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Raz AA, Vida GS, Stern SR, Mahadevaraju S, Fingerhut JM, Viveiros JM, Pal S, Grey JR, Grace MR, Berry CW, Li H, Janssens J, Saelens W, Shao Z, Hu C, Yamashita YM, Przytycka T, Oliver B, Brill JA, Krause H, Matunis EL, White-Cooper H, DiNardo S, Fuller MT. Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes. eLife 2023; 12:e82201. [PMID: 36795469 PMCID: PMC9934865 DOI: 10.7554/elife.82201] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/19/2023] [Indexed: 02/17/2023] Open
Abstract
Proper differentiation of sperm from germline stem cells, essential for production of the next generation, requires dramatic changes in gene expression that drive remodeling of almost all cellular components, from chromatin to organelles to cell shape itself. Here, we provide a single nucleus and single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq (snRNA-seq) data from the Fly Cell Atlas (FCA) study. With over 44,000 nuclei and 6000 cells analyzed, the data provide identification of rare cell types, mapping of intermediate steps in differentiation, and the potential to identify new factors impacting fertility or controlling differentiation of germline and supporting somatic cells. We justify assignment of key germline and somatic cell types using combinations of known markers, in situ hybridization, and analysis of extant protein traps. Comparison of single cell and single nucleus datasets proved particularly revealing of dynamic developmental transitions in germline differentiation. To complement the web-based portals for data analysis hosted by the FCA, we provide datasets compatible with commonly used software such as Seurat and Monocle. The foundation provided here will enable communities studying spermatogenesis to interrogate the datasets to identify candidate genes to test for function in vivo.
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Affiliation(s)
- Amelie A Raz
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical InstituteCambridgeUnited States
| | - Gabriela S Vida
- Department of Cell and Developmental Biology, The Perelman School of Medicine and The Penn Institute for Regenerative MedicinePhiladelphiaUnited States
| | - Sarah R Stern
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
| | - Sharvani Mahadevaraju
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Jaclyn M Fingerhut
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical InstituteCambridgeUnited States
| | - Jennifer M Viveiros
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Soumitra Pal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Jasmine R Grey
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Mara R Grace
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Cameron W Berry
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
| | - Hongjie Li
- Huffington Center on Aging and Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Jasper Janssens
- JVIB Center for Brain & Disease Research, and the Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Wouter Saelens
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, and Department of Applied Mathematics, Computer Science and Statistics, Ghent UniversityGhentBelgium
| | - Zhantao Shao
- Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Chun Hu
- Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical InstituteCambridgeUnited States
| | - Teresa Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Julie A Brill
- Cell Biology Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Molecular Genetics, University of TorontoTorontoCanada
- Institute of Medical Science, University of TorontoTorontoCanada
| | - Henry Krause
- Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Erika L Matunis
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | | | - Stephen DiNardo
- Department of Cell and Developmental Biology, The Perelman School of Medicine and The Penn Institute for Regenerative MedicinePhiladelphiaUnited States
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
- Department of Genetics, Stanford UniversityStanfordUnited States
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2
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Chakravarti A, Thirimanne HN, Brown S, Calvi BR. Drosophila p53 isoforms have overlapping and distinct functions in germline genome integrity and oocyte quality control. eLife 2022; 11:61389. [PMID: 35023826 PMCID: PMC8758136 DOI: 10.7554/elife.61389] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
p53 gene family members in humans and other organisms encode a large number of protein isoforms whose functions are largely undefined. Using Drosophila as a model, we find that a p53B isoform is expressed predominantly in the germline where it colocalizes with p53A into subnuclear bodies. It is only p53A, however, that mediates the apoptotic response to ionizing radiation in the germline and soma. In contrast, p53A and p53B are both required for the normal repair of meiotic DNA breaks, an activity that is more crucial when meiotic recombination is defective. We find that in oocytes with persistent DNA breaks p53A is also required to activate a meiotic pachytene checkpoint. Our findings indicate that Drosophila p53 isoforms have DNA lesion and cell type-specific functions, with parallels to the functions of mammalian p53 family members in the genotoxic stress response and oocyte quality control.
