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Kohram M, Sanderson AE, Loui A, Thompson PV, Vashistha H, Shomar A, Oltvai ZN, Salman H. Nonlethal deleterious mutation-induced stress accelerates bacterial aging. Proc Natl Acad Sci U S A 2024; 121:e2316271121. [PMID: 38709929 PMCID: PMC11098108 DOI: 10.1073/pnas.2316271121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/29/2024] [Indexed: 05/08/2024] Open
Abstract
Random mutagenesis, including when it leads to loss of gene function, is a key mechanism enabling microorganisms' long-term adaptation to new environments. However, loss-of-function mutations are often deleterious, triggering, in turn, cellular stress and complex homeostatic stress responses, called "allostasis," to promote cell survival. Here, we characterize the differential impacts of 65 nonlethal, deleterious single-gene deletions on Escherichia coli growth in three different growth environments. Further assessments of select mutants, namely, those bearing single adenosine triphosphate (ATP) synthase subunit deletions, reveal that mutants display reorganized transcriptome profiles that reflect both the environment and the specific gene deletion. We also find that ATP synthase α-subunit deleted (ΔatpA) cells exhibit elevated metabolic rates while having slower growth compared to wild-type (wt) E. coli cells. At the single-cell level, compared to wt cells, individual ΔatpA cells display near normal proliferation profiles but enter a postreplicative state earlier and exhibit a distinct senescence phenotype. These results highlight the complex interplay between genomic diversity, adaptation, and stress response and uncover an "aging cost" to individual bacterial cells for maintaining population-level resilience to environmental and genetic stress; they also suggest potential bacteriostatic antibiotic targets and -as select human genetic diseases display highly similar phenotypes, - a bacterial origin of some human diseases.
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Affiliation(s)
- Maryam Kohram
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Amy E. Sanderson
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Alicia Loui
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | | | - Harsh Vashistha
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Aseel Shomar
- Department of Chemical Engineering, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Zoltán N. Oltvai
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA15260
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA15260
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY14627
| | - Hanna Salman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
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2
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Andrawus M, Sharvit L, Touitou N, Lerrer B, Cohen HY, Atzmon G. Copy number variation as a tool for implementing pregnancy as an aging model. Aging (Albany NY) 2023; 15:7922-7932. [PMID: 37639552 PMCID: PMC10496986 DOI: 10.18632/aging.204936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/10/2023] [Indexed: 08/31/2023]
Abstract
Copy number variations (CNV) are a major contributor to genome variability and have been linked to aging and other degradable phenotypes such as pregnancy physiology. To demonstrate how pregnancy can be used as a model of aging, we used CNVs from pregnant mice. Candidate CNVs were selected by applying case-control analysis in human centenarians compared with control groups. These CNVs were aligned with the mouse genome and their copy variation was assessed using qRT-PCR in liver and blood tissue samples from pregnant mice throughout pregnancy (baseline; first, second, and third trimester; post-partum). Eight of the ten selected CNVs demonstrated a significant decline/increase trend throughout the pregnancy followed by opposite direction soon after delivery in the liver and blood of the mouse tissues. Furthermore, significant differential expression was detected among the candidate CNVs' close vicinity genes (APA2A, LSS, RBDHF1, PLAAT1, and SCL17A2), but not in the WSCD2 gene. Establishing a genetic link between longevity and pregnancy is a significant step toward implementing the pregnancy process as a model for aging. These results in pregnant mice highlight the mechanism and similarities between pregnancy and aging. Investigating the mechanisms that cause such rejuvenation after labor could change our aging treatment paradigm.
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Affiliation(s)
- Mariana Andrawus
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
| | - Lital Sharvit
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
| | - Noga Touitou
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Batia Lerrer
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Haim Y. Cohen
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Gil Atzmon
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
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3
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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4
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Michnowska A, Hart SFM, Smolarz K, Hallmann A, Metzger MJ. Horizontal transmission of disseminated neoplasia in the widespread clam
Macoma balthica
from the Southern Baltic Sea. Mol Ecol 2022; 31:3128-3136. [DOI: 10.1111/mec.16464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Alicja Michnowska
- Department of Marine Ecosystems Functioning Institute of Oceanography Faculty of Oceanography and Geography University of Gdańsk Piłsudskiego 46 81‐378 Gdynia
| | - Samuel F. M. Hart
- Pacific Northwest Research Institute 720 Broadway Seattle WA 98122 USA
- Molecular and Cellular Biology Program University of Washington 1959 NE Pacific Street, HSB T‐466 Seattle WA 98195 USA
| | - Katarzyna Smolarz
- Department of Marine Ecosystems Functioning Institute of Oceanography Faculty of Oceanography and Geography University of Gdańsk Piłsudskiego 46 81‐378 Gdynia
| | - Anna Hallmann
- Department of Pharmaceutical Biochemistry Medical University of Gdańsk Dębinki 1 80‐211 Gdańsk
| | - Michael J. Metzger
- Pacific Northwest Research Institute 720 Broadway Seattle WA 98122 USA
- Molecular and Cellular Biology Program University of Washington 1959 NE Pacific Street, HSB T‐466 Seattle WA 98195 USA
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5
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Keller A, Spits C. The Impact of Acquired Genetic Abnormalities on the Clinical Translation of Human Pluripotent Stem Cells. Cells 2021; 10:cells10113246. [PMID: 34831467 PMCID: PMC8625075 DOI: 10.3390/cells10113246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/07/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
Human pluripotent stem cells (hPSC) are known to acquire chromosomal abnormalities, which range from point mutations to large copy number changes, including full chromosome aneuploidy. These aberrations have a wide-ranging influence on the state of cells, in both the undifferentiated and differentiated state. Currently, very little is known on how these abnormalities will impact the clinical translation of hPSC, and particularly their potential to prime cells for oncogenic transformation. A further complication is that many of these abnormalities exist in a mosaic state in culture, which complicates their detection with conventional karyotyping methods. In this review we discuss current knowledge on how these aberrations influence the cell state and how this may impact the future of research and the cells’ clinical potential.
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Valencia-Morales MDP, Sanchez-Flores A, Colín-Castelán D, Alvarado-Caudillo Y, Fragoso-Bargas N, López-González G, Peña-López T, Ramírez-Nava M, de la Rocha C, Rodríguez-Ríos D, Lund G, Zaina S. Somatic Genetic Mosaicism in the Apolipoprotein E-null Mouse Aorta. Thromb Haemost 2021; 121:1541-1553. [PMID: 33677828 DOI: 10.1055/a-1414-4840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In addition to genetic and epigenetic inheritance, somatic variation may contribute to cardiovascular disease (CVD) risk. CVD-associated somatic mutations have been reported in human clonal hematopoiesis, but evidence in the atheroma is lacking. To probe for somatic variation in atherosclerosis, we sought single-nucleotide private variants (PVs) in whole-exome sequencing (WES) data of aorta, liver, and skeletal muscle of two C57BL/6J coisogenic male ApoE null/wild-type (WT) sibling pairs, and RNA-seq data of one of the two pairs. Relative to the C57BL/6 reference genome, we identified 9 and 11 ApoE null aorta- and liver-specific PVs that were shared by all WES and RNA-seq datasets. Corresponding PVs in WT sibling aorta and liver were 1 and 0, respectively, and not overlapping with ApoE null PVs. Pyrosequencing analysis of 4 representative PVs in 17 ApoE null aortas and livers confirmed tissue-specific shifts toward the alternative allele, in addition to significant deviations from mendelian allele ratios. Notably, all aorta and liver PVs were present in the dbSNP database and were predominantly transition mutations within atherosclerosis-related genes. The majority of PVs were in discrete clusters approximately 3 Mb and 65 to 73 Mb away from hypermutable immunoglobin loci in chromosome 6. These features were largely shared with previously reported CVD-associated somatic mutations in human clonal hematopoiesis. The observation that SNPs exhibit tissue-specific somatic DNA mosaicism in ApoE null mice is potentially relevant for genetic association study design. The proximity of PVs to hypermutable loci suggests testable mechanistic hypotheses.
