1
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DeCasien AR, Chiou KL, Testard C, Mercer A, Negrón-Del Valle JE, Bauman Surratt SE, González O, Stock MK, Ruiz-Lambides AV, Martínez MI, Antón SC, Walker CS, Sallet J, Wilson MA, Brent LJN, Montague MJ, Sherwood CC, Platt ML, Higham JP, Snyder-Mackler N. Evolutionary and biomedical implications of sex differences in the primate brain transcriptome. CELL GENOMICS 2024; 4:100589. [PMID: 38942023 DOI: 10.1016/j.xgen.2024.100589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/28/2023] [Accepted: 05/31/2024] [Indexed: 06/30/2024]
Abstract
Humans exhibit sex differences in the prevalence of many neurodevelopmental disorders and neurodegenerative diseases. Here, we generated one of the largest multi-brain-region bulk transcriptional datasets for the rhesus macaque and characterized sex-biased gene expression patterns to investigate the translatability of this species for sex-biased neurological conditions. We identify patterns similar to those in humans, which are associated with overlapping regulatory mechanisms, biological processes, and genes implicated in sex-biased human disorders, including autism. We also show that sex-biased genes exhibit greater genetic variance for expression and more tissue-specific expression patterns, which may facilitate rapid evolution of sex-biased genes. Our findings provide insights into the biological mechanisms underlying sex-biased disease and support the rhesus macaque model for the translational study of these conditions.
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Affiliation(s)
- Alex R DeCasien
- Department of Anthropology, New York University, New York, NY, USA; New York Consortium in Evolutionary Primatology, New York, NY, USA; Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA.
| | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Department of Psychology, University of Washington, Seattle, WA, USA; Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Washington, Seattle, WA, USA.
| | - Camille Testard
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Arianne Mercer
- Department of Psychology, University of Washington, Seattle, WA, USA
| | | | | | - Olga González
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Michala K Stock
- Department of Sociology and Anthropology, Metropolitan State University of Denver, Denver, CO, USA
| | | | - Melween I Martínez
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, PR, USA
| | - Susan C Antón
- Department of Anthropology, New York University, New York, NY, USA; New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Christopher S Walker
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jérôme Sallet
- Stem Cell and Brain Research Institute, Université Lyon, Lyon, France
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behavior, University of Exeter, Exeter, UK
| | - Michael J Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Michael L Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA; Department of Marketing, University of Pennsylvania, Philadelphia, PA, USA
| | - James P Higham
- Department of Anthropology, New York University, New York, NY, USA; New York Consortium in Evolutionary Primatology, New York, NY, USA.
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Department of Psychology, University of Washington, Seattle, WA, USA; Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Washington, Seattle, WA, USA; ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA.
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2
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Tharp ME, Han CZ, Balak CD, Fitzpatrick C, O'Connor C, Preissl S, Buchanan J, Nott A, Escoubet L, Mavrommatis K, Gupta M, Schwartz MS, Sang UH, Jones PS, Levy ML, Gonda DD, Ben-Haim S, Ciacci J, Barba D, Khalessi A, Coufal NG, Chen CC, Glass CK, Page DC. The inactive X chromosome drives sex differences in microglial inflammatory activity in human glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597433. [PMID: 38895459 PMCID: PMC11185629 DOI: 10.1101/2024.06.06.597433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Biological sex is an important risk factor in cancer, but the underlying cell types and mechanisms remain obscure. Since tumor development is regulated by the immune system, we hypothesize that sex-biased immune interactions underpin sex differences in cancer. The male-biased glioblastoma multiforme (GBM) is an aggressive and treatment-refractory tumor in urgent need of more innovative approaches, such as considering sex differences, to improve outcomes. GBM arises in the specialized brain immune environment dominated by microglia, so we explored sex differences in this immune cell type. We isolated adult human TAM-MGs (tumor-associated macrophages enriched for microglia) and control microglia and found sex-biased inflammatory signatures in GBM and lower-grade tumors associated with pro-tumorigenic activity in males and anti-tumorigenic activity in females. We demonstrated that genes expressed or modulated by the inactive X chromosome facilitate this bias. Together, our results implicate TAM-MGs, specifically their sex chromosomes, as drivers of male bias in GBM.
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Affiliation(s)
- Marla E Tharp
- Whitehead Institute, Cambridge, MA 02142, USA
- These authors contributed equally
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- These authors contributed equally
| | - Chris D Balak
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Conor Fitzpatrick
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Carolyn O'Connor
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sebastian Preissl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
- Present address: Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Justin Buchanan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexi Nott
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Brain Sciences, Imperial College London, London, United Kingdom
- UK Dementia Research Institute, Imperial College London, London, United Kingdom
| | | | | | - Mihir Gupta
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
- Present address: Department of Neurosurgery, Yale University, New Haven, CT 06520, USA
| | - Marc S Schwartz
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - U Hoi Sang
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - Pamela S Jones
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
- Present address: Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Michael L Levy
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - David D Gonda
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sharona Ben-Haim
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - Joseph Ciacci
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - David Barba
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexander Khalessi
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - Nicole G Coufal
- Department of Pediatrics University of California, San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Clark C Chen
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
- Present address: Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
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3
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Luo Y, Safabakhsh S, Palumbo A, Fiset C, Shen C, Parker J, Foster LJ, Laksman Z. Sex-Based Mechanisms of Cardiac Development and Function: Applications for Induced-Pluripotent Stem Cell Derived-Cardiomyocytes. Int J Mol Sci 2024; 25:5964. [PMID: 38892161 PMCID: PMC11172775 DOI: 10.3390/ijms25115964] [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: 05/06/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Males and females exhibit intrinsic differences in the structure and function of the heart, while the prevalence and severity of cardiovascular disease vary in the two sexes. However, the mechanisms of this sex-based dimorphism are yet to be elucidated. Sex chromosomes and sex hormones are the main contributors to sex-based differences in cardiac physiology and pathophysiology. In recent years, the advances in induced pluripotent stem cell-derived cardiac models and multi-omic approaches have enabled a more comprehensive understanding of the sex-specific differences in the human heart. Here, we provide an overview of the roles of these two factors throughout cardiac development and explore the sex hormone signaling pathways involved. We will also discuss how the employment of stem cell-based cardiac models and single-cell RNA sequencing help us further investigate sex differences in healthy and diseased hearts.
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Affiliation(s)
- Yinhan Luo
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; (Y.L.); (J.P.)
| | - Sina Safabakhsh
- Centre for Cardiovascular Innovation, Division of Cardiology, University of British Columbia, Vancouver, BC V6T 2A1, Canada;
| | - Alessia Palumbo
- Michael Smith Laboratories, Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (A.P.); (L.J.F.)
| | - Céline Fiset
- Research Centre, Montreal Heart Institute, Faculty of Pharmacy, Université de Montréal, Montréal, QC H1T 1C8, Canada;
| | - Carol Shen
- Department of Integrated Sciences, University of British Columbia, Vancouver, BC V6T 1Z2, Canada;
| | - Jeremy Parker
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; (Y.L.); (J.P.)
| | - Leonard J. Foster
- Michael Smith Laboratories, Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (A.P.); (L.J.F.)
| | - Zachary Laksman
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; (Y.L.); (J.P.)
- Centre for Cardiovascular Innovation, Division of Cardiology, University of British Columbia, Vancouver, BC V6T 2A1, Canada;
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4
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Wu J, Duan C, Lan L, Chen W, Mao X. Sex Differences in Cochlear Transcriptomes in Horseshoe Bats. Animals (Basel) 2024; 14:1177. [PMID: 38672325 PMCID: PMC11047584 DOI: 10.3390/ani14081177] [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: 02/01/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Sexual dimorphism of calls is common in animals, whereas studies on the molecular basis underlying this phenotypic variation are still scarce. In this study, we used comparative transcriptomics of cochlea to investigate the sex-related difference in gene expression and alternative splicing in four Rhinolophus taxa. Based on 31 cochlear transcriptomes, we performed differential gene expression (DGE) and alternative splicing (AS) analyses between the sexes in each taxon. Consistent with the degree of difference in the echolocation pulse frequency between the sexes across the four taxa, we identified the largest number of differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) in R. sinicus. However, we also detected multiple DEGs and ASGs in taxa without sexual differences in echolocation pulse frequency, suggesting that these genes might be related to other parameters of echolocation pulse rather than the frequency component. Some DEGs and ASGs are related to hearing loss or deafness genes in human or mice and they can be considered to be candidates associated with the sexual differences of echolocation pulse in bats. We also detected more than the expected overlap of DEGs and ASGs in two taxa. Overall, our current study supports the important roles of both DGE and AS in generating or maintaining sexual differences in animals.
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Affiliation(s)
| | | | | | | | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China; (J.W.); (C.D.); (L.L.); (W.C.)
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5
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Wang Y, Sano S. Why Y matters? The implication of loss of Y chromosome in blood and cancer. Cancer Sci 2024; 115:706-714. [PMID: 38258457 PMCID: PMC10921008 DOI: 10.1111/cas.16072] [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: 10/23/2023] [Revised: 12/23/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Hematopoietic mosaic loss of Y chromosome (mLOY) has emerged as a potential male-specific accelerator of biological aging, increasing the risk of various age-related diseases, including cancer. Importantly, mLOY is not confined to hematopoietic cells; its presence has also been observed in nonhematological cancer cells, with the impact of this presence previously unknown. Recent studies have revealed that, whether occurring in leukocytes or cancer cells, mLOY plays a role in promoting the development of an immunosuppressive tumor microenvironment. This occurs through the modulation of tumor-infiltrating immune cells, ultimately enabling cancer cells to evade the vigilant immune system. In this review, we illuminate recent progress concerning the effects of hematopoietic mLOY and cancer mLOY on cancer progression. Examining cancer progression from the perspective of LOY adds a new layer to our understanding of cancer immunity, promising insights that hold the potential to identify innovative and potent immunotherapy targets for cancer.
