1
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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2
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Wu J, Lin D, Jiu L, Liu Q, Gu Z, Luo J, Zhao Y. Exploring epigenetic biomarkers of universal specificities and commonalities among pan-cancer cohorts in The Cancer Genome Atlas. Epigenomics 2021; 13:599-612. [PMID: 33787302 DOI: 10.2217/epi-2021-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To explore the mechanism of cancer by employing a comprehensive analysis of DNA methylation patterns and variations among pan-cancer cohorts. Materials & methods: This research focused on the discovery of universally specific or common biomarkers by mathematical statistics and machine learning methods in The Cancer Genome Atlas. Results: We found 138 differently methylated CpGs (DMCs) with a common methylation trend and eight common differently methylated regions in different cancer cohorts. Additionally, we found 99 DMCs to distinguish 32 different cancer cohorts in random forest analysis because of the specificity mechanism, but each DMC still had high instability. Conclusion: Our results could facilitate the development of biomarkers that are universally specific and common features across pan-cancer cohorts.
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Affiliation(s)
- Jie Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Deng Lin
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Liandi Jiu
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Qi Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Zhenglong Gu
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China.,Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Junjie Luo
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
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3
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Painter DT, van der Wouden F, Laubichler MD, Youn H. Quantifying simultaneous innovations in evolutionary medicine. Theory Biosci 2020; 139:319-335. [PMID: 33241494 PMCID: PMC7719117 DOI: 10.1007/s12064-020-00333-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/13/2020] [Indexed: 01/23/2023]
Abstract
To what extent do simultaneous innovations occur and are independently from each other? In this paper we use a novel persistent keyword framework to systematically identify innovations in a large corpus containing academic papers in evolutionary medicine between 2007 and 2011. We examine whether innovative papers occurring simultaneously are independent from each other by evaluating the citation and co-authorship information gathered from the corpus metadata. We find that 19 out of 22 simultaneous innovative papers do, in fact, occur independently from each other. In particular, co-authors of simultaneous innovative papers are no more geographically concentrated than the co-authors of similar non-innovative papers in the field. Our result suggests producing innovative work draws from a collective knowledge pool, rather than from knowledge circulating in distinct localized collaboration networks. Therefore, new ideas can appear at multiple locations and with geographically dispersed co-authorship networks. Our findings support the perspective that simultaneous innovations are the outcome of collective behavior.
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Affiliation(s)
- Deryc T. Painter
- School of Complex Adaptive System, Arizona State University, Tempe, AZ 85281 USA
| | | | - Manfred D. Laubichler
- School of Complex Adaptive System, Arizona State University, Tempe, AZ 85281 USA
- Santa Fe Institute, Santa Fe, NM 87501 USA
| | - Hyejin Youn
- Kellogg School of Management, Northwestern University, Evanston, IL 60208 USA
- Northwestern Institute on Complex Systems, Evanston, IL 60208 USA
- London Mathematical Lab, London, WC2N 6DF UK
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4
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Dritsoula A, Kislikova M, Oomatia A, Webster AP, Beck S, Ponticos M, Lindsey B, Norman J, Wheeler DC, Oates T, Caplin B. "Epigenome-wide methylation profile of chronic kidney disease-derived arterial DNA uncovers novel pathways in disease-associated cardiovascular pathology.". Epigenetics 2020; 16:718-728. [PMID: 32930636 DOI: 10.1080/15592294.2020.1819666] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chronic kidney disease (CKD) related cardiovascular disease (CVD) is characterized by vascular remodelling with well-established structural and functional changes in the vascular wall such as arterial stiffness, matrix deposition, and calcification. These phenotypic changes resemble pathology seen in ageing, and are likely to be mediated by sustained alterations in gene expression, which may be caused by epigenetic changes such as tissue-specific DNA methylation. We aimed to investigate tissue specific changes in DNA methylation that occur in CKD-related CVD. Genome-wide DNA methylation changes were examined in bisulphite converted genomic DNA isolated from the vascular media of CKD and healthy arteries. Methylation-specific PCR was used to validate the array data, and the association between DNA methylation and gene and protein expression was examined. The DNA methylation age was compared to the chronological age in both cases and controls. Three hundred and nineteen differentially methylated regions (DMR) were identified spread across the genome. Pathway analysis revealed that DMRs associated with genes were involved in embryonic and vascular development, and signalling pathways such as TGFβ and FGF. Expression of top differentially methylated gene HOXA5 showed a significant negative correlation with DNA methylation. Interestingly, DNA methylation age and chronological age were highly correlated, but there was no evidence of accelerated age-related DNA methylation in the arteries of CKD patients. In conclusion, we demonstrated that differential DNA methylation in the arterial tissue of CKD patients represents a potential mediator of arterial pathology and may be used to uncover novel pathways in the genesis of CKD-associated complications.
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Affiliation(s)
- Athina Dritsoula
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - Maria Kislikova
- Department of Renal Medicine, Division of Medicine, UCL, London, UK.,Department of Nephrology, University Hospital Marqués de Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Amin Oomatia
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - Amy P Webster
- Department of Cancer Biology, Cancer Institute, UCL, London, UK
| | - Stephan Beck
- Department of Cancer Biology, Cancer Institute, UCL, London, UK
| | - Markella Ponticos
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, UCL, London, UK
| | - Ben Lindsey
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - Jill Norman
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - David C Wheeler
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - Thomas Oates
- Department of Renal Medicine, Division of Medicine, UCL, London, UK.,Departments of Nephrology and General Medicine, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Ben Caplin
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
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5
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Hoehe MR, Morris-Rosendahl DJ. The role of genetics and genomics in clinical psychiatry. DIALOGUES IN CLINICAL NEUROSCIENCE 2019. [PMID: 30581286 PMCID: PMC6296395 DOI: 10.31887/dcns.2018.20.3/mhoehe] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The enormous successes in the genetics and genomics of many diseases have provided the basis for the advancement of precision medicine. Thus, the detection of genetic variants associated with neuropsychiatric disorders, as well as treatment outcome, has raised growing expectations that these findings could soon be translated into the clinic to improve diagnosis, the prediction of disease risk and individual response to drug therapy. In this article, we will provide an introduction to the search for genes involved in psychiatric illness and summarize the present findings in major psychiatric disorders. We will review the genetic variants in genes encoding drug metabolizing enzymes and specific drug targets which were found to be associated with variable drug response and severe side effects. We will evaluate the clinical translatability of these findings, whether there is currently any role for genetic testing and in this context, make valuable sources of information available to the clinician seeking guidance and advice in this rapidly developing field of psychiatric genetics.
