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Gazzellone A, Sangiorgi E. From Churchill to Elephants: The Role of Protective Genes against Cancer. Genes (Basel) 2024; 15:118. [PMID: 38255007 PMCID: PMC10815068 DOI: 10.3390/genes15010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Richard Peto's paradox, first described in 1975 from an epidemiological perspective, established an inverse correlation between the probability of developing cancer in multicellular organisms and the number of cells. Larger animals exhibit fewer tumors compared to smaller ones, though exceptions exist. Mice are more susceptible to cancer than humans, while elephants and whales demonstrate significantly lower cancer prevalence rates than humans. How nature and evolution have addressed the issue of cancer in the animal kingdom remains largely unexplored. In the field of medicine, much attention has been devoted to cancer-predisposing genes, as they offer avenues for intervention, including blocking, downregulating, early diagnosis, and targeted treatment. Predisposing genes also tend to manifest clinically earlier and more aggressively, making them easier to identify. However, despite significant strides in modern medicine, the role of protective genes lags behind. Identifying genes with a mild predisposing effect poses a significant challenge. Consequently, comprehending the protective function conferred by genes becomes even more elusive, and their very existence is subject to questioning. While the role of variable expressivity and penetrance defects of the same variant in a family is well-documented for many hereditary cancer syndromes, attempts to delineate the function of protective/modifier alleles have been restricted to a few instances. In this review, we endeavor to elucidate the role of protective genes observed in the animal kingdom, within certain genetic syndromes that appear to act as cancer-resistant/repressor alleles. Additionally, we explore the role of protective alleles in conditions predisposing to cancer. The ultimate goal is to discern why individuals, like Winston Churchill, managed to live up to 91 years of age, despite engaging in minimal physical activity, consuming large quantities of alcohol daily, and not abstaining from smoking.
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Affiliation(s)
| | - Eugenio Sangiorgi
- Sezione di Medicina Genomica, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
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Rejuvenation: Turning Back Time by Enhancing CISD2. Int J Mol Sci 2022; 23:ijms232214014. [PMID: 36430496 PMCID: PMC9695557 DOI: 10.3390/ijms232214014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
The aging human population with age-associated diseases has become a problem worldwide. By 2050, the global population of those who are aged 65 years and older will have tripled. In this context, delaying age-associated diseases and increasing the healthy lifespan of the aged population has become an important issue for geriatric medicine. CDGSH iron-sulfur domain 2 (CISD2), the causative gene for Wolfram syndrome 2 (WFS2; MIM 604928), plays a pivotal role in mediating lifespan and healthspan by maintaining mitochondrial function, endoplasmic reticulum integrity, intracellular Ca2+ homeostasis, and redox status. Here, we summarize the most up-to-date publications on CISD2 and discuss the crucial role that this gene plays in aging and age-associated diseases. This review mainly focuses on the following topics: (1) CISD2 is one of the few pro-longevity genes identified in mammals. Genetic evidence from loss-of-function (knockout mice) and gain-of-function (transgenic mice) studies have demonstrated that CISD2 is essential to lifespan control. (2) CISD2 alleviates age-associated disorders. A higher level of CISD2 during natural aging, when achieved by transgenic overexpression, improves Alzheimer's disease, ameliorates non-alcoholic fatty liver disease and steatohepatitis, and maintains corneal epithelial homeostasis. (3) CISD2, the expression of which otherwise decreases during natural aging, can be pharmaceutically activated at a late-life stage of aged mice. As a proof-of-concept, we have provided evidence that hesperetin is a promising CISD2 activator that is able to enhance CISD2 expression, thus slowing down aging and promoting longevity. (4) The anti-aging effect of hesperetin is mainly dependent on CISD2 because transcriptomic analysis of the skeletal muscle reveals that most of the differentially expressed genes linked to hesperetin are regulated by hesperetin in a CISD2-dependent manner. Furthermore, three major metabolic pathways that are affected by hesperetin have been identified in skeletal muscle, namely lipid metabolism, protein homeostasis, and nitrogen and amino acid metabolism. This review highlights the urgent need for CISD2-based pharmaceutical development to be used as a potential therapeutic strategy for aging and age-associated diseases.