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Affiliation(s)
- Ying Wang
- Department of CardiologyThe Second Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Soichi Sano
- Laboratory of Cardiovascular MosaicismNational Cerebral and Cardiovascular CenterOsakaJapan
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6
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Vergnes L, Wiese CB, Zore T, Riestenberg C, Avetisyan R, Reue K. Gene Regulation and Mitochondrial Activity During White and Brown Adipogenesis Are Modulated by KDM5 Histone Demethylase. J Endocr Soc 2024; 8:bvae029. [PMID: 38425435 PMCID: PMC10904225 DOI: 10.1210/jendso/bvae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 03/02/2024] Open
Abstract
Body fat accumulation differs between males and females and is influenced by both gonadal sex (ovaries vs testes) and chromosomal sex (XX vs XY). We previously showed that an X chromosome gene, Kdm5c, is expressed at higher levels in females compared to males and correlates with adiposity in mice and humans. Kdm5c encodes a KDM5 histone demethylase that regulates gene expression by modulating histone methylation at gene promoters and enhancers. Here, we use chemical inhibition and genetic knockdown to identify a role for KDM5 activity during early stages of white and brown preadipocyte differentiation, with specific effects on white adipocyte clonal expansion, and white and brown adipocyte gene expression and mitochondrial activity. In white adipogenesis, KDM5 activity modulates H3K4 histone methylation at the Dlk1 gene promoter to repress gene expression and promote progression from preadipocytes to mature adipocytes. In brown adipogenesis, KDM5 activity modulates H3K4 methylation and gene expression of Ucp1, which is required for thermogenesis. Unbiased transcriptome analysis revealed that KDM5 activity regulates genes associated with cell cycle regulation and mitochondrial function, and this was confirmed by functional analyses of cell proliferation and cellular bioenergetics. Using genetic knockdown, we demonstrate that KDM5C is the likely KDM5 family member that is responsible for regulation of white and brown preadipocyte programming. Given that KDM5C levels are higher in females compared to males, our findings suggest that sex differences in white and brown preadipocyte gene regulation may contribute to sex differences in adipose tissue function.
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Affiliation(s)
- Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carrie B Wiese
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Temeka Zore
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carrie Riestenberg
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Rozeta Avetisyan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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7
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Nucera S, Sindoni MM, Bugarin C, Villa T, Biondi A, Balduzzi A, Gaipa G. A novel flow-cytometric based method to assess post-HSCT donor chimerism exploiting RNA hybridization. Bone Marrow Transplant 2024; 59:171-177. [PMID: 37935782 PMCID: PMC10849949 DOI: 10.1038/s41409-023-02143-9] [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: 07/07/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
Analysis of donor-recipient chimerism after hematopoietic stem cell transplantation (HSCT) is of pivotal importance for patient's clinical management, especially in the context of mixed chimerism. Patients are routinely monitored for chimerism in sorted subsets of peripheral blood cells. However, measurement of chimerism in sorted immune cell subsets is technically challenging and time consuming. We here propose a novel, flow cytometry-based approach to detect donor cell chimerism in sex-mismatched HSCT. We exploit RNA PrimeFlow™ system, based on RNA hybridization, to detect mRNA from a lysine demethylase encoded by Y chromosome, KDM5D. This approach allows to distinguish male and female derived cells with around 1% sensitivity. The procedure can be coupled with multiparametric immunophenotyping to assess chimerism in specific immune cell subsets without the need for prior FACS-sorting. We apply this method to a cohort of HSCT patients (n = 10) and we show that it is consistent with standard PCR-based method. We also show that different T lymphocyte subsets display variable degrees of donor chimerism, especially in CD8+ T cell compartment where we observe an enrichment for recipient chimerism in central memory T cells. This method can be exploited to advance current knowledge on immune reconstitution focusing on specific subsets avoiding prior FACS-sorting.
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Affiliation(s)
- Silvia Nucera
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy.
- School of Medicine and Surgery, University of Milano Bicocca, Milan, Italy.
| | - Marco M Sindoni
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milano Bicocca, Milan, Italy
| | - Cristina Bugarin
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Tiziana Villa
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Andrea Biondi
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy.
- School of Medicine and Surgery, University of Milano Bicocca, Milan, Italy.
| | - Adriana Balduzzi
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milano Bicocca, Milan, Italy
| | - Giuseppe Gaipa
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
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8
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. CELL GENOMICS 2024; 4:100462. [PMID: 38190107 PMCID: PMC10794785 DOI: 10.1016/j.xgen.2023.100462] [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: 06/01/2023] [Revised: 08/15/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Alexander K Godfrey
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neha V Bokil
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Shanlee M Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Developmental Pediatrics, eXtraOrdinarY Kids Program, Children's Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA; Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA.
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9
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Lan L, Zhang X, Yang S, Li L, Mao X. Chromosome-level genome assembly of the Stoliczka's Asian trident bat (Aselliscus stoliczkanus). Sci Data 2023; 10:902. [PMID: 38102156 PMCID: PMC10724287 DOI: 10.1038/s41597-023-02838-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
Stoliczka's Asian trident bat (Aselliscus stoliczkanus) is a small-bodied species and very sensitive to climate change. Here, we presented a chromosome-level genome assembly of A. stoliczkanus by combining Illumina sequencing, Nanopore sequencing and high-throughput chromatin conformation capture (Hi-C) sequencing technology. The genome assembly was 2.18 Gb in size with 98.26% of the genome sequences anchored onto 14 autosomes and two sex chromosomes (X and Y). The quality of the genome assembly is very high with a contig and scaffold N50 of 72.98 and 162 Mb, respectively, Benchmarking Universal Single-Copy Orthologs (BUSCO) score of 96.6%, and the consensus quality value (QV) of 47.44. A total of 20,567 genes were predicted and 98.8% of these genes were functionally annotated. Syntenic blocks between A. stoliczkanus and Homo sapiens, together with previous comparative cytogenetic studies, provide valuable foundations for further comparative genomic and cytogenetic studies in mammals. The reference-quality genome of A. stoliczkanus contributes an important resource for conservative genomics and landscape genomics in predicting adaptation and vulnerability to climate change.
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Affiliation(s)
- Linjing Lan
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062, China
| | - Xin Zhang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062, China
| | - Shanxiu Yang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062, China
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062, China.
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10
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Owens MC, Shen H, Yanas A, Mendoza-Figueroa MS, Lavorando E, Wei X, Shweta H, Tang HY, Goldman YE, Liu KF. Mutant forms of DDX3X with diminished catalysis form hollow condensates that exhibit sex-specific regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.533240. [PMID: 38076929 PMCID: PMC10705264 DOI: 10.1101/2023.03.19.533240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Mutations in the RNA helicase DDX3X, implicated in various cancers and neurodevelopmental disorders, often impair RNA unwinding and translation. However, the mechanisms underlying this impairment and the differential interactions of DDX3X mutants with wild-type (WT) X-linked DDX3X and Y-linked homolog DDX3Y remain elusive. This study reveals that specific DDX3X mutants more frequently found in disease form distinct hollow condensates in cells. Using a combined structural, biochemical, and single-molecule microscopy study, we show that reduced ATPase and RNA release activities contribute to condensate formation and the catalytic deficits result from inhibiting the catalytic cycle at multiple steps. Proteomic investigations further demonstrate that these hollow condensates sequester WT DDX3X/DDX3Y and other proteins crucial for diverse signaling pathways. WT DDX3X enhances the dynamics of heterogeneous mutant/WT hollow condensates more effectively than DDX3Y. These findings offer valuable insights into the catalytic defects of specific DDX3X mutants and their differential interactions with wild-type DDX3X and DDX3Y, potentially explaining sex biases in disease.
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11
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Brandt L, Angelino P, Martinez R, Cristinelli S, Ciuffi A. Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro through Cell Activation Dynamics. Cells 2023; 12:2689. [PMID: 38067117 PMCID: PMC10706042 DOI: 10.3390/cells12232689] [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: 10/13/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men's. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers' expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure.
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Affiliation(s)
- Ludivine Brandt
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Paolo Angelino
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
- Translational Data Science (TDS)-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Raquel Martinez
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
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12
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Kabbej N, Ashby FJ, Riva A, Gamlin PD, Mandel RJ, Kunta A, Rouse CJ, Heldermon CD. Sex differences in brain transcriptomes of juvenile Cynomolgus macaques. RESEARCH SQUARE 2023:rs.3.rs-3422091. [PMID: 38045237 PMCID: PMC10690328 DOI: 10.21203/rs.3.rs-3422091/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background: Behavioral, social, and physical characteristics are posited to distinguish the sexes, yet research on transcription-level sexual differences in the brain is limited. Here, we investigated sexually divergent brain transcriptomics in prepubertal cynomolgus macaques, a commonly used surrogate species to humans. Methods: A transcriptomic profile using RNA sequencing was generated for the temporal lobe, ventral midbrain, and cerebellum of 3 female and 3 male cynomolgus macaques previously treated with an Adeno-associated virus vector mix. Statistical analyses to determine differentially expressed protein-coding genes in all three lobes were conducted using DeSeq2 with a false discovery rate corrected P value of .05. Results: We identified target genes in the temporal lobe, ventral midbrain, and cerebellum with functions in translation, immunity, behavior, and neurological disorders that exhibited statistically significant sexually divergent expression. Conclusions: We provide potential mechanistic insights to the epidemiological differences observed between the sexes with regards to mental health and infectious diseases, such as COVID19. Our results provide pre-pubertal information on sexual differences in non-human primate brain transcriptomics and may provide insight to health disparities between the biological sexes in humans.
