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Riaz M, Mattisson J, Polekhina G, Bakshi A, Halvardson J, Danielsson M, Ameur A, McNeil J, Forsberg LA, Lacaze P. A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells. Cell Biosci 2021; 11:205. [PMID: 34895331 PMCID: PMC8667399 DOI: 10.1186/s13578-021-00716-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background Mosaic loss of Y chromosome (LOY) is the most common somatic change that occurs in circulating white blood cells of older men. LOY in leukocytes is associated with increased risk for all-cause mortality and a range of common disease such as hematological and non-hematological cancer, Alzheimer’s disease, and cardiovascular events. Recent genome-wide association studies identified up to 156 germline variants associated with risk of LOY. The objective of this study was to use these variants to calculate a novel polygenic risk score (PRS) for LOY, and to assess the predictive performance of this score in a large independent population of older men. Results We calculated a PRS for LOY in 5131 men aged 70 years and older. Levels of LOY were estimated using microarrays and validated by whole genome sequencing. After adjusting for covariates, the PRS was a significant predictor of LOY (odds ratio [OR] = 1.74 per standard deviation of the PRS, 95% confidence intervals [CI] 1.62–1.86, p < 0.001). Men in the highest quintile of the PRS distribution had > fivefold higher risk of LOY than the lowest (OR = 5.05, 95% CI 4.05–6.32, p < 0.001). Adding the PRS to a LOY prediction model comprised of age, smoking and alcohol consumption significantly improved prediction (AUC = 0.628 [CI 0.61–0.64] to 0.695 [CI 0.67–0.71], p < 0.001). Conclusions Our results suggest that a PRS for LOY could become a useful tool for risk prediction and targeted intervention for common disease in men. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00716-z.
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Affiliation(s)
- Moeen Riaz
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Galina Polekhina
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Andrew Bakshi
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - John McNeil
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,The Beijer Laboratory, Uppsala University, Uppsala, Sweden.
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia.
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Liu B, Chen M, Yang Y, Huang Y, Qian Y, Dong M. Identification of of a PAX2 mutation from maternal mosaicism causes recurrent renal disorder in siblings. Clin Chim Acta 2021; 525:23-28. [PMID: 34906559 DOI: 10.1016/j.cca.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND PAX2-related disorder is an autosomal dominant disorder characterized by renal and eye abnormalities. Some patients may present with isolated renal abnormalities without obvious ocular abnormalities. It is associated with mutations in paired box gene 2 (PAX2), which is one of the families of paired box transcription factor genes. Studies on mosaicism have been limited in PAX2-related disorder, as only three families with mosaic PAX2 mutations have been reported in the literature. METHODS The proband with multicystic dysplastic kidneys from a Chinese family was recruited in our study. Detailed clinical symptoms were enquired. Trio-based whole exome sequencing (WES), SNP array, sanger sequencing and droplet digital PCR (ddPCR) were used to characterize etiology in the proband. Prenatal diagnosis was performed through amniocentesis and prenatal ultrasound when the proband's mother was further pregnant at 20 weeks. RESULTS A heterozygous missense mutation in PAX2 (c.194 T > C) was identified in the proband. His asymptomatic mother has the same mutation with somatic mosaicism ratio of 22%. The mutation was also detected in the fetus. Prenatal ultrasound showed that bilateral hyperechogenic kidneys with decrease of renal size. CONCLUSIONS This is the first report on PAX2 mosaicism in a Chinese family. Identifying PAX2 mosaicism provides more evidence for estimating recurrence risk. Our findings have important implications on genetic counseling for patients with PAX2-related disorder and provide an effective diagnostic technology for mosaicism.
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Affiliation(s)
- Bei Liu
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Mengjia Chen
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yanmei Yang
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yingzhi Huang
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yeqing Qian
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Minyue Dong
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China.
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53
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Martín-Campos JM. Genetic Determinants of Plasma Low-Density Lipoprotein Cholesterol Levels: Monogenicity, Polygenicity, and "Missing" Heritability. Biomedicines 2021; 9:biomedicines9111728. [PMID: 34829957 PMCID: PMC8615680 DOI: 10.3390/biomedicines9111728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Changes in plasma low-density lipoprotein cholesterol (LDL-c) levels relate to a high risk of developing some common and complex diseases. LDL-c, as a quantitative trait, is multifactorial and depends on both genetic and environmental factors. In the pregenomic age, targeted genes were used to detect genetic factors in both hyper- and hypolipidemias, but this approach only explained extreme cases in the population distribution. Subsequently, the genetic basis of the less severe and most common dyslipidemias remained unknown. In the genomic age, performing whole-exome sequencing in families with extreme plasma LDL-c values identified some new candidate genes, but it is unlikely that such genes can explain the majority of inexplicable cases. Genome-wide association studies (GWASs) have identified several single-nucleotide variants (SNVs) associated with plasma LDL-c, introducing the idea of a polygenic origin. Polygenic risk scores (PRSs), including LDL-c-raising alleles, were developed to measure the contribution of the accumulation of small-effect variants to plasma LDL-c. This paper discusses other possibilities for unexplained dyslipidemias associated with LDL-c, such as mosaicism, maternal effect, and induced epigenetic changes. Future studies should consider gene-gene and gene-environment interactions and the development of integrated information about disease-driving networks, including phenotypes, genotypes, transcription, proteins, metabolites, and epigenetics.
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Affiliation(s)
- Jesús Maria Martín-Campos
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau (IR-HSCSP)-Biomedical Research Institute Sant Pau (IIB-Sant Pau), C/Sant Quintí 77-79, 08041 Barcelona, Spain
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Lähnemann D, Köster J, Fischer U, Borkhardt A, McHardy AC, Schönhuth A. Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo. Nat Commun 2021; 12:6744. [PMID: 34795237 PMCID: PMC8602313 DOI: 10.1038/s41467-021-26938-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/22/2021] [Indexed: 01/14/2023] Open
Abstract
Accurate single cell mutational profiles can reveal genomic cell-to-cell heterogeneity. However, sequencing libraries suitable for genotyping require whole genome amplification, which introduces allelic bias and copy errors. The resulting data violates assumptions of variant callers developed for bulk sequencing. Thus, only dedicated models accounting for amplification bias and errors can provide accurate calls. We present ProSolo for calling single nucleotide variants from multiple displacement amplified (MDA) single cell DNA sequencing data. ProSolo probabilistically models a single cell jointly with a bulk sequencing sample and integrates all relevant MDA biases in a site-specific and scalable-because computationally efficient-manner. This achieves a higher accuracy in calling and genotyping single nucleotide variants in single cells in comparison to state-of-the-art tools and supports imputation of insufficiently covered genotypes, when downstream tools cannot handle missing data. Moreover, ProSolo implements the first approach to control the false discovery rate reliably and flexibly. ProSolo is implemented in an extendable framework, with code and usage at: https://github.com/prosolo/prosolo.
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Affiliation(s)
- David Lähnemann
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106, Braunschweig, Germany
- Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Algorithms for Reproducible Bioinformatics, Institute of Human Genetics, University of Duisburg-Essen, 45147, Essen, Germany
| | - Johannes Köster
- Algorithms for Reproducible Bioinformatics, Institute of Human Genetics, University of Duisburg-Essen, 45147, Essen, Germany
- Genome Data Science, Life Sciences Group, Centrum Wiskunde & Informatica, 1098 XG, Amsterdam, The Netherlands
| | - Ute Fischer
- Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106, Braunschweig, Germany.
- Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Alexander Schönhuth
- Genome Data Science, Life Sciences Group, Centrum Wiskunde & Informatica, 1098 XG, Amsterdam, The Netherlands.
- Genome Data Science, Faculty of Technology, Bielefeld University, 33615, Bielefeld, Germany.
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Johansson M, Pedersen A, Cole JW, Lagging C, Lindgren A, Maguire JM, Rost NS, Söderholm M, Worrall BB, Stanne TM, Jern C. Genetic Predisposition to Mosaic Chromosomal Loss Is Associated With Functional Outcome After Ischemic Stroke. NEUROLOGY-GENETICS 2021; 7:e634. [PMID: 34786478 PMCID: PMC8589264 DOI: 10.1212/nxg.0000000000000634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/15/2021] [Indexed: 11/27/2022]
Abstract
Background and Objectives To test the hypothesis that a predisposition to acquired genetic alterations is associated with ischemic stroke outcome by investigating the association between a polygenic risk score (PRS) for mosaic loss of chromosome Y (mLOY) and outcome in a large international data set. Methods We used data from the genome-wide association study performed within the Genetics of Ischemic Stroke Functional Outcome network, which included 6,165 patients (3,497 men and 2,668 women) with acute ischemic stroke of mainly European ancestry. We assessed a weighted PRS for mLOY and examined possible associations with the modified Rankin Scale (mRS) score 3 months poststroke in logistic regression models. We investigated the whole study sample as well as men and women separately. Results Increasing PRS for mLOY was associated with poor functional outcome (mRS score >2) with an odds ratio (OR) of 1.11 (95% confidence interval [CI] 1.03–1.19) per 1 SD increase in the PRS after adjustment for age, sex, ancestry, stroke severity (NIH Stroke Scale), smoking, and diabetes mellitus. In sex-stratified analyses, we found a statistically significant association in women (adjusted OR 1.20, 95% CI 1.08–1.33). In men, the association was in the same direction (adjusted OR 1.04, 95% CI 0.95–1.14), and we observed no significant genotype-sex interaction. Discussion In this exploratory study, we found associations between genetic variants predisposing to mLOY and stroke outcome. The significant association in women suggests underlying mechanisms related to genomic instability that operate in both sexes. These findings need replication and mechanistic exploration.