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Rahit KMTH, Tarailo-Graovac M. Genetic Modifiers and Rare Mendelian Disease. Genes (Basel) 2020; 11:E239. [PMID: 32106447 PMCID: PMC7140819 DOI: 10.3390/genes11030239] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022] Open
Abstract
Despite advances in high-throughput sequencing that have revolutionized the discovery of gene defects in rare Mendelian diseases, there are still gaps in translating individual genome variation to observed phenotypic outcomes. While we continue to improve genomics approaches to identify primary disease-causing variants, it is evident that no genetic variant acts alone. In other words, some other variants in the genome (genetic modifiers) may alleviate (suppress) or exacerbate (enhance) the severity of the disease, resulting in the variability of phenotypic outcomes. Thus, to truly understand the disease, we need to consider how the disease-causing variants interact with the rest of the genome in an individual. Here, we review the current state-of-the-field in the identification of genetic modifiers in rare Mendelian diseases and discuss the potential for future approaches that could bridge the existing gap.
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Affiliation(s)
- K. M. Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
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Pleiman JK, Irving AA, Wang Z, Toraason E, Clipson L, Dove WF, Deming DA, Newton MA. The conserved protective cyclic AMP-phosphodiesterase function PDE4B is expressed in the adenoma and adjacent normal colonic epithelium of mammals and silenced in colorectal cancer. PLoS Genet 2018; 14:e1007611. [PMID: 30188895 PMCID: PMC6143270 DOI: 10.1371/journal.pgen.1007611] [Citation(s) in RCA: 12] [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: 12/19/2017] [Revised: 09/18/2018] [Accepted: 08/06/2018] [Indexed: 12/31/2022] Open
Abstract
Conservation over three mammalian genera-the mouse, rat, and human-has been found for a subset of the transcripts whose level differs between the adenoma and normal epithelium of the colon. Pde4b is one of the triply conserved transcripts whose level is enhanced both in the colonic adenoma and in the normal colonic epithelium, especially adjacent to adenomas. It encodes the phosphodiesterase PDE4B, specific for cAMP. Loss of PDE4B function in the ApcMin/+ mouse leads to a significant increase in the number of colonic adenomas. Similarly, Pde4b-deficient ApcMin/+ mice are hypersensitive to treatment by the inflammatory agent DSS, becoming moribund soon after treatment. These observations imply that the PDE4B function protects against ApcMin-induced adenomagenesis and inflammatory lethality. The paradoxical enhancement of the Pde4b transcript in the adenoma versus this inferred protective function of PDE4B can be rationalized by a feedback model in which PDE4B is first activated by early oncogenic stress involving cAMP and then, as reported for frank human colon cancer, inactivated by epigenetic silencing.
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Affiliation(s)
- Jennifer K. Pleiman
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Amy A. Irving
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Molecular and Environmental Toxicology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Zhishi Wang
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Erik Toraason
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Linda Clipson
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - William F. Dove
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Dustin A. Deming
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Division of Hematology and Medical Oncology, Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Michael A. Newton
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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Vukovic V, Stojanovic J, Vecchioni A, Pastorino R, Boccia S. Systematic Review and Meta-analysis of SNPs from Genome-Wide Association Studies of Head and Neck Cancer. Otolaryngol Head Neck Surg 2018; 159:615-624. [PMID: 30126334 DOI: 10.1177/0194599818792262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objective Various genome-wide association studies (GWASs) identified new head and neck cancer (HNC) susceptibility loci, although the evidence has not been systematically summarized. We performed a systematic review and meta-analyses of the GWASs to identify the most commonly reported genetic loci associated with a risk of HNC. Data Sources We searched the PubMed, ISI Web of Science, SCOPUS, and GWAS databases to retrieve eligible studies, in English or Italian, published until June 1, 2017. Review Methods Only GWASs reporting data on the association between single-nucleotide polymorphisms (SNPs) and HNC were included. The quality of included studies was evaluated using the Q-Genie tool. Random-effect meta-analyses were performed considering only SNPs with at least 1 significant result from the included articles, and pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. Results Seven studies of case-control design were included in the review. Five studies on nasopharyngeal cancer (NPC) in Chinese, reporting on 27 different SNPs, were included in meta-analyses. Results show that 6 SNPs ( rs2076483, rs2975042, rs9258122, rs29232, and rs9510787) had an increased pooled estimates for A risk alleles (OR [95% CI]: 1.55 [1.36-1.77], 1.90 [1.69-2.14], 1.47 [1.31-1.65], 1.52 [1.32-1.76], and 1.22 [1.13-1.31], respectively) while G risk allele of rs3129055 reported an OR of 1.49 (95% CI, 1.33-1.67). Conclusion Our systematic review identified 5 SNPs located on chromosome 6 ( rs2076483, rs2975042, rs3129055, rs9258122, and rs29232) and 1 ( rs9510787) on chromosome 13 as significantly associated with an increased risk of NPC in Chinese.