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13
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Abstract
Unreliable protein-based tools are impeding sex-based research.
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Affiliation(s)
- Bradley D Gelfand
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jayakrishna Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
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14
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Umino K, Morita K, Ikeda T, Kawaguchi SI, Nagayama T, Ito S, Minakata D, Ashizawa M, Yamamoto C, Hatano K, Sato K, Ohmine K, Fujiwara SI, Kimura SI, Kako S, Doki N, Ozawa Y, Mori Y, Eto T, Hiramoto N, Nakamae H, Kanda J, Ichinohe T, Atsuta Y, Nakasone H, Morishima S, Kanda Y. Antibody-mediated pathogenesis of chronic GVHD through DBY/HLA class II complexes and induction of a GVL effect. Blood 2023; 142:1008-1021. [PMID: 37363859 DOI: 10.1182/blood.2023019799] [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: 01/19/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
Chronic graft-versus-host disease (cGVHD) is a multiorgan syndrome with clinical features resembling those of autoimmune diseases. Thus, understanding commonalities in the pathophysiology of cGVHD and autoimmune diseases, such as the presence of disease-risk HLA alleles, is imperative for developing novel therapies against cGVHD. Alloantibodies against H-Y antigens encoded on the Y-chromosome are well-described risk factors for cGVHD in female-to-male transplantation. However, because H-Y antigens generally localize intracellularly in the male reproductive organs, how they emerge at affected organ levels remains elusive. Here, by analyzing nationwide registry data stratified per donor-recipient sex, we identified specific HLA class II alleles that contributed to susceptibility to male cGVHD after transplantation from HLA-identical female siblings (HLA-DRB1∗15:02: hazard ratio, 1.28; 95% confidence interval, 1.03-1.58; P = .025). Coexpression of HLA-DRB1∗15:02 efficiently transported full-length H-Y antigens, especially DBY, to the surface. The presence of alloantibodies against DBY/HLA class II complexes significantly predicted the occurrence of cGVHD (68.8% vs 31.7% at 1 year; P = .002). Notably, the ability of HLA class II molecules to transport and present DBY to alloantibodies was closely associated with the susceptibility of HLA class II alleles to cGVHD. DBY specifically colocalized with HLA class II molecules on the dermal vascular endothelium in cGVHD and provoked complement-dependent cytotoxicity. Moreover, these complexes were observed in some male leukemic cells. Altogether, these findings suggest that vascular endothelial cells facilitate alloantibody-mediated cGVHD and highlight that alloantibodies against DBY/HLA class II complexes could be common targets for cGVHD and a graft-versus-leukemia effect.
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Affiliation(s)
- Kento Umino
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Kaoru Morita
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Takashi Ikeda
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Shin-Ichiro Kawaguchi
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Takashi Nagayama
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Shoko Ito
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Daisuke Minakata
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Masahiro Ashizawa
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Chihiro Yamamoto
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Kaoru Hatano
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Kazuya Sato
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Ken Ohmine
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Shin-Ichiro Fujiwara
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Shun-Ichi Kimura
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Shinichi Kako
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Noriko Doki
- Division of Hematology, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Yukiyasu Ozawa
- Department of Hematology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Japan
| | - Yasuo Mori
- Hematology, Oncology & Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Tetsuya Eto
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Nobuhiro Hiramoto
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Hirohisa Nakamae
- Department of Hematology, Osaka Metropolitan University Hospital, Osaka, Japan
| | - Junya Kanda
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tatsuo Ichinohe
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yoshiko Atsuta
- Japanese Data Center for Hematopoietic Cell Transplantation, Nagakute, Japan
- Department of Registry Science for Transplant and Cellular Therapy, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Hideki Nakasone
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Satoko Morishima
- Division of Endocrinology, Diabetes and Metabolism, Hematology and Rheumatology, Second Department of Internal Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Yoshinobu Kanda
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
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15
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Gadek M, Sherr EH, Floor SN. The variant landscape and function of DDX3X in cancer and neurodevelopmental disorders. Trends Mol Med 2023; 29:726-739. [PMID: 37422363 DOI: 10.1016/j.molmed.2023.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/10/2023]
Abstract
RNA molecules rely on proteins across their life cycle. DDX3X encodes an X-linked DEAD-box RNA helicase with a Y-linked paralog, DDX3Y. DDX3X is central to the RNA life cycle and is implicated in many conditions, including cancer and the neurodevelopmental disorder DDX3X syndrome. DDX3X-linked conditions often exhibit sex differences, possibly due to differences between expression or function of the X- and Y-linked paralogs DDX3X and DDX3Y. DDX3X-related diseases have different mutational landscapes, indicating different roles of DDX3X. Understanding the role of DDX3X in normal and disease states will inform the understanding of DDX3X in disease. We review the function of DDX3X and DDX3Y, discuss how mutation type and sex bias contribute to human diseases involving DDX3X, and review possible DDX3X-targeting treatments.
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Affiliation(s)
- Margaret Gadek
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA.
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16
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Torres EM. Consequences of gaining an extra chromosome. Chromosome Res 2023; 31:24. [PMID: 37620607 PMCID: PMC10449985 DOI: 10.1007/s10577-023-09732-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: 05/11/2023] [Revised: 07/18/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023]
Abstract
Mistakes in chromosome segregation leading to aneuploidy are the primary cause of miscarriages in humans. Excluding sex chromosomes, viable aneuploidies in humans include trisomies of chromosomes 21, 18, or 13, which cause Down, Edwards, or Patau syndromes, respectively. While individuals with trisomy 18 or 13 die soon after birth, people with Down syndrome live to adulthood but have intellectual disabilities and are prone to multiple diseases. At the cellular level, mistakes in the segregation of a single chromosome leading to a cell losing a chromosome are lethal. In contrast, the cell that gains a chromosome can survive. Several studies support the hypothesis that gaining an extra copy of a chromosome causes gene-specific phenotypes and phenotypes independent of the identity of the genes encoded within that chromosome. The latter, referred to as aneuploidy-associated phenotypes, are the focus of this review. Among the conserved aneuploidy-associated phenotypes observed in yeast and human cells are lower viability, increased gene expression, increased protein synthesis and turnover, abnormal nuclear morphology, and altered metabolism. Notably, abnormal nuclear morphology of aneuploid cells is associated with increased metabolic demand for de novo synthesis of sphingolipids. These findings reveal important insights into the possible pathological role of aneuploidy in Down syndrome. Despite the adverse effects on cell physiology, aneuploidy is a hallmark of cancer cells. Understanding how aneuploidy affects cell physiology can reveal insights into the selective pressure that aneuploid cancer cells must overcome to support unlimited proliferation.
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Affiliation(s)
- Eduardo M Torres
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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17
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Kuroki Y, Fukami M. Y Chromosome Genomic Variations and Biological Significance in Human Diseases and Health. Cytogenet Genome Res 2023; 163:5-13. [PMID: 37562362 DOI: 10.1159/000531933] [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: 01/19/2023] [Accepted: 07/10/2023] [Indexed: 08/12/2023] Open
Abstract
The Y chromosome is a haploid genome unique to males with no genes essential for life. It is easily transmitted to the next generation without being repaired by recombination, even if a major genomic structural alteration occurs. On the other hand, the Y chromosome genome is basically a region transmitted only from father to son, reflecting a male-specific inheritance between generations. The Y chromosome exhibits genomic structural differences among different ethnic groups and individuals. The Y chromosome was previously thought to affect only male-specific phenotypes, but recent studies have revealed associations between the Y chromosomes and phenotypes common to both males and females, such as certain types of cancer and neuropsychiatric disorders. This evidence was discovered with the finding of the mosaic loss of the Y chromosome in somatic cells. This phenomenon is also affected by environmental factors, such as smoking and aging. In the past, functional analysis of the Y chromosome has been elucidated by assessing the function of Y chromosome-specific genes and the association between Y chromosome haplogroups and human phenotypes. These studies are currently being conducted intensively. Additionally, the recent advance of large-scale genome cohort studies has increased the amount of Y chromosome genomic information available for analysis, making it possible to conduct more precise studies of the relationship between genome structures and phenotypes. In this review, we will introduce recent analyses using large-scale genome cohort data and previously reported association studies between Y chromosome haplogroups and human phenotypes, such as male infertility, cancer, cardiovascular system traits, and neuropsychiatric disorders. The function and biological role of the Y chromosome in human phenotypes will also be discussed.
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Affiliation(s)
- Yoko Kuroki
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
- Division of Collaborative Research, National Center for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Center for Child Health and Development, Tokyo, Japan
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18
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Schaffer L, Rau S, Clasen L, Warling A, Whitman ET, Nadig A, McDermott C, Xenophontos A, Wilson K, Blumenthal J, Torres E, Raznahan A. X- vs. Y-Chromosome Influences on Human Behavior: A Deep Phenotypic Comparison of Psychopathology in XXY and XYY Syndromes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.19.23291614. [PMID: 37502878 PMCID: PMC10371113 DOI: 10.1101/2023.06.19.23291614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Do different genetic disorders impart different psychiatric risk profiles? This question has major implications for biological and translational aspects of psychiatry, but has been difficult to tackle given limited access to shared batteries of fine-grained clinical data across genetic disorders. Using a new suite of generalizable analytic approaches, we examine gold-standard diagnostic ratings, scores on 66 dimensional measures of psychopathology, and measures of cognition and functioning in two different sex chromosome aneuploidies (SCAs) - Klinefelter (XXY/KS) and XYY syndrome (n=102 and 64 vs. n=74 and 60 matched XY controls, total n=300). We focus on SCAs for their high collective prevalence, informativeness regarding differential X- vs. Y-chromosome effects, and potential relevance for normative sex differences. We show that XXY/KS elevates rates for most psychiatric diagnoses as previously reported for XYY, but disproportionately so for anxiety disorders. Fine-mapping across all 66 traits provides a detailed profile of psychopathology in XXY/KS which is strongly correlated with that of XYY (r=.75 across traits) and robust to ascertainment biases, but reveals: (i) a greater penetrance of XYY than KS/XXY for most traits except mood/anxiety problems, and (ii) a disproportionate impact of XYY vs. XXY/KS on social problems. XXY/KS and XXY showed a similar coupling of psychopathology with adaptive function and caregiver strain, but not IQ. This work provides new tools for deep-phenotypic comparisons of genetic disorders in psychiatry and uses these to detail unique and shared effects of the X- and Y-chromosome on human behavior.
