miao W. Dynamics and timing of diversification events of ciliated eukaryotes from a large phylogenomic perspective. Mol Phylogenet Evol 2024; 197:108110. [PMID: 38768875 DOI: 10.1016/j.ympev.2024.108110] [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: 01/07/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Ciliophora, an exceptionally diverse lineage of unicellular eukaryotes, exhibits a remarkable range of species richness across classes in the ciliate Tree of Life. In this study, we have acquired transcriptome and genome data from 40 representative species in seven ciliate classes. Utilizing 247 genes and 105 taxa, we devised a comprehensive phylogenomic tree for Ciliophora, encompassing over 60 % of orders and constituting the most extensive dataset of ciliate species to date. We established a robust phylogenetic framework that encompasses ambiguous taxa and the major classes within the phylum. Our findings support the monophyly of each of two subphyla (Postciliodesmatophora and Intramacronucleata), along with three subclades (Protocruzia, CONTHREEP, and SAPML) nested within Intramacronucleata, and elucidate evolutionary positions among the major classes within the phylum. Drawing on the robust ciliate Tree of Life and three constraints, we estimated the radiation of Ciliophora around 1175 Ma during the middle of the Proterozoic Eon, and most of the ciliate classes diverged from their sister lineage during the latter half of this period. Additionally, based on the time-calibrated tree and species richness pattern, we investigated net diversification rates of Ciliophora and its classes. The global net diversification rate for Ciliophora was estimated at 0.004979 species/Ma. Heterogeneity in net diversification rates was evident at the class level, with faster rates observed in Oligohymenophorea and Spirotrichea than other classes within the subclades CONTHREEP and SAPML, respectively. Notably, our analysis suggests that variations in net diversification rates, rather than clade ages, appear to contribute to the differences in species richness in Ciliophora at the class level.
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Affiliation(s)
- Chuanqi Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Siyu Gu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Pan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xueyan Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weiwei Qin
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Guangying Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xinxin Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kai Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China.
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Naratadam GT, Mecklenburg J, Shein SA, Zou Y, Lai Z, Tumanov AV, Price TJ, Akopian AN. Degenerative and regenerative peripheral processes are associated with persistent painful chemotherapy-induced neuropathies in males and females. Sci Rep 2024; 14:17543. [PMID: 39080341 PMCID: PMC11289433 DOI: 10.1038/s41598-024-68485-6] [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: 12/21/2023] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
This study investigated the time course of gene expression changes during the progression of persistent painful neuropathy caused by paclitaxel (PTX) in male and female mouse hindpaws and dorsal root ganglia (DRG). Bulk RNA-seq was used to examine these gene expression changes at 1, 16, and 31 days post-last PTX. At these time points, differentially expressed genes (DEGs) were predominantly related to the reduction or increase in epithelial, skin, bone, and muscle development and to angiogenesis, myelination, axonogenesis, and neurogenesis. These processes are accompanied by the regulation of DEGs related to the cytoskeleton, extracellular matrix organization, and cellular energy production. This gene plasticity during the progression of persistent painful neuropathy could be interpreted as a biological process linked to tissue regeneration/degeneration. In contrast, gene plasticity related to immune processes was minimal at 1-31 days after PTX. It was also noted that despite similarities in biological processes and pain chronicity between males and females, specific DEGs differed dramatically according to sex. The main conclusions of this study are that gene expression plasticity in hindpaw and DRG during PTX neuropathy progression similar to tissue regeneration and degeneration, minimally affects immune system processes and is heavily sex-dependent at the individual gene level.
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Affiliation(s)
- George T Naratadam
- South Texas Medical Scientist Training Program (STX-MSTP), Integrated Biomedical Sciences (IBMS) Program, The Long School of Medicine, University of Texas Health Science Center at San Antonio (UTHSCSA), 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Jennifer Mecklenburg
- Department of Endodontics, School of Dentistry, University of Texas Health Science Center at San Antonio (UTHSCSA), 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Sergey A Shein
- Department of Microbiology, Immunology and Molecular Genetics, The Long School of Medicine, UTHSCSA, San Antonio, TX, 78229, USA
| | - Yi Zou
- Department of Molecular Medicine, The Long School of Medicine, UTHSCSA, San Antonio, TX, 78229, USA
| | - Zhao Lai
- Department of Molecular Medicine, The Long School of Medicine, UTHSCSA, San Antonio, TX, 78229, USA
- Greehey Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, 78229, USA
| | - Alexei V Tumanov
- South Texas Medical Scientist Training Program (STX-MSTP), Integrated Biomedical Sciences (IBMS) Program, The Long School of Medicine, University of Texas Health Science Center at San Antonio (UTHSCSA), 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
- Department of Microbiology, Immunology and Molecular Genetics, The Long School of Medicine, UTHSCSA, San Antonio, TX, 78229, USA.