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Affiliation(s)
- María Del Pilar Valencia-Morales
- Department of Genetic Engineering, CINVESTAV Irapuato Unit, Irapuato, Mexico
- Department of Developmental Genetics and Molecular Physiology, "Unidad Universitaria de Secuenciación Masiva y Bioinformática", Biotechnology Institute, UNAM, Cuernavaca, Mexico
| | - Alejandro Sanchez-Flores
- "Unidad Universitaria de Secuenciación Masiva y Bioinformática", Biotechnology Institute, UNAM, Cuernavaca, Mexico
| | | | | | | | - Gladys López-González
- Bachelor's Degree in Nutrition Programme, Division of Health Sciences, Leon Campus, University of Guanajuato, Leon, Mexico
| | - Tania Peña-López
- Department of Medical Sciences, Leon Campus, University of Guanajuato, Leon, Mexico
| | - Magda Ramírez-Nava
- Bachelor's Degree in Nutrition Programme, Division of Health Sciences, Leon Campus, University of Guanajuato, Leon, Mexico
| | - Carmen de la Rocha
- Department of Genetic Engineering, CINVESTAV Irapuato Unit, Irapuato, Mexico
| | | | - Gertrud Lund
- Department of Genetic Engineering, CINVESTAV Irapuato Unit, Irapuato, Mexico
| | - Silvio Zaina
- Department of Medical Sciences, Leon Campus, University of Guanajuato, Leon, Mexico
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7
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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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8
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Sharma A, Jain M, Halder A, Kaushal S. Identification of genomic imbalances (CNVs as well as LOH) in sertoli cell only syndrome cases through cytoscan microarray. Gene 2021; 801:145851. [PMID: 34274474 DOI: 10.1016/j.gene.2021.145851] [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: 08/07/2020] [Revised: 06/01/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Sertoli cell only syndrome (SCOS) is characterized by complete absence of germ cells in seminiferous tubules of testis. SCOS is multifactorial but genetic factors play a major role in pathogenesis of the disorder with idiopathic origin. Genetic factors majorly include sex chromosomal aneuploidy and Yq Microdeletion. But a large number of cases are still idiopathic. The study aimed to evaluate the genomic imbalances (CNVs and LOH) in idiopathic SCOS patients. The study is based on 28 apparent idiopathic SCOS cases and 10 controls. Molecular cytogenetic techniques viz., FISH, STS-Multiplex PCR and Affymetrix cytoscan microarray (750 K) were used. The microarray screened whole genomic imbalances in DNA from peripheral blood of 25 cases (excluded Klinefelter syndrome patients) and testicular FNAC sample of 2 cases. High FSH and low Inhibin B were observed in cases as compared to control controls groups. Four cases of sex chromosomal abnormality (i.e., three non-mosaic 47, XXY males and one non-mosaic 46, XX male) as well as four cases of Yq microdeletion (i.e., three cases with AZFc deletion and one case with complete AZFa, b and c deletion) were identified. Microarray detected unbalanced translocation of two segments of Y-chromosome i.e., Yp11.31-p11.2 (~4.o mb region, involving SRY) and Yp11.2 (~2.5 mb region) on X-chromosome in XX male. Also, loss of segment on same X-chromosome involving PAR1 region was identified. We have identified both autosomal and sex chromosomal CNVs (recurrent as well as private) involving candidate genes like SYCE1, ZFPM2, SRPK1, DAZ1, BPY2, HSFY1, VCY1 etc. All these CNVs are possibly associated with SCOS pathogenesis. CNVs identified in cases were already reported as pathogenic variant in clinical database DECIPHER. Microarray also detected many LOH (all autosomal, >3.0 mb size) that covered genes with spermatogenesis related function. The mechanism of action of LOH in pathogenesis of SCOS still remains unravelled. CNVs and LOH related to spermatogenesis identified from two different sample types (blood vs. testicular tissue) were discordant. This study should be extended for larger cohort of patients.
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Affiliation(s)
- Aiyush Sharma
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Jain
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India.
| | - Ashutosh Halder
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Kaushal
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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9
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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: 5] [Impact Index Per Article: 1.7] [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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10
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Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol 2021; 22:92. [PMID: 33781308 PMCID: PMC8006362 DOI: 10.1186/s13059-021-02285-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. RESULTS Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. CONCLUSIONS This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.
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Affiliation(s)
- Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Taejeong Bae
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jeremy Thorpe
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Maxwell A Sherman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- MIT Department of Electrical Engineering and Computer Science, Cambridge, MA, USA
| | - Attila G Jones
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sean Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Present Address: Arcus Biosciences, Hayward, CA, 94545, USA
| | | | - Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Irene Lobon
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chaggai Rosenbluh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Simone Tomasi
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Livia Tomasini
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ryan Doan
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Yeongjun Jang
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rujuta Narurkar
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Matthew T Oetjens
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shobana Sekar
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
- Vall d'Hebron Institut de Recerca, 08035, Barcelona, Spain
- Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
- ICREA Academia, 08010 Barcelona, Spain
| | - Richard E Straub
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Andrew Chess
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Tomas Marquès-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel R Weinberger
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University, New Haven, 06520, CT, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Tashia and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford, CA, 94305, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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11
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Guo SW. Cancer-associated mutations in endometriosis: shedding light on the pathogenesis and pathophysiology. Hum Reprod Update 2020; 26:423-449. [PMID: 32154564 DOI: 10.1093/humupd/dmz047] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/22/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Endometriosis is a benign gynaecological disease. Thus, it came as a complete surprise when it was reported recently that the majority of deep endometriosis lesions harbour somatic mutations and a sizeable portion of them contain known cancer-associated mutations (CAMs). Four more studies have since been published, all demonstrating the existence of CAMs in different subtypes of endometriosis. While the field is still evolving, the confirmation of CAMs has raised many questions that were previously overlooked. OBJECTIVE AND RATIONALE A comprehensive overview of CAMs in endometriosis has been produced. In addition, with the recently emerged understanding of the natural history of endometriotic lesions as well as CAMs in normal and apparently healthy tissues, this review attempts to address the following questions: Why has there been such a wild discrepancy in reported mutation frequencies? Why does ectopic endometrium have a higher mutation rate than that of eutopic endometrium? Would the presence of CAMs in endometriotic lesions increase the risk of cancer to the bearers? Why do endometriotic epithelial cells have much higher mutation frequencies than their stromal counterpart? What clinical implications, if any, do the CAMs have for the bearers? Do these CAMs tell us anything about the pathogenesis and/or pathophysiology of endometriosis? SEARCH METHODS The PubMed database was searched, from its inception to September 2019, for all papers in English using the term 'endometriosis and CAM', 'endometriosis and cancer-driver mutation', 'somatic mutations', 'fibrosis', 'fibrosis and epigenetic', 'CAMs and tumorigenesis', 'somatic mutation and normal tissues', 'oestrogen receptor and fibrosis', 'oxidative stress and fibrosis', 'ARID1A mutation', and 'Kirsten rat sarcoma mutation and therapeutics'. All retrieved papers were read and, when relevant, incorporated into the review results. OUTCOMES Seven papers that identified CAMs in endometriosis using various sequencing methods were retrieved, and their results were somewhat different. Yet, it is apparent that those using microdissection techniques and more accurate sequencing methods found more CAMs, echoing recent discoveries that apparently healthy tissues also harbour CAMs as a result of the replicative aging process. Hence endometriotic lesions, irrespective of subtype, if left intact, would generate CAMs as part of replicative aging, oxidative stress and perhaps other factors yet to be identified and, in some rare cases, develop cancer. The published data still are unable to paint a clear picture on pathogenesis of endometriosis. However, since endometriotic epithelial cells have a higher turnover than their stromal counterpart due to cyclic bleeding, and since the endometriotic stromal component can be formed by refresh influx of mesenchymal cells through epithelial-mesenchymal transition, endothelial-mesenchymal transition, mesothelial-mesenchymal transition and other processes as well as recruitment of bone-marrow-derived stem cells and outflow due to smooth muscle metaplasia, endometriotic epithelial cells have much higher mutation frequencies than their stromal counterpart. The epithelial and stromal cellular components develop in a dependent and co-evolving manner. Genes involved in CAMs are likely to be active players in lesional fibrogenesis, and hyperestrogenism and oxidative stress are likely drivers of both CAMs and fibrogenesis. Finally, endometriotic lesions harbouring CAMs would conceivably be more refractory to medical treatment, due, in no small part, to their high fibrotic content and reduced vascularity and cellularity. WIDER IMPLICATIONS The accumulating data on CAMs in endometriosis have shed new light on the pathogenesis and pathophysiology of endometriosis. They also suggest new challenges in management. The distinct yet co-evolving developmental trajectories of endometriotic stroma and epithelium underscore the importance of the lesional microenvironment and ever-changing cellular identity. Mutational profiling of normal endometrium from women of different ages and reproductive history is needed in order to gain a deeper understanding of the pathogenesis. Moreover, one area that has conspicuously received scant attention is the epigenetic landscape of ectopic, eutopic and normal endometrium.
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Affiliation(s)
- Sun-Wei Guo
- Shanghai Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China.,Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai 200011, China
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12
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Fiala C, Diamandis EP. Mutations in normal tissues-some diagnostic and clinical implications. BMC Med 2020; 18:283. [PMID: 33115454 PMCID: PMC7594459 DOI: 10.1186/s12916-020-01763-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/25/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND It has long been known that mutations are at the core of many diseases, most notably cancer. Mutational analysis of tissues and fluids is useful for cancer and other disease diagnosis and management. MAIN BODY The prevailing cancer development hypothesis posits that cancer originates from mutations in cancer-driving genes that accumulate in tissues over time. These mutations then confer special characteristics to cancer cells, known as the hallmarks of cancer. Mutations in specific driver genes can lead to the formation of cancerous subclones and mutation risk increases with age. New research has revealed an unexpectedly large number of mutations in normal tissues; these findings could have significant implications to the understanding of the pathobiology of cancer and for disease diagnosis and therapy. Here, we discuss how the prevalence of mutations in normal tissues provides novel and relevant insights about clonal development in cancer and other diseases. Specifically, this review will focus on discussing mutations in normal tissues in the context of developing specific, circulating tumor DNA (ctDNA) tests for cancer, and evaluating clonal hematopoiesis as a predictor of blood cancers and cardiovascular pathology, as well as their implications to the phenomena of neural mosaicism in the context of Alzheimer's disease. CONCLUSIONS In view of these new findings, the fundamental differences between the accumulation of genetic alterations in healthy, aging tissues compared to cancer and cardiovascular or neural diseases will need to be better delineated in the future.
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Affiliation(s)
- Clare Fiala
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Department of Clinical Biochemistry, Mount Sinai Hospital and University Health Network, 60 Murray St. Box 32, Floor 6, Rm L6-201, Toronto, ON, MST 3L9, Canada.