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Affiliation(s)
- Margret R Hoehe
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Deborah J Morris-Rosendahl
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, UK, NHLI, Imperial College London, UK
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6
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Wang Q, Peng WX, Wang L, Ye L. Toward multiomics-based next-generation diagnostics for precision medicine. Per Med 2019; 16:157-170. [PMID: 30816060 DOI: 10.2217/pme-2018-0085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Our healthcare system is experiencing a paradigm shift to precision medicine, aiming at an early prediction of individual disease risks and targeted interventions. Whole-genome sequencing is currently gaining momentum, as it has the potential to capture all classes of genetic variation, thus providing a more complete picture of the individual's genetic makeup, which could be utilized in genetic testing; however, this will also lead to difficulties in interpreting the test results, necessitating careful integration of genomic data with other layers of information, both molecular multiomics measurements of epigenome, transcriptome, proteome, metabolome and even microbiome, as well as comprehensive information on diet, lifestyle and environment. Overall, the translation of patient-specific data into actionable diagnostic tools will be a challenging task, requiring expertise from multiple disciplines, secure data sharing in large reference databases and a strong computational infrastructure.
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Affiliation(s)
- Qi Wang
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Wei-Xian Peng
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Lu Wang
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Li Ye
- Department of Nursing, Tongde Hospital of Zhejiang Province, Hangzhou 310012, Zhejiang Province, China
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7
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Garg P, Joshi RS, Watson C, Sharp AJ. A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome. PLoS Genet 2018; 14:e1007707. [PMID: 30273333 PMCID: PMC6181428 DOI: 10.1371/journal.pgen.1007707] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 10/11/2018] [Accepted: 09/08/2018] [Indexed: 12/22/2022] Open
Abstract
While population studies have resulted in detailed maps of genetic variation in humans, to date there are few robust maps of epigenetic variation. We identified sites containing clusters of CpGs with high inter-individual epigenetic variation, termed Variably Methylated Regions (VMRs) in five purified cell types. We observed that VMRs occur preferentially at enhancers and 3' UTRs. While the majority of VMRs have high heritability, a subset of VMRs within the genome show highly correlated variation in trans, forming co-regulated networks that have low heritability, differ between cell types and are enriched for specific transcription factor binding sites and biological pathways of functional relevance to each tissue. For example, in T cells we defined a network of 95 co-regulated VMRs enriched for genes with roles in T-cell activation; in fibroblasts a network of 34 co-regulated VMRs comprising all four HOX gene clusters enriched for control of tissue growth; and in neurons a network of 18 VMRs enriched for roles in synaptic signaling. By culturing genetically-identical fibroblasts under varying environmental conditions, we experimentally demonstrated that some VMR networks are responsive to the environment, with methylation levels at these loci changing in a coordinated fashion in trans dependent on cellular growth. Intriguingly these environmentally-responsive VMRs showed a strong enrichment for imprinted loci (p<10-80), suggesting that these are particularly sensitive to environmental conditions. Our study provides a detailed map of common epigenetic variation in the human genome, showing that both genetic and environmental causes underlie this variation.
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Affiliation(s)
- Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ricky S. Joshi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Corey Watson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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8
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Volkova PY, Geras'kin SA. 'Omic' technologies as a helpful tool in radioecological research. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 189:156-167. [PMID: 29677564 DOI: 10.1016/j.jenvrad.2018.04.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.
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Affiliation(s)
- Polina Yu Volkova
- Institute of Radiology and Agroecology, 249032, Kievskoe shosse, 109 km, Obninsk, Russia.
| | - Stanislav A Geras'kin
- Institute of Radiology and Agroecology, 249032, Kievskoe shosse, 109 km, Obninsk, Russia
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9
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Hoehe MR. The role of genetics and genomics in clinical psychiatry. DIALOGUES IN CLINICAL NEUROSCIENCE 2018; 20:169-177. [PMID: 30581286 PMCID: PMC6296395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
The enormous successes in the genetics and genomics of many diseases have provided the basis for the advancement of precision medicine. Thus, the detection of genetic variants associated with neuropsychiatric disorders, as well as treatment outcome, has raised growing expectations that these findings could soon be translated into the clinic to improve diagnosis, the prediction of disease risk and individual response to drug therapy. In this article, we will provide an introduction to the search for genes involved in psychiatric illness and summarize the present findings in major psychiatric disorders. We will review the genetic variants in genes encoding drug metabolizing enzymes and specific drug targets which were found to be associated with variable drug response and severe side effects. We will evaluate the clinical translatability of these findings, whether there is currently any role for genetic testing and in this context, make valuable sources of information available to the clinician seeking guidance and advice in this rapidly developing field of psychiatric genetics.
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10
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Abstract
Pregnancy is known to induce rapid, progressive, and substantial changes to the cardiovascular system, ultimately facilitating successful pregnancy outcomes. Women who develop hypertensive disorders during pregnancy are considered to have "failed" the cardiovascular stress test of pregnancy and likely represent a subpopulation with inadequate cardiovascular accommodation. Preeclampsia is a serious complication with a myriad of manifestations in both mother and offspring. This pregnancy syndrome is a polygenic disease and has now been linked to a greater incidence of cardiovascular disease. Moreover, offsprings born to preeclamptic mothers exhibit an elevated risk of cardiovascular disease, stroke, and mental disorders during adulthood. This suggests that preeclampsia not only exposes the mother and the fetus to complications during pregnancy but also programs chronic diseases during adulthood in the offspring. The etiology of preeclampsia remains unknown, with various theories being suggested to explain its origin. It is primarily thought to be associated with poor placentation and entails excessive maternal inflammation and endothelial dysfunction. It is well established now that the maternal immune system and the placenta are involved in a highly choreographed cross talk that underlies adequate spiral artery remodeling required for uteroplacental perfusion and free flow of nutrients to the fetus. Although it is not clear whether immunological alterations occur early during pregnancy, studies have proposed that dysregulated systemic and placental immunity contribute to impaired angiogenesis and the onset of preeclampsia. Recently emerged strong evidence suggests a potential link among epigenetics, microRNAs (miRNAs), and pregnancy complications. This chapter will focus on important aspects of epigenetics, immunological aspects, and cardiovascular and vascular remodeling of preeclampsia.