| | - Theodore J Price
- School of Behavioral and Brain Sciences and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, 75080, USA.
| | - Armen N Akopian
- South Texas Medical Scientist Training Program (STX-MSTP), Integrated Biomedical Sciences (IBMS) Program, The Long School of Medicine, University of Texas Health Science Center at San Antonio (UTHSCSA), 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
- Department of Endodontics, School of Dentistry, University of Texas Health Science Center at San Antonio (UTHSCSA), 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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35
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Sypek EI, Tassou A, Collins HY, Huang K, McCallum WM, Bourdillon AT, Barres BA, Bohlen CJ, Scherrer G. Diversity of microglial transcriptional responses during opioid exposure and neuropathic pain. Pain 2024:00006396-990000000-00672. [PMID: 39073407 DOI: 10.1097/j.pain.0000000000003275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/14/2024] [Indexed: 07/30/2024]
Abstract
ABSTRACT Microglia take on an altered morphology during chronic opioid treatment. This morphological change is broadly used to identify the activated microglial state associated with opioid side effects, including tolerance and opioid-induced hyperalgesia (OIH). Microglia display similar morphological responses in the spinal cord after peripheral nerve injury (PNI). Consistent with this observation, functional studies have suggested that microglia activated by opioids or PNI engage common molecular mechanisms to induce hypersensitivity. In this article, we conducted deep RNA sequencing (RNA-seq) and morphological analysis of spinal cord microglia in male mice to comprehensively interrogate transcriptional states and mechanistic commonality between multiple models of OIH and PNI. After PNI, we identify an early proliferative transcriptional event across models that precedes the upregulation of histological markers of microglial activation. However, we found no proliferative transcriptional response associated with opioid-induced microglial activation, consistent with histological data, indicating that the number of microglia remains stable during morphine treatment, whereas their morphological response differs from PNI models. Collectively, these results establish the diversity of pain-associated microglial transcriptomic responses and point towards the targeting of distinct insult-specific microglial responses to treat OIH, PNI, or other central nervous system pathologies.
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Affiliation(s)
- Elizabeth I Sypek
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, United States
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States
- Stanford Neurosciences Institute, Stanford, CA, United States
- Stanford University Neurosciences Graduate Program, Stanford, CA, United States
| | - Adrien Tassou
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Hannah Y Collins
- Department of Neurobiology, Stanford University, Stanford, CA, United States. Bohlen is now with the Department of Neuroscience, Genentech, South San Francisco, CA, United States
| | - Karen Huang
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - William M McCallum
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, United States
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Ben A Barres
- Department of Neurobiology, Stanford University, Stanford, CA, United States. Bohlen is now with the Department of Neuroscience, Genentech, South San Francisco, CA, United States
| | - Christopher J Bohlen
- Department of Neurobiology, Stanford University, Stanford, CA, United States. Bohlen is now with the Department of Neuroscience, Genentech, South San Francisco, CA, United States
| | - Grégory Scherrer
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- New York Stem Cell Foundation-Robertson Investigator Chapel Hill, NC, United States
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36
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Song Y, Parada G, Lee JTH, Hemberg M. Mining alternative splicing patterns in scRNA-seq data using scASfind. Genome Biol 2024; 25:197. [PMID: 39075577 PMCID: PMC11285346 DOI: 10.1186/s13059-024-03323-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 06/26/2024] [Indexed: 07/31/2024] Open
Abstract
Single-cell RNA-seq (scRNA-seq) is widely used for transcriptome profiling, but most analyses focus on gene-level events, with less attention devoted to alternative splicing. Here, we present scASfind, a novel computational method to allow for quantitative analysis of cell type-specific splicing events using full-length scRNA-seq data. ScASfind utilizes an efficient data structure to store the percent spliced-in value for each splicing event. This makes it possible to exhaustively search for patterns among all differential splicing events, allowing us to identify marker events, mutually exclusive events, and events involving large blocks of exons that are specific to one or more cell types.