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Affiliation(s)
- Malin Johansson
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Annie Pedersen
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - John W Cole
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Cecilia Lagging
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Arne Lindgren
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Jane M Maguire
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Natalia S Rost
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Martin Söderholm
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Bradford B Worrall
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Tara M Stanne
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Christina Jern
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
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Lebedev IN, Zhigalina DI. From contemplation to classification of chromosomal mosaicism in human preimplantation embryos. J Assist Reprod Genet 2021; 38:2833-2848. [PMID: 34518954 PMCID: PMC8609036 DOI: 10.1007/s10815-021-02304-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022] Open
Abstract
Chromosomal mosaicism is a hallmark of early human embryo development. The last decade yielded an enormous amount of information about diversity and prevalence of mosaicism in preimplantation embryos due to progress in preimplantation genetic testing of aneuploidies (PGT-A) based exclusively on molecular karyotyping of trophectoderm biopsy. However, the inner cell mass karyotype is still missing for mosaic embryos affecting the success rate of assisted reproductive medicine. Here, a classification model of chromosomal mosaicism is proposed based on the analysis of the primary zygote karyotype, the timing and types of primary and secondary chromosome segregation errors, and the distribution of mosaic cell clones between different embryonic and extraembryonic compartments of the blastocyst. Five basic principles for mosaicism analysis are introduced, namely, the estimation of the primary zygote karyotype, the investigation of additional sample point, the requirement of the second time point analysis, the delineating of reciprocity of chromosome segregation, and comprehensive chromosome screening at the single-cell level. The suggested model allows the prediction of the inner cell mass karyotype of the blastocyst and its developmental potential based on information from trophectoderm biopsy and non-invasive PGT-A using blastocoele fluid sample or spent culture medium as additional sample and time points for analysis and considering the reciprocity as a basic process in chromosome segregation errors between daughter cells in postzygotic cell divisions.
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Affiliation(s)
- Igor N. Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050 Russia
| | - Daria I. Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050 Russia
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Swiatczak B. Struggle within: evolution and ecology of somatic cell populations. Cell Mol Life Sci 2021; 78:6797-6806. [PMID: 34477897 PMCID: PMC11073125 DOI: 10.1007/s00018-021-03931-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/31/2021] [Accepted: 08/25/2021] [Indexed: 12/19/2022]
Abstract
The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable multicellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts at the cellular level. On the other hand, the example of clonal selection of lymphocytes indicates that certain forms of somatic mutation and selection are concordant with the organism-level fitness. Recent DNA sequencing and tissue physiology studies suggest that in addition to adaptive immune cells also neurons, epithelial cells, epidermal cells, hematopoietic stem cells and functional cells in solid bodily organs are subject to evolutionary forces during the lifetime of an organism. Here we refer to these recent studies and suggest that the expanding list of somatically evolving cells modifies idealized views of biological individuals as radically different from collectives.
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Affiliation(s)
- Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, 96 Jinzhai Rd., Hefei, 230026, China.
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58
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Hong Y, Zhang D, Zhou X, Chen A, Abliz A, Bai J, Wang L, Hu Q, Gong K, Guan X, Liu M, Zheng X, Lai S, Qu H, Zhao F, Hao S, Wu Z, Cai H, Hu S, Ma Y, Zhang J, Ke Y, Wang QF, Chen W, Zeng C. Common Postzygotic Mutational Signatures in Healthy Adult Tissues Related to Embryonic Hypoxia. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 20:177-191. [PMID: 34624550 PMCID: PMC9510933 DOI: 10.1016/j.gpb.2021.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 12/04/2022]
Abstract
Postzygotic mutations are acquired in normal tissues throughout an individual’s lifetime and hold clues for identifying mutagenic factors. Here, we investigated postzygotic mutation spectra of healthy individuals using optimized ultra-deep exome sequencing of the time-series samples from the same volunteer as well as the samples from different individuals. In blood, sperm, and muscle cells, we resolved three common types of mutational signatures. Signatures A and B represent clock-like mutational processes, and the polymorphisms of epigenetic regulation genes influence the proportion of signature B in mutation profiles. Notably, signature C, characterized by C>T transitions at GpCpN sites, tends to be a feature of diverse normal tissues. Mutations of this type are likely to occur early during embryonic development, supported by their relatively high allelic frequencies, presence in multiple tissues, and decrease in occurrence with age. Almost none of the public datasets for tumors feature this signature, except for 19.6% of samples of clear cell renal cell carcinoma with increased activation of the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Moreover, the accumulation of signature C in the mutation profile was accelerated in a human embryonic stem cell line with drug-induced activation of HIF-1α. Thus, embryonic hypoxia may explain this novel signature across multiple normal tissues. Our study suggests that hypoxic condition in an early stage of embryonic development is a crucial factor inducing C>T transitions at GpCpN sites; and individuals’ genetic background may also influence their postzygotic mutation profiles.
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Affiliation(s)
- Yaqiang Hong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dake Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xiangtian Zhou
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou 325035, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou 325035, China
| | - Aili Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Amir Abliz
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jian Bai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Liang Wang
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Qingtao Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Kenan Gong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Xiaonan Guan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Mengfei Liu
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xinchang Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujuan Lai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Fuxin Zhao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou 325035, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou 325035, China
| | - Shuang Hao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhen Wu
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Hong Cai
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Shaoyan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou 215025, China
| | - Yue Ma
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Junting Zhang
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Qian-Fei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Collaborative Innovation Center for Genetics and Development, Shanghai 200438, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Aging and Cancer: The Waning of Community Bonds. Cells 2021; 10:cells10092269. [PMID: 34571918 PMCID: PMC8468626 DOI: 10.3390/cells10092269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer often arises in the context of an altered tissue landscape. We argue that a major contribution of aging towards increasing the risk of neoplastic disease is conveyed through effects on the microenvironment. It is now firmly established that aged tissues are prone to develop clones of altered cells, most of which are compatible with a normal histological appearance. Such increased clonogenic potential results in part from a generalized decrease in proliferative fitness, favoring the emergence of more competitive variant clones. However, specific cellular genotypes can emerge with reduced cooperative and integrative capacity, leading to disruption of tissue architecture and paving the way towards progression to overt neoplastic phenotypes.
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Gutierrez-Rodrigues F, Sahoo SS, Wlodarski MW, Young NS. Somatic mosaicism in inherited bone marrow failure syndromes. Best Pract Res Clin Haematol 2021; 34:101279. [PMID: 34404533 DOI: 10.1016/j.beha.2021.101279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/01/2021] [Accepted: 06/12/2021] [Indexed: 12/20/2022]
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a heterogenous group of diseases caused by pathogenic germline variants in key pathways associated with haematopoiesis and genomic stability. Germline variants in IBMFS-related genes are known to reduce the fitness of hematopoietic stem and progenitor cells (HSPC), which has been hypothesized to drive clonal selection in these diseases. In many IBMFS, somatic mosaicism predominantly impacts cells by two distinct mechanisms, with contrasting effects. An acquired variation can improve cell fitness towards baseline levels, providing rescue of a deleterious phenotype. Alternatively, somatic mosaicism may result in a fitness advantage that results in malignant transformation. This review will describe these phenomena in IBMFS and delineate their relevance for diagnosis and clinical management. In addition, we will discuss which samples and methods can be used for detection of mosaicism according to clinical phenotype, type of mosaicism, and sample availability.
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Affiliation(s)
| | - Sushree S Sahoo
- Department of Hematology, St. Jude Children's Research Hospital, TN, USA
| | - Marcin W Wlodarski
- Department of Hematology, St. Jude Children's Research Hospital, TN, USA; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
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61
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Fang H, Deng X, Disteche CM. X-factors in human disease: Impact of gene content and dosage regulation. Hum Mol Genet 2021; 30:R285-R295. [PMID: 34387327 DOI: 10.1093/hmg/ddab221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
The gene content of the X and Y chromosomes has dramatically diverged during evolution. The ensuing dosage imbalance within the genome of males and females has led to unique chromosome-wide regulatory mechanisms with significant and sex-specific impacts on X-linked gene expression. X inactivation or silencing of most genes on one X chromosome chosen at random in females profoundly affects the manifestation of X-linked diseases, as males inherit a single maternal allele, while females express maternal and paternal alleles in a mosaic manner. An additional complication is the existence of genes that escape X inactivation and thus are ubiquitously expressed from both alleles in females. The mosaic nature of X-linked gene expression and the potential for escape can vary between individuals, tissues, cell types, and stages of life. Our understanding of the specialized nature of X-linked genes and of the multilayer epigenetic regulation that influence their expression throughout the organism has been helped by molecular studies conducted by tissue-specific and single-cell-specific approaches. In turn, the definition of molecular events that control X silencing has helped develop new approaches for the treatment of some X-linked disorders. This review focuses on the peculiarities of the X chromosome genetic content and epigenetic regulation in shaping the manifestation of congenital and acquired X-linked disorders in a sex-specific manner.
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Affiliation(s)
- He Fang
- Department of Laboratory Medicine and Pathology
| | | | - Christine M Disteche
- Department of Laboratory Medicine and Pathology.,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
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Latorre-Pellicer A, Gil-Salvador M, Parenti I, Lucia-Campos C, Trujillano L, Marcos-Alcalde I, Arnedo M, Ascaso Á, Ayerza-Casas A, Antoñanzas-Pérez R, Gervasini C, Piccione M, Mariani M, Weber A, Kanber D, Kuechler A, Munteanu M, Khuller K, Bueno-Lozano G, Puisac B, Gómez-Puertas P, Selicorni A, Kaiser FJ, Ramos FJ, Pié J. Clinical relevance of postzygotic mosaicism in Cornelia de Lange syndrome and purifying selection of NIPBL variants in blood. Sci Rep 2021; 11:15459. [PMID: 34326454 PMCID: PMC8322329 DOI: 10.1038/s41598-021-94958-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
Postzygotic mosaicism (PZM) in NIPBL is a strong source of causality for Cornelia de Lange syndrome (CdLS) that can have major clinical implications. Here, we further delineate the role of somatic mosaicism in CdLS by describing a series of 11 unreported patients with mosaic disease-causing variants in NIPBL and performing a retrospective cohort study from a Spanish CdLS diagnostic center. By reviewing the literature and combining our findings with previously published data, we demonstrate a negative selection against somatic deleterious NIPBL variants in blood. Furthermore, the analysis of all reported cases indicates an unusual high prevalence of mosaicism in CdLS, occurring in 13.1% of patients with a positive molecular diagnosis. It is worth noting that most of the affected individuals with mosaicism have a clinical phenotype at least as severe as those with constitutive pathogenic variants. However, the type of genetic change does not vary between germline and somatic events and, even in the presence of mosaicism, missense substitutions are located preferentially within the HEAT repeat domain of NIPBL. In conclusion, the high prevalence of mosaicism in CdLS as well as the disparity in tissue distribution provide a novel orientation for the clinical management and genetic counselling of families.