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11
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Stotz K, Griffiths P. Epigenetics: ambiguities and implications. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2016; 38:22. [PMID: 27854053 DOI: 10.1007/s40656-016-0121-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
Everyone has heard of 'epigenetics', but the term means different things to different researchers. Four important contemporary meanings are outlined in this paper. Epigenetics in its various senses has implications for development, heredity, and evolution, and also for medicine. Concerning development, it cements the vision of a reactive genome strongly coupled to its environment. Concerning heredity, both narrowly epigenetic and broader 'exogenetic' systems of inheritance play important roles in the construction of phenotypes. A thoroughly epigenetic model of development and evolution was Waddington's aim when he introduced the term 'epigenetics' in the 1940s, but it has taken the modern development of molecular epigenetics to realize this aim. In the final sections of the paper we briefly outline some further implications of epigenetics for medicine and for the nature/nurture debate.
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Affiliation(s)
- Karola Stotz
- Department of Philosophy, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Paul Griffiths
- Department of Philosophy and Charles Perkins Centre, University of Sydney, Sydney, NSW, 2006, Australia
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12
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Creemers SG, van Koetsveld PM, van Kemenade FJ, Papathomas TG, Franssen GJH, Dogan F, Eekhoff EMW, van der Valk P, de Herder WW, Janssen JAMJL, Feelders RA, Hofland LJ. Methylation of IGF2 regulatory regions to diagnose adrenocortical carcinomas. Endocr Relat Cancer 2016; 23:727-37. [PMID: 27535174 DOI: 10.1530/erc-16-0266] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 01/20/2023]
Abstract
Adrenocortical carcinoma (ACC) is a rare malignancy with a poor prognosis. Discrimination of ACCs from adrenocortical adenomas (ACAs) is challenging on both imaging and histopathological grounds. High IGF2 expression is associated with malignancy, but shows large variability. In this study, we investigate whether specific methylation patterns of IGF2 regulatory regions could serve as a valuable biomarker in distinguishing ACCs from ACAs. Pyrosequencing was used to analyse methylation percentages in DMR0, DMR2, imprinting control region (ICR) (consisting of CTCF3 and CTCF6) and the H19 promoter. Expression of IGF2 and H19 mRNA was assessed by real-time quantitative PCR. Analyses were performed in 24 ACCs, 14 ACAs and 11 normal adrenals. Using receiver operating characteristic (ROC) analysis, we evaluated which regions showed the best predictive value for diagnosis of ACC and determined the diagnostic accuracy of these regions. In ACCs, the DMR0, CTCF3, CTCF6 and the H19 promoter were positively correlated with IGF2 mRNA expression (P<0.05). Methylation in the most discriminating regions distinguished ACCs from ACAs with a sensitivity of 96%, specificity of 100% and an area under the curve (AUC) of 0.997±0.005. Our findings were validated in an independent cohort of 9 ACCs and 13 ACAs, resulting in a sensitivity of 89% and a specificity of 92%. Thus, methylation patterns of IGF2 regulatory regions can discriminate ACCs from ACAs with high diagnostic accuracy. This proposed test may become the first objective diagnostic tool to assess malignancy in adrenal tumours and facilitate the choice of therapeutic strategies in this group of patients.
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Affiliation(s)
- S G Creemers
- Department of Internal MedicineDivision of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - P M van Koetsveld
- Department of Internal MedicineDivision of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - F J van Kemenade
- Department of PathologyErasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - T G Papathomas
- Department of PathologyErasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands Department of HistopathologyKing's College Hospital, Denmark Hill, London, UK
| | - G J H Franssen
- Department of SurgeryErasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - F Dogan
- Department of Internal MedicineDivision of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - E M W Eekhoff
- Department of PathologyVU University Medical Center, Amsterdam, The Netherlands
| | - P van der Valk
- Department of PathologyVU University Medical Center, Amsterdam, The Netherlands
| | - W W de Herder
- Department of Internal MedicineDivision of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J A M J L Janssen
- Department of Internal MedicineDivision of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - R A Feelders
- Department of Internal MedicineDivision of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - L J Hofland
- Department of Internal MedicineDivision of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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13
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Cofer ZC, Cui S, EauClaire SF, Kim C, Tobias JW, Hakonarson H, Loomes KM, Matthews RP. Methylation Microarray Studies Highlight PDGFA Expression as a Factor in Biliary Atresia. PLoS One 2016; 11:e0151521. [PMID: 27010479 PMCID: PMC4806872 DOI: 10.1371/journal.pone.0151521] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 02/27/2016] [Indexed: 01/21/2023] Open
Abstract
Biliary atresia (BA) is a progressive fibro-inflammatory disorder that is the leading indication for liver transplantation in children. Although there is evidence implicating genetic, infectious, environmental, and inflammatory causes, the etiology of BA remains unknown. We have recently reported that cholangiocytes from BA patients showed decreased DNA methylation relative to disease- and non-disease controls, supporting a potential role for DNA hypomethylation in BA etiopathogenesis. In the current study, we examined the methylation status of specific genes in human BA livers using methylation microarray technology. We found global DNA hypomethylation in BA samples as compared to disease- and non-disease controls at specific genetic loci. Hedgehog pathway members, SHH and GLI2, known to be upregulated in BA, were both hypomethylated, validating this approach as an investigative tool. Another region near the PDGFA locus was the most significantly hypomethylated in BA, suggesting potential aberrant expression. Validation assays confirmed increased transcriptional and protein expression of PDGFA in BA livers. We also show that PDGF-A protein is specifically localized to cholangiocytes in human liver samples. Injection of PDGF-AA protein dimer into zebrafish larvae caused biliary developmental and functional defects. In addition, activation of the Hedgehog pathway caused increased expression of PDGF-A in zebrafish larvae, providing a previously unrecognized link between PDGF and the Hedgehog pathway. Our findings implicate DNA hypomethylation as a specific factor in mediating overexpression of genes associated with BA and identify PDGF as a new candidate in BA pathogenesis.