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Affiliation(s)
- Yuyao Song
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Guillermo Parada
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | | | - Martin Hemberg
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, 02115, USA.
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37
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Yang X, Mann KK, Wu H, Ding J. scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration. Genome Biol 2024; 25:198. [PMID: 39075536 PMCID: PMC11285326 DOI: 10.1186/s13059-024-03338-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: 12/15/2023] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
Single-cell multi-omics data reveal complex cellular states, providing significant insights into cellular dynamics and disease. Yet, integration of multi-omics data presents challenges. Some modalities have not reached the robustness or clarity of established transcriptomics. Coupled with data scarcity for less established modalities and integration intricacies, these challenges limit our ability to maximize single-cell omics benefits. We introduce scCross, a tool leveraging variational autoencoders, generative adversarial networks, and the mutual nearest neighbors (MNN) technique for modality alignment. By enabling single-cell cross-modal data generation, multi-omics data simulation, and in silico cellular perturbations, scCross enhances the utility of single-cell multi-omics studies.
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Affiliation(s)
- Xiuhui Yang
- School of Software, Shandong University, 1500 Shunhua, Jinan, 250101, Shandong, China
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, H4A 3J1, QC, Canada
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Koren K Mann
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Hao Wu
- School of Software, Shandong University, 1500 Shunhua, Jinan, 250101, Shandong, China.
| | - Jun Ding
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, H4A 3J1, QC, Canada.
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Mila-Quebec AI Institute, Montreal, QC, H2S 3H1, Canada.
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38
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Lause J, Ziegenhain C, Hartmanis L, Berens P, Kobak D. Compound models and Pearson residuals for single-cell RNA-seq data without UMIs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.02.551637. [PMID: 37577688 PMCID: PMC10418209 DOI: 10.1101/2023.08.02.551637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Recent work employed Pearson residuals from Poisson or negative binomial models to normalize UMI data. To extend this approach to non-UMI data, we model the additional amplification step with a compound distribution: we assume that sequenced RNA molecules follow a negative binomial distribution, and are then replicated following an amplification distribution. We show how this model leads to compound Pearson residuals, which yield meaningful gene selection and embeddings of Smart-seq2 datasets. Further, we suggest that amplification distributions across several sequencing protocols can be described by a broken power law. The resulting compound model captures previously unexplained overdispersion and zero-inflation patterns in non-UMI data.
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39
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Ye K, Chang W, Xu J, Guo Y, Qin Q, Dang K, Han X, Zhu X, Ge Q, Cui Q, Xu Y, Zhao X. Spatial transcriptomic profiling of isolated microregions in tissue sections utilizing laser-induced forward transfer. PLoS One 2024; 19:e0305977. [PMID: 39052564 PMCID: PMC11271912 DOI: 10.1371/journal.pone.0305977] [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: 12/29/2023] [Accepted: 06/07/2024] [Indexed: 07/27/2024] Open
Abstract
Profiling gene expression while preserving cell locations aids in the comprehensive understanding of cell fates in multicellular organisms. However, simple and flexible isolation of microregions of interest (mROIs) for spatial transcriptomics is still challenging. We present a laser-induced forward transfer (LIFT)-based method combined with a full-length mRNA-sequencing protocol (LIFT-seq) for profiling region-specific tissues. LIFT-seq demonstrated that mROIs from two adjacent sections could reliably and sensitively detect and display gene expression. In addition, LIFT-seq can identify region-specific mROIs in the mouse cortex and hippocampus. Finally, LIFT-seq identified marker genes in different layers of the cortex with very similar expression patterns. These genes were then validated using in situ hybridization (ISH) results. Therefore, LIFT-seq will be a valuable and efficient technique for profiling the spatial transcriptome in various tissues.