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Affiliation(s)
- Lukas Schaffer
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Srishti Rau
- Center for Autism Spectrum Disorders and Division of Neuropsychology, Children’s National Hospital, Washington DC, USA
| | - Liv Clasen
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Allysa Warling
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Ethan T. Whitman
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Ajay Nadig
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Cassidy McDermott
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Anastasia Xenophontos
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Kathleen Wilson
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Jonathan Blumenthal
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Erin Torres
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
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19
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Qi M, Pang J, Mitsiades I, Lane AA, Rheinbay E. Loss of chromosome Y in primary tumors. Cell 2023; 186:S0092-8674(23)00646-3. [PMID: 37385248 DOI: 10.1016/j.cell.2023.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/17/2023] [Accepted: 06/08/2023] [Indexed: 07/01/2023]
Abstract
Certain cancer types afflict female and male patients disproportionately. The reasons include differences in male/female physiology, effect of sex hormones, risk behavior, environmental exposures, and genetics of the sex chromosomes X and Y. Loss of Y (LOY) is common in peripheral blood cells in aging men, and this phenomenon is associated with several diseases. However, the frequency and role of LOY in tumors is little understood. Here, we present a comprehensive catalog of LOY in >5,000 primary tumors from male patients in the TCGA. We show that LOY rates vary by tumor type and provide evidence for LOY being either a passenger or driver event depending on context. LOY in uveal melanoma specifically is associated with age and survival and is an independent predictor of poor outcome. LOY creates common dependencies on DDX3X and EIF1AX in male cell lines, suggesting that LOY generates unique vulnerabilities that could be therapeutically exploited.
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Affiliation(s)
- Meifang Qi
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiali Pang
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Irene Mitsiades
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Andrew A Lane
- Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Esther Rheinbay
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital Department of Pathology, Boston, MA 02114, USA.
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20
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543763. [PMID: 37333288 PMCID: PMC10274745 DOI: 10.1101/2023.06.05.543763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex-chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors - ZFX and ZFY - encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Alexander K. Godfrey
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Neha V. Bokil
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute; Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892 USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | | | | | - Shanlee M. Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E. Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R. Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Developmental Pediatrics, eXtraOrdinarY Kids Program, Children’s Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA
- Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - David C. Page
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
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21
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Horeth E, Bard J, Che M, Wrynn T, Song E, Marzullo B, Burke M, Popat S, Loree T, Zemer J, Tapia J, Frustino J, Kramer J, Sinha S, Romano R. High-Resolution Transcriptomic Landscape of the Human Submandibular Gland. J Dent Res 2023; 102:525-535. [PMID: 36726292 PMCID: PMC10249006 DOI: 10.1177/00220345221147908] [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] [Indexed: 02/03/2023] Open
Abstract
Saliva-secreting and transporting cells are part of the complex cellular milieu of the human salivary gland, where they play important roles in normal glandular physiology and diseased states. However, comprehensive molecular characterization, particularly at single-cell resolution, is still incomplete, in part due to difficulty in procuring normal human tissues. Here, we perform an in-depth analysis of male and female adult human submandibular gland (SMG) samples by bulk RNA sequencing (RNA-seq) and examine the molecular underpinnings of the heterogeneous cell populations by single-cell (sc) RNA-seq. Our results from scRNA-seq highlight the remarkable diversity of clusters of epithelial and nonepithelial cells that reside in the SMG that is also faithfully recapitulated by deconvolution of the bulk-RNA data sets. Our analyses reveal complex transcriptomic heterogeneity within both the ductal and acinar subpopulations and identify atypical SMG cell types, such as mucoacinar cells that are unique to humans and ionocytes that have been recently described in the mouse. We use CellChat to explore ligand-receptor interactome predictions that likely mediate crucial cell-cell communications between the various cell clusters. Finally, we apply a trajectory inference method to investigate specific cellular branching points and topology that offers insights into the dynamic and complex differentiation process of the adult SMG. The data sets and the analyses herein comprise an extensive wealth of high-resolution information and a valuable resource for a deeper mechanistic understanding of human SMG biology and pathophysiology.
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Affiliation(s)
- E. Horeth
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - J. Bard
- Genomics and Bioinformatics Core, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - M. Che
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - T. Wrynn
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - E.A.C. Song
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - B. Marzullo
- Genomics and Bioinformatics Core, State University of New York at Buffalo, Buffalo, NY, USA
| | - M.S. Burke
- Erie County Medical Center, Department of Head & Neck/Plastic & Reconstructive Surgery, Buffalo, NY, USA
| | - S. Popat
- Erie County Medical Center, Department of Head & Neck/Plastic & Reconstructive Surgery, Buffalo, NY, USA
| | - T. Loree
- Erie County Medical Center, Department of Head & Neck/Plastic & Reconstructive Surgery, Buffalo, NY, USA
| | - J. Zemer
- Erie County Medical Center Division of Oral Oncology & Maxillofacial Prosthetics, Buffalo, NY, USA
| | - J.L. Tapia
- Department of Oral Diagnostic Sciences, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - J. Frustino
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
- Erie County Medical Center Division of Oral Oncology & Maxillofacial Prosthetics, Buffalo, NY, USA
| | - J.M. Kramer
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - S. Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - R.A. Romano
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
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22
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Chen W, Zhou W, Li Q, Mao X. Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat. PeerJ 2023; 11:e15231. [PMID: 37123006 PMCID: PMC10135408 DOI: 10.7717/peerj.15231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Sexually dimorphic traits are common in sexually reproducing organisms and can be encoded by differential gene regulation between males and females. Although alternative splicing is common mechanism in generating transcriptional diversity, its role in generating sex differences relative to differential gene expression is less clear. Here, we investigate the relative roles of differential gene expression and alternative splicing between male and female the horseshoe bat species, Rhinolophus sinicus. Horseshoe bats are an excellent model to study acoustic differences between sexes. Using RNA-seq analyses of two somatic tissues (brain and liver) from males and females of the same population, we identified 3,471 and 2,208 differentially expressed genes between the sexes (DEGs) in the brain and liver, respectively. DEGs were enriched with functional categories associated with physiological difference of the sexes (e.g.,gamete generation and energy production for reproduction in females). In addition, we also detected many differentially spliced genes between the sexes (DSGs, 2,231 and 1,027 in the brain and liver, respectively) which were mainly involved in regulation of RNA splicing and mRNA metabolic process. Interestingly, we found a significant enrichment of DEGs on the X chromosome, but not for DSGs. As for the extent of overlap between the two sets of genes, more than expected overlap of DEGs and DSGs was observed in the brain but not in the liver. This suggests that more complex tissues, such as the brain, may require the intricate and simultaneous interplay of both differential gene expression and splicing of genes to govern sex-specific functions. Overall, our results support that variation in gene expression and alternative splicing are important and complementary mechanisms governing sex differences.
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Affiliation(s)
- Wenli Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Qianqian Li
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
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23
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Nix JL, Schettini GP, Biase FH. Sexing of cattle embryos using RNA-sequencing data or polymerase chain reaction based on a complete sequence of cattle chromosome Y. Front Genet 2023; 14:1038291. [PMID: 37077537 PMCID: PMC10106624 DOI: 10.3389/fgene.2023.1038291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
When necessary, RNA-sequencing data or polymerase chain reaction (PCR) assays can be used to determine the presence of the chromosome Y (ChrY) in samples. This information allows for biological variation due to sexual dimorphism to be studied. A prime example is when researchers conduct RNA-sequencing of single embryos, or conceptuses, prior to the development of gonads. A recent publication of a complete sequence of the ChrY has removed limitations for the development of these procedures in cattle, otherwise imposed by the absence of a ChrY in the reference genome. Using the sequence of the cattle ChrY and transcriptome data, we conducted a systematic search for genes in the ChrY that are exclusively expressed in male tissues. The genes ENSBIXG00000029763, ENSBIXG00000029774, ENSBIXG00000029788, and ENSBIXG00000029892 were consistently expressed across male tissues and lowly expressed or absent in female samples. We observed that the cumulative values of counts per million were 2688-fold greater in males than the equivalent values in female samples. Thus, we deemed these genes suitable for the sexing of samples using RNA-sequencing data. We successfully used this set of genes to infer the sex of 22 cattle blastocysts (8 females and 14 males). Additionally, the completed sequence of the cattle ChrY has segments in the male-specific region that are not repeated. We designed a pair of oligonucleotides that targets one of these non-repeated regions in the male-specific sequence of the ChrY. Using this pair of oligonucleotides, in a multiplexed PCR assay with oligonucleotides that anneal to an autosome chromosome, we accurately identified the sex of cattle blastocysts. We developed efficient procedures for the sexing of samples in cattle using either transcriptome data or their DNA. The procedures using RNA-sequencing will greatly benefit researchers who work with samples limited in cell numbers which are only sufficient to produce transcriptome data. The oligonucleotides used for the accurate sexing of samples using PCR are transferable to other cattle tissue samples.