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Affiliation(s)
- Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Marta Gil-Salvador
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Cristina Lucia-Campos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Laura Trujillano
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28049, Madrid, Spain
- Biosciences Research Institute, School of Experimental Sciences, Universidad Francisco de Vitoria, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - María Arnedo
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ángela Ascaso
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ariadna Ayerza-Casas
- Unit of Paediatric Cardiology, Service of Paediatrics, Hospital Universitario Miguel Servet, 50009, Zaragoza, Spain
| | - Rebeca Antoñanzas-Pérez
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Cristina Gervasini
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Milena Mariani
- Centro Fondazione Mariani per il Bambino Fragile, Department of Pediatrics, ASST-Lariana Sant'Anna Hospital, San Fermo della Battaglia (Como), Italy
| | - Axel Weber
- Institute of Human Genetics, Justus-Liebig-University, Giessen, Germany
| | - Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Martin Munteanu
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Katharina Khuller
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Gloria Bueno-Lozano
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28049, Madrid, Spain
| | - Angelo Selicorni
- Centro Fondazione Mariani per il Bambino Fragile, Department of Pediatrics, ASST-Lariana Sant'Anna Hospital, San Fermo della Battaglia (Como), Italy
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsmedizin Essen, Universitätsklinikum Essen, Essen, Germany
| | - Feliciano J Ramos
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain.
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain.
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63
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Liu YL, Stadler ZK. The Future of Parallel Tumor and Germline Genetic Testing: Is There a Role for All Patients With Cancer? J Natl Compr Canc Netw 2021; 19:871-878. [PMID: 34340209 PMCID: PMC11123333 DOI: 10.6004/jnccn.2021.7044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 04/09/2021] [Indexed: 11/17/2022]
Abstract
Under the traditional paradigm of genetic testing in cancer, the role of germline testing was to assess for the inherited risk of cancer, whereas the role of tumor testing was to determine therapeutic selection. Parallel tumor-normal genetic testing uses simultaneous genetic testing of the tumor and normal tissue to identify mutations and allows their classification as either germline or somatic. The increasing adoption of parallel testing has revealed a greater number of germline findings in patients who otherwise would not have met clinical criteria for testing. This result has widespread implications for the screening and further testing of at-risk relatives and for gene discovery. It has also revealed the importance of germline testing in therapeutic actionability. Herein, we describe the pros and cons of tumor-only versus parallel tumor-normal testing and summarize the data on the prevalence of incidental actionable germline findings. Because germline testing in patients with cancer continues to expand, it is imperative that systems be in place for the proper interpretation, dissemination, and counseling for patients and at-risk relatives. We also review new therapeutic approvals with germline indications and highlight the increasing importance of germline testing in selecting therapies. Because recommendations for universal genetic testing are increasing in multiple cancer types and the number of approved therapies with germline indications is also increasing, a gradual transition toward parallel tumor-normal genetic testing in all patients with cancer is foreseeable.
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Affiliation(s)
- Ying L. Liu
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K. Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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64
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Genetics of autosomal mosaic chromosomal alteration (mCA). J Hum Genet 2021; 66:879-885. [PMID: 34321609 DOI: 10.1038/s10038-021-00964-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/11/2022]
Abstract
Mosaic chromosomal alterations (mCAs) are frequently observed in cancer cells and are regarded as one of the common features of cancers. Strikingly, accumulating studies demonstrated that mCAs are also prevalent in elderly individuals without cancer, implying mCA could be a feature of aging and not necessarily a cancerous state. However, the genetic basis of mCA has been mostly unknown. Recent studies of autosomal mCA based on biobank-scale datasets, including UK Biobank and Biobank Japan, provided a glimpse into the underlying genetic mechanism. In this concise review, we briefly introduced mCA, its link with cancer and aging, and the emerging genetic mechanisms of this phenomenon. We highlighted the following aspects: (1) the interplay between somatic and inherited germline mutations in generating mosaicism; (2) monogenic and polygenic architectures of mCA; and (3) population-specific profiles of mCA. We provided a future perspective emphasizing the need to understand the connection between mCA and other characteristics of aging, in particular, the epigenetic and immunologic features.
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65
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Mattisson J, Danielsson M, Hammond M, Davies H, Gallant CJ, Nordlund J, Raine A, Edén M, Kilander L, Ingelsson M, Dumanski JP, Halvardson J, Forsberg LA. Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99. Sci Rep 2021; 11:15160. [PMID: 34312421 PMCID: PMC8313698 DOI: 10.1038/s41598-021-94588-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
Mosaic loss of chromosome Y (LOY) in immune cells is a male-specific mutation associated with increased risk for morbidity and mortality. The CD99 gene, positioned in the pseudoautosomal regions of chromosomes X and Y, encodes a cell surface protein essential for several key properties of leukocytes and immune system functions. Here we used CITE-seq for simultaneous quantification of CD99 derived mRNA and cell surface CD99 protein abundance in relation to LOY in single cells. The abundance of CD99 molecules was lower on the surfaces of LOY cells compared with cells without this aneuploidy in all six types of leukocytes studied, while the abundance of CD proteins encoded by genes located on autosomal chromosomes were independent from LOY. These results connect LOY in single cells with immune related cellular properties at the protein level, providing mechanistic insight regarding disease vulnerability in men affected with mosaic chromosome Y loss in blood leukocytes.
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Affiliation(s)
- Jonas Mattisson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Hammond
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Caroline J Gallant
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Malin Edén
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Lena Kilander
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Jan P Dumanski
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Faculty of Pharmacy, 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,The Beijer Laboratory, Uppsala University, Uppsala, Sweden.
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66
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Lin SH, Brown DW, Rose B, Day F, Lee OW, Khan SM, Hislop J, Chanock SJ, Perry JRB, Machiela MJ. Incident disease associations with mosaic chromosomal alterations on autosomes, X and Y chromosomes: insights from a phenome-wide association study in the UK Biobank. Cell Biosci 2021; 11:143. [PMID: 34301302 PMCID: PMC8299574 DOI: 10.1186/s13578-021-00651-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Mosaic chromosomal alterations (mCAs) are large chromosomal gains, losses and copy-neutral losses of heterozygosity (LOH) in peripheral leukocytes. While many individuals with detectable mCAs have no notable adverse outcomes, mCA-associated gene dosage alterations as well as clonal expansion of mutated leukocyte clones could increase susceptibility to disease. RESULTS We performed a phenome-wide association study (PheWAS) using existing data from 482,396 UK Biobank (UKBB) participants to investigate potential associations between mCAs and incident disease. Of the 1290 ICD codes we examined, our adjusted analysis identified a total of 50 incident disease outcomes associated with mCAs at PheWAS significance levels. We observed striking differences in the diseases associated with each type of alteration, with autosomal mCAs most associated with increased hematologic malignancies, incident infections and possibly cancer therapy-related conditions. Alterations of chromosome X were associated with increased lymphoid leukemia risk and, mCAs of chromosome Y were linked to potential reduced metabolic disease risk. CONCLUSIONS Our findings demonstrate that a wide range of diseases are potential sequelae of mCAs and highlight the critical importance of careful covariate adjustment in mCA disease association studies.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Brandon Rose
- University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Felix Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Jada Hislop
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA.
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Maani N, Panabaker K, McCuaig JM, Buckley K, Semotiuk K, Farncombe KM, Ainsworth P, Panchal S, Sadikovic B, Armel SR, Lin H, Kim RH. Incidental findings from cancer next generation sequencing panels. NPJ Genom Med 2021; 6:63. [PMID: 34282142 PMCID: PMC8289933 DOI: 10.1038/s41525-021-00224-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/09/2021] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have facilitated multi-gene panel (MGP) testing to detect germline DNA variants in hereditary cancer patients. This sensitive technique can uncover unexpected, non-germline incidental findings indicative of mosaicism, clonal hematopoiesis (CH), or hematologic malignancies. A retrospective chart review was conducted to identify cases of incidental findings from NGS-MGP testing. Inclusion criteria included: 1) multiple pathogenic variants in the same patient; 2) pathogenic variants at a low allele fraction; and/or 3) the presence of pathogenic variants not consistent with family history. Secondary tissue analysis, complete blood count (CBC) and medical record review were conducted to further delineate the etiology of the pathogenic variants. Of 6060 NGS-MGP tests, 24 cases fulfilling our inclusion criteria were identified. Pathogenic variants were detected in TP53, ATM, CHEK2, BRCA1 and APC. 18/24 (75.0%) patients were classified as CH, 3/24 (12.5%) as mosaic, 2/24 (8.3%) related to a hematologic malignancy, and 1/24 (4.2%) as true germline. We describe a case-specific workflow to identify and interpret the nature of incidental findings on NGS-MGP. This workflow will provide oncology and genetic clinics a practical guide for the management and counselling of patients with unexpected NGS-MGP findings.
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Affiliation(s)
- Nika Maani
- Program for Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jeanna M McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada
| | | | - Kara Semotiuk
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, ON, Canada
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada
| | - Seema Panchal
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Breast Cancer Clinic, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Susan Randall Armel
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Raymond H Kim
- Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, ON, Canada.
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GIGYF1 loss of function is associated with clonal mosaicism and adverse metabolic health. Nat Commun 2021; 12:4178. [PMID: 34234147 PMCID: PMC8263756 DOI: 10.1038/s41467-021-24504-y] [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: 02/24/2021] [Accepted: 06/21/2021] [Indexed: 12/01/2022] Open
Abstract
Mosaic loss of chromosome Y (LOY) in leukocytes is the most common form of clonal mosaicism, caused by dysregulation in cell-cycle and DNA damage response pathways. Previous genetic studies have focussed on identifying common variants associated with LOY, which we now extend to rarer, protein-coding variation using exome sequences from 82,277 male UK Biobank participants. We find that loss of function of two genes—CHEK2 and GIGYF1—reach exome-wide significance. Rare alleles in GIGYF1 have not previously been implicated in any complex trait, but here loss-of-function carriers exhibit six-fold higher susceptibility to LOY (OR = 5.99 [3.04–11.81], p = 1.3 × 10−10). These same alleles are also associated with adverse metabolic health, including higher susceptibility to Type 2 Diabetes (OR = 6.10 [3.51–10.61], p = 1.8 × 10−12), 4 kg higher fat mass (p = 1.3 × 10−4), 2.32 nmol/L lower serum IGF1 levels (p = 1.5 × 10−4) and 4.5 kg lower handgrip strength (p = 4.7 × 10−7) consistent with proposed GIGYF1 enhancement of insulin and IGF-1 receptor signalling. These associations are mirrored by a common variant nearby associated with the expression of GIGYF1. Our observations highlight a potential direct connection between clonal mosaicism and metabolic health. Mosaic loss of chromosome Y (LOY) is a common form of clonal mosaicism in leukocytes. Here, the authors extend genetic association analyses to rare variation using exome-sequence data from 82,277 males, finding that loss-of-function alleles in GIGYF1 are associated with six-fold higher susceptibility to both LOY and Type 2 Diabetes.
