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Kita K, Morkos C, Nolan K. Maintenance of stem cell self-renewal by sex chromosomal zinc-finger transcription factors. World J Methodol 2024; 14:97664. [DOI: 10.5662/wjm.v14.i4.97664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 07/26/2024] Open
Abstract
In this Editorial review, we would like to focus on a very recent discovery showing the global autosomal gene regulation by Y- and inactivated X-chromosomal transcription factors, zinc finger gene on the Y chromosome (ZFY) and zinc finger protein X-linked (ZFX). ZFX and ZFY are both zinc-finger proteins that encode general transcription factors abundant in hematopoietic and embryonic stem cells. Although both proteins are homologs, interestingly, the regulation of self-renewal by these transcriptional factors is almost exclusive to ZFX. This fact implies that there are some differential roles between ZFX and ZFY in regulating the maintenance of self-renewal activity in stem cells. Besides the maintenance of stemness, ZFX overexpression or mutations may be linked to certain cancers. Although cancers and stem cells are double-edged swords, there is no study showing the link between ZFX activity and the telomere. Thus, stemness or cancers with ZFX may be linked to other molecules, such as Oct4, Sox2, Klf4, and others. Based on very recent studies and a few lines of evidence in the past decade, it appears that the ZFX is linked to the canonical Wnt signaling, which is one possible mechanism to explain the role of ZFX in the self-renewal of stem cells.
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Affiliation(s)
- Katsuhiro Kita
- Department of Biology, St. Francis College, Brooklyn, NY 11201, United States
| | - Celine Morkos
- Department of Biology, St. Francis College, Brooklyn, NY 11201, United States
| | - Kathleen Nolan
- Department of Biology, St. Francis College, Brooklyn, NY 11201, United States
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2
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Pavlinek A, Adhya D, Tsompanidis A, Warrier V, Vernon AC, Lancaster M, Mill J, Srivastava DP, Baron-Cohen S. Using Organoids to Model Sex Differences in the Human Brain. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100343. [PMID: 39092139 PMCID: PMC11292257 DOI: 10.1016/j.bpsgos.2024.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 08/04/2024] Open
Abstract
Sex differences are widespread during neurodevelopment and play a role in neuropsychiatric conditions such as autism, which is more prevalent in males than females. In humans, males have been shown to have larger brain volumes than females with development of the hippocampus and amygdala showing prominent sex differences. Mechanistically, sex steroids and sex chromosomes drive these differences in brain development, which seem to peak during prenatal and pubertal stages. Animal models have played a crucial role in understanding sex differences, but the study of human sex differences requires an experimental model that can recapitulate complex genetic traits. To fill this gap, human induced pluripotent stem cell-derived brain organoids are now being used to study how complex genetic traits influence prenatal brain development. For example, brain organoids from individuals with autism and individuals with X chromosome-linked Rett syndrome and fragile X syndrome have revealed prenatal differences in cell proliferation, a measure of brain volume differences, and excitatory-inhibitory imbalances. Brain organoids have also revealed increased neurogenesis of excitatory neurons due to androgens. However, despite growing interest in using brain organoids, several key challenges remain that affect its validity as a model system. In this review, we discuss how sex steroids and the sex chromosomes each contribute to sex differences in brain development. Then, we examine the role of X chromosome inactivation as a factor that drives sex differences. Finally, we discuss the combined challenges of modeling X chromosome inactivation and limitations of brain organoids that need to be taken into consideration when studying sex differences.
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Affiliation(s)
- Adam Pavlinek
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Dwaipayan Adhya
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Alex Tsompanidis
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Anthony C. Vernon
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | | | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Deepak P. Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
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Rengarajan S, Derks J, Bellott DW, Slavov N, Page DC. Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602613. [PMID: 39026797 PMCID: PMC11257633 DOI: 10.1101/2024.07.08.602613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The Y-linked gene DDX3Y and its X-linked homolog DDX3X survived the evolution of the human sex chromosomes from ordinary autosomes. DDX3X encodes a multi-functional RNA helicase, with mutations causing developmental disorders and cancers. We find that, among X-linked genes with surviving Y homologs, DDX3X is extraordinarily dosage-sensitive. Studying cells of individuals with sex chromosome aneuploidy, we observe that when the number of Y chromosomes increases, DDX3X transcript levels fall; conversely, when the number of X chromosomes increases, DDX3Y transcript levels fall. In 46,XY cells, CRISPRi knockdown of either DDX3X or DDX3Y causes transcript levels of the homologous gene to rise. In 46,XX cells, chemical inhibition of DDX3X protein activity elicits an increase in DDX3X transcript levels. Thus, perturbation of either DDX3X or DDX3Y expression is buffered - by negative cross-regulation of DDX3X and DDX3Y in 46,XY cells, and by negative auto-regulation of DDX3X in 46,XX cells. DDX3X-DDX3Y cross-regulation is mediated through mRNA destabilization - as shown by metabolic labeling of newly transcribed RNA - and buffers total levels of DDX3X and DDX3Y protein in human cells. We infer that post-transcriptional auto-regulation of the ancestral (autosomal) DDX3 gene transmuted into auto- and cross-regulation of DDX3X and DDX3Y as these sex-linked genes evolved from ordinary alleles of their autosomal precursor.
