1
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Fadra N, Schultz-Rogers LE, Chanana P, Cousin MA, Macke EL, Ferrer A, Pinto E Vairo F, Olson RJ, Oliver GR, Mulvihill LA, Jenkinson G, Klee EW. Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease. BMC Genomics 2024; 25:371. [PMID: 38627676 PMCID: PMC11020449 DOI: 10.1186/s12864-024-10240-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential inactivation of either the maternal or paternal copy of the X chromosome in a majority of cells results in a skewed or non-random pattern of X inactivation and is observed in over 25% of adult females. Identifying skewed X inactivation is of clinical significance in patients with suspected rare genetic diseases due to the possibility of biased expression of disease-causing genes present on the active X chromosome. The current clinical test for the detection of skewed XCI relies on the methylation status of the methylation-sensitive restriction enzyme (Hpall) binding site present in proximity of short tandem polymorphic repeats on the androgen receptor (AR) gene. This approach using one locus results in uninformative or inconclusive data for 10-20% of tests. Further, recent studies have shown inconsistency between methylation of the AR locus and the state of inactivation of the X chromosome. Herein, we develop a method for estimating X inactivation status, using exome and transcriptome sequencing data derived from blood in 227 female samples. We built a reference model for evaluation of XCI in 135 females from the GTEx consortium. We tested and validated the model on 11 female individuals with different types of undiagnosed rare genetic disorders who were clinically tested for X-skew using the AR gene assay and compared results to our outlier-based analysis technique. RESULTS In comparison to the AR clinical test for identification of X inactivation, our method was concordant with the AR method in 9 samples, discordant in 1, and provided a measure of X inactivation in 1 sample with uninformative clinical results. We applied this method on an additional 81 females presenting to the clinic with phenotypes consistent with different hereditary disorders without a known genetic diagnosis. CONCLUSIONS This study presents the use of transcriptome and exome sequencing data to provide an accurate and complete estimation of X-inactivation and skew status in a cohort of female patients with different types of suspected rare genetic disease.
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Affiliation(s)
- Numrah Fadra
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Pritha Chanana
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Margot A Cousin
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Garrett Jenkinson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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2
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Dori A, Scutifero M, Passamano L, Zoppi D, Ruggiero L, Trabacca A, Politano L. Treatment with ataluren in four symptomatic Duchenne carriers. A pilot study. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2024; 43:8-15. [PMID: 38586166 PMCID: PMC10997039 DOI: 10.36185/2532-1900-398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/01/2024] [Indexed: 04/09/2024]
Abstract
Duchenne muscular dystrophy (DMD) is a devastating X-linked neuromuscular disorder caused by dystrophin gene deletions (75%), duplications (15-20%) and point mutations (5-10%), a small portion of which are nonsense mutations. Women carrying dystrophin gene mutations are commonly unaffected because the wild X allele may produce a sufficient amount of the dystrophin protein. However, approximately 8-10% of them may experience muscle symptoms and 50% of those over 40 years develop cardiomyopathy. The presence of symptoms defines the individual as an affected "symptomatic or manifesting carrier". Though there is no effective cure for DMD, therapies are available to slow the decline of muscle strength and delay the onset and progression of cardiac and respiratory impairment. These include ataluren for patients with nonsense mutations, and antisense oligonucleotides therapies, for patients with specific deletions. Symptomatic DMD female carriers are not included in these indications and little data documenting their management, often entrusted to the discretion of individual doctors, is present in the literature. In this article, we report the clinical and instrumental outcomes of four symptomatic DMD carriers, aged between 26 and 45 years, who were treated with ataluren for 21 to 73 months (average 47.3), and annually evaluated for muscle strength, respiratory and cardiological function. Two patients retain independent ambulation at ages 33 and 45, respectively. None of them developed respiratory involvement or cardiomyopathy. No clinical adverse effects or relevant abnormalities in routine laboratory values, were observed.
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Affiliation(s)
- Amir Dori
- Department of Neurology, Chaim Sheba Medical Center, HaShomer, and Joseph Sagol Neuroscience Center, Faculty of Medicine, Aviv University, Aviv, Israel
| | - Marianna Scutifero
- Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Luigia Passamano
- Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Dario Zoppi
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, Naples, Italy
| | - Lucia Ruggiero
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples “Federico II”, Naples, Italy
| | - Antonio Trabacca
- Scientific Institute IRCCS “E. Medea”, Unit for Severe disabilities in developmental age and young adults (Developmental Neurology and Neurorehabilitation), Brindisi, Italy
| | - Luisa Politano
- Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
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Matsumoto A, Kano S, Kobayashi N, Matsuki M, Furukawa R, Yamagishi H, Yoshinari H, Nakata W, Wakabayashi H, Tsuda H, Watanabe K, Takahashi H, Yamagata T, Matsumura T, Osaka H, Mori H, Iwamoto S. Unfavorable switching of skewed X chromosome inactivation leads to Menkes disease in a female infant. Sci Rep 2024; 14:440. [PMID: 38172222 PMCID: PMC10764769 DOI: 10.1038/s41598-023-50668-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Menkes disease is an X-linked disorder of copper metabolism caused by mutations in the ATP7A gene, and female carriers are usually asymptomatic. We describe a 7-month-old female patient with severe intellectual disability, epilepsy, and low levels of serum copper and ceruloplasmin. While heterozygous deletion of exons 16 and 17 of the ATP7A gene was detected in the proband, her mother, and her grandmother, only the proband suffered from Menkes disease clinically. Intriguingly, X chromosome inactivation (XCI) analysis demonstrated that the grandmother and the mother showed skewing of XCI toward the allele with the ATP7A deletion and that the proband had extremely skewed XCI toward the normal allele, resulting in exclusive expression of the pathogenic ATP7A mRNA transcripts. Expression bias analysis and recombination mapping of the X chromosome by the combination of whole genome and RNA sequencing demonstrated that meiotic recombination occurred at Xp21-p22 and Xq26-q28. Assuming that a genetic factor on the X chromosome enhanced or suppressed XCI of its allele, the factor must be on either of the two distal regions derived from her grandfather. Although we were unable to fully uncover the molecular mechanism, we concluded that unfavorable switching of skewed XCI caused Menkes disease in the proband.
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Affiliation(s)
- Ayumi Matsumoto
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Shintaro Kano
- Department of Radiology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Natsumi Kobayashi
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Mitsuru Matsuki
- Department of Radiology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Rieko Furukawa
- Department of Radiology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hirokazu Yamagishi
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hiroki Yoshinari
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Waka Nakata
- Department of Radiology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hiroko Wakabayashi
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hidetoshi Tsuda
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Kazuhisa Watanabe
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hironori Takahashi
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Takanori Yamagata
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Takayoshi Matsumura
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
- Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Harushi Mori
- Department of Radiology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Sadahiko Iwamoto
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan.
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Moysés-Oliveira M, Favilla BP, Melaragno MI, Tufik S. X-Chromosome Dependent Differences in the Neuronal Molecular Signatures and Their Implications in Sleep Patterns. Sleep Med Clin 2023; 18:521-531. [PMID: 38501524 DOI: 10.1016/j.jsmc.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Biological factors and mechanisms that drive sex differences observed in sleep disturbances are understudied and poorly understood. The extent to which sex chromosome constitution impacts on sex differences in circadian patterns is still a knowledge void in the sleep medicine field. Here we focus on the neurological consequences of X-chromosome functional imbalances between males and females and how this molecular inequality might affect sex divergencies on sleep. In light of the X-chromosome inactivation mechanism in females and its implications in gene regulation, we describe sleep-related neuronal circuits and brain regions impacted by sex-biased modulations of the transcriptome and the epigenome. Benefited from recent large-scale genetic studies on the interplay between X-chromosome and brain function, we list clinically relevant genes that might play a role in sex differences in neuronal pathways. Those molecular signatures are put into the context of sleep and sleep-associated neurological phenotypes, aiming to identify biological mechanisms that link X-chromosome gene regulation to sex-biased human traits. These findings are a significant step forward in understanding how X-linked genes manifest in sleep-associated transcriptional networks and point to future research opportunities to address female-specific clinical manifestations and therapeutic responses.
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Affiliation(s)
- Mariana Moysés-Oliveira
- Sleep Institute, Associação Fundo de Incentivo à Pesquisa, Rua Marselhea, 500, São Paulo, São Paulo, Brazil
| | - Bianca Pereira Favilla
- Genetics Division, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sergio Tufik
- Sleep Institute, Associação Fundo de Incentivo à Pesquisa, Rua Marselhea, 500, São Paulo, São Paulo, Brazil; Departamento de Psicobiologia, Universidade Federal de São Paulo, São Paulo, Brazil.
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5
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Peeters SB, Posynick BJ, Brown CJ. Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation. EPIGENOMES 2023; 7:29. [PMID: 38131901 PMCID: PMC10742877 DOI: 10.3390/epigenomes7040029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be expressed from the otherwise inactive X chromosome-in some cases constitutively, while other genes are variable between individuals, tissues or cells. In this review we discuss the advantages and disadvantages of the approaches that have been used to identify escapees. The identity of escapees provides important clues to mechanisms underlying escape from XCI, an arena of study now moving from correlation to functional studies. As most escapees show greater expression in females, the not-so-inactive X chromosome is a substantial contributor to sex differences in humans, and we highlight some examples of such impact.
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Affiliation(s)
| | | | - Carolyn J. Brown
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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6
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Ballouz S, Kawaguchi RK, Pena MT, Fischer S, Crow M, French L, Knight FM, Adams LB, Gillis J. The transcriptional legacy of developmental stochasticity. Nat Commun 2023; 14:7226. [PMID: 37940702 PMCID: PMC10632366 DOI: 10.1038/s41467-023-43024-5] [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: 01/06/2022] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Genetic and environmental variation are key contributors during organism development, but the influence of minor perturbations or noise is difficult to assess. This study focuses on the stochastic variation in allele-specific expression that persists through cell divisions in the nine-banded armadillo (Dasypus novemcinctus). We investigated the blood transcriptome of five wild monozygotic quadruplets over time to explore the influence of developmental stochasticity on gene expression. We identify an enduring signal of autosomal allelic variability that distinguishes individuals within a quadruplet despite their genetic similarity. This stochastic allelic variation, akin to X-inactivation but broader, provides insight into non-genetic influences on phenotype. The presence of stochastically canalized allelic signatures represents a novel axis for characterizing organismal variability, complementing traditional approaches based on genetic and environmental factors. We also developed a model to explain the inconsistent penetrance associated with these stochastically canalized allelic expressions. By elucidating mechanisms underlying the persistence of allele-specific expression, we enhance understanding of development's role in shaping organismal diversity.