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Affiliation(s)
- Zenobia C. Cofer
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
| | - Shuang Cui
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
| | - Steven F. EauClaire
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
| | - Cecilia Kim
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - John W. Tobias
- Penn Center for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kathleen M. Loomes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Randolph P. Matthews
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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14
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Lahiri DK, Maloney B, Bayon BL, Chopra N, White FA, Greig NH, Nurnberger JI. Transgenerational latent early-life associated regulation unites environment and genetics across generations. Epigenomics 2016; 8:373-87. [PMID: 26950428 DOI: 10.2217/epi.15.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The origin of idiopathic diseases is still poorly understood. The latent early-life associated regulation (LEARn) model unites environmental exposures and gene expression while providing a mechanistic underpinning for later-occurring disorders. We propose that this process can occur across generations via transgenerational LEARn (tLEARn). In tLEARn, each person is a 'unit' accumulating preclinical or subclinical 'hits' as in the original LEARn model. These changes can then be epigenomically passed along to offspring. Transgenerational accumulation of 'hits' determines a sporadic disease state. Few significant transgenerational hits would accompany conception or gestation of most people, but these may suffice to 'prime' someone to respond to later-life hits. Hits need not produce symptoms or microphenotypes to have a transgenerational effect. Testing tLEARn requires longitudinal approaches. A recently proposed longitudinal epigenome/envirome-wide association study would unite genetic sequence, epigenomic markers, environmental exposures, patient personal history taken at multiple time points and family history.
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Affiliation(s)
- Debomoy K Lahiri
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA.,Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Bryan Maloney
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Baindu L Bayon
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Nipun Chopra
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Fletcher A White
- Department of Anesthesia, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Nigel H Greig
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - John I Nurnberger
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA.,Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
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15
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Guarrera S, Fiorito G, Onland-Moret NC, Russo A, Agnoli C, Allione A, Di Gaetano C, Mattiello A, Ricceri F, Chiodini P, Polidoro S, Frasca G, Verschuren MWM, Boer JMA, Iacoviello L, van der Schouw YT, Tumino R, Vineis P, Krogh V, Panico S, Sacerdote C, Matullo G. Gene-specific DNA methylation profiles and LINE-1 hypomethylation are associated with myocardial infarction risk. Clin Epigenetics 2015; 7:133. [PMID: 26705428 PMCID: PMC4690365 DOI: 10.1186/s13148-015-0164-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 12/15/2015] [Indexed: 12/16/2022] Open
Abstract
Background DNA methylation profiles are responsive to environmental stimuli and metabolic shifts. This makes DNA methylation a potential biomarker of environmental-related and lifestyle-driven diseases of adulthood. Therefore, we investigated if white blood cells’ (WBCs) DNA methylation profiles are associated with myocardial infarction (MI) occurrence. Whole-genome DNA methylation was investigated by microarray analysis in 292 MI cases and 292 matched controls from the large prospective Italian European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (EPICOR study). Significant signals (false discovery rate (FDR) adjusted P < 0.05) were replicated by mass spectrometry in 317 MI cases and 262 controls from the Dutch EPIC cohort (EPIC-NL). Long interspersed nuclear element-1 (LINE-1) methylation profiles were also evaluated in both groups. Results A differentially methylated region (DMR) within the zinc finger and BTB domain-containing protein 12 (ZBTB12) gene body and LINE-1 hypomethylation were identified in EPICOR MI cases and replicated in the EPIC-NL sample (ZBTB12-DMR meta-analysis: effect size ± se = −0.016 ± 0.003, 95 % CI = −0.021;−0.011, P = 7.54 × 10−10; LINE-1 methylation meta-analysis: effect size ± se = −0.161 ± 0.040, 95 % CI = −0.239;−0.082, P = 6.01 × 10−5). Moreover, cases with shorter time to disease had more pronounced ZBTB12-DMR hypomethylation (meta-analysis, men: effect size ± se = −0.0059 ± 0.0017, PTREND = 5.0 × 10−4; women: effect size ± se = −0.0053 ± 0.0019, PTREND = 6.5 × 10−3) and LINE-1 hypomethylation (meta-analysis, men: effect size ± se = −0.0010 ± 0.0003, PTREND = 1.6 × 10−3; women: effect size ± se = −0.0008 ± 0.0004, PTREND = 0.026) than MI cases with longer time to disease. In the EPIC-NL replication panel, DNA methylation profiles improved case-control discrimination and reclassification when compared with traditional MI risk factors only (net reclassification improvement (95 % CI) between 0.23 (0.02–0.43), P = 0.034, and 0.89 (0.64–1.14), P < 1 × 10−5). Conclusions Our data suggest that specific methylation profiles can be detected in WBCs, in a preclinical condition, several years before the occurrence of MI, providing an independent signature of cardiovascular risk. We showed that prediction accuracy can be improved when DNA methylation is taken into account together with traditional MI risk factors, although further confirmation on a larger sample is warranted. Our findings support the potential use of DNA methylation patterns in peripheral blood white cells as promising early biomarkers of MI. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0164-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simonetta Guarrera
- Human Genetics Foundation (HuGeF), Via Nizza 52, Turin, I-10126 Torino Italy.,Medical Sciences Department, University of Turin, Turin, Italy
| | - Giovanni Fiorito
- Human Genetics Foundation (HuGeF), Via Nizza 52, Turin, I-10126 Torino Italy.,Medical Sciences Department, University of Turin, Turin, Italy
| | | | - Alessia Russo
- Human Genetics Foundation (HuGeF), Via Nizza 52, Turin, I-10126 Torino Italy.,Medical Sciences Department, University of Turin, Turin, Italy
| | - Claudia Agnoli
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Alessandra Allione
- Human Genetics Foundation (HuGeF), Via Nizza 52, Turin, I-10126 Torino Italy.,Medical Sciences Department, University of Turin, Turin, Italy
| | - Cornelia Di Gaetano
- Human Genetics Foundation (HuGeF), Via Nizza 52, Turin, I-10126 Torino Italy.,Medical Sciences Department, University of Turin, Turin, Italy
| | - Amalia Mattiello
- Department of Clinical and Experimental Medicine, Federico II University, Naples, Italy
| | | | - Paolo Chiodini
- Department of Public Health, Second University of Naples, Naples, Italy
| | - Silvia Polidoro
- Human Genetics Foundation (HuGeF), Via Nizza 52, Turin, I-10126 Torino Italy
| | - Graziella Frasca
- Cancer Registry and Histopathology Unit, "Civile-M.P. Arezzo" Hospital, ASP 7, Ragusa, Italy
| | - Monique W M Verschuren
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands.,Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Jolanda M A Boer
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, IS Italy
| | | | - Rosario Tumino
- Cancer Registry and Histopathology Unit, "Civile-M.P. Arezzo" Hospital, ASP 7, Ragusa, Italy
| | - Paolo Vineis
- Human Genetics Foundation (HuGeF), Via Nizza 52, Turin, I-10126 Torino Italy.,Epidemiology and Public Health, Imperial College London, London, UK
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Salvatore Panico
- Department of Clinical and Experimental Medicine, Federico II University, Naples, Italy
| | | | - Giuseppe Matullo
- Human Genetics Foundation (HuGeF), Via Nizza 52, Turin, I-10126 Torino Italy.,Medical Sciences Department, University of Turin, Turin, Italy
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16
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Wagner LE, Evans RG, Noland D, Barkley R, Sullivan DK, Drisko J. The Next Generation of Dietitians: Implementing Dietetics Education and Practice in Integrative Medicine. J Am Coll Nutr 2015; 34:430-5. [DOI: 10.1080/07315724.2014.979514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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17
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Satterlee JS, Beckel-Mitchener A, McAllister K, Procaccini DC, Rutter JL, Tyson FL, Chadwick LH. Community resources and technologies developed through the NIH Roadmap Epigenomics Program. Methods Mol Biol 2015; 1238:27-49. [PMID: 25421653 DOI: 10.1007/978-1-4939-1804-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This chapter describes resources and technologies generated by the NIH Roadmap Epigenomics Program that may be useful to epigenomics researchers investigating a variety of diseases including cancer. Highlights include reference epigenome maps for a wide variety of human cells and tissues, the development of new technologies for epigenetic assays and imaging, the identification of novel epigenetic modifications, and an improved understanding of the role of epigenetic processes in a diversity of human diseases. We also discuss future needs in this area including exploration of epigenomic variation between individuals, single-cell epigenomics, environmental epigenomics, exploration of the use of surrogate tissues, and improved technologies for epigenome manipulation.