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Affiliation(s)
- Shruthi Rengarajan
- Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jason Derks
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | | | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, 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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4
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Bansal P, Banda EC, Glatt-Deeley HR, Stoddard CE, Linsley JW, Arora N, Deleschaux C, Ahern DT, Kondaveeti Y, Massey RE, Nicouleau M, Wang S, Sabariego-Navarro M, Dierssen M, Finkbeiner S, Pinter SF. A dynamic in vitro model of Down syndrome neurogenesis with trisomy 21 gene dosage correction. SCIENCE ADVANCES 2024; 10:eadj0385. [PMID: 38848354 PMCID: PMC11160455 DOI: 10.1126/sciadv.adj0385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Excess gene dosage from chromosome 21 (chr21) causes Down syndrome (DS), spanning developmental and acute phenotypes in terminal cell types. Which phenotypes remain amenable to intervention after development is unknown. To address this question in a model of DS neurogenesis, we derived trisomy 21 (T21) human induced pluripotent stem cells (iPSCs) alongside, otherwise, isogenic euploid controls from mosaic DS fibroblasts and equipped one chr21 copy with an inducible XIST transgene. Monoallelic chr21 silencing by XIST is near-complete and irreversible in iPSCs. Differential expression reveals that T21 neural lineages and iPSCs share suppressed translation and mitochondrial pathways and activate cellular stress responses. When XIST is induced before the neural progenitor stage, T21 dosage correction suppresses a pronounced skew toward astrogenesis in neural differentiation. Because our transgene remains inducible in postmitotic T21 neurons and astrocytes, we demonstrate that XIST efficiently represses genes even after terminal differentiation, which will empower exploration of cell type-specific T21 phenotypes that remain responsive to chr21 dosage.
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Affiliation(s)
- Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Erin C. Banda
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Heather R. Glatt-Deeley
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Christopher E. Stoddard
- Cell and Genome Engineering Core, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Jeremy W. Linsley
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Neha Arora
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Cécile Deleschaux
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Darcy T. Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Rachael E. Massey
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Michael Nicouleau
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Shijie Wang
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Miguel Sabariego-Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Human Pharmacology and Clinical Neurosciences Research Group, Neurosciences Research Program, Hospital Del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA, USA
- Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA, USA
- Neuroscience and Biomedical Sciences Graduate Programs, University of California San Francisco, San Francisco, CA, USA
| | - Stefan F. Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
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5
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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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6
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Zhang S, Wang R, Zhang L, Birchler JA, Sun L. Inverse and Proportional Trans Modulation of Gene Expression in Human Aneuploidies. Genes (Basel) 2024; 15:637. [PMID: 38790266 PMCID: PMC11121296 DOI: 10.3390/genes15050637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Genomic imbalance in aneuploidy is often detrimental to organisms. To gain insight into the molecular basis of aneuploidies in humans, we analyzed transcriptome data from several autosomal and sex chromosome aneuploidies. The results showed that in human aneuploid cells, genes located on unvaried chromosomes are inversely or proportionally trans-modulated, while a subset of genes on the varied chromosomes are compensated. Less genome-wide modulation is found for sex chromosome aneuploidy compared with autosomal aneuploidy due to X inactivation and the retention of dosage sensitive regulators on both sex chromosomes to limit the effective dosage change. We also found that lncRNA and mRNA can have different responses to aneuploidy. Furthermore, we analyzed the relationship between dosage-sensitive transcription factors and their targets, which illustrated the modulations and indicates genomic imbalance is related to stoichiometric changes in components of gene regulatory complexes.In summary, this study demonstrates the existence of trans-acting effects and compensation mechanisms in human aneuploidies and contributes to our understanding of gene expression regulation in unbalanced genomes and disease states.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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7
