1
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Kaufmann P, Wiberg RAW, Papachristos K, Scofield DG, Tellgren-Roth C, Immonen E. Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles. Mol Biol Evol 2023; 40:msad167. [PMID: 37479678 PMCID: PMC10414808 DOI: 10.1093/molbev/msad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023] Open
Abstract
The Y chromosome is theorized to facilitate evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is scarce. Due to the lack of recombination, Y chromosomes are prone to degenerative processes, which poses a constraint on their adaptive potential. Yet, in the seed beetle, Callosobruchus maculatus segregating Y linked variation affects male body size and thereby sexual size dimorphism (SSD). Here, we assemble C. maculatus sex chromosome sequences and identify molecular differences associated with Y-linked SSD variation. The assembled Y chromosome is largely euchromatic and contains over 400 genes, many of which are ampliconic with a mixed autosomal and X chromosome ancestry. Functional annotation suggests that the Y chromosome plays important roles in males beyond primary reproductive functions. Crucially, we find that, besides an autosomal copy of the gene target of rapamycin (TOR), males carry an additional TOR copy on the Y chromosome. TOR is a conserved regulator of growth across taxa, and our results suggest that a Y-linked TOR provides a male specific opportunity to alter body size. A comparison of Y haplotypes associated with male size difference uncovers a copy number variation for TOR, where the haplotype associated with decreased male size, and thereby increased sexual dimorphism, has two additional TOR copies. This suggests that sexual conflict over growth has been mitigated by autosome to Y translocation of TOR followed by gene duplications. Our results reveal that despite of suppressed recombination, the Y chromosome can harbor adaptive potential as a male-limited supergene.
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Affiliation(s)
- Philipp Kaufmann
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Uppsala, Sweden
| | - R Axel W Wiberg
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Uppsala, Sweden
- Ecology Division, Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Douglas G Scofield
- Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, Sweden
| | - Christian Tellgren-Roth
- National Genomics Infrastructure, Uppsala Genome Center, SciLifeLab, BioMedical Centre, Uppsala University, Uppsala, Sweden
| | - Elina Immonen
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Uppsala, Sweden
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2
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Abdel-Hafiz HA, Schafer JM, Chen X, Xiao T, Gauntner TD, Li Z, Theodorescu D. Y chromosome loss in cancer drives growth by evasion of adaptive immunity. Nature 2023; 619:624-631. [PMID: 37344596 PMCID: PMC10975863 DOI: 10.1038/s41586-023-06234-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
Loss of the Y chromosome (LOY) is observed in multiple cancer types, including 10-40% of bladder cancers1-6, but its clinical and biological significance is unknown. Here, using genomic and transcriptomic studies, we report that LOY correlates with poor prognoses in patients with bladder cancer. We performed in-depth studies of naturally occurring LOY mutant bladder cancer cells as well as those with targeted deletion of Y chromosome by CRISPR-Cas9. Y-positive (Y+) and Y-negative (Y-) tumours grew similarly in vitro, whereas Y- tumours were more aggressive than Y+ tumours in immune-competent hosts in a T cell-dependent manner. High-dimensional flow cytometric analyses demonstrated that Y- tumours promote striking dysfunction or exhaustion of CD8+ T cells in the tumour microenvironment. These findings were validated using single-nuclei RNA sequencing and spatial proteomic evaluation of human bladder cancers. Of note, compared with Y+ tumours, Y- tumours exhibited an increased response to anti-PD-1 immune checkpoint blockade therapy in both mice and patients with cancer. Together, these results demonstrate that cancer cells with LOY mutations alter T cell function, promoting T cell exhaustion and sensitizing them to PD-1-targeted immunotherapy. This work provides insights into the basic biology of LOY mutation and potential biomarkers for improving cancer immunotherapy.
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Affiliation(s)
- Hany A Abdel-Hafiz
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johanna M Schafer
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
- Roche Diagnostics Solutions, Oro Valley, AZ, USA
| | - Xingyu Chen
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tong Xiao
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Timothy D Gauntner
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Cedars-Sinai Cancer Center, Los Angeles, CA, USA.
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3
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Nielsen TM, Baldwin J, Fedorka KM. Gene-poor Y-chromosomes substantially impact male trait heritabilities and may help shape sexually dimorphic evolution. Heredity (Edinb) 2023; 130:236-241. [PMID: 36759734 PMCID: PMC10076275 DOI: 10.1038/s41437-023-00596-8] [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: 07/20/2022] [Revised: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
How natural selection facilitates sexually dimorphic evolution despite a shared genome is unclear. The patrilineal inheritance of Y-chromosomes makes them an appealing solution. However, they have largely been dismissed due to their gene-poor, heterochromatic nature and because the additive genetic variation necessary for adaptive evolution is theoretically difficult to maintain. Further, previous empirical work has revealed mostly Y-linked sign epistatic variance segregating within populations, which can often impede adaptive evolution. To assess the evolutionary impact of Y-linked variation, we established replicate populations in Drosophila simulans containing multiple Y-chromosomes (YN populations) or a single Y-chromosome variant (Y1 populations) drawn from a single population. We estimated male and female heritabilities for several traits known to be influenced by Y-chromosomes, including the number of sternopleural bristles, abdominal bristles, sex comb teeth, and tibia length. A decrease in YN heritabilities compared with Y1 would be consistent with Y-chromosome variation being sign epistatic. A decrease in Y1 heritabilities would be consistent with Y-chromosome variation being additive, though additive-by-additive epistatic variation cannot be entirely dismissed. Female heritability estimates served as controls and were not expected to differ. We found male Y1 populations exhibited lower heritabilities for all traits except tibia length; consistent with Y-linked additivity (on average YN trait heritabilities were 25% greater than Y1). Female estimates showed no difference. These data suggest Y-chromosomes should play an important role in male trait evolution and may even influence sexually dimorphic evolution by shaping traits shared by both sexes.
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Affiliation(s)
- Tobias Møgelvang Nielsen
- University of Central Florida, Biological Sciences Building, 4110 Libra Dr., Orlando, FL, 32816, USA
| | - Jaden Baldwin
- University of Central Florida, Biological Sciences Building, 4110 Libra Dr., Orlando, FL, 32816, USA
| | - Kenneth M Fedorka
- University of Central Florida, Biological Sciences Building, 4110 Libra Dr., Orlando, FL, 32816, USA.
