1
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Song QH, Zhao KX, Huang S, Chen T, He L. Escape from X-chromosome inactivation and sex differences in Alzheimer's disease. Rev Neurosci 2024; 35:341-354. [PMID: 38157427 DOI: 10.1515/revneuro-2023-0108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
Sex differences exist in the onset and progression of Alzheimer's disease. Globally, women have a higher prevalence, while men with Alzheimer's disease experience earlier mortality and more pronounced cognitive decline than women. The cause of sex differences in Alzheimer's disease remains unclear. Accumulating evidence suggests the potential role of X-linked genetic factors in the sex difference of Alzheimer's disease (AD). During embryogenesis, a remarkable process known as X-chromosome inactivation (XCI) occurs in females, leading to one of the X chromosomes undergoing transcriptional inactivation, which balances the effects of two X chromosomes in females. Nevertheless, certain genes exceptionally escape from XCI, which provides a basis for dual expression dosage of specific genes in females. Based on recent research findings, we explore key escape genes and their potential therapeutic use associated with Alzheimer's disease. Also, we discuss their possible role in driving the sex differences in Alzheimer's disease. This will provide new perspectives for precision medicine and gender-specific treatment of AD.
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Affiliation(s)
- Qing-Hua Song
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Ke-Xuan Zhao
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Shuai Huang
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Tong Chen
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Ling He
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
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2
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Gocuk SA, Jolly JK, Edwards TL, Ayton LN. Female carriers of X-linked inherited retinal diseases - Genetics, diagnosis, and potential therapies. Prog Retin Eye Res 2023; 96:101190. [PMID: 37406879 DOI: 10.1016/j.preteyeres.2023.101190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
Inherited retinal diseases (IRDs) are a group of heterogeneous conditions that cause progressive vision loss, typically due to monogenic mutations. Female carriers of X-linked IRDs have a single copy of the disease-causing gene, and therefore, may exhibit variable clinical signs that vary from near normal retina to severe disease and vision loss. The relationships between individual genetic mutations and disease severity in X-linked carriers requires further study. This review summarises the current literature surrounding the spectrum of disease seen in female carriers of choroideremia and X-linked retinitis pigmentosa. Various classification systems are contrasted to accurately grade retinal disease. Furthermore, genetic mechanisms at the early embryonic stage are explored to potentially explain the variability of disease seen in female carriers. Future research in this area will provide insight into the association between genotype and retinal phenotypes of female carriers, which will guide in the management of these patients. This review acknowledges the importance of identifying which patients may be at high risk of developing severe symptoms, and therefore should be considered for emerging treatments, such as retinal gene therapy.
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Affiliation(s)
- Sena A Gocuk
- Department of Optometry and Vision Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jasleen K Jolly
- Vision and Eye Research Institute, Anglia Ruskin University, Cambridge, UK
| | - Thomas L Edwards
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lauren N Ayton
- Department of Optometry and Vision Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia.
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3
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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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4
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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 PMCID: PMC10324263 DOI: 10.1186/s13293-023-00527-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [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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5
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Inkster AM, Wong MT, Matthews AM, Brown CJ, Robinson WP. Who's afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data. Epigenetics Chromatin 2023; 16:1. [PMID: 36609459 PMCID: PMC9825011 DOI: 10.1186/s13072-022-00477-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Many human disease phenotypes manifest differently by sex, making the development of methods for incorporating X and Y-chromosome data into analyses vital. Unfortunately, X and Y chromosome data are frequently excluded from large-scale analyses of the human genome and epigenome due to analytical complexity associated with sex chromosome dosage differences between XX and XY individuals, and the impact of X-chromosome inactivation (XCI) on the epigenome. As such, little attention has been given to considering the methods by which sex chromosome data may be included in analyses of DNA methylation (DNAme) array data. RESULTS With Illumina Infinium HumanMethylation450 DNAme array data from 634 placental samples, we investigated the effects of probe filtering, normalization, and batch correction on DNAme data from the X and Y chromosomes. Processing steps were evaluated in both mixed-sex and sex-stratified subsets of the analysis cohort to identify whether including both sexes impacted processing results. We found that identification of probes that have a high detection p-value, or that are non-variable, should be performed in sex-stratified data subsets to avoid over- and under-estimation of the quantity of probes eligible for removal, respectively. All normalization techniques investigated returned X and Y DNAme data that were highly correlated with the raw data from the same samples. We found no difference in batch correction results after application to mixed-sex or sex-stratified cohorts. Additionally, we identify two analytical methods suitable for XY chromosome data, the choice between which should be guided by the research question of interest, and we performed a proof-of-concept analysis studying differential DNAme on the X and Y chromosome in the context of placental acute chorioamnionitis. Finally, we provide an annotation of probe types that may be desirable to filter in X and Y chromosome analyses, including probes in repetitive elements, the X-transposed region, and cancer-testis gene promoters. CONCLUSION While there may be no single "best" approach for analyzing DNAme array data from the X and Y chromosome, analysts must consider key factors during processing and analysis of sex chromosome data to accommodate the underlying biology of these chromosomes, and the technical limitations of DNA methylation arrays.
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Affiliation(s)
- Amy M Inkster
- BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC, V6H 3N1, Canada.
- Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, V6H 3N1, Canada.
| | - Martin T Wong
- Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, V6H 3N1, Canada
| | - Allison M Matthews
- BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC, V6H 3N1, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, V6T 1Z7, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, V6H 3N1, Canada
| | - Wendy P Robinson
- BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC, V6H 3N1, Canada
- Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, V6H 3N1, Canada
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6
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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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7
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Günthner R, Knipping L, Jeruschke S, Satanoskij R, Lorenz-Depiereux B, Hemmer C, Braunisch MC, Riedhammer KM, Ćomić J, Tönshoff B, Tasic V, Abazi-Emini N, Nushi-Stavileci V, Buiting K, Gjorgjievski N, Momirovska A, Patzer L, Kirschstein M, Gross O, Lungu A, Weber S, Renders L, Heemann U, Meitinger T, Büscher AK, Hoefele J. Renal X-inactivation in female individuals with X-linked Alport syndrome primarily determined by age. Front Med (Lausanne) 2022; 9:953643. [PMID: 36341250 PMCID: PMC9630586 DOI: 10.3389/fmed.2022.953643] [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: 05/26/2022] [Accepted: 09/21/2022] [Indexed: 08/29/2023] Open
Abstract
X-linked Alport syndrome (AS) caused by hemizygous disease-causing variants in COL4A5 primarily affects males. Females with a heterozygous state show a diverse phenotypic spectrum ranging from microscopic hematuria to end-stage kidney disease (ESKD) and extrarenal manifestations. In other X-linked diseases, skewed X-inactivation leads to preferential silencing of one X-chromosome and thus can determine the phenotype in females. We aimed to show a correlation between X-inactivation in blood and urine-derived renal cells and clinical phenotype of females with a heterozygous disease-causing variant in COL4A5 compared to healthy controls. A total of 56 females with a heterozygous disease-causing COL4A5 variant and a mean age of 31.6 ± 18.3 SD years were included in this study. A total of 94% had hematuria, 62% proteinuria >200 mg/day, yet only 7% had decreased eGFR. Using human androgen receptor assay X-inactivation was examined in blood cells of all 56 individuals, in urine-derived cells of 27 of these individuals and in all healthy controls. X-inactivation did not correlate with age of first manifestation, proteinuria or eGFR neither in blood, nor in urine. The degree of X-inactivation showed a moderate association with age, especially in urine-derived cells of the patient cohort (rho = 0.403, p = 0.037). Determination of X-inactivation allelity revealed a shift of X-inactivation toward the COL4A5 variant bearing allele. This is the first study examining X-inactivation of urine-derived cells from female individuals with AS. A correlation between phenotype and X-inactivation could not be observed suspecting other genetic modifiers shaping the phenotype in female individuals with AS. The association of X-inactivation with age in urine-derived cells suggests an escape-mechanism inactivating the COL4A5 variant carrying allele in female individuals with AS.
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Affiliation(s)
- Roman Günthner
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Lea Knipping
- Pediatric Nephrology, University Hospital Essen, Essen, Germany
| | | | - Robin Satanoskij
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | | | - Clara Hemmer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Matthias C. Braunisch
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Korbinian M. Riedhammer
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Jasmina Ćomić
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Burkhard Tönshoff
- Department of Pediatrics I, University Children’s Hospital Heidelberg, Heidelberg, Germany
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, North Macedonia
| | - Nora Abazi-Emini
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, North Macedonia
| | | | - Karin Buiting
- Institute for Human Genetics, University Hospital Essen, Essen, Germany
| | - Nikola Gjorgjievski
- University Hospital of Nephrology, Faculty of Medicine, University “Ss Cyril and Methodius,” Skopje, North Macedonia
| | | | - Ludwig Patzer
- Department of Pediatrics, Children’s Hospital St. Elisabeth and St. Barbara, Halle (Saale), Germany
| | | | - Oliver Gross
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Göttingen, Germany
| | - Adrian Lungu
- Fundeni Clinical Institute, Pediatric Nephrology Department, Bucharest, Romania
| | - Stefanie Weber
- Department of Pediatrics II, University Children’s Hospital, Philipps-University Marburg, Marburg, Germany
| | - Lutz Renders
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Uwe Heemann
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Anja K. Büscher
- Pediatric Nephrology, University Hospital Essen, Essen, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
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8
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Pallier PN, Ferrara M, Romagnolo F, Ferretti MT, Soreq H, Cerase A. Chromosomal and environmental contributions to sex differences in the vulnerability to neurological and neuropsychiatric disorders: Implications for therapeutic interventions. Prog Neurobiol 2022; 219:102353. [PMID: 36100191 DOI: 10.1016/j.pneurobio.2022.102353] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/22/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Neurological and neuropsychiatric disorders affect men and women differently. Multiple sclerosis, Alzheimer's disease, anxiety disorders, depression, meningiomas and late-onset schizophrenia affect women more frequently than men. By contrast, Parkinson's disease, autism spectrum condition, attention-deficit hyperactivity disorder, Tourette's syndrome, amyotrophic lateral sclerosis and early-onset schizophrenia are more prevalent in men. Women have been historically under-recruited or excluded from clinical trials, and most basic research uses male rodent cells or animals as disease models, rarely studying both sexes and factoring sex as a potential source of variation, resulting in a poor understanding of the underlying biological reasons for sex and gender differences in the development of such diseases. Putative pathophysiological contributors include hormones and epigenetics regulators but additional biological and non-biological influences may be at play. We review here the evidence for the underpinning role of the sex chromosome complement, X chromosome inactivation, and environmental and epigenetic regulators in sex differences in the vulnerability to brain disease. We conclude that there is a pressing need for a better understanding of the genetic, epigenetic and environmental mechanisms sustaining sex differences in such diseases, which is critical for developing a precision medicine approach based on sex-tailored prevention and treatment.