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Affiliation(s)
- John S Satterlee
- Division of Basic Neuroscience and Behavioral Research, National Institute on Drug Abuse, National Institutes of Health, 6001 Executive Boulevard, NIH, MSC 9555, Bethesda, MD, 20892-9555, USA,
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18
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Abstract
Epigenetics, the study of functionally relevant chemical modifications to DNA that do not involve a change in the DNA nucleotide sequence, is at the interface between research and clinical medicine. Research on epigenetic marks, which regulate gene expression independently of the underlying genetic code, has dramatically changed our understanding of the interplay between genes and the environment. This interplay alters human biology and developmental trajectories, and can lead to programmed human disease years after the environmental exposure. In addition, epigenetic marks are potentially heritable. In this article, we discuss the underlying concepts of epigenetics and address its current and potential applicability for primary care providers.
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Affiliation(s)
- Robert Wright
- FAAP, Departments of Preventive Medicine and Pediatrics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Pl, Box 1057, New York, NY 10029.
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19
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Abstract
It is becoming increasingly clear that genomics is beginning to have a major impact in guiding diagnoses and treatment of many disorders. As the cost of DNA sequencing continues to drop and more patient genomes are sequenced, the challenge is to deliver this knowledge to the clinic, particularly in cancer. DNA sequencing of patients with rare disease is revealing novel druggable pathways for more common disorders. Genetic tools for treating disease are also advancing rapidly. Genetic approaches, thought to be pipedreams five years ago for diseases such as Duchenne muscular dystrophy, are now showing promise in clinical trials and many of these methodologies are being applied more widely for other diseases. The era of genomic medicine has arrived.
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20
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Lessans S, Dorsey SG. The role for epigenetic modifications in pain and analgesia response. Nurs Res Pract 2013; 2013:961493. [PMID: 24228176 PMCID: PMC3817675 DOI: 10.1155/2013/961493] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/12/2013] [Indexed: 12/12/2022] Open
Abstract
Pain remains a poorly understood and managed symptom. A limited mechanistic understanding of interindividual differences in pain and analgesia response shapes current approaches to assessment and treatment. Opportunities exist to improve pain care through increased understanding of how dynamic epigenomic remodeling shapes injury, illness, pain, and treatment response. Tightly regulated alterations of the DNA-histone chromatin complex enable cells to control transcription, replication, gene expression, and protein production. Pathological alterations to chromatin shape the ability of the cell to respond to physiologic and environmental cues leading to disease and reduced treatment effectiveness. This review provides an overview of critical epigenetic processes shaping pathology and pain, highlights current research support for the role of epigenomic modification in the development of chronic pain, and summarizes the therapeutic potential to alter epigenetic processes to improve health outcomes.
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Affiliation(s)
- Sherrie Lessans
- School of Nursing, University of Maryland, Baltimore, USA
- Program in Neuroscience, University of Maryland, Baltimore, USA
| | - Susan G. Dorsey
- School of Nursing, University of Maryland, Baltimore, USA
- Program in Neuroscience, University of Maryland, Baltimore, USA
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21
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Zhang Z, Zhao Z, Liu B, Li D, Zhang D, Chen H, Liu D. Systems biomedicine: It’s your turn—Recent progress in systems biomedicine. QUANTITATIVE BIOLOGY 2013. [DOI: 10.1007/s40484-013-0009-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Young DA, Bui C, Barter MJ. Understanding CpG methylation in the context of osteoarthritis. Epigenomics 2013; 4:593-5. [PMID: 23244304 DOI: 10.2217/epi.12.63] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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23
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Lahiri DK, Maloney B. Gene × environment interaction by a longitudinal epigenome-wide association study (LEWAS) overcomes limitations of genome-wide association study (GWAS). Epigenomics 2013; 4:685-99. [PMID: 23244313 DOI: 10.2217/epi.12.60] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The goal of genome-wide association studies is to identify SNPs unique to disease. It usually involves a single sampling from subjects' lifetimes. While primary DNA sequence variation influences gene-expression levels, expression is also influenced by epigenetics, including the 'somatic epitype' (G(SE)), an epigenotype acquired postnatally. While genes are inherited, and novel polymorphisms do not routinely appear, G(SE) is fluid. Furthermore, G(SE) could respond to environmental factors (such as heavy metals) and to differences in exercise, maternal care and dietary supplements - all of which postnatally modify oxidation or methylation of DNA, leading to altered gene expression. Change in epigenetic status may be critical for the development of many diseases. We propose a 'longitudinal epigenome-wide association study', wherein G(SE) are measured at multiple time points along with subjects' histories. This Longitudinal epigenome-wide association study, based on the 'dynamic' somatic epitype over the 'static' genotype, merits further investigation.