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Affiliation(s)
- Sara Ballouz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Risa Karakida Kawaguchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Maria T Pena
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare System Bureau, National Hansen's Disease Program, Baton Rouge, LA, 70803, USA
| | - Stephan Fischer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, F-75015, France
| | - Megan Crow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Genentech, Inc., South San Francisco, CA, USA
| | - Leon French
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | | | - Linda B Adams
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare System Bureau, National Hansen's Disease Program, Baton Rouge, LA, 70803, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
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7
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Giovenino C, Trajkova S, Pavinato L, Cardaropoli S, Pullano V, Ferrero E, Sukarova-Angelovska E, Carestiato S, Salmin P, Rinninella A, Battaglia A, Bertoli L, Fadda A, Palermo F, Carli D, Mussa A, Dimartino P, Bruselles A, Froukh T, Mandrile G, Pasini B, De Rubeis S, Buxbaum JD, Pippucci T, Tartaglia M, Rossato M, Delledonne M, Ferrero GB, Brusco A. Skewed X-chromosome inactivation in unsolved neurodevelopmental disease cases can guide re-evaluation For X-linked genes. Eur J Hum Genet 2023; 31:1228-1236. [PMID: 36879111 PMCID: PMC10620389 DOI: 10.1038/s41431-023-01324-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/24/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Despite major advances in genome technology and analysis, >50% of patients with a neurodevelopmental disorder (NDD) remain undiagnosed after extensive evaluation. A point in case is our clinically heterogeneous cohort of NDD patients that remained undiagnosed after FRAXA testing, chromosomal microarray analysis and trio exome sequencing (ES). In this study, we explored the frequency of non-random X chromosome inactivation (XCI) in the mothers of male patients and affected females, the rationale being that skewed XCI might be masking previously discarded genetic variants found on the X chromosome. A multiplex fluorescent PCR-based assay was used to analyse the pattern of XCI after digestion with HhaI methylation-sensitive restriction enzyme. In families with skewed XCI, we re-evaluated trio-based ES and identified pathogenic variants and a deletion on the X chromosome. Linkage analysis and RT-PCR were used to further study the inactive X chromosome allele, and Xdrop long-DNA technology was used to define chromosome deletion boundaries. We found skewed XCI (>90%) in 16/186 (8.6%) mothers of NDD males and in 12/90 (13.3%) NDD females, far beyond the expected rate of XCI in the normal population (3.6%, OR = 4.10; OR = 2.51). By re-analyzing ES and clinical data, we solved 7/28 cases (25%) with skewed XCI, identifying variants in KDM5C, PDZD4, PHF6, TAF1, OTUD5 and ZMYM3, and a deletion in ATRX. We conclude that XCI profiling is a simple assay that targets a subgroup of patients that can benefit from re-evaluation of X-linked variants, thus improving the diagnostic yield in NDD patients and identifying new X-linked disorders.
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Affiliation(s)
- Chiara Giovenino
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Verdiana Pullano
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Pediatric Diseases, Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, 1000, Skopje, Republic of North Macedonia
| | - Silvia Carestiato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Paola Salmin
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | - Antonina Rinninella
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 94124, Catania, Italy
| | - Anthony Battaglia
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Luca Bertoli
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Antonio Fadda
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Flavia Palermo
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Alessandro Bruselles
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, University of Torino, Orbassano, TO, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tommaso Pippucci
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italia
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marzia Rossato
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Massimo Delledonne
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | | | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy.
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8
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Werner JM, Hover J, Gillis J. Population variability in X-chromosome inactivation across 9 mammalian species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562732. [PMID: 37904929 PMCID: PMC10614859 DOI: 10.1101/2023.10.17.562732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
One of the two X chromosomes in female mammals is epigenetically silenced in embryonic stem cells by X chromosome inactivation (XCI). This creates a mosaic of cells expressing either the maternal or the paternal X allele. The XCI ratio, the proportion of inactivated parental alleles, varies widely among individuals, representing the largest instance of epigenetic variability within mammalian populations. While various contributing factors to XCI variability are recognized, namely stochastic and/or genetic effects, their relative contributions are poorly understood. This is due in part to limited cross-species analysis, making it difficult to distinguish between generalizable or species-specific mechanisms for XCI ratio variability. To address this gap, we measured XCI ratios in nine mammalian species (9,143 individual samples), ranging from rodents to primates, and compared the strength of stochastic models or genetic factors for explaining XCI variability. Our results demonstrate the embryonic stochasticity of XCI is a general explanatory model for population XCI variability in mammals, while genetic factors play a minor role.
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Affiliation(s)
- Jonathan M Werner
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - John Hover
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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9
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Johansson J, Lidéus S, Höijer I, Ameur A, Gudmundsson S, Annerén G, Bondeson ML, Wilbe M. A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing. Sci Rep 2023; 13:12856. [PMID: 37553382 PMCID: PMC10409790 DOI: 10.1038/s41598-023-34413-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/29/2023] [Indexed: 08/10/2023] Open
Abstract
X-chromosome inactivation (XCI) analyses often assist in diagnostics of X-linked traits, however accurate assessment remains challenging with current methods. We developed a novel strategy using amplification-free Cas9 enrichment and Oxford nanopore technologies sequencing called XCI-ONT, to investigate and rigorously quantify XCI in human androgen receptor gene (AR) and human X-linked retinitis pigmentosa 2 gene (RP2). XCI-ONT measures methylation over 116 CpGs in AR and 58 CpGs in RP2, and separate parental X-chromosomes without PCR bias. We show the usefulness of the XCI-ONT strategy over the PCR-based golden standard XCI technique that only investigates one or two CpGs per gene. The results highlight the limitations of using the golden standard technique when the XCI pattern is partially skewed and the advantages of XCI-ONT to rigorously quantify XCI. This study provides a universal XCI-method on DNA, which is highly valuable in clinical and research framework of X-linked traits.
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Affiliation(s)
- Josefin Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Sarah Lidéus
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Ida Höijer
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Sanna Gudmundsson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Marie-Louise Bondeson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Maria Wilbe
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden.
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10
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Buono MF, Benavente ED, Daniels M, Mol BM, Mekke JM, de Borst GJ, de Kleijn DPV, van der Laan SW, Pasterkamp G, Onland-Moret C, Mokry M, den Ruijter HM. X chromosome inactivation skewing is common in advanced carotid atherosclerotic lesions in females and predicts secondary peripheral artery events. Biol Sex Differ 2023; 14:43. [PMID: 37408072 DOI: 10.1186/s13293-023-00527-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/24/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND AND AIM Sex differences in atherosclerosis have been described with female plaques being mostly perceived as stable and fibrous. Sex-specific mechanisms such as mosaic loss of the Y chromosome in men have been linked to cardiovascular health. In women, X-linked mechanisms such as X chromosome inactivation (XCI) skewing is common in several tissues. Yet, information on the role of XCI in female atherosclerotic plaques is lacking. Here, we investigated the presence of XCI skewing in advanced atherosclerotic lesions and its association with cardiovascular risk factors, histological plaque data, and clinical data. METHODS XCI skewing was quantified in 154 atherosclerotic plaque and 55 blood DNA samples of women included in the Athero-Express study. The skewing status was determined performing the HUMARA assay. Then, we studied the relationship of XCI skewing in female plaque and cardiovascular risk factors using regression models. In addition, we studied if plaque XCI predicted plaque composition, and adverse events during 3-years follow-up using Cox proportional hazard models. RESULTS XCI skewing was detected in 76 of 154 (49.4%) plaques and in 27 of 55 (67%) blood samples. None of the clinical risk factors were associated with plaque skewing. Plaque skewing was more often detected in plaques with a plaque hemorrhage (OR [95% CI]: 1.44 [1.06-1.98], P = 0.02). Moreover, skewed plaques were not associated with a higher incidence of composite and major events but were specifically associated with peripheral artery events during a 3-year follow-up period in a multivariate model (HR [95%CI]: 1.46 [1.09-1.97]; P = 0.007). CONCLUSIONS XCI skewing is common in carotid plaques of females and is predictive for the occurrence of peripheral artery events within 3 years after carotid endarterectomy.
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Affiliation(s)
- Michele F Buono
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark Daniels
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Barend M Mol
- Department of Vascular Surgery, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joost M Mekke
- Department of Vascular Surgery, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Gert J de Borst
- Department of Vascular Surgery, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Charlotte Onland-Moret
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Michal Mokry
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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11
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Minić S, Cerovac N, Novaković I, Gazikalović S, Popadić S, Trpinac D. The Impact of the IKBKG Gene on the Appearance of the Corpus Callosum Abnormalities in Incontinentia Pigmenti. Diagnostics (Basel) 2023; 13:diagnostics13071300. [PMID: 37046518 PMCID: PMC10093331 DOI: 10.3390/diagnostics13071300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/19/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Incontinentia pigmenti (IP) is a rare skin disease combined with anomalies of the teeth, eyes, and central nervous system (CNS). Mutations of the IKBKG gene are responsible for IP. Among the most frequent CNS abnormalities found in IP using magnetic resonance imaging (MRI) are corpus callosum (CC) abnormalities. The aim of the study was to determine the presence of CC abnormalities, their relationship with the IKBKG mutations, and the possible presence of mutations of other genes. A group of seven IP patients was examined. Analyses of the IKBKG gene and the X-chromosome inactivation pattern were performed, as well as MRI and whole exome sequencing (WES) with the focus on the genes relevant for neurodegeneration. WES analysis showed IKBKG mutation in all examined patients. A patient who had a mutation of a gene other than IKBKG was excluded from further study. Four of the seven patients had clinically diagnosed CNS anomalies; two out of four had MRI-diagnosed CC anomalies. The simultaneous presence of IKBKG mutation and CC abnormalities and the absence of other mutations indicate that IKBKG may be the cause of CC abnormalities and should be included in the list of genes responsible for CC abnormalities.
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12
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Kong YF, Li SZ, Wang KW, Zhu B, Yuan YX, Li MK, Zhou JY. An Efficient Bayesian Method for Estimating the Degree of the Skewness of X Chromosome Inactivation Based on the Mixture of General Pedigrees and Unrelated Females. Biomolecules 2023; 13:biom13030543. [PMID: 36979477 PMCID: PMC10046098 DOI: 10.3390/biom13030543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Skewed X chromosome inactivation (XCI-S) has been reported to be associated with some X-linked diseases. Several methods have been proposed to estimate the degree of XCI-S (denoted as γ) for quantitative and qualitative traits based on unrelated females. However, there is no method available for estimating γ based on general pedigrees. Therefore, in this paper, we propose a Bayesian method to obtain the point estimate and the credible interval of γ based on the mixture of general pedigrees and unrelated females (called mixed data for brevity), which is also suitable for only general pedigrees. We consider the truncated normal prior and the uniform prior for γ. Further, we apply the eigenvalue decomposition and Cholesky decomposition to our proposed methods to accelerate the computation speed. We conduct extensive simulation studies to compare the performances of our proposed methods and two existing Bayesian methods which are only applicable to unrelated females. The simulation results show that the incorporation of general pedigrees can improve the efficiency of the point estimation and the precision and the accuracy of the interval estimation of γ. Finally, we apply the proposed methods to the Minnesota Center for Twin and Family Research data for their practical use.
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Affiliation(s)
- Yi-Fan Kong
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Shi-Zhu Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Kai-Wen Wang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Bin Zhu
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Yu-Xin Yuan
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Meng-Kai Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Ji-Yuan Zhou
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
- Correspondence:
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13
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Escape from X-inactivation in twins exhibits intra- and inter-individual variability across tissues and is heritable. PLoS Genet 2023; 19:e1010556. [PMID: 36802379 PMCID: PMC9942974 DOI: 10.1371/journal.pgen.1010556] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/06/2022] [Indexed: 02/23/2023] Open
Abstract
X-chromosome inactivation (XCI) silences one X in female cells to balance sex-differences in X-dosage. A subset of X-linked genes escape XCI, but the extent to which this phenomenon occurs and how it varies across tissues and in a population is as yet unclear. To characterize incidence and variability of escape across individuals and tissues, we conducted a transcriptomic study of escape in adipose, skin, lymphoblastoid cell lines and immune cells in 248 healthy individuals exhibiting skewed XCI. We quantify XCI escape from a linear model of genes' allelic fold-change and XIST-based degree of XCI skewing. We identify 62 genes, including 19 lncRNAs, with previously unknown patterns of escape. We find a range of tissue-specificity, with 11% of genes escaping XCI constitutively across tissues and 23% demonstrating tissue-restricted escape, including cell type-specific escape across immune cells of the same individual. We also detect substantial inter-individual variability in escape. Monozygotic twins share more similar escape than dizygotic twins, indicating that genetic factors may underlie inter-individual differences in escape. However, discordant escape also occurs within monozygotic co-twins, suggesting environmental factors also influence escape. Altogether, these data indicate that XCI escape is an under-appreciated source of transcriptional differences, and an intricate phenotype impacting variable trait expressivity in females.