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Affiliation(s)
- Patrick N Pallier
- Blizard Institute, Centre for Neuroscience, Surgery and Trauma, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
| | - Maria Ferrara
- Institute of Psychiatry, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy; Department of Psychiatry, Yale University, School of Medicine, New Haven, CT, United States; Women's Brain Project (WBP), Switzerland
| | - Francesca Romagnolo
- Institute of Psychiatry, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | | | - Hermona Soreq
- The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, 9190401, Israel
| | - Andrea Cerase
- EMBL-Rome, Via Ramarini 32, 00015 Monterotondo, RM, Italy; Blizard Institute, Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; Department of Biology, University of Pisa, SS12 Abetone e Brennero 4, 56127 Pisa, Italy.
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9
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Wang YC, Wu Y, Choi J, Allington G, Zhao S, Khanfar M, Yang K, Fu PY, Wrubel M, Yu X, Mekbib KY, Ocken J, Smith H, Shohfi J, Kahle KT, Lu Q, Jin SC. Computational Genomics in the Era of Precision Medicine: Applications to Variant Analysis and Gene Therapy. J Pers Med 2022; 12:175. [PMID: 35207663 PMCID: PMC8878256 DOI: 10.3390/jpm12020175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid methodological advances in statistical and computational genomics have enabled researchers to better identify and interpret both rare and common variants responsible for complex human diseases. As we continue to see an expansion of these advances in the field, it is now imperative for researchers to understand the resources and methodologies available for various data types and study designs. In this review, we provide an overview of recent methods for identifying rare and common variants and understanding their roles in disease etiology. Additionally, we discuss the strategy, challenge, and promise of gene therapy. As computational and statistical approaches continue to improve, we will have an opportunity to translate human genetic findings into personalized health care.
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Affiliation(s)
- Yung-Chun Wang
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Yuchang Wu
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Julie Choi
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Garrett Allington
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA; (H.S.); (K.T.K.)
| | - Shujuan Zhao
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Mariam Khanfar
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Kuangying Yang
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Po-Ying Fu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Max Wrubel
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Xiaobing Yu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA
| | - Kedous Y. Mekbib
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; (K.Y.M.); (J.O.); (J.S.)
| | - Jack Ocken
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; (K.Y.M.); (J.O.); (J.S.)
| | - Hannah Smith
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA; (H.S.); (K.T.K.)
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; (K.Y.M.); (J.O.); (J.S.)
| | - John Shohfi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; (K.Y.M.); (J.O.); (J.S.)
| | - Kristopher T. Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA; (H.S.); (K.T.K.)
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Sheng Chih Jin
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
- Department of Pediatrics, School of Medicine, Washington University, St. Louis, MO 63110, USA
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10
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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: 19] [Impact Index Per Article: 6.3] [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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11
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Kananen L, Marttila S. Ageing-associated changes in DNA methylation in X and Y chromosomes. Epigenetics Chromatin 2021; 14:33. [PMID: 34215292 PMCID: PMC8254238 DOI: 10.1186/s13072-021-00407-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Ageing displays clear sexual dimorphism, evident in both morbidity and mortality. Ageing is also associated with changes in DNA methylation, but very little focus has been on the sex chromosomes, potential biological contributors to the observed sexual dimorphism. Here, we sought to identify DNA methylation changes associated with ageing in the Y and X chromosomes, by utilizing datasets available in data repositories, comprising in total of 1240 males and 1191 females, aged 14–92 years. Results In total, we identified 46 age-associated CpG sites in the male Y, 1327 age-associated CpG sites in the male X, and 325 age-associated CpG sites in the female X. The X chromosomal age-associated CpGs showed significant overlap between females and males, with 122 CpGs identified as age-associated in both sexes. Age-associated X chromosomal CpGs in both sexes were enriched in CpG islands and depleted from gene bodies and showed no strong trend towards hypermethylation nor hypomethylation. In contrast, the Y chromosomal age-associated CpGs were enriched in gene bodies, and showed a clear trend towards hypermethylation with age. Conclusions Significant overlap in X chromosomal age-associated CpGs identified in males and females and their shared features suggest that despite the uneven chromosomal dosage, differences in ageing-associated DNA methylation changes in the X chromosome are unlikely to be a major contributor of sex dimorphism in ageing. While age-associated CpGs showed good replication across datasets in the present study, only a limited set of previously reported age-associated CpGs were replicated. One contributor to the limited overlap are differences in the age range of individuals included in each data set. Further study is needed to identify biologically significant age-associated CpGs in the sex chromosomes. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00407-6.
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Affiliation(s)
- Laura Kananen
- Faculty of Social Sciences (Health Sciences), Tampere University, Tampere, Finland. .,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. .,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. .,Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Saara Marttila
- Gerontology Research Center, Tampere University, Tampere, Finland. .,Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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12
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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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13
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Mengel-From J, Lindahl-Jacobsen R, Nygaard M, Soerensen M, Ørstavik KH, Hertz JM, Andersen-Ranberg K, Tan Q, Christensen K. Skewness of X-chromosome inactivation increases with age and varies across birth cohorts in elderly Danish women. Sci Rep 2021; 11:4326. [PMID: 33619309 PMCID: PMC7900237 DOI: 10.1038/s41598-021-83702-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/04/2021] [Indexed: 01/26/2023] Open
Abstract
Mosaicism in blood varies with age, and cross-sectional studies indicate that for women, skewness of X-chromosomal mosaicism increases with age. This pattern could, however, also be due to less X-inactivation in more recent birth cohorts. Skewed X-chromosome inactivation was here measured longitudinally by the HUMARA assay in 67 septuagenarian and octogenarian women assessed at 2 time points, 10 years apart, and in 10 centenarian women assessed at 2 time points, 2–7 years apart. Skewed X-chromosome inactivation was also compared in 293 age-matched septuagenarian twins born in 1917–1923 and 1931–1937, and 212 centenarians born in 1895, 1905 and 1915. The longitudinal study of septuagenarians and octogenarians revealed that 16% (95% CI 7–29%) of the women developed skewed X-inactivation over a 10-year period. In the cross-sectional across-birth cohort study, the earlier-born septuagenarian (1917–1923) and centenarian women (1895) had a higher degree of skewness than the respective recent age-matched birth cohorts, which indicates that the women in the more recent cohorts, after the age of 70, had not only changed degree of skewness with age, they had also undergone less age-related hematopoietic sub-clone expansion. This may be a result of improved living conditions and better medical treatment in the more recent birth cohorts.
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Affiliation(s)
- Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, the Danish Twin Registry, and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9, 5000, Odense C, Denmark. .,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
| | - Rune Lindahl-Jacobsen
- Epidemiology, Biostatistics and Biodemography, the Danish Twin Registry, and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9, 5000, Odense C, Denmark.,Interdisciplinary Centre on Population Dynamics (CPop), University of Southern Denmark, Odense, Denmark
| | - Marianne Nygaard
- Epidemiology, Biostatistics and Biodemography, the Danish Twin Registry, and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9, 5000, Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, the Danish Twin Registry, and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9, 5000, Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | | | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Karen Andersen-Ranberg
- Epidemiology, Biostatistics and Biodemography, the Danish Twin Registry, and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9, 5000, Odense C, Denmark.,Geriatric Research Unit, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, the Danish Twin Registry, and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9, 5000, Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, the Danish Twin Registry, and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9, 5000, Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
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14
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Han D, Hao M, Qu L, Xu W. A novel model for the X-chromosome inactivation association on survival data. Stat Methods Med Res 2020; 29:1305-1314. [PMID: 31258049 DOI: 10.1177/0962280219859037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The X-linked genetic association is overlooked in most of the genetic studies because of the complexity of X-chromosome inactivation process. In fact, the biological process of the gene at the same locus can vary across different subjects. Besides, the skewness of X-chromosome inactivation is inherently subject-specific (even tissue-specific within subjects) and cannot be accurately represented by a population-level parameter. To tackle this issue, a new model is proposed to incorporate the X-linked genetic association into right-censored survival data. The novel model can present that the X-linked genes on different subjects may go through different biological processes via a mixed distribution. Further, a random effect is employed to describe the uncertainty of the biological process for every subject. The proposed method can derive the probability for the escape of X-chromosome inactivation and derive the unbiased estimates of the model parameters. The Legendre-Gauss Quadrature method is used to approximate the integration over the random effect. Finite sample performance of this method is examined via extensive simulation studies. An application is illustrated with the implementation on a cancer genetic study with right-censored survival data.
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Affiliation(s)
- Dongxiao Han
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Meiling Hao
- School of Statistics, University of International Business and Economics, Beijing, China
| | - Lianqiang Qu
- School of Mathematics and Statistics, Central China Normal University, Wuhan, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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15
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Li S, Lund JB, Christensen K, Baumbach J, Mengel-From J, Kruse T, Li W, Mohammadnejad A, Pattie A, Marioni RE, Deary IJ, Tan Q. Exploratory analysis of age and sex dependent DNA methylation patterns on the X-chromosome in whole blood samples. Genome Med 2020; 12:39. [PMID: 32345361 PMCID: PMC7189689 DOI: 10.1186/s13073-020-00736-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/07/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Large numbers of autosomal sites are found differentially methylated in the aging genome. Due to analytical difficulties in dealing with sex differences in X-chromosome content and X-inactivation (XCI) in females, this has not been explored for the X chromosome. METHODS Using data from middle age to elderly individuals (age 55+ years) from two Danish cohorts of monozygotic twins and the Scottish Lothian Birth Cohort 1921, we conducted an X-chromosome-wide analysis of age-associated DNA methylation patterns with consideration of stably inferred XCI status. RESULTS Through analysing and comparing sex-specific X-linked DNA methylation changes over age late in life, we identified 123, 293 and 55 CpG sites significant (FDR < 0.05) only in males, only in females and in both sexes of Danish twins. All findings were significantly replicated in the two Danish twin cohorts. CpG sites escaping XCI are predominantly de-methylated with increasing age across cohorts. In contrast, CpGs highly methylated in both sexes are methylated even further with increasing age. Among the replicated sites in Danish samples, 16 (13%), 24 (8.2%) and 3 (5.5%) CpGs were further validated in LBC1921 (FDR < 0.05). CONCLUSIONS The X-chromosome of whole blood leukocytes displays age- and sex-dependent DNA methylation patterns in relation to XCI across cohorts.