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24
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Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
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Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
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25
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Escalona M, VanCampen J, Maurer NW, Haukness M, Okhovat M, Harris RS, Watwood A, Hartley GA, O’Neill RJ, Medvedev P, Makova KD, Vollmers C, Carbone L, Green RE. Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J Hered 2023; 114:35-43. [PMID: 36146896 PMCID: PMC10019027 DOI: 10.1093/jhered/esac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/08/2022] [Indexed: 02/04/2023] Open
Abstract
The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.
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Affiliation(s)
- Merly Escalona
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jake VanCampen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - Marina Haukness
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Allison Watwood
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06296, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06296, USA
| | - Rachel J O’Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06296, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06296, USA
| | - Paul Medvedev
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA
- Department of Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
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26
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Arnold AP, Chen X, Grzybowski MN, Ryan JM, Sengelaub DR, Mohanroy T, Furlan VA, Grisham W, Malloy L, Takizawa A, Wiese CB, Vergnes L, Skaletsky H, Page DC, Reue K, Harley VR, Dwinell MR, Geurts AM. A "Four Core Genotypes" rat model to distinguish mechanisms underlying sex-biased phenotypes and diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527738. [PMID: 36798326 PMCID: PMC9934672 DOI: 10.1101/2023.02.09.527738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Background We have generated a rat model similar to the Four Core Genotypes mouse model, allowing comparison of XX and XY rats with the same type of gonad. The model detects novel sex chromosome effects (XX vs. XY) that contribute to sex differences in any rat phenotype. Methods XY rats were produced with an autosomal transgene of Sry , the testis-determining factor gene, which were fathers of XX and XY progeny with testes. In other rats, CRISPR-Cas9 technology was used to remove Y chromosome factors that initiate testis differentiation, producing fertile XY gonadal females that have XX and XY progeny with ovaries. These groups can be compared to detect sex differences caused by sex chromosome complement (XX vs. XY) and/or by gonadal hormones (rats with testes vs. ovaries). Results We have measured numerous phenotypes to characterize this model, including gonadal histology, breeding performance, anogenital distance, levels of reproductive hormones, body and organ weights, and central nervous system sexual dimorphisms. Serum testosterone levels were comparable in adult XX and XY gonadal males. Numerous phenotypes previously found to be sexually differentiated by the action of gonadal hormones were found to be similar in XX and XY rats with the same type of gonad, suggesting that XX and XY rats with the same type of gonad have comparable levels of gonadal hormones at various stages of development. Conclusion The results establish a powerful new model to discriminate sex chromosome and gonadal hormone effects that cause sexual differences in rat physiology and disease.
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27
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The human inactive X chromosome modulates expression of the active X chromosome. CELL GENOMICS 2023; 3:100259. [PMID: 36819663 PMCID: PMC9932992 DOI: 10.1016/j.xgen.2023.100259] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/12/2022] [Accepted: 01/06/2023] [Indexed: 02/11/2023]
Abstract
The "inactive" X chromosome (Xi) has been assumed to have little impact, in trans, on the "active" X (Xa). To test this, we quantified Xi and Xa gene expression in individuals with one Xa and zero to three Xis. Our linear modeling revealed modular Xi and Xa transcriptomes and significant Xi-driven expression changes for 38% (162/423) of expressed X chromosome genes. By integrating allele-specific analyses, we found that modulation of Xa transcript levels by Xi contributes to many of these Xi-driven changes (≥121 genes). By incorporating metrics of evolutionary constraint, we identified 10 X chromosome genes most likely to drive sex differences in common disease and sex chromosome aneuploidy syndromes. We conclude that human X chromosomes are regulated both in cis, through Xi-wide transcriptional attenuation, and in trans, through positive or negative modulation of individual Xa genes by Xi. The sum of these cis and trans effects differs widely among genes.
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28
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Parallel Evolution of Sex-Linked Genes across XX/XY and ZZ/ZW Sex Chromosome Systems in the Frog Glandirana rugosa. Genes (Basel) 2023; 14:genes14020257. [PMID: 36833183 PMCID: PMC9956060 DOI: 10.3390/genes14020257] [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: 12/24/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Genetic sex-determination features male (XX/XY) or female heterogamety (ZZ/ZW). To identify similarities and differences in the molecular evolution of sex-linked genes between these systems, we directly compared the sex chromosome systems existing in the frog Glandirana rugosa. The heteromorphic X/Y and Z/W sex chromosomes were derived from chromosomes 7 (2n = 26). RNA-Seq, de novo assembly, and BLASTP analyses identified 766 sex-linked genes. These genes were classified into three different clusters (XW/YZ, XY/ZW, and XZ/YW) based on sequence identities between the chromosomes, probably reflecting each step of the sex chromosome evolutionary history. The nucleotide substitution per site was significantly higher in the Y- and Z-genes than in the X- and W- genes, indicating male-driven mutation. The ratio of nonsynonymous to synonymous nucleotide substitution rates was higher in the X- and W-genes than in the Y- and Z-genes, with a female bias. Allelic expression in gonad, brain, and muscle was significantly higher in the Y- and W-genes than in the X- and Z-genes, favoring heterogametic sex. The same set of sex-linked genes showed parallel evolution across the two distinct systems. In contrast, the unique genomic region of the sex chromosomes demonstrated a difference between the two systems, with even and extremely high expression ratios of W/Z and Y/X, respectively.
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29
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Pre-T cell receptor self-MHC sampling restricts thymocyte dedifferentiation. Nature 2023; 613:565-574. [PMID: 36410718 PMCID: PMC9851994 DOI: 10.1038/s41586-022-05555-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/11/2022] [Indexed: 11/22/2022]
Abstract
Programming T cells to distinguish self from non-self is a vital, multi-step process that occurs in the thymus1-4. Signalling through the pre-T cell receptor (preTCR), a CD3-associated heterodimer comprising an invariant pTα chain and a clone-specific β chain, is a critical early checkpoint in thymocyte development within the αβ T cell lineage5,6. PreTCRs arrayed on CD4-CD8- double-negative thymocytes ligate peptides bound to major histocompatibility complex molecules (pMHC) on thymic stroma, similar to αβ T cell receptors that appear on CD4+CD8+ double-positive thymocytes, but via a different molecular docking strategy7-10. Here we show the consequences of these distinct interactions for thymocyte progression using synchronized fetal thymic progenitor cultures that differ in the presence or absence of pMHC on support stroma, and single-cell transcriptomes at key thymocyte developmental transitions. Although major histocompatibility complex (MHC)-negative stroma fosters αβ T cell differentiation, the absence of preTCR-pMHC interactions leads to deviant thymocyte transcriptional programming associated with dedifferentiation. Highly proliferative double-negative and double-positive thymocyte subsets emerge, with antecedent characteristics of T cell lymphoblastic and myeloid malignancies. Compensatory upregulation of diverse MHC class Ib proteins in B2m/H2-Ab1 MHC-knockout mice partially safeguards in vivo thymocyte progression, although disseminated double-positive thymic tumours may develop with ageing. Thus, as well as promoting β chain repertoire broadening for subsequent αβ T cell receptor utilization, preTCR-pMHC interactions limit cellular plasticity to facilitate normal thymocyte differentiation and proliferation that, if absent, introduce developmental vulnerabilities.
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30
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Olney KC, Plaisier SB, Phung TN, Silasi M, Perley L, O'Bryan J, Ramirez L, Kliman HJ, Wilson MA. Sex differences in early and term placenta are conserved in adult tissues. Biol Sex Differ 2022; 13:74. [PMID: 36550527 PMCID: PMC9773522 DOI: 10.1186/s13293-022-00470-y] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pregnancy complications vary based on the fetus's genetic sex, which may, in part, be modulated by the placenta. Furthermore, developmental differences early in life can have lifelong health outcomes. Yet, sex differences in gene expression within the placenta at different timepoints throughout pregnancy and comparisons to adult tissues remains poorly characterized. METHODS Here, we collect and characterize sex differences in gene expression in term placentas (≥ 36.6 weeks; 23 male XY and 27 female XX). These are compared with sex differences in previously collected first trimester placenta samples and 42 non-reproductive adult tissues from GTEx. RESULTS We identify 268 and 53 sex-differentially expressed genes in the uncomplicated late first trimester and term placentas, respectively. Of the 53 sex-differentially expressed genes observed in the term placentas, 31 are also sex-differentially expressed genes in the late first trimester placentas. Furthermore, sex differences in gene expression in term placentas are highly correlated with sex differences in the late first trimester placentas. We found that sex-differential gene expression in the term placenta is significantly correlated with sex differences in gene expression in 42 non-reproductive adult tissues (correlation coefficient ranged from 0.892 to 0.957), with the highest correlation in brain tissues. Sex differences in gene expression were largely driven by gene expression on the sex chromosomes. We further show that some gametologous genes (genes with functional copies on X and Y) will have different inferred sex differences if the X-linked gene expression in females is compared to the sum of the X-linked and Y-linked gene expression in males. CONCLUSIONS We find that sex differences in gene expression are conserved in late first trimester and term placentas and that these sex differences are conserved in adult tissues. We demonstrate that there are sex differences associated with innate immune response in late first trimester placentas but there is no significant difference in gene expression of innate immune genes between sexes in healthy full-term placentas. Finally, sex differences are predominantly driven by expression from sex-linked genes.
