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Caspar SM, Dubacher N, Kopps AM, Meienberg J, Henggeler C, Matyas G. Clinical sequencing: From raw data to diagnosis with lifetime value. Clin Genet 2019; 93:508-519. [PMID: 29206278 DOI: 10.1111/cge.13190] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022]
Abstract
High-throughput sequencing (HTS) has revolutionized genetics by enabling the detection of sequence variants at hitherto unprecedented large scale. Despite these advances, however, there are still remaining challenges in the complete coverage of targeted regions (genes, exome or genome) as well as in HTS data analysis and interpretation. Moreover, it is easy to get overwhelmed by the plethora of available methods and tools for HTS. Here, we review the step-by-step process from the generation of sequence data to molecular diagnosis of Mendelian diseases. Highlighting advantages and limitations, this review addresses the current state of (1) HTS technologies, considering targeted, whole-exome, and whole-genome sequencing on short- and long-read platforms; (2) read alignment, variant calling and interpretation; as well as (3) regulatory issues related to genetic counseling, reimbursement, and data storage.
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Affiliation(s)
- S M Caspar
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - N Dubacher
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - A M Kopps
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - J Meienberg
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - C Henggeler
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - G Matyas
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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2
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Gendrel AV, Attia M, Chen CJ, Diabangouaya P, Servant N, Barillot E, Heard E. Developmental dynamics and disease potential of random monoallelic gene expression. Dev Cell 2014; 28:366-80. [PMID: 24576422 DOI: 10.1016/j.devcel.2014.01.016] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/23/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022]
Abstract
X chromosome inactivation (XCI) and allelic exclusion of olfactory receptors or immunoglobulin loci represent classic examples of random monoallelic expression (RME). RME of some single copy genes has also been reported, but the in vivo relevance of this remains unclear. Here we identify several hundred RME genes in clonal neural progenitor cell lines derived from embryonic stem cells. RME occurs during differentiation, and, once established, the monoallelic state can be highly stable. We show that monoallelic expression also occurs in vivo, in the absence of DNA sequence polymorphism. Several of the RME genes identified play important roles in development and have been implicated in human autosomal-dominant disorders. We propose that monoallelic expression of such genes contributes to the fine-tuning of the developmental regulatory pathways they control, and, in the context of a mutation, RME can predispose to loss of function in a proportion of cells and thus contribute to disease.
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Affiliation(s)
- Anne-Valerie Gendrel
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France
| | - Mikael Attia
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France
| | - Chong-Jian Chen
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France; Bioinformatics and Computational Systems Biology of Cancer, INSERM U900, Paris 75248, France; Mines ParisTech, Fontainebleau 77300, France
| | - Patricia Diabangouaya
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France
| | - Nicolas Servant
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Bioinformatics and Computational Systems Biology of Cancer, INSERM U900, Paris 75248, France; Mines ParisTech, Fontainebleau 77300, France
| | - Emmanuel Barillot
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Bioinformatics and Computational Systems Biology of Cancer, INSERM U900, Paris 75248, France; Mines ParisTech, Fontainebleau 77300, France
| | - Edith Heard
- Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France.
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Variable allelic expression of imprinted genes in human pluripotent stem cells during differentiation into specialized cell types in vitro. Biochem Biophys Res Commun 2014; 446:493-8. [DOI: 10.1016/j.bbrc.2014.02.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 02/28/2014] [Indexed: 12/27/2022]
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4
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Masui O, Bonnet I, Le Baccon P, Brito I, Pollex T, Murphy N, Hupé P, Barillot E, Belmont AS, Heard E. Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell 2011; 145:447-58. [PMID: 21529716 DOI: 10.1016/j.cell.2011.03.032] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/23/2011] [Accepted: 03/18/2011] [Indexed: 01/08/2023]
Abstract
Random X inactivation represents a paradigm for monoallelic gene regulation during early ES cell differentiation. In mice, the choice of X chromosome to inactivate in XX cells is ensured by monoallelic regulation of Xist RNA via its antisense transcription unit Tsix/Xite. Homologous pairing events have been proposed to underlie asymmetric Tsix expression, but direct evidence has been lacking owing to their dynamic and transient nature. Here we investigate the live-cell dynamics and outcome of Tsix pairing in differentiating mouse ES cells. We find an overall increase in genome dynamics including the Xics during early differentiation. During pairing, however, Xic loci show markedly reduced movements. Upon separation, Tsix expression becomes transiently monoallelic, providing a window of opportunity for monoallelic Xist upregulation. Our findings reveal the spatiotemporal choreography of the X chromosomes during early differentiation and indicate a direct role for pairing in facilitating symmetry-breaking and monoallelic regulation of Xist during random X inactivation.