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Affiliation(s)
- Shuxia Li
- Epidemiology and Biostatistics, Department of Public Health, Faculty of Health Science, University of Southern Denmark, J. B. Winsløws Vej 9B, DK-5000, Odense C, Denmark
| | - Jesper B Lund
- Epidemiology and Biostatistics, Department of Public Health, Faculty of Health Science, University of Southern Denmark, J. B. Winsløws Vej 9B, DK-5000, Odense C, Denmark
| | - Kaare Christensen
- Epidemiology and Biostatistics, Department of Public Health, Faculty of Health Science, University of Southern Denmark, J. B. Winsløws Vej 9B, DK-5000, Odense C, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Jonas Mengel-From
- Epidemiology and Biostatistics, Department of Public Health, Faculty of Health Science, University of Southern Denmark, J. B. Winsløws Vej 9B, DK-5000, Odense C, Denmark
| | - Torben Kruse
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Weilong Li
- Epidemiology and Biostatistics, Department of Public Health, Faculty of Health Science, University of Southern Denmark, J. B. Winsløws Vej 9B, DK-5000, Odense C, Denmark
| | - Afsaneh Mohammadnejad
- Epidemiology and Biostatistics, Department of Public Health, Faculty of Health Science, University of Southern Denmark, J. B. Winsløws Vej 9B, DK-5000, Odense C, Denmark
| | - Alison Pattie
- Department of Psychology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.,Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Scotland, UK
| | - Ian J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, Scotland, UK.,Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Scotland, UK
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, Faculty of Health Science, University of Southern Denmark, J. B. Winsløws Vej 9B, DK-5000, Odense C, Denmark. .,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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16
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Heritability of skewed X-inactivation in female twins is tissue-specific and associated with age. Nat Commun 2019; 10:5339. [PMID: 31767861 PMCID: PMC6877649 DOI: 10.1038/s41467-019-13340-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 11/04/2019] [Indexed: 12/16/2022] Open
Abstract
Female somatic X-chromosome inactivation (XCI) balances the X-linked transcriptional dosages between the sexes. Skewed XCI toward one parental X has been observed in several complex human traits, but the extent to which genetics and environment influence skewed XCI is largely unexplored. To address this, we quantify XCI-skew in multiple tissues and immune cell types in a twin cohort. Within an individual, XCI-skew differs between blood, fat and skin tissue, but is shared across immune cell types. XCI skew increases with age in blood, but not other tissues, and is associated with smoking. XCI-skew is increased in twins with Rheumatoid Arthritis compared to unaffected identical co-twins. XCI-skew is heritable in blood of females >55 years old (h2 = 0.34), but not in younger individuals or other tissues. This results in a Gene x Age interaction that shifts the functional dosage of all X-linked heterozygous loci in a tissue-restricted manner. Skewing of X chromosome inactivation (XCI) occurs when the silencing of one parental X chromosome is non-random. Here, Zito et al. report XCI patterns in lymphoblastoid cell lines, blood, subcutaneous adipose tissue samples and skin samples of monozygotic and dizygotic twins and find XCI skew to associate with tissue and age.
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17
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Fahim AT, Sullivan LS, Bowne SJ, Jones KD, Wheaton DKH, Khan NW, Heckenlively JR, Jayasundera KT, Branham KH, Andrews CA, Othman MI, Karoukis AJ, Birch DG, Daiger SP. X-Chromosome Inactivation Is a Biomarker of Clinical Severity in Female Carriers of RPGR-Associated X-Linked Retinitis Pigmentosa. Ophthalmol Retina 2019; 4:510-520. [PMID: 31953110 DOI: 10.1016/j.oret.2019.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE X-linked retinitis pigmentosa can manifest in female carriers with widely variable severity, whereas others remain unaffected. The contribution of X-chromosome inactivation (XCI) to phenotypic variation has been postulated but not demonstrated. Furthermore, the impact of genotype and genetic modifiers has been demonstrated in affected males but has not been well established in female carriers. The purpose of this study was to describe the scope of clinical phenotype in female carriers with mutations in RPGR and quantify the contribution of genotype, genetic modifiers, and XCI to phenotypic severity. DESIGN Cohort study. PARTICIPANTS Seventy-seven female carriers with RPGR mutations from 41 pedigrees. METHODS Coding single nucleotide polymorphisms were sequenced in candidate genetic modifier genes encoding known RPGR-interacting proteins. X-chromosome inactivation ratios were determined in genomic DNA isolated from blood (n = 42) and saliva (n = 20) using methylation status of X-linked polymorphic repeats. These genetic data were compared with disease severity based on quantitative clinical parameters. MAIN OUTCOME MEASURES Visual acuity, Humphrey visual field (HVF) results, full-field electroretinography results, and dark adaptation. RESULTS Most individuals at all ages were mildly affected or unaffected, whereas those who progressed to moderate or severe vision loss were older than 30 years. RPGR genotype was not associated with clinical severity. The D1264N variant in RPGRIP1L was associated with more severe disease. Skewed XCI toward inactivation of the normal RPGR allele was associated with more severe disease. The XCI ratio in both blood and saliva was a predictor of visual function as measured by HVF diameter, rod amplitude, flicker amplitude, and flicker implicit time. For carriers with extreme XCI skewing of 80:20 or more, 57% were affected severely compared with 8% for those with XCI of less than 80:20 (P = 0.002). CONCLUSIONS Female carriers with mutations in RPGR demonstrate widely variable clinical severity. X-chromosome inactivation ratios correlate with clinical severity and may serve as a predictor of clinically significant disease. Because RPGR gene therapy trials are underway, a future imperative exists to determine which carriers require intervention and when to intervene. X-chromosome inactivation analysis may be useful for identifying candidates for early intervention.
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Affiliation(s)
- Abigail T Fahim
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan.
| | - Lori S Sullivan
- Department of Genetics, University of Texas Health Science Center, Houston, Texas
| | - Sara J Bowne
- Department of Genetics, University of Texas Health Science Center, Houston, Texas
| | | | | | - Naheed W Khan
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - K Thiran Jayasundera
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Kari H Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Chris A Andrews
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Mohammad I Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Athanasios J Karoukis
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | | | - Stephen P Daiger
- Department of Genetics, University of Texas Health Science Center, Houston, Texas
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18
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Espin-Garcia O, Croitoru K, Xu W. A finite mixture model for X-chromosome association with an emphasis on microbiome data analysis. Genet Epidemiol 2019; 43:427-439. [PMID: 30657195 DOI: 10.1002/gepi.22190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 12/14/2022]
Abstract
Analysis of the X chromosome has been largely neglected in genetic studies mainly because of complex underlying biological mechanisms. On the other hand, the study of human microbiome data (typically over-dispersed counts with an excess of zeros) has generated great interest recently because of advancements in next-generation sequencing technologies. We propose a novel approach to infer the association between host genetic variants in the X-chromosome and microbiome data. The method accounts for random X-chromosome inactivation (XCI), skewed (or nonrandom) XCI (XCI-S), and escape of XCI (XCI-E). The inference is performed through a finite mixture model (FMM), in which an indicator variable denoting the "true" biological mechanism is treated as missing data. An expectation-maximization algorithm on zero-inflated and two-part models is implemented to estimate genetic effects. We investigate the performance of the FMM along with strategies that assume XCI and XCI-E mechanisms for all subjects compared with alternative approaches. Briefly, an XCI mechanism codes males' genotypes as homozygous females, whereas under XCI-E, males are treated as heterozygous females. By comprehensive simulations, we evaluate tests of the hypothesis under a computationally efficient score statistic. In summary, the FMM renders reduced bias and commensurate power compared to XCI, XCI-E, and alternative strategies while maintaining adequate Type 1 error control. The proposed method has far-reaching applications. In particular, we illustrate its usage on a large-scale human microbiome study, the Genetic, Environmental and Microbial (GEM) project, to test for the genetic association on the X chromosome.
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Affiliation(s)
- Osvaldo Espin-Garcia
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Kenneth Croitoru
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada.,Division of Gastroenterology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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19
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Eaddy Norton A, Broyles AD. Drug allergy in children and adults: Is it the double X chromosome? Ann Allergy Asthma Immunol 2018; 122:148-155. [PMID: 30465863 DOI: 10.1016/j.anai.2018.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE This article reviews the latest science and epidemiologic studies related to drug allergy in children and adults to explore possible mechanisms related to female propensity for drug allergy. DATA SOURCES PubMed literature review, focusing primarily on the last 5 years. STUDY SELECTIONS Articles reviewing the science behind female predisposition to atopic and asthmatic conditions and epidemiologic studies reviewing drug allergy and drug-induced anaphylaxis. RESULTS Despite adult female predilection for atopic conditions, few laboratory studies explore sex-specific mechanisms in atopic/allergic diseases, and most are focused on autoimmunity and asthma. Drug allergy is more frequently reported in adult females compared with adult males. Adult females are also more likely to have drug-induced anaphylaxis (DIA), although no clear sex predominance has been reported in fatal or severe DIA. Studies in children suggest the reverse picture, with prepubertal males more likely to have drug allergy and DIA than prepubertal girls. CONCLUSION Possible explanations for female predisposition for drug allergy are multifactorial and include disproportionate utilization of health care with more exposure to antibiotics or medications, genetic factors related to the X chromosome, epigenetic changes, and discrepant hormonal interactions with immune cells.
