1
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Chen J, Landback P, Arsala D, Guzzetta A, Xia S, Atlas J, Sosa D, Zhang YE, Cheng J, Shen B, Long M. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567139. [PMID: 38045239 PMCID: PMC10690195 DOI: 10.1101/2023.11.14.567139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are genetic novelties pivotal in mammalian evolution. Their phenotypic impacts and evolutionary pattern over time, however, remain elusive in humans due to the technical and ethical complexities in functional studies. By combining human gene age dating and Mendelian disease phenotyping, our research reveals a gradual increase in disease gene proportions with gene age. Logistic regression modeling indicates that this increase could be related to longer protein lengths and higher burdens of deleterious de novo germline variants (DNVs) for older genes. We also find a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (~0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Notably, young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit disease-related functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. We further reveal a logistic growth pattern of pleiotropy over evolutionary time, indicating a diminishing marginal growth of new functions for older genes due to intensifying selective constraints over time. We propose a "pleiotropy-barrier" model that delineates higher potentials of phenotypic innovation for young genes than for older genes, a process subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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Affiliation(s)
- Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Patrick Landback
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Alexander Guzzetta
- Department of Pathology, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Jared Atlas
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Yong E. Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingqiu Cheng
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
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2
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Öling S, Struck E, Noreen-Thorsen M, Zwahlen M, von Feilitzen K, Odeberg J, Pontén F, Lindskog C, Uhlén M, Dusart P, Butler LM. A human stomach cell type transcriptome atlas. BMC Biol 2024; 22:36. [PMID: 38355543 PMCID: PMC10865703 DOI: 10.1186/s12915-024-01812-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single-cell sequencing-based atlases. RESULTS Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell, and plasma cells, identifying over 1600 cell type-enriched genes. CONCLUSIONS We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.
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Affiliation(s)
- S Öling
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - E Struck
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - M Noreen-Thorsen
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - M Zwahlen
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - K von Feilitzen
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - J Odeberg
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
- The University Hospital of North Norway (UNN), 9019, Tromsø, Norway
- Department of Haematology, Coagulation Unit, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - F Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - C Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - M Uhlén
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - P Dusart
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
- Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76, Stockholm, Sweden
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - L M Butler
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway.
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden.
- Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76, Stockholm, Sweden.
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, 171 76, Stockholm, Sweden.
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3
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Chen J. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. RESEARCH SQUARE 2023:rs.3.rs-3632644. [PMID: 38045389 PMCID: PMC10690325 DOI: 10.21203/rs.3.rs-3632644/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are structural novelties pivotal in mammalian evolution. Their phenotypic impact on humans, however, remains elusive due to the technical and ethical complexities in functional studies. Through combining gene age dating with Mendelian disease phenotyping, our research reveals that new genes associated with disease phenotypes steadily integrate into the human genome at a rate of ~ 0.07% every million years over macroevolutionary timescales. Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures between young and old genes. Notably, young genes show significant enrichment in the male reproductive system, indicating strong sexual selection. Young genes also exhibit functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, bipedal locomotion, and color vision. Our findings further reveal increasing levels of pleiotropy over evolutionary time, which accompanies stronger selective constraints. We propose a "pleiotropy-barrier" model that delineates different potentials for phenotypic innovation between young and older genes subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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4
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Mendelian inheritance revisited: dominance and recessiveness in medical genetics. Nat Rev Genet 2023:10.1038/s41576-023-00574-0. [PMID: 36806206 DOI: 10.1038/s41576-023-00574-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/22/2023]
Abstract
Understanding the consequences of genotype for phenotype (which ranges from molecule-level effects to whole-organism traits) is at the core of genetic diagnostics in medicine. Many measures of the deleteriousness of individual alleles exist, but these have limitations for predicting the clinical consequences. Various mechanisms can protect the organism from the adverse effects of functional variants, especially when the variant is paired with a wild type allele. Understanding why some alleles are harmful in the heterozygous state - representing dominant inheritance - but others only with the biallelic presence of pathogenic variants - representing recessive inheritance - is particularly important when faced with the deluge of rare genetic alterations identified by high throughput DNA sequencing. Both awareness of the specific quantitative and/or qualitative effects of individual variants and the elucidation of allelic and non-allelic interactions are essential to optimize genetic diagnosis and counselling.