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Ahern DT, Bansal P, Faustino IV, Glatt-Deeley HR, Massey R, Kondaveeti Y, Banda EC, Pinter SF. Isogenic hiPSC models of Turner syndrome development reveal shared roles of inactive X and Y in the human cranial neural crest network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.08.531747. [PMID: 36945647 PMCID: PMC10028916 DOI: 10.1101/2023.03.08.531747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Modeling the developmental etiology of viable human aneuploidy can be challenging in rodents due to syntenic boundaries, or primate-specific biology. In humans, monosomy-X (45,X) causes Turner syndrome (TS), altering craniofacial, skeletal, endocrine, and cardiovascular development, which in contrast remain unaffected in 39,X-mice. To learn how human monosomy-X may impact early embryonic development, we turned to human 45,X and isogenic euploid induced pluripotent stem cells (hiPSCs) from male and female mosaic donors. Because neural crest (NC) derived cell types are hypothesized to underpin craniofacial and cardiovascular changes in TS, we performed a highly-powered differential expression study on hiPSC-derived anterior neural crest cells (NCCs). Across three independent isogenic panels, 45,X NCCs show impaired acquisition of PAX7+SOX10+ markers, and disrupted expression of other NCC-specific genes, relative to their isogenic euploid controls. In particular, 45,X NCCs increase cholesterol biosynthesis genes while reducing transcripts that feature 5' terminal oligopyrimidine (TOP) motifs, including those of ribosomal protein and nuclear-encoded mitochondrial genes. Such metabolic pathways are also over-represented in weighted co-expression gene modules that are preserved in monogenic neurocristopathy. Importantly, these gene modules are also significantly enriched in 28% of all TS-associated terms of the human phenotype ontology. Our analysis identifies specific sex-linked genes that are expressed from two copies in euploid males and females alike and qualify as candidate haploinsufficient drivers of TS phenotypes in NC-derived lineages. This study demonstrates that isogenic hiPSC-derived NCC panels representing monosomy-X can serve as a powerful model of early NC development in TS and inform new hypotheses towards its etiology.
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Affiliation(s)
- Darcy T. Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Isaac V. Faustino
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Heather R. Glatt-Deeley
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Rachael Massey
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Erin C. Banda
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Stefan F. Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
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8
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Blanton LV, San Roman AK, Wood G, Buscetta A, Banks N, Skaletsky H, Godfrey AK, Pham TT, Hughes JF, Brown LG, Kruszka P, Lin AE, Kastner DL, Muenke M, Page DC. Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585578. [PMID: 38562807 PMCID: PMC10983990 DOI: 10.1101/2024.03.18.585578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recent in vitro studies of human sex chromosome aneuploidy showed that the Xi ("inactive" X) and Y chromosomes broadly modulate autosomal and Xa ("active" X) gene expression in two cell types. We tested these findings in vivo in two additional cell types. Using linear modeling in CD4+ T cells and monocytes from individuals with one to three X chromosomes and zero to two Y chromosomes, we identified 82 sex-chromosomal and 344 autosomal genes whose expression changed significantly with Xi and/or Y dosage in vivo . Changes in sex-chromosomal expression were remarkably constant in vivo and in vitro across all four cell types examined. In contrast, autosomal responses to Xi and/or Y dosage were largely cell-type-specific, with up to 2.6-fold more variation than sex-chromosomal responses. Targets of the X- and Y-encoded transcription factors ZFX and ZFY accounted for a significant fraction of these autosomal responses both in vivo and in vitro . We conclude that the human Xi and Y transcriptomes are surprisingly robust and stable across the four cell types examined, yet they modulate autosomal and Xa genes - and cell function - in a cell-type-specific fashion. These emerging principles offer a foundation for exploring the wide-ranging regulatory roles of the sex chromosomes across the human body.
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9
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Sugrue JA, Duffy D. Systems vaccinology studies - achievements and future potential. Microbes Infect 2024:105318. [PMID: 38460935 DOI: 10.1016/j.micinf.2024.105318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Human immune responses to vaccination are variable both within and between populations. Systems vaccinology, which is the application of multi-omics technologies to vaccine studies, seeks to understand such variation and predict responses to optimise vaccine strategies. Here, we outline new approaches to systems vaccinology, focusing on the incorporation of additional cohorts, endpoints and technologies.