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Affiliation(s)
- Allison Eaddy Norton
- Vanderbilt Children's Hospital, Division of Pediatric Pulmonary, Allergy and Immunology, School of Medicine, Nashville, Tennessee
| | - Ana Dioun Broyles
- Boston Children's Hospital, Division of Allergy and Immunology, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts.
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20
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Cloake NC, Yan J, Aminian A, Pender MP, Greer JM. PLP1 Mutations in Patients with Multiple Sclerosis: Identification of a New Mutation and Potential Pathogenicity of the Mutations. J Clin Med 2018; 7:jcm7100342. [PMID: 30314286 PMCID: PMC6210135 DOI: 10.3390/jcm7100342] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/20/2022] Open
Abstract
PLP1 is located on the X-chromosome and encodes myelin proteolipid protein (PLP), the most abundant protein in central nervous system myelin. Generally, point mutations in PLP1 result in X-linked dysmyelinating disorders, such as Pelizaeus-Merzbacher disease (PMD) or spastic paraplegia type 2 (SPG2). However, several case studies have identified patients with missense point mutations in PLP1 and clinical symptoms and signs compatible with a diagnosis of multiple sclerosis (MS). To investigate if PLP1 mutations occur relatively frequently in MS, we sequenced the coding regions of PLP1 in 22 female MS patients who had developed disease after the age of 40 and in 42 healthy women, and identified a missense mutation in exon 2 of PLP1 resulting in a Leu30Val mutation in the protein in one of the MS patients. mCherry-tagged plasmids containing wild type or mutant PLP1 sequences of PLP, including two known PMD/SPG2-related mutations as positive controls, were constructed and transfected into Cos-7 cells. In comparison with cells transfected with wild type PLP1, all mutations caused significant accumulation of PLP in the endoplasmic reticulum of the cells and induction of the unfolded protein response-a mechanism that leads to apoptosis of cells expressing mutant proteins. Additionally, in silico analysis of the binding of peptides containing the Leu30Val mutation to the human leukocyte antigen (HLA) molecules carried by the patient harboring this mutation suggested that the mutation could produce several novel immunogenic epitopes in this patient. These results support the idea that mutations in myelin-related genes could contribute to the development of MS in a small proportion of patients.
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Affiliation(s)
- Nancy C Cloake
- UQ Centre for Clinical Research, the University of Queensland, Brisbane, QLD 4029, Australia.
| | - Jun Yan
- UQ Centre for Clinical Research, the University of Queensland, Brisbane, QLD 4029, Australia.
| | - Atefeh Aminian
- UQ Centre for Clinical Research, the University of Queensland, Brisbane, QLD 4029, Australia.
- School of Medicine, Tehran University of Medical Sciences, Tehran 15119-43943, Iran.
| | - Michael P Pender
- Faculty of Medicine, the University of Queensland, Brisbane, QLD 4029, Australia.
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia.
| | - Judith M Greer
- UQ Centre for Clinical Research, the University of Queensland, Brisbane, QLD 4029, Australia.
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21
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Eguchi M, Yagi C, Tauchi H, Kobayashi M, Ishii E, Eguchi-Ishimae M. Exon skipping in CYBB mRNA and skewed inactivation of X chromosome cause late-onset chronic granulomatous disease. Pediatr Hematol Oncol 2018; 35:341-349. [PMID: 30633606 DOI: 10.1080/08880018.2018.1522402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Chronic granulomatous disease (CGD) is a hereditary immunodeficiency syndrome caused by a defect in the NADPH oxidase complex, which is essential for bactericidal function of phagocytes. Approximately 70% of patients with CGD have a mutation in the CYBB gene on the X chromosome, resulting in defective expression of gp91phox, one of the membrane-bound subunits of NADPH oxidase. Although most patients with X-linked CGD are males, owing to transmission of this disease as an X-linked recessive trait, there are female patients with X-linked CGD. Here, we report the case of a teenage girl with X-linked CGD associated with a heterozygous mutation in exon 5 of the CYBB gene (c.389G > C; R130P), which causes skipping of exon 5, resulting in a premature stop codon in exon 6 of CYBB. Accurate pro-mRNA splicing for mature mRNA formation is regulated by several splicing mechanisms that are essential for appropriate recognition of exonic sequences. The c.389G > C mutation disrupts exonic-splicing regulator sequences, thereby resulting in the aberrant skipping of exon 5 in the CYBB transcript of the patient. The patient showed an extremely skewed (≥96%) X inactivation pattern of the HUMARA locus; this inactivation is thought to be responsible for the development of CGD not only in neutrophils but also in monocytic, T-cell, and B-cell lineages and in CD34-positive immature hematopoietic cells. Our case and other reports indicate that the onset of X-linked CGD in female patients tends to occur later in life, and that the symptoms tend to be milder as compared to male patients.
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Affiliation(s)
- Mariko Eguchi
- a Department of Pediatrics , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Chihiro Yagi
- a Department of Pediatrics , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Hisamichi Tauchi
- a Department of Pediatrics , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Masao Kobayashi
- b Department of Pediatrics , Hiroshima University Graduate School of Biomedical Sciences , Hiroshima , Hiroshima , Japan
| | - Eiichi Ishii
- a Department of Pediatrics , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Minenori Eguchi-Ishimae
- a Department of Pediatrics , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
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22
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Parsons BL. Multiclonal tumor origin: Evidence and implications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:1-18. [PMID: 30115427 DOI: 10.1016/j.mrrev.2018.05.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/11/2018] [Accepted: 05/05/2018] [Indexed: 12/31/2022]
Abstract
An accurate understanding of the clonal origins of tumors is critical for designing effective strategies to treat or prevent cancer and for guiding the field of cancer risk assessment. The intent of this review is to summarize evidence of multiclonal tumor origin and, thereby, contest the commonly held assumption of monoclonal tumor origin. This review describes relevant studies of X chromosome inactivation, analyses of tumor heterogeneity using other markers, single cell sequencing, and lineage tracing studies in aggregation chimeras and engineered rodent models. Methods for investigating tumor clonality have an inherent bias against detecting multiclonality. Despite this, multiclonality has been observed within all tumor stages and within 53 different types of tumors. For myeloid tumors, monoclonal tumor origin may be the predominant path to cancer and a monoclonal tumor origin cannot be ruled out for a fraction of other cancer types. Nevertheless, a large body of evidence supports the conclusion that most cancers are multiclonal in origin. Cooperation between different cell types and between clones of cells carrying different genetic and/or epigenetic lesions is discussed, along with how polyclonal tumor origin can be integrated with current perspectives on the genesis of tumors. In order to develop biologically sound and useful approaches to cancer risk assessment and precision medicine, mathematical models of carcinogenesis are needed, which incorporate multiclonal tumor origin and the contributions of spontaneous mutations in conjunction with the selective advantages conferred by particular mutations and combinations of mutations. Adherence to the idea that a growth must develop from a single progenitor cell to be considered neoplastic has outlived its usefulness. Moving forward, explicit examination of tumor clonality, using advanced tools, like lineage tracing models, will provide a strong foundation for future advances in clinical oncology and better training for the next generation of oncologists and pathologists.
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Affiliation(s)
- Barbara L Parsons
- US Food and Drug Administration, National Center for Toxicological Research, Division of Genetic and Molecular Toxicology, 3900 NCTR Rd., Jefferson, AR 72079, United States.
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23
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Carè A, Bellenghi M, Matarrese P, Gabriele L, Salvioli S, Malorni W. Sex disparity in cancer: roles of microRNAs and related functional players. Cell Death Differ 2018; 25:477-485. [PMID: 29352271 PMCID: PMC5864217 DOI: 10.1038/s41418-017-0051-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 11/13/2017] [Accepted: 11/24/2017] [Indexed: 01/08/2023] Open
Abstract
A sexual dimorphism at the cellular level has been suggested to play a role in cancer onset and progression. In particular, very recent studies have unraveled striking differences between cells carrying XX or XY chromosomes in terms of response to stressful stimuli, indicating the presence of genetic and epigenetic differences determining sex-specific metabolic or phenotypic traits. Although this field of investigation is still in its infancy, available data suggest a key role of sexual chromosomes in determining cell life or death. In particular, cells carrying XX chromosomes exhibit a higher adaptive potential and survival behavior in response to microenvironmental variations with respect to XY cells. Cells from females also appear to be equipped with more efficient epigenetic machinery than the male counterpart. In particular, the X chromosome contains an unexpected high number of microRNAs (miRs), at present 118, in comparison with only two miRs localized on chromosome Y, and an average of 40-50 on the autosomes. The regulatory power of these small non-coding RNAs is well recognized, as 30-50% of all protein-coding genes are targeted by miRs and their role in cell fate has been well demonstrated. In addition, several further insights, including DNA methylation patterns that are different in males and females, claim for a significant gender disparity in cancer and in the immune system activity against tumors. In this brief paper, we analyze the state of the art of our knowledge on the implication of miRs encoded on sex chromosomes, and their related functional paths, in the regulation of cell homeostasis and depict possible perspectives for the epigenetic research in the field.
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Affiliation(s)
- Alessandra Carè
- Oncology Unit, Center for Gender-specific Medicine Istituto Superiore di Sanita', Viale Regina Elena, 299 00161, Rome, Italy
| | - Maria Bellenghi
- Oncology Unit, Center for Gender-specific Medicine Istituto Superiore di Sanita', Viale Regina Elena, 299 00161, Rome, Italy
| | - Paola Matarrese
- Oncology Unit, Center for Gender-specific Medicine Istituto Superiore di Sanita', Viale Regina Elena, 299 00161, Rome, Italy
| | - Lucia Gabriele
- Immunotherapy Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanita', Viale Regina Elena, 299 00161, Rome, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Walter Malorni
- Oncology Unit, Center for Gender-specific Medicine Istituto Superiore di Sanita', Viale Regina Elena, 299 00161, Rome, Italy.