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4
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Underwood A, Rasicci DT, Hinds D, Mitchell JT, Zieba JK, Mills J, Arnold NE, Cook TW, Moustaqil M, Gambin Y, Sierecki E, Fontaine F, Vanderweele S, Das AS, Cvammen W, Sirpilla O, Soehnlen X, Bricker K, Alokaili M, Green M, Heeringa S, Wilstermann AM, Freeland TM, Qutob D, Milsted A, Jauch R, Triche TJ, Krawczyk CM, Bupp CP, Rajasekaran S, Francois M, Prokop JW. Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships. Genes (Basel) 2023; 14:222. [PMID: 36672963 PMCID: PMC9859272 DOI: 10.3390/genes14010222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood-brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
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Affiliation(s)
- Adam Underwood
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Daniel T Rasicci
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - David Hinds
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jackson T Mitchell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jacob K Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Joshua Mills
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Nicholas E Arnold
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Taylor W Cook
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mehdi Moustaqil
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Yann Gambin
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Emma Sierecki
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Frank Fontaine
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Vanderweele
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Akansha S Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - William Cvammen
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Olivia Sirpilla
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Xavier Soehnlen
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Kristen Bricker
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Maram Alokaili
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Morgan Green
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Sadie Heeringa
- Department of Biology, Calvin University, Grand Rapids, MI 49546, USA
| | - Amy M Wilstermann
- Department of Biology, Calvin University, Grand Rapids, MI 49546, USA
| | - Thomas M. Freeland
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Dinah Qutob
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Amy Milsted
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 518057, China
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Division of Medical Genetics, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Mathias Francois
- The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Sydney, NSW 2006, Australia
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
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5
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Nanda I, Schröder SK, Steinlein C, Haaf T, Buhl EM, Grimm DG, Weiskirchen R. Rat Hepatic Stellate Cell Line CFSC-2G: Genetic Markers and Short Tandem Repeat Profile Useful for Cell Line Authentication. Cells 2022; 11:cells11182900. [PMID: 36139474 PMCID: PMC9497204 DOI: 10.3390/cells11182900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Hepatic stellate cells (HSCs) are also known as lipocytes, fat-storing cells, perisinusoidal cells, or Ito cells. These liver-specific mesenchymal cells represent about 5% to 8% of all liver cells, playing a key role in maintaining the microenvironment of the hepatic sinusoid. Upon chronic liver injury or in primary culture, these cells become activated and transdifferentiate into a contractile phenotype, i.e., the myofibroblast, capable of producing and secreting large quantities of extracellular matrix compounds. Based on their central role in the initiation and progression of chronic liver diseases, cultured HSCs are valuable in vitro tools to study molecular and cellular aspects of liver diseases. However, the isolation of these cells requires special equipment, trained personnel, and in some cases needs approval from respective authorities. To overcome these limitations, several immortalized HSC lines were established. One of these cell lines is CFSC, which was originally established from cirrhotic rat livers induced by carbon tetrachloride. First introduced in 1991, this cell line and derivatives thereof (i.e., CFSC-2G, CFSC-3H, CFSC-5H, and CFSC-8B) are now used in many laboratories as an established in vitro HSC model. We here describe molecular features that are suitable for cell authentication. Importantly, chromosome banding and multicolor spectral karyotyping (SKY) analysis demonstrate that the CFSC-2G genome has accumulated extensive chromosome rearrangements and most chromosomes exist in multiple copies producing a pseudo-triploid karyotype. Furthermore, our study documents a defined short tandem repeat (STR) profile including 31 species-specific markers, and a list of genes expressed in CFSC-2G established by bulk mRNA next-generation sequencing (NGS).
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Affiliation(s)
- Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University of Würzburg, D-97074 Würzburg, Germany
| | - Sarah K. Schröder
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany
| | - Claus Steinlein
- Institute of Human Genetics, Julius Maximilians University of Würzburg, D-97074 Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University of Würzburg, D-97074 Würzburg, Germany
| | - Eva M. Buhl
- Electron Microscopy Facility, Institute of Pathology, RWTH Aachen University Hospital, D-52074 Aachen, Germany
| | - Domink G. Grimm
- Campus Straubing for Biotechnology and Sustainability & Weihenstephan-Triesdorf University of Applied Sciences, Technical University of Munich, D-94315 Straubing, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany
- Correspondence: ; Tel.: +49-(0)241-808-8683
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6
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Cīrulis A, Hansson B, Abbott JK. Sex-limited chromosomes and non-reproductive traits. BMC Biol 2022; 20:156. [PMID: 35794589 PMCID: PMC9261002 DOI: 10.1186/s12915-022-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 06/22/2022] [Indexed: 12/03/2022] Open
Abstract
Sex chromosomes are typically viewed as having originated from a pair of autosomes, and differentiated as the sex-limited chromosome (e.g. Y) has degenerated by losing most genes through cessation of recombination. While often thought that degenerated sex-limited chromosomes primarily affect traits involved in sex determination and sex cell production, accumulating evidence suggests they also influence traits not sex-limited or directly involved in reproduction. Here, we provide an overview of the effects of sex-limited chromosomes on non-reproductive traits in XY, ZW or UV sex determination systems, and discuss evolutionary processes maintaining variation at sex-limited chromosomes and molecular mechanisms affecting non-reproductive traits.
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Affiliation(s)
- Aivars Cīrulis
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Bengt Hansson
- Department of Biology, Lund University, 223 62, Lund, Sweden
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7
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Rainville JR, Lipuma T, Hodes GE. Translating the Transcriptome: Sex Differences in the Mechanisms of Depression and Stress, Revisited. Biol Psychiatry 2022; 91:25-35. [PMID: 33865609 PMCID: PMC10197090 DOI: 10.1016/j.biopsych.2021.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 12/28/2022]
Abstract
The past decade has produced a plethora of studies examining sex differences in the transcriptional profiles of stress and mood disorders. As we move forward from accepting the existence of extensive molecular sex differences in the brain to exploring the purpose of these sex differences, our approach must become more systemic and less reductionist. Earlier studies have examined specific brain regions and/or cell types. To use this knowledge to develop the next generation of personalized medicine, we need to comprehend how transcriptional changes across the brain and/or the body relate to each other. We provide an overview of the relationships between baseline and depression/stress-related transcriptional sex differences and explore contributions of preclinically identified mechanisms and their impacts on behavior.
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Affiliation(s)
- Jennifer R Rainville
- Department of Neuroscience, Virginia Polytechnic and State University, Blacksburg, Virginia
| | - Timothy Lipuma
- Department of Neuroscience, Virginia Polytechnic and State University, Blacksburg, Virginia
| | - Georgia E Hodes
- Department of Neuroscience, Virginia Polytechnic and State University, Blacksburg, Virginia.