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Stoffregen EP, Donley N, Stauffer D, Smith L, Thayer MJ. An autosomal locus that controls chromosome-wide replication timing and mono-allelic expression. Hum Mol Genet 2011; 20:2366-78. [PMID: 21459774 DOI: 10.1093/hmg/ddr138] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mammalian DNA replication initiates at multiple sites along chromosomes at different times, following a temporal replication program. Homologous alleles typically replicate synchronously; however, mono-allelically expressed genes such as imprinted genes, allelically excluded genes and genes on the female X chromosome replicate asynchronously. We have used a chromosome engineering strategy to identify a human autosomal locus that controls this replication timing program in cis. We show that Cre/loxP-mediated rearrangements at a discrete locus at 6q16.1 result in delayed replication of the entire chromosome. This locus displays asynchronous replication timing that is coordinated with other mono-allelically expressed genes on chromosome 6. Characterization of this locus revealed mono-allelic expression of a large intergenic non-coding RNA, which we have named asynchronous replication and autosomal RNA on chromosome 6, ASAR6. Finally, disruption of this locus results in the activation of the previously silent alleles of linked mono-allelically expressed genes. We previously found that chromosome rearrangements involving eight different autosomes display delayed replication timing, and that cells containing chromosomes with delayed replication timing have a 30-80-fold increase in the rate at which new gross chromosomal rearrangements occurred. Taken together, these observations indicate that human autosomes contain discrete cis-acting loci that control chromosome-wide replication timing, mono-allelic expression and the stability of entire chromosomes.
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Affiliation(s)
- Eric P Stoffregen
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, 3181 S W Sam Jackson Park Road, Portland, OR 97239, USA
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Abstract
Alzheimer’s disease (AD) and Parkinson’s disease (PD) are two common neurodegenerative diseases that result in the progressive damage or death of neurons. Environmental agents have the potential to damage the developing and mature nervous system, resulting in neurodegenerative diseases. Heritable changes in gene expression that do not involve coding sequence modifications are referred to as ‘epigenetic’. These modifications include DNA methylation and downstream modification of histones. Environmental factors, including heavy metals and dietary folate intake, perturb neurodegenerative genes by epigenetic means, leading to altered gene expression and late-onset neurodegenerative diseases. Research into the genetic control of DNA methylation indicates an allelic skewing in a significant proportion of genes. This phenomenon may determine how an individual’s genetic makeup can alter the effect an environmental factor has on their risk of developing neurodegeneration. Finally, preliminary evidence using cell culture and transgenic animal models suggests that whole classes of pan-epigenetic modifiers will have significant protective effects against common neurodegenerative diseases.
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Affiliation(s)
- John BJ Kwok
- Neuroscience Research Australia, Randwick, NSW, Australia and University of New South Wales, Kensington, NSW, Australia
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Prestel M, Feller C, Becker PB. Dosage compensation and the global re-balancing of aneuploid genomes. Genome Biol 2010; 11:216. [PMID: 20804581 PMCID: PMC2945780 DOI: 10.1186/gb-2010-11-8-216] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Diploid genomes are exquisitely balanced systems of gene expression. The dosage-compensation systems that evolved along with monosomic sex chromosomes exemplify the intricacies of compensating for differences in gene copy number by transcriptional regulation.