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Affiliation(s)
- Debomoy K Lahiri
- Department of Psychiatry, Laboratory of Molecular Neurogenetics, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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24
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Young DA. Editorial: More evidence for a role of CpG methylation in the pathogenesis of osteoarthritis. ACTA ACUST UNITED AC 2013; 65:555-8. [PMID: 23233319 DOI: 10.1002/art.37811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 11/20/2012] [Indexed: 11/05/2022]
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25
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González-Recio O, Ugarte E, Bach A. Trans-generational effect of maternal lactation during pregnancy: a Holstein cow model. PLoS One 2012; 7:e51816. [PMID: 23284777 PMCID: PMC3527476 DOI: 10.1371/journal.pone.0051816] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/06/2012] [Indexed: 11/19/2022] Open
Abstract
Epigenetic regulation in mammals begins in the first stages of embryogenesis. This prenatal programming determines, in part, phenotype expression in adult life. Some species, particularly dairy cattle, are conceived during the maternal lactation, which is a period of large energy and nutrient needs. Under these circumstances, embryo and fetal development compete for nutrients with the mammary gland, which may affect prenatal programming and predetermine phenotype at adulthood. Data from a specialized dairy breed were used to determine the transgenerational effect when embryo development coincides with maternal lactation. Longitudinal phenotypic data for milk yield (kg), ratio of fat-protein content in milk during first lactation, and lifespan (d) from 40,065 cows were adjusted for environmental and genetic effects using a Bayesian framework. Then, the effect of different maternal circumstances was determined on the residuals. The maternal-related circumstances were 1) presence of lactation, 2) maternal milk yield level, and 3) occurrence of mastitis during embryogenesis. Females born to mothers that were lactating while pregnant produced 52 kg (MonteCarlo standard error; MCs.e. = 0.009) less milk, lived 16 d (MCs.e. = 0.002) shorter and were metabolically less efficient (+0.42% milk fat/protein ratio; MCs.e.<0.001) than females whose fetal life developed in the absence of maternal lactation. The greater the maternal milk yield during embryogenesis, the larger the negative effects of prenatal programming, precluding the offspring born to the most productive cows to fully express their potential additive genetic merit during their adult life. Our data provide substantial evidence of transgenerational effect when pregnancy and lactation coincide. Although this effect is relatively low, it should not be ignored when formulating rations for lactating and pregnant cows. Furthermore, breeding, replacement, and management strategies should also take into account whether the individuals were conceived during maternal lactation because, otherwise, their performance may deviate from what it could be expected.
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26
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Fernandez-Jimenez N, Plaza-Izurieta L, Lopez-Euba T, Jauregi-Miguel A, Ramon Bilbao J. Cubic regression-based degree of correction predicts the performance of whole bisulfitome amplified DNA methylation analysis. Epigenetics 2012; 7:1349-54. [PMID: 23154537 PMCID: PMC3528690 DOI: 10.4161/epi.22846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Epigenetic mechanisms, including DNA methylation, are important determinants in development and disease. There is a need for technologies capable of detecting small variations in methylation levels in an accurate and reproducible manner, even if only limited amounts of DNA are available (which is the case in many studies in humans). Quantitative methylation analysis of minute DNA amounts after whole bisulfitome amplification (qMAMBA) has been proposed as an alternative, but this technique has not been adequately standardized and no comparative study against conventional methods has been performed, that includes a wide range of methylation percentages and different target assays. We designed an experiment to compare the performance of qMAMBA and bisulfite-treated genomic (non-amplified) DNA pyrosequencing. Reactions were performed in duplicate for each technique in eight different target genes, using nine artificially constructed DNA samples with methylation levels ranging between 0% and 100% with intervals of 12.5%. Cubic polynomial curves were plotted from the experimental results and the real methylation values and the resulting equation was used to estimate new corrected data points. The use of the cubic regression-based correction benefits the accuracy and the power of discrimination in methylation studies. Additionally, dispersion of the new estimated data around a y = x line (R ( 2) ) served to fix a cutoff that can discriminate, with a single 9-point curve experiment, whether whole bisulfitome amplification and subsequent qMAMBA can produce accurate methylation results. Finally, even with an optimized reagent kit, DNA samples subjected to whole bisulfitome amplification enhance the preferential amplification of unmethylated alleles, and subtle changes in methylation levels cannot be detected confidently.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, BioCruces Health Research Institute, University of the Basque Country UPV/EHU, Leioa, Basque Country, Spain
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27
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Blair LP, Yan Q. Epigenetic mechanisms in commonly occurring cancers. DNA Cell Biol 2012; 31 Suppl 1:S49-61. [PMID: 22519822 PMCID: PMC3460614 DOI: 10.1089/dna.2012.1654] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/20/2012] [Accepted: 03/20/2012] [Indexed: 12/11/2022] Open
Abstract
Cancer is a collection of very complex diseases that share many traits while differing in many ways as well. This makes a universal cure difficult to attain, and it highlights the importance of understanding each type of cancer at a molecular level. Although many strides have been made in identifying the genetic causes for some cancers, we now understand that simple changes in the primary DNA sequence cannot explain the many steps that are necessary to turn a normal cell into a rouge cancer cell. In recent years, some research has shifted to focusing on detailing epigenetic contributions to the development and progression of cancer. These changes occur apart from primary genomic sequences and include DNA methylation, histone modifications, and miRNA expression. Since these epigenetic modifications are reversible, drugs targeting epigenetic changes are becoming more common in clinical settings. Daily discoveries elucidating these complex epigenetic processes are leading to advances in the field of cancer research. These advances, however, come at a rapid and often overwhelming pace. This review specifically summarizes the main epigenetic mechanisms currently documented in solid tumors common in the United States and Europe.
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Affiliation(s)
- Lauren P Blair
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520-8023, USA.
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28
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Buchheit T, Van de Ven T, Shaw A. Epigenetics and the transition from acute to chronic pain. PAIN MEDICINE 2012; 13:1474-90. [PMID: 22978429 DOI: 10.1111/j.1526-4637.2012.01488.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVE The objective of this study was to review the epigenetic modifications involved in the transition from acute to chronic pain and to identify potential targets for the development of novel, individualized pain therapeutics. BACKGROUND Epigenetics is the study of heritable modifications in gene expression and phenotype that do not require a change in genetic sequence to manifest their effects. Environmental toxins, medications, diet, and psychological stresses can alter epigenetic processes such as DNA methylation, histone acetylation, and RNA interference. As epigenetic modifications potentially play an important role in inflammatory cytokine metabolism, steroid responsiveness, and opioid sensitivity, they are likely key factors in the development of chronic pain. Although our knowledge of the human genetic code and disease-associated polymorphisms has grown significantly in the past decade, we have not yet been able to elucidate the mechanisms that lead to the development of persistent pain after nerve injury or surgery. DESIGN This is a focused literature review of epigenetic science and its relationship to chronic pain. RESULTS Significant laboratory and clinical data support the notion that epigenetic modifications are affected by the environment and lead to differential gene expression. Similar to mechanisms involved in the development of cancer, neurodegenerative disease, and inflammatory disorders, the literature endorses an important potential role for epigenetics in chronic pain. CONCLUSIONS Epigenetic analysis may identify mechanisms critical to the development of chronic pain after injury, and may provide new pathways and target mechanisms for future drug development and individualized medicine.