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5
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Shirokova O, Zaborskaya O, Pchelin P, Kozliaeva E, Pershin V, Mukhina I. Genetic and Epigenetic Sexual Dimorphism of Brain Cells during Aging. Brain Sci 2023; 13:brainsci13020195. [PMID: 36831738 PMCID: PMC9954625 DOI: 10.3390/brainsci13020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
In recent years, much of the attention paid to theoretical and applied biomedicine, as well as neurobiology, has been drawn to various aspects of sexual dimorphism due to the differences that male and female brain cells demonstrate during aging: (a) a dimorphic pattern of response to therapy for neurodegenerative disorders, (b) different age of onset and different degrees of the prevalence of such disorders, and (c) differences in their symptomatic manifestations in men and women. The purpose of this review is to outline the genetic and epigenetic differences in brain cells during aging in males and females. As a result, we hereby show that the presence of brain aging patterns in males and females is due to a complex of factors associated with the effects of sex chromosomes, which subsequently entails a change in signal cascades in somatic cells.
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Affiliation(s)
- Olesya Shirokova
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Correspondence:
| | - Olga Zaborskaya
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
| | - Pavel Pchelin
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
| | - Elizaveta Kozliaeva
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
| | - Vladimir Pershin
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
| | - Irina Mukhina
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
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6
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A human adipose tissue cell-type transcriptome atlas. Cell Rep 2022; 40:111046. [PMID: 35830816 DOI: 10.1016/j.celrep.2022.111046] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 04/29/2022] [Accepted: 06/13/2022] [Indexed: 12/19/2022] Open
Abstract
The importance of defining cell-type-specific genes is well acknowledged. Technological advances facilitate high-resolution sequencing of single cells, but practical challenges remain. Adipose tissue is composed primarily of adipocytes, large buoyant cells requiring extensive, artefact-generating processing for separation and analysis. Thus, adipocyte data are frequently absent from single-cell RNA sequencing (scRNA-seq) datasets, despite being the primary functional cell type. Here, we decipher cell-type-enriched transcriptomes from unfractionated human adipose tissue RNA-seq data. We profile all major constituent cell types, using 527 visceral adipose tissue (VAT) or 646 subcutaneous adipose tissue (SAT) samples, identifying over 2,300 cell-type-enriched transcripts. Sex-subset analysis uncovers a panel of male-only cell-type-enriched genes. By resolving expression profiles of genes differentially expressed between SAT and VAT, we identify mesothelial cells as the primary driver of this variation. This study provides an accessible method to profile cell-type-enriched transcriptomes using bulk RNA-seq, generating a roadmap for adipose tissue biology.
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7
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Hu Y, Lauffer P, Stewart M, Codner G, Mayerl S, Heuer H, Ng L, Forrest D, Trotsenburg P, Jongejan A, Fliers E, Hennekam R, Boelen A. An animal model for Pierpont syndrome; a mouse bearing the Tbl1xr1Y446C/Y446C mutation. Hum Mol Genet 2022; 31:2951-2963. [PMID: 35416977 PMCID: PMC9433735 DOI: 10.1093/hmg/ddac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/23/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
Pierpont syndrome is a rare disorder characterized mainly by global developmental delay, unusual facial features, altered fat distribution in the limbs and hearing loss. A specific mutation (p.Tyr446Cys) in TBL1XR1, encoding a WD40 repeat-containing protein, which is a component of the SMRT/NCoR (silencing mediator retinoid and thyroid hormone receptors/nuclear receptor corepressors), has been reported as the genetic cause of Pierpont syndrome. Here, we used CRISPR-cas9 technology to generate a mutant mouse with the Y446C mutation in Tbl1xr1, which is also present in Pierpont syndrome. Several aspects of the phenotype were studied in the mutant mice: growth, body composition, hearing, motor behavior, thyroid hormone state and lipid and glucose metabolism. The mutant mice (Tbl1xr1Y446C/Y446C) displayed delayed growth, altered body composition with increased relative lean mass and impaired hearing. Expression of several genes involved in fatty acid metabolism differed in white adipose tissue, but not in liver or muscle of mutant mice compared to wild-type mice (Tbl1xr1+/+). No difference in thyroid hormone plasma concentrations was observed. Tbl1xr1Y446C/Y446C mice can be used as a model for distinct features of Pierpont syndrome, which will enable future studies on the pathogenic mechanisms underlying the various phenotypic characteristics.