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69
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Kawashima Y, Nishikomori R, Ohara O. Multiomic technologies for analyses of inborn errors of immunity: from snapshot of the average cell to dynamic temporal picture at single-cell resolution. Inflamm Regen 2021; 41:19. [PMID: 34193319 PMCID: PMC8247241 DOI: 10.1186/s41232-021-00169-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022] Open
Abstract
Advances in DNA sequencing technology have significantly impacted human genetics; they have enabled the analysis of genetic causes of rare diseases, which are usually pathogenic variants in a single gene at the nucleotide sequence level. However, since the quantity of data regarding the relationship between genotype and phenotype is insufficient to diagnose some rare immune diseases definitively, genetic information alone cannot help obtain a mechanistic understanding of the disease etiology. For such cases, exploring the molecular phenotype using multiomic analyses could be the approach of choice. In this review, we first overview current technologies for multiomic analysis, particularly focusing on RNA and protein profiling of bulk cell ensembles. We then discuss the measurement modality and granularity issue because it is critical to design multiomic experiments properly. Next, we illustrate the importance of bioimaging by describing our experience with the analysis of an autoinflammatory disease, cryopyrin-associated periodic fever syndrome, which could be caused by low-frequency somatic mosaicism and cannot be well characterized only by multiomic snapshot analyses of an ensemble of many immune cells. We found it powerful to complement the multiomic data with bioimaging data that can provide us with indispensable time-specific dynamic information of every single cell in the "immune cell society." Because we now have many measurement tools in different modalities and granularity to tackle the etiology of rare hereditary immune diseases, we might gain a deeper understanding of the pathogenic mechanisms of these diseases by taking full advantage of these tools in an integrated manner.
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Affiliation(s)
- Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan.
- Future Medicine Education and Research Organization, Chiba University, Chiba, 260-8670, Japan.
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70
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Ibanez B, Fernández-Ortiz A, Fernández-Friera L, García-Lunar I, Andrés V, Fuster V. Progression of Early Subclinical Atherosclerosis (PESA) Study: JACC Focus Seminar 7/8. J Am Coll Cardiol 2021; 78:156-179. [PMID: 34238438 DOI: 10.1016/j.jacc.2021.05.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 12/23/2022]
Abstract
Atherosclerosis starts early in life and progresses silently for decades. Considering atherosclerosis as a "systemic disease" invites the use of noninvasive methodologies to detect disease in various regions before symptoms appear. The PESA-(Progression of Early Subclinical Atherosclerosis) CNIC-SANTANDER study is an ongoing prospective cohort study examining imaging, biological, and behavioral parameters associated with the presence and progression of early subclinical atherosclerosis. Between 2010 and 2014, PESA enrolled 4,184 asymptomatic middle-aged participants who undergo serial 3-yearly follow-up examinations including clinical interviews, lifestyle questionnaires, sampling, and noninvasive imaging assessment of multiterritorial subclinical atherosclerosis (carotids, iliofemorals, aorta, and coronaries). PESA tracks the trajectories of atherosclerosis and associated disorders from early stages to the transition to symptomatic phases. A joint venture between the CNIC and the Santander Bank, PESA is expected to run until at least 2029, and its significant contributions to date are presented in this review paper.
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Affiliation(s)
- Borja Ibanez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Cardiology Department, IIS-Fundación Jiménez Díaz University Hospital, Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Antonio Fernández-Ortiz
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Hospital Clínico San Carlos, IdISSC, Universidad Complutense, Madrid, Spain
| | - Leticia Fernández-Friera
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Hospital Universitario HM Montepríncipe-CIEC, Universidad San Pablo CEU, Madrid, Spain
| | - Inés García-Lunar
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Cardiology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Vicente Andrés
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Valentín Fuster
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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71
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Yan YH, Chen SX, Cheng LY, Rodriguez AY, Tang R, Cabrera K, Zhang DY. Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing. Sci Rep 2021; 11:11640. [PMID: 34079006 PMCID: PMC8172533 DOI: 10.1038/s41598-021-91142-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022] Open
Abstract
Whole exome sequencing (WES) is used to identify mutations in a patient's tumor DNA that are predictive of tumor behavior, including the likelihood of response or resistance to cancer therapy. WES has a mutation limit of detection (LoD) at variant allele frequencies (VAF) of 5%. Putative mutations called at ≤ 5% VAF are frequently due to sequencing errors, therefore reporting these subclonal mutations incurs risk of significant false positives. Here we performed ~ 1000 × WES on fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue biopsy samples from a non-small cell lung cancer patient, and identified 226 putative mutations at between 0.5 and 5% VAF. Each variant was then tested using NuProbe NGSure, to confirm the original WES calls. NGSure utilizes Blocker Displacement Amplification to first enrich the allelic fraction of the mutation and then uses Sanger sequencing to determine mutation identity. Results showed that 52% of the 226 (117) putative variants were disconfirmed, among which 2% (5) putative variants were found to be misidentified in WES. In the 66 cancer-related variants, the disconfirmed rate was 82% (54/66). This data demonstrates Blocker Displacement Amplification allelic enrichment coupled with Sanger sequencing can be used to confirm putative mutations ≤ 5% VAF. By implementing this method, next-generation sequencing can reliably report low-level variants at a high sensitivity, without the cost of high sequencing depth.
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Affiliation(s)
| | - Sherry X Chen
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA
| | - Lauren Y Cheng
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA
| | | | - Rui Tang
- NuProbe USA, Inc., Houston, TX, USA
| | | | - David Yu Zhang
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA.
- Systems, Synthetic, and Physical Biology, Rice University, 6500 Main St, Houston, TX, 77030, USA.
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72
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Affiliation(s)
- Satu Mustjoki
- From the Translational Immunology Research Program and the Department of Clinical Chemistry and Hematology, University of Helsinki, the Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, and the iCAN Digital Precision Cancer Medicine Flagship - all in Helsinki (S.M.); and the Hematology Branch, National Heart, Lung, and Blood Institute, Bethesda, MD (N.S.Y.)
| | - Neal S Young
- From the Translational Immunology Research Program and the Department of Clinical Chemistry and Hematology, University of Helsinki, the Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, and the iCAN Digital Precision Cancer Medicine Flagship - all in Helsinki (S.M.); and the Hematology Branch, National Heart, Lung, and Blood Institute, Bethesda, MD (N.S.Y.)
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73
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Chesneau B, Plancke A, Rolland G, Chassaing N, Coubes C, Brischoux-Boucher E, Edouard T, Dulac Y, Aubert-Mucca M, Lavabre-Bertrand T, Plaisancié J, Khau Van Kien P. Parental mosaicism in Marfan and Ehlers-Danlos syndromes and related disorders. Eur J Hum Genet 2021; 29:771-779. [PMID: 33414558 PMCID: PMC8110803 DOI: 10.1038/s41431-020-00797-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
Marfan syndrome (MFS) is a heritable connective tissue disorder (HCTD) caused by pathogenic variants in FBN1 that frequently occur de novo. Although individuals with somatogonadal mosaicisms have been reported with respect to MFS and other HCTD, the overall frequency of parental mosaicism in this pathology is unknown. In an attempt to estimate this frequency, we reviewed all the 333 patients with a disease-causing variant in FBN1. We then used direct sequencing, combined with High Resolution Melting Analysis, to detect mosaicism in their parents, complemented by NGS when a mosaicism was objectivized. We found that (1) the number of apparently de novo events is much higher than the classically admitted number (around 50% of patients and not 25% as expected for FBN1) and (2) around 5% of the FBN1 disease-causing variants were not actually de novo as anticipated, but inherited in a context of somatogonadal mosaicisms revealed in parents from three families. High Resolution Melting Analysis and NGS were more efficient at detecting and evaluating the level of mosaicism compared to direct Sanger sequencing. We also investigated individuals with a causal variant in another gene identified through our "aortic diseases genes" NGS panel and report, for the first time, on an individual with a somatogonadal mosaicism in COL5A1. Our study shows that parental mosaicism is not that rare in Marfan syndrome and should be investigated with appropriate methods given its implications in patient's management.
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Affiliation(s)
- Bertrand Chesneau
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Universitaire de Nîmes, Nîmes, France ,Centre de Référence du Syndrome de Marfan et des Syndromes Apparentés, Hôpital des Enfants, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Aurélie Plancke
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
| | - Guillaume Rolland
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
| | - Nicolas Chassaing
- Service de Génétique Médicale, Hôpital Purpan, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Christine Coubes
- Service de Génétique Clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | | | - Thomas Edouard
- Centre de Référence du Syndrome de Marfan et des Syndromes Apparentés, Hôpital des Enfants, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Yves Dulac
- Centre de Référence du Syndrome de Marfan et des Syndromes Apparentés, Hôpital des Enfants, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Marion Aubert-Mucca
- Centre de Référence du Syndrome de Marfan et des Syndromes Apparentés, Hôpital des Enfants, Centre Hospitalier Universitaire de Toulouse, Toulouse, France ,Service de Génétique Médicale, Hôpital Purpan, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Thierry Lavabre-Bertrand
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
| | - Julie Plaisancié
- Centre de Référence du Syndrome de Marfan et des Syndromes Apparentés, Hôpital des Enfants, Centre Hospitalier Universitaire de Toulouse, Toulouse, France ,Service de Génétique Médicale, Hôpital Purpan, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Philippe Khau Van Kien
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
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74
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Tiemann‐Boege I, Mair T, Yasari A, Zurovec M. Pathogenic postzygotic mosaicism in the tyrosine receptor kinase pathway: potential unidentified human disease hidden away in a few cells. FEBS J 2021; 288:3108-3119. [PMID: 32810928 PMCID: PMC8247027 DOI: 10.1111/febs.15528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/17/2020] [Accepted: 08/14/2020] [Indexed: 01/19/2023]
Abstract
Mutations occurring during embryonic development affect only a subset of cells resulting in two or more distinct cell populations that are present at different levels, also known as postzygotic mosaicism (PZM). Although PZM is a common biological phenomenon, it is often overlooked as a source of disease due to the challenges associated with its detection and characterization, especially for very low-frequency variants. Moreover, PZM can cause a different phenotype compared to constitutional mutations. Especially, lethal mutations in receptor tyrosine kinase (RTK) pathway genes, which exist only in a mosaic state, can have completely new clinical manifestations and can look very different from the associated monogenic disorder. However, some key questions are still not addressed, such as the level of mosaicism resulting in a pathogenic phenotype and how the clinical outcome changes with the development and age. Addressing these questions is not trivial as we require methods with the sensitivity to capture some of these variants hidden away in very few cells. Recent ultra-accurate deep-sequencing approaches can now identify these low-level mosaics and will be central to understand systemic and local effects of mosaicism in the RTK pathway. The main focus of this review is to highlight the importance of low-level mosaics and the need to include their detection in studies of genomic variation associated with disease.