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Affiliation(s)
- Vladimir Vukovic
- 1 Section of Hygiene, Institute of Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Jovana Stojanovic
- 1 Section of Hygiene, Institute of Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessia Vecchioni
- 1 Section of Hygiene, Institute of Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Roberta Pastorino
- 1 Section of Hygiene, Institute of Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefania Boccia
- 1 Section of Hygiene, Institute of Public Health, Università Cattolica del Sacro Cuore, Rome, Italy.,2 Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Riordan JD, Nadeau JH. From Peas to Disease: Modifier Genes, Network Resilience, and the Genetics of Health. Am J Hum Genet 2017; 101:177-191. [PMID: 28777930 PMCID: PMC5544383 DOI: 10.1016/j.ajhg.2017.06.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Phenotypes are rarely consistent across genetic backgrounds and environments, but instead vary in many ways depending on allelic variants, unlinked genes, epigenetic factors, and environmental exposures. In the extreme, individuals carrying the same causal DNA sequence variant but on different backgrounds can be classified as having distinct conditions. Similarly, some individuals that carry disease alleles are nevertheless healthy despite affected family members in the same environment. These genetic background effects often result from the action of so-called "modifier genes" that modulate the phenotypic manifestation of target genes in an epistatic manner. While complicating the prospects for gene discovery and the feasibility of mechanistic studies, such effects are opportunities to gain a deeper understanding of gene interaction networks that provide organismal form and function as well as resilience to perturbation. Here, we review the principles of modifier genetics and assess progress in studies of modifier genes and their targets in both simple and complex traits. We propose that modifier effects emerge from gene interaction networks whose structure and function vary with genetic background and argue that these effects can be exploited as safe and effective ways to prevent, stabilize, and reverse disease and dysfunction.
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Affiliation(s)
- Jesse D Riordan
- Pacific Northwest Research Institute, Seattle, WA 98122, USA.
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, WA 98122, USA.
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Abstract
The combination of next-generation sequencing technologies and high-throughput genotyping platforms has revolutionized the pursuit of genetic variants that contribute towards disease. Furthermore, these technologies have provided invaluable insight into the genetic factors that prevent individuals from developing disease. Exploiting the evolutionary mechanisms that were designed by nature to help prevent disease is an attractive line of enquiry. Such efforts have the potential to generate a therapeutic target roadmap and rejuvenate the current drug-discovery pathway. By delineating the genomic factors that are protective against disease, there is potential to derive highly effective, genomically anchored medicines that assist in maintaining health.
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Spiezio SH, Amon LM, McMillen TS, Vick CM, Houston BA, Caldwell M, Ogimoto K, Morton GJ, Kirk EA, Schwartz MW, Nadeau JH, LeBoeuf RC. Genetic determinants of atherosclerosis, obesity, and energy balance in consomic mice. Mamm Genome 2014; 25:549-63. [PMID: 25001233 DOI: 10.1007/s00335-014-9530-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/11/2014] [Indexed: 12/18/2022]
Abstract
Metabolic diseases such as obesity and atherosclerosis result from complex interactions between environmental factors and genetic variants. A panel of chromosome substitution strains (CSSs) was developed to characterize genetic and dietary factors contributing to metabolic diseases and other biological traits and biomedical conditions. Our goal here was to identify quantitative trait loci (QTLs) contributing to obesity, energy expenditure, and atherosclerosis. Parental strains C57BL/6 and A/J together with a panel of 21 CSSs derived from these progenitors were subjected to chronic feeding of rodent chow and atherosclerotic (females) or diabetogenic (males) test diets, and evaluated for a variety of metabolic phenotypes including several traits unique to this report, namely fat pad weights, energy balance, and atherosclerosis. A total of 297 QTLs across 35 traits were discovered, two of which provided significant protection from atherosclerosis, and several dozen QTLs modulated body weight, body composition, and circulating lipid levels in females and males. While several QTLs confirmed previous reports, most QTLs were novel. Finally, we applied the CSS quantitative genetic approach to energy balance, and identified three novel QTLs controlling energy expenditure and one QTL modulating food intake. Overall, we identified many new QTLs and phenotyped several novel traits in this mouse model of diet-induced metabolic diseases.