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13
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Zamai L. Unveiling Human Non-Random Genome Editing Mechanisms Activated in Response to Chronic Environmental Changes: I. Where Might These Mechanisms Come from and What Might They Have Led To? Cells 2020; 9:E2362. [PMID: 33121045 PMCID: PMC7693803 DOI: 10.3390/cells9112362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
This article challenges the notion of the randomness of mutations in eukaryotic cells by unveiling stress-induced human non-random genome editing mechanisms. To account for the existence of such mechanisms, I have developed molecular concepts of the cell environment and cell environmental stressors and, making use of a large quantity of published data, hypothesised the origin of some crucial biological leaps along the evolutionary path of life on Earth under the pressure of natural selection, in particular, (1) virus-cell mating as a primordial form of sexual recombination and symbiosis; (2) Lamarckian CRISPR-Cas systems; (3) eukaryotic gene development; (4) antiviral activity of retrotransposon-guided mutagenic enzymes; and finally, (5) the exaptation of antiviral mutagenic mechanisms to stress-induced genome editing mechanisms directed at "hyper-transcribed" endogenous genes. Genes transcribed at their maximum rate (hyper-transcribed), yet still unable to meet new chronic environmental demands generated by "pollution", are inadequate and generate more and more intronic retrotransposon transcripts. In this scenario, RNA-guided mutagenic enzymes (e.g., Apolipoprotein B mRNA editing catalytic polypeptide-like enzymes, APOBECs), which have been shown to bind to retrotransposon RNA-repetitive sequences, would be surgically targeted by intronic retrotransposons on opened chromatin regions of the same "hyper-transcribed" genes. RNA-guided mutagenic enzymes may therefore "Lamarkianly" generate single nucleotide polymorphisms (SNP) and gene copy number variations (CNV), as well as transposon transposition and chromosomal translocations in the restricted areas of hyper-functional and inadequate genes, leaving intact the rest of the genome. CNV and SNP of hyper-transcribed genes may allow cells to surgically explore a new fitness scenario, which increases their adaptability to stressful environmental conditions. Like the mechanisms of immunoglobulin somatic hypermutation, non-random genome editing mechanisms may generate several cell mutants, and those codifying for the most environmentally adequate proteins would have a survival advantage and would therefore be Darwinianly selected. Non-random genome editing mechanisms represent tools of evolvability leading to organismal adaptation including transgenerational non-Mendelian gene transmission or to death of environmentally inadequate genomes. They are a link between environmental changes and biological novelty and plasticity, finally providing a molecular basis to reconcile gene-centred and "ecological" views of evolution.
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Affiliation(s)
- Loris Zamai
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; ; Tel./Fax: +39-0722-304-319
- National Institute for Nuclear Physics (INFN)-Gran Sasso National Laboratory (LNGS), 67100 Assergi, L’Aquila, Italy
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14
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Sharma A, Halder A, Kaushal S, Jain M. Intra-individual Genomic Variation Analysis in Tissues (Blood vs. Testis) Through SNP Microarray: A Case Report of Two Patients with Idiopathic Sertoli Cell Only Syndrome (SCOS). J Reprod Infertil 2020; 21:308-311. [PMID: 33209739 PMCID: PMC7648869 DOI: 10.18502/jri.v21i4.4325] [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] [Indexed: 11/25/2022] Open
Abstract
Background: Inflammatory responses within the peritoneal cavity may result in endometrial dysfunction in women with endometriosis. The true causes of this disease remain poorly understood. It is hypothesized that downstream toll-like receptors (TLRs) inflammatory cytokines in response to pathogens may be associated with endometriosis. So, this study was aimed at evaluating the expression of TLRs signaling and endometriosis-associated inflammatory responses. Methods: Totally, 20 infertile endometriosis patients and 20 normal women undergoing controlled ovarian stimulation were enrolled. The cellular pellet and supernatant were obtained by centrifugation of follicular fluid (FF). Evaluation of TLRs and their signaling pathway gene expression was performed on cellular pellets using quantitative-PCR. The supernatant was used for determination of cytokine protein expression by ELISA. The results are expressed as mean±SEM and a p<0.05 was considered statistically significant. Results: Quantitative-PCR analysis suggested that TLR1, 5, 6, 7, 8, 10, MYD88, NF-ĸB, IL-10 and TGF-β genes expression significantly increased in patients compared to the control group (p<0.05). TLR3, 9, INF-β genes expression was significantly lower in endometriosis than control group (p<0.05). There was no significant difference in the expression of TLR2, TLR4, TIRAP, TRIF, TRAM, and IRF3 between two groups. Also, significant increase in the levels of IL-6, IL-8 and MIF protein in FF of endometriosis group was detected in comparison with normal women (p<0.05). Conclusion: The expression of TLR downstream signaling in the follicular cells can initiate inflammatory responses and changes in the FF cytokine profile which in turn may induce endometriosis and infertility disorder.
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Affiliation(s)
- Aiyush Sharma
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Ashutosh Halder
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Kaushal
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Jain
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
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15
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Al Zouabi L, Bardin AJ. Stem Cell DNA Damage and Genome Mutation in the Context of Aging and Cancer Initiation. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036210. [PMID: 31932318 DOI: 10.1101/cshperspect.a036210] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Adult stem cells fuel tissue homeostasis and regeneration through their unique ability to self-renew and differentiate into specialized cells. Thus, their DNA provides instructions that impact the tissue as a whole. Since DNA is not an inert molecule, but rather dynamic, interacting with a myriad of chemical and physical factors, it encounters damage from both endogenous and exogenous sources. Damage to DNA introduces deviations from its normal intact structure and, if left unrepaired, may result in a genetic mutation. In turn, mutant genomes of stem and progenitor cells are inherited in cells of the lineage, thus eroding the genetic information that maintains homeostasis of the somatic cell population. Errors arising in stem and progenitor cells will have a substantially larger impact on the tissue in which they reside than errors occurring in postmitotic differentiated cells. Therefore, maintaining the integrity of genomic DNA within our stem cells is essential to protect the instructions necessary for rebuilding healthy tissues during homeostatic renewal. In this review, we will first discuss DNA damage arising in stem cells and cell- and tissue-intrinsic mechanisms that protect against harmful effects of this damage. Secondly, we will examine how erroneous DNA repair and persistent DNA damage in stem and progenitor cells impact stem cells and tissues in the context of cancer initiation and aging. Finally, we will discuss the use of invertebrate and vertebrate model systems to address unanswered questions on the role that DNA damage and mutation may play in aging and precancerous conditions.
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Affiliation(s)
- Lara Al Zouabi
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75248 Paris, France.,Sorbonne Universités, UPMC University, Paris 6, France
| | - Allison J Bardin
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75248 Paris, France.,Sorbonne Universités, UPMC University, Paris 6, France
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16
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Groza C, Kwan T, Soranzo N, Pastinen T, Bourque G. Personalized and graph genomes reveal missing signal in epigenomic data. Genome Biol 2020; 21:124. [PMID: 32450900 PMCID: PMC7249353 DOI: 10.1186/s13059-020-02038-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/08/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias downstream results. RESULTS We show that accounting for genetic variation using a modified reference genome or a de novo assembled genome can alter histone H3K4me1 and H3K27ac ChIP-seq peak calls either by creating new personal peaks or by the loss of reference peaks. Using permissive cutoffs, modified reference genomes are found to alter approximately 1% of peak calls while de novo assembled genomes alter up to 5% of peaks. We also show statistically significant differences in the amount of reads observed in regions associated with the new, altered, and unchanged peaks. We report that short insertions and deletions (indels), followed by single nucleotide variants (SNVs), have the highest probability of modifying peak calls. We show that using a graph personalized genome represents a reasonable compromise between modified reference genomes and de novo assembled genomes. We demonstrate that altered peaks have a genomic distribution typical of other peaks. CONCLUSIONS Analyzing epigenomic datasets with personalized and graph genomes allows the recovery of new peaks enriched for indels and SNVs. These altered peaks are more likely to differ between individuals and, as such, could be relevant in the study of various human phenotypes.
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Affiliation(s)
| | - Tony Kwan
- Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambdridge, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambdridge, UK
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambdridge, UK
| | - Tomi Pastinen
- Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
- Center for Pediatric Genomic Medicine, Kansas City, MO, USA
| | - Guillaume Bourque
- Human Genetics, McGill University, Montreal, QC, Canada.
- McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada.
- Canadian Centre for Computational Genomics, Montreal, QC, Canada.
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan.
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17
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Ramírez-Plascencia HHF, Gutiérrez-Angulo M, Suárez-Villanueva AS, Peregrina-Sandoval J, Ayala-Madrigal MDLL. Variación somática intraindividual del polimorfismo rs669 del gen A2M en pacientes con cáncer colorrectal. REVISTA DE LA FACULTAD DE MEDICINA 2020. [DOI: 10.15446/revfacmed.v68n1.79864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La variación somática intraindividual (VSI) se describe como la diferencia genética entre los tejidos de un mismo individuo. La VSI se incrementa conforme avanza la edad y se asocia con alteraciones neurológicas, hematológicas e inmunes y, de manera especial, con cáncer, aunque puede no manifestar un fenotipo definido.1Para analizar la posible VSI en pacientes mexicanos con cáncer colorrectal (CCR), Yang et al.2 estudiaron el polimorfismo rs669 (c.2998 A>G, p.Ile1000Val) del gen A2M que codifica para la proteína alfa-2 macroglobulina, una inhibidora de proteasas involucrada en la progresión y proliferación del tumor. Esta variante se localiza cerca de un sitio tioéster, necesario para la función inhibidora de la proteína.