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Affiliation(s)
- Kimberly C Olney
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Seema B Plaisier
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Tanya N Phung
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Michelle Silasi
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Mercy Hospital St. Louis, St. Louis, MO, 63141, USA
| | - Lauren Perley
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Jane O'Bryan
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Lucia Ramirez
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Harvey J Kliman
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA.
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA.
- The Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85282, USA.
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31
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Gast M, Nageswaran V, Kuss AW, Tzvetkova A, Wang X, Mochmann LH, Rad PR, Weiss S, Simm S, Zeller T, Voelzke H, Hoffmann W, Völker U, Felix SB, Dörr M, Beling A, Skurk C, Leistner DM, Rauch BH, Hirose T, Heidecker B, Klingel K, Nakagawa S, Poller WC, Swirski FK, Haghikia A, Poller W. tRNA-like Transcripts from the NEAT1-MALAT1 Genomic Region Critically Influence Human Innate Immunity and Macrophage Functions. Cells 2022; 11:cells11243970. [PMID: 36552736 PMCID: PMC9777231 DOI: 10.3390/cells11243970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
The evolutionary conserved NEAT1-MALAT1 gene cluster generates large noncoding transcripts remaining nuclear, while tRNA-like transcripts (mascRNA, menRNA) enzymatically generated from these precursors translocate to the cytosol. Whereas functions have been assigned to the nuclear transcripts, data on biological functions of the small cytosolic transcripts are sparse. We previously found NEAT1-/- and MALAT1-/- mice to display massive atherosclerosis and vascular inflammation. Here, employing selective targeted disruption of menRNA or mascRNA, we investigate the tRNA-like molecules as critical components of innate immunity. CRISPR-generated human ΔmascRNA and ΔmenRNA monocytes/macrophages display defective innate immune sensing, loss of cytokine control, imbalance of growth/angiogenic factor expression impacting upon angiogenesis, and altered cell-cell interaction systems. Antiviral response, foam cell formation/oxLDL uptake, and M1/M2 polarization are defective in ΔmascRNA/ΔmenRNA macrophages, defining first biological functions of menRNA and describing new functions of mascRNA. menRNA and mascRNA represent novel components of innate immunity arising from the noncoding genome. They appear as prototypes of a new class of noncoding RNAs distinct from others (miRNAs, siRNAs) by biosynthetic pathway and intracellular kinetics. Their NEAT1-MALAT1 region of origin appears as archetype of a functionally highly integrated RNA processing system.
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Affiliation(s)
- Martina Gast
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
| | - Vanasa Nageswaran
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 12200 Berlin, Germany
| | - Andreas W Kuss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Ana Tzvetkova
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Xiaomin Wang
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Liliana H Mochmann
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Pegah Ramezani Rad
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Tanja Zeller
- University Center of Cardiovascular Science, University Heart and Vascular Center, 20246 Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, 20246 Hamburg, Germany
| | - Henry Voelzke
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Wolfgang Hoffmann
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
| | - Stefan B Felix
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Department of Cardiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Marcus Dörr
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Department of Cardiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Antje Beling
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Institute for Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10178 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Carsten Skurk
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
| | - David-Manuel Leistner
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Bernhard H Rauch
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Pharmacology, University Medicine Greifswald, 17487 Greifswald, Germany
- Department Human Medicine, Section Pharmacology and Toxicology, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Bettina Heidecker
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Karin Klingel
- Institute for Pathology and Neuropathology, Department of Pathology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Wolfram C Poller
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Filip K Swirski
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arash Haghikia
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany
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Grenn FP, Makarious MB, Bandres-Ciga S, Iwaki H, Singleton AB, Nalls MA, Blauwendraat C. Analysis of Y chromosome haplogroups in Parkinson's disease. Brain Commun 2022; 4:fcac277. [PMID: 36387750 PMCID: PMC9665271 DOI: 10.1093/braincomms/fcac277] [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: 03/03/2022] [Revised: 07/01/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson's disease is a complex neurodegenerative disorder that is about 1.5 times more prevalent in males than females. Extensive work has been done to identify the genetic risk factors behind Parkinson's disease on autosomes and more recently on Chromosome X, but work remains to be done on the male-specific Y chromosome. In an effort to explore the role of the Y chromosome in Parkinson's disease, we analysed whole-genome sequencing data from the Accelerating Medicines Partnership-Parkinson's disease initiative (1466 cases and 1664 controls), genotype data from NeuroX (3491 cases and 3232 controls) and genotype data from UKBiobank (182 517 controls, 1892 cases and 3783 proxy cases), all consisting of male European ancestry samples. We classified sample Y chromosomes by haplogroup using three different tools for comparison (Snappy, Yhaplo and Y-LineageTracker) and meta-analysed this data to identify haplogroups associated with Parkinson's disease. This was followed up with a Y-chromosome association study to identify specific variants associated with disease. We also analysed blood-based RNASeq data obtained from the Accelerating Medicines Partnership-Parkinson's disease initiative (1020 samples) and RNASeq data obtained from the North American Brain Expression Consortium (171 samples) to identify Y-chromosome genes differentially expressed in cases, controls, specific haplogroups and specific tissues. RNASeq analyses suggest Y-chromosome gene expression differs between brain and blood tissues but does not differ significantly in cases, controls or specific haplogroups. Overall, we did not find any strong associations between Y-chromosome genetics and Parkinson's disease, suggesting the explanation for the increased prevalence in males may lie elsewhere.
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Affiliation(s)
- Francis P Grenn
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mary B Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hirotaka Iwaki
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mike A Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Sakka R, Abdelhedi F, Sellami H, Pichon B, Lajmi Y, Mnif M, Kebaili S, Derbel R, Kamoun H, Gdoura R, Delbaere A, Desir J, Abramowicz M, Vialard F, Dupont JM, Ammar-Keskes L. An unusual familial Xp22.12 microduplication including EIF1AX: A novel candidate dosage-sensitive gene for premature ovarian insufficiency. Eur J Med Genet 2022; 65:104613. [PMID: 36113757 DOI: 10.1016/j.ejmg.2022.104613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 07/22/2022] [Accepted: 09/09/2022] [Indexed: 11/19/2022]
Abstract
We report on the results of array-CGH and Whole exome sequencing (WES) studies carried out in a Tunisian family with 46,XX premature ovarian insufficiency (POI). This study has led to the identification of a familial Xp22.12 tandem duplication with a size of 559.4 kb, encompassing only three OMIM genes (RPS6KA3, SH3KBP1and EIF1AX), and a new heterozygous variant in SPIDR gene: NM_001080394.3:c.1845_1853delTATAATTGA (p.Ile616_Asp618del) segregating with POI. Increased mRNA expression levels were detected for SH3KBP1 and EIF1AX, while a normal transcript level for RPS6KA3 was detected in the three affected family members, explaining the absence of intellectual disability (ID). To the best of our knowledge, this is the first duplication involving the Xp22.12 region, reported in a family without ID, but rather with secondary amenorrhea (SA) and female infertility. As EIF1AX is a regulatory gene escaping X-inactivation, which has an extreme dosage sensitivity and highly expressed in the ovary, we suggest that this gene might be a candidate gene for ovarian function. Homozygous nonsense pathogenic variants of SPIDR gene have been reported in familial cases in POI. It has been suggested that chromosomal instability associated with SPIDR molecular defects supports the role of SPIDR protein in double-stranded DNA damage repair in vivo in humans and its causal role in POI. In this family, the variant (p.Ile616_Asp618del), present in a heterozygous state, is located in the domain that interacts with BLM and might disrupt the BLM binding ability of SPIDR protein. These findings strengthen the hypothesis that the additional effect of this variant could lead to POI in this family. Although the work represents the first evidence that EIF1AX duplication might be responsible for POI through its over-expression, further functional studies are needed to clarify and prove EIF1AX involvement in POI phenotype.
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Affiliation(s)
- Rim Sakka
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia; Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Fatma Abdelhedi
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia; Medical Genetics Department, Hedi Chaker Hospital, Sfax, Tunisia.
| | - Hanen Sellami
- Water Researches and Technologies Center (CERTE), University of Carthage, Tourist Road Soliman, Nabeul, Tunisia; Toxicology, Environmental Microbiology and Health Research Laboratory (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Bruno Pichon
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Yosra Lajmi
- Cytogenetics Department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris, Sorbonne Paris Cité, Paris Descartes University, Medical School, Paris, France
| | - Mouna Mnif
- Department of Endocrinology, Hedi Chaker Hospital, Sfax, Tunisia
| | - Sahbi Kebaili
- Department of Gynecology, HediChaker Hospital, Sfax, Tunisia
| | - Rihab Derbel
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetics Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Radhouane Gdoura
- Toxicology, Environmental Microbiology and Health Research Laboratory (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Anne Delbaere
- Fertility Clinic, Department of Gynecology and Obstetrics, Erasme Hospital, UniversitéLibre de Bruxelles, Brussels, Belgium
| | - Julie Desir
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Marc Abramowicz
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - François Vialard
- Genetics Department, CHI Poissy St Germain-en-Laye, F-78300, Poissy, France; RHuMA Team, UMR-BREED, INRAE-UVSQ-ENVA, UFR-SVS, F-78180, Montigny le Bretonneux, France
| | - Jean-Michel Dupont
- Cytogenetics Department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris, Sorbonne Paris Cité, Paris Descartes University, Medical School, Paris, France
| | - Leila Ammar-Keskes
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia
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Abstract
Understanding sex differences in physiology and disease requires the identification of the molecular agents that cause phenotypic sex differences. Two groups of such agents are genes located on the sex chromosomes, and gonadal hormones. The former have coherent linkage to chromosomes that form differently in the two sexes under the influence of genomic forces that are not related to reproductive function, whereas the latter have a direct or indirect relationship to reproduction. Evidence published in the past 5 years supports the identification of several agents of sexual differentiation encoded by the X chromosome in mice, including Kdm5c, Kdm6a, Ogt and Xist. These X chromosome agents have wide pleiotropic effects, potentially influencing sex differences in many different tissues, a characteristic shared with the gonadal hormones. The identification of X chromosome agents of sexual differentiation will facilitate understanding of complex intersecting gene pathways underlying sex differences in disease.