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14
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Dystrophin myonuclear domain restoration governs treatment efficacy in dystrophic muscle. Proc Natl Acad Sci U S A 2023; 120:e2206324120. [PMID: 36595689 PMCID: PMC9926233 DOI: 10.1073/pnas.2206324120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Dystrophin is essential for muscle health: its sarcolemmal absence causes the fatal, X-linked condition, Duchenne muscular dystrophy (DMD). However, its normal, spatial organization remains poorly understood, which hinders the interpretation of efficacy of its therapeutic restoration. Using female reporter mice heterozygous for fluorescently tagged dystrophin (DmdEGFP), we here reveal that dystrophin distribution is unexpectedly compartmentalized, being restricted to myonuclear-defined sarcolemmal territories extending ~80 µm, which we called "basal sarcolemmal dystrophin units (BSDUs)." These territories were further specialized at myotendinous junctions, where both Dmd transcripts and dystrophin protein were enriched. Genome-level correction in X-linked muscular dystrophy mice via CRISPR/Cas9 gene editing restored a mosaic of separated dystrophin domains, whereas transcript-level Dmd correction, following treatment with tricyclo-DNA antisense oligonucleotides, restored dystrophin initially at junctions before extending along the entire fiber-with levels ~2% sufficient to moderate the dystrophic process. We conclude that widespread restoration of fiber dystrophin is likely critical for therapeutic success in DMD, perhaps most importantly, at muscle-tendon junctions.
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15
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Juchniewicz P, Kloska A, Portalska K, Jakóbkiewicz-Banecka J, Węgrzyn G, Liss J, Głodek P, Tukaj S, Piotrowska E. X-chromosome inactivation patterns depend on age and tissue but not conception method in humans. Chromosome Res 2023; 31:4. [PMID: 36695960 PMCID: PMC9877087 DOI: 10.1007/s10577-023-09717-9] [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: 09/16/2022] [Revised: 11/27/2022] [Accepted: 12/06/2022] [Indexed: 01/26/2023]
Abstract
Female somatic X-chromosome inactivation (XCI) balances the X-linked transcriptional dosages between the sexes, randomly silencing the maternal or paternal X chromosome in each cell of 46,XX females. Skewed XCI toward one parental X has been observed in association with ageing and in some female carriers of X-linked diseases. To address the problem of non-random XCI, we quantified the XCI skew in different biological samples of naturally conceived females of different age groups and girls conceived after in vitro fertilization (IVF). Generally, XCI skew differed between saliva, blood, and buccal swabs, while saliva and blood had the most similar XCI patterns in individual females. XCI skew increased with age in saliva, but not in other tissues. We showed no significant differences in the XCI patterns in tissues of naturally conceived and IVF females. The gene expression profile of the placenta and umbilical cord blood was determined depending on the XCI pattern. The increased XCI skewing in the placental tissue was associated with the differential expression of several genes out of 40 considered herein. Notably, skewed XCI patterns (> 80:20) were identified with significantly increased expression levels of four genes: CD44, KDM6A, PHLDA2, and ZRSR2. The differences in gene expression patterns between samples with random and non-random XCI may shed new light on factors contributing to the XCI pattern outcome and indicate new paths in future research on the phenomenon of XCI skewing.
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Affiliation(s)
- Patrycja Juchniewicz
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Anna Kloska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Karolina Portalska
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Joanna Jakóbkiewicz-Banecka
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Joanna Liss
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland ,Research and Development Center, INVICTA, Sopot, Poland
| | - Piotr Głodek
- Research and Development Center, INVICTA, Sopot, Poland
| | - Stefan Tukaj
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Ewa Piotrowska
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
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16
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Voskuhl R, Itoh Y. The X factor in neurodegeneration. J Exp Med 2022; 219:e20211488. [PMID: 36331399 PMCID: PMC9641640 DOI: 10.1084/jem.20211488] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/22/2022] [Accepted: 10/12/2022] [Indexed: 07/25/2023] Open
Abstract
Given the aging population, it is important to better understand neurodegeneration in aging healthy people and to address the increasing incidence of neurodegenerative diseases. It is imperative to apply novel strategies to identify neuroprotective therapeutics. The study of sex differences in neurodegeneration can reveal new candidate treatment targets tailored for women and men. Sex chromosome effects on neurodegeneration remain understudied and represent a promising frontier for discovery. Here, we will review sex differences in neurodegeneration, focusing on the study of sex chromosome effects in the context of declining levels of sex hormones during aging.
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Affiliation(s)
- Rhonda Voskuhl
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Yuichiro Itoh
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
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17
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Szűcs Z, Pinti É, Haltrich I, Szén OP, Nagy T, Barta E, Méhes G, Bidiga L, Török O, Ujfalusi A, Koczok K, Balogh I. An Ultra-Rare Manifestation of an X-Linked Recessive Disorder: Duchenne Muscular Dystrophy in a Female Patient. Int J Mol Sci 2022; 23:ijms232113076. [PMID: 36361862 PMCID: PMC9655586 DOI: 10.3390/ijms232113076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is the most common inherited muscle dystrophy. Patients are characterized by muscle weakness, gross motor delay, and elevated serum creatinine kinase (CK) levels. The disease is caused by mutations in the DMD gene located on the X chromosome. Due to the X-linked recessive inheritance pattern, DMD most commonly affects males, who are generally diagnosed between the age of 3–5 years. Here we present an ultra-rare manifestation of DMD in a female patient. Cytogenetic examination showed that she has a t(X;10)(p21.1;p12.1) translocation, which turned out to affect the DMD gene with one of the breakpoints located in exon 54 (detected by genome sequencing). The X-inactivation test revealed skewed X-inactivation (ratio 99:1). Muscle histology and dystrophin immunohistochemistry showed severe dystrophic changes and highly reduced dystrophin expression, respectively. These results, in accordance with the clinical picture and a highly elevated serum CK, led to the diagnosis of DMD. In conclusion, although in very rare cases, DMD can manifest in female patients as well. In this case, a balanced X-autosome reciprocal translocation disrupts the DMD gene and skewed X-inactivation leads to the manifestation of the DMD phenotype.
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Affiliation(s)
- Zsuzsanna Szűcs
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Éva Pinti
- 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - Irén Haltrich
- 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - Orsolya Pálné Szén
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Tibor Nagy
- Bioinformatics and Functional Genome Analysis Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Endre Barta
- Bioinformatics and Functional Genome Analysis Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - László Bidiga
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Olga Török
- Medical and Health Science Centre, Department of Obstetrics and Gynaecology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Anikó Ujfalusi
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Katalin Koczok
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (K.K.); (I.B.)
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (K.K.); (I.B.)
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18
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Yang ZY, Liu W, Yuan YX, Kong YF, Zhao PZ, Fung WK, Zhou JY. Robust association tests for quantitative traits on the X chromosome. Heredity (Edinb) 2022; 129:244-256. [PMID: 36085362 PMCID: PMC9519943 DOI: 10.1038/s41437-022-00560-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
The genome-wide association study is an elementary tool to assess the genetic contribution to complex human traits. However, such association tests are mainly proposed for autosomes, and less attention has been given to methods for identifying loci on the X chromosome due to their distinct biological features. In addition, the existing association tests for quantitative traits on the X chromosome either fail to incorporate the information of males or only detect variance heterogeneity. Therefore, we propose four novel methods, which are denoted as QXcat, QZmax, QMVXcat and QMVZmax. When using these methods, it is assumed that the risk alleles for females and males are the same and that the locus being studied satisfies the generalized genetic model for females. The first two methods are based on comparing the means of the trait value across different genotypes, while the latter two methods test for the difference of both means and variances. All four methods effectively incorporate the information of X chromosome inactivation. Simulation studies demonstrate that the proposed methods control the type I error rates well. Under the simulated scenarios, the proposed methods are generally more powerful than the existing methods. We also apply our proposed methods to data from the Minnesota Center for Twin and Family Research and find 10 single nucleotide polymorphisms that are statistically significantly associated with at least two traits at the significance level of 1 × 10-3.
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Affiliation(s)
- Zi-Ying Yang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Wei Liu
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yu-Xin Yuan
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yi-Fan Kong
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Pei-Zhen Zhao
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wing Kam Fung
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, China.
| | - Ji-Yuan Zhou
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China.
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19
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Skewed X-Chromosome Inactivation and Parental Gonadal Mosaicism Are Implicated in X-Linked Recessive Female Hemophilia Patients. Diagnostics (Basel) 2022; 12:diagnostics12102267. [PMID: 36291957 PMCID: PMC9600608 DOI: 10.3390/diagnostics12102267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/09/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Hemophilia A (HA) and B (HB) are X-linked recessive disorders that mainly affect males born from a mother carrier. Females are rarely affected but a number of mechanisms have been suggested in symptomatic females, such as skewed X-chromosome inactivation (XCI), chromosomal rearrangements, and hermaphrodites. Different methodologies are required to elucidate the underlying causes of such diseases in female patients. Methods: Three families with female hemophilia patients, including two HA and one HB, were enrolled for genetic analyses. Cytogenetics, molecular examinations on F8 and F9 genes, XCI assay, and linkage analysis were performed. Results: All three female patients are demonstrated to be heterozygous for an F8, or F9 mutation: one patient is inherited from her unaffected mother and the other two are sporadic cases. All three patients exhibit skewed XCI. The inherited patient is found to be unmethylated in the maternal X chromosome, which increases the potential for the expression of the mutant allele. The two sporadic cases are hypomethylated or unmethylated in the paternal X chromosome, suggesting that paternal gonadal mosaicism may exist in these families. Conclusions: In addition to screening for coagulation function, different genetic analyses are mandatory to explore the nature of mechanisms responsible for the X-linked recessive disorders in female patients as shown in this study. Our results confirm that skewed XCI is responsible for hemophilia in heterozygous female patients. Likewise, our results implicate that parental gonadal mosaicism, followed by skewed XCI, contributes to hemophilia in “sporadic” female patients.