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Affiliation(s)
- Sabrina H Spiezio
- Institute for Systems Biology, 401 North Terry Ave, Seattle, WA, 98109, USA
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Shimomura K, Kumar V, Koike N, Kim TK, Chong J, Buhr ED, Whiteley AR, Low SS, Omura C, Fenner D, Owens JR, Richards M, Yoo SH, Hong HK, Vitaterna MH, Bass J, Pletcher MT, Wiltshire T, Hogenesch J, Lowrey PL, Takahashi JS. Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice. eLife 2013; 2:e00426. [PMID: 23580255 PMCID: PMC3622178 DOI: 10.7554/elife.00426] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/12/2013] [Indexed: 11/13/2022] Open
Abstract
Genetic and molecular approaches have been critical for elucidating the mechanism of the mammalian circadian clock. Here, we demonstrate that the ClockΔ19 mutant behavioral phenotype is significantly modified by mouse strain genetic background. We map a suppressor of the ClockΔ19 mutation to a ∼900 kb interval on mouse chromosome 1 and identify the transcription factor, Usf1, as the responsible gene. A SNP in the promoter of Usf1 causes elevation of its transcript and protein in strains that suppress the Clock mutant phenotype. USF1 competes with the CLOCK:BMAL1 complex for binding to E-box sites in target genes. Saturation binding experiments demonstrate reduced affinity of the CLOCKΔ19:BMAL1 complex for E-box sites, thereby permitting increased USF1 occupancy on a genome-wide basis. We propose that USF1 is an important modulator of molecular and behavioral circadian rhythms in mammals. DOI:http://dx.doi.org/10.7554/eLife.00426.001.
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Affiliation(s)
- Kazuhiro Shimomura
- Center for Functional Genomics, Department of Neurobiology, Center for Sleep and Circadian Biology, Northwestern University, Evanston, United States
| | - Vivek Kumar
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nobuya Koike
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Tae-Kyung Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jason Chong
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Ethan D Buhr
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Andrew R Whiteley
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Sharon S Low
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Chiaki Omura
- Department of Neurobiology, Center for Functional Genomics, Northwestern University, Evanston, United States
| | - Deborah Fenner
- Department of Neurobiology, Center for Functional Genomics, Northwestern University, Evanston, United States
| | - Joseph R Owens
- Department of Neurobiology, Center for Sleep and Circadian Biology, Northwestern University, Evanston, United States
| | - Marc Richards
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Seung-Hee Yoo
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Hee-Kyung Hong
- Department of Neurobiology, Center for Functional Genomics, Northwestern University, Evanston, United States
| | - Martha H Vitaterna
- Center for Functional Genomics, Department of Neurobiology, Center for Sleep and Circadian Biology, Northwestern University, Evanston, United States
| | - Joseph Bass
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Mathew T Pletcher
- Department of Genomics, Genomics Institute of the Novartis Research Foundation, San Diego, United States
| | - Tim Wiltshire
- Department of Genomics, Genomics Institute of the Novartis Research Foundation, San Diego, United States
| | - John Hogenesch
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Phillip L Lowrey
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Joseph S Takahashi
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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Non-Mendelian etiologic factors in neuropsychiatric illness: pleiotropy, epigenetics, and convergence. Behav Brain Sci 2013; 35:363-4. [PMID: 23095384 DOI: 10.1017/s0140525x12001392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The target article by Charney on behavior genetics/genomics discusses how numerous molecular factors can inform heritability estimations and genetic association studies. These factors find application in the search for genes for behavioral phenotypes, including neuropsychiatric disorders. We elaborate upon how single causal factors can generate multiple phenotypes, and discuss how multiple causal factors may converge on common neurodevelopmental mechanisms.