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Affiliation(s)
| | - Theresa Mair
- Institute of BiophysicsJohannes Kepler UniversityLinzAustria
| | - Atena Yasari
- Institute of BiophysicsJohannes Kepler UniversityLinzAustria
| | - Michal Zurovec
- Biology Centre of the Czech Academy of SciencesInstitute of EntomologyCeske BudejoviceCzech Republic
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75
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Chavkin NW, Min KD, Walsh K. Importance of clonal hematopoiesis in heart failure. Trends Cardiovasc Med 2021; 32:198-203. [PMID: 33892102 PMCID: PMC8526615 DOI: 10.1016/j.tcm.2021.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 01/28/2023]
Abstract
Heart failure is prevalent in the elderly population. Inflammatory processes can contribute to the progression of heart failure by altering the balance of tissue healing and pathological remodeling during the injury response. New findings show that aging can alter immune cell phenotypes through the process of clonal hematopoiesis. This condition results from acquired somatic DNA mutations in specific driver genes that give rise to clonal expansions of mutant hematopoietic cells with overactive inflammatory properties. Recent clinical and experimental studies have shown that clonal hematopoiesis is prevalent in heart failure patients and associated with poor prognosis. In this review, we summarize current evidence that associates clonal hematopoiesis with the progression of heart failure. We further describe the mechanistic links between clonal hematopoiesis and the pro-inflammatory responses that can contribute to pathological outcomes in the heart. Finally, we provide perspectives on future research directions in the area of clonal hematopoiesis and heart failure.
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Affiliation(s)
- Nicholas W Chavkin
- Berne Cardiovascular Research Center USA; Department of Cardiology USA; Hematovascular Biology Center, University of Virginia, School of Medicine, Charlottesville, VA, 22908 USA
| | - Kyung-Duk Min
- Berne Cardiovascular Research Center USA; Department of Cardiology USA; Hematovascular Biology Center, University of Virginia, School of Medicine, Charlottesville, VA, 22908 USA
| | - Kenneth Walsh
- Berne Cardiovascular Research Center USA; Department of Cardiology USA; Hematovascular Biology Center, University of Virginia, School of Medicine, Charlottesville, VA, 22908 USA.
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Epigenome Chaos: Stochastic and Deterministic DNA Methylation Events Drive Cancer Evolution. Cancers (Basel) 2021; 13:cancers13081800. [PMID: 33918773 PMCID: PMC8069666 DOI: 10.3390/cancers13081800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Cancer is a group of diseases characterized by abnormal cell growth with a high potential to invade other tissues. Genetic abnormalities and epigenetic alterations found in tumors can be due to high levels of DNA damage and repair. These can be transmitted to daughter cells, which assuming other alterations as well, will generate heterogeneous and complex populations. Deciphering this complexity represents a central point for understanding the molecular mechanisms of cancer and its therapy. Here, we summarize the genomic and epigenomic events that occur in cancer and discuss novel approaches to analyze the epigenetic complexity of cancer cell populations. Abstract Cancer evolution is associated with genomic instability and epigenetic alterations, which contribute to the inter and intra tumor heterogeneity, making genetic markers not accurate to monitor tumor evolution. Epigenetic changes, aberrant DNA methylation and modifications of chromatin proteins, determine the “epigenome chaos”, which means that the changes of epigenetic traits are randomly generated, but strongly selected by deterministic events. Disordered changes of DNA methylation profiles are the hallmarks of all cancer types, but it is not clear if aberrant methylation is the cause or the consequence of cancer evolution. Critical points to address are the profound epigenetic intra- and inter-tumor heterogeneity and the nature of the heterogeneity of the methylation patterns in each single cell in the tumor population. To analyze the methylation heterogeneity of tumors, new technological and informatic tools have been developed. This review discusses the state of the art of DNA methylation analysis and new approaches to reduce or solve the complexity of methylated alleles in DNA or cell populations.
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77
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Brown DW, Machiela MJ. Why Y? Downregulation of Chromosome Y Genes Potentially Contributes to Elevated Cancer Risk. J Natl Cancer Inst 2021; 112:871-872. [PMID: 31945785 DOI: 10.1093/jnci/djz236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 11/15/2022] Open
Affiliation(s)
- Derek W Brown
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.,Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Mitchell J Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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78
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Abstract
In this review, Pilley et al. examine the impact of different p53 mutations and focus on how heterogeneity of p53 status can affect relationships between cells within a tumor. p53 is an important tumor suppressor, and the complexities of p53 function in regulating cancer cell behaviour are well established. Many cancers lose or express mutant forms of p53, with evidence that the type of alteration affecting p53 may differentially impact cancer development and progression. It is also clear that in addition to cell-autonomous functions, p53 status also affects the way cancer cells interact with each other. In this review, we briefly examine the impact of different p53 mutations and focus on how heterogeneity of p53 status can affect relationships between cells within a tumor.
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Affiliation(s)
- Steven Pilley
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Tristan A Rodriguez
- National Heart and Lung Institute, Imperial College, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
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79
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Min YK, Lee YK, Nam SH, Kim JK, Park KS, Kim JW. Quantitative and Qualitative QC of Next-Generation Sequencing for Detecting Somatic Variants: An Example of Detecting Clonal Hematopoiesis of Indeterminate Potential. Clin Chem 2021; 66:832-841. [PMID: 32395759 DOI: 10.1093/clinchem/hvaa088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Because next-generation sequencing (NGS) for detecting somatic mutations has been adopted in clinical fields, both qualitative and quantitative QC of the somatic variants through whole coding regions detected by NGS is crucial. However, specific applications or guidelines, especially for quantitative QC, are currently insufficient. Our goal was to devise a practical approach for both quantitative and qualitative QC using an example of detecting clonal hematopoiesis of indeterminate potential (CHIP). METHODS We applied the QC scheme using commercial reference materials and in-house QC materials (IQCM) composed of haplotype map and cancer cell lines for monitoring CHIP. RESULTS This approach efficiently validated a customized CHIP NGS assay. Accuracy, analytical sensitivity, analytical specificity, qualitative precision (concordance), and limit of detection achieved were 99.87%, 98.53%, 100.00%, 100.00%, and 1.00%, respectively. The quantitative precision analysis also had a higher CV percentage at a lower alternative read depth (R2 = 0.749∼0.858). Use of IQCM ensured more than 100-fold reduction in the cost per run compared with that achieved using commercial reference materials. CONCLUSION Our approach determined the general analytical performance of NGS for detecting CHIP and recognized limitations such as lower precision at a lower level of variant burden. This approach could also be theoretically expanded to a general NGS assay for detecting somatic variants. Considering the reliable NGS results and cost-effectiveness, we propose the use of IQCM for QC of NGS assays at clinical laboratories.
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Affiliation(s)
- Young Kyu Min
- Department of Biomedical Laboratory Science, Dankook University, Chungnam, Korea
| | - Young Kee Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea
| | | | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, Dankook University, Chungnam, Korea
| | - Kyung Sun Park
- Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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80
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Hammond D, Loghavi S. Clonal haematopoiesis of emerging significance. Pathology 2021; 53:300-311. [PMID: 33685721 DOI: 10.1016/j.pathol.2021.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/17/2022]
Abstract
Clonal haematopoiesis (CH) is a ubiquitous feature of aging and provides mechanistic insight into the inextricable relationship between chronic inflammation and age-related diseases. Although CH confers a cumulative risk of subsequent haematological malignancy, particularly myeloid neoplasms, that risk is heavily mutation- and context-specific. Individuals with mutations in DNA damage response pathway genes receiving select cytotoxic therapies for solid tumours are among the highest risk groups for subsequent development of myeloid neoplasms. Multiple lines of evidence suggest that TET2-mutated macrophages causally contribute to cardiometabolic disease through the generation of proinflammatory cytokines. It is speculated that such CH-related inflammation is a shared driver of several other chronic diseases. Whether we can intervene in individuals with CH to diminish the risk of subsequent haematological malignancy or non-haematological disease remains to be seen. However, precision anti-cytokine therapies are a rational starting point to break the feedforward loop between clonal myeloid expansion, inflammation, and end-organ damage.
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Affiliation(s)
- Danielle Hammond
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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81
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Glessner JT, Chang X, Liu Y, Li J, Khan M, Wei Z, Sleiman PMA, Hakonarson H. MONTAGE: a new tool for high-throughput detection of mosaic copy number variation. BMC Genomics 2021; 22:133. [PMID: 33627065 PMCID: PMC7905641 DOI: 10.1186/s12864-021-07395-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/19/2021] [Indexed: 01/21/2023] Open
Abstract
Background Not all cells in a given individual are identical in their genomic makeup. Mosaicism describes such a phenomenon where a mixture of genotypic states in certain genomic segments exists within the same individual. Mosaicism is a prevalent and impactful class of non-integer state copy number variation (CNV). Mosaicism implies that certain cell types or subset of cells contain a CNV in a segment of the genome while other cells in the same individual do not. Several studies have investigated the impact of mosaicism in single patients or small cohorts but no comprehensive scan of mosaic CNVs has been undertaken to accurately detect such variants and interpret their impact on human health and disease. Results We developed a tool called Montage to improve the accuracy of detection of mosaic copy number variants in a high throughput fashion. Montage directly interfaces with ParseCNV2 algorithm to establish disease phenotype genome-wide association and determine which genomic ranges had more or less than expected frequency of mosaic events. We screened for mosaic events in over 350,000 samples using 1% allele frequency as the detection limit. Additionally, we uncovered disease associations of multiple phenotypes with mosaic CNVs at several genomic loci. We additionally investigated the allele imbalance observations genome-wide to define non-diploid and non-integer copy number states. Conclusions Our novel algorithm presents an efficient tool with fast computational runtime and high levels of accuracy of mosaic CNV detection. A curated mosaic CNV callset of 3716 events in 2269 samples is presented with comparability to previous reports and disease phenotype associations. The new algorithm can be freely accessed via: https://github.com/CAG-CNV/MONTAGE. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07395-7.