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8
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Kaufmann P, Wolak ME, Husby A, Immonen E. Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance. Nat Ecol Evol 2021; 5:1394-1402. [PMID: 34413504 DOI: 10.1038/s41559-021-01530-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023]
Abstract
Sexual dimorphism is ubiquitous in nature but its evolution is puzzling given that the mostly shared genome constrains independent evolution in the sexes. Sex differences should result from asymmetries between the sexes in selection or genetic variation but studies investigating both simultaneously are lacking. Here, we combine a quantitative genetic analysis of body size variation, partitioned into autosomal and sex chromosome contributions and ten generations of experimental evolution to dissect the evolution of sexual body size dimorphism in seed beetles (Callosobruchus maculatus) subjected to sexually antagonistic or sex-limited selection. Female additive genetic variance (VA) was primarily linked to autosomes, exhibiting a strong intersexual genetic correlation with males ([Formula: see text] = 0.926), while X- and Y-linked genes further contributed to the male VA and X-linked genes contributed to female dominance variance. Consistent with these estimates, sexual body size dimorphism did not evolve in response to female-limited selection but evolved by 30-50% under male-limited and sexually antagonistic selection. Remarkably, Y-linked variance alone could change dimorphism by 30%, despite the C. maculatus Y chromosome being small and heterochromatic. Our results demonstrate how the potential for sexual dimorphism to evolve depends on both its underlying genetic basis and the nature of sex-specific selection.
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Affiliation(s)
- Philipp Kaufmann
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | - Matthew E Wolak
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Elina Immonen
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
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9
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Moriggi M, Belloli S, Barbacini P, Murtaj V, Torretta E, Chaabane L, Canu T, Penati S, Malosio ML, Esposito A, Gelfi C, Moresco RM, Capitanio D. Skeletal Muscle Proteomic Profile Revealed Gender-Related Metabolic Responses in a Diet-Induced Obesity Animal Model. Int J Mol Sci 2021; 22:ijms22094680. [PMID: 33925229 PMCID: PMC8125379 DOI: 10.3390/ijms22094680] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/15/2021] [Accepted: 04/27/2021] [Indexed: 02/08/2023] Open
Abstract
Obesity is a chronic, complex pathology associated with a risk of developing secondary pathologies, including cardiovascular diseases, cancer, type 2 diabetes (T2DM) and musculoskeletal disorders. Since skeletal muscle accounts for more than 70% of total glucose disposal, metabolic alterations are strictly associated with the onset of insulin resistance and T2DM. The present study relies on the proteomic analysis of gastrocnemius muscle from 15 male and 15 female C56BL/J mice fed for 14 weeks with standard, 45% or 60% high-fat diets (HFD) adopting a label-free LC–MS/MS approach followed by bioinformatic pathway analysis. Results indicate changes in males due to HFD, with increased muscular stiffness (Col1a1, Col1a2, Actb), fiber-type switch from slow/oxidative to fast/glycolytic (decreased Myh7, Myl2, Myl3 and increased Myh2, Mylpf, Mybpc2, Myl1), increased oxidative stress and mitochondrial dysfunction (decreased respiratory chain complex I and V and increased complex III subunits). At variance, females show few alterations and activation of compensatory mechanisms to counteract the increase of fatty acids. Bioinformatics analysis allows identifying upstream molecules involved in regulating pathways identified at variance in our analysis (Ppargc1a, Pparg, Cpt1b, Clpp, Tp53, Kdm5a, Hif1a). These findings underline the presence of a gender-specific response to be considered when approaching obesity and related comorbidities.
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Affiliation(s)
- Manuela Moriggi
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy;
| | - Sara Belloli
- Institute of Molecular Bioimaging and Physiology, CNR, 20090 Segrate, Italy; (S.B.); (R.M.M.)
- Department of Nuclear Medicine, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Pietro Barbacini
- Department of Biomedical Sciences for Health, University of Milan, 20090 Segrate, Italy; (P.B.); (C.G.)
| | - Valentina Murtaj
- Department of Nuclear Medicine, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
- PhD Program in Neuroscience, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | | | - Linda Chaabane
- Experimental Imaging Center, Preclinical Imaging Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (L.C.); (T.C.); (A.E.)
| | - Tamara Canu
- Experimental Imaging Center, Preclinical Imaging Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (L.C.); (T.C.); (A.E.)
| | - Silvia Penati
- Laboratory of Pharmacology and Brain Pathology, Neuro Center, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy; (S.P.); (M.L.M.)
- Institute of Neuroscience, Humanitas Mirasole S.p.A, 20089 Rozzano, Italy
| | - Maria Luisa Malosio
- Laboratory of Pharmacology and Brain Pathology, Neuro Center, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy; (S.P.); (M.L.M.)
- Institute of Neuroscience, Humanitas Mirasole S.p.A, 20089 Rozzano, Italy
| | - Antonio Esposito
- Experimental Imaging Center, Preclinical Imaging Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (L.C.); (T.C.); (A.E.)
- Experimental Imaging Center, Radiology Department, IRCCS San Raffaele Scientific Institute, School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, 20090 Segrate, Italy; (P.B.); (C.G.)
- IRCCS Istituto Ortopedico Galeazzi, 20161 Milan, Italy;
| | - Rosa Maria Moresco
- Institute of Molecular Bioimaging and Physiology, CNR, 20090 Segrate, Italy; (S.B.); (R.M.M.)
- Department of Nuclear Medicine, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, 20090 Segrate, Italy; (P.B.); (C.G.)
- Correspondence: ; Tel.: +39-0250330411
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10
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Hartog N, Faber W, Frisch A, Bauss J, Bupp CP, Rajasekaran S, Prokop JW. SARS-CoV-2 infection: molecular mechanisms of severe outcomes to suggest therapeutics. Expert Rev Proteomics 2021; 18:105-118. [PMID: 33779460 PMCID: PMC8022340 DOI: 10.1080/14789450.2021.1908894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Introduction:The year 2020 was defined by the 29,903 base pairs of RNA that codes for the SARS-CoV-2 genome. SARS-CoV-2 infects humans to cause COVID-19, spreading from patient-to-patient yet impacts patients very divergently.Areas covered: Within this review, we address the known molecular mechanisms and supporting data for COVID-19 clinical course and pathology, clinical risk factors and molecular signatures, therapeutics of severe COVID-19, and reinfection/vaccination. Literature and published datasets were reviewed using PubMed, Google Scholar, and NCBI SRA tools. The combination of exaggerated cytokine signaling, pneumonia, NETosis, pyroptosis, thrombocytopathy, endotheliopathy, multiple organ dysfunction syndrome (MODS), and acute respiratory distress syndrome (ARDS) create a positive feedback loop of severe damage in patients with COVID-19 that impacts the entire body and may persist for months following infection. Understanding the molecular pathways of severe COVID-19 opens the door for novel therapeutic design. We summarize the current insights into pathology, risk factors, secondary infections, genetics, omics, and drugs being tested to treat severe COVID-19.Expert opinion: A growing level of support suggests the need for stronger integration of biomarkers and precision medicine to guide treatment strategies of severe COVID-19, where each patient has unique outcomes and thus require guided treatment.