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Affiliation(s)
- Thomas Buchheit
- Department of Anesthesiology, Duke University Medical Center, Durham VA Medical Center, Durham, NC 27710, USA.
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29
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Botana-Rial M, De Chiara L, Valverde D, Leiro-Fernández V, Represas-Represas C, Del Campo-Pérez V, Fernández-Villar A. Prognostic value of aberrant hypermethylation in pleural effusion of lung adenocarcinoma. Cancer Biol Ther 2012; 13:1436-42. [PMID: 22954699 DOI: 10.4161/cbt.22004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lung adenocarcinoma is one of the most frequent causes of malignant pleural effusions (MPE). The presence of MPE bears a poor prognosis. Although epigenetic changes are commonly related to human neoplasia, scarce date is available on patients with MPE. We aimed to estimate the prognostic value of DNA methylation of tumor suppressor genes from pleural fluid. Thirty patients with MPE due to lung adenocarcinoma were prospectively included. Methylation-specific (MS) PCR was used to study the methylation status of the promoter region of tumor suppressor genes p16/INK4a, MGMT, BRCA1 and RARβ in pleural fluid. Clinical data and survival were collected. Survival analysis was performed using Kaplan-Meier plots and Cox regression. Hypermethylation in at least one gene was detected in 25 patients (83.3%). On multivariate analysis factors significantly associated with shorter survival were the lack of hypermethylation in any of the studied genes (hazard ratio = 9.3; p = 0.001), Charlson index ≥ 3 (hazard ratio = 9.6, p = 0.002) and no oncological treatment (hazard ratio = 11.1; p < 0.001). Analysis of aberrant promoter hypermethylation of tumor suppressor genes may be useful in predicting prognosis, but further studies are needed to validate our findings.
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Affiliation(s)
- Maribel Botana-Rial
- Bronchopleural Unit, Respiratory and Infectious Disease Research Group, Pneumology Service of Complexo Hospitalario Universitario de Vigo, Bio-medical Research Institute of Vigo, Vigo, Spain.
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30
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Hewitt KJ, Garlick JA. Cellular reprogramming to reset epigenetic signatures. Mol Aspects Med 2012; 34:841-8. [PMID: 22982217 DOI: 10.1016/j.mam.2012.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 08/27/2012] [Indexed: 12/25/2022]
Abstract
The controlled differentiation of induced pluripotent stem cells (iPSC) towards clinically-relevant cell types has benefitted from epigenetic profiling of lineage-specific markers to confirm the phenotype of iPSC-derived cells. Mapping epigenetic marks throughout the genome has identified unique changes which occur in the DNA methylation profile of cells as they differentiate to specific cell types. Beyond characterizing the development of cells derived from pluripotent stem cells, the process of reprogramming cells to iPSC resets lineage-specific DNA methylation marks established during differentiation to specific somatic cell types. This property of reprogramming has potential utility in reverting aberrant epigenetic alterations in nuclear organization that are linked to disease progression. Since DNA methylation marks are reset following reprogramming, and contribute to restarting developmental programs, it is possible that DNA methylation marks associated with the disease state may also be erased in these cells. The subsequent differentiation of such cells could result in cell progeny that will function effectively as therapeutically-competent cell types for use in regenerative medicine. This suggests that through reprogramming it may be possible to directly modify the epigenetic memory of diseased cells and help to normalize their cellular phenotype, while also broadening our understanding of disease pathogenesis.
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Affiliation(s)
- Kyle J Hewitt
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI 53705, USA
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31
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Tuo J, Grob S, Zhang K, Chan CC. Genetics of immunological and inflammatory components in age-related macular degeneration. Ocul Immunol Inflamm 2012; 20:27-36. [PMID: 22324898 DOI: 10.3109/09273948.2011.628432] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Age-related macular degeneration (AMD), affecting 30 to 50 million elder individuals worldwide, is a disease affecting the macular retina and choroid that can lead to irreversible central vision loss and blindness. Recent findings support a role for immunologic processes in AMD pathogenesis, including generation of inflammatory related molecules in the Bruch's membrane, recruitment of macrophages, complement activation, microglial activation and accumulation in the macular lesions. Pro-inflammatory effects of chronic inflammation and oxidative stress can result in abnormal retinal pigment epithelium, photoreceptor atrophy and choroidal neovascularization. The associations of immunological and inflammatory genes, in particular the genes related to innate immunity with AMD support the involvement of various immunological pathways in the AMD pathogenesis. We review the literature on the involvements of inflammatory genes in AMD, highlight recent genetic discoveries, and discuss the potential application of such knowledge in the management of patients with AMD.
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Affiliation(s)
- Jingsheng Tuo
- Immunopathology Section, Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-1857, USA
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32
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Scholz B, Marschalek R. Epigenetics and blood disorders. Br J Haematol 2012; 158:307-22. [DOI: 10.1111/j.1365-2141.2012.09193.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/09/2012] [Indexed: 12/25/2022]
Affiliation(s)
- Bastian Scholz
- Institute of Pharmaceutical Biology/DCAL; Biocentre; Goethe-University; Frankfurt/Main; Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/DCAL; Biocentre; Goethe-University; Frankfurt/Main; Germany
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33
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Abstract
Strong evidence suggests a potential link among epigenetics, microRNAs (miRNAs), and pregnancy complications. Much research still needs to be carried out to determine whether epigenetic factors are predictive in the pathogenesis of preeclampsia (PE), a life-threatening disease during pregnancy. Recently, the importance of maternal epigenetic features, including DNA methylation, histone modifications, epigenetically regulated miRNA, and the effect of imprinted or non-imprinted genes on trophoblast growth, invasion, as well as fetal development and hypertension in pregnancy, has been demonstrated in a series of articles. This article discusses the current evidence of this complicated network of miRNA and epigenetic factors as potential mechanisms that may underlie the theories of disease for PE. Translating these basic epigenetic findings to clinical practice could potentially serve as prognostic biomarkers for diagnosis in its early stages and could help in the development of prophylactic strategies.