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Affiliation(s)
- Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Xiao Chang
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Yichuan Liu
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Jin Li
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Munir Khan
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Patrick M A Sleiman
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
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82
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Baliakas P, Forsberg LA. Chromosome Y loss and drivers of clonal hematopoiesis in myelodysplastic syndrome. Haematologica 2021; 106:329-331. [PMID: 33522783 PMCID: PMC7849334 DOI: 10.3324/haematol.2020.266601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; The Beijer Laboratory, Uppsala University, Uppsala.
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83
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A New Perspective on the Origin of DNA Double-Strand Breaks and Its Implications for Ageing. Genes (Basel) 2021; 12:genes12020163. [PMID: 33530310 PMCID: PMC7912064 DOI: 10.3390/genes12020163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
It is estimated that 10-50 DNA double-strand breaks (DSBs) occur in a nucleated human cell per cell cycle. We reviewed the present state of knowledge and hypothesized that the currently accepted mechanisms cannot explain such high frequency of DSBs occurring daily under normal physiological conditions. We propose an alternative model that implicates illegitimate genomic integration into healthy cells of cell-free chromatin (cfCh) particles released from the billions of cells that die in the body every day. Repeated genomic integration of cfCh may have catastrophic consequences for the cell, such as DSBs, their faulty repair by nonhomologous end joining (NHEJ) followed by apoptosis with release of more cfCh which would integrate into genomes of surrounding cells. This can creates a vicious cycle of cfCh integration, DSBs, NHEJ, and more apoptosis, thereby providing a potential explanation as to why so many billions of cells die in the body on a daily basis. We also recount the recent observation that cfCh integration and the resulting DSBs activate inflammatory cytokines. This leads us to propose that concurrent DSBs and induction of inflammation occurring throughout life may be the underlying cause of ageing, degenerative disorders, and cancer. Finally, we discuss the prospect that agents that can inactivate/degrade cfCh may hold the key to making healthy ageing a realizable goal.
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84
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Reply to Veitia. Eur J Hum Genet 2021; 29:1323-1324. [PMID: 33462398 PMCID: PMC8440652 DOI: 10.1038/s41431-020-00802-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/10/2022] Open
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85
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Proshkina EN, Solovev IA, Shaposhnikov MV, Moskalev AA. Key Molecular Mechanisms of Aging, Biomarkers, and Potential Interventions. Mol Biol 2021. [DOI: 10.1134/s0026893320060096] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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86
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James BD, Guerin P, Allen JB. Let's Talk About Sex-Biological Sex Is Underreported in Biomaterial Studies. Adv Healthc Mater 2021; 10:e2001034. [PMID: 33043626 PMCID: PMC7791002 DOI: 10.1002/adhm.202001034] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/26/2020] [Indexed: 12/13/2022]
Abstract
Precision medicine aims to better individualize healthcare. It requires that biomaterials be designed for the physiological characteristics of a specific patient. To make this a reality, biomaterials research and development must address differences of biological sex. More specifically, biomaterials should be designed with properties optimized and appropriate for male and female patients. In analyzing research articles from seven prominent biomaterials journals, sex as a biological variable is missing from an overwhelming majority of in vitro biomaterial studies. From the survey, the reporting of the sex of primary cell cultures happened only 10.3% of the time. Contributing to this trend is that commercial vendors bias cell lines toward one sex or another by not disclosing information of cell line sex at the time of purchase; researchers do not communicate this pertinent information in published studies; and many journal policies have little to no requirements for reporting cell line characteristics. Omitting this valuable information leads to a gap in the understanding of sex-specific cell-biomaterial interactions and it creates a bias in research findings towards one sex or another. To curb this concerning trend and make precision biomaterials a reality will require the biomaterials field to "talk about sex" by reporting cell sex more broadly.
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Affiliation(s)
- Bryan D James
- Department of Materials Science and Engineering, University of Florida, 206 Rhines Hall, PO Box 116400, Gainesville, FL, 32611-6400, USA
| | - Paxton Guerin
- Department of Materials Science and Engineering, University of Florida, 206 Rhines Hall, PO Box 116400, Gainesville, FL, 32611-6400, USA
| | - Josephine B Allen
- Department of Materials Science and Engineering, University of Florida, 206 Rhines Hall, PO Box 116400, Gainesville, FL, 32611-6400, USA
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87
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Affiliation(s)
- Ephrat Levy-Lahad
- From the Shaare Zedek Medical Center and the Hebrew University of Jerusalem, Jerusalem (E.L.-L.); and the University of Washington, Seattle (M.-C.K.)
| | - Mary-Claire King
- From the Shaare Zedek Medical Center and the Hebrew University of Jerusalem, Jerusalem (E.L.-L.); and the University of Washington, Seattle (M.-C.K.)
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88
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Rydzanicz M, Olszewski P, Kedra D, Davies H, Filipowicz N, Bruhn-Olszewska B, Cavalli M, Szczałuba K, Młynek M, Machnicki MM, Stawiński P, Kostrzewa G, Krajewski P, Śladowski D, Chrzanowska K, Dumanski JP, Płoski R. Variable degree of mosaicism for tetrasomy 18p in phenotypically discordant monozygotic twins-Diagnostic implications. Mol Genet Genomic Med 2020; 9:e1526. [PMID: 33319479 PMCID: PMC7963419 DOI: 10.1002/mgg3.1526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Abstract
Background Phenotypically discordant monozygotic twins (PDMZTs) offer a unique opportunity to study post‐zygotic genetic variation and provide insights into the linkage between genotype and phenotype. We report a comprehensive analysis of a pair of PDMZTs. Methods Dysmorphic features and delayed neuro‐motor development were observed in the proband, whereas her twin sister was phenotypically normal. Four tissues (blood, skin, hair follicles, and buccal mucosa) from both twins were studied using four complementary methods, including whole‐exome sequencing, karyotyping, array CGH, and SNP array. Results In the proband, tetrasomy 18p affecting all studied tissues except for blood was identified. Karyotyping of fibroblasts revealed isochromosome 18p [i(18p)] in all metaphases. The corresponding analysis of the phenotypically normal sister surprisingly revealed low‐level mosaicism (5.4%) for i(18p) in fibroblasts. Conclusion We emphasize that when mosaicism is suspected, multiple tissues should be studied and we highlight the usefulness of non‐invasive sampling of hair follicles and buccal mucosa as a convenient source of non‐mesoderm‐derived DNA, which complements the analysis of mesoderm using blood. Moreover, low‐level mosaic tetrasomy 18p is well tolerated and such low‐level mosaicism, readily detected by karyotyping, can be missed by other methods. Finally, mosaicism for low‐level tetrasomy 18p might be more common in the general population than it is currently recognized, due to detection limitations.
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Affiliation(s)
| | - Pawel Olszewski
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Darek Kedra
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Natalia Filipowicz
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Bozena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marco Cavalli
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Marlena Młynek
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marcin M Machnicki
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Paweł Krajewski
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Dariusz Śladowski
- Department of Transplantology and Central Tissue Bank, Centre for Biostructure, Medical University of Warsaw, Warsaw, Poland
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Jan P Dumanski
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland.,Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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89
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Trovato F, Parra R, Pracucci E, Landi S, Cozzolino O, Nardi G, Cruciani F, Pillai V, Mosti L, Cwetsch AW, Cancedda L, Gritti L, Sala C, Verpelli C, Maset A, Lodovichi C, Ratto GM. Modelling genetic mosaicism of neurodevelopmental disorders in vivo by a Cre-amplifying fluorescent reporter. Nat Commun 2020; 11:6194. [PMID: 33273479 PMCID: PMC7713426 DOI: 10.1038/s41467-020-19864-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic mosaicism, a condition in which an organ includes cells with different genotypes, is frequently present in monogenic diseases of the central nervous system caused by the random inactivation of the X-chromosome, in the case of X-linked pathologies, or by somatic mutations affecting a subset of neurons. The comprehension of the mechanisms of these diseases and of the cell-autonomous effects of specific mutations requires the generation of sparse mosaic models, in which the genotype of each neuron is univocally identified by the expression of a fluorescent protein in vivo. Here, we show a dual-color reporter system that, when expressed in a floxed mouse line for a target gene, leads to the creation of mosaics with tunable degree. We demonstrate the generation of a knockout mosaic of the autism/epilepsy related gene PTEN in which the genotype of each neuron is reliably identified, and the neuronal phenotype is accurately characterized by two-photon microscopy.
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Affiliation(s)
- Francesco Trovato
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy.
| | - Riccardo Parra
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Enrico Pracucci
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Silvia Landi
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
- Institute of Neuroscience CNR, Pisa, Italy
| | - Olga Cozzolino
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Gabriele Nardi
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Federica Cruciani
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Vinoshene Pillai
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Laura Mosti
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Andrzej W Cwetsch
- Istituto Italiano di Tecnologia, Genoa, Italy
- Università degli studi di Genova, Genoa, Italy
| | - Laura Cancedda
- Istituto Italiano di Tecnologia, Genoa, Italy
- Istituto Telethon Dulbecco, Rome, Italy
| | | | - Carlo Sala
- Institute of Neuroscience CNR, Milan, Italy
| | | | - Andrea Maset
- Veneto Institute of Molecular Medicine, Padua, Italy
- Padova Neuroscience Center, Padova Università di Padova, Padua, Italy
| | - Claudia Lodovichi
- Veneto Institute of Molecular Medicine, Padua, Italy
- Padova Neuroscience Center, Padova Università di Padova, Padua, Italy
- Institute of Neuroscience CNR, Padua, Italy
| | - Gian Michele Ratto
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy.