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Affiliation(s)
- Nicholas Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Allergy & Immunology, Spectrum Health, Grand Rapids, MI, USA
| | - William Faber
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Chemistry, Grand Rapids Community College, Grand Rapids, MI, USA
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI, USA
- Office of Research, Office of Research, Spectrum Health, Grand Rapids, MI, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
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11
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Deschepper CF. Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells. Sci Rep 2020; 10:14900. [PMID: 32913328 PMCID: PMC7484786 DOI: 10.1038/s41598-020-71447-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/13/2020] [Indexed: 12/22/2022] Open
Abstract
In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes that include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes. However, no study to date has investigated the functional impact of targeted mutations of any of these genes within adult non-reproductive somatic cells. We thus compared adult male mice carrying a gene trap within their Uty gene (UtyGT) to their wild-type (WT) isogenic controls, and performed deep sequencing of RNA and genome-wide profiling of chromatin features in extracts from either cardiac tissue, cardiomyocyte-specific nuclei or purified cardiomyocytes. The apparent impact of UtyGT on gene transcription concentrated mostly on chrY genes surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs) contained within their introns and Eif2s3y, in addition to possible effects on the autosomal Malat1 lncRNA. Notwithstanding, UtyGT also caused coordinate changes in the abundance of hundreds of mRNA transcripts related to coherent cell functions, including RNA processing and translation. The results altogether indicated that tightly co-regulated chrY genes had nonetheless more widespread effects on the autosomal transcriptome in adult somatic cells, most likely due to mechanisms other than just transcriptional regulation of corresponding protein-coding genes.
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Affiliation(s)
- Christian F Deschepper
- Cardiovascular Biology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM) and Université de Montréal, 100 Pine Ave West, Montréal, QC, H2W 1R7, Canada.
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12
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Perrino C, Ferdinandy P, Bøtker HE, Brundel BJJM, Collins P, Davidson SM, den Ruijter HM, Engel FB, Gerdts E, Girao H, Gyöngyösi M, Hausenloy DJ, Lecour S, Madonna R, Marber M, Murphy E, Pesce M, Regitz-Zagrosek V, Sluijter JPG, Steffens S, Gollmann-Tepeköylü C, Van Laake LW, Van Linthout S, Schulz R, Ytrehus K. Improving translational research in sex-specific effects of comorbidities and risk factors in ischaemic heart disease and cardioprotection: position paper and recommendations of the ESC Working Group on Cellular Biology of the Heart. Cardiovasc Res 2020; 117:367-385. [PMID: 32484892 DOI: 10.1093/cvr/cvaa155] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/29/2020] [Accepted: 05/27/2020] [Indexed: 12/17/2022] Open
Abstract
Ischaemic heart disease (IHD) is a complex disorder and a leading cause of death and morbidity in both men and women. Sex, however, affects several aspects of IHD, including pathophysiology, incidence, clinical presentation, diagnosis as well as treatment and outcome. Several diseases or risk factors frequently associated with IHD can modify cellular signalling cascades, thus affecting ischaemia/reperfusion injury as well as responses to cardioprotective interventions. Importantly, the prevalence and impact of risk factors and several comorbidities differ between males and females, and their effects on IHD development and prognosis might differ according to sex. The cellular and molecular mechanisms underlying these differences are still poorly understood, and their identification might have important translational implications in the prediction or prevention of risk of IHD in men and women. Despite this, most experimental studies on IHD are still undertaken in animal models in the absence of risk factors and comorbidities, and assessment of potential sex-specific differences are largely missing. This ESC WG Position Paper will discuss: (i) the importance of sex as a biological variable in cardiovascular research, (ii) major biological mechanisms underlying sex-related differences relevant to IHD risk factors and comorbidities, (iii) prospects and pitfalls of preclinical models to investigate these associations, and finally (iv) will provide recommendations to guide future research. Although gender differences also affect IHD risk in the clinical setting, they will not be discussed in detail here.
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Affiliation(s)
- Cinzia Perrino
- Department of Advanced Biomedical Sciences, Federico II University, Via Pansini 5, 80131 Naples, Italy
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary.,Pharmahungary Group, Hajnoczy str. 6., H-6722 Szeged, Hungary
| | - Hans E Bøtker
- Department of Cardiology, Aarhus University Hospital, Palle Juul-Jensens Blvd. 161, 8200 Aarhus, Denmark
| | - Bianca J J M Brundel
- Department of Physiology, Amsterdam UMC, Vrije Universiteit, Amsterdam Cardiovascular Sciences, De Boelelaan 1117, Amsterdam, 1108 HV, the Netherlands
| | - Peter Collins
- Imperial College, Faculty of Medicine, National Heart & Lung Institute, South Kensington Campus, London SW7 2AZ, UK.,Royal Brompton Hospital, Sydney St, Chelsea, London SW3 6NP, UK
| | - Sean M Davidson
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, WC1E 6HX London, UK
| | - Hester M den Ruijter
- Experimental Cardiology Laboratory, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Felix B Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Muscle Research Center Erlangen (MURCE), Schwabachanlage 12, 91054 Erlangen, Germany
| | - Eva Gerdts
- Department for Clinical Science, University of Bergen, PO Box 7804, 5020 Bergen, Norway
| | - Henrique Girao
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, Azinhaga Santa Comba, Celas, 3000-548 Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, and Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Mariann Gyöngyösi
- Department of Cardiology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Derek J Hausenloy
- Cardiovascular & Metabolic Disorders Program, Duke-National University of Singapore Medical School, 8 College Road, 169857, Singapore.,National Heart Research Institute Singapore, National Heart Centre Singapore, 5 Hospital Drive, 169609, Singapore.,Yong Loo Lin School of Medicine, National University Singapore, 1E Kent Ridge Road, 119228, Singapore.,The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London WC1E 6HX, UK.,Cardiovascular Research Center, College of Medical and Health Sciences, Asia University, 500, Lioufeng Rd., Wufeng, Taichung 41354, Taiwan
| | - Sandrine Lecour
- Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, Chris Barnard Building, University of Cape Town, Private Bag X3 7935 Observatory, Cape Town, South Africa
| | - Rosalinda Madonna
- Institute of Cardiology, University of Pisa, Lungarno Antonio Pacinotti 43, 56126 Pisa, Italy.,Department of Internal Medicine, University of Texas Medical School in Houston, 6410 Fannin St #1014, Houston, TX 77030, USA
| | - Michael Marber
- King's College London BHF Centre, The Rayne Institute, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK
| | - Elizabeth Murphy
- Laboratory of Cardiac Physiology, Cardiovascular Branch, NHLBI, NIH, 10 Center Drive, Bethesda, MD 20892, USA
| | - Maurizio Pesce
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS Via Parea, 4, I-20138 Milan, Italy
| | - Vera Regitz-Zagrosek
- Berlin Institute of Gender in Medicine, Center for Cardiovascular Research, DZHK, partner site Berlin, Geschäftsstelle Potsdamer Str. 58, 10785 Berlin, Germany.,University of Zürich, Rämistrasse 71, 8006 Zürich, Germany