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Affiliation(s)
| | | | - Savanna Brown
- Department of Biology, Indiana University, Bloomington, United States
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, United States
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Mahadevaraju S, Fear JM, Akeju M, Galletta BJ, Pinheiro MMLS, Avelino CC, Cabral-de-Mello DC, Conlon K, Dell'Orso S, Demere Z, Mansuria K, Mendonça CA, Palacios-Gimenez OM, Ross E, Savery M, Yu K, Smith HE, Sartorelli V, Yang H, Rusan NM, Vibranovski MD, Matunis E, Oliver B. Dynamic sex chromosome expression in Drosophila male germ cells. Nat Commun 2021; 12:892. [PMID: 33563972 PMCID: PMC7873209 DOI: 10.1038/s41467-021-20897-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
Given their copy number differences and unique modes of inheritance, the evolved gene content and expression of sex chromosomes is unusual. In many organisms the X and Y chromosomes are inactivated in spermatocytes, possibly as a defense mechanism against insertions into unpaired chromatin. In addition to current sex chromosomes, Drosophila has a small gene-poor X-chromosome relic (4th) that re-acquired autosomal status. Here we use single cell RNA-Seq on fly larvae to demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes, based on measuring all genes or a set of broadly expressed genes in testis we identified. In contrast, genes on the single Y chromosome become maximally active in primary spermatocytes. Reduced X transcript levels are due to failed activation of RNA-Polymerase-II by phosphorylation of Serine 2 and 5.
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Affiliation(s)
- Sharvani Mahadevaraju
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Justin M Fear
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Miriam Akeju
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Brian J Galletta
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mara M L S Pinheiro
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
| | - Camila C Avelino
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
| | - Diogo C Cabral-de-Mello
- Instituto de Biociências/IB, Departamento de Biologia Geral e Aplicada, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Katie Conlon
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Stafania Dell'Orso
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zelalem Demere
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Kush Mansuria
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Carolina A Mendonça
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
| | - Octavio M Palacios-Gimenez
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
- Department of Evolutionary Biology and Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden
| | - Eli Ross
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Max Savery
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kevin Yu
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Harold E Smith
- Genomics Core, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Haiwang Yang
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Nasser M Rusan
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maria D Vibranovski
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
| | - Erika Matunis
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Brian Oliver
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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Napoletano F, Gibert B, Yacobi-Sharon K, Vincent S, Favrot C, Mehlen P, Girard V, Teil M, Chatelain G, Walter L, Arama E, Mollereau B. p53-dependent programmed necrosis controls germ cell homeostasis during spermatogenesis. PLoS Genet 2017; 13:e1007024. [PMID: 28945745 PMCID: PMC5629030 DOI: 10.1371/journal.pgen.1007024] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/05/2017] [Accepted: 09/15/2017] [Indexed: 01/02/2023] Open
Abstract
The importance of regulated necrosis in pathologies such as cerebral stroke and myocardial infarction is now fully recognized. However, the physiological relevance of regulated necrosis remains unclear. Here, we report a conserved role for p53 in regulating necrosis in Drosophila and mammalian spermatogenesis. We found that Drosophila p53 is required for the programmed necrosis that occurs spontaneously in mitotic germ cells during spermatogenesis. This form of necrosis involved an atypical function of the initiator caspase Dronc/Caspase 9, independent of its catalytic activity. Prevention of p53-dependent necrosis resulted in testicular hyperplasia, which was reversed by restoring necrosis in spermatogonia. In mouse testes, p53 was required for heat-induced germ cell necrosis, indicating that regulation of necrosis is a primordial function of p53 conserved from invertebrates to vertebrates. Drosophila and mouse spermatogenesis will thus be useful models to identify inducers of necrosis to treat cancers that are refractory to apoptosis.