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90
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Min KD, Kour A, Sano S, Walsh K. The role of clonal haematopoiesis in cardiovascular diseases: epidemiology and experimental studies. J Intern Med 2020; 288:507-517. [PMID: 32715520 PMCID: PMC8375669 DOI: 10.1111/joim.13130] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/27/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022]
Abstract
Clonal haematopoiesis results from acquired mutations in haematopoietic stem and progenitor cells (HSPCs). These mutations can confer the HSPC with a competitive advantage, leading to their clonal expansion within the limiting bone marrow niche. This process is often insufficient to produce a haematologic malignancy; however, the expanding HSPC clones increasingly give rise to progeny leucocytes whose phenotypes can be altered by the somatic mutations that they harbour. Key findings from multiple human studies have shown that clonal haematopoiesis in the absence of overt haematologic alterations is common amongst the ageing population and associated with mortality and cardiovascular disease. Key findings from experimental studies have provided evidence for a causative role for clonal haematopoiesis in cardiovascular diseases, and aspects of these mechanisms have been elucidated. Whilst our understanding of the impact and biology of clonal haematopoiesis is in its infancy, analyses of some of the most commonly mutated driver genes suggest promising clinical scenarios involving the development of personalized therapies with immunomodulatory drugs that exploit the perturbation caused by the particular mutation. Herein, we review the accumulating epidemiological and experimental evidence, and summarize our current understanding of the importance of clonal haematopoiesis as a new causal risk factor for atherosclerotic cardiovascular disease and heart failure.
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Affiliation(s)
- K D Min
- From the, Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - A Kour
- From the, Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - S Sano
- From the, Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - K Walsh
- From the, Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
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91
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Gebert M, Jaśkiewicz M, Moszyńska A, Collawn JF, Bartoszewski R. The Effects of Single Nucleotide Polymorphisms in Cancer RNAi Therapies. Cancers (Basel) 2020; 12:E3119. [PMID: 33113880 PMCID: PMC7694039 DOI: 10.3390/cancers12113119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Tremendous progress in RNAi delivery methods and design has allowed for the effective development of siRNA-based therapeutics that are currently under clinical investigation for various cancer treatments. This approach has the potential to revolutionize cancer therapy by providing the ability to specifically downregulate or upregulate the mRNA of any protein of interest. This exquisite specificity, unfortunately, also has a downside. Genetic variations in the human population are common because of the presence of single nucleotide polymorphisms (SNPs). SNPs lead to synonymous and non-synonymous changes and they occur once in every 300 base pairs in both coding and non-coding regions in the human genome. Much less common are the somatic mosaicism variations associated with genetically distinct populations of cells within an individual that is derived from postzygotic mutations. These heterogeneities in the population can affect the RNAi's efficacy or more problematically, which can lead to unpredictable and sometimes adverse side effects. From a more positive viewpoint, both SNPs and somatic mosaicisms have also been implicated in human diseases, including cancer, and these specific changes could offer the ability to effectively and, more importantly, selectively target the cancer cells. In this review, we discuss how SNPs in the human population can influence the development and success of novel anticancer RNAi therapies and the importance of why SNPs should be carefully considered.
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Affiliation(s)
- Magdalena Gebert
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.G.); (M.J.); (A.M.)
| | - Maciej Jaśkiewicz
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.G.); (M.J.); (A.M.)
| | - Adrianna Moszyńska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.G.); (M.J.); (A.M.)
| | - James F. Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.G.); (M.J.); (A.M.)
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92
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Singh SM, Castellani CA, Hill KA. Postzygotic Somatic Mutations in the Human Brain Expand the Threshold-Liability Model of Schizophrenia. Front Psychiatry 2020; 11:587162. [PMID: 33192734 PMCID: PMC7642466 DOI: 10.3389/fpsyt.2020.587162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
The search for what causes schizophrenia has been onerous. This research has included extensive assessment of a variety of genetic and environmental factors using ever emerging high-resolution technologies and traditional understanding of the biology of the brain. These efforts have identified a large number of schizophrenia-associated genes, some of which are altered by mutational and epi-mutational mechanisms in a threshold liability model of schizophrenia development. The results, however, have limited predictability and the actual cause of the disease remains unknown. This current state asks for conceptualizing the problem differently in light of novel insights into the nature of mutations, the biology of the brain and the fine precision and resolution of emerging technologies. There is mounting evidence that mutations acquired during postzygotic development are more common than germline mutations. Also, the postzygotic somatic mutations including epimutations (PZMs), which often lead to somatic mosaicism, are relatively common in the mammalian brain in comparison to most other tissues and PZMs are more common in patients with neurodevelopmental mental disorders, including schizophrenia. Further, previously inaccessible, detection of PZMs is becoming feasible with the advent of novel technologies that include single-cell genomics and epigenomics and the use of exquisite experimental designs including use of monozygotic twins discordant for the disease. These developments allow us to propose a working hypothesis and expand the threshold liability model of schizophrenia that already encompasses familial genetic, epigenetic and environmental factors to include somatic de novo PZMs. Further, we offer a test for this expanded model using currently available genome sequences and methylome data on monozygotic twins discordant for schizophrenia (MZD) and their parents. The results of this analysis argue that PZMs play a significant role in the development of schizophrenia and explain extensive heterogeneity seen across patients. It also offers the potential to convincingly link PZMs to both nervous system health and disease, an area that has remained challenging to study and relatively under explored.
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Affiliation(s)
- Shiva M. Singh
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada
| | | | - Kathleen A. Hill
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada
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93
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Jung C, Evans MA, Walsh K. Genetics of age-related clonal hematopoiesis and atherosclerotic cardiovascular disease. Curr Opin Cardiol 2020; 35:219-225. [PMID: 32073406 DOI: 10.1097/hco.0000000000000726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW While advanced age is the major risk factor for the development of atherosclerotic cardiovascular disease (ASCVD), we have a poor understanding of how aging promotes the progression of this disease. Recent evidence suggests that the age-dependent accumulation of somatic mutations in hematopoietic cells may represent a new causal risk factor for ASCVD. RECENT FINDINGS A hallmark of aging is the accumulation of somatic DNA mutations in all tissues of the body. Accordingly, evidence shows that hematopoietic stem/progenitor cells accumulate somatic mutations as a function of age in nonsymptomatic individuals. When these mutations occur in driver genes that provide a selective advantage to the hematopoietic stem/progenitor cells, they undergo a clonal expansion and progressively give rise to blood leukocytes that harbor these mutations. This phenomenon, referred to as clonal hematopoiesis, has been associated with the increased risk of mortality, hematologic malignancy, ASCVD, and related diseases. Notably, many individuals exhibiting clonal hematopoiesis carry single 'driver' mutations in preleukemic genes including DNA methyltransferase 3a, ten-eleven translocation 2, additional sex combs like 1, and Janus kinase 2. Experimental studies show that these mutations in some of these genes can alter the inflammatory properties of the leukocyte and contribute to the pathogenesis of ASCVD. SUMMARY We review recent epidemiological and experimental findings on the association between age-related clonal hematopoiesis and ASCVD by focusing on prevalent driver gene mutations.
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Affiliation(s)
- Changhee Jung
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Megan A Evans
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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94
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Abstract
Mosaicism refers to the occurrence of two or more genomes in an individual derived from a single zygote. Germline mosaicism is a mutation that is limited to the gonads and can be transmitted to offspring. Somatic mosaicism is a postzygotic mutation that occurs in the soma, and it may occur at any developmental stage or in adult tissues. Mosaic variation may be classified in six ways: (a) germline or somatic origin, (b) class of DNA mutation (ranging in scale from single base pairs to multiple chromosomes), (c) developmental context, (d) body location(s), (e) functional consequence (including deleterious, neutral, or advantageous), and (f) additional sources of mosaicism, including mitochondrial heteroplasmy, exogenous DNA sources such as vectors, and epigenetic changes such as imprinting and X-chromosome inactivation. Technological advances, including single-cell and other next-generation sequencing, have facilitated improved sensitivity and specificity to detect mosaicism in a variety of biological contexts.
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Affiliation(s)
- Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA;
| | - Ikeoluwa A Osei-Owusu
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
| | | | - Rossella Tupler
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA; .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA; .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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95
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Gong P, Jiao X, Zhang Y, Yang Z. Complex Mosaicism of Two Distinct Mutations in a Female Patient With KCNA2-Related Encephalopathy: A Case Report. Front Genet 2020; 11:911. [PMID: 32903602 PMCID: PMC7438874 DOI: 10.3389/fgene.2020.00911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/22/2020] [Indexed: 12/29/2022] Open
Abstract
KCNA2 gene mutations were described to cause a new molecular entity within the developmental and epileptic or epileptic encephalopathies. Here, we firstly reported a patient with an unusual mosaicism for KCNA2, presenting two distinct mosaic missense mutations at the same loci. Clinical trio-based whole-exome sequencing using next-generation sequencing (NGS) revealed two novel mutations in KCNA2: c.1225A > T [p.(Ile409Phe)] and c.1225A > C [p.(Ile409Leu)]. Both missense mutations were in mosaic status and Sanger sequencing confirmed them as de novo. The affected 5-year-old girl presented as seizures with fever sensitivity, and mild cognitive and behavioral disorders. EEG showed focal centrotemporal epileptiform discharges accompanied by nocturnal focal seizures at the age of slightly older than 5 years, more likely carrying a loss-of-function mutation of KCNA2-related phenotype. Further NGS with a mean coverage of 6950 × showed 26% (mosaic mutation reads/total reads) of the c.1225A > T mutation and 23% of the c.1225A > C mutation. The sum of their allele fractions was close to 50%, approximately equal to a heterozygous variant. The patient had no seizures for 8 months on combination of levetiracetam (18.75 mg/kg/d) and valproate (20 mg/kg/d) till the last follow-up at the age of 5 years and 11 months. Our findings highlighted the two mosaic mutations responsible for the pathogenesis of KCNA2-related encephalopathy. The patient expanded the mutational spectrum of KCNA2-related encephalopathy and provided new insight into the complex genetic disorder.