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20
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Summers V. Sex differences in number of X chromosomes and X-chromosome inactivation in females promote greater variability in hearing among males. Biol Sex Differ 2022; 13:49. [PMID: 36114557 PMCID: PMC9482204 DOI: 10.1186/s13293-022-00457-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/27/2022] [Indexed: 01/19/2023] Open
Abstract
Background For more than 150 years, research studies have documented greater variability across males than across females (“greater male variability”—GMV) over a broad range of behavioral and morphological measures. In placental mammals, an ancient difference between males and females that may make an important contribution to GMV is the different pattern of activation of X chromosomes across cells in females (mosaic inactivation of one the two X chromosomes across cells) vs males (consistent activation of a single X chromosome in all cells). In the current study, variability in hearing thresholds was examined for human listeners with thresholds within the normal range. Initial analyses compared variability in thresholds across males vs. across females. If greater across-male than across-female variability was present, and if these differences in variability related to the different patterns X-chromosome activation in males vs. females, it was expected that correlations between related measures within a given subject (e.g., hearing thresholds at given frequency in the two ears) would be greater in males than females. Methods Hearing thresholds at audiometric test frequencies (500–6000 or 500–8000 Hz) were extracted from two datasets representing more than 8500 listeners with normal hearing (4590 males, 4376 females). Separate data analyses were carried out on each dataset to compare: (1) relative variability in hearing thresholds across males vs. across females at each test frequency; (2) correlations between both across-ear and within-ear hearing thresholds within males vs. within females, and (3) mean thresholds for females vs. males at each frequency. Results A consistent pattern of GMV in hearing thresholds was seen across frequencies in both datasets. In addition, both across-ear and within-ear correlations between thresholds were consistently greater in males than females. Previous studies have frequently reported lower mean thresholds for females than males for listeners with normal hearing. One of the datasets replicated this result, showing a clear and consistent pattern of lower mean thresholds for females. The second data set did not show clear evidence of this female advantage. Conclusions Hearing thresholds showed clear evidence of greater variability across males than across females and higher correlations across related threshold measures within males than within females. The results support a link between the observed GMV and the mosaic pattern of X-activation for females that is not present in males. Supplementary Information The online version contains supplementary material available at 10.1186/s13293-022-00457-9. Greater variability in hearing thresholds across males than females for human listeners with thresholds within the normal range. Higher within-ear and between-ear correlations between thresholds for males than females consistent with sex chromosome effects on variability NIH-mandated inclusion of sex as a biological variable should include sex differences in variability and underlying mechanisms
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21
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Werner JM, Ballouz S, Hover J, Gillis J. Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events. Dev Cell 2022; 57:1995-2008.e5. [PMID: 35914524 PMCID: PMC9398941 DOI: 10.1016/j.devcel.2022.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/11/2022] [Accepted: 07/07/2022] [Indexed: 12/14/2022]
Abstract
X-chromosome inactivation (XCI) is a random, permanent, and developmentally early epigenetic event that occurs during mammalian embryogenesis. We harness these features to investigate characteristics of early lineage specification events during human development. We initially assess the consistency of X-inactivation and establish a robust set of XCI-escape genes. By analyzing variance in XCI ratios across tissues and individuals, we find that XCI is shared across all tissues, suggesting that XCI is completed in the epiblast (in at least 6-16 cells) prior to specification of the germ layers. Additionally, we exploit tissue-specific variability to characterize the number of cells present during tissue-lineage commitment, ranging from approximately 20 cells in liver and whole blood tissues to 80 cells in brain tissues. By investigating the variability of XCI ratios using adult tissue, we characterize embryonic features of human XCI and lineage specification that are otherwise difficult to ascertain experimentally.
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Affiliation(s)
- Jonathan M Werner
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sara Ballouz
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW Australia
| | - John Hover
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
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22
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Minić S, Trpinac D, Novaković I, Cerovac N, Dobrosavljević Vukojević D, Rosain J. Challenges in Rare Diseases Diagnostics: Incontinentia Pigmenti with Heterozygous GBA Mutation. Diagnostics (Basel) 2022; 12:diagnostics12071711. [PMID: 35885615 PMCID: PMC9318020 DOI: 10.3390/diagnostics12071711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases represent a diagnostic challenge due to their number, variety of clinical phenomena, and possibility of a simultaneous presence of two or more diseases. An illustration of this challenge is an occurrence of a late diagnosis of a proband initially diagnosed with West syndrome, later revealed to be caused by Incontinentia pigmenti (IP). Furthermore, 20 years later, it was discovered that the proband was also a carrier of a heterozygous GBA gene mutation. The methods used in diagnostics were as follows: IKBKG gene analysis, the X-chromosome inactivation assay, analyses of the genes relevant for neurodegeneration, WES analysis, analysis of biochemical parameters typical for Gaucher disease (GD), and autoantibodies including IFN-α2a and IFN-ω. To avoid overlooking IP and other possible rare disease diagnoses, carefully searching for dermatological signs in these conditions is recommended. It is important that the diagnostic criteria are based on quality and extensive data from multiple studies of each rare disease. Establishing precise diagnostic criteria for as many rare diseases as possible and establishing a publicly accessible database of rare diseases with a search possibility according to phenotypic abnormalities and genetic mutations would greatly facilitate and speed up the establishment of an accurate diagnosis.
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Affiliation(s)
- Snežana Minić
- A Clinics of Dermatovenerology, University Clinical Center of Serbia, Deligradska 34, 11000 Belgrade, Serbia;
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
- Correspondence: ; Tel.: +38-164-199-8867
| | - Dušan Trpinac
- Institute of Histology and Embryology, Faculty of Medicine, University of Belgrade, Višegradska 26, 11000 Belgrade, Serbia;
| | - Ivana Novaković
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Višegradska 26, 11000 Belgrade, Serbia;
| | - Nataša Cerovac
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
- Clinic for Neurology and Psychiatry for Children and Youth, University Clinical Center of Serbia, Dr. Subotica 6a, 11000 Belgrade, Serbia
| | - Danijela Dobrosavljević Vukojević
- A Clinics of Dermatovenerology, University Clinical Center of Serbia, Deligradska 34, 11000 Belgrade, Serbia;
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France;
- Imagine Institute, University of Paris, 75015 Paris, France
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23
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Jiwrajka N, Anguera MC. The X in seX-biased immunity and autoimmune rheumatic disease. J Exp Med 2022; 219:e20211487. [PMID: 35510951 PMCID: PMC9075790 DOI: 10.1084/jem.20211487] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/04/2022] [Accepted: 03/31/2022] [Indexed: 01/07/2023] Open
Abstract
Sexual dimorphism in the composition and function of the human immune system has important clinical implications, as males and females differ in their susceptibility to infectious diseases, cancers, and especially systemic autoimmune rheumatic diseases. Both sex hormones and the X chromosome, which bears a number of immune-related genes, play critical roles in establishing the molecular basis for the observed sex differences in immune function and dysfunction. Here, we review our current understanding of sex differences in immune composition and function in health and disease, with a specific focus on the contribution of the X chromosome to the striking female bias of three autoimmune rheumatic diseases.
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Affiliation(s)
- Nikhil Jiwrajka
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Montserrat C. Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
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24
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Pozojevic J, von Holt BH, Westenberger A. Factors influencing reduced penetrance and variable expressivity in X-linked dystonia-parkinsonism. MED GENET-BERLIN 2022; 34:97-102. [PMID: 38835911 PMCID: PMC11007627 DOI: 10.1515/medgen-2022-2135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
X-linked dystonia-parkinsonism (XDP) is a neurodegenerative movement disorder that primarily affects adult Filipino men. It is caused by a founder retrotransposon insertion in TAF1 that contains a hexanucleotide repeat, the number of which differs among the patients and correlates with the age at disease onset (AAO) and other clinical parameters. A recent work has identified additional genetic modifiers of age-associated penetrance in XDP, bringing to light the DNA mismatch repair genes MSH3 and PMS2. Despite X-linked recessive inheritance, a minor subset of patients are female, manifesting the disease via various mechanisms such as homozygosity, imbalanced X-chromosome inactivation, or aneuploidy. Here, we summarize and discuss clinical and genetic aspects of XDP, with a focus on variable disease expressivity as a consequence of subtle genetic differences within a seemingly homogenous population of patients.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, BMF, Building 67; Ratzeburger Allee 160, 23538 Lübeck, Germany
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Björn-Hergen von Holt
- Institute of Medical Biometry and Statistics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, BMF, Building 67; Ratzeburger Allee 160, 23538 Lübeck, Germany
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25
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Fonova EA, Tolmacheva EN, Kashevarova AA, Sazhenova EA, Nikitina TV, Lopatkina ME, Vasilyeva OY, Zarubin AА, Aleksandrova TN, Yuriev SY, Skryabin NA, Stepanov VA, Lebedev IN. Skewed X-Chromosome Inactivation as a Possible Marker of X-Linked CNV in Women with Pregnancy Loss. Cytogenet Genome Res 2022; 162:97-108. [PMID: 35636401 DOI: 10.1159/000524342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
Skewed X-chromosome inactivation (sXCI) can be a marker of lethal genetic variants on the X chromosome in a woman since sXCI modifies the pathological phenotype. The aim of this study was to search for CNVs in women with miscarriages and sXCI. XCI was assayed using the classical method based on the amplification of highly polymorphic exon 1 of the androgen receptor (AR) gene. The XCI status was analysed in 313 women with pregnancy loss and in 87 spontaneously aborted embryos with 46,XX karyotype, as well as in control groups of 135 women without pregnancy loss and 64 embryos with 46,XX karyotype from induced abortions in women who terminated a normal pregnancy. The frequency of sXCI differed significantly between women with miscarriages and women without pregnancy losses (6.3% and 2.2%, respectively; p = 0.019). To exclude primary causes of sXCI, sequencing of the XIST and XACT genes was performed. The XIST and XACT gene sequencing revealed no known pathogenic variants that could lead to sXCI. Molecular karyotyping was performed using aCGH, followed by verification of X-linked CNVs by RT-PCR and MLPA. Microdeletions at Xp11.23 and Xq24 as well as gains of Xq28 were detected in women with sXCI and pregnancy loss.
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Affiliation(s)
- Elizaveta A Fonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Elena A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Tatyana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Maria E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Aleksei А Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Tatyana N Aleksandrova
- Department of Obstetrics and Gynecology, Siberian State Medical University, Tomsk, Russian Federation
| | - Sergey Yu Yuriev
- Department of Obstetrics and Gynecology, Siberian State Medical University, Tomsk, Russian Federation
| | - Nikolay A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Vadim A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
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26
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Yu WY, Zhang Y, Li MK, Yang ZY, Fung WK, Zhao PZ, Zhou JY. BEXCIS: Bayesian methods for estimating the degree of the skewness of X chromosome inactivation. BMC Bioinformatics 2022; 23:193. [PMID: 35610583 PMCID: PMC9128296 DOI: 10.1186/s12859-022-04721-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background X chromosome inactivation (XCI) is an epigenetic phenomenon that one of two X chromosomes in females is transcriptionally silenced during early embryonic development. Skewed XCI has been reported to be associated with some X-linked diseases. There have been several methods measuring the degree of the skewness of XCI. However, these methods may still have several limitations. Results We propose a Bayesian method to obtain the point estimate and the credible interval of the degree of XCI skewing by incorporating its prior information of being between 0 and 2. We consider a normal prior and a uniform prior for it (respectively denoted by BN and BU). We also propose a penalized point estimate based on the penalized Fieller’s method and derive the corresponding confidence interval. Simulation results demonstrate that the BN and BU methods can solve the problems of extreme point estimates, noninformative intervals, empty sets and discontinuous intervals. The BN method generally outperforms other methods with the lowest mean squared error in the point estimation, and well controls the coverage probability with the smallest median and the least variation of the interval width in the interval estimation. We apply all the methods to the Graves’ disease data and the Minnesota Center for Twin and Family Research data, and find that SNP rs3827440 in the Graves’ disease data may undergo skewed XCI towards the allele C. Conclusions We recommend the BN method for measuring the degree of the skewness of XCI in practice. The R package BEXCIS is publicly available at https://github.com/Wen-YiYu/BEXCIS. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04721-y.
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Affiliation(s)
- Wen-Yi Yu
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yu Zhang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Meng-Kai Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Zi-Ying Yang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Wing Kam Fung
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, China
| | - Pei-Zhen Zhao
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ji-Yuan Zhou
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China. .,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China.
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27
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Weyand AC, Sidonio RF, Sholzberg M. Health issues in women and girls affected by haemophilia with a focus on nomenclature, heavy menstrual bleeding, and musculoskeletal issues. Haemophilia 2022; 28 Suppl 4:18-25. [PMID: 35521724 PMCID: PMC9321707 DOI: 10.1111/hae.14535] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 12/26/2022]
Abstract
Introduction Women and girls affected by haemophilia, including haemophilia carriers (WGH) are at risk of bleeding symptoms that may go unrecognized, including heavy menstrual bleeding (HMB) and musculoskeletal bleeding. Terminology continues to evolve. Aim To describe the current recommendations for nomenclature surrounding WGH, and the current understanding of HMB, iron deficiency, and musculoskeletal complaints in these patients. Methods Literature was reviewed and summarized. Results With regards to nomenclature, women with factor levels less than 50% should be classified as having haemophilia, while carriers with normal levels should be characterized accordingly to symptomatology. HMB and resultant iron deficiency are common among WGH, have a multitude of downstream effects, and maybe overlooked due to stigma around menstruation. Musculoskeletal bleeding and resultant joint changes are increasingly recognized in this population but do not necessarily correlate with factor levels. Conclusion Although progress has been made in the care of WGH, much work remains to further improve their care.