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Affiliation(s)
- Jamie A Sugrue
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France.
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10
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Kundakovic M, Tickerhoof M. Epigenetic mechanisms underlying sex differences in the brain and behavior. Trends Neurosci 2024; 47:18-35. [PMID: 37968206 PMCID: PMC10841872 DOI: 10.1016/j.tins.2023.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/21/2023] [Accepted: 09/26/2023] [Indexed: 11/17/2023]
Abstract
Sex differences are found across brain regions, behaviors, and brain diseases. Sexual differentiation of the brain is initiated prenatally but it continues throughout life, as a result of the interaction of three major factors: gonadal hormones, sex chromosomes, and the environment. These factors are thought to act, in part, via epigenetic mechanisms which control chromatin and transcriptional states in brain cells. In this review, we discuss evidence that epigenetic mechanisms underlie sex-specific neurobehavioral changes during critical organizational periods, across the estrous cycle, and in response to diverse environments throughout life. We further identify future directions for the field that will provide novel mechanistic insights into brain sex differences, inform brain disease treatments and women's brain health in particular, and apply to people across genders.
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Affiliation(s)
- Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA.
| | - Maria Tickerhoof
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
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11
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Reed EG, Keller-Norrell PR. Minding the Gap: Exploring Neuroinflammatory and Microglial Sex Differences in Alzheimer's Disease. Int J Mol Sci 2023; 24:17377. [PMID: 38139206 PMCID: PMC10743742 DOI: 10.3390/ijms242417377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Research into Alzheimer's Disease (AD) describes a link between AD and the resident immune cells of the brain, the microglia. Further, this suspected link is thought to have underlying sex effects, although the mechanisms of these effects are only just beginning to be understood. Many of these insights are the result of policies put in place by funding agencies such as the National Institutes of Health (NIH) to consider sex as a biological variable (SABV) and the move towards precision medicine due to continued lackluster therapeutic options. The purpose of this review is to provide an updated assessment of the current research that summarizes sex differences and the research pertaining to microglia and their varied responses in AD.
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Affiliation(s)
- Erin G. Reed
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44242, USA
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12
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Peeters SB, Posynick BJ, Brown CJ. Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation. EPIGENOMES 2023; 7:29. [PMID: 38131901 PMCID: PMC10742877 DOI: 10.3390/epigenomes7040029] [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: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be expressed from the otherwise inactive X chromosome-in some cases constitutively, while other genes are variable between individuals, tissues or cells. In this review we discuss the advantages and disadvantages of the approaches that have been used to identify escapees. The identity of escapees provides important clues to mechanisms underlying escape from XCI, an arena of study now moving from correlation to functional studies. As most escapees show greater expression in females, the not-so-inactive X chromosome is a substantial contributor to sex differences in humans, and we highlight some examples of such impact.
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Affiliation(s)
| | | | - Carolyn J. Brown
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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13
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Jevit MJ, Castaneda C, Paria N, Das PJ, Miller D, Antczak DF, Kalbfleisch TS, Davis BW, Raudsepp T. Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep 2023; 13:20180. [PMID: 37978222 PMCID: PMC10656420 DOI: 10.1038/s41598-023-47583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
We generated single haplotype assemblies from a hinny hybrid which significantly improved the gapless contiguity for horse and donkey autosomal genomes and the X chromosomes. We added over 15 Mb of missing sequence to both X chromosomes, 60 Mb to donkey autosomes and corrected numerous errors in donkey and some in horse reference genomes. We resolved functionally important X-linked repeats: the DXZ4 macrosatellite and ampliconic Equine Testis Specific Transcript Y7 (ETSTY7). We pinpointed the location of the pseudoautosomal boundaries (PAB) and determined the size of the horse (1.8 Mb) and donkey (1.88 Mb) pseudoautosomal regions (PARs). We discovered distinct differences in horse and donkey PABs: a testis-expressed gene, XKR3Y, spans horse PAB with exons1-2 located in Y and exon3 in the X-Y PAR, whereas the donkey XKR3Y is Y-specific. DXZ4 had a similar ~ 8 kb monomer in both species with 10 copies in horse and 20 in donkey. We assigned hundreds of copies of ETSTY7, a sequence horizontally transferred from Parascaris and massively amplified in equids, to horse and donkey X chromosomes and three autosomes. The findings and products contribute to molecular studies of equid biology and advance research on X-linked conditions, sex chromosome regulation and evolution in equids.