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Affiliation(s)
- Yalan Hu
- Endocrine Laboratory, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Lauffer
- Department of Pediatric Endocrinology, Emma Children's Hospital, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Michelle Stewart
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Gemma Codner
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Steffen Mayerl
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Heike Heuer
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lily Ng
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Douglas Forrest
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Paul Trotsenburg
- Department of Pediatric Endocrinology, Emma Children's Hospital, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health, Methodology Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Eric Fliers
- Department of Endocrinology, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Raoul Hennekam
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anita Boelen
- Endocrine Laboratory, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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8
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Li G, Wang C, Guan X, Bai Y, Feng Y, Wei W, Meng H, Fu M, He M, Zhang X, Lu Y, Lin Y, Guo H. Age-related DNA methylation on Y chromosome and their associations with total mortality among Chinese males. Aging Cell 2022; 21:e13563. [PMID: 35120273 PMCID: PMC8920452 DOI: 10.1111/acel.13563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
In view of the sex differences in aging‐related diseases, sex chromosomes may play a critical role during aging process. This study aimed to identify age‐related DNA methylation changes on Y chromosome (ChrY). A two‐stage study design was conducted in this study. The discovery stage contained 419 Chinese males, including 205 from the Wuhan‐Zhuhai cohort panel, 107 from the coke oven workers panel, and 107 from the Shiyan panel. The validation stage contained 587 Chinese males from the Dongfeng‐Tongji sub‐cohort. We used the Illumina HumanMethylation BeadChip to determine genome‐wide DNA methylation in peripheral blood of the study participants. The associations between age and methylation levels of ChrY CpGs were investigated by using linear regression models with adjustment for potential confounders. Further, associations of age‐related ChrY CpGs with all‐cause mortality were tested in the validation stage. We identified the significant associations of 41 ChrY CpGs with age at false discovery rate (FDR) <0.05 in the discovery stage, and 18 of them were validated in the validation stage (p < 0.05). Meta‐analysis of both stages confirmed the robust positive associations of 14 CpGs and negative associations of 4 CpGs with age (FDR<0.05). Among them, cg03441493 and cg17816615 were significantly associated with all‐cause mortality risk [HR(95% CI) = 1.37 (1.04, 1.79) and 0.70 (0.54, 0.93), respectively]. Our results highlighted the importance of ChrY CpGs on male aging.
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Affiliation(s)
- Guyanan Li
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Department of Clinical Laboratory Medicine Shanghai Fifth People's Hospital Fudan University Shanghai China
| | - Chenming Wang
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xin Guan
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yansen Bai
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yue Feng
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wei Wei
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Hua Meng
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Ming Fu
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Meian He
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yanjun Lu
- Department of Laboratory Medicine Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yong Lin
- Department of Clinical Laboratory Medicine Shanghai Fifth People's Hospital Fudan University Shanghai China
- Department of Laboratory Medicine Huashan Hospital Fudan University Shanghai China
- National Clinical Research Center for Aging and Medicine Huashan Hospital Fudan University Shanghai China
| | - Huan Guo
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
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Identification of a New Mutation in RSK2, the Gene for Coffin-Lowry Syndrome (CLS), in Two Related Patients with Mild and Atypical Phenotypes. Brain Sci 2021; 11:brainsci11081105. [PMID: 34439726 PMCID: PMC8394959 DOI: 10.3390/brainsci11081105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Coffin–Lowry syndrome (CLS) is a syndromic form of X-linked intellectual disability, in which specific associated facial, hand, and skeletal abnormalities are diagnostic features. Methods: In the present study, an unreported missense genetic variant of the ribosomal S6 kinase 2 (RSK2) gene has been identified, by next-generation sequencing, in two related males with two different phenotypes of intellectual disability (ID) and peculiar facial dysmorphisms. We performed functional studies on this variant and another one, already reported in the literature, involving the same amino acid residue but, to date, without an efficient characterization. Results: Our study demonstrated that the two variants involving residue 189 significantly impaired its kinase activity. Conclusions: We detected a loss-of-function RSK2 mutation with loss in kinase activity in a three-generation family with an X-linked ID.