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Affiliation(s)
- Angela C Weyand
- Department of Pediatrics, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Robert F Sidonio
- Department of Pediatrics, Division of Hematology/Oncology, Emory University, Atlanta, Georgia, USA
| | - Michelle Sholzberg
- Departments of Medicine, and Laboratory Medicine and Pathobiology, St. Michael's Hospital, Li Ka Shing Knowledge Institute, University of Toronto, Toronto, Ontario, Canada
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28
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Li MK, Yuan YX, Zhu B, Wang KW, Fung WK, Zhou JY. Gene-Based Methods for Estimating the Degree of the Skewness of X Chromosome Inactivation. Genes (Basel) 2022; 13:genes13050827. [PMID: 35627212 PMCID: PMC9140558 DOI: 10.3390/genes13050827] [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: 04/14/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Skewed X chromosome inactivation (XCI-S) has been reported to be associated with some X-linked diseases, and currently several methods have been proposed to estimate the degree of the XCI-S (denoted as γ) for a single locus. However, no method has been available to estimate γ for genes. Therefore, in this paper, we first propose the point estimate and the penalized point estimate of γ for genes, and then derive its confidence intervals based on the Fieller’s and penalized Fieller’s methods, respectively. Further, we consider the constraint condition of γ∈[0, 2] and propose the Bayesian methods to obtain the point estimates and the credible intervals of γ, where a truncated normal prior and a uniform prior are respectively used (denoted as GBN and GBU). The simulation results show that the Bayesian methods can avoid the extreme point estimates (0 or 2), the empty sets, the noninformative intervals ([0, 2]) and the discontinuous intervals to occur. GBN performs best in both the point estimation and the interval estimation. Finally, we apply the proposed methods to the Minnesota Center for Twin and Family Research data for their practical use. In summary, in practical applications, we recommend using GBN to estimate γ of genes.
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Affiliation(s)
- Meng-Kai Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Yu-Xin Yuan
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Bin Zhu
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Kai-Wen Wang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Wing Kam Fung
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, China;
| | - Ji-Yuan Zhou
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
- Correspondence:
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29
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Evaluation of FMR4, FMR5 and FMR6 Expression Levels as Non-Invasive Biomarkers for the Diagnosis of Fragile X-Associated Primary Ovarian Insufficiency (FXPOI). J Clin Med 2022; 11:jcm11082186. [PMID: 35456280 PMCID: PMC9025681 DOI: 10.3390/jcm11082186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Female FMR1 (Fragile X mental retardation 1) premutation carriers are at risk for developing fragile X-associated primary ovarian insufficiency (FXPOI), a condition characterized by amenorrhea before age 40 years. Not all women with a FMR1 premutation suffer from primary ovarian insufficiency and nowadays there are no molecular or other biomarkers that can help predict the occurrence of FXPOI. Long non-coding RNAs (lncRNAs) comprise a group of regulatory transcripts which have versatile molecular functions, making them important regulators in all aspects of gene expression. In recent medical studies, lncRNAs have been described as potential diagnostic biomarkers in many diseases. The present study was designed to determine the expression profile of three lncRNAs derived from the FMR1 locus, FMR4, FMR5 and FMR6, in female FMR1 premutation carriers in order: (i) to determine a possible role in the pathogenesis of FXPOI and (ii) to investigate whether they could serve as a biomarker for the diagnosis of FXPOI. FMR4, FMR5 and FMR6 transcripts levels were evaluated in total RNA extracted from peripheral blood by digital droplet PCR and compared between FMR1 premutation carriers with FXPOI and without FXPOI. The diagnostic value of lncRNAs was evaluated by receiver operating characteristic (ROC) analysis. Results revealed a significant association between FXPOI and high expression levels of FMR4. No association was obtained for FMR5 or FMR6. ROC curve analysis revealed that FMR4 can distinguish FMR1 premutation carrier with FXPOI with a diagnostic power of 0.67. These findings suggest a potential role of FMR4 as a possible biomarker for FXPOI.
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30
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Řeboun M, Sikora J, Magner M, Wiederlechnerová H, Černá A, Poupětová H, Štorkánova G, Mušálková D, Dostálová G, Goláň L, Linhart A, Dvořáková L. Pitfalls of X-chromosome inactivation testing in females with Fabry disease. Am J Med Genet A 2022; 188:1979-1989. [PMID: 35338595 DOI: 10.1002/ajmg.a.62728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/09/2022] [Accepted: 03/04/2022] [Indexed: 11/07/2022]
Abstract
Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the GLA gene encoding alpha-galactosidase A (AGAL). The impact of X-chromosome inactivation (XCI) on the phenotype of female FD patients remains unclear. In this study we aimed to determine pitfalls of XCI testing in a cohort of 35 female FD patients. XCI was assessed by two methylation-based and two allele-specific expression assays. The results correlated, although some variance among the four assays was observed. GLA transcript analyses identified crossing-over in three patients and detected mRNA instability in three out of four analyzed null alleles. AGAL activity correlated with XCI pattern and was not influenced by the mutation type or by reduced mRNA stability. Therefore, AGAL activity may help to detect crossing-over in patients with unstable GLA alleles. Tissue-specific XCI patterns in six patients, and age-related changes in two patients were observed. To avoid misinterpretation of XCI results in female FD patients we show that (i) a combination of several XCI assays generates more reliable results and minimizes possible biases; (ii) correlating XCI to GLA expression and AGAL activity facilitates identification of cross-over events; (iii) age- and tissue-related XCI specificities of XCI patterning should be considered.
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Affiliation(s)
- Martin Řeboun
- Diagnostic laboratories of IMD, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jakub Sikora
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Martin Magner
- Diagnostic laboratories of IMD, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Department of Pediatrics, Thomayer University Hospital and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Helena Wiederlechnerová
- Diagnostic laboratories of IMD, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Alena Černá
- Diagnostic laboratories of IMD, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Helena Poupětová
- Diagnostic laboratories of IMD, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Gabriela Štorkánova
- Diagnostic laboratories of IMD, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Gabriela Dostálová
- Second Department of Internal Cardiovascular Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lubor Goláň
- Second Department of Internal Cardiovascular Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Aleš Linhart
- Second Department of Internal Cardiovascular Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lenka Dvořáková
- Diagnostic laboratories of IMD, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
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Fang X, Butler KM, Abidi F, Gass J, Beisang A, Feyma T, Ryther RC, Standridge S, Heydemann P, Jones M, Haas R, Lieberman DN, Marsh E, Benke TA, Skinner S, Neul JL, Percy AK, Friez MJ, Caylor RC. Analysis of X-inactivation status in a Rett syndrome natural history study cohort. Mol Genet Genomic Med 2022; 10:e1917. [PMID: 35318820 PMCID: PMC9034674 DOI: 10.1002/mgg3.1917] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a rare neurodevelopmental disorder associated with pathogenic MECP2 variants. Because the MECP2 gene is subject to X-chromosome inactivation (XCI), factors including MECP2 genotypic variation, tissue differences in XCI, and skewing of XCI all likely contribute to the clinical severity of individuals with RTT. METHODS We analyzed the XCI patterns from blood samples of 320 individuals and their mothers. It includes individuals with RTT (n = 287) and other syndromes sharing overlapping phenotypes with RTT (such as CDKL5 Deficiency Disorder [CDD, n = 16]). XCI status in each proband/mother duo and the parental origin of the preferentially inactivated X chromosome were analyzed. RESULTS The average XCI ratio in probands was slightly increased compared to their unaffected mothers (73% vs. 69%, p = .0006). Among the duos with informative XCI data, the majority of individuals with classic RTT had their paternal allele preferentially inactivated (n = 180/220, 82%). In sharp contrast, individuals with CDD had their maternal allele preferentially inactivated (n = 10/12, 83%). Our data indicate a weak positive correlation between XCI skewing ratio and clinical severity scale (CSS) scores in classic RTT patients with maternal allele preferentially inactivated XCI (rs = 0.35, n = 40), but not in those with paternal allele preferentially inactivated XCI (rs = -0.06, n = 180). The most frequent MECP2 pathogenic variants were enriched in individuals with highly/moderately skewed XCI patterns, suggesting an association with higher levels of XCI skewing. CONCLUSION These results extend our understanding of the pathogenesis of RTT and other syndromes with overlapping clinical features by providing insight into the both XCI and the preferential XCI of parental alleles.
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Affiliation(s)
- Xiaolan Fang
- Greenwood Genetic CenterGreenwoodSouth CarolinaUSA
| | | | - Fatima Abidi
- Greenwood Genetic CenterGreenwoodSouth CarolinaUSA
| | - Jennifer Gass
- Florida Cancer Specialists & Research InstituteFort MyersFLUSA,Present address:
Florida Cancer Specialists & Research InstituteFort MyersFloridaUSA
| | - Arthur Beisang
- Gillette Children’s Specialty HealthcareSt. PaulMinnesotaUSA
| | - Timothy Feyma
- Gillette Children’s Specialty HealthcareSt. PaulMinnesotaUSA
| | - Robin C. Ryther
- Department of NeurologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Shannon Standridge
- Division of NeurologyCincinnati Children’s Hospital Medical CenterCincinnatiOhioUSA,Department of Pediatrics, College of MedicineUniversity of CincinnatiCincinnatiOhioUSA
| | | | - Mary Jones
- Oakland Children’s Hospital, UCSFOaklandCaliforniaUSA
| | - Richard Haas
- University of California San DiegoSan DiegoCaliforniaUSA
| | - David N Lieberman
- Department of NeurologyBoston Children’s HospitalBostonMassachusettsUSA
| | - Eric D. Marsh
- Children’s Hospital of Philadelphia and University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Tim A. Benke
- University of Colorado School of Medicine, Children’s Hospital Colorado‐AuroraDenverColoradoUSA
| | | | - Jeffrey L. Neul
- Vanderbilt Kennedy CenterVanderbilt University Medical CenterNashville TN
| | - Alan K. Percy
- The University of Alabama at BirminghamBirminghamAlabamaUSA
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32
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Catino G, Genovese S, Di Tommaso S, Orlando V, Petti MT, De Bernardi ML, Dallapiccola B, Novelli A, Ulgheri L, Piscopo C, Alesi V. Reciprocal Xp11.4p11.3 microdeletion/microduplication spanning USP9X, DDX3X, and CASK genes in two patients with syndromic intellectual disability. Am J Med Genet A 2022; 188:1836-1847. [PMID: 35238482 DOI: 10.1002/ajmg.a.62694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 12/13/2022]
Abstract
Only a few patients with deletions or duplications at Xp11.4, bridging USP9X, DDX3X, and CASK genes, have been described so far. Here, we report on a female harboring a de novo Xp11.4p11.3 deletion and a male with an overlapping duplication inherited from an unaffected mother, presenting with syndromic intellectual disability. We discuss the role of USP9X, DDX3X, and CASK genes in human development and describe the effects of Xp11.4 deletion and duplications in female and male patients, respectively.