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Affiliation(s)
- Matthew J Jevit
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Caitlin Castaneda
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Nandina Paria
- Texas Scottish Rite Hospital for Children, Dallas, TX, 75219, USA
| | - Pranab J Das
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Donald Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Theodore S Kalbfleisch
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Brian W Davis
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
| | - Terje Raudsepp
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
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14
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Moyano Rodriguez Y, Borensztein M. X-chromosome inactivation: a historic topic that's still hot. Development 2023; 150:dev202072. [PMID: 37997921 DOI: 10.1242/dev.202072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The last edition of the X-chromosome inactivation (XCI) meeting was held as an EMBO workshop in Berlin on 19-22 June 2023. The conference took place at the Harnack-haus in the Dahlem district, birthplace of the first modern research campus, where notable scientists such as Lise Meitner, Hans Krebs and, briefly, Albert Einstein conducted their research. This special edition, also accessible online, was organized by Rafael Galupa (Centre for Integrative Biology of Toulouse, France), Joost Gribnau (Erasmus MC Rotterdam, The Netherlands), Claire Rougeulle (Université Paris Cité/CNRS, Epigenetics and Cell Fate Center, Paris, France), Edda Schulz (Max Planck Institute for Molecular Genetics, Berlin, Germany) and James Turner (The Francis Crick Institute, London, UK). Originally scheduled for 2021, to commemorate the 60th anniversary of Mary Lyon's hypothesis on X-chromosome inactivation in mammals and the 30th anniversary of XIST/Xist discovery, the meeting had to be postponed because of the COVID-19 pandemic. Seven years after the latest XCI meeting in London, the enthusiasm and expectations of the community were at their highest, bringing together over 160 scientists from around the world to share and discuss their research. Eighty posters and more than 40 talks were presented at this event, in a collegial and collaborative atmosphere. A historical session and several breakout discussions were also organized, as well as the now traditional boat trip, all thanks to great organization. Here, we debrief readers on this fantastic conference.
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Affiliation(s)
| | - Maud Borensztein
- IGMM, University of Montpellier, CNRS, 34090 Montpellier, France
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15
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Wiese CB, Avetisyan R, Reue K. The impact of chromosomal sex on cardiometabolic health and disease. Trends Endocrinol Metab 2023; 34:652-665. [PMID: 37598068 PMCID: PMC11090013 DOI: 10.1016/j.tem.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 08/21/2023]
Abstract
Many aspects of metabolism are sex-biased, from gene expression in metabolic tissues to the prevalence and presentation of cardiometabolic diseases. The influence of hormones produced by male and female gonads has been widely documented, but recent studies have begun to elucidate the impact of genetic sex (XX or XY chromosomes) on cellular and organismal metabolism. XX and XY cells have differential gene dosage conferred by specific genes that escape X chromosome inactivation or the presence of Y chromosome genes that are absent from XX cells. Studies in mouse models that dissociate chromosomal and gonadal sex have uncovered mechanisms for sex-biased epigenetic, transcriptional, and post-transcriptional regulation of gene expression in conditions such as obesity, atherosclerosis, pulmonary hypertension, autoimmune disease, and Alzheimer's disease.
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Affiliation(s)
- Carrie B Wiese
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Rozeta Avetisyan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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16
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Deviatiiarov R, Nagai H, Ismagulov G, Stupina A, Wada K, Ide S, Toji N, Zhang H, Sukparangsi W, Intarapat S, Gusev O, Sheng G. Dosage compensation of Z sex chromosome genes in avian fibroblast cells. Genome Biol 2023; 24:213. [PMID: 37730643 PMCID: PMC10510239 DOI: 10.1186/s13059-023-03055-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
In birds, sex is genetically determined; however, the molecular mechanism is not well-understood. The avian Z sex chromosome (chrZ) lacks whole chromosome inactivation, in contrast to the mammalian chrX. To investigate chrZ dosage compensation and its role in sex specification, we use a highly quantitative method and analyze transcriptional activities of male and female fibroblast cells from seven bird species. Our data indicate that three fourths of chrZ genes are strictly compensated across Aves, similar to mammalian chrX. We also present a complete list of non-compensated chrZ genes and identify Ribosomal Protein S6 (RPS6) as a conserved sex-dimorphic gene in birds.