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Molecular characterization of the Yp11.2 region deletion in the Chinese Han population. Int J Legal Med 2021; 135:1351-1358. [PMID: 33903958 PMCID: PMC8205872 DOI: 10.1007/s00414-021-02596-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/03/2021] [Indexed: 12/28/2022]
Abstract
The Y chromosome is male-specific and is important for spermatogenesis and male fertility. However, the Y chromosome is poorly characterized due to massive palindromes and inverted repeats, which increase the likelihood of genomic rearrangements, resulting in short tandem repeats on the Y chromosome or long fragment deletions. The present study reports a large-scale (2.573~2.648 Mb) deletion in the Yp11.2 region in a Chinese population based on the analysis of 34 selected Y-specific sequence-tagged sites and subsequent sequencing of the breakpoint junctions on the Y chromosome from 5,068,482–5,142,391 bp to 7,715,462–7,716,695 bp. The results of sequence analysis indicated that the deleted region included part or all of the following five genes: PCDH11Y, TSPY, AMELY, TBL1Y, and RKY. These genes are associated with spermatogenesis or amelogenesis and various other processes; however, specific physiological functions and molecular mechanisms of these genes remain unclear. Notably, individuals with this deletion pattern did not have an obvious pathological phenotype but manifested some degree of amelogenesis imperfecta.
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11
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Lauffer P, Zwaveling-Soonawala N, Naafs JC, Boelen A, van Trotsenburg ASP. Diagnosis and Management of Central Congenital Hypothyroidism. Front Endocrinol (Lausanne) 2021; 12:686317. [PMID: 34566885 PMCID: PMC8458656 DOI: 10.3389/fendo.2021.686317] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/13/2021] [Indexed: 11/21/2022] Open
Abstract
Central congenital hypothyroidism (CH) is defined as thyroid hormone (TH) deficiency at birth due to insufficient stimulation by the pituitary of the thyroid gland. The incidence of central CH is currently estimated at around 1:13,000. Central CH may occur in isolation, but in the majority of cases (60%) it is part of combined pituitary hormone deficiencies (CPHD). In recent years several novel genetic causes of isolated central CH have been discovered (IGSF1, TBL1X, IRS4), and up to 90% of isolated central CH cases can be genetically explained. For CPHD the etiology usually remains unknown, although pituitary stalk interruption syndrome does seem to be the most common anatomic pituitary malformation associated with CPHD. Recent studies have shown that central CH is a more severe condition than previously thought, and that early detection and treatment leads to good neurodevelopmental outcome. However, in the neonatal period the clinical diagnosis is often missed despite hospital admission because of feeding problems, hypoglycemia and prolonged jaundice. This review provides an update on the etiology and prognosis of central CH, and a practical approach to diagnosis and management of this intriguing condition.
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Affiliation(s)
- Peter Lauffer
- Emma Children’s Hospital, Amsterdam University Medical Centers (UMC), Department of Pediatric Endocrinology, University of Amsterdam, Amsterdam, Netherlands
| | - Nitash Zwaveling-Soonawala
- Emma Children’s Hospital, Amsterdam University Medical Centers (UMC), Department of Pediatric Endocrinology, University of Amsterdam, Amsterdam, Netherlands
| | - Jolanda C. Naafs
- Emma Children’s Hospital, Amsterdam University Medical Centers (UMC), Department of Pediatric Endocrinology, University of Amsterdam, Amsterdam, Netherlands
| | - Anita Boelen
- Endocrine Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - A. S. Paul van Trotsenburg
- Emma Children’s Hospital, Amsterdam University Medical Centers (UMC), Department of Pediatric Endocrinology, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: A. S. Paul van Trotsenburg,
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12
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Godfrey AK, Naqvi S, Chmátal L, Chick JM, Mitchell RN, Gygi SP, Skaletsky H, Page DC. Quantitative analysis of Y-Chromosome gene expression across 36 human tissues. Genome Res 2020; 30:860-873. [PMID: 32461223 PMCID: PMC7370882 DOI: 10.1101/gr.261248.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Little is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across 36 human tissues from hundreds of individuals. Although it is often said that Y-Chromosome genes are lowly expressed outside the testis, we report many instances of elevated Y-Chromosome gene expression in a nonreproductive tissue. A notable example is EIF1AY, which encodes eukaryotic translation initiation factor 1A Y-linked, together with its X-linked homolog EIF1AX. Evolutionary loss of a Y-linked microRNA target site enabled up-regulation of EIF1AY, but not of EIF1AX, in the heart. Consequently, this essential translation initiation factor is nearly twice as abundant in male as in female heart tissue at the protein level. Divergence between the X and Y Chromosomes in regulatory sequence can therefore lead to tissue-specific Y-Chromosome-driven sex biases in expression of critical, dosage-sensitive regulatory genes.