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24
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Sharma A, Kaut O, Pavlova A, Fröhlich H, Ahmad A, Schmitt I, El-Maarri O, Oldenburg J, Wüllner U. Skewed X-chromosome inactivation and XIST locus methylation levels do not contribute to the lower prevalence of Parkinson's disease in females. Neurobiol Aging 2017; 57:248.e1-248.e5. [PMID: 28663000 DOI: 10.1016/j.neurobiolaging.2017.05.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 05/19/2017] [Accepted: 05/27/2017] [Indexed: 10/19/2022]
Abstract
Parkinson's disease (PD) is a degenerative disorder of the nervous system and the cause of the majority of sporadic cases is unknown. Females are relatively protected from PD as compared with males and linkage studies suggested a PD susceptibility locus on the X chromosome. To determine a putative association of skewed X-chromosome inactivation (XCI) and PD, we examined XCI patterns using a human androgen receptor gene-based assay (HUMARA) and did not identify any association of skewed or random X inactivation with clinical heterogeneity among female PD patients. In addition, we sought to determine methylation-specific changes at the X-inactive specific transcript (XIST) locus, which is known to be responsible for initiating X inactivation. We observed a trend towards hypomethylation in the gene body region of the XIST locus in PD females which did not reach significance. Furthermore, we extended our analysis of DNA methylation across the entire X-chromosome which revealed no methylation-specific differences between PD females and healthy controls. Thus, we propose that skewed XCI and methylation levels on the entire X chromosome did not reveal changes which could account for the decreased PD susceptibility in females or suitable to use as a biomarker.
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Affiliation(s)
- Amit Sharma
- Department of Neurology, University Clinic Bonn, Bonn, Germany; Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany
| | - Oliver Kaut
- Department of Neurology, University Clinic Bonn, Bonn, Germany
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany
| | - Holger Fröhlich
- Bonn-Aachen International Center for IT (B-IT), Bonn, Germany; UCB Biosciences GmbH, Monheim, Germany
| | - Ashar Ahmad
- Bonn-Aachen International Center for IT (B-IT), Bonn, Germany
| | - Ina Schmitt
- Department of Neurology, University Clinic Bonn, Bonn, Germany
| | - Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany; Department of Natural Sciences, Lebanese American University, Byblos, Beirut, Lebanon
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany
| | - Ullrich Wüllner
- Department of Neurology, University Clinic Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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25
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Have humans lost control: The elusive X-controlling element. Semin Cell Dev Biol 2016; 56:71-77. [DOI: 10.1016/j.semcdb.2016.01.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/22/2016] [Accepted: 01/28/2016] [Indexed: 02/01/2023]
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26
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Choi S, Lee S, Qiao D, Hardin M, Cho MH, Silverman EK, Park T, Won S. FARVATX: Family-Based Rare Variant Association Test for X-Linked Genes. Genet Epidemiol 2016; 40:475-85. [PMID: 27325607 DOI: 10.1002/gepi.21979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 03/05/2016] [Accepted: 04/04/2016] [Indexed: 11/06/2022]
Abstract
Although the X chromosome has many genes that are functionally related to human diseases, the complicated biological properties of the X chromosome have prevented efficient genetic association analyses, and only a few significantly associated X-linked variants have been reported for complex traits. For instance, dosage compensation of X-linked genes is often achieved via the inactivation of one allele in each X-linked variant in females; however, some X-linked variants can escape this X chromosome inactivation. Efficient genetic analyses cannot be conducted without prior knowledge about the gene expression process of X-linked variants, and misspecified information can lead to power loss. In this report, we propose new statistical methods for rare X-linked variant genetic association analysis of dichotomous phenotypes with family-based samples. The proposed methods are computationally efficient and can complete X-linked analyses within a few hours. Simulation studies demonstrate the statistical efficiency of the proposed methods, which were then applied to rare-variant association analysis of the X chromosome in chronic obstructive pulmonary disease. Some promising significant X-linked genes were identified, illustrating the practical importance of the proposed methods.
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Affiliation(s)
- Sungkyoung Choi
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
| | - Sungyoung Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Megan Hardin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.,Department of Statistics, Seoul National University, Seoul, Korea
| | - Sungho Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.,Department of Public Health Science, Seoul National University, Seoul, Korea.,Institute of Health and Environment, Seoul National University, Seoul, Korea
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27
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Gentilini D, Garagnani P, Pisoni S, Bacalini MG, Calzari L, Mari D, Vitale G, Franceschi C, Di Blasio AM. Stochastic epigenetic mutations (DNA methylation) increase exponentially in human aging and correlate with X chromosome inactivation skewing in females. Aging (Albany NY) 2016; 7:568-78. [PMID: 26342808 PMCID: PMC4586102 DOI: 10.18632/aging.100792] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study we applied a new analytical strategy to investigate the relations between stochastic epigenetic mutations (SEMs) and aging. We analysed methylation levels through the Infinium HumanMethylation27 and HumanMethylation450 BeadChips in a population of 178 subjects ranging from 3 to 106 years. For each CpG probe, epimutated subjects were identified as the extreme outliers with methylation level exceeding three times interquartile ranges the first quartile (Q1-(3 × IQR)) or the third quartile (Q3+(3 × IQR)). We demonstrated that the number of SEMs was low in childhood and increased exponentially during aging. Using the HUMARA method, skewing of X chromosome inactivation (XCI) was evaluated in heterozygotes women. Multivariate analysis indicated a significant correlation between log(SEMs) and degree of XCI skewing after adjustment for age (β = 0.41; confidence interval: 0.14, 0.68; p-value = 0.0053). The PATH analysis tested the complete model containing the variables: skewing of XCI, age, log(SEMs) and overall CpG methylation. After adjusting for the number of epimutations we failed to confirm the well reported correlation between skewing of XCI and aging. This evidence might suggest that the known correlation between XCI skewing and aging could not be a direct association but mediated by the number of SEMs.
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Affiliation(s)
- Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum- University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Serena Pisoni
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum- University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Luciano Calzari
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy
| | - Daniela Mari
- Geriatric Unit, IRCCS Ca' Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Giovanni Vitale
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum- University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
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28
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Viggiano E, Ergoli M, Picillo E, Politano L. Determining the role of skewed X-chromosome inactivation in developing muscle symptoms in carriers of Duchenne muscular dystrophy. Hum Genet 2016; 135:685-98. [PMID: 27098336 DOI: 10.1007/s00439-016-1666-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/29/2016] [Indexed: 11/24/2022]
Abstract
Duchenne and Becker dystrophinopathies (DMD and BMD) are X-linked recessive disorders caused by mutations in the dystrophin gene that lead to absent or reduced expression of dystrophin in both skeletal and heart muscles. DMD/BMD female carriers are usually asymptomatic, although about 8 % may exhibit muscle or cardiac symptoms. Several mechanisms leading to a reduced dystrophin have been hypothesized to explain the clinical manifestations and, in particular, the role of the skewed XCI is questioned. In this review, the mechanism of XCI and its involvement in the phenotype of BMD/DMD carriers with both a normal karyotype or with X;autosome translocations with breakpoints at Xp21 (locus of the DMD gene) will be analyzed. We have previously observed that DMD carriers with moderate/severe muscle involvement, exhibit a moderate or extremely skewed XCI, in particular if presenting with an early onset of symptoms, while DMD carriers with mild muscle involvement present a random XCI. Moreover, we found that among 87.1 % of the carriers with X;autosome translocations involving the locus Xp21 who developed signs and symptoms of dystrophinopathy such as proximal muscle weakness, difficulty to run, jump and climb stairs, 95.2 % had a skewed XCI pattern in lymphocytes. These data support the hypothesis that skewed XCI is involved in the onset of phenotype in DMD carriers, the X chromosome carrying the normal DMD gene being preferentially inactivated and leading to a moderate-severe muscle involvement.
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Affiliation(s)
- Emanuela Viggiano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, I Policlinico, Second University of Naples, Piazza Miraglia, 80138, Naples, Italy
| | - Manuela Ergoli
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, I Policlinico, Second University of Naples, Piazza Miraglia, 80138, Naples, Italy
| | - Esther Picillo
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, I Policlinico, Second University of Naples, Piazza Miraglia, 80138, Naples, Italy
| | - Luisa Politano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, I Policlinico, Second University of Naples, Piazza Miraglia, 80138, Naples, Italy.
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29
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Wu C, Sun Z. X chromosome abnormal inactivation: a unique factor for women's diseases? Epigenomics 2016; 8:447-50. [DOI: 10.2217/epi.16.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Cuijiao Wu
- Department of Histology & Embryology, Qingdao University Medical School, Qingdao, Shandong, China
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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30
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Fahim AT, Daiger SP. The Role of X-Chromosome Inactivation in Retinal Development and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 854:325-31. [PMID: 26427428 DOI: 10.1007/978-3-319-17121-0_43] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The expression of X-linked genes is equalized between males and females in mammalian species through X-Chromosome inactivation (XCI). Every cell in a female mammalian embryo randomly chooses one X Chromosome for epigenetic silencing at the 8-16 cell stage, resulting in a Gaussian distribution of XCI ratios with a peak at 50:50. At the tail extremes of this distribution, X-linked recessive mutations can manifest in disease in female carriers if the mutant allele is disproportionately active. The role of XCI skewing, if any, in X-linked retinal disease is still unknown, although many have speculated that such skewing accounts for phenotypic variation in female carriers of X-linked retinitis pigmentosa (XlRP). Some investigators have used clinical findings such as tapetal-like reflex, pigmentary changes, and multifocal ERG parameters to approximate XCI patches in the retina. These studies are limited by small cohorts and the relative inaccessibility of retinal tissue for genetic and epigenetic analysis. Although blood has been used as a proxy for other tissues in determining XCI ratios, blood XCI skews with age out of proportion to other tissues and may not accurately reflect retinal XCI ratios. Future investigations in determining retinal XCI ratios and the contribution of XCI to phenotype could potentially impact prognosis for female carriers of X-linked retinal disease.
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Affiliation(s)
- Abigail T Fahim
- Department of Ophthalmology and Visual Sciences, University of Michigan, Kellogg Eye Center, 1000 Wall Street, 48105, Ann Arbor, MI, USA.
| | - Stephen P Daiger
- School of Public Health, University of Texas Health Science Center, 1200 Herman Pressler Drive, RAS W-522, 77030, Houston, TX, USA.