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Affiliation(s)
- Kaiqiang Ye
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Wanqing Chang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Jitao Xu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Yunxia Guo
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Qingyang Qin
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Kaitong Dang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Xiaofeng Han
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Xiaolei Zhu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Qiannan Cui
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Yun Xu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Xiangwei Zhao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
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40
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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41
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Shin SW, Mudvari P, Thaploo S, Wheeler MA, Douek DC, Quintana FJ, Boritz EA, Abate AR, Clark IC. FIND-seq: high-throughput nucleic acid cytometry for rare single-cell transcriptomics. Nat Protoc 2024:10.1038/s41596-024-01021-y. [PMID: 39039320 DOI: 10.1038/s41596-024-01021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 05/09/2024] [Indexed: 07/24/2024]
Abstract
Rare cells have an important role in development and disease, and methods for isolating and studying cell subsets are therefore an essential part of biology research. Such methods traditionally rely on labeled antibodies targeted to cell surface proteins, but large public databases and sophisticated computational approaches increasingly define cell subsets on the basis of genomic, epigenomic and transcriptomic sequencing data. Methods for isolating cells on the basis of nucleic acid sequences powerfully complement these approaches by providing experimental access to cell subsets discovered in cell atlases, as well as those that cannot be otherwise isolated, including cells infected with pathogens, with specific DNA mutations or with unique transcriptional or splicing signatures. We recently developed a nucleic acid cytometry platform called 'focused interrogation of cells by nucleic acid detection and sequencing' (FIND-seq), capable of isolating rare cells on the basis of RNA or DNA markers, followed by bulk or single-cell transcriptomic analysis. This platform has previously been used to characterize the splicing-dependent activation of the transcription factor XBP1 in astrocytes and HIV persistence in memory CD4 T cells from people on long-term antiretroviral therapy. Here, we outline the molecular and microfluidic steps involved in performing FIND-seq, including protocol updates that allow detection and whole transcriptome sequencing of rare HIV-infected cells that harbor genetically intact virus genomes. FIND-seq requires knowledge of microfluidics, optics and molecular biology. We expect that FIND-seq, and this comprehensive protocol, will enable mechanistic studies of rare HIV+ cells, as well as other cell subsets that were previously difficult to recover and sequence.
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Affiliation(s)
- Seung Won Shin
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA
| | - Prakriti Mudvari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
| | - Iain C Clark
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA.
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42
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Tooley K, Jerby L, Escobar G, Krovi SH, Mangani D, Dandekar G, Cheng H, Madi A, Goldschmidt E, Lambden C, Krishnan RK, Rozenblatt-Rosen O, Regev A, Anderson AC. Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity. Cell Rep Med 2024; 5:101640. [PMID: 38959885 PMCID: PMC11293343 DOI: 10.1016/j.xcrm.2024.101640] [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: 05/31/2023] [Revised: 01/05/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
CD8+ T cells must persist and function in diverse tumor microenvironments to exert their effects. Thus, understanding common underlying expression programs could better inform the next generation of immunotherapies. We apply a generalizable matrix factorization algorithm that recovers both shared and context-specific expression programs from diverse datasets to a single-cell RNA sequencing (scRNA-seq) compendium of 33,161 CD8+ T cells from 132 patients with seven human cancers. Our meta-single-cell analyses uncover a pan-cancer T cell dysfunction program that predicts clinical non-response to checkpoint blockade in melanoma and highlights CXCR6 as a pan-cancer marker of chronically activated T cells. Cxcr6 is trans-activated by AP-1 and repressed by TCF1. Using mouse models, we show that Cxcr6 deletion in CD8+ T cells increases apoptosis of PD1+TIM3+ cells, dampens CD28 signaling, and compromises tumor growth control. Our study uncovers a TCF1:CXCR6 axis that counterbalances PD1-mediated suppression of CD8+ cell responses and is essential for effective anti-tumor immunity.