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Affiliation(s)
- Francesco Napoletano
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Benjamin Gibert
- Apoptosis, Cancer and Development Laboratory- Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - Keren Yacobi-Sharon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Stéphane Vincent
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Clémentine Favrot
- Apoptosis, Cancer and Development Laboratory- Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory- Equipe labellisée ‘La Ligue’, LabEx DEVweCAN, Centre de Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - Victor Girard
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Margaux Teil
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Gilles Chatelain
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Ludivine Walter
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Eli Arama
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Bertrand Mollereau
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
- * E-mail:
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5
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D’Brot A, Kurtz P, Regan E, Jakubowski B, Abrams JM. A platform for interrogating cancer-associated p53 alleles. Oncogene 2017; 36:286-291. [PMID: 26996664 PMCID: PMC5031501 DOI: 10.1038/onc.2016.48] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 01/06/2016] [Accepted: 01/19/2016] [Indexed: 12/13/2022]
Abstract
p53 is the most frequently mutated gene in human cancer. Compelling evidence argues that full transformation involves loss of growth suppression encoded by wild-type p53 together with poorly understood oncogenic activity encoded by missense mutations. Furthermore, distinguishing disease alleles from natural polymorphisms is an important clinical challenge. To interrogate the genetic activity of human p53 variants, we leveraged the Drosophila model as an in vivo platform. We engineered strains that replace the fly p53 gene with human alleles, producing a collection of stocks that are, in effect, 'humanized' for p53 variants. Like the fly counterpart, human p53 transcriptionally activated a biosensor and induced apoptosis after DNA damage. However, all humanized strains representing common alleles found in cancer patients failed to complement in these assays. Surprisingly, stimulus-dependent activation of hp53 occurred without stabilization, demonstrating that these two processes can be uncoupled. Like its fly counterpart, hp53 formed prominent nuclear foci in germline cells but cancer-associated p53 variants did not. Moreover, these same mutant alleles disrupted hp53 foci and inhibited biosensor activity, suggesting that these properties are functionally linked. Together these findings establish a functional platform for interrogating human p53 alleles and suggest that simple phenotypes could be used to stratify disease variants.
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Affiliation(s)
- Alejandro D’Brot
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paula Kurtz
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Erin Regan
- Department of Physical Therapy, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - John M Abrams
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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6
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Abstract
The dramatic changes that male germ cells in the adult testis undergo in gene expression profile and morphology as they transition from spermatogonial stem cells through to mature spermatozoa is dependent upon their association with Sertoli cells. Sertoli cells are crucial for survival and maturation of male germ cells. Two recent papers, Holembowski et al.1 and Inoue et al.2 have described a surprising role for the p53 family member, p73, in regulation of germ cell-Sertoli cell adhesion.
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Affiliation(s)
| | - Gary R Hime
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC 3010, Australia
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7
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Titen SWA, Lin HC, Bhandari J, Golic KG. Chk2 and p53 regulate the transmission of healed chromosomes in the Drosophila male germline. PLoS Genet 2014; 10:e1004130. [PMID: 24586185 PMCID: PMC3937212 DOI: 10.1371/journal.pgen.1004130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/04/2013] [Indexed: 01/12/2023] Open
Abstract
When a dicentric chromosome breaks in mitosis, the broken ends cannot be repaired by normal mechanisms that join two broken ends since each end is in a separate daughter cell. However, in the male germline of Drosophila melanogaster, a broken end may be healed by de novo telomere addition. We find that Chk2 (encoded by lok) and P53, major mediators of the DNA damage response, have strong and opposite influences on the transmission of broken-and-healed chromosomes: lok mutants exhibit a large increase in the recovery of healed chromosomes relative to wildtype control males, but p53 mutants show a strong reduction. This contrasts with the soma, where mutations in lok and p53 have the nearly identical effect of allowing survival and proliferation of cells with irreparable DNA damage. Examination of testes revealed a transient depletion of germline cells after dicentric chromosome induction in the wildtype controls, and further showed that P53 is required for the germline to recover. Although lok mutant males transmit healed chromosomes at a high rate, broken chromosome ends can also persist through spermatogonial divisions without healing in lok mutants, giving rise to frequent dicentric bridges in Meiosis II. Cytological and genetic analyses show that spermatid nuclei derived from such meiotic divisions are eliminated during spermiogenesis, resulting in strong meiotic drive. We conclude that the primary responsibility for maintaining genome integrity in the male germline lies with Chk2, and that P53 is required to reconstitute the germline when cells are eliminated owing to unrepaired DNA damage.
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Affiliation(s)
- Simon W. A. Titen
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Ho-Chen Lin
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Jayaram Bhandari
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Kent G. Golic
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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