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18
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Narisu N, Rothwell R, Vrtačnik P, Rodríguez S, Didion J, Zöllner S, Erdos MR, Collins FS, Eriksson M. Analysis of somatic mutations identifies signs of selection during in vitro aging of primary dermal fibroblasts. Aging Cell 2019; 18:e13010. [PMID: 31385397 PMCID: PMC6826141 DOI: 10.1111/acel.13010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 06/20/2019] [Accepted: 06/30/2019] [Indexed: 12/13/2022] Open
Abstract
Somatic mutations are critical for cancer development and may play a role in age-related functional decline. Here, we used deep sequencing to analyze the prevalence of somatic mutations during in vitro cell aging. Primary dermal fibroblasts from healthy subjects of young and advanced age, from Hutchinson-Gilford progeria syndrome and from xeroderma pigmentosum complementation groups A and C, were first restricted in number and then expanded in vitro. DNA was obtained from cells pre- and post-expansion and sequenced at high depth (1656× mean coverage), over a cumulative 290 kb target region, including the exons of 44 aging-related genes. Allele frequencies of 58 somatic mutations differed between the pre- and post-cell culture expansion passages. Mathematical modeling revealed that the frequency change of three of the 58 mutations was unlikely to be explained by genetic drift alone, indicative of positive selection. Two of these three mutations, CDKN2A c.53C>T (T18M) and ERCC8 c.*772T>A, were identified in cells from a patient with XPA. The allele frequency of the CDKN2A mutation increased from 0% to 55.3% with increasing cell culture passage. The third mutation, BRCA2 c.6222C>T (H2074H), was identified in a sample from a healthy individual of advanced age. However, further validation of the three mutations suggests that other unmeasured variants probably provide the selective advantage in these cells. Our results reinforce the notions that somatic mutations occur during aging and that some are under positive selection, supporting the model of increased tissue heterogeneity with increased age.
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Affiliation(s)
- Narisu Narisu
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | | | - Peter Vrtačnik
- Department of Biosciences and Nutrition, Center for Innovative MedicineKarolinska InstitutetHuddingeSweden
| | - Sofía Rodríguez
- Department of Biosciences and Nutrition, Center for Innovative MedicineKarolinska InstitutetHuddingeSweden
| | - John Didion
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Sebastian Zöllner
- Department of BiostatisticsUniversity of MichiganAnn ArborMIUSA
- Department of PsychiatryUniversity of MichiganAnn ArborMIUSA
| | - Michael R. Erdos
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Francis S. Collins
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Maria Eriksson
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
- Department of Biosciences and Nutrition, Center for Innovative MedicineKarolinska InstitutetHuddingeSweden
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19
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Innan H, Veitia R, Govindaraju DR. Genetic and epigenetic Muller's ratchet as a mechanism of frailty and morbidity during aging: a demographic genetic model. Hum Genet 2019; 139:409-420. [PMID: 31713020 DOI: 10.1007/s00439-019-02067-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022]
Abstract
Mutation accumulation has been proposed as a cause of senescence. During this process, age-related genetic and epigenetic mutations steadily accumulate. Cascading deleterious effects of mutations might initiate a steady "accumulation of deficits" in cells, despite the existence of repair mechanisms, leading to cellular senescence and functional decline of tissues and organs, which ultimately manifest as frailty and disease. Here, we investigate several of these aspects in differentiating cell populations through modeling and simulation using the Moran birth-death (demographic) process, under several scenarios of mutation accumulation. Deleterious mutations seem to rapidly accumulate particularly early in the course of life, during which the rate of cell division is high, thereby exerting a greater effect on subsequent cellular senescence. Our results are compatible with the principle of the Muller's ratchet taking place in asexually reproducing organisms. The ratchet speed in a given tissue depends on the size of the cell population, mutation rate and the impact of such mutations on cell phenotypes. It varies substantially among cells in different tissues and organs due to heterogeneity in relation to cell and organ-specific demographic features. Ratchet accelerates particularly after middle age, resulting in a synergistic fitness decay at the level of cell populations. We extend Fisher's average excess concept and rank order scale to interpret differential phenotypic effects of the increase of the mutation load among cell populations within a given tissue. We postulate that classical evolutionary genetic models can explain, at least in part, the origins of frailty, subclinical conditions, morbidity and the health consequences of senescence.
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Affiliation(s)
- Hideki Innan
- Graduate University for Advanced Studies, Hayama, Kanagawa, 240-0193, Japan.
| | - Reiner Veitia
- Institute Jacques Monod, Paris, France.,Universite Paris Diderot, Paris, France
| | - Diddahally R Govindaraju
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA. .,The Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY, 10460, USA.
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20
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Brazilian forensic casework analysis through MPS applications: Statistical weight-of-evidence and biological nature of criminal samples as an influence factor in quality metrics. Forensic Sci Int 2019; 303:109938. [DOI: 10.1016/j.forsciint.2019.109938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/22/2019] [Indexed: 12/18/2022]
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21
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Heitzer E, Haque IS, Roberts CES, Speicher MR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat Rev Genet 2019; 20:71-88. [PMID: 30410101 DOI: 10.1038/s41576-018-0071-5] [Citation(s) in RCA: 787] [Impact Index Per Article: 157.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Precision oncology seeks to leverage molecular information about cancer to improve patient outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by constraints on sampling frequency and their incomplete representation of the entire tumour bulk. Now, attention is turning to minimally invasive liquid biopsies, which enable analysis of tumour components (including circulating tumour cells and circulating tumour DNA) in bodily fluids such as blood. The potential of liquid biopsies is highlighted by studies that show they can track the evolutionary dynamics and heterogeneity of tumours and can detect very early emergence of therapy resistance, residual disease and recurrence. However, the analytical validity and clinical utility of liquid biopsies must be rigorously demonstrated before this potential can be realized.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria. .,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | | | | | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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22
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Ferris E, Abegglen LM, Schiffman JD, Gregg C. Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance. Cell Rep 2019. [PMID: 29514101 PMCID: PMC6294302 DOI: 10.1016/j.celrep.2018.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genomewide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat, and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ~33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched near elephant DNA damage response genes. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi anemia complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species.
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Affiliation(s)
- Elliott Ferris
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Lisa M Abegglen
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84132-3401, USA; Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Joshua D Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84132-3401, USA; Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Christopher Gregg
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT 84132-3401, USA; New York Stem Cell Foundation, New York, NY, USA.
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23
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Bowman RL, Busque L, Levine RL. Clonal Hematopoiesis and Evolution to Hematopoietic Malignancies. Cell Stem Cell 2019; 22:157-170. [PMID: 29395053 DOI: 10.1016/j.stem.2018.01.011] [Citation(s) in RCA: 300] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Clonal hematopoiesis (CH) broadly describes the expansion of a clonal population of blood cells with one or more somatic mutations. Individuals with CH are at greater risk for hematological malignancies, cardiovascular disease, and increased mortality from non-hematological cancers. Understanding the causes of CH and how these mutant cells interact with cells of other tissues will provide critical insights into preleukemic development, stem cell biology, host-immune interactions, and cancer evolution. Here we discuss the clinical manifestations of CH, mechanisms contributing to its development, the role of CH in clonal evolution toward leukemia, and the contribution of CH to non-hematological disease states.
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Affiliation(s)
- Robert L Bowman
- Human Oncology and Pathogenesis Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lambert Busque
- Research Centre, Hôpital Maisonneuve-Rosemont, Université de Montréal, Montréal, QC, Canada
| | - Ross L Levine
- Human Oncology and Pathogenesis Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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24
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Liu R, Mignardi M, Jones R, Enge M, Kim SK, Quake SR, Zou J. Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas. Sci Rep 2019; 9:5592. [PMID: 30944357 PMCID: PMC6447534 DOI: 10.1038/s41598-019-41951-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/21/2019] [Indexed: 12/20/2022] Open
Abstract
Recently high-throughput image-based transcriptomic methods were developed and enabled researchers to spatially resolve gene expression variation at the molecular level for the first time. In this work, we develop a general analysis tool to quantitatively study the spatial correlations of gene expression in fixed tissue sections. As an illustration, we analyze the spatial distribution of single mRNA molecules measured by in situ sequencing on human fetal pancreas at three developmental time points–80, 87 and 117 days post-fertilization. We develop a density profile-based method to capture the spatial relationship between gene expression and other morphological features of the tissue sample such as position of nuclei and endocrine cells of the pancreas. In addition, we build a statistical model to characterize correlations in the spatial distribution of the expression level among different genes. This model enables us to infer the inhibitory and clustering effects throughout different time points. Our analysis framework is applicable to a wide variety of spatially-resolved transcriptomic data to derive biological insights.
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Affiliation(s)
- Ruishan Liu
- Department of Electrical Engineering, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA
| | - Marco Mignardi
- Department of Bioengineering and Applied Physics, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA. .,Department of Information Technology, Uppsala University, Lgerhyddsvgen 2, Uppsala, SE-751 05, Sweden. .,Chan-Zuckerberg Biohub, 499 Illinois St., San Francisco, CA, 94158, USA.
| | - Robert Jones
- Department of Bioengineering and Applied Physics, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA
| | - Martin Enge
- Department of Bioengineering and Applied Physics, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Stephen R Quake
- Department of Information Technology, Uppsala University, Lgerhyddsvgen 2, Uppsala, SE-751 05, Sweden.,Chan-Zuckerberg Biohub, 499 Illinois St., San Francisco, CA, 94158, USA
| | - James Zou
- Department of Biomedical Data Science, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA. .,Chan-Zuckerberg Biohub, 499 Illinois St., San Francisco, CA, 94158, USA.