| | - Joost P G Sluijter
- Experimental Cardiology Laboratory, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 8, 3584 CS Utrecht, the Netherlands.,Circulatory Health Laboratory, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht University, Heidelberglaan 8, 3584 CS Utrecht, the Netherlands
| | - Sabine Steffens
- Institute for Cardiovascular Prevention and German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Pettenkoferstr. 9, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Can Gollmann-Tepeköylü
- Department of Cardiac Surgery, Medical University of Innsbruck, Anichstr.35, A - 6020 Innsbruck, Austria
| | - Linda W Van Laake
- Cardiology and UMC Utrecht Regenerative Medicine Center, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Sophie Van Linthout
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité, University Medicine Berlin, 10178 Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité, University Medicine Berlin, 10178 Berlin, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Rainer Schulz
- Institute of Physiology, Justus-Liebig University Giessen, Ludwigstraße 23, 35390 Giessen, Germany
| | - Kirsti Ytrehus
- Department of Medical Biology, UiT The Arctic University of Norway, Hansine Hansens veg 18, 9037 Tromsø, Norway
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13
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Prokop JW, Chhetri SB, van Veen JE, Chen X, Underwood AC, Uhl K, Dwinell MR, Geurts AM, Correa SM, Arnold AP. Transcriptional analysis of the multiple Sry genes and developmental program at the onset of testis differentiation in the rat. Biol Sex Differ 2020; 11:28. [PMID: 32398044 PMCID: PMC7216353 DOI: 10.1186/s13293-020-00305-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The commonly used laboratory rat, Rattus norvegicus, is unique in having multiple Sry gene copies found on the Y chromosome, with different copies encoding amino acid variations that influence the resulting protein function. It is not clear which Sry genes are expressed at the onset of testis differentiation or how their expression correlates with that of other genes in testis-determination pathways. METHODS Here, two independent E11-E14 developmental RNAseq datasets show that multiple Sry genes are expressed at E12-E13. RESULTS The identified copies expressed during testis initiation include Sry4A, Sry1, and Sry3C, which are conserved in every strain of Rattus norvegicus with genomes sequenced to date. CONCLUSIONS This work represents a first step in defining the complex environment of rat testis differentiation that can open the door for generating sex reversal model systems using embryo manipulation techniques that have been available in the mouse but not the rat.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.,Johns Hopkins University, Baltimore, MD, 21218, USA
| | - J Edward van Veen
- Department of Integrative Biology & Physiology, Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, 610 Charles Young Drive South, Los Angeles, CA, 90095, USA
| | - Xuqi Chen
- Department of Integrative Biology & Physiology, Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, 610 Charles Young Drive South, Los Angeles, CA, 90095, USA
| | - Adam C Underwood
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.,Division of Mathematics and Science, Walsh University, North Canton, OH, 44720, USA
| | - Katie Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Stephanie M Correa
- Department of Integrative Biology & Physiology, Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, 610 Charles Young Drive South, Los Angeles, CA, 90095, USA
| | - Arthur P Arnold
- Department of Integrative Biology & Physiology, Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, 610 Charles Young Drive South, Los Angeles, CA, 90095, USA.
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14
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Cowley AW, Dwinell MR. Chromosomal Substitution Strategies to Localize Genomic Regions Related to Complex Traits. Compr Physiol 2020; 10:365-388. [PMID: 32163204 DOI: 10.1002/cphy.c180029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chromosomal substitution strategies provide a powerful tool to anonymously reveal the relationship between DNA sequence variants and a normal or disease phenotype of interest. Even in this age of CRISPR-Cas9 genome engineering, the knockdown or overexpression of a gene provides relevant information to our understanding of complex disease only when a close association of an allelic variant with the phenotype has first been established. Limitations of genetic linkage approaches led to the development of more efficient breeding strategies to substitute chromosomal segments from one animal strain into the genetic background of a different strain, enabling a direct comparison of the phenotypes of the strains with variant(s) that differ only at a defined locus. This substitution can be a whole chromosome (consomic), a part of a chromosome (congenic), or as small as only a single or several alleles (subcongenics). In contrast to complete knockout of a specific candidate gene of interest, which simply studies the effects of complete elimination of the gene, the substitution of naturally occurring variants can provide special insights into the functional actions of wild-type alleles. Strategies for production of these inbred strains are reviewed, and a number of examples are used to illustrate the utility of these model systems. Consomic/congenic strains provide a number of experimental advantages in the study of functions of genes and their variants, which are emphasized in this article, such as replication of experimental studies; determination of temporal relationships throughout a life; rigorously controlled experiments in which relations between genotype and phenotype can be tested with the confounding effects of heterogeneous genetic backgrounds, both targeted and multilayered; and "omic" studies performed at many levels of functionality, from molecules to organelles, cells to organs, and organs to organismal behavior across the life span. The application of chromosomal substitution strategies and development of consomic/congenic rat and mouse strains have greatly expanded our knowledge of genomic variants and their phenotypic relationship to physiological functions and to complex diseases such as hypertension and cancer. © 2020 American Physiological Society. Compr Physiol 10:365-388, 2020.
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Affiliation(s)
- Allen W Cowley
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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15
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Lusis AJ. Y-Chromosome Genetic Variation Associated With Atherosclerosis and Inflammation. Arterioscler Thromb Vasc Biol 2019; 39:2201-2202. [PMID: 31644351 DOI: 10.1161/atvbaha.119.313369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Aldons J Lusis
- Department of Medicine/Division of Cardiology, Department of Human Genetics, Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles
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16
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Eales JM, Maan AA, Xu X, Michoel T, Hallast P, Batini C, Zadik D, Prestes PR, Molina E, Denniff M, Schroeder J, Bjorkegren JLM, Thompson J, Maffia P, Guzik TJ, Keavney B, Jobling MA, Samani NJ, Charchar FJ, Tomaszewski M. Human Y Chromosome Exerts Pleiotropic Effects on Susceptibility to Atherosclerosis. Arterioscler Thromb Vasc Biol 2019; 39:2386-2401. [PMID: 31644355 PMCID: PMC6818981 DOI: 10.1161/atvbaha.119.312405] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Supplemental Digital Content is available in the text. The male-specific region of the Y chromosome (MSY) remains one of the most unexplored regions of the genome. We sought to examine how the genetic variants of the MSY influence male susceptibility to coronary artery disease (CAD) and atherosclerosis.