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Affiliation(s)
- Katherine Tooley
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Livnat Jerby
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulia Escobar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - S Harsha Krovi
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Davide Mangani
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gitanjali Dandekar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanning Cheng
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Goldschmidt
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Conner Lambden
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajesh K Krishnan
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ana C Anderson
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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43
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Fang S, Ji Y, Shen Y, Yang S, Zhang H, Xin W, Shi W, Chen W. TET3 Contributes to Exercise-Induced Functional Axon Regeneration and Visual Restoration. Adv Biol (Weinh) 2024:e2400145. [PMID: 39007414 DOI: 10.1002/adbi.202400145] [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: 05/27/2024] [Indexed: 07/16/2024]
Abstract
Axons have intrinsically poor regenerative capacity in the mature central nervous system (CNS), leading to permanent neurological impairments in individuals. There is growing evidence that exercise is a powerful physiological intervention that can obviously enhance cell rejuvenate capacity, but its molecular mechanisms that mediate the axonal regenerative benefits remain largely unclear. Using the eye as the CNS model, here it is first indicated that placing mice in an exercise stimulation environment induced DNA methylation patterns and transcriptomes of retinal ganglion cell, promoted axon regeneration after injury, and reversed vision loss in aged mice. These beneficial effects are dependent on the DNA demethylases TET3-mediated epigenetic effects, which increased the expression of genes associated with the regenerative growth programs, such as STAT3, Wnt5a, Klf6. Exercise training also shows with the improved mitochondrial and metabolic dysfunction in retinas and optic nerves via TET3. Collectively, these results suggested that the increased regenerative capacity induced by enhancing physical activity is mediated through epigenetic reprogramming in mouse model of optic nerve injury and in aged mouse. Understanding the molecular mechanism underlying exercise-dependent neuronal plasticity led to the identification of novel targets for ameliorating pathologies associated with etiologically diverse diseases.
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Affiliation(s)
- Si Fang
- Multiscale Research Institute of Complex Systems, Department of Integrative Oncology in Fudan University Shanghai Cancer Center, Jingan District Central Hospital of Shanghai, Department of Otorhinolaryngology-Head and Neck Surgery in Huashan Hospital, Fudan University, Shanghai, 200433, China
| | - Yunxiang Ji
- Multiscale Research Institute of Complex Systems, Department of Integrative Oncology in Fudan University Shanghai Cancer Center, Jingan District Central Hospital of Shanghai, Department of Otorhinolaryngology-Head and Neck Surgery in Huashan Hospital, Fudan University, Shanghai, 200433, China
| | - Yilan Shen
- Department of Nephrology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Simin Yang
- Multiscale Research Institute of Complex Systems, Department of Integrative Oncology in Fudan University Shanghai Cancer Center, Jingan District Central Hospital of Shanghai, Department of Otorhinolaryngology-Head and Neck Surgery in Huashan Hospital, Fudan University, Shanghai, 200433, China
- Department of Pharmacology, Basic Medical College, Anhui Medical University, Hefei, 230032, China
| | - Hongli Zhang
- Multiscale Research Institute of Complex Systems, Department of Integrative Oncology in Fudan University Shanghai Cancer Center, Jingan District Central Hospital of Shanghai, Department of Otorhinolaryngology-Head and Neck Surgery in Huashan Hospital, Fudan University, Shanghai, 200433, China
- Department of Nephrology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Wenfeng Xin
- College of Notoginseng Medicine and Pharmacy, Wenshan University, Wenshan, 663000, China
| | - Weidong Shi
- Multiscale Research Institute of Complex Systems, Department of Integrative Oncology in Fudan University Shanghai Cancer Center, Jingan District Central Hospital of Shanghai, Department of Otorhinolaryngology-Head and Neck Surgery in Huashan Hospital, Fudan University, Shanghai, 200433, China
| | - Wei Chen
- Multiscale Research Institute of Complex Systems, Department of Integrative Oncology in Fudan University Shanghai Cancer Center, Jingan District Central Hospital of Shanghai, Department of Otorhinolaryngology-Head and Neck Surgery in Huashan Hospital, Fudan University, Shanghai, 200433, China
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44
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Niu Y, Luo J, Zong C. Single-cell total-RNA profiling unveils regulatory hubs of transcription factors. Nat Commun 2024; 15:5941. [PMID: 39009595 PMCID: PMC11251146 DOI: 10.1038/s41467-024-50291-3] [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: 09/27/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from unspliced RNA to spliced RNA (i.e., mature RNA) to degradation. To feed this kinetic analysis, simultaneous measurement of unspliced RNA and spliced RNA in single cells is greatly desired. However, the majority of single-cell RNA-seq chemistry primarily captures mature RNA species to measure gene expressions. Here, we develop a one-step total-RNA chemistry-based single-cell RNA-seq method: snapTotal-seq. We benchmark this method with multiple single-cell RNA-seq assays in their performance in kinetic analysis of cell cycle by RNA velocity. Next, with LASSO regression between transcription factors, we identify the critical regulatory hubs mediating the cell cycle dynamics. We also apply snapTotal-seq to profile the oncogene-induced senescence and identify the key regulatory hubs governing the entry of senescence. Furthermore, from the comparative analysis of unspliced RNA and spliced RNA, we identify a significant portion of genes whose expression changes occur in spliced RNA but not to the same degree in unspliced RNA, indicating these gene expression changes are mainly controlled by post-transcriptional regulation. Overall, we demonstrate that snapTotal-seq can provide enriched information about gene regulation, especially during the transition between cell states.