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Affiliation(s)
- Matthias Prestel
- Adolf-Butenandt-Institute and Centre for Integrated Protein Science (CiPSM), Ludwig-Maximilians-University, Schillerstrasse 44, 80336 Munich, Germany
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Nagler A, Cytron S, Mashevich M, Korenstein-Ilan A, Avivi L. The aberrant asynchronous replication - characterizing lymphocytes of cancer patients - is erased following stem cell transplantation. BMC Cancer 2010; 10:230. [PMID: 20497575 PMCID: PMC2887401 DOI: 10.1186/1471-2407-10-230] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 05/24/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aberrations of allelic replication timing are epigenetic markers observed in peripheral blood cells of cancer patients. The aberrant markers are non-cancer-type-specific and are accompanied by increased levels of sporadic aneuploidy. The study aimed at following the epigenetic markers and aneuploidy levels in cells of patients with haematological malignancies from diagnosis to full remission, as achieved by allogeneic stem cell transplantation (alloSCT). METHODS TP53 (a tumor suppressor gene assigned to chromosome 17), AML1 (a gene assigned to chromosome 21 and involved in the leukaemia-abundant 8;21 translocation) and the pericentomeric satellite sequence of chromosome 17 (CEN17) were used for replication timing assessments. Aneuploidy was monitored by enumerating the copy numbers of chromosomes 17 and 21. Replication timing and aneuploidy were detected cytogenetically using fluorescence in situ hybridization (FISH) technology applied to phytohemagglutinin (PHA)-stimulated lymphocytes. RESULTS We show that aberrant epigenetic markers are detected in patients with hematological malignancies from the time of diagnosis through to when they are scheduled to undergo alloSCT. These aberrations are unaffected by the clinical status of the disease and are displayed both during accelerated stages as well as in remission. Yet, these markers are eradicated completely following stem cell transplantation. In contrast, the increased levels of aneuploidy (irreversible genetic alterations) displayed in blood lymphocytes at various stages of disease are not eliminated following transplantation. However, they do not elevate and remain unchanged (stable state). A demethylating anti-cancer drug, 5-azacytidine, applied in vitro to lymphocytes of patients prior to transplantation mimics the effect of transplantation: the epigenetic aberrations disappear while aneuploidy stays unchanged. CONCLUSIONS The reversible nature of the replication aberrations may serve as potential epigenetic blood markers for evaluating the success of transplant or other treatments and for long-term follow up of the patients who have overcome a hematological malignancy.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Aneuploidy
- Azacitidine/pharmacology
- Cells, Cultured
- Child
- Child, Preschool
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 21
- Core Binding Factor Alpha 2 Subunit/genetics
- DNA Modification Methylases/antagonists & inhibitors
- DNA Modification Methylases/metabolism
- DNA Replication Timing/drug effects
- Enzyme Inhibitors/pharmacology
- Epigenesis, Genetic/drug effects
- Female
- Hematologic Neoplasms/diagnosis
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/pathology
- Hematologic Neoplasms/surgery
- Humans
- In Situ Hybridization, Fluorescence
- Lymphocytes/drug effects
- Lymphocytes/pathology
- Male
- Middle Aged
- Stem Cell Transplantation
- Time Factors
- Transplantation, Homologous
- Treatment Outcome
- Tumor Suppressor Protein p53/genetics
- Young Adult
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Affiliation(s)
- Arnon Nagler
- Bone Marrow Transplantation Department, Institute of Hematology, Chaim Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Samuel Cytron
- Department of Urology, Barzilai Medical Center, affiliated to the Faculty of Health Sciences, Ben-Gurion University of The Negev, Askelon 78306, Israel
| | - Maya Mashevich
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Avital Korenstein-Ilan
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Lydia Avivi
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
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Abstract
The multifunctional zinc-finger protein CCCTC-binding factor (CTCF) is a very strong candidate for the role of coordinating the expression level of coding sequences with their three-dimensional position in the nucleus, apparently responding to a "code" in the DNA itself. Dynamic interactions between chromatin fibers in the context of nuclear architecture have been implicated in various aspects of genome functions. However, the molecular basis of these interactions still remains elusive and is a subject of intense debate. Here we discuss the nature of CTCF-DNA interactions, the CTCF-binding specificity to its binding sites and the relationship between CTCF and chromatin, and we examine data linking CTCF with gene regulation in the three-dimensional nuclear space. We discuss why these features render CTCF a very strong candidate for the role and propose a unifying model, the "CTCF code," explaining the mechanistic basis of how the information encrypted in DNA may be interpreted by CTCF into diverse nuclear functions.