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Affiliation(s)
- James M Eales
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.)
| | - Akhlaq A Maan
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.)
| | - Xiaoguang Xu
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.)
| | - Tom Michoel
- The Roslin Institute, The University of Edinburgh, United Kingdom (T.M.).,Computational Biology Unit and Department of Informatics, University of Bergen, Norway (T.M.)
| | - Pille Hallast
- Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (P.H.)
| | - Chiara Batini
- Department of Health Sciences (C.B., J.T.), University of Leicester, United Kingdom
| | - Daniel Zadik
- Department of Genetics and Genome Biology (D.Z., M.A.J.), University of Leicester, United Kingdom
| | - Priscilla R Prestes
- School of Health and Life Sciences, Federation University Australia, Ballarat, Victoria (P.R.P., E.M., F.J.C.)
| | - Elsa Molina
- School of Health and Life Sciences, Federation University Australia, Ballarat, Victoria (P.R.P., E.M., F.J.C.)
| | - Matthew Denniff
- Department of Cardiovascular Sciences (M.D., N.J.S., F.J.C.), University of Leicester, United Kingdom
| | - Juliane Schroeder
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation (J.S., P.M.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom.,Institute of Cardiovascular and Medical Sciences (J.S., P.M., T.J.G.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Johan L M Bjorkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.)
| | - John Thompson
- Department of Health Sciences (C.B., J.T.), University of Leicester, United Kingdom
| | - Pasquale Maffia
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation (J.S., P.M.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom.,Institute of Cardiovascular and Medical Sciences (J.S., P.M., T.J.G.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom.,Department of Pharmacy, University of Naples Federico II, Italy (P.M.)
| | - Tomasz J Guzik
- Institute of Cardiovascular and Medical Sciences (J.S., P.M., T.J.G.), College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom.,Jagiellonian University College of Medicine, Kraków, Poland (T.J.G.)
| | - Bernard Keavney
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.).,Division of Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom (B.K., M.T.)
| | - Mark A Jobling
- Department of Genetics and Genome Biology (D.Z., M.A.J.), University of Leicester, United Kingdom
| | - Nilesh J Samani
- Department of Cardiovascular Sciences (M.D., N.J.S., F.J.C.), University of Leicester, United Kingdom.,NIHR Leicester Biomedical Research Centre, United Kingdom (N.J.S.)
| | - Fadi J Charchar
- Department of Cardiovascular Sciences (M.D., N.J.S., F.J.C.), University of Leicester, United Kingdom.,School of Health and Life Sciences, Federation University Australia, Ballarat, Victoria (P.R.P., E.M., F.J.C.).,Department of Physiology, University of Melbourne, Parkville, Victoria, Australia (F.J.C.)
| | - Maciej Tomaszewski
- From the Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom (J.M.E., A.A.M., X.X., B.K., M.T.).,Division of Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom (B.K., M.T.)
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17
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Prokop JW, May T, Strong K, Bilinovich SM, Bupp C, Rajasekaran S, Worthey EA, Lazar J. Genome sequencing in the clinic: the past, present, and future of genomic medicine. Physiol Genomics 2018; 50:563-579. [PMID: 29727589 PMCID: PMC6139636 DOI: 10.1152/physiolgenomics.00046.2018] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomic sequencing has undergone massive expansion in the past 10 yr, from a rarely used research tool into an approach that has broad applications in a clinical setting. From rare disease to cancer, genomics is transforming our knowledge of biology. The transition from targeted gene sequencing, to whole exome sequencing, to whole genome sequencing has only been made possible due to rapid advancements in technologies and informatics that have plummeted the cost per base of DNA sequencing and analysis. The tools of genomics have resolved the etiology of disease for previously undiagnosable conditions, identified cancer driver gene variants, and have impacted the understanding of pathophysiology for many diseases. However, this expansion of use has also highlighted research's current voids in knowledge. The lack of precise animal models for gene-to-function association, lack of tools for analysis of genomic structural changes, skew in populations used for genetic studies, publication biases, and the "Unknown Proteome" all contribute to voids needing filled for genomics to work in a fast-paced clinical setting. The future will hold the tools to fill in these voids, with new data sets and the continual development of new technologies allowing for expansion of genomic medicine, ushering in the days to come for precision medicine. In this review we highlight these and other points in hopes of advancing and guiding precision medicine into the future for optimal success.
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Affiliation(s)
- Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology , Huntsville, Alabama
- Department of Pediatrics and Human Development, Michigan State University , East Lansing, Michigan
- Department of Pharmacology and Toxicology, Michigan State University , East Lansing, Michigan
| | - Thomas May
- HudsonAlpha Institute for Biotechnology , Huntsville, Alabama
- Institute for Health and Aging, University of California San Francisco , San Francisco, California
- Elson S. Floyd College of Medicine, Washington State University , Spokane, Washington
| | - Kim Strong
- HudsonAlpha Institute for Biotechnology , Huntsville, Alabama
| | - Stephanie M Bilinovich
- Department of Pediatrics and Human Development, Michigan State University , East Lansing, Michigan
| | - Caleb Bupp
- Department of Pediatrics and Human Development, Michigan State University , East Lansing, Michigan
- Department of Genetics, Helen DeVos Children's Hospital, Spectrum Health, Grand Rapids, Michigan
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, Michigan State University , East Lansing, Michigan
- Department of Pediatric Critical Care Medicine, Helen DeVos Children's Hospital, Spectrum Health, Grand Rapids, Michigan
| | | | - Jozef Lazar
- HudsonAlpha Institute for Biotechnology , Huntsville, Alabama
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18
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Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads. Sci Rep 2018; 8:9436. [PMID: 29930304 PMCID: PMC6013464 DOI: 10.1038/s41598-018-27819-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
This study is a comparison of the efficiency of three technologies used for Y chromosome capture and the next-generation sequencing (NGS) technologies applied for determining its whole sequence. Our main findings disclose that streptavidin-biotin magnetic particle-based capture methodology offers better and a deeper sequence coverage for Y chromosome capture, compared to chromosome sorting and microdissection procedures. Moreover, this methodology is less time consuming and the most selective for capturing only Y chromosomal material, in contrast with other methodologies that result in considerable background material from other, non-targeted chromosomes. NGS results compared between two platforms, NextSeq 500 and SOLID 5500xl, produce the same coverage results. This is the first study to explore a methodological comparison of Y chromosome capture and genetic analysis. Our results indicate an improved strategy for Y chromosome research with applications in several scientific fields where this chromosome plays an important role, such as forensics, medical sciences, molecular anthropology and cancer sciences.