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Affiliation(s)
- Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Silvia Di Tommaso
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Valeria Orlando
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Maria Teresa Petti
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | | | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Bambino Gesu Children Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Lucia Ulgheri
- Department of Biomedical Sciences, Clinical Genetics Service, Azienda Ospedaliero-Universitaria, Sassari, Italy
| | - Carmelo Piscopo
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
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Rodrigues B, Gonçalves A, Sousa V, Maia N, Marques I, Vale-Fernandes E, Santos R, Nogueira AJA, Jorge P. Use of the FMR1 Gene Methylation Status to Assess the X-Chromosome Inactivation Pattern: A Stepwise Analysis. Genes (Basel) 2022; 13:419. [PMID: 35327973 PMCID: PMC8951761 DOI: 10.3390/genes13030419] [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: 01/31/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
X-chromosome inactivation (XCI) is a developmental process to compensate the imbalance in the dosage of X-chromosomal genes in females. A skewing of the XCI pattern may suggest a carrier status for an X-linked disease or explain the presence of a severe phenotype. In these cases, it is important to determine the XCI pattern, conventionally using the gold standard Human Androgen-Receptor Assay (HUMARA), based on the analysis of the methylation status at a polymorphic CAG region in the first exon of the human androgen receptor gene (AR). The aim of this study was to evaluate whether the methylation status of the fragile mental retardation protein translational regulator gene (FMR1) can provide an XCI pattern similar to that obtained by HUMARA. A set of 48 female carriers of FMR1 gene normal-sized alleles was examined using two assays: HUMARA and a FMR1 methylation PCR (mPCR). Ranges were defined to establish the XCI pattern using the methylation pattern of the FMR1 gene by mPCR. Overall, a 77% concordance of the XCI patterns was obtained between the two assays, which led us to propose a set of key points and a stepwise analysis towards obtaining an accurate result for the XCI pattern and to minimize the underlying pitfalls.
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Affiliation(s)
- Bárbara Rodrigues
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - Ana Gonçalves
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - Vanessa Sousa
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
| | - Nuno Maia
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - Isabel Marques
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - Emídio Vale-Fernandes
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
- Centre for Medically Assisted Procreation/Public Gamete Bank, Centro Materno-Infantil do Norte Dr. Albino Aroso (CMIN), Centro Hospitalar Universitário do Porto (CHUPorto), 4050-651 Porto, Portugal
| | - Rosário Santos
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - António J. A. Nogueira
- CESAM—Center for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Paula Jorge
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
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Qin S, Wang X, Wang J. Identification of an SRY-negative 46,XX infertility male with a heterozygous deletion downstream of SOX3 gene. Mol Cytogenet 2022; 15:2. [PMID: 35164824 PMCID: PMC8842887 DOI: 10.1186/s13039-022-00580-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/28/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
A male individual with a karyotype of 46,XX is very rare. We explored the genetic aetiology of an infertility male with a kayrotype of 46,XX and SRY negative.
Methods
The peripheral blood sample was collected from the patient and subjected to a few genetic testing, including chromosomal karyotyping, azoospermia factor (AZF) deletion, short tandem repeat (STR) analysis for AMELX, AMELY and SRY, fluorescence in situ hybridization (FISH) with specific probes for CSP 18/CSP X/CSP Y/SRY, chromosomal microarray analysis (CMA) for genomic copy number variations(CNVs), whole-genome analysis(WGA) for genomic SNV&InDel mutation, and X chromosome inactivation (XCI) analysis.
Results
The patient had a karyotype of 46,XX. AZF analysis showed that he missed the AZF region (including a, b and c) and SRY gene. STR assay revealed he possessed the AMELX in the X chromosome, but he had no the AMELY and SRY in the Y chromosome. FISH analysis with CSP X/CSP Y/SRY showed only two X centromeric signals, but none Y chromosome and SRY. The above results of the karyotype, FISH and STR analysis did not suggest a Y chromosome chimerism existed in the patient's peripheral blood. The result of the CMA indicated a heterozygous deletion with an approximate size of 867 kb in Xq27.1 (hg19: chrX: 138,612,879–139,480,163 bp), located at 104 kb downstream of SOX3 gene, including F9, CXorf66, MCF2 and ATP11C. WGA also displayed the above deletion fragment but did not present known pathogenic or likely pathogenic SNV&InDel mutation responsible for sex determination and development. XCI assay showed that he had about 75% of the X chromosome inactivated.
Conclusions
Although the pathogenicity of 46,XX male patients with SRY negative remains unclear, SOX3 expression of the acquired function may be associated with partial testis differentiation of these patients. Therefore, the CNVs analysis of the SOX3 gene and its regulatory region should be performed routinely for these patients.
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Santamaria R, Ballester M, Garcia-Llorens G, Martinez F, Blazquez M, Ribes-Koninckx C, Castell JV, Wuestefeld T, Bort R. Derivation of healthy hepatocyte-like cells from a female patient with ornithine transcarbamylase deficiency through X-inactivation selection. Sci Rep 2022; 12:2308. [PMID: 35145162 PMCID: PMC8831560 DOI: 10.1038/s41598-022-06184-w] [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: 07/12/2021] [Accepted: 01/18/2022] [Indexed: 11/09/2022] Open
Abstract
Autologous cell replacement therapy for inherited metabolic disorders requires the correction of the underlying genetic mutation in patient's cells. An unexplored alternative for females affected from X-linked diseases is the clonal selection of cells randomly silencing the X-chromosome containing the mutant allele, without in vivo or ex vivo genome editing. In this report, we have isolated dermal fibroblasts from a female patient affected of ornithine transcarbamylase deficiency and obtained clones based on inactivation status of either maternally or paternally inherited X chromosome, followed by differentiation to hepatocytes. Hepatocyte-like cells derived from these clones display indistinct features characteristic of hepatocytes, but express either the mutant or wild type OTC allele depending on X-inactivation pattern. When clonally derived hepatocyte-like cells were transplanted into FRG® KO mice, they were able to colonize the liver and recapitulate OTC-dependent phenotype conditioned by X-chromosome inactivation pattern. This approach opens new strategies for cell therapy of X-linked metabolic diseases and experimental in vitro models for drug development for such diseases.
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Affiliation(s)
- Ramon Santamaria
- Experimental Hepatology Unit, Instituto de Investigación Sanitaria La Fe, CIBERehd, Hospital Universitari i Politècnic La Fe, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Maria Ballester
- Experimental Hepatology Unit, Instituto de Investigación Sanitaria La Fe, CIBERehd, Hospital Universitari i Politècnic La Fe, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Guillem Garcia-Llorens
- Experimental Hepatology Unit, Instituto de Investigación Sanitaria La Fe, CIBERehd, Hospital Universitari i Politècnic La Fe, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Biochemistry and Molecular Biology Department, Universidad de Valencia, Valencia, Spain
| | - Francisco Martinez
- Genetics Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, 46026, Valencia, Spain
| | - Marina Blazquez
- Experimental Hepatology Unit, Instituto de Investigación Sanitaria La Fe, CIBERehd, Hospital Universitari i Politècnic La Fe, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Carmen Ribes-Koninckx
- Coeliac Disease and Inmunopathology Research Unit, Instituto de Investigación Sanitaria La Fe, Pediatric Gastroenterology, Hospital Universitari i Politècnic La Fe, 46026, Valencia, Spain
| | - Jose V Castell
- Experimental Hepatology Unit, Instituto de Investigación Sanitaria La Fe, CIBERehd, Hospital Universitari i Politècnic La Fe, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Biochemistry and Molecular Biology Department, Universidad de Valencia, Valencia, Spain
| | - Torsten Wuestefeld
- Laboratory for In Vivo Genetics & Gene Therapy, Genome Institute of Singapore, A*STAR & National Cancer Centre Singapore, School of Biological Science, SingHealth & Adj. Ass.-Prof. Nanyang Technological University, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Roque Bort
- Experimental Hepatology Unit, Instituto de Investigación Sanitaria La Fe, CIBERehd, Hospital Universitari i Politècnic La Fe, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain.
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36
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Mechanisms of Choice in X-Chromosome Inactivation. Cells 2022; 11:cells11030535. [PMID: 35159344 PMCID: PMC8833938 DOI: 10.3390/cells11030535] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 12/04/2022] Open
Abstract
Early in development, placental and marsupial mammals harbouring at least two X chromosomes per nucleus are faced with a choice that affects the rest of their lives: which of those X chromosomes to transcriptionally inactivate. This choice underlies phenotypical diversity in the composition of tissues and organs and in their response to the environment, and can determine whether an individual will be healthy or affected by an X-linked disease. Here, we review our current understanding of the process of choice during X-chromosome inactivation and its implications, focusing on the strategies evolved by different mammalian lineages and on the known and unknown molecular mechanisms and players involved.
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Liu L, Chen H, Sun C, Zhang J, Wang J, Du M, Li J, Di L, Shen J, Geng S, Pang Y, Luo Y, Wu C, Fu Y, Zheng Z, Wang J, Huang Y. Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling. Genome Res 2021; 32:44-54. [PMID: 34963662 PMCID: PMC8744674 DOI: 10.1101/gr.275453.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 11/15/2021] [Indexed: 11/29/2022]
Abstract
Genomic-scale somatic copy number alterations in healthy humans are difficult to investigate because of low occurrence rates and the structural variations’ stochastic natures. Using a Tn5-transposase-assisted single-cell whole-genome sequencing method, we sequenced over 20,000 single lymphocytes from 16 individuals. Then, with the scale increased to a few thousand single cells per individual, we found that about 7.5% of the cells had large-size copy number alterations. Trisomy 21 was the most prevalent aneuploid event among all autosomal copy number alterations, whereas monosomy X occurred most frequently in over-30-yr-old females. In the monosomy X single cells from individuals with phased genomes and identified X-inactivation ratios in bulk, the inactive X Chromosomes were lost more often than the active ones.
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Harrison LM, Noble DWA, Jennions MD. A meta-analysis of sex differences in animal personality: no evidence for the greater male variability hypothesis. Biol Rev Camb Philos Soc 2021; 97:679-707. [PMID: 34908228 DOI: 10.1111/brv.12818] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022]
Abstract
The notion that men are more variable than women has become embedded into scientific thinking. For mental traits like personality, greater male variability has been partly attributed to biology, underpinned by claims that there is generally greater variation among males than females in non-human animals due to stronger sexual selection on males. However, evidence for greater male variability is limited to morphological traits, and there is little information regarding sex differences in personality-like behaviours for non-human animals. Here, we meta-analysed sex differences in means and variances for over 2100 effects (204 studies) from 220 species (covering five broad taxonomic groups) across five personality traits: boldness, aggression, activity, sociality and exploration. We also tested if sexual size dimorphism, a proxy for sex-specific sexual selection, explains variation in the magnitude of sex differences in personality. We found no significant differences in personality between the sexes. In addition, sexual size dimorphism did not explain variation in the magnitude of the observed sex differences in the mean or variance in personality for any taxonomic group. In sum, we find no evidence for widespread sex differences in variability in non-human animal personality.
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Affiliation(s)
- Lauren M Harrison
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia
| | - Daniel W A Noble
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia
| | - Michael D Jennions
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia
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Upadia J, Walano N, Noh GS, Liu J, Li Y, Deputy S, Elliott LT, Wong J, Lee JA, Caylor RC, Andersson HC. HSD10 disease in a female: A case report and review of literature. JIMD Rep 2021; 62:35-43. [PMID: 34765396 PMCID: PMC8574182 DOI: 10.1002/jmd2.12250] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/07/2022] Open
Abstract
HSD10 disease is a rare X-linked mitochondrial disorder caused by pathogenic variants in the HSD17B10 gene. The phenotype results from impaired 17β-hydroxysteroid dehydrogenase 10 (17β-HSD10) protein structure and function. HSD10 is a multifunctional protein involved in enzymatic degradation of isoleucine and branched-chain fatty acids, the metabolism of sex hormones and neurosteroids, as well as in regulating mitochondrial RNA maturation. HSD10 disease is characterised by progressive neurologic impairment. Disease onset is varied and includes neonatal-onset, infantile-onset and late-onset in males. Females can also be affected. Our index case is a 45-month-old female, who initially presented at 11 months of age with global developmental delay. She subsequently began to lose previously acquired cognitive and motor skills starting around 29 months of age. Brain MRI showed abnormalities in the basal ganglia indicative of possible mitochondrial disease. Urine organic acid analysis revealed elevations of 2-methyl-3-hydroxybutyric acid and tiglyglycine. HSD17B10 gene sequencing revealed a likely pathogenic variant, NM_001037811.2:c.439C>T (p.Arg147Cys) inherited from her mother, expected to be causative of HSD10 disease. Her X-chromosome inactivation study is consistent with a skewed X-inactivation pattern. We report a female patient with HSD10 disease caused by a missense pathogenic variant, Arg147Cys in the HSD17B10 gene. The patient is the fifth severely affected female with this disease. This case adds to the small number of known affected families with this highly variable disease in the literature. These findings support the possibility of X-inactivation patterns influencing the penetrance of HSD10 disease in females.