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25
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Approaches and Methods for Variant Analysis in the Genome of a Single Cell. HEALTHY AGEING AND LONGEVITY 2019. [DOI: 10.1007/978-3-030-24970-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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26
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Nishioka M, Bundo M, Iwamoto K, Kato T. Somatic mutations in the human brain: implications for psychiatric research. Mol Psychiatry 2019; 24:839-856. [PMID: 30087451 PMCID: PMC6756205 DOI: 10.1038/s41380-018-0129-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/27/2018] [Accepted: 05/25/2018] [Indexed: 01/18/2023]
Abstract
Psychiatric disorders such as schizophrenia and bipolar disorder are caused by complex gene-environment interactions. While recent advances in genomic technologies have enabled the identification of several risk variants for psychiatric conditions, including single-nucleotide variants and copy-number variations, these factors can explain only a portion of the liability to these disorders. Although non-inherited factors had previously been attributed to environmental causes, recent genomic analyses have demonstrated that de novo mutations are among the main non-inherited risk factors for several psychiatric conditions. Somatic mutations in the brain may also explain how stochastic developmental events and environmental insults confer risk for a psychiatric disorder following fertilization. Here, we review evidence regarding somatic mutations in the brains of individuals with and without neuropsychiatric diseases. We further discuss the potential biological mechanisms underlying somatic mutations in the brain as well as the technical issues associated with the detection of somatic mutations in psychiatric research.
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Affiliation(s)
- Masaki Nishioka
- 0000 0001 2151 536Xgrid.26999.3dDivision for Counseling and Support, The University of Tokyo, Tokyo, Japan
| | - Miki Bundo
- 0000 0001 0660 6749grid.274841.cDepartment of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan ,0000 0004 1754 9200grid.419082.6PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama, Japan.
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27
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Zhang D, Osborne JM, Abu-Bonsrah KD, Cheeseman BL, Landman KA, Jurkowicz B, Newgreen DF. Stochastic clonal expansion of “superstars” enhances the reserve capacity of enteric nervous system precursor cells. Dev Biol 2018; 444 Suppl 1:S287-S296. [DOI: 10.1016/j.ydbio.2018.01.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 10/18/2022]
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28
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Bazrgar M, Gourabi H, Karimpour-Fard A, Boroujeni PB, Anisi K, Movaghar B, Valojerdi MR. Origins of Intraindividual Genetic Variation in Human Fetuses. Reprod Sci 2018; 26:1139-1145. [PMID: 30453833 DOI: 10.1177/1933719118808919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Intraindividual copy number variation (CNV) origin is largely unknown. They might be due to aging and/or common genome instability at the preimplantation stage while contribution of preimplantation in human intraindividual CNVs occurrence is unknown. To address this question, we investigated mosaicism and its origin in the fetuses of natural conception. METHODS We studied normal fetuses following therapeutic abortion due to maternal indications. We analyzed the genome of 22 tissues of each fetus by array comparative genomic hybridization for intraindividual CNVs. Each tissue was studied in 2 microarray experiments; the reciprocal aberrations larger than 40 Kb, identified by comparing tissues of each fetus, were subsequently validated using quantitative polymerase chain reaction. RESULTS Through intraindividual comparison, frequency of reciprocal events varied from 2 to 9. According to the distribution pattern of the frequent CNV in derivatives of different germ layers, we found that its origin is early development including preimplantation, whereas CNVs with low frequency have occurred in later stages. Shared CNVs in both fetuses were belonged to thymus and related to the functional role of genes located in these CNVs. CONCLUSIONS The origin of some of fetal CNVs is preimplantation stage. Each organ might inherit CNVs with an unpredictable pattern due to the extensive cell mixing/migration in embryonic development.
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Affiliation(s)
- Masood Bazrgar
- 1 Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, Tehran, Iran
- authors share the first authorship for this article
| | - Hamid Gourabi
- 1 Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, Tehran, Iran
- authors share the first authorship for this article
| | - Anis Karimpour-Fard
- 2 Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Parnaz Borjian Boroujeni
- 1 Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, Tehran, Iran
| | - Khadije Anisi
- 1 Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, Tehran, Iran
| | - Bahar Movaghar
- 3 Department of Embryology, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Mojtaba Rezazadeh Valojerdi
- 3 Department of Embryology, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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29
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Algady W, Louzada S, Carpenter D, Brajer P, Färnert A, Rooth I, Ngasala B, Yang F, Shaw MA, Hollox EJ. The Malaria-Protective Human Glycophorin Structural Variant DUP4 Shows Somatic Mosaicism and Association with Hemoglobin Levels. Am J Hum Genet 2018; 103:769-776. [PMID: 30388403 PMCID: PMC6218809 DOI: 10.1016/j.ajhg.2018.10.008] [Citation(s) in RCA: 18] [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: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 01/23/2023] Open
Abstract
Glycophorin A and glycophorin B are red blood cell surface proteins and are both receptors for the parasite Plasmodium falciparum, which is the principal cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that carries extra copies of a glycophorin A-glycophorin B fusion gene and has a dramatic effect on malaria risk by reducing the risk of severe malaria by up to 40%. Using fiber-FISH and Illumina sequencing, we validate the structural arrangement of the glycophorin locus in the DUP4 variant and reveal somatic variation in copy number of the glycophorin B-glycophorin A fusion gene. By developing a simple, specific, PCR-based assay for DUP4, we show that the DUP4 variant reaches a frequency of 13% in the population of a malaria-endemic village in south-eastern Tanzania. We genotype a substantial proportion of that village and demonstrate an association of DUP4 genotype with hemoglobin levels, a phenotype related to malaria, using a family-based association test. Taken together, we show that DUP4 is a complex structural variant that may be susceptible to somatic variation and show that DUP4 is associated with a malarial-related phenotype in a longitudinally followed population.
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Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Sandra Louzada
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Danielle Carpenter
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Paulina Brajer
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Ingegerd Rooth
- Nyamisati Malaria Research, Rufiji, National Institute for Medical Research, Dar-es-Salaam, Tanzania
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania; Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala Universitet, 75185 Uppsala, Sweden
| | - Fengtang Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds LS9 7TF, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
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30
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Komkov AY, Minervina AA, Nugmanov GA, Saliutina MV, Khodosevich KV, Lebedev YB, Mamedov IZ. An advanced enrichment method for rare somatic retroelement insertions sequencing. Mob DNA 2018; 9:31. [PMID: 30450130 PMCID: PMC6208084 DOI: 10.1186/s13100-018-0136-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/15/2018] [Indexed: 12/18/2022] Open
Abstract
Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells. Electronic supplementary material The online version of this article (10.1186/s13100-018-0136-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Y Komkov
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia.,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela str. 1, Moscow, 117997 Russia
| | - Anastasia A Minervina
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia
| | - Gaiaz A Nugmanov
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia
| | - Mariia V Saliutina
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia
| | - Konstantin V Khodosevich
- 3Biotech Research and Innovation Centre, Copenhagen University, Ole Maaløes Vej 5, Copenhagen, 2200 Denmark
| | - Yuri B Lebedev
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia
| | - Ilgar Z Mamedov
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia.,4Pirogov Russian National Research Medical University, Ostrovitianov str. 1, Moscow, 117997 Russia
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31
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Watahiki M, Trewavas A. Systems, variation, individuality and plant hormones. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 146:3-22. [PMID: 30312622 DOI: 10.1016/j.pbiomolbio.2018.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/06/2018] [Indexed: 02/02/2023]
Abstract
Inter-individual variation in plants and particularly in hormone content, figures strongly in evolution and behaviour. Homo sapiens and Arabidopsis exhibit similar and substantial phenotypic and molecular variation. Whereas there is a very substantial degree of hormone variation in mankind, reports of inter-individual variation in plant hormone content are virtually absent but are likely to be as large if not larger than that in mankind. Reasons for this absence are discussed. Using an example of inter-individual variation in ethylene content in ripening, the article shows how biological time is compressed by hormones. It further resolves an old issue of very wide hormone dose response that result directly from negative regulation in hormone (and light) transduction. Negative regulation is used because of inter-individual variability in hormone synthesis, receptors and ancillary proteins, a consequence of substantial genomic and environmental variation. Somatic mosaics have been reported for several plant tissues and these too contribute to tissue variation and wide variation in hormone response. The article concludes by examining what variation exists in gravitropic responses. There are multiple sensing systems of gravity vectors and multiple routes towards curvature. These are an aspect of the need for reliability in both inter-individual variation and unpredictable environments. Plant hormone inter-individuality is a new area for research and is likely to change appreciation of the mechanisms that underpin individual behaviour.
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Affiliation(s)
- Masaaki Watahiki
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Anthony Trewavas
- Institute of Plant Molecular Science, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3 JH, Scotland, United Kingdom.
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32
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Hehir-Kwa JY, Tops BBJ, Kemmeren P. The clinical implementation of copy number detection in the age of next-generation sequencing. Expert Rev Mol Diagn 2018; 18:907-915. [PMID: 30221560 DOI: 10.1080/14737159.2018.1523723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The role of copy number variants (CNVs) in disease is now well established. In parallel NGS technologies, such as long-read technologies, there is continual development and data analysis methods continue to be refined. Clinical exome sequencing data is now a reality for many diagnostic laboratories in both congenital genetics and oncology. This provides the ability to detect and report both SNVs and structural variants, including CNVs, using a single assay for a wide range of patient cohorts. Areas covered: Currently, whole-genome sequencing is mainly restricted to research applications and clinical utility studies. Furthermore, detecting the full-size spectrum of CNVs as well as somatic events remains difficult for both exome and whole-genome sequencing. As a result, the full extent of genomic variants in an individual's genome is still largely unknown. Recently, new sequencing technologies have been introduced which maintain the long-range genomic context, aiding the detection of CNVs and structural variants. Expert commentary: The development of long-read sequencing promises to resolve many CNV and SV detection issues but is yet to become established. The current challenge for clinical CNV detection is how to fully exploit all the data which is generated by high throughput sequencing technologies.