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Affiliation(s)
- Rolf Ohlsson
- Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Victor Lobanenkov
- Molecular Pathology Section, Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (LIP/NIAID/NIH), Twinbrook Building, Room 1329, MSC-8152, 5640 Fisher Lane, Rockville, MD 20852, USA
| | - Elena Klenova
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
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Sandhu KS, Shi C, Sjölinder M, Zhao Z, Göndör A, Liu L, Tiwari VK, Guibert S, Emilsson L, Imreh MP, Ohlsson R. Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development. Genes Dev 2009; 23:2598-603. [PMID: 19933149 DOI: 10.1101/gad.552109] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent observations highlight that the mammalian genome extensively communicates with itself via long-range chromatin interactions. The causal link between such chromatin cross-talk and epigenetic states is, however, poorly understood. We identify here a network of physically juxtaposed regions from the entire genome with the common denominator of being genomically imprinted. Moreover, CTCF-binding sites within the H19 imprinting control region (ICR) not only determine the physical proximity among imprinted domains, but also transvect allele-specific epigenetic states, identified by replication timing patterns, to interacting, nonallelic imprinted regions during germline development. We conclude that one locus can directly or indirectly pleiotropically influence epigenetic states of multiple regions on other chromosomes with which it interacts.
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Affiliation(s)
- Kuljeet Singh Sandhu
- Department of Development and Genetics, Evolution Biology Centre, Uppsala University, S-752 36 Uppsala, Sweden
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Abstract
The genome forms extensive and dynamic physical interactions with itself in the form of chromosome loops and bridges, thus exploring the three-dimensional space of the nucleus. It is now possible to examine these interactions at the molecular level, and we have gained glimpses of their functional implications. Chromosomal interactions can contribute to the silencing and activation of genes within the three-dimensional context of the nuclear architecture. Technical advances in detecting these interactions contribute to our understanding of the functional organization of the genome, as well as its adaptive plasticity in response to environmental changes during development and disease.
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Affiliation(s)
- Anita Göndör
- Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden.
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Happle R. Monoallelic expression on autosomes may explain an unusual heritable form of pigmentary mosaicism: a historical case revisited. Clin Exp Dermatol 2009; 34:834-7. [DOI: 10.1111/j.1365-2230.2009.03543.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Yin S, Wang P, Deng W, Zheng H, Hu L, Hurst LD, Kong X. Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals. Genome Biol 2009; 10:R74. [PMID: 19594925 PMCID: PMC2728528 DOI: 10.1186/gb-2009-10-7-r74] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 06/13/2009] [Accepted: 07/13/2009] [Indexed: 01/14/2023] Open
Abstract
Comparison of gene expression variation in autosomal and X-linked genes reveals that high transcriptional noise is not a necessary consequence of haploid expression. Background Theory predicts that haploid-expressed genes should have noisier expression than comparable diploid-expressed ones with the same expression level. However, in mammals there are several classes of gene that are monoallelically expressed, including X-linked genes, imprinted genes and some other autosomal genes. Does it follow that the evolution of X chromosomes in eukaryotes comes at the cost of increased transcriptional noise in the heterogametic sex? Moreover, is escaping X-inactivation in mammalian females associated with an increase in transcriptional variation? To address these questions, we analyze gene expression variation between replicate samples of diverse mammalian cell lines in steady-state using microarray data. Results We observe that transcriptional variation of X-linked genes is no different to that of autosomal genes both before and after control for transcript abundance. By contrast, autosomal genes subject to allelic exclusion do have unusually high noise levels even allowing for their low transcript abundance. The prior theory we suggest was insufficient, at least as regards X-chromosomes, as it failed to appreciate the regulatory complexity of gene expression, not least the effects of genomic neighborhood. Conclusions These results suggest that high noise is not a necessary consequence of haploid expression and emphasize the primacy of expression level as a determinant of noise. The latter has consequences for understanding the etiology of haplo-insufficiency and the evolution of gene expression levels. Given the coupling between expression level and noise on the X-chromosome, we suggest that part of the selective advantage of dosage compensation is noise abatement of X-linked genes.