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Association of skewed X chromosome inactivation and idiopathic recurrent spontaneous abortion: a systematic review and meta-analysis. Reprod Biomed Online 2015; 31:140-8. [DOI: 10.1016/j.rbmo.2015.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 11/20/2022]
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Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes. Blood 2015; 126:9-16. [PMID: 25931582 DOI: 10.1182/blood-2015-03-631747] [Citation(s) in RCA: 1301] [Impact Index Per Article: 144.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/26/2015] [Indexed: 12/12/2022] Open
Abstract
Recent genetic analyses of large populations have revealed that somatic mutations in hematopoietic cells leading to clonal expansion are commonly acquired during human aging. Clonally restricted hematopoiesis is associated with an increased risk of subsequent diagnosis of myeloid or lymphoid neoplasia and increased all-cause mortality. Although myelodysplastic syndromes (MDS) are defined by cytopenias, dysplastic morphology of blood and marrow cells, and clonal hematopoiesis, most individuals who acquire clonal hematopoiesis during aging will never develop MDS. Therefore, acquisition of somatic mutations that drive clonal expansion in the absence of cytopenias and dysplastic hematopoiesis can be considered clonal hematopoiesis of indeterminate potential (CHIP), analogous to monoclonal gammopathy of undetermined significance and monoclonal B-cell lymphocytosis, which are precursor states for hematologic neoplasms but are usually benign and do not progress. Because mutations are frequently observed in healthy older persons, detection of an MDS-associated somatic mutation in a cytopenic patient without other evidence of MDS may cause diagnostic uncertainty. Here we discuss the nature and prevalence of CHIP, distinction of this state from MDS, and current areas of uncertainty regarding diagnostic criteria for myeloid malignancies.
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Gallot V, Nedellec S, Capmas P, Legendre G, Lejeune-Saada V, Subtil D, Nizard J, Levêque J, Deffieux X, Hervé B, Vialard F. Fausses couches précoces « à répétition » : bilan et prise en charge. ACTA ACUST UNITED AC 2014; 43:812-41. [DOI: 10.1016/j.jgyn.2014.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Guillén-Navarro E, Domingo-Jiménez MR, Alcalde-Martín C, Cancho-Candela R, Couce ML, Galán-Gómez E, Alonso-Luengo O. Clinical manifestations in female carriers of mucopolysaccharidosis type II: a Spanish cross-sectional study. Orphanet J Rare Dis 2013; 8:92. [PMID: 23800320 PMCID: PMC3697996 DOI: 10.1186/1750-1172-8-92] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/20/2013] [Indexed: 01/02/2023] Open
Abstract
Background Mucopolysaccharidosis type II (MPS II) is an inherited X-linked disease associated with a deficiency in the enzyme iduronate 2-sulfatase due to iduronate 2-sulfatase gene (IDS) mutations. Recent studies in MPS II carriers did not find clinical involvement, but these were mainly performed by anamnesis and patients’ self-reported description of signs and symptoms. So although it is rare in heterozygous carriers, investigations in other types of inherited X-linked disorders suggest that some clinical manifestations may be a possibility. The aim of this study was to evaluate the clinical pattern in female carriers of MPS II and to determine whether clinical symptoms were associated with the X-chromosome inactivation (XCI) pattern and age. Methods Female carriers of MPS II were genetically identified by molecular analysis of IDS. The clinical evaluation protocol included pedigree analysis, a comprehensive anamnesis, complete physical examination, ophthalmological evaluation, brain-evoked auditory response, electrocardiogram, echocardiogram, pulmonary function tests, abdominal sonogram, skeletal survey, neurophysiological studies, blood cell counts and biochemistry, urine glycosaminoglycan (GAGs) quantification, karyotype and pattern of XCI. Results Ten women were included in the study. The mean age of the participants was 40.2 ± 13.1 years. Six carriers presented a skewed XCI pattern, 3 of whom (aged 38, 42 and 52 years) had increased levels of GAGs in the urine and showed typical MPS II clinical manifestations, such as skeletal anomalies, liver abnormalities, carpal tunnel syndrome, recurrent ear infection, hypoacusia and more frequent severe odontological problems without coarse facial features. Conclusions This is the first study performing a comprehensive evaluation of heterozygous MPS II carriers. Our results provide evidence of possible progressive, age-dependent, mild clinical manifestations in MPS II female carriers with a skewed XCI pattern, most likely affecting the normal allele. Further comparative studies with systematized clinical examinations in larger age-stratified populations of MPS II female carriers are required.
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Guillén-Navarro E, Domingo-Jiménez MR, Alcalde-Martín C, Cancho-Candela R, Couce ML, Galán-Gómez E, Alonso-Luengo O. Clinical manifestations in female carriers of mucopolysaccharidosis type II: a Spanish cross-sectional study. Orphanet J Rare Dis 2013. [PMID: 23800320 DOI: 10.1186/1750‐1172‐8‐92] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mucopolysaccharidosis type II (MPS II) is an inherited X-linked disease associated with a deficiency in the enzyme iduronate 2-sulfatase due to iduronate 2-sulfatase gene (IDS) mutations. Recent studies in MPS II carriers did not find clinical involvement, but these were mainly performed by anamnesis and patients' self-reported description of signs and symptoms. So although it is rare in heterozygous carriers, investigations in other types of inherited X-linked disorders suggest that some clinical manifestations may be a possibility. The aim of this study was to evaluate the clinical pattern in female carriers of MPS II and to determine whether clinical symptoms were associated with the X-chromosome inactivation (XCI) pattern and age. METHODS Female carriers of MPS II were genetically identified by molecular analysis of IDS. The clinical evaluation protocol included pedigree analysis, a comprehensive anamnesis, complete physical examination, ophthalmological evaluation, brain-evoked auditory response, electrocardiogram, echocardiogram, pulmonary function tests, abdominal sonogram, skeletal survey, neurophysiological studies, blood cell counts and biochemistry, urine glycosaminoglycan (GAGs) quantification, karyotype and pattern of XCI. RESULTS Ten women were included in the study. The mean age of the participants was 40.2 ± 13.1 years. Six carriers presented a skewed XCI pattern, 3 of whom (aged 38, 42 and 52 years) had increased levels of GAGs in the urine and showed typical MPS II clinical manifestations, such as skeletal anomalies, liver abnormalities, carpal tunnel syndrome, recurrent ear infection, hypoacusia and more frequent severe odontological problems without coarse facial features. CONCLUSIONS This is the first study performing a comprehensive evaluation of heterozygous MPS II carriers. Our results provide evidence of possible progressive, age-dependent, mild clinical manifestations in MPS II female carriers with a skewed XCI pattern, most likely affecting the normal allele. Further comparative studies with systematized clinical examinations in larger age-stratified populations of MPS II female carriers are required.
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Li G, Jin T, Liang H, Tu Y, Zhang W, Gong L, Su Q, Gao G. Skewed X-chromosome inactivation in patients with esophageal carcinoma. Diagn Pathol 2013; 8:55. [PMID: 23556484 PMCID: PMC3640911 DOI: 10.1186/1746-1596-8-55] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 04/01/2013] [Indexed: 11/15/2022] Open
Abstract
Abstract Skewed X-chromosome inactivation (SXCI) was found in some apparently healthy females mainly from Western countries. It has been linked to development of ovarian, breast and pulmonary carcinomas. The present study aimed to observe the SXCI frequencies in apparently healthy Chinese females and patients with esophageal carcinoma. DNA was extracted from the peripheral blood cells from 401 Chinese females without a detectable tumor and 143 female patients with esophageal carcinoma. Exon 1 of androgen receptor (AR) gene was amplified, and the products of different CAG alleles were resolved on denaturing polyacrylamide gels and visualized after silver staining. The corrected ratios (CR) of the products before and after HpaII digestion were calculated. As to the healthy females, when CR ≥ 3 was used as a criterion, SXCI was found in two (4.3%) of the 46 neonates, 13 (7.8%) of the 166 younger adults (16–50 years) and 37 (25.7%) of the 144 elderly females (51–96 years), with the frequency higher in the elderly subjects than in the two former groups (P < 0.05). When a more stringent criterion (CR ≥ 10) was used, SXCI was found in one (2.2%), two (1.2%) and 16 (11.1%) of the subjects in the three age groups, respectively, itsfrequency being higher in the elderly than in the younger age groups (P < 0.05). Occurrence of SXCI was detected in both the patients and controls at similar frequencies. However, the phenomenon, as defined as CR ≥ 3, was more frequent in the patients aging <40 years (35.7%) compared to the corresponding reference group (7.6%, P = 0.006). When CR ≥ 10 was adopted, the frequencies were 7.1% and 1.2%, respectively. Their difference did not attain statistical significance (P = 0. 217). SXCI also occurs in apparently healthy Chinese females, and is associated with age. It may be considered as a predisposing factor for the early development of esophageal carcinoma. Virtual slides The virtual slide(s) for this article can be found here http://www.diagnosticpathology.diagnomx.eu/vs/1542364337927656
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Affiliation(s)
- Gang Li
- Department of Neurosurgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an, China
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Gentilini D, Castaldi D, Mari D, Monti D, Franceschi C, Di Blasio AM, Vitale G. Age-dependent skewing of X chromosome inactivation appears delayed in centenarians' offspring. Is there a role for allelic imbalance in healthy aging and longevity? Aging Cell 2012; 11:277-83. [PMID: 22292741 DOI: 10.1111/j.1474-9726.2012.00790.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Recently, it has been proposed that age-related X chromosome inactivation (XCI) skewing can clinically result in late-onset X-linked disorders. This observation leads to hypothesize that age-related skewed XCI might also influence lifespan in women. To investigate this issue, we employed a new experimental model of longevity and healthy aging including 55 female centenarians, 40 of their offspring, 33 age-matched offspring of both non-long-lived parents and 41 young women. Peripheral blood DNA from 169 females was screened for heterozygosity at the HUMARA locus. We confirmed that skewing of XCI is an age-dependent phenomenon. However, skewed XCI was significantly less severe and frequent in centenarians' offspring [degree of skewing (DS) = 0.16 ± 0.02] compared to age-matched offspring of both non-long-lived parents (DS = 0.24 ± 0.02) (P < 0.05). A second goal was to assess whether changes in XCI pattern could be a consequence of loss of methylation on X chromosome. Using a methylation array evaluating 1085 CpG sites across X chromosome and eleven CpG sites located at HUMARA locus, no differences in methylation levels and profiles emerged between all groups analysed, thus suggesting that age-associated epigenetic changes could not influence HUMARA results. In conclusion, the results presented herein highlight for the first time an interesting link between skewing of XCI and healthy aging and longevity. We speculate that the allelic imbalance produced by XCI skewing may compromise the cooperative and compensatory organization occurring between the two cell populations that make up the female mosaic.