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Affiliation(s)
- Jayne Y Hehir-Kwa
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Bastiaan B J Tops
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Patrick Kemmeren
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
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33
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Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Improved molecular karyotyping in glioblastoma. Mutat Res 2018; 811:16-26. [PMID: 30055482 DOI: 10.1016/j.mrfmmm.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
Uneven replication creates artifacts during whole genome amplification (WGA) that confound molecular karyotype assignment in single cells. Here, we present an improved WGA recipe that increased coverage and detection of copy number variants (CNVs) in single cells. We examined serial resections of glioblastoma (GBM) tumor from the same patient and found low-abundance clones containing CNVs in clinically relevant loci that were not observable using bulk DNA sequencing. We discovered extensive genomic variability in this class of tumor and provide a practical approach for investigating somatic mosaicism.
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Affiliation(s)
- Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Matt Wolpert
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Mark Haakenson
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Maria-Beatriz Lopes
- Department of Pathology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - David Schiff
- Department of Neurology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - James Hicks
- Michelson Center, University of Southern California, Los Angeles, CA, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Justin Loe
- Full Genomes Corp, Inc., Rockville, MD, United States
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Brain Immunology and Glia, University of Virginia, School of Medicine, Charlottesville, VA, United States.
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34
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Mokretar K, Pease D, Taanman JW, Soenmez A, Ejaz A, Lashley T, Ling H, Gentleman S, Houlden H, Holton JL, Schapira AHV, Nacheva E, Proukakis C. Somatic copy number gains of α-synuclein (SNCA) in Parkinson’s disease and multiple system atrophy brains. Brain 2018; 141:2419-2431. [DOI: 10.1093/brain/awy157] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/16/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Katya Mokretar
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
- Department of Academic Haematology, University College London, UK
| | - Daniel Pease
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Jan-Willem Taanman
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Aynur Soenmez
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Ayesha Ejaz
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurodegenerative diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Helen Ling
- Queen Square Brain Bank for Neurodegenerative diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurodegenerative diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Anthony H V Schapira
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | | | - Christos Proukakis
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
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35
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Nishioka M, Bundo M, Ueda J, Yoshikawa A, Nishimura F, Sasaki T, Kakiuchi C, Kasai K, Kato T, Iwamoto K. Identification of somatic mutations in monozygotic twins discordant for psychiatric disorders. NPJ SCHIZOPHRENIA 2018; 4:7. [PMID: 29654278 PMCID: PMC5899160 DOI: 10.1038/s41537-018-0049-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/05/2018] [Accepted: 03/20/2018] [Indexed: 12/30/2022]
Abstract
Monozygotic twins are assumed to have identical genomes. Based on this assumption, phenotypic discordance in monozygotic twins has been previously attributed to environmental factors. However, recent genomic studies have identified characteristic somatic mutations in monozygotic twins discordant for Darier disease, Van der Woude syndrome, and Dravet syndrome. Here, we explored somatic mutations in four pairs of monozygotic twins discordant for schizophrenia or delusional disorder. We analyzed whole exome sequence data obtained from blood samples and identified seven somatic mutations in one twin pair discordant for delusional disorder. All seven of these mutations were validated by independent amplicon sequencing, and five of them were further validated by pyrosequencing. One somatic mutation in the patient with delusional disorder showed a missense variant in ABCC9 with an allele fraction of 7.32%. Although an association between the somatic mutations and phenotypic discordance could not be established conclusively in this study, our results suggest that somatic mutations in monozygotic twins may contribute to the development of psychiatric disorders, and can serve as high-priority candidates for genetic studies. Identical twins are not always identical when it comes to psychiatric disorders—and DNA mutations that arise after birth could explain why. Researchers in Japan led by Tadafumi Kato from the RIKEN Brain Science Institute and
Kazuya Iwamoto from Kumamoto University searched for DNA differences between four pairs of identical twins discordant for schizophrenia or delusional disorder by sequencing the entire protein-coding portion of the genome from the study subjects’ blood. In one sibling pair, they found seven genetic differences, including one in the sister with the delusional disorder that altered the sequence of a protein implicated in sleep and other brain functions. The findings suggest that, alongside epigenetic and environmental differences, acquired mutations can account for discordances in psychiatric illnesses among otherwise genetically identical twins.
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Affiliation(s)
- Masaki Nishioka
- Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division for Counseling and Support, The University of Tokyo, Tokyo, Japan
| | - Miki Bundo
- Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Junko Ueda
- Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama, Japan
| | - Akane Yoshikawa
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumichika Nishimura
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Chihiro Kakiuchi
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. .,Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
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36
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Shu Z, Row S, Deng WM. Endoreplication: The Good, the Bad, and the Ugly. Trends Cell Biol 2018; 28:465-474. [PMID: 29567370 DOI: 10.1016/j.tcb.2018.02.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 01/08/2023]
Abstract
To battle adverse internal and external conditions and maintain homeostasis, diploid organisms employ various cellular processes, such as proliferation and apoptosis. In some tissues, an alternative mechanism, endoreplication, is employed toward similar goals. Endoreplication is an evolutionarily conserved cell cycle program during which cells replicate their genomes without division, resulting in polyploid cells. Importantly, endoreplication is reported to be indispensable for normal development and organ formation across various organisms, from fungi to humans. In recent years, more attention has been drawn to delineating its connections to wound healing and tumorigenesis. In this Review, we discuss mechanisms of endoreplication and polyploidization, their essential and positive roles in normal development and tissue homeostasis, and the relationship between polyploidy and cancer.
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Affiliation(s)
- Zhiqiang Shu
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Sarayu Row
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
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37
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Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science 2018; 359:550-555. [PMID: 29217587 PMCID: PMC6311130 DOI: 10.1126/science.aan8690] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/28/2017] [Indexed: 12/20/2022]
Abstract
Somatic mosaicism in the human brain may alter function of individual neurons. We analyzed genomes of single cells from the forebrains of three human fetuses (15 to 21 weeks postconception) using clonal cell populations. We detected 200 to 400 single-nucleotide variations (SNVs) per cell. SNV patterns resembled those found in cancer cell genomes, indicating a role of background mutagenesis in cancer. SNVs with a frequency of >2% in brain were also present in the spleen, revealing a pregastrulation origin. We reconstructed cell lineages for the first five postzygotic cleavages and calculated a mutation rate of ~1.3 mutations per division per cell. Later in development, during neurogenesis, the mutation spectrum shifted toward oxidative damage, and the mutation rate increased. Both neurogenesis and early embryogenesis exhibit substantially more mutagenesis than adulthood.
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Affiliation(s)
- Taejeong Bae
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Livia Tomasini
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Jessica Mariani
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Bo Zhou
- Departments of Psychiatry and Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Tanmoy Roychowdhury
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel Franjic
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Mihovil Pletikos
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Reenal Pattni
- Departments of Psychiatry and Genetics, Stanford University, Palo Alto, CA 94305, USA
| | | | | | | | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
- Yale Kavli Institute for Neuroscience, New Haven, CT 06520, USA
| | - Alexander E Urban
- Departments of Psychiatry and Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520, USA.
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
- Yale Kavli Institute for Neuroscience, New Haven, CT 06520, USA
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38
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Abstract
DNA mutations are inevitable. Despite proficient DNA repair mechanisms, somatic cells accumulate mutations during development and aging, generating cells with different genotypes within the same individual, a phenomenon known as somatic mosaicism. While the existence of somatic mosaicism has long been recognized, in the last five years, advances in sequencing have provided unprecedented resolution to characterize the extent and nature of somatic genetic variation. Collectively, these new studies are revealing a previously uncharacterized aging phenotype: the accumulation of clones with cancer driver mutations. Here, we summarize the most recent findings, which converge in the novel notion that cancer-associated mutations are prevalent in normal tissue and accumulate with aging.
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Affiliation(s)
- Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott R. Kennedy
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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39
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Lessard S, Francioli L, Alfoldi J, Tardif JC, Ellinor PT, MacArthur DG, Lettre G, Orkin SH, Canver MC. Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci. Proc Natl Acad Sci U S A 2017; 114:E11257-E11266. [PMID: 29229813 PMCID: PMC5748207 DOI: 10.1073/pnas.1714640114] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The CRISPR-Cas9 nuclease system holds enormous potential for therapeutic genome editing of a wide spectrum of diseases. Large efforts have been made to further understanding of on- and off-target activity to assist the design of CRISPR-based therapies with optimized efficacy and safety. However, current efforts have largely focused on the reference genome or the genome of cell lines to evaluate guide RNA (gRNA) efficiency, safety, and toxicity. Here, we examine the effect of human genetic variation on both on- and off-target specificity. Specifically, we utilize 7,444 whole-genome sequences to examine the effect of variants on the targeting specificity of ∼3,000 gRNAs across 30 therapeutically implicated loci. We demonstrate that human genetic variation can alter the off-target landscape genome-wide including creating and destroying protospacer adjacent motifs (PAMs). Furthermore, single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) can result in altered on-target sites and novel potent off-target sites, which can predispose patients to treatment failure and adverse effects, respectively; however, these events are rare. Taken together, these data highlight the importance of considering individual genomes for therapeutic genome-editing applications for the design and evaluation of CRISPR-based therapies to minimize risk of treatment failure and/or adverse outcomes.