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Affiliation(s)
- Shanye Yin
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, South Chongqing Road, Shanghai 200025, PR China
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Dotan ZA, Dotan A, Ramon J, Avivi L. Aberrant allele-specific replication, independent of parental origin, in blood cells of cancer patients. BMC Cancer 2008; 8:390. [PMID: 19109880 PMCID: PMC2629776 DOI: 10.1186/1471-2407-8-390] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 12/25/2008] [Indexed: 11/10/2022] Open
Abstract
Background Allelic counterparts of biallelically expressed genes display an epigenetic symmetry normally manifested by synchronous replication, different from genes subjected to monoallelic expression, which normally are characterized by an asynchronous mode of replication (well exemplified by the SNRPN imprinted locus). Malignancy was documented to be associated with gross modifications in the inherent replication-timing coordination between allelic counterparts of imprinted genes as well as of biallelically expressed loci. The cancer-related allelic replication timing aberrations are non-disease specific and appear in peripheral blood cells of cancer patients, including those with solid tumors. As such they offer potential blood markers for non-invasive cancer test. The present study was aimed to gain some insight into the mechanism leading to the replication timing alterations of genes in blood lymphocytes of cancer patients. Methods Peripheral blood samples derived from patients with prostate cancer were chosen to represent the cancerous status, and samples taken from patients with no cancer but with benign prostate hyperplasia were used to portray the normal status. Fluorescence In Situ Hybridization (FISH) replication assay, applied to phytohemagglutinin (PHA)-stimulated blood lymphocytes, was used to evaluate the temporal order (either synchronous or asynchronous) of genes in the patients' cells. Results We demonstrated that: (i) the aberrant epigenetic profile, as delineated by the cancer status, is a reversible modification, evidenced by our ability to restore the normal patterns of replication in three unrelated loci (CEN15, SNRPN and RB1) by introducing an archetypical demethylating agent, 5-azacytidine; (ii) following the rehabilitating effect of demethylation, an imprinted gene (SNRPN) retains its original parental imprint; and (iii) the choice of an allele between early or late replication in the aberrant asynchronous replication, delineated by the cancer status, is not random but is independent of the parental origin. Conclusion The non-disease specific aberrant epigenetic profile displayed in peripheral blood cells of patients with a solid tumour (unlike genetic aberrations) can be reversed, by an epigenetic drug applied in vitro, to the normal. It appears that the cancerous status differentiates between two allelic counterparts in a non-random manner, but independent of the parental origin
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Affiliation(s)
- Zohar A Dotan
- Department of Urology, Sheba Medical Center, Tel-Hashomer 52621, Israel.
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15
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Wang SC, Oelze B, Schumacher A. Age-specific epigenetic drift in late-onset Alzheimer's disease. PLoS One 2008; 3:e2698. [PMID: 18628954 PMCID: PMC2444024 DOI: 10.1371/journal.pone.0002698] [Citation(s) in RCA: 297] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 06/13/2008] [Indexed: 11/18/2022] Open
Abstract
Despite an enormous research effort, most cases of late-onset Alzheimer's disease (LOAD) still remain unexplained and the current biomedical science is still a long way from the ultimate goal of revealing clear risk factors that can help in the diagnosis, prevention and treatment of the disease. Current theories about the development of LOAD hinge on the premise that Alzheimer's arises mainly from heritable causes. Yet, the complex, non-Mendelian disease etiology suggests that an epigenetic component could be involved. Using MALDI-TOF mass spectrometry in post-mortem brain samples and lymphocytes, we have performed an analysis of DNA methylation across 12 potential Alzheimer's susceptibility loci. In the LOAD brain samples we identified a notably age-specific epigenetic drift, supporting a potential role of epigenetic effects in the development of the disease. Additionally, we found that some genes that participate in amyloid-beta processing (PSEN1, APOE) and methylation homeostasis (MTHFR, DNMT1) show a significant interindividual epigenetic variability, which may contribute to LOAD predisposition. The APOE gene was found to be of bimodal structure, with a hypomethylated CpG-poor promoter and a fully methylated 3'-CpG-island, that contains the sequences for the epsilon4-haplotype, which is the only undisputed genetic risk factor for LOAD. Aberrant epigenetic control in this CpG-island may contribute to LOAD pathology. We propose that epigenetic drift is likely to be a substantial mechanism predisposing individuals to LOAD and contributing to the course of disease.
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Affiliation(s)
- Sun-Chong Wang
- Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taiwan
| | | | - Axel Schumacher
- Epigenetics Lab, Department of Medicine II, Klinikum rechts der Isar, Munich, Germany
- * E-mail:
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