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Affiliation(s)
- Yichi Niu
- Department of Molecular and Human Genetics, Houston, TX, USA
- Genetics & Genomics Program, Houston, TX, USA
| | - Jiayi Luo
- Department of Molecular and Human Genetics, Houston, TX, USA
- Cancer and Cell Biology Program, Houston, TX, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Houston, TX, USA.
- Genetics & Genomics Program, Houston, TX, USA.
- Cancer and Cell Biology Program, Houston, TX, USA.
- Integrative Molecular and Biomedical Sciences Program, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Houston, TX, USA.
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, USA.
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Bakina O, Conrad T, Mitic N, Vidal RO, Obrusnik T, Sai S, Nolte C, Semtner M, Kettenmann H. In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia. PLoS One 2024; 19:e0302376. [PMID: 38990806 PMCID: PMC11239014 DOI: 10.1371/journal.pone.0302376] [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: 08/16/2023] [Accepted: 04/02/2024] [Indexed: 07/13/2024] Open
Abstract
We applied the patch-seq technique to harvest transcripts from individual microglial cells from cortex, hippocampus and corpus callosum of acute brain slices from adult mice. After recording membrane currents with the patch-clamp technique, the cytoplasm was collected via the pipette and underwent adapted SMART-seq2 preparation with subsequent sequencing. On average, 4138 genes were detected in 113 cells from hippocampus, corpus callosum and cortex, including microglia markers such as Tmem119, P2ry12 and Siglec-H. Comparing our dataset to previously published single cell mRNA sequencing data from FACS-isolated microglia indicated that two clusters of cells were absent in our patch-seq dataset. Pathway analysis of marker genes in FACS-specific clusters revealed association with microglial activation and stress response. This indicates that under normal conditions microglia in situ lack transcripts associated with a stress-response, and that the microglia-isolation procedure by mechanical dissociation and FACS triggers the expression of genes related to activation and stress.
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Affiliation(s)
- Olga Bakina
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Humboldt Universität, Berlin, Germany
| | - Thomas Conrad
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nina Mitic
- Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ramon Oliveira Vidal
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Tessa Obrusnik
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Somesh Sai
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christiane Nolte
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marcus Semtner
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Helmut Kettenmann
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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46
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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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Liu B, Liu Y, Li S, Chen P, Zhang J, Feng L. Depletion of placental brain-derived neurotrophic factor (BDNF) is attributed to premature ovarian insufficiency (POI) in mice offspring. J Ovarian Res 2024; 17:141. [PMID: 38982490 PMCID: PMC11232340 DOI: 10.1186/s13048-024-01467-4] [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: 12/11/2023] [Accepted: 06/29/2024] [Indexed: 07/11/2024] Open
Abstract
INTRODUCTION Premature ovarian insufficiency (POI) is one of the causes of female infertility. Unexplained POI is increasingly affecting women in their reproductive years. However, the etiology of POI is diverse and remains elusive. We and others have shown that brain-derived neurotrophic factor (BDNF) plays an important role in adult ovarian function. Here, we report on a novel role of BDNF in the Developmental Origins of POI. METHODS Placental BDNF knockout mice were created using CRISPR/CAS9. Homozygous knockout (cKO(HO)) mice didn't survive, while heterozygous knockout (cKO(HE)) mice did. BDNF reduction in cKO(HE) mice was confirmed via immunohistochemistry and Western blots. Ovaries were collected from cKO(HE) mice at various ages, analyzing ovarian metrics, FSH expression, and litter sizes. In one-month-old mice, oocyte numbers were assessed using super-ovulation, and oocyte gene expression was analyzed with smart RNAseq. Ovaries of P7 mice were studied with SEM, and gene expression was confirmed with RT-qPCR. Alkaline phosphatase staining at E11.5 and immunofluorescence for cyclinD1 assessed germ cell number and cell proliferation. RESULTS cKO(HE) mice had decreased ovarian function and litter size in adulthood. They were insensitive to ovulation induction drugs manifested by lower oocyte release after superovulation in one-month-old cKO(HE) mice. The transcriptome and SEM results indicate that mitochondria-mediated cell death or aging might occur in cKO(HE) ovaries. Decreased placental BDNF led to diminished primordial germ cell proliferation at E11.5 and ovarian reserve which may underlie POI in adulthood. CONCLUSION The current results showed decreased placental BDNF diminished primordial germ cell proliferation in female fetuses during pregnancy and POI in adulthood. Our findings can provide insights into understanding the underlying mechanisms of POI.