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Affiliation(s)
- Pan Gong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xianru Jiao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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96
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Rodríguez-Nóvoa S, Rodríguez-Jiménez C, Alonso C, Rodriguez-Laguna L, Gordo G, Martinez-Glez V, García Polo I. Familial hypercholesterolemia: A single-nucleotide variant (SNV) in mosaic at the low density lipoprotein receptor (LDLR). Atherosclerosis 2020; 311:37-43. [PMID: 32937241 DOI: 10.1016/j.atherosclerosis.2020.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/03/2020] [Accepted: 08/20/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND AND AIMS Familial hypercholesterolemia is most frequently caused by genetic variants in the LDLR gene. Most of LDLR pathogenic variants are missense, followed by splicing and deletion/insertions variants. Mosaicism is a genetic condition in which an individual shows more than one clone of cells with different genotypes. The objective of this article was the molecular characterization of a patient with hypercholesterolemia. METHODS AND RESULTS Genetic analysis of DNA from peripheral blood and saliva was performed by NGS, Sanger sequencing and pyrosequencing technologies. NGS analysis detected the pathogenic variant LDLR:c.1951G > T:p.(Asp651Tyr) in 9%-12% of reads. The presence of the variant was confirmed by pyrosequencing analysis. The variant found was functional characterized using an in vitro model (CHO-ldlA7 cells). Activity and expression of cell surface LDLR were measured by flow cytometry. Colocalization LDLR-Dil-LDL was detected by immunofluorescence. The LDLR activity showed 80% uptake, 50% binding and 53% expression of cell surface LDLR regarding wild type. CONCLUSIONS Herein, we report the first case of a mosaic single nucleotide variant affecting the LDLR gene in a patient with familial hypercholesterolemia. As it has been described for other pathologies, mosaicism could be underestimated in FH and its detection will improve with the introduction of NGS technologies in the diagnostic routine.
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Affiliation(s)
- Sonia Rodríguez-Nóvoa
- Genetics of Metabolic Diseases Laboratory, Department of Genetics, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain.
| | - Carmen Rodríguez-Jiménez
- Genetics of Metabolic Diseases Laboratory, Department of Genetics, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | | | - Lara Rodriguez-Laguna
- Vascular Malformations Section, Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Spain
| | - Gema Gordo
- Vascular Malformations Section, Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Spain
| | - Victor Martinez-Glez
- Vascular Malformations Section, Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Spain
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97
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Martínez-Glez V, Tenorio J, Nevado J, Gordo G, Rodríguez-Laguna L, Feito M, de Lucas R, Pérez-Jurado LA, Ruiz Pérez VL, Torrelo A, Spinner NB, Happle R, Biesecker LG, Lapunzina P. A six-attribute classification of genetic mosaicism. Genet Med 2020; 22:1743-1757. [PMID: 32661356 PMCID: PMC8581815 DOI: 10.1038/s41436-020-0877-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Mosaicism denotes an individual who has at least two populations of cells with distinct genotypes that are derived from a single fertilized egg. Genetic variation among the cell lines can involve whole chromosomes, structural or copy number variants, small or single nucleotide variants, or epigenetic variants. The mutational events that underlie mosaic variants occur during mitotic cell divisions after fertilization and zygote formation. The initiating mutational event can occur in any types of cell at any time in development, leading to enormous variation in the distribution and phenotypic effect of mosaicism. A number of classification proposals have been put forward to classify genetic mosaicism into categories based on the location, pattern, and mechanisms of the disease. We here propose a new classification of genetic mosaicism that considers the affected tissue, the pattern and distribution of the mosaicism, the pathogenicity of the variant, the direction of the change (benign to pathogenic vs. pathogenic to benign), and the postzygotic mutational mechanism. The accurate and comprehensive categorization and subtyping of mosaicisms is important and has potential clinical utility to define the natural history of these disorders, tailor follow-up frequency and interventions, estimate recurrence risks, and guide therapeutic decisions.
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Affiliation(s)
- Víctor Martínez-Glez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| | - Jair Tenorio
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Gema Gordo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Lara Rodríguez-Laguna
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Marta Feito
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Raúl de Lucas
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra and Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Women's and Children's Hospital, South Australia Medical and Health Research Institute (SAHMRI) and University of Adelaide, Adelaide, SA, Australia
| | - Víctor L Ruiz Pérez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.,Instituto de Investigaciones Biomédicas de Madrid (CSIC-UAM), Madrid, Spain
| | - Antonio Torrelo
- Department of Pediatrics, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicines at The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rudolf Happle
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
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98
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Spinetti G, Sangalli E, Tagliabue E, Maselli D, Colpani O, Ferland-McCollough D, Carnelli F, Orlando P, Paccagnella A, Furlan A, Stefani PM, Sambado L, Sambataro M, Madeddu P. MicroRNA-21/PDCD4 Proapoptotic Signaling From Circulating CD34 + Cells to Vascular Endothelial Cells: A Potential Contributor to Adverse Cardiovascular Outcomes in Patients With Critical Limb Ischemia. Diabetes Care 2020; 43:1520-1529. [PMID: 32358022 PMCID: PMC7305013 DOI: 10.2337/dc19-2227] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/30/2020] [Indexed: 02/03/2023]
Abstract
OBJECTIVE In patients with type 2 diabetes (T2D) and critical limb ischemia (CLI), migration of circulating CD34+ cells predicted cardiovascular mortality at 18 months after revascularization. This study aimed to provide long-term validation and mechanistic understanding of the biomarker. RESEARCH DESIGN AND METHODS The association between CD34+ cell migration and cardiovascular mortality was reassessed at 6 years after revascularization. In a new series of T2D-CLI and control subjects, immuno-sorted bone marrow CD34+ cells were profiled for miRNA expression and assessed for apoptosis and angiogenesis activity. The differentially regulated miRNA-21 and its proapoptotic target, PDCD4, were titrated to verify their contribution in transferring damaging signals from CD34+ cells to endothelial cells. RESULTS Multivariable regression analysis confirmed that CD34+ cell migration forecasts long-term cardiovascular mortality. CD34+ cells from T2D-CLI patients were more apoptotic and less proangiogenic than those from control subjects and featured miRNA-21 downregulation, modulation of several long noncoding RNAs acting as miRNA-21 sponges, and upregulation of the miRNA-21 proapoptotic target PDCD4. Silencing miR-21 in control CD34+ cells phenocopied the T2D-CLI cell behavior. In coculture, T2D-CLI CD34+ cells imprinted naive endothelial cells, increasing apoptosis, reducing network formation, and modulating the TUG1 sponge/miRNA-21/PDCD4 axis. Silencing PDCD4 or scavenging reactive oxygen species protected endothelial cells from the negative influence of T2D-CLI CD34+ cells. CONCLUSIONS Migration of CD34+ cells predicts long-term cardiovascular mortality in T2D-CLI patients. An altered paracrine signaling conveys antiangiogenic and proapoptotic features from CD34+ cells to the endothelium. This damaging interaction may increase the risk for life-threatening complications.
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99
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Chromosomal alterations among age-related haematopoietic clones in Japan. Nature 2020; 584:130-135. [PMID: 32581364 DOI: 10.1038/s41586-020-2426-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 04/02/2020] [Indexed: 12/26/2022]
Abstract
The extent to which the biology of oncogenesis and ageing are shaped by factors that distinguish human populations is unknown. Haematopoietic clones with acquired mutations become common with advancing age and can lead to blood cancers1-10. Here we describe shared and population-specific patterns of genomic mutations and clonal selection in haematopoietic cells on the basis of 33,250 autosomal mosaic chromosomal alterations that we detected in 179,417 Japanese participants in the BioBank Japan cohort and compared with analogous data from the UK Biobank. In this long-lived Japanese population, mosaic chromosomal alterations were detected in more than 35.0% (s.e.m., 1.4%) of individuals older than 90 years, which suggests that such clones trend towards inevitability with advancing age. Japanese and European individuals exhibited key differences in the genomic locations of mutations in their respective haematopoietic clones; these differences predicted the relative rates of chronic lymphocytic leukaemia (which is more common among European individuals) and T cell leukaemia (which is more common among Japanese individuals) in these populations. Three different mutational precursors of chronic lymphocytic leukaemia (including trisomy 12, loss of chromosomes 13q and 13q, and copy-neutral loss of heterozygosity) were between two and six times less common among Japanese individuals, which suggests that the Japanese and European populations differ in selective pressures on clones long before the development of clinically apparent chronic lymphocytic leukaemia. Japanese and British populations also exhibited very different rates of clones that arose from B and T cell lineages, which predicted the relative rates of B and T cell cancers in these populations. We identified six previously undescribed loci at which inherited variants predispose to mosaic chromosomal alterations that duplicate or remove the inherited risk alleles, including large-effect rare variants at NBN, MRE11 and CTU2 (odds ratio, 28-91). We suggest that selective pressures on clones are modulated by factors that are specific to human populations. Further genomic characterization of clonal selection and cancer in populations from around the world is therefore warranted.
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100
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Proshkina E, Shaposhnikov M, Moskalev A. Genome-Protecting Compounds as Potential Geroprotectors. Int J Mol Sci 2020; 21:E4484. [PMID: 32599754 PMCID: PMC7350017 DOI: 10.3390/ijms21124484] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Throughout life, organisms are exposed to various exogenous and endogenous factors that cause DNA damages and somatic mutations provoking genomic instability. At a young age, compensatory mechanisms of genome protection are activated to prevent phenotypic and functional changes. However, the increasing stress and age-related deterioration in the functioning of these mechanisms result in damage accumulation, overcoming the functional threshold. This leads to aging and the development of age-related diseases. There are several ways to counteract these changes: 1) prevention of DNA damage through stimulation of antioxidant and detoxification systems, as well as transition metal chelation; 2) regulation of DNA methylation, chromatin structure, non-coding RNA activity and prevention of nuclear architecture alterations; 3) improving DNA damage response and repair; 4) selective removal of damaged non-functional and senescent cells. In the article, we have reviewed data about the effects of various trace elements, vitamins, polyphenols, terpenes, and other phytochemicals, as well as a number of synthetic pharmacological substances in these ways. Most of the compounds demonstrate the geroprotective potential and increase the lifespan in model organisms. However, their genome-protecting effects are non-selective and often are conditioned by hormesis. Consequently, the development of selective drugs targeting genome protection is an advanced direction.
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Affiliation(s)
- Ekaterina Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
| | - Mikhail Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
- Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky prosp., 167001 Syktyvkar, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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