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Affiliation(s)
- Samuel Lessard
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Laurent Francioli
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Jessica Alfoldi
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Jean-Claude Tardif
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Guillaume Lettre
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115;
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Boston, MA 02115
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115;
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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40
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Stranger BE, Brigham LE, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber WF, Lonsdale JT, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas JA, Walters G, Washington M, Wheeler J, Bridge J, Foster BA, Gillard BM, Karasik E, Kumar R, Miklos M, Moser MT, Jewell SD, Montroy RG, Rohrer DC, Valley D, Davis DA, Mash DC, Gould SE, Guan P, Koester S, Little AR, Martin C, Moore HM, Rao A, Struewing JP, Volpi S, Hansen KD, Hickey PF, Rizzardi LF, Hou L, Liu Y, Molinie B, Park Y, Rinaldi N, Wang LB, Van Wittenberghe N, Claussnitzer M, Gelfand ET, Li Q, Linder S, Smith KS, Tsang EK, Demanelis K, Doherty JA, Jasmine F, Kibriya MG, Jiang L, Lin S, Wang M, Jian R, Li X, Chan J, Bates D, Diegel M, Halow J, Haugen E, Johnson A, Kaul R, Lee K, Maurano MT, Nelson J, Neri FJ, Sandstrom R, Fernando MS, Linke C, Oliva M, Skol A, Wu F, Akey JM, Feinberg AP, Li JB, Pierce BL, Stamatoyannopoulos JA, Tang H, Ardlie KG, Kellis M, Snyder MP, Montgomery SB. Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. Nat Genet 2017; 49:1664-1670. [PMID: 29019975 PMCID: PMC6636856 DOI: 10.1038/ng.3969] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic variants have been associated with myriad molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and diseases. Identifying any particular genetic variant's cascade of effects, from molecule to individual, requires assaying multiple layers of molecular complexity. We introduce the Enhancing GTEx (eGTEx) project that extends the GTEx project to combine gene expression with additional intermediate molecular measurements on the same tissues to provide a resource for studying how genetic differences cascade through molecular phenotypes to impact human health.
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Affiliation(s)
- Barbara E. Stranger
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
- Center for Data Intensive Science, The University of Chicago, Chicago, IL 60637, USA
| | - Lori E. Brigham
- Washington Regional Transplant Community, Annandale, VA 22003, USA
| | - Richard Hasz
- Gift of Life Donor Program, Philadelphia, PA 19103, USA
| | | | | | | | - Gene Kopen
- National Disease Research Interchange, Philadelphia, PA 19103, USA
| | | | - John T. Lonsdale
- National Disease Research Interchange, Philadelphia, PA 19103, USA
| | - Alisa McDonald
- National Disease Research Interchange, Philadelphia, PA 19103, USA
| | | | | | | | | | - Saboor Shad
- National Disease Research Interchange, Philadelphia, PA 19103, USA
| | | | | | | | - Joseph Wheeler
- Center for Organ Recovery and Education, Pittsburgh, PA 15238, USA
| | | | - Barbara A. Foster
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Bryan M. Gillard
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Ellen Karasik
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Rachna Kumar
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Mark Miklos
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Michael T. Moser
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | | | | | | | - Dana Valley
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A. Davis
- Brain Endowment Bank, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Deborah C. Mash
- Brain Endowment Bank, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sarah E. Gould
- Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD 20852, USA
| | - Ping Guan
- Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Susan Koester
- Division of Neuroscience and Basic Behavioral Science, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - A. Roger Little
- National Institute on Drug Abuse, NIH, Bethesda, MD 20892, USA
| | - Casey Martin
- Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD 20852, USA
| | - Helen M. Moore
- Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Abhi Rao
- Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jeffery P. Struewing
- Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD 20852, USA
| | - Simona Volpi
- Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD 20852, USA
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Peter F. Hickey
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lindsay F. Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lei Hou
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Yaping Liu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Benoit Molinie
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Yongjin Park
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Nicola Rinaldi
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Li B. Wang
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Nicholas Van Wittenberghe
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Melina Claussnitzer
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Technical University Munich, 8350 Freising, Germany
| | - Ellen T. Gelfand
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sandra Linder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kevin S. Smith
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Emily K. Tsang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
| | - Kathryn Demanelis
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Jennifer A. Doherty
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G. Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shin Lin
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Meng Wang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Xiao Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joanne Chan
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Bates
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Morgan Diegel
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Jessica Halow
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Audra Johnson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Kristen Lee
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY 10016, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Fidencio J. Neri
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | | | - Marian S. Fernando
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Caroline Linke
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Meritxell Oliva
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Andrew Skol
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
- Center for Data Intensive Science, The University of Chicago, Chicago, IL 60637, USA
| | - Fan Wu
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Brandon L. Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | | | - Hua Tang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kristin G. Ardlie
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
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41
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Castellani CA, Melka MG, Gui JL, Gallo AJ, O'Reilly RL, Singh SM. Post-zygotic genomic changes in glutamate and dopamine pathway genes may explain discordance of monozygotic twins for schizophrenia. Clin Transl Med 2017; 6:43. [PMID: 29181591 PMCID: PMC5704032 DOI: 10.1186/s40169-017-0174-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/05/2017] [Indexed: 01/06/2023] Open
Abstract
Background Monozygotic twins are valuable in assessing the genetic vs environmental contribution to diseases. In the era of complete genome sequences, they allow identification of mutational mechanisms and specific genes and pathways that offer predisposition to the development of complex diseases including schizophrenia. Methods We sequenced the complete genomes of two pairs of monozygotic twins discordant for schizophrenia (MZD), including one representing a family tetrad. The family specific complete sequences have allowed identification of post zygotic mutations between MZD genomes. It allows identification of affected genes including relevant network and pathways that may account for the diseased state in pair specific patient. Results We found multiple twin specific sequence differences between co-twins that included small nucleotides [single nucleotide variants (SNV), small indels and block substitutions], copy number variations (CNVs) and structural variations. The genes affected by these changes belonged to a number of canonical pathways, the most prominent ones are implicated in schizophrenia and related disorders. Although these changes were found in both twins, they were more frequent in the affected twin in both pairs. Two specific pathway defects, glutamate receptor signaling and dopamine feedback in cAMP signaling pathways, were uniquely affected in the two patients representing two unrelated families. Conclusions We have identified genome-wide post zygotic mutations in two MZD pairs affected with schizophrenia. It has allowed us to use the threshold model and propose the most likely cause of this disease in the two patients studied. The results support the proposition that each schizophrenia patient may be unique and heterogeneous somatic de novo events may contribute to schizophrenia threshold and discordance of the disease in monozygotic twins. Electronic supplementary material The online version of this article (10.1186/s40169-017-0174-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C A Castellani
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - M G Melka
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - J L Gui
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - A J Gallo
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - R L O'Reilly
- Department of Psychiatry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - S M Singh
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada.,Department of Psychiatry, The University of Western Ontario, London, ON, N6A 5B7, Canada
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42
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The potential of liquid biopsies for the early detection of cancer. NPJ Precis Oncol 2017; 1:36. [PMID: 29872715 PMCID: PMC5871864 DOI: 10.1038/s41698-017-0039-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023] Open
Abstract
Precision medicine refers to the choosing of targeted therapies based on genetic data. Due to the increasing availability of data from large-scale tumor genome sequencing projects, genome-driven oncology may have enormous potential to change the clinical management of patients with cancer. To this end, components of tumors, which are shed into the circulation, i.e., circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), or extracellular vesicles, are increasingly being used for monitoring tumor genomes. A growing number of publications have documented that these “liquid biopsies” are informative regarding response to given therapies, are capable of detecting relapse with lead time compared to standard measures, and reveal mechanisms of resistance. However, the majority of published studies relate to advanced tumor stages and the use of liquid biopsies for detection of very early malignant disease stages is less well documented. In early disease stages, strategies for analysis are in principle relatively similar to advanced stages. However, at these early stages, several factors pose particular difficulties and challenges, including the lower frequency and volume of aberrations, potentially confounding phenomena such as clonal expansions of non-tumorous tissues or the accumulation of cancer-associated mutations with age, and the incomplete insight into driver alterations. Here we discuss biology, technical complexities and clinical significance for early cancer detection and their impact on precision oncology.
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Chen A, Lynch KB, Ren J, Jia Z, Yang Y, Lu JJ, Liu S. Tunable Electroosmosis-Based Femto-Liter Pipette: A Promising Tool toward Living-Cell Surgery. Anal Chem 2017; 89:10806-10812. [DOI: 10.1021/acs.analchem.7b02132] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Apeng Chen
- Department
of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kyle B. Lynch
- Department
of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jiangtao Ren
- Department
of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhijian Jia
- School
of Materials and Chemical Engineering, Ningbo University of Technology, Ningbo, Zhejiang 315016, P.R. China
| | - Yu Yang
- Department
of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Joann J. Lu
- Department
of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Shaorong Liu
- Department
of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation. PLoS One 2017; 12:e0180467. [PMID: 28683077 PMCID: PMC5500342 DOI: 10.1371/journal.pone.0180467] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array "waves", and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.