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Unexpected X chromosome skewing during culture and reprogramming of human somatic cells can be alleviated by exogenous telomerase. Cell Stem Cell 2012; 9:156-65. [PMID: 21816366 DOI: 10.1016/j.stem.2011.06.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/13/2011] [Accepted: 06/07/2011] [Indexed: 12/28/2022]
Abstract
Somatic tissues in female eutherian mammals are mosaic due to random X inactivation. In contrast to mice, X chromosome reactivation does not occur during the reprogramming of human female somatic cells to induced pluripotent stem cells (iPSCs), although this view is contested. Using balanced populations of female Rett patient and control fibroblasts, we confirm that all cells in iPSC colonies contain an inactive X, and additionally find that all colonies made from the same donor fibroblasts contain the same inactive X chromosome. Notably, this extreme "skewing" toward a particular dominant, active X is also a general feature of primary female fibroblasts during proliferation, and the skewing seen in reprogramming and fibroblast culture can be alleviated by overexpression of telomerase. These results have important implications for in vitro modeling of X-linked diseases and the interpretation of long-term culture studies in cancer and senescence using primary female fibroblast cell lines.
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Skewed X inactivation and survival: a 13-year follow-up study of elderly twins and singletons. Eur J Hum Genet 2011; 20:361-4. [PMID: 22146940 DOI: 10.1038/ejhg.2011.215] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In mammalian females, one of the two X chromosomes is inactivated in early embryonic life. Females are therefore mosaics for two cell populations, one with the maternal and one with the paternal X as the active X chromosome. A skewed X inactivation is a marked deviation from a 50:50 ratio. In populations of women past 55-60 years of age, an increased degree of skewing (DS) is found. Here the association between age-related skewing and mortality is analyzed in a 13-year follow-up study of 500 women from three cohorts (73-100 years of age at intake). Women with low DS had significantly higher mortality than the majority of women who had a more skewed DS (hazard ratio: 1.30; 95% CI: 1.04-1.64). The association between X inactivation and mortality was replicated in dizygotic twin pairs for which the co-twin with the lowest DS also had a statistically significant tendency to die first in the twin pairs with the highest intra-pair differences in DS (proportion: 0.71; 95% CI: 0.52-0.86). Both results suggest that lower DS is associated with higher mortality. We therefore propose that age-related skewing may be partly due to a population selection with lower mortality among those with higher DS.
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Chronic hemolytic anemia is associated with a new glucose-6-phosphate dehydrogenase in-frame deletion in an older woman. Blood Cells Mol Dis 2011; 46:288-93. [DOI: 10.1016/j.bcmd.2011.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 01/25/2011] [Accepted: 02/03/2011] [Indexed: 11/22/2022]
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Wong CCY, Caspi A, Williams B, Houts R, Craig IW, Mill J. A longitudinal twin study of skewed X chromosome-inactivation. PLoS One 2011; 6:e17873. [PMID: 21445353 PMCID: PMC3062559 DOI: 10.1371/journal.pone.0017873] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 02/11/2011] [Indexed: 01/10/2023] Open
Abstract
X-chromosome inactivation (XCI) is a pivotal epigenetic mechanism involved in the dosage compensation of X-linked genes between males and females. In any given cell, the process of XCI in early female development is thought to be random across alleles and clonally maintained once established. Recent studies, however, suggest that XCI might not always be random and that skewed inactivation may become more prevalent with age. The factors influencing such XCI skewing and its changes over time are largely unknown. To elucidate the influence of stochastic, heritable and environmental factors in longitudinal changes in XCI, we examined X inactivation profiles in a sample of monozygotic (MZ) (n = 23) and dizygotic (DZ) (n = 22) female twin-pairs at ages 5 and 10 years. Compared to MZ twins who were highly concordant for allelic XCI ratios, DZ twins showed much lower levels of concordance. Whilst XCI patterns were moderately stable between ages 5 and 10 years, there was some drift over time with an increased prevalence of more extreme XCI skewing at age 10. To our knowledge, this study represents the earliest longitudinal assessment of skewed XCI patterns, and suggests that skewed XCI may already be established in early childhood. Our data also suggest a link between MZ twinning and the establishment of allelic XCI ratios, and demonstrate that acquired skewing in XCI after establishment is primarily mediated by stochastic mechanisms. These data have implications for our understanding about sex differences in complex disease, and the potential causes of phenotypic discordance between MZ female twins.
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Affiliation(s)
- Chloe Chung Yi Wong
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Avshalom Caspi
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
- Departments of Psychology and Neuroscience, Psychiatry and Behavioral Sciences, Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Benjamin Williams
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
- Departments of Psychology and Neuroscience, Psychiatry and Behavioral Sciences, Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Renate Houts
- Departments of Psychology and Neuroscience, Psychiatry and Behavioral Sciences, Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Ian W. Craig
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Jonathan Mill
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
- * E-mail:
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El-Maarri O, Walier M, Behne F, van Üüm J, Singer H, Diaz-Lacava A, Nüsgen N, Niemann B, Watzka M, Reinsberg J, van der Ven H, Wienker T, Stoffel-Wagner B, Schwaab R, Oldenburg J. Methylation at global LINE-1 repeats in human blood are affected by gender but not by age or natural hormone cycles. PLoS One 2011; 6:e16252. [PMID: 21311577 PMCID: PMC3023801 DOI: 10.1371/journal.pone.0016252] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 12/19/2010] [Indexed: 01/13/2023] Open
Abstract
Previously, we reported on inter-individual and gender specific variations of LINE-1 methylation in healthy individuals. In this study, we investigated whether this variability could be influenced by age or sex hormones in humans. To this end, we studied LINE-1 methylation in vivo in blood-derived DNA from individuals aged 18 to 64 years and from young healthy females at various hormone levels during the menstrual cycle. Our results show that no significant association with age was observed. However, the previously reported increase of LINE-1 methylation in males was reconfirmed. In females, although no correlation between LINE-1 or Alu methylation and hormone levels was observed, a significant stable individual specific level of methylation was noted. In vitro results largely confirmed these findings, as neither estrogen nor dihydrotestosterone affected LINE-1 or Alu methylation in Hek293T, HUVEC, or MDA-kb2 cell lines. In contrast, a decrease in methylation was observed in estrogen-treated T47-Kbluc cell lines strongly expressing estrogen receptor. The very low expression of estrogen receptor in blood cells could explain the observed insensitivity of methylation at LINE-1 to natural hormonal variations in females. In conclusion, neither natural cycle of hormones nor age has a detectable effect on the LINE-1 methylation in peripheral blood cells, while gender remains an important factor.
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Affiliation(s)
- Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany.
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Abstract
Autoimmune diseases appear to have multiple contributing factors including genetics, epigenetics, environmental factors, and aging. The predominance of females among patients with autoimmune diseases suggests possible involvement of the X chromosome and X chromosome inactivation. X chromosome inactivation is an epigenetic event resulting in multiple levels of control for modulation of the expression of X-linked genes in normal female cells such that there remains only one active X chromosome in the cell. The extent of this control is unique among the chromosomes and has the potential for problems when regulation is disrupted. Here we discuss the X chromosome inactivation process and how the X chromosome and X chromosome inactivation may be involved in development of autoimmune disorders.
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Affiliation(s)
- Wesley H Brooks
- Experimental HTS, Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612-9416, USA.
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Siddiqui RA, Sauermann U, Altmüller J, Fritzer E, Nothnagel M, Dalibor N, Fellay J, Kaup FJ, Stahl-Hennig C, Nürnberg P, Krawczak M, Platzer M. X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women. Am J Hum Genet 2009; 85:228-39. [PMID: 19679225 DOI: 10.1016/j.ajhg.2009.07.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 07/07/2009] [Accepted: 07/21/2009] [Indexed: 11/26/2022] Open
Abstract
AIDS has changed from a mostly male-specific health problem to one that predominantly affects females. Although sex differences in HIV-1 susceptibility are beyond doubt, the extent to which sex affects the onset and progression of AIDS has remained elusive. Here, we provide evidence for an influence of X chromosomal variation on the course of retroviral infection, both in HIV-1-infected patients and in the rhesus macaque model of AIDS. A two-stage, microsatellite-based GWAS of SIV-infected monkeys revealed MHC class I markers and a hitherto-unknown X chromosomal locus as being associated with a nominal score measuring progression to AIDS (Fisher's exact p < 10(-6)). The X chromosomal association was subsequently confirmed in HIV-1-infected patients with published SNP genotype data. SNP rs5968255, located at human Xq21.1 in a conserved sequence element near the RPS6KA6 and CYLC1 genes, was identified as a significant genetic determinant of disease progression in females (ANOVA p = 8.8 x 10(-5)), but not in males (p = 0.19). Heterozygous female carriers of the C allele showed significantly slower CD4 cell decline and a lower viral load at set point than TT homozygous females and than males. Inspection of HapMap revealed that the CT genotype is significantly more frequent among Asians than among Europeans or Africans. Our results suggest that, in addition to the individual innate and adaptive immunity status, sex-linked genetic variation impacts upon the rate of progression to AIDS. Elucidating the mechanisms underlying this sex-specific effect will promote the development of antiretroviral therapies with high efficacy in both sexes.