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Affiliation(s)
- Mahua Choudhury
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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Chinnery PF, Elliott HR, Hudson G, Samuels DC, Relton CL. Epigenetics, epidemiology and mitochondrial DNA diseases. Int J Epidemiol 2012; 41:177-87. [PMID: 22287136 DOI: 10.1093/ije/dyr232] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Over the last two decades, the mutation of mitochondrial DNA (mtDNA) has emerged as a major cause of inherited human disease. The disorders present clinically in at least 1 in 10,000 adults, but pathogenic mutations are found in approximately 1 in 200 of the background population. Mitochondrial DNA is maternally inherited and there can be marked phenotypic variability within the same family. Heteroplasmy is a significant factor and environmental toxins also appear to modulate the phenotype. Although genetic and biochemical studies have provided part of the explanation, a comprehensive understanding of the incomplete penetrance of these diseases is lacking--both at the population and family levels. Here, we review the potential role of epigenetic factors in the pathogenesis of mtDNA diseases and the contribution that epidemiological approaches can make to improve our understanding in this area. Despite being previously dismissed, there is an emerging evidence that mitochondria contain the machinery required to epigenetically modify mtDNA expression. In addition, the increased production of reactive oxygen species seen in several mtDNA diseases could lead to the epigenetic modification of the nuclear genome, including chromatin remodelling and alterations to DNA methylation and microRNA expression, thus contributing to the diverse pathophysiology observed in this group of diseases. These observations open the door to future studies investigating the role of mtDNA methylation in human disease.
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Affiliation(s)
- Patrick F Chinnery
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK.
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Abstract
The beginning of this century was not only marked by the publication of the first draft of the human genome but also set off a decade of intense research on epigenetic phenomena. Apart from DNA methylation, it became clear that many other factors including a wide range of histone modifications, different shades of chromatin accessibility, and a vast suite of noncoding RNAs comprise the epigenome. With the recent advances in sequencing technologies, it has now become possible to analyze many of these features in depth, allowing for the first time the establishment of complete epigenomic profiles for basically every cell type of interest. Here, we will discuss the recent advances that allow comprehensive epigenetic mapping, highlight several projects that set out to better understand the epigenome, and discuss the impact that epigenomic mapping can have on our understanding of both healthy and diseased cells.
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Affiliation(s)
- Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
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Klemcke HG, Joe B, Rose R, Ryan KL. Life or death? A physiogenomic approach to understand individual variation in responses to hemorrhagic shock. Curr Genomics 2011; 12:428-42. [PMID: 22379396 PMCID: PMC3178911 DOI: 10.2174/138920211797248574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 06/29/2011] [Accepted: 07/06/2011] [Indexed: 11/22/2022] Open
Abstract
Severe hemorrhage due to trauma is a major cause of death throughout the world. It has often been observed that some victims are able to withstand hemorrhage better than others. For decades investigators have attempted to identify physiological mechanisms that distinguish survivors from nonsurvivors for the purpose of providing more informed therapies. As an alternative approach to address this issue, we have initiated a research program to identify genes and genetic mechanisms that contribute to this phenotype of survival time after controlled hemorrhage. From physiogenomic studies using inbred rat strains, we have demonstrated that this phenotype is a heritable quantitative trait, and is therefore a complex trait regulated by multiple genes. Our work continues to identify quantitative trait loci as well as potential epigenetic mechanisms that might influence survival time after severe hemorrhage. Our ultimate goal is to improve survival to traumatic hemorrhage and attendant shock via regulation of genetic mechanisms and to provide knowledge that will lead to genetically-informed personalized treatments.
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Affiliation(s)
- Harold G Klemcke
- U.S. Army Institute of Surgical Research, Fort Sam Houston, TX 78234, USA
| | - Bina Joe
- Physiological Genomics Laboratory, Department of Physiology and Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Rajiv Rose
- U.S. Army Institute of Surgical Research, Fort Sam Houston, TX 78234, USA
| | - Kathy L Ryan
- U.S. Army Institute of Surgical Research, Fort Sam Houston, TX 78234, USA
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Johnson W, Penke L, Spinath FM. Understanding Heritability: What it is and What it is Not. EUROPEAN JOURNAL OF PERSONALITY 2011. [DOI: 10.1002/per.835] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Commentators generally found our exposition of the concept of heritability helpful for psychologists, suggesting that we largely accomplished our primary goal. Many provided supplemental and helpful perspectives on concepts we addressed. A few of the comments indicated that we may not have been completely successful in making clear our secondary goal, which was to outline how heritability estimates confound a plethora of influences. In this response, we thus emphasize that we do not claim that specific kinds of complexity, or, even worse, intractable complexity, pervade the genetics of behavioural traits. Rather, our claim is that genetics is riddled with complexity of many degrees and kinds, and heritability is a poor indicator of either degree or kind of underlying genetic complexity. Copyright © 2011 John Wiley & Sons, Ltd.
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Affiliation(s)
- Wendy Johnson
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, Scotland, UK
- Department of Psychology, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Lars Penke
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Frank M. Spinath
- Department of Psychology, Saarland University, Saarbruecken, Germany
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Schindl R, Mayer K, Aigner K. [Computer experience and further developments in the respiratory function laboratory (author's transl)]. MEDIZINISCHE KLINIK 1975; 70:1815-20. [PMID: 594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reported is on satisfactory results obtained with a small-size computer consisting of punching and scanning device, as well as plain writing machine in the respiratory function laboratory. Developed in on- as well as off-line processing by an own technical staff, a diagnostic and teaching program was established for all respiratory function routine methods with the advantages of a large number of cases examined, elimination of sources of error, considerable supply of data and information, automatic documentation and filing, plain writing, interpretation and evaluation of findings. In continuation of such works also the blood gas analysis has been included. These values as the total of disturbances of the pathophysiological acid-base status are considered and interpreted. Clinical correction is forced in this man-machine dialogue by automatic stops of the whole machinery before going on. Subsequently and in addition are computer alveolar-arterial oxygen pressure gradient, venous shunt and oxygen saturation and expressed utilizing the capacity of the small-size computer. Further developments in the respiratory function diagnostic- and teaching program for small-size computers--not too expensive in the building block principle - are intended.
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