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Affiliation(s)
- Arthur P Arnold
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
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Linsky JMJ, Dunlop RA, Noad MJ, McMichael LA. A mammalian messenger RNA sex determination method from humpback whale ( Megaptera novaeangliae) blubber biopsies. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220556. [PMID: 36016912 PMCID: PMC9399696 DOI: 10.1098/rsos.220556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The large size of free-ranging mysticetes, such as humpback whales (Megaptera novaeangliae), make capture and release health assessments unfeasible for conservation research. However, individual energetic condition or reproductive health may be assessed from the gene expression of remotely biopsied tissue. To do this, researchers must reliably extract RNA and interpret gene expression measurements within the context of an individual's sex. Here, we outline an RNA extraction protocol from blubber tissue and describe a novel mammalian RNA sex determination method. Our method consists of a duplex reverse transcription-quantitative (real-time) polymerase chain reaction (RT-qPCR) with primer sets for a control gene (ACTB) and the X-chromosome inactivation gene (XIST). Products of each RT-qPCR had distinct melting temperature profiles based on the presence (female) or absence (male) of the XIST transcript. Using high-resolution melt analysis, reactions were sorted into one of two clusters (male/female) based on their melting profiles. We validated the XIST method by comparing results with a standard DNA-based method. With adequate quantities of RNA (minimum of approx. 9 ng µl-1), the XIST sex determination method shows 100% agreement with traditional DNA sex determination. Using the XIST method, future cetacean health studies can interpret gene expression within the context of an individual's sex, all from a single extraction.
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Affiliation(s)
- Jacob M. J. Linsky
- School of Biological Sciences The University of Queensland, St Lucia, Queensland 4072, Australia
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Rebecca A. Dunlop
- School of Biological Sciences The University of Queensland, St Lucia, Queensland 4072, Australia
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Michael J. Noad
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
| | - Lee A. McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
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36
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Shen H, Yanas A, Owens MC, Zhang C, Fritsch C, Fare CM, Copley KE, Shorter J, Goldman YE, Liu KF. Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation. Mol Cell 2022; 82:2588-2603.e9. [PMID: 35588748 PMCID: PMC9308757 DOI: 10.1016/j.molcel.2022.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/09/2022] [Accepted: 04/19/2022] [Indexed: 02/05/2023]
Abstract
Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs remains elusive. Herein, using ensemble and single-molecule techniques, we report that the sex chromosome-encoded RNA helicases DDX3X and DDX3Y are distinct in their propensities for liquid-liquid phase separation (LLPS), dissolution, and translation repression. We demonstrate that the N-terminal intrinsically disordered region of DDX3Y more strongly promotes LLPS than the corresponding region of DDX3X and that the weaker ATPase activity of DDX3Y, compared with DDX3X, contributes to the slower disassembly dynamics of DDX3Y-positive condensates. Interestingly, DDX3Y-dependent LLPS represses mRNA translation and enhances aggregation of FUS more strongly than DDX3X-dependent LLPS. Our study provides a platform for future comparisons of sex chromosome-encoded protein homologs, providing insights into sex differences in RNA metabolism and human disease.
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Affiliation(s)
- Hui Shen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amber Yanas
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Owens
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Celia Zhang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clark Fritsch
- Graduate Group in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yale E Goldman
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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37
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The evolution of gene regulation on sex chromosomes. Trends Genet 2022; 38:844-855. [DOI: 10.1016/j.tig.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022]
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38
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Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
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Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
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39
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Okwuosa TM, Zaha VG. Sex Differences in Cardio-Oncology: Considerations for the Practicing Clinician and Researcher. Circulation 2022; 145:510-512. [PMID: 35157522 DOI: 10.1161/circulationaha.122.058906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Tochukwu M Okwuosa
- Department of Internal Medicine, Division of Cardiovascular Medicine, Rush University Medical Center, Chicago, IL (T.M.)
| | - Vlad G Zaha
- Department of Internal Medicine, Cardiology Division, Cardio-Oncology Program, Harold C. Simmons Comprehensive Cancer Center, and Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas (V.G.Z).,Parkland Health and Hospital System, Dallas, TX (V.G.Z)
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Maggi A. Sex and Liver Disease: The Necessity of an Overarching Theory to Explain the Effect of Sex on Nonreproductive Functions. Endocrinology 2022; 163:6425114. [PMID: 34758075 PMCID: PMC8826248 DOI: 10.1210/endocr/bqab229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 11/19/2022]
Abstract
The number of studies illuminating major sex differences in liver metabolic activities is growing, but we still lack a theory to explain the origin of the functional differences we are identifying. In the animal kingdom, energy metabolism is tightly associated with reproduction; conceivably, the major evolutionary step that occurred about 200 million years ago with placentation determined a significant change in female physiology, as females had to create new energy strategies to allow the growth of the embryo in the womb and the lactation of the newborn. In vertebrates the liver is the metabolic organ most tuned to gonadal functions because the liver synthesizes and transports of all the components necessary for the maturation of the egg upon estrogenic stimulation. Thus, in mammals, evolution must have worked on the already strict gonad-liver relationship fostering these novel reproductive needs. As a consequence, the functions of mammalian liver in females diverged from that in males to acquire the flexibility necessary to tailor metabolism according to reproductive status and to ensure the parsimonious exploitation and storage of energy for the continuation of gestation in case of food scarcity. Indeed, several studies show that male and female livers adopt very different strategies when confronted with nutritional stress of varied origins. Considering the role of liver and energy metabolism in most pathologies, a better focus on liver functions in the 2 sexes might be of considerable help in personalizing medicine and pharmacology for male and female needs.
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Affiliation(s)
- Adriana Maggi
- Correspondence: Adriana Maggi, PhD, Department of Pharmaceutical Sciences, University of Milan, Via Balzaretti 9, 20219 Milan, Italy.
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41
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Venkataramanan S, Gadek M, Calviello L, Wilkins K, Floor SN. DDX3X and DDX3Y are redundant in protein synthesis. RNA (NEW YORK, N.Y.) 2021; 27:1577-1588. [PMID: 34535544 PMCID: PMC8594478 DOI: 10.1261/rna.078926.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
DDX3 is a DEAD-box RNA helicase that regulates translation and is encoded by the X- and Y-linked paralogs DDX3X and DDX3Y While DDX3X is ubiquitously expressed in human tissues and essential for viability, DDX3Y is male-specific and shows lower and more variable expression than DDX3X in somatic tissues. Heterozygous genetic lesions in DDX3X mediate a class of developmental disorders called DDX3X syndrome, while loss of DDX3Y is implicated in male infertility. One possible explanation for female-bias in DDX3X syndrome is that DDX3Y encodes a polypeptide with different biochemical activity. In this study, we use ribosome profiling and in vitro translation to demonstrate that the X- and Y-linked paralogs of DDX3 play functionally redundant roles in translation. We find that transcripts that are sensitive to DDX3X depletion or mutation are rescued by complementation with DDX3Y. Our data indicate that DDX3X and DDX3Y proteins can functionally complement each other in the context of mRNA translation in human cells. DDX3Y is not expressed in a large fraction of the central nervous system. These findings suggest that expression differences, not differences in paralog-dependent protein synthesis, underlie the sex-bias of DDX3X-associated diseases.
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Affiliation(s)
- Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Margaret Gadek
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kevin Wilkins
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143, USA
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42
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Lock R, Al Asafen H, Fleischer S, Tamargo M, Zhao Y, Radisic M, Vunjak-Novakovic G. A framework for developing sex-specific engineered heart models. NATURE REVIEWS. MATERIALS 2021; 7:295-313. [PMID: 34691764 PMCID: PMC8527305 DOI: 10.1038/s41578-021-00381-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 05/02/2023]
Abstract
The convergence of tissue engineering and patient-specific stem cell biology has enabled the engineering of in vitro tissue models that allow the study of patient-tailored treatment modalities. However, sex-related disparities in health and disease, from systemic hormonal influences to cellular-level differences, are often overlooked in stem cell biology, tissue engineering and preclinical screening. The cardiovascular system, in particular, shows considerable sex-related differences, which need to be considered in cardiac tissue engineering. In this Review, we analyse sex-related properties of the heart muscle in the context of health and disease, and discuss a framework for including sex-based differences in human cardiac tissue engineering. We highlight how sex-based features can be implemented at the cellular and tissue levels, and how sex-specific cardiac models could advance the study of cardiovascular diseases. Finally, we define design criteria for sex-specific cardiac tissue engineering and provide an outlook to future research possibilities beyond the cardiovascular system.
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Affiliation(s)
- Roberta Lock
- Department of Biomedical Engineering, Columbia University, New York, NY USA
| | - Hadel Al Asafen
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario Canada
| | - Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY USA
| | - Manuel Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY USA
| | - Yimu Zhao
- Department of Biomedical Engineering, Columbia University, New York, NY USA
| | - Milica Radisic
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario Canada
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY USA
- Department of Medicine, Columbia University, New York, NY USA
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43
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Subrini J, Turner J. Y chromosome functions in mammalian spermatogenesis. eLife 2021; 10:67345. [PMID: 34606444 PMCID: PMC8489898 DOI: 10.7554/elife.67345] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
The mammalian Y chromosome is critical for male sex determination and spermatogenesis. However, linking each Y gene to specific aspects of male reproduction has been challenging. As the Y chromosome is notoriously hard to sequence and target, functional studies have mostly relied on transgene-rescue approaches using mouse models with large multi-gene deletions. These experimental limitations have oriented the field toward the search for a minimum set of Y genes necessary for male reproduction. Here, considering Y-chromosome evolutionary history and decades of discoveries, we review the current state of research on its function in spermatogenesis and reassess the view that many Y genes are disposable for male reproduction.