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Affiliation(s)
- Jariya Upadia
- Hayward Genetics Center, Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
- Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
| | - Nicolette Walano
- Hayward Genetics Center, Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
- Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
| | - Grace S. Noh
- Hayward Genetics Center, Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
- Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
| | - Jiao Liu
- Hayward Genetics Center, Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
| | - Yuwen Li
- Hayward Genetics Center, Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
- Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
| | - Stephen Deputy
- Division of Pediatric Neurology, Department of PediatricsLouisiana State University Health Sciences Center/Children's HospitalNew OrleansLouisianaUSA
| | - Lindsay T. Elliott
- Department of Pediatric Physical Medicine and RehabilitationLouisiana State University Health Sciences Center/Children's HospitalNew OrleansLouisianaUSA
| | - Joaquin Wong
- Division of Pediatric Neurology, Department of PediatricsLouisiana State University Health Sciences Center/Children's HospitalNew OrleansLouisianaUSA
| | | | | | - Hans C. Andersson
- Hayward Genetics Center, Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
- Department of PediatricsTulane University School of MedicineNew OrleansLouisianaUSA
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Simonetti L, Ferreira LGA, Vidi AC, de Souza JS, Kunii IS, Melaragno MI, de Mello CB, Carvalheira G, Dias da Silva MR. Intelligence Quotient Variability in Klinefelter Syndrome Is Associated With GTPBP6 Expression Under Regulation of X-Chromosome Inactivation Pattern. Front Genet 2021; 12:724625. [PMID: 34616429 PMCID: PMC8488338 DOI: 10.3389/fgene.2021.724625] [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: 06/15/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022] Open
Abstract
Klinefelter syndrome (KS) displays a broad dysmorphological, endocrinological, and neuropsychological clinical spectrum. We hypothesized that the neurocognitive dysfunction present in KS relies on an imbalance in X-chromosome gene expression. Thus, the X-chromosome inactivation (XCI) pattern and neurocognitive X-linked gene expression were tested and correlated with intelligence quotient (IQ) scores. We evaluated 11 KS patients by (a) IQ assessment, (b) analyzing the XCI patterns using both HUMARA and ZDHHC15 gene assays, and (c) blood RT-qPCR to investigate seven X-linked genes related to neurocognitive development (GTPBP6, EIF2S3, ITM2A, HUWE1, KDM5C, GDI1, and VAMP7) and XIST in comparison with 14 (male and female) controls. Considering IQ 80 as the standard minimum reference, we verified that the variability in IQ scores in KS patients seemed to be associated with the XCI pattern. Seven individuals in the KS group presented a random X-inactivation (RXI) and lower average IQ than the four individuals who presented a skewed X-inactivation (SXI) pattern. The evaluation of gene expression showed higher GTPBP6 expression in KS patients with RXI than in controls (p = 0.0059). Interestingly, the expression of GTPBP6 in KS patients with SXI did not differ from that observed in controls. Therefore, our data suggest for the first time that GTPBP6 expression is negatively associated with full-scale IQ under the regulation of the type of XCI pattern. The SXI pattern may regulate GTPBP6 expression, thereby dampening the impairment in cognitive performance and playing a role in intelligence variability in individuals with KS, which warrants further mechanistic investigations.
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Affiliation(s)
- Luciane Simonetti
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Lucas G A Ferreira
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Angela Cristina Vidi
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Janaina Sena de Souza
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ilda S Kunii
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Claudia Berlim de Mello
- Department of Psychobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gianna Carvalheira
- Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Magnus R Dias da Silva
- Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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León NY, Harley VR. ATR-X syndrome: genetics, clinical spectrum, and management. Hum Genet 2021; 140:1625-1634. [PMID: 34524523 DOI: 10.1007/s00439-021-02361-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022]
Abstract
ATR-X, an acronym for alpha thalassemia and mental retardation X-linked, syndrome is a congenital condition predominantly affecting males, characterized by mild to severe intellectual disability, facial, skeletal, urogenital, and hematopoietic anomalies. Less common are heart defects, eye anomalies, renal abnormalities, and gastrointestinal dysfunction. ATR-X syndrome is caused by germline variants in the ATRX gene. Until recently, the diagnosis of the ATR-X syndrome had been guided by the classical clinical manifestations and confirmed by molecular techniques. However, our new systematic analysis shows that the only clinical sign shared by all affected individuals is intellectual disability, with the other manifestations varying even within the same family. More than 190 different germline ATRX mutations in some 200 patients have been analyzed. With improved and more frequent analysis by molecular technologies, more subtle deletions and insertions have been detected recently. Moreover, emerging technologies reveal non-classic phenotypes of ATR-X syndrome as well as the description of a new clinical feature, the development of osteosarcoma which suggests an increased cancer risk in ATR-X syndrome. This review will focus on the different types of inherited ATRX mutations and their relation to clinical features in the ATR-X syndrome. We will provide an update of the frequency of clinical manifestations, the affected organs, and the genotype-phenotype correlations. Finally, we propose a shift in the diagnosis of ATR-X patients, from a clinical diagnosis to a molecular-based approach. This may assist clinicians in patient management, risk assessment and genetic counseling.
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Affiliation(s)
- Nayla Y León
- Sex Development Laboratory, Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, 27-31 Wright Street, Melbourne, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
| | - Vincent R Harley
- Sex Development Laboratory, Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, 27-31 Wright Street, Melbourne, VIC, 3168, Australia. .,Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia.
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Zhang Y, Li X, Gibson A, Edberg J, Kimberly RP, Absher DM. Skewed allelic expression on X chromosome associated with aberrant expression of XIST on systemic lupus erythematosus lymphocytes. Hum Mol Genet 2021; 29:2523-2534. [PMID: 32628254 DOI: 10.1093/hmg/ddaa131] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/27/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
A common feature of autoimmune diseases, including systemic lupus erythematosus (SLE), is an increased prevalence in women. However, the molecular basis for sex disparity in SLE remains poorly understood. To examine the role of X-linked transcription in SLE adaptive immune cells, we performed RNA-seq in T cell and B cell subsets from either healthy donors or patients with SLE. Analyses of allelic expression (AE) profiles identified a pattern of increased allelic imbalance across the entire X chromosome in SLE lymphocytes. X-linked genes exhibiting AE in SLE had an extensive overlap with genes known to escape X chromosome inactivation (XCI). XIST RNA was overexpressed in SLE patients. Differential XIST expression correlated with AE profiles more positively at X-linked genes than the genome-wide background. Analysis of three independent RNA-seq data verified the XIST-associated skewed AE on X chromosome in SLE. Integrative analyses of DNA methylation profiles showed an increased variability of DNA methylation levels at these AE-related X-linked genes. In cultured lymphoblastic cells, knockdown of XIST specifically altered allelic imbalance patterns between X chromosomes. Our study provides genetic evidence that upregulation of XIST accompanied with more skewed allelic expression on X chromosome is associated with the pathogenesis of SLE and may provide mechanistic insights into the increased incidence of SLE in females.
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Affiliation(s)
- Yanfeng Zhang
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Xinrui Li
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Andrew Gibson
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeffrey Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Sauteraud R, Stahl JM, James J, Englebright M, Chen F, Zhan X, Carrel L, Liu DJ. Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases. Genome Res 2021; 31:1629-1637. [PMID: 34426515 PMCID: PMC8415373 DOI: 10.1101/gr.275677.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/23/2021] [Indexed: 01/07/2023]
Abstract
The X Chromosome plays an important role in human development and disease. However, functional genomic and disease association studies of X genes greatly lag behind autosomal gene studies, in part owing to the unique biology of X-Chromosome inactivation (XCI). Because of XCI, most genes are only expressed from one allele. Yet, ∼30% of X genes “escape” XCI and are transcribed from both alleles, many only in a proportion of the population. Such interindividual differences are likely to be disease relevant, particularly for sex-biased disorders. To understand the functional biology for X-linked genes, we developed X-Chromosome inactivation for RNA-seq (XCIR), a novel approach to identify escape genes using bulk RNA-seq data. Our method, available as an R package, is more powerful than alternative approaches and is computationally efficient to handle large population-scale data sets. Using annotated XCI states, we examined the contribution of X-linked genes to the disease heritability in the United Kingdom Biobank data set. We show that escape and variable escape genes explain the largest proportion of X heritability, which is in large part attributable to X genes with Y homology. Finally, we investigated the role of each XCI state in sex-biased diseases and found that although XY homologous gene pairs have a larger overall effect size, enrichment for variable escape genes is significantly increased in female-biased diseases. Our results, for the first time, quantitate the importance of variable escape genes for the etiology of sex-biased disease, and our pipeline allows analysis of larger data sets for a broad range of phenotypes.
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Affiliation(s)
- Renan Sauteraud
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Jill M Stahl
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Jesica James
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Marisa Englebright
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Fang Chen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Xiaowei Zhan
- Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8821, USA
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
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Viggiano E, Politano L. X Chromosome Inactivation in Carriers of Fabry Disease: Review and Meta-Analysis. Int J Mol Sci 2021; 22:ijms22147663. [PMID: 34299283 PMCID: PMC8304911 DOI: 10.3390/ijms22147663] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 12/27/2022] Open
Abstract
Anderson-Fabry disease is an X-linked inborn error of glycosphingolipid catabolism caused by a deficiency of α-galactosidase A. The incidence ranges between 1: 40,000 and 1:117,000 of live male births. In Italy, an estimate of incidence is available only for the north-western Italy, where it is of approximately 1:4000. Clinical symptoms include angiokeratomas, corneal dystrophy, and neurological, cardiac and kidney involvement. The prevalence of symptomatic female carriers is about 70%, and in some cases, they can exhibit a severe phenotype. Previous studies suggest a correlation between skewed X chromosome inactivation and symptoms in carriers of X-linked disease, including Fabry disease. In this review, we briefly summarize the disease, focusing on the clinical symptoms of carriers and analysis of the studies so far published in regards to X chromosome inactivation pattern, and manifesting Fabry carriers. Out of 151 records identified, only five reported the correlation between the analysis of XCI in leukocytes and the related phenotype in Fabry carriers, in particular evaluating the Mainz Severity Score Index or cardiac involvement. The meta-analysis did not show any correlation between MSSI or cardiac involvement and skewed XCI, likely because the analysis of XCI in leukocytes is not useful for predicting the phenotype in Fabry carriers.
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Affiliation(s)
- Emanuela Viggiano
- Department of Prevention, UOC Hygiene Service and Public Health, ASL Roma 2, 00142 Rome, Italy
- Correspondence: (E.V.); (L.P.)
| | - Luisa Politano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, Luigi Vanvitelli University, 80138 Naples, Italy
- Correspondence: (E.V.); (L.P.)