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Skewed X chromosome inactivation and trisomic spontaneous abortion: no association. Am J Hum Genet 2009; 85:179-93. [PMID: 19646676 DOI: 10.1016/j.ajhg.2009.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 06/29/2009] [Accepted: 07/01/2009] [Indexed: 11/21/2022] Open
Abstract
Several studies suggest that highly skewed X chromosome inactivation (HSXI) is associated with recurrent spontaneous abortion. We hypothesized that this association reflects an increased rate of trisomic conceptions due to anomalies on the X chromosome that lead both to HSXI and to a diminished oocyte pool. We compared the distribution of X chromosome inactivation (XCI) skewing percentages (range: 50%-100%) among women with spontaneous abortions in four karyotype groups-trisomy (n = 154), chromosomally normal male (n = 43), chromosomally normal female (n = 38), nontrisomic chromosomally abnormal (n = 61)-to the distribution for age-matched controls with chromosomally normal births (n = 388). In secondary analyses, we subdivided the nontrisomic chromosomally abnormal group, divided trisomies by chromosome, and classified women by reproductive history. Our data support neither an association of HSXI with all trisomies nor an association of HSXI with chromosomally normal male spontaneous abortions. We also find no association between HSXI and recurrent abortion (n = 45).
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46
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Chabchoub G, Uz E, Maalej A, Mustafa CA, Rebai A, Mnif M, Bahloul Z, Farid NR, Ozcelik T, Ayadi H. Analysis of skewed X-chromosome inactivation in females with rheumatoid arthritis and autoimmune thyroid diseases. Arthritis Res Ther 2009; 11:R106. [PMID: 19589151 PMCID: PMC2745787 DOI: 10.1186/ar2759] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 06/22/2009] [Accepted: 07/09/2009] [Indexed: 12/12/2022] Open
Abstract
Introduction The majority of autoimmune diseases such as rheumatoid arthritis (RA) and autoimmune thyroid diseases (AITDs) are characterized by a striking female predominance superimposed on a predisposing genetic background. The role of extremely skewed X-chromosome inactivation (XCI) has been questioned in the pathogenesis of several autoimmune diseases. Methods We examined XCI profiles of females affected with RA (n = 106), AITDs (n = 145) and age-matched healthy women (n = 257). XCI analysis was performed by enzymatic digestion of DNA with a methylation sensitive enzyme (HpaII) followed by PCR of a polymorphic CAG repeat in the androgen receptor (AR) gene. The XCI pattern was classified as skewed when 80% or more of the cells preferentially inactivated the same X-chromosome. Results Skewed XCI was observed in 26 of the 76 informative RA patients (34.2%), 26 of the 100 informative AITDs patients (26%), and 19 of the 170 informative controls (11.2%) (P < 0.0001; P = 0.0015, respectively). More importantly, extremely skewed XCI, defined as > 90% inactivation of one allele, was present in 17 RA patients (22.4%), 14 AITDs patients (14.0%), and in only seven controls (4.1%, P < 0.0001; P = 0.0034, respectively). Stratifying RA patients according to laboratory profiles (rheumatoid factor and anti-citrullinated protein antibodies), clinical manifestations (erosive disease and nodules) and the presence of others autoimmune diseases did not reveal any statistical significance (P > 0.05). Conclusions These results suggest a possible role for XCI mosaicism in the pathogenesis of RA and AITDs and may in part explain the female preponderance of these diseases.
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Affiliation(s)
- Ghazi Chabchoub
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Avenue Majida Boulila, Sfax, Tunisia.
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Orstavik KH. X chromosome inactivation in clinical practice. Hum Genet 2009; 126:363-73. [PMID: 19396465 DOI: 10.1007/s00439-009-0670-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Accepted: 04/07/2009] [Indexed: 01/19/2023]
Abstract
X chromosome inactivation (XCI) is the transcriptional silencing of the majority of genes on one of the two X chromosomes in mammalian females. Females are, therefore, mosaics for two cell lines, one with the maternal X and one with the paternal X as the active chromosome. The relative proportion of the two cell lines, the X inactivation pattern, may be analyzed by simple assays in DNA from available tissues. This review focuses on medical issues related to XCI in X-linked disorders, and on the value of X inactivation analysis in clinical practice.
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Affiliation(s)
- Karen Helene Orstavik
- Department of Medical Genetics, Oslo University Hospital, Rikshospitalet and Faculty Division Rikshospitalet, University of Oslo, Forskningsveien 2B, 0027, Oslo, Norway.
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Brix TH, Hansen PS, Knudsen GPS, Kringen MK, Kyvik KO, Orstavik KH, Hegedüs L. No link between X chromosome inactivation pattern and simple goiter in females: evidence from a twin study. Thyroid 2009; 19:165-9. [PMID: 19191747 DOI: 10.1089/thy.2008.0380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Simple goiter (SG) comprises diffuse (DG) and nodular (NG) benign nonautoimmune nontoxic goiter. In nonendemic goiter areas, the ratio of females to males may exceed 5:1, indicating that gender and/or sex hormones may play a role in the etiology of SG in these areas. Theoretically, as shown for autoimmune thyroid disease, X chromosome inactivation (XCI) and resultant tissue chimerism could offer a novel explanation for the female preponderance of SG. To examine whether skewed XCI is associated with SG, we first compared XCI in 71 twin individuals with SG with that in 142 unrelated healthy control twin individuals, and then performed a within-pair comparison of XCI in 48 twin pairs discordant for SG. METHODS DNA was extracted from peripheral blood cells. XCI analysis was performed by predigestion of DNA using the methylation-sensitive enzyme Hpall, followed by polymerase chain reaction of the polymorphic CAG repeat of the androgen receptor gene. A polymerase chain reaction product is obtained from the inactive X chromosome only. The XCI pattern was classified as skewed when 80% or more of the cells preferentially inactivated the same X chromosome. Twin zygosity was established by DNA fingerprinting. RESULTS The frequency of skewed XCI in female twins with SG, DG, and NG was 11% (8/71), 13% (6/46), and 8% (2/25), respectively, which was not significantly different from the prevalences in the corresponding control populations, 14% (20/142, p = 0.56), 14% (13/92, p = 1.00), and 14% (7/50, p = 0.71), respectively. Essentially, similar results were obtained when comparing the prevalence of skewed XCI in twin pairs discordant for SG (48 pairs), DG (30 pairs), and NG (18 pairs). CONCLUSION In a sample of Danish female twins, we did not find evidence for involvement of skewed XCI in the etiology or the female preponderance of SG.
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Affiliation(s)
- Thomas Heiberg Brix
- Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark.
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Lose F, Duffy DL, Kay GF, Kedda MA, Spurdle AB. Skewed X chromosome inactivation and breast and ovarian cancer status: evidence for X-linked modifiers of BRCA1. J Natl Cancer Inst 2008; 100:1519-29. [PMID: 18957670 DOI: 10.1093/jnci/djn345] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND X chromosome inactivation, which silences gene expression from one of the two X chromosomes in females, is usually random. Skewed X inactivation has been implicated in both the expression and the suppression of X-linked disease phenotypes and has been reported to occur more frequently in breast and ovarian cancer patients, including BRCA1 or BRCA2 mutation carriers, than in control subjects. METHODS We assessed the pattern of X chromosome inactivation using methylation-specific polymerase chain reaction amplification of the exon 1 microsatellite region of the X-linked androgen receptor (AR) gene in DNA from blood samples obtained from control subjects without a personal history of breast or ovarian cancer (n = 735), ovarian cancer patients (n = 313), familial breast cancer patients who did not carry mutations in BRCA1 or BRCA2 (n = 235), and affected and unaffected carriers of mutations in BRCA1 (n = 260) or BRCA2 (n = 63). We defined the pattern of X chromosome inactivation as skewed when the same X chromosome was active in at least 90% of cells. The association between skewed X inactivation and disease and/or BRCA mutation status was assessed by logistic regression analysis. The association between skewed X inactivation and age at cancer diagnosis was assessed by Cox proportional hazards regression analysis. All statistical tests were two-sided. RESULTS The age-adjusted frequency of skewed X inactivation was not statistically significantly higher in ovarian cancer or familial breast cancer case subjects compared with control subjects. Skewed X inactivation was higher in BRCA1 mutation carriers than in control subjects (odds ratio [OR] = 2.7, 95% confidence interval [CI] = 1.1 to 6.2; P = .02), particularly among unaffected women (OR = 6.1, 95% CI = 1.5 to 31.8; P = .005). Among BRCA1 mutation carriers, those with skewed X inactivation were older at diagnosis of breast or ovarian cancer than those without skewed X inactivation (hazard ratio [HR] of breast or ovarian cancer = 0.37, 95% CI = 0.14 to 0.95; P = .04). Among BRCA2 mutation carriers, skewed X inactivation also occurred more frequently in unaffected carriers than in those diagnosed with breast or ovarian cancer (OR = 5.2, 95% CI = 0.5 to 28.9; P = .08) and was associated with delayed age at onset (HR = 0.59, 95% CI = 0.37 to 0.94; P = .03). CONCLUSIONS Skewed X inactivation occurs at an increased frequency in BRCA1 (and possibly BRCA2) mutation carriers compared with control subjects and is associated with a statistically significant increase in age at diagnosis of breast and ovarian cancer.
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Affiliation(s)
- Felicity Lose
- Cancer and Cell Biology Division, Queensland Institute of Medical Research, Herston, Brisbane, Queensland, Australia
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Developmental and epigenetic regulation of the human TLR3 gene. Mol Immunol 2008; 46:27-36. [PMID: 18715647 DOI: 10.1016/j.molimm.2008.06.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/17/2008] [Accepted: 06/19/2008] [Indexed: 02/02/2023]
Abstract
The receptor encoded by the human TLR3 gene recognizes double-strand RNAs (dsRNAs) associated with viral infection. TLR3 expression is strongly activated upon differentiation of monocytes to dendritic cells, and can be further stimulated by the dsRNA analog polyinosine:polycytosine (PI:C). We report evidence for developmental regulation of the TLR3 gene. In dendritic cells derived from cord blood, both differentiation- and PI:C-associated TLR3 transcriptional activation are impaired as compared to cells from adults. Consistent with relative expression patterns, chromatin states and remodeling differ between newborn and adult samples. TLR3 expression in newborn dendritic cells exhibits heterocellularity and allelic imbalance (skewing), features characteristic of cis-acting epigenetic control. These findings reveal a new source for variability in innate immune system function and provide a model for further study of perinatal epigenetic transitions during development.
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