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Affiliation(s)
- Jeremie Subrini
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - James Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
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Jackson EK, Bellott DW, Cho TJ, Skaletsky H, Hughes JF, Pyntikova T, Page DC. Large palindromes on the primate X Chromosome are preserved by natural selection. Genome Res 2021; 31:1337-1352. [PMID: 34290043 PMCID: PMC8327919 DOI: 10.1101/gr.275188.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/17/2021] [Indexed: 12/27/2022]
Abstract
Mammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples of sex-chromosome palindromes conserved between species. We identified 26 palindromes on the human X Chromosome, constituting more than 2% of its sequence, and characterized orthologous palindromes in the chimpanzee and the rhesus macaque using a clone-based sequencing approach that incorporates full-length nanopore reads. Many of these palindromes are missing or misassembled in the current reference assemblies of these species' genomes. We find that 12 human X palindromes have been conserved for at least 25 million years, with orthologs in both chimpanzee and rhesus macaque. Insertions and deletions between species are significantly depleted within the X palindromes' protein-coding genes compared to their noncoding sequence, demonstrating that natural selection has preserved these gene families. The spacers that separate the left and right arms of palindromes are a site of localized structural instability, with seven of 12 conserved palindromes showing no spacer orthology between human and rhesus macaque. Analysis of the 1000 Genomes Project data set revealed that human X-palindrome spacers are enriched for deletions relative to arms and flanking sequence, including a common spacer deletion that affects 13% of human X Chromosomes. This work reveals an abundance of conserved palindromes on primate X Chromosomes and suggests that protein-coding gene families in palindromes (most of which remain poorly characterized) promote X-palindrome survival in the face of ongoing structural instability.
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Affiliation(s)
- Emily K Jackson
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | | | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Balaton BP, Brown CJ. Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation. Epigenetics Chromatin 2021; 14:30. [PMID: 34187555 PMCID: PMC8244145 DOI: 10.1186/s13072-021-00404-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/17/2021] [Indexed: 01/26/2023] Open
Abstract
Background X-chromosome inactivation (XCI) is the epigenetic inactivation of one of two X chromosomes in XX eutherian mammals. The inactive X chromosome is the result of multiple silencing pathways that act in concert to deposit chromatin changes, including DNA methylation and histone modifications. Yet over 15% of genes escape or variably escape from inactivation and continue to be expressed from the otherwise inactive X chromosome. To the extent that they have been studied, epigenetic marks correlate with this expression. Results Using publicly available data, we compared XCI status calls with DNA methylation, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3. At genes subject to XCI we found heterochromatic marks enriched, and euchromatic marks depleted on the inactive X when compared to the active X. Genes escaping XCI were more similar between the active and inactive X. Using sample-specific XCI status calls, we found some marks differed significantly with variable XCI status, but which marks were significant was not consistent between genes. A model trained to predict XCI status from these epigenetic marks obtained over 75% accuracy for genes escaping and over 90% for genes subject to XCI. This model made novel XCI status calls for genes without allelic differences or CpG islands required for other methods. Examining these calls across a domain of variably escaping genes, we saw XCI status vary across individual genes rather than at the domain level. Lastly, we compared XCI status calls to genetic polymorphisms, finding multiple loci associated with XCI status changes at variably escaping genes, but none individually sufficient to induce an XCI status change. Conclusion The control of expression from the inactive X chromosome is multifaceted, but ultimately regulated at the individual gene level with detectable but limited impact of distant polymorphisms. On the inactive X, at silenced genes euchromatic marks are depleted while heterochromatic marks are enriched. Genes escaping inactivation show a less significant enrichment of heterochromatic marks and depletion of H3K27ac. Combining all examined marks improved XCI status prediction, particularly for genes without CpG islands or polymorphisms, as no single feature is a consistent feature of silenced or expressed genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00404-9.
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Affiliation(s)
- Bradley P Balaton
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada.
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Wang J, Lan Y, He L, Tang R, Li Y, Huang Y, Liang S, Gao Z, Price M, Yue B, He M, Guo T, Fan Z. Sex-specific gene expression in the blood of four primates. Genomics 2021; 113:2605-2613. [PMID: 34116169 DOI: 10.1016/j.ygeno.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/03/2021] [Accepted: 06/06/2021] [Indexed: 10/21/2022]
Abstract
Blood is an important non-reproductive tissue, but little is known about the sex-specific gene expressions in the blood. Therefore, we investigated sex-specific gene expression differences in the blood tissues of four primates, rhesus macaques (Macaca mulatta), Tibetan macaques (M. thibetana), yellow baboons (Papio cynocephalus), and humans. We identified seven sex-specific differentially expressed genes (SDEGs) in each non-human primate and 31 SDEGs in humans. The four primates had only one common SDEG, MAP7D2. In humans, immune-related SDEGs were identified as up-regulated, but also down-regulated in females. We also found that most of the X-Y gene pairs had similar expression levels between species, except pair EIF1AY/EIF1AX. The expression level of X-Y gene pairs of rhesus and Tibetan macaques showed no significant differential expression levels, while humans had six significant XY-biased and three XX-biased X-Y gene pairs. Our observed sex differences in blood should increase understanding of sex differences in primate blood tissue.
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Affiliation(s)
- Jiao Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yue Lan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Lewei He
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ruixiang Tang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Yuhui Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Yuan Huang
- Medical Laboratory Department of West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Shan Liang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Zhan Gao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China.
| | - Tao Guo
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
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Vogt PH, Bender U, Deibel B, Kiesewetter F, Zimmer J, Strowitzki T. Human AZFb deletions cause distinct testicular pathologies depending on their extensions in Yq11 and the Y haplogroup: new cases and review of literature. Cell Biosci 2021; 11:60. [PMID: 33766143 PMCID: PMC7995748 DOI: 10.1186/s13578-021-00551-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/06/2021] [Indexed: 02/07/2023] Open
Abstract
Genomic AZFb deletions in Yq11 coined “classical” (i.e. length of Y DNA deletion: 6.23 Mb) are associated with meiotic arrest (MA) of patient spermatogenesis, i.e., absence of any postmeiotic germ cells. These AZFb deletions are caused by non-allelic homologous recombination (NAHR) events between identical sequence blocks located in the proximal arm of the P5 palindrome and within P1.2, a 92 kb long sequence block located in the P1 palindrome structure of AZFc in Yq11. This large genomic Y region includes deletion of 6 protein encoding Y genes, EIFA1Y, HSFY, PRY, RBMY1, RPS4Y, SMCY. Additionally, one copy of CDY2 and XKRY located in the proximal P5 palindrome and one copy of BPY1, two copies of DAZ located in the P2 palindrome, and one copy of CDY1 located proximal to P1.2 are included within this AZFb microdeletion. It overlaps thus distally along 2.3 Mb with the proximal part of the genomic AZFc deletion. However, AZFb deletions have been also reported with distinct break sites in the proximal and/or distal AZFb breakpoint intervals on the Y chromosome of infertile men. These so called “non-classical” AZFb deletions are associated with variable testicular pathologies, including meiotic arrest, cryptozoospermia, severe oligozoospermia, or oligoasthenoteratozoospermia (OAT syndrome), respectively. This raised the question whether there are any specific length(s) of the AZFb deletion interval along Yq11 required to cause meiotic arrest of the patient’s spermatogenesis, respectively, whether there is any single AZFb Y gene deletion also able to cause this “classical” AZFb testicular pathology? Review of the literature and more cases with “classical” and “non-classical” AZFb deletions analysed in our lab since the last 20 years suggests that the composition of the genomic Y sequence in AZFb is variable in men with distinct Y haplogroups especially in the distal AZFb region overlapping with the proximal AZFc deletion interval and that its extension can be “polymorphic” in the P3 palindrome. That means this AZFb subinterval can be rearranged or deleted also on the Y chromosome of fertile men. Any AZFb deletion observed in infertile men with azoospermia should therefore be confirmed as “de novo” mutation event, i.e., not present on the Y chromosome of the patient’s father or fertile brother before it is considered as causative agent for man’s infertility. Moreover, its molecular length in Yq11 should be comparable to that of the “classical” AZFb deletion, before meiotic arrest is prognosed as the patient’s testicular pathology.
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Affiliation(s)
- P H Vogt
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany.
| | - U Bender
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - B Deibel
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - F Kiesewetter
- Department of Andrology, University Clinic of Dermatology, Erlangen, Germany
| | - J Zimmer
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - T Strowitzki
- Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Heidelberg, Germany
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Martínez-Pacheco M, Tenorio M, Almonte L, Fajardo V, Godínez A, Fernández D, Cornejo-Páramo P, Díaz-Barba K, Halbert J, Liechti A, Székely T, Urrutia AO, Cortez D. Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals. Genome Biol Evol 2020; 12:2015-2028. [PMID: 32790864 PMCID: PMC7674692 DOI: 10.1093/gbe/evaa173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.
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Affiliation(s)
| | | | - Laura Almonte
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | - Alan Godínez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | | | | | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Tamas Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom.,Ecology Institute, UNAM, Mexico
| | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
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