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Affiliation(s)
- Alexander K Godfrey
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sahin Naqvi
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Lukáš Chmátal
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard N Mitchell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
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13
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Molecular Characterization of Mosaicism for a Small Supernumerary Marker Chromosome Derived from Chromosome Y in an Infertile Male with Apparently Normal Phenotype: A Case Report and Literature Review. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9398275. [PMID: 31828149 PMCID: PMC6885818 DOI: 10.1155/2019/9398275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/14/2019] [Accepted: 11/01/2019] [Indexed: 01/31/2023]
Abstract
Small supernumerary marker chromosomes (sSMCs), equal in size or smaller than chromosome 20 of the same metaphase, can hardly be identified through traditional banding technique. They are usually associated with intelligent disability, growth retardation, and infertility, but the genotype-phenotype correlations are still complicated for their complex origins and constitutions. Herein, we identified a 26-year-old Chinese infertile male who carried a mosaic sSMC and was diagnosed as severe oligospermia. The G-banding analysis initially described his karyotype as mos 47, XY, +mar[32]/46, XY[18]. The chromosomal microarray analysis results showed a 25.5 Mb gain in Yp11.31q11.23 and a 0.15 Mb loss in Yq12. Two SRY signals were discovered in the “seemingly” normal chromosome Y in both cell lines using SRY probe: one normal SRY was located on the distal tip of the short arm of chromosome Y while the other SRY was located on the terminal of long arm in the same chromosome Y. The sSMC(Y) was finally identified as der(Y) (pter ⟶ q11.23) (SRY-). To our knowledge, the chromosomal Y anomalies, SRY gene translocated from der(Y) (pter ⟶ q11.23) to qter of normal chromosome Y, were not reported before. Our findings indicated that the mosaic presence of sSMC(Y) may be the main cause of severe oligospermia although no other apparent abnormalities were observed in the proband. Further research on association between sSMC(Y) and spermatogenesis impairment should be investigated. It is recommended measures of traditional and molecular cytogenetic analysis should be taken to determine the origins and constitutions of sSMC so as to offer more appropriate genetic counseling for the infertile sSMC carriers.
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14
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Naz S, Friedman TB. Growth factor and receptor malfunctions associated with human genetic deafness. Clin Genet 2019; 97:138-155. [PMID: 31506927 DOI: 10.1111/cge.13641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/22/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022]
Abstract
A variety of different signaling pathways are necessary for development and maintenance of the human auditory system. Normal hearing allows for the detection of soft sounds within the frequency range of 20 to 20 000 Hz, but more importantly to perceive the human voice frequency band of 250 to 6000 Hz. Loss of hearing is common, and is a clinically heterogeneous disorder that can be caused by environmental factors such as exposure to loud noise, infections and ototoxic drugs. In addition, variants of hundreds of genes have been reported to disrupt processes required for hearing. Noncoding regulatory variants and variants of additional genes necessary for hearing remain to be discovered as many individuals with inherited deafness are without a genetic diagnosis, despite the advent of whole exome sequencing. Here, we discuss in detail some of these deafness-causing variants of genes encoding a ligand or its receptor. Spotlighted in this review are three growth factor-receptor-pairs EDN3/EDNRB, HGF/MET and JAG/NOTCH, which individually are necessary for normal hearing. We also offer our perspective on unanswered questions, future challenges and potential opportunities for treatments emerging from molecular genetic and mechanistic studies of deafness due to these causes.
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Affiliation(s)
- Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
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15
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San Roman AK, Page DC. A strategic research alliance: Turner syndrome and sex differences. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:59-67. [PMID: 30790449 DOI: 10.1002/ajmg.c.31677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 12/11/2022]
Abstract
Sex chromosome constitution varies in the human population, both between the sexes (46,XX females and 46,XY males), and within the sexes (e.g., 45,X and 46,XX females, and 47,XXY and 46,XY males). Coincident with this genetic variation are numerous phenotypic differences between males and females, and individuals with sex chromosome aneuploidy. However, the molecular mechanisms by which sex chromosome constitution impacts phenotypes at the cellular, tissue, and organismal levels remain largely unexplored. Thus, emerges a fundamental question connecting the study of sex differences and sex chromosome aneuploidy syndromes: How does sex chromosome constitution influence phenotype? Here, we focus on Turner syndrome (TS), associated with the 45,X karyotype, and its synergies with the study of sex differences. We review findings from evolutionary studies of the sex chromosomes, which identified genes that are most likely to contribute to phenotypes as a result of variation in sex chromosome constitution. We then explore strategies for investigating the direct effects of the sex chromosomes, and the evidence for specific sex chromosome genes impacting phenotypes. In sum, we argue that integrating the study of TS with sex differences offers a mutually beneficial alliance to identify contributions of the sex chromosomes to human development, health, and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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