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Huang AY, Zhang Z, Ye AY, Dou Y, Yan L, Yang X, Zhang Y, Wei L. MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples. Nucleic Acids Res 2017; 45:e76. [PMID: 28132024 PMCID: PMC5449543 DOI: 10.1093/nar/gkx024] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/24/2016] [Accepted: 01/26/2017] [Indexed: 02/07/2023] Open
Abstract
Genomic mosaicism arising from postzygotic mutations has long been associated with cancer and more recently with non-cancer diseases. It has also been detected in healthy individuals including healthy parents of children affected with genetic disorders, highlighting its critical role in the origin of genetic mutations. However, most existing software for the genome-wide identification of single-nucleotide mosaicisms (SNMs) requires a paired control tissue obtained from the same individual which is often unavailable for non-cancer individuals and sometimes missing in cancer studies. Here, we present MosaicHunter (http://mosaichunter.cbi.pku.edu.cn), a bioinformatics tool that can identify SNMs in whole-genome and whole-exome sequencing data of unpaired samples without matched controls using Bayesian genotypers. We evaluate the accuracy of MosaicHunter on both simulated and real data and demonstrate that it has improved performance compared with other somatic mutation callers. We further demonstrate that incorporating sequencing data of the parents can be an effective approach to significantly improve the accuracy of detecting SNMs in an individual when a matched control sample is unavailable. Finally, MosaicHunter also has a paired mode that can take advantage of matched control samples when available, making it a useful tool for detecting SNMs in both non-cancer and cancer studies.
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Affiliation(s)
- August Yue Huang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Zheng Zhang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- Peking-Tsinghua Center for Life Sciences, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Yanmei Dou
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Linlin Yan
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yuehua Zhang
- Peking University First Hospital, Peking University, Beijing 100034, People's Republic of China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science 2017; 356:356/6336/eaal1641. [PMID: 28450582 DOI: 10.1126/science.aal1641] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neuropsychiatric disorders have a complex genetic architecture. Human genetic population-based studies have identified numerous heritable sequence and structural genomic variants associated with susceptibility to neuropsychiatric disease. However, these germline variants do not fully account for disease risk. During brain development, progenitor cells undergo billions of cell divisions to generate the ~80 billion neurons in the brain. The failure to accurately repair DNA damage arising during replication, transcription, and cellular metabolism amid this dramatic cellular expansion can lead to somatic mutations. Somatic mutations that alter subsets of neuronal transcriptomes and proteomes can, in turn, affect cell proliferation and survival and lead to neurodevelopmental disorders. The long life span of individual neurons and the direct relationship between neural circuits and behavior suggest that somatic mutations in small populations of neurons can significantly affect individual neurodevelopment. The Brain Somatic Mosaicism Network has been founded to study somatic mosaicism both in neurotypical human brains and in the context of complex neuropsychiatric disorders.
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Emami NC, Leong L, Wan E, Van Blarigan EL, Cooperberg MR, Tenggara I, Carroll PR, Chan JM, Witte JS, Simko JP. Tissue Sources for Accurate Measurement of Germline DNA Genotypes in Prostate Cancer Patients Treated With Radical Prostatectomy. Prostate 2017; 77:425-434. [PMID: 27900799 PMCID: PMC5479703 DOI: 10.1002/pros.23283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/03/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Benign tissue from a tumor-containing organ is commonly the only available source for obtaining a patient's unmutated genome for use in cancer research. While it is critical to identify histologically normal tissue that is independent of the tumor lineage, few additional considerations are applied to the choice of this material for such measurements. METHODS Normal formalin-fixed, paraffin-embedded seminal vesicle, and urethral tissues, in addition to whole blood, were collected from 31 prostate cancer patients having undergone radical prostatectomy. Genotype concordance was evaluated for DNA from each tissue source in relation to whole blood. RESULTS Overall, there was a greater genotype call rate for DNA derived from urethral tissue (97.0%) in comparison with patient-matched seminal vesicle tissues (95.9%, P = 0.0015). Furthermore, with reference to patient-matched whole blood, urethral samples exhibited higher genotype concordance (94.1%) than that of seminal vesicle samples (92.5%, P = 0.035). CONCLUSIONS These findings highlight the heterogeneity between diverse sources of DNA in genotype measurement and motivate the consideration of normal tissue biases in tumor-normal analyses. Prostate 77: 425-434, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nima C. Emami
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Lancelote Leong
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Eunice Wan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Erin L. Van Blarigan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Matthew R. Cooperberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Imelda Tenggara
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Peter R. Carroll
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - June M. Chan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - John S. Witte
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Correspondence to: Jeffry P. Simko, 1825 4th St., Room M2360, San Francisco, CA 94158, 415-353-7171 (Phone), 415-353-7094 (Fax), . John S. Witte, 1450 3rd St., San Francisco, CA 94158, 415-502-6882 (Phone), 415-476-1356 (Fax),
| | - Jeffry P. Simko
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Anatomic Pathology, University of California, San Francisco, San Francisco, California
- Correspondence to: Jeffry P. Simko, 1825 4th St., Room M2360, San Francisco, CA 94158, 415-353-7171 (Phone), 415-353-7094 (Fax), . John S. Witte, 1450 3rd St., San Francisco, CA 94158, 415-502-6882 (Phone), 415-476-1356 (Fax),
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One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin. Genome Res 2017; 27:512-523. [PMID: 28235832 PMCID: PMC5378170 DOI: 10.1101/gr.215517.116] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/24/2017] [Indexed: 01/01/2023]
Abstract
Few studies have been conducted to understand post-zygotic accumulation of mutations in cells of the healthy human body. We reprogrammed 32 skin fibroblast cells from families of donors into human induced pluripotent stem cell (hiPSC) lines. The clonal nature of hiPSC lines allows a high-resolution analysis of the genomes of the founder fibroblast cells without being confounded by the artifacts of single-cell whole-genome amplification. We estimate that on average a fibroblast cell in children has 1035 mostly benign mosaic SNVs. On average, 235 SNVs could be directly confirmed in the original fibroblast population by ultradeep sequencing, down to an allele frequency (AF) of 0.1%. More sensitive droplet digital PCR experiments confirmed more SNVs as mosaic with AF as low as 0.01%, suggesting that 1035 mosaic SNVs per fibroblast cell is the true average. Similar analyses in adults revealed no significant increase in the number of SNVs per cell, suggesting that a major fraction of mosaic SNVs in fibroblasts arises during development. Mosaic SNVs were distributed uniformly across the genome and were enriched in a mutational signature previously observed in cancers and in de novo variants and which, we hypothesize, is a hallmark of normal cell proliferation. Finally, AF distribution of mosaic SNVs had distinct narrow peaks, which could be a characteristic of clonal cell selection, clonal expansion, or both. These findings reveal a large degree of somatic mosaicism in healthy human tissues, link de novo and cancer mutations to somatic mosaicism, and couple somatic mosaicism with cell proliferation.
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Sharma A, Ansari AH, Kumari R, Pandey R, Rehman R, Mehani B, Varma B, Desiraju BK, Mabalirajan U, Agrawal A, Mukhopadhyay A. Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress. F1000Res 2017; 5:2520. [PMID: 28149503 DOI: 10.12688/f1000research.9495.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2016] [Indexed: 12/11/2022] Open
Abstract
Somatic variation in DNA can cause cells to deviate from the preordained genomic path in both disease and healthy conditions. Here, using exome sequencing of paired tissue samples, we show that the normal human brain harbors somatic single base variations measuring up to 0.48% of the total variations. Interestingly, about 64% of these somatic variations in the brain are expected to lead to non-synonymous changes, and as much as 87% of these represent G:C>T:A transversion events. Further, the transversion events in the brain were mostly found in the frontal cortex, whereas the corpus callosum from the same individuals harbors the reference genotype. We found a significantly higher amount of 8-OHdG (oxidative stress marker) in the frontal cortex compared to the corpus callosum of the same subjects (p<0.01), correlating with the higher G:C>T:A transversions in the cortex. We found significant enrichment for axon guidance and related pathways for genes harbouring somatic variations. This could represent either a directed selection of genetic variations in these pathways or increased susceptibility of some loci towards oxidative stress. This study highlights that oxidative stress possibly influence single nucleotide somatic variations in normal human brain.
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Affiliation(s)
- Anchal Sharma
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Asgar Hussain Ansari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Renu Kumari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Rakhshinda Rehman
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bharati Mehani
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Binuja Varma
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bapu K Desiraju
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Ulaganathan Mabalirajan
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Anurag Agrawal
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Arijit Mukhopadhyay
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; School of Environment and Life Sciences, University of Salford, Manchester, UK
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Genomic structural variations for cardiovascular and metabolic comorbidity. Sci Rep 2017; 7:41268. [PMID: 28120895 PMCID: PMC5264603 DOI: 10.1038/srep41268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/19/2016] [Indexed: 12/19/2022] Open
Abstract
The objective of this study was to identify genes targeted by both copy number and copy-neutral changes in the right coronary arteries in the area of advanced atherosclerotic plaques and intact internal mammary arteries derived from the same individuals with comorbid coronary artery disease and metabolic syndrome. The artery samples from 10 patients were screened for genomic imbalances using array comparative genomic hybridization. Ninety high-confidence, identical copy number variations (CNVs) were detected. We also identified eight copy-neutral changes (cn-LOHs) > 1.5 Mb in paired arterial samples in 4 of 10 individuals. The frequencies of the two gains located in the 10q24.31 (ERLIN1) and 12q24.11 (UNG, ACACB) genomic regions were evaluated in 33 paired arteries and blood samples. Two patients contained the gain in 10q24.31 (ERLIN1) and one patient contained the gain in 12q24.11 (UNG, ACACB) that affected only the blood DNA. An additional two patients harboured these CNVs in both the arteries and blood. In conclusion, we discovered and confirmed a gain of the 10q24.31 (ERLIN1) and 12q24.11 (UNG, ACACB) genomic regions in patients with coronary artery disease and metabolic comorbidity. Analysis of DNA extracted from blood indicated a possible somatic origin for these CNVs.
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