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19
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Same-Sex Twin Pair Phenotypic Correlations are Consistent with Human Y Chromosome Promoting Phenotypic Heterogeneity. Evol Biol 2018. [DOI: 10.1007/s11692-018-9454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Zore T, Palafox M, Reue K. Sex differences in obesity, lipid metabolism, and inflammation-A role for the sex chromosomes? Mol Metab 2018; 15:35-44. [PMID: 29706320 PMCID: PMC6066740 DOI: 10.1016/j.molmet.2018.04.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/26/2018] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sex differences in obesity and related diseases are well established. Gonadal hormones are a major determinant of these sex differences. However, sex differences in body size and composition are evident prior to exposure to gonadal hormones, providing evidence for gonadal-independent contributions attributable to the XX or XY sex chromosome complement. Large-scale genetic studies have revealed male/female differences in the genetic architecture of adipose tissue amount and anatomical distribution. However, these studies have typically neglected the X and Y chromosomes. SCOPE OF THE REVIEW Here we discuss how the sex chromosome complement may influence obesity, lipid levels, and inflammation. Human sex chromosome anomalies such as Klinefelter syndrome (XXY), as well as mouse models with engineered alterations in sex chromosome complement, support an important role for sex chromosomes in obesity and metabolism. In particular, the Four Core Genotypes mouse model-consisting of XX mice with either ovaries or testes, and XY mice with either ovaries or testes-has revealed an effect of X chromosome dosage on adiposity, hyperlipidemia, and inflammation irrespective of male or female gonads. Mechanisms may include enhanced expression of genes that escape X chromosome inactivation. MAJOR CONCLUSIONS Although less well studied than effects of gonadal hormones, sex chromosomes exert independent and interactive effects on adiposity, lipid metabolism, and inflammation. In particular, the presence of two X chromosomes has been associated with increased adiposity and dyslipidemia in mouse models and in XXY men. The enhanced expression of genes that escape X chromosome inactivation may contribute, but more work is required.
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Affiliation(s)
- Temeka Zore
- Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Maria Palafox
- Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Maan AA, Eales J, Akbarov A, Rowland J, Xu X, Jobling MA, Charchar FJ, Tomaszewski M. The Y chromosome: a blueprint for men's health? Eur J Hum Genet 2017; 25:1181-1188. [PMID: 28853720 PMCID: PMC5643963 DOI: 10.1038/ejhg.2017.128] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/16/2017] [Accepted: 06/28/2017] [Indexed: 12/22/2022] Open
Abstract
The Y chromosome has long been considered a 'genetic wasteland' on a trajectory to completely disappear from the human genome. The perception of its physiological function was restricted to sex determination and spermatogenesis. These views have been challenged in recent times with the identification of multiple ubiquitously expressed Y-chromosome genes and the discovery of several unexpected associations between the Y chromosome, immune system and complex polygenic traits. The collected evidence suggests that the Y chromosome influences immune and inflammatory responses in men, translating into genetically programmed susceptibility to diseases with a strong immune component. Phylogenetic studies reveal that carriers of a common European lineage of the Y chromosome (haplogroup I) possess increased risk of coronary artery disease. This occurs amidst upregulation of inflammation and suppression of adaptive immunity in this Y lineage, as well as inferior outcomes in human immunodeficiency virus infection. From structural analysis and experimental data, the UTY (Ubiquitously Transcribed Tetratricopeptide Repeat Containing, Y-Linked) gene is emerging as a promising candidate underlying the associations between Y-chromosome variants and the immunity-driven susceptibility to complex disease. This review synthesises the recent structural, experimental and clinical insights into the human Y chromosome in the context of men's susceptibility to disease (with a particular emphasis on cardiovascular disease) and provides an overview of the paradigm shift in the perception of the Y chromosome.
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Affiliation(s)
- Akhlaq A Maan
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - James Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Joshua Rowland
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK
| | - Fadi J Charchar
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University, Mount Helen Campus, Ballarat, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Division of Medicine, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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Trombetta B, D'Atanasio E, Cruciani F. Patterns of Inter-Chromosomal Gene Conversion on the Male-Specific Region of the Human Y Chromosome. Front Genet 2017; 8:54. [PMID: 28515739 PMCID: PMC5413550 DOI: 10.3389/fgene.2017.00054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/18/2017] [Indexed: 12/31/2022] Open
Abstract
The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized. The main effect of ICGC is to increase the allelic diversity of MSY by generating a significant excess of clustered single nucleotide polymorphisms (SNPs) (defined as groups of two or more SNPs occurring in close proximity and on the same branch of the Y phylogeny). On the human MSY, 13 inter-chromosomal gene conversion hotspots (GCHs) have been identified so far, involving donor sequences mainly from the X-chromosome and, to a lesser extent, from autosomes. Most of the GCHs are evolutionary conserved and overlap with regions involved in aberrant X–Y crossing-over. This review mainly focuses on the dynamics and the current knowledge concerning the recombinational landscape of the human MSY in the form of ICGC, on how this molecular mechanism may influence the evolution of the MSY, and on how it could affect the information enclosed within a genomic region which, until recently, appeared to be an evolutionary independent unit.
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Affiliation(s)
- Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di RomaRome, Italy
| | - Eugenia D'Atanasio
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di RomaRome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di RomaRome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche (CNR),Rome, Italy
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23
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Genetic variation in chromosome Y regulates susceptibility to influenza A virus infection. Proc Natl Acad Sci U S A 2017; 114:3491-3496. [PMID: 28242695 DOI: 10.1073/pnas.1620889114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Males of many species, ranging from humans to insects, are more susceptible than females to parasitic, fungal, bacterial, and viral infections. One mechanism that has been proposed to account for this difference is the immunocompetence handicap model, which posits that the greater infectious disease burden in males is due to testosterone, which drives the development of secondary male sex characteristics at the expense of suppressing immunity. However, emerging data suggest that cell-intrinsic (chromosome X and Y) sex-specific factors also may contribute to the sex differences in infectious disease burden. Using a murine model of influenza A virus (IAV) infection and a panel of chromosome Y (ChrY) consomic strains on the C57BL/6J background, we present data showing that genetic variation in ChrY influences IAV pathogenesis in males. Specific ChrY variants increase susceptibility to IAV in males and augment pathogenic immune responses in the lung, including activation of proinflammatory IL-17-producing γδ T cells, without affecting viral replication. In addition, susceptibility to IAV segregates independent of copy number variation in multicopy ChrY gene families that influence susceptibility to other immunopathological phenotypes, including survival after infection with coxsackievirus B3. These results demonstrate a critical role for genetic variation in ChrY in regulating susceptibility to infectious disease.