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Abstract
PURPOSE OF REVIEW To summarize the recent literature related to female hemophilia A carriers with respect to prevalence in the population, the impact of baseline factor VIII levels and other influences on bleeding phenotype, and clinical management needs. RECENT FINDINGS Many female hemophilia A carriers are at risk for abnormal bleeding, yet they are underrecognized by healthcare providers and their bleeding symptoms are underreported. Low FVIII levels are consistently associated with clinically significant bleeding and correlate well with skewed X chromosome inactivation (XCI). Most interestingly, bleeding tendency is also observed in some hemophilia A carriers with normal factor VIII levels and requires further investigation. Well controlled studies investigating peripartum and periprocedural FVIII levels and adequate hemostatic treatment are necessary to inform management guidelines. SUMMARY Prevalence and bleeding tendency of hemophilia A carriers remain underreported, despite a significant proportion having low FVIII levels. Skewed XCI may explain low FVIII but does not explain the bleeding risk encountered in a larger proportion of hemophilia A carriers with random XCI and borderline/normal FVIII.
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A statistical measure for the skewness of X chromosome inactivation for quantitative traits and its application to the MCTFR data. BMC Genom Data 2021; 22:24. [PMID: 34215184 PMCID: PMC8254321 DOI: 10.1186/s12863-021-00978-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 06/17/2021] [Indexed: 11/24/2022] Open
Abstract
Background X chromosome inactivation (XCI) is that one of two chromosomes in mammalian females is silenced during early development of embryos. There has been a statistical measure for the degree of the skewness of XCI for qualitative traits. However, no method is available for such task at quantitative trait loci. Results In this article, we extend the existing statistical measure for the skewness of XCI for qualitative traits, and the likelihood ratio, Fieller’s and delta methods for constructing the corresponding confidence intervals, and make them accommodate quantitative traits. The proposed measure is a ratio of two linear regression coefficients when association exists. Noting that XCI may cause variance heterogeneity of the traits across different genotypes in females, we obtain the point estimate and confidence intervals of the measure by incorporating such information. The hypothesis testing of the proposed methods is also investigated. We conduct extensive simulation studies to assess the performance of the proposed methods. Simulation results demonstrate that the median of the point estimates of the measure is very close to the pre-specified true value. The likelihood ratio and Fieller’s methods control the size well, and have the similar test power and accurate coverage probability, which perform better than the delta method. So far, we are not aware of any association study for the X-chromosomal loci in the Minnesota Center for Twin and Family Research data. So, we apply our proposed methods to these data for their practical use and find that only the rs792959 locus, which is simultaneously associated with the illicit drug composite score and behavioral disinhibition composite score, may undergo XCI skewing. However, this needs to be confirmed by molecular genetics. Conclusions We recommend the Fieller’s method in practical use because it is a non-iterative procedure and has the similar performance to the likelihood ratio method. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00978-z.
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A novel mutation of the RPGR gene in a Chinese X-linked retinitis pigmentosa family and possible involvement of X-chromosome inactivation. Eye (Lond) 2021; 35:1688-1696. [PMID: 32839555 PMCID: PMC8169654 DOI: 10.1038/s41433-020-01150-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/14/2020] [Accepted: 08/13/2020] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES The objective of this study is to investigate the molecular mechanisms and genotype-phenotype correlations of a Chinese family with X-linked retinitis pigmentosa (XLRP). METHODS A four-generation family with a total of 41 individuals including 7 affected males was recruited. All subjects in this pedigree underwent a complete ophthalmic examination. Targeted capture and next-generation sequencing were performed on the proband using a multigene panel containing 57 known causative genes of retinitis pigmentosa (RP), including RP1, RP2, RPGR, RHO, PRPH2, CRB1 among others. All variants were verified in the remaining family members by polymerase chain reaction amplification and Sanger sequencing. Blood DNA was used for X-chromosome inactivation analysis in female carriers. RESULTS All the affected individuals were diagnosed with RP. The affected males showed symptoms from the first decade, while the female carriers had onset in the second decade or later. A frameshift mutation c.345_348delTGAA in the RPGR gene was identified in all affected males and female carriers. By XCI analysis, we found that there was little correlation between their phenotype and the methylation status of their X chromosomes. CONCLUSIONS A novel mutation c.345_348delTGAA of the RPGR gene was identified, expanding the spectrum of RPGR mutations causing XLRP. In this pedigree, the phenotype extended to female carriers, in whom RP was milder and its onset delayed compared to hemizygous males. Although lack of strong correlation between X-inactivation and the severity of the disease, the milder, variable effects in female carriers still could reflect X-inactivation patterns in the retina of each individual.
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Juchniewicz P, Piotrowska E, Kloska A, Podlacha M, Mantej J, Węgrzyn G, Tukaj S, Jakóbkiewicz-Banecka J. Dosage Compensation in Females with X-Linked Metabolic Disorders. Int J Mol Sci 2021; 22:ijms22094514. [PMID: 33925963 PMCID: PMC8123450 DOI: 10.3390/ijms22094514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 01/19/2023] Open
Abstract
Through the use of new genomic and metabolomic technologies, our comprehension of the molecular and biochemical etiologies of genetic disorders is rapidly expanding, and so are insights into their varying phenotypes. Dosage compensation (lyonization) is an epigenetic mechanism that balances the expression of genes on heteromorphic sex chromosomes. Many studies in the literature have suggested a profound influence of this phenomenon on the manifestation of X-linked disorders in females. In this review, we summarize the clinical and genetic findings in female heterozygotic carriers of a pathogenic variant in one of ten selected X-linked genes whose defects result in metabolic disorders.
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Affiliation(s)
- Patrycja Juchniewicz
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (P.J.); (A.K.); (J.J.-B.)
| | - Ewa Piotrowska
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (M.P.); (J.M.); (G.W.); (S.T.)
- Correspondence: ; Tel.: +48-58-523-6040
| | - Anna Kloska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (P.J.); (A.K.); (J.J.-B.)
| | - Magdalena Podlacha
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (M.P.); (J.M.); (G.W.); (S.T.)
| | - Jagoda Mantej
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (M.P.); (J.M.); (G.W.); (S.T.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (M.P.); (J.M.); (G.W.); (S.T.)
| | - Stefan Tukaj
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (M.P.); (J.M.); (G.W.); (S.T.)
| | - Joanna Jakóbkiewicz-Banecka
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (P.J.); (A.K.); (J.J.-B.)
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Miller CH, Bean CJ. Genetic causes of haemophilia in women and girls. Haemophilia 2021; 27:e164-e179. [PMID: 33314404 PMCID: PMC8132474 DOI: 10.1111/hae.14186] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/07/2020] [Accepted: 10/19/2020] [Indexed: 01/19/2023]
Abstract
Women and girls reported as "haemophilic females" may have complex genetic causes for their haemophilia phenotype. In addition, women and girls may have excessive bleeding requiring treatment simply because they are heterozygous for haemophilia alleles. While severe and moderate haemophilia are rare in females, 16% of patients with mild haemophilia A and almost one-quarter of those with mild haemophilia B seen in U.S. haemophilia treatment centres are women and girls. A phenotypic female with a low level of factor VIII or factor IX may be classified into one of the following categories of causality: homozygosity (two identical haemophilia alleles), compound heterozygosity (two different haemophilia alleles), hemizygosity (one haemophilia allele and no normal allele), heterozygosity (one haemophilia allele and one normal allele), genetic causes other than haemophilia and non-genetic causes. Studies required for classification may include coagulation parameters, F8 or F9 sequencing, F8 inversion testing, multiplex ligation-dependent probe amplification, karyotyping and X chromosome inactivation studies performed on the patient and parents. Women and girls who are homozygous, compound heterozygous or hemizygous clearly have haemophilia, as they do not have a normal allele. Heterozygous women and girls with factor levels below the haemostatic range also meet the definitions used for haemophilia treatment.
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Affiliation(s)
- Connie H Miller
- Division of Blood Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christopher J Bean
- Division of Blood Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
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50
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Kousal B, Majer F, Vlaskova H, Dvorakova L, Piherova L, Meliska M, Langrova H, Palecek T, Kubanek M, Krebsova A, Gurka J, Stara V, Michaelides M, Kalina T, Sikora J, Liskova P. Pigmentary retinopathy can indicate the presence of pathogenic LAMP2 variants even in somatic mosaic carriers with no additional signs of Danon disease. Acta Ophthalmol 2021; 99:61-68. [PMID: 32533651 DOI: 10.1111/aos.14478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/29/2020] [Indexed: 11/28/2022]
Abstract
PURPOSE Danon disease (DD) is a rare X-linked disorder caused by pathogenic variants in LAMP2. DD primarily manifests as a severe cardiomyopathy. An early diagnosis is crucial for patient survival. The aim of the study was to determine the usefulness of ocular examination for identification of DD. METHODS Detailed ocular examination in 10 patients with DD (3 males, 7 females) and a 45-year-old asymptomatic female somatic mosaic carrier of a LAMP2 disease-causing variant. RESULTS All patients with manifest cardiomyopathy had pigmentary retinopathy with altered autofluorescence and diffuse visual field loss. Best corrected visual acuity (BCVA) was decreased (<0.63) in 8 (40%) out of 20 eyes. The severity of retinal pathology increased with age, resulting in marked cone-rod involvement overtime. Spectral-domain optical coherence tomography in younger patients revealed focal loss of photoreceptors, disruption and deposition at the retinal pigment epithelium/Bruch's membrane layer (corresponding to areas of marked increased autofluorescence), and hyperreflective foci in the outer nuclear layer. Cystoid macular oedema was seen in one eye. In the asymptomatic female with somatic mosaicism, the BCVA was 1.0 bilaterally. An abnormal autofluorescence pattern in the left eye was present; while full-field electroretinography was normal. CONCLUSIONS Detailed ocular examination may represent a sensitive and quick screening tool for the identification of carriers of LAMP2 pathogenic variants, even in somatic mosaicism. Hence, further investigation should be undertaken in all patients with pigmentary retinal dystrophy as it may be a sign of a life-threatening disease.
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Affiliation(s)
- Bohdan Kousal
- Department of Ophthalmology First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
- Research Unit for Rare Diseases Department of Pediatrics and Adolescent Medicine First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
| | - Filip Majer
- Research Unit for Rare Diseases Department of Pediatrics and Adolescent Medicine First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
| | - Hana Vlaskova
- Research Unit for Rare Diseases Department of Pediatrics and Adolescent Medicine First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
| | - Lenka Dvorakova
- Research Unit for Rare Diseases Department of Pediatrics and Adolescent Medicine First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
| | - Lenka Piherova
- Research Unit for Rare Diseases Department of Pediatrics and Adolescent Medicine First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
| | - Martin Meliska
- Department of Ophthalmology First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
| | - Hana Langrova
- Department of Ophthalmology Faculty of Medicine in Hradec Kralove Charles University and University Hospital Hradec Kralove Hradec Kralove Czech Republic
| | - Tomas Palecek
- 2nd Department of Medicine ‐ Department of Cardiovascular Medicine First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
| | - Milos Kubanek
- Department of Cardiology Institute for Clinical and Experimental Medicine Prague Czech Republic
| | - Alice Krebsova
- Department of Cardiology Institute for Clinical and Experimental Medicine Prague Czech Republic
| | - Jiri Gurka
- Department of Cardiology Institute for Clinical and Experimental Medicine Prague Czech Republic
| | - Veronika Stara
- Department of Paediatrics Second Faculty of Medicine Charles University and Motol University Hospital Prague Czech Republic
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust London UK
- UCL Institute of Ophthalmology University College London London UK
| | - Tomas Kalina
- Department of Paediatric Haematology and Oncology Childhood Leukaemia Investigation Prague Second Faculty of Medicine Charles University and Motol University Hospital Prague Czech Republic
| | - Jakub Sikora
- Research Unit for Rare Diseases Department of Pediatrics and Adolescent Medicine First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
- Institute of Pathology First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
| | - Petra Liskova
- Department of Ophthalmology First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
- Research Unit for Rare Diseases Department of Pediatrics and Adolescent Medicine First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic
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