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Affiliation(s)
- Bin Liu
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Reproduction, School of Medicine, Xinhua Hospital, Shanghai Jiao-Tong University, Shanghai, China
| | - Yongjie Liu
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shuman Li
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Pingping Chen
- Department of Reproduction, School of Medicine, Xinhua Hospital, Shanghai Jiao-Tong University, Shanghai, China
| | - Jun Zhang
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Liping Feng
- Department of Obstetrics and Gynaecology, Duke University, Durham, NC, USA.
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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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Xu H, Ye Y, Duan R, Gao Y, Hu Y, Gao L. Beaconet: A Reference-Free Method for Integrating Multiple Batches of Single-Cell Transcriptomic Data in Original Molecular Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306770. [PMID: 38711214 PMCID: PMC11234410 DOI: 10.1002/advs.202306770] [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: 09/17/2023] [Revised: 04/02/2024] [Indexed: 05/08/2024]
Abstract
Integrating multiple single-cell datasets is essential for the comprehensive understanding of cell heterogeneity. Batch effect is the undesired systematic variations among technologies or experimental laboratories that distort biological signals and hinder the integration of single-cell datasets. However, existing methods typically rely on a selected dataset as a reference, leading to inconsistent integration performance using different references, or embed cells into uninterpretable low-dimensional feature space. To overcome these limitations, a reference-free method, Beaconet, for integrating multiple single-cell transcriptomic datasets in original molecular space by aligning the global distribution of each batch using an adversarial correction network is presented. Through extensive comparisons with 13 state-of-the-art methods, it is demonstrated that Beaconet can effectively remove batch effect while preserving biological variations and is superior to existing unsupervised methods using all possible references in overall performance. Furthermore, Beaconet performs integration in the original molecular feature space, enabling the characterization of cell types and downstream differential expression analysis directly using integrated data with gene-expression features. Additionally, when applying to large-scale atlas data integration, Beaconet shows notable advantages in both time- and space-efficiencies. In summary, Beaconet serves as an effective and efficient batch effect removal tool that can facilitate the integration of single-cell datasets in a reference-free and molecular feature-preserved mode.
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Affiliation(s)
- Han Xu
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Yusen Ye
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Ran Duan
- School of Electrical and Information EngineeringBeijing University of Civil Engineering and ArchitectureBeijing102616China
| | - Yong Gao
- Department of Computer ScienceThe University of British Columbia OkanaganKelownaBritish ColumbiaV1V 1V7Canada
| | - Yuxuan Hu
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Lin Gao
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
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50
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Giaccari C, Cecere F, Argenziano L, Pagano A, Riccio A. New insights into oocyte cytoplasmic lattice-associated proteins. Trends Genet 2024:S0168-9525(24)00149-5. [PMID: 38955588 DOI: 10.1016/j.tig.2024.06.002] [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: 04/16/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
Oocyte maturation and preimplantation embryo development are critical to successful pregnancy outcomes and the correct establishment and maintenance of genomic imprinting. Thanks to novel technologies and omics studies in human patients and mouse models, the importance of the proteins associated with the cytoplasmic lattices (CPLs), highly abundant structures found in the cytoplasm of mammalian oocytes and preimplantation embryos, in the maternal to zygotic transition is becoming increasingly evident. This review highlights the recent discoveries on the role of these proteins in protein storage and other oocyte cytoplasmic processes, epigenetic reprogramming, and zygotic genome activation (ZGA). A better comprehension of these events may significantly improve clinical diagnosis and pave the way for targeted interventions aiming to correct or mitigate female fertility issues and genomic imprinting disorders.
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Affiliation(s)
- Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy
| | - Lucia Argenziano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy
| | - Angela Pagano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy; Institute of Genetics and Biophysics (IGB) 'Adriano Buzzati-Traverso,' Consiglio Nazionale delle Ricerche (CNR), Naples, Italy.
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