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Praktiknjo SD, Picard S, Deschepper CF. Comparisons of chromosome Y-substituted mouse strains reveal that the male-specific chromosome modulates the effects of androgens on cardiac functions. Biol Sex Differ 2016; 7:61. [PMID: 27980711 PMCID: PMC5143463 DOI: 10.1186/s13293-016-0116-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/09/2016] [Indexed: 01/06/2023] Open
Abstract
Background The C57BL/6J.YA/J mouse strain is a chromosome-substituted line where the original male-specific portion of chromosome Y (MSY) from C57BL/6J mice was substituted for that from A/J mice. In hearts from male C57BL/6J.YA/J and C57BL/6J mice, orchidectomy (ORX) affected in a strictly strain-specific fashion the expression a subset of genes showing enrichment for functional categories, including that of circadian rhythms and cardiac contractility. We further tested whether: (1) there were strain-specific differences in cardiac circadian rhythms; (2) strain-dependent differences in the effects of ORX on contractility genes translated into differences in cardiac functions; and (3) differential contractility responses occurred preferentially at times when circadian rhythms also showed strain-specific differences. Methods In hearts from the two above strains, we (1) profiled the expression levels of 15 circadian genes at 4-h intervals across a 24 h period; (2) tested the effects of either ORX or androgen replacement on expression of cardiac contractility genes, and that of ORX on myocardial functional reserve; and (3) verified whether the effects of MSY variants on cardiac contractility-related responses showed synchronicity with differences in circadian rhythms. Results Among the 15 tested circadian genes, a subset of them were affected by strain (and thus the genetic origin of MSY), which interacted with the amplitude of their peak of maximal expression at 2:00 PM. At that same time-point, ORX decreased (and androgen supplementation increased) the expression of three contractility-related genes, and decreased myocardial relaxation reserve in C57BL/6J.YA/J, but not in C57BL/6J mice. These effects were not detected at 10:00 AM, i.e., at another time-point when circadian genes showed no strain-specific differences. Conclusions The results indicate that in mice, androgens have activational effects on cardiac circadian rhythms, contractile gene expression, and myocardial functional reserve. All effects occurred preferentially at the same time of the day, but varied as a function of the genetic origin of MSY. Androgens may therefore be necessary but not sufficient to impart male-specific characteristics to some particular cardiac functions, with genetic material from MSY being one other necessary factor to fully define their range of actions. Electronic supplementary material The online version of this article (doi:10.1186/s13293-016-0116-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samantha D Praktiknjo
- Institut de recherches cliniques de Montréal (IRCM) and Dept of Medicine, Cardiovascular Biology Research Unit, Université de Montréal, 100 Pine Ave West, Montreal, QC H2W 1R7 Canada ; Present address: Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, D-13125 Berlin, Germany
| | - Sylvie Picard
- Institut de recherches cliniques de Montréal (IRCM) and Dept of Medicine, Cardiovascular Biology Research Unit, Université de Montréal, 100 Pine Ave West, Montreal, QC H2W 1R7 Canada
| | - Christian F Deschepper
- Institut de recherches cliniques de Montréal (IRCM) and Dept of Medicine, Cardiovascular Biology Research Unit, Université de Montréal, 100 Pine Ave West, Montreal, QC H2W 1R7 Canada
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25
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Sex bias in paediatric autoimmune disease – Not just about sex hormones? J Autoimmun 2016; 69:12-23. [DOI: 10.1016/j.jaut.2016.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/25/2016] [Accepted: 02/29/2016] [Indexed: 02/06/2023]
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26
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Prokop JW, Tsaih SW, Faber AB, Boehme S, Underwood AC, Troyer S, Playl L, Milsted A, Turner ME, Ely D, Martins AS, Tutaj M, Lazar J, Dwinell MR, Jacob HJ. The phenotypic impact of the male-specific region of chromosome-Y in inbred mating: the role of genetic variants and gene duplications in multiple inbred rat strains. Biol Sex Differ 2016; 7:10. [PMID: 26848384 PMCID: PMC4740989 DOI: 10.1186/s13293-016-0064-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/26/2016] [Indexed: 12/22/2022] Open
Abstract
Backgound The male-specific region of chromosome-Y (MSY) contributes to phenotypes outside of testis development and has a high rate of evolution between mammalian species. With a lack of genomic crossover, MSY is one of the few genomic areas under similar variation and evolutionary selection in inbred and outbred animal populations, allowing for an assessment of evolutionary mechanisms to translate between the populations. Methods Using next-generation sequencing, MSY consomic strains, molecular characterization, and large-scale phenotyping, we present here regions of MSY that contribute to inbred strain phenotypes. Results We have shown that (1) MSY of rat has nine autosomal gene transposition events with strain-specific selection; (2) sequence variants in MSY occur with a 1.98-fold higher number of variants than other chromosomes in seven sequenced rat strains; (3) Sry, the most studied MSY gene, has undergone extensive gene duplications, driving ubiquitous expression not seen in human or mouse; (4) the expression profile of Sry in the rat is driven by the insertion of the Sry2 copy into an intron of the ubiquitously expressed Kdm5d gene in antisense orientation, but due to several loss of function mutations in the Sry2 protein, nuclear localization and transcriptional control are decreased; (5) expression of Sry copies other than Sry2 in the rat overlaps with the expression profile for human SRY; (6) gene duplications and sequence variants (P76T) of Sry can be selected for phenotypes such as high blood pressure and androgen receptor signaling within inbred mating; and most importantly, (7) per chromosome size, MSY contributes to higher strain-specific phenotypic variation relative to all other chromosomes, with 53 phenotypes showing both a male to female and consomic cross significance. Conclusion The data presented supports a high probability of MSY genetic variation altering a broad range of inbred rat phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s13293-016-0064-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ; Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Shirng-Wern Tsaih
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Allison B Faber
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Shannon Boehme
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Adam C Underwood
- Department of Mathematics and Science, Walsh University, North Canton, OH 44720 USA
| | - Samuel Troyer
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Lauren Playl
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Amy Milsted
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Monte E Turner
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Daniel Ely
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Almir S Martins
- Núcleo de Fisiologia Geral e Genômica Funcional-ICB-Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais Brazil
| | - Marek Tutaj
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Jozef Lazar
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ; Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Melinda R Dwinell
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Howard J Jacob
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ; Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
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