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Affiliation(s)
- Ruslan Deviatiiarov
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Life Improvement by Future Technologies Institute, Moscow, Russian Federation
| | - Hiroki Nagai
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Galym Ismagulov
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Anastasia Stupina
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Kazuhiro Wada
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Shinji Ide
- Kumamoto City Zoo and Botanical Garden, Kumamoto, Japan
| | - Noriyuki Toji
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Heng Zhang
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Woranop Sukparangsi
- Department of Biology, Faculty of Science, Burapha University, Chonburi, Thailand
| | | | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation.
- Graduate School of Medicine, Juntendo University, Tokyo, Japan.
- Life Improvement by Future Technologies Institute, Moscow, Russian Federation.
| | - Guojun Sheng
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.
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17
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Sisoudiya SD, Mishra P, Li H, Schraw JM, Scheurer ME, Salvi S, Doddapaneni H, Muzny D, Mitchell D, Taylor O, Sabo A, Lupo PJ, Plon SE. Identification of USP9X as a leukemia susceptibility gene. Blood Adv 2023; 7:4563-4575. [PMID: 37289514 PMCID: PMC10425687 DOI: 10.1182/bloodadvances.2023009814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/10/2023] Open
Abstract
We recently reported that children with multiple birth defects have a significantly higher risk of childhood cancer. We performed whole-genome sequencing on a cohort of probands from this study with birth defects and cancer and their parents. Structural variant analysis identified a novel 5 kb de novo heterozygous inframe deletion overlapping the catalytic domain of USP9X in a female proband with multiple birth defects, developmental delay, and B-cell acute lymphoblastic leukemia (B-ALL). Her phenotype was consistent with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F). Genotype-phenotype analysis including previously reported female probands (n = 42) demonstrated that MRXS99F probands with B-ALL (n = 3) clustered with subjects with loss-of-function (LoF) USP9X variants and multiple anomalies. The cumulative incidence of B-ALL among these female probands (7.1%) was significantly higher than an age- and sex-matched cohort (0.003%) from the Surveillance, Epidemiology, and End Results database (P < .0001, log-rank test). There are no reports of LoF variants in males. Males with hypomorphic missense variants have neurodevelopmental disorders without birth defects or leukemia risk. In contrast, in sporadic B-ALL, somatic LoF USP9X mutations occur in both males and females, and expression levels are comparable in leukemia samples from both sexes (P = .54), with the highest expressors being female patients with extra copies of the X-chromosome. Overall, we describe USP9X as a novel female-specific leukemia predisposition gene associated with multiple congenital, neurodevelopmental anomalies, and B-ALL risk. In contrast, USP9X serves as a tumor suppressor in sporadic pediatric B-ALL in both sexes, with low expression associated with poorer survival in patients with high-risk B-ALL.
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Affiliation(s)
- Saumya Dushyant Sisoudiya
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Pamela Mishra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Jeremy M. Schraw
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Michael E. Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | | | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Danielle Mitchell
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Olga Taylor
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Philip J. Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
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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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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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20
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Gal-Oz ST, Shay T. Genetics of Sex Differences in Immunity. Curr Top Microbiol Immunol 2023; 441:1-19. [PMID: 37695423 DOI: 10.1007/978-3-031-35139-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Women have a stronger immune response and a higher frequency of most autoimmune diseases than men. While much of the difference between men and women is due to the effect of gonadal hormones, genetic differences play a major role in the difference between the immune response and disease frequencies in women and men. Here, we focus on the immune differences between the sexes that are not downstream of the gonadal hormones. These differences include the gene content of the sex chromosomes, the inactivation of chromosome X in women, the consequences of non-random X inactivation and escape from inactivation, and the states that are uniquely met by the immune system of women-pregnancy, birth, and breast feeding. While these female-specific states are temporary and involve gonadal hormonal changes, they may leave a long-lasting footprint on the health of women, for example, by fetal cells that remain in the mother's body for decades. We also briefly discuss the immune phenotype of congenital sex chromosomal aberrations and experimental models that enable hormonal and the non-hormonal effects of the sex chromosomes to be disentangled. The increasing human life expectancy lengthens the period during which gonadal hormones levels are reduced in both sexes. A better understanding of the non-hormonal effects of sex chromosomes thus becomes more important for improving the life quality during that period.
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Affiliation(s)
- Shani T Gal-Oz
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Tal Shay
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
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