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Abstract
Modifier genes are an integral part of the genetic landscape in both humans and experimental organisms, but have been less well explored in mammals than other systems. A growing number of modifier genes in mouse models of disease nonetheless illustrate the potential for novel findings, while new technical advances promise many more to come. Modifier genes in mouse models include induced mutations and spontaneous or wild-derived variations captured in inbred strains. Identification of modifiers among wild-derived variants in particular should detect disease modifiers that have been shaped by selection and might therefore be compatible with high fitness and function. Here we review selected examples and argue that modifier genes derived from natural variation may provide a bias for nodes in genetic networks that have greater intrinsic plasticity and whose therapeutic manipulation may therefore be more resilient to side effects than conventional targets.
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Affiliation(s)
- Bruce A Hamilton
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America.
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Abstract
Common cardiovascular diseases, such as atherosclerosis and congestive heart failure, are exceptionally complex, involving a multitude of environmental and genetic factors that often show nonlinear interactions as well as being highly dependent on sex, age, and even the maternal environment. Although focused, reductionistic approaches have led to progress in elucidating the pathophysiology of cardiovascular diseases, such approaches are poorly powered to address complex interactions. Over the past decade, technological advances have made it possible to interrogate biological systems on a global level, raising hopes that, in combination with computational approaches, it may be possible to more fully address the complexities of cardiovascular diseases. In this Review, we provide an overview of such systems-based approaches to cardiovascular disease and discuss their translational implications.
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Affiliation(s)
- W Robb MacLellan
- Cardiovascular Research Laboratories, University of California Los Angeles, 675 Charles E. Young Drive South, MRL 3645, University of California Los Angeles, Los Angeles, CA 90095-1760, USA
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Abstract
BACKGROUND Advances in diagnostic and treatment regimens that aim to reduce fracture incidence will benefit from a better understanding of how bone morphology and tissue quality define whole-bone mechanical properties. QUESTIONS/PURPOSES The goal of this article was to review what is known about the interactions among morphologic and tissue quality traits and how these interactions contribute to bone quality (ie, whole-bone mechanical function). Several questions were addressed. First, how do interactions among morphology and tissue quality traits relate to functional adaptation? Second, what are the emergent patterns of functionally adapted trait sets in long bones? Third, how effective is phenotypic integration at establishing function across a population? Fourth, what are the emergent patterns of functionally adapted trait sets in corticocancellous structures? Fifth, how do functional interactions change with aging? METHODS A literature review was conducted with papers identified primarily through citations listed in reference sections as well as general searches using Google Scholar and PubMed. RESULTS The interactions among adult traits or phenotypic integration are an emergent property of the compensatory mechanisms complex systems used to establish function or homeostasis. Traits are not regulated independently but vary simultaneously (ie, covary) in specific ways to establish function. This covariation results in individuals acquiring unique sets of traits to establish bone quality. CONCLUSIONS AND CLINICAL RELEVANCE Biologic constraints imposed on the skeletal system result in a population showing a pattern of trait sets that is predictable based on external bone size and that can be used to identify individuals with reduced bone quality relative to their bone size and body size.
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Affiliation(s)
- Karl J Jepsen
- Leni and Peter W. May Department of Orthopaedics, Mount Sinai School of Medicine, Box 1188, One Gustave Levy Place, New York, NY 10029, USA.
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15
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Alcaraz WA, Chen E, Valdes P, Kim E, Lo YH, Vo J, Hamilton BA. Modifier genes and non-genetic factors reshape anatomical deficits in Zfp423-deficient mice. Hum Mol Genet 2011; 20:3822-30. [PMID: 21729880 DOI: 10.1093/hmg/ddr300] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Development of neural circuitry depends on the integration of signaling pathways to coordinate specification, proliferation and differentiation of cell types in the right number, in the right place, at the right time. Zinc finger protein 423 (Zfp423), a 30-zinc finger transcription factor, forms alternate complexes with components of several developmental signaling pathways, suggesting it as a point of signal integration during brain development. We previously showed that mice lacking Zfp423 have reduced proliferation of cerebellar precursor cells, resulting in complete loss of vermis and variable hypoplasia of cerebellar hemispheres. Here, we show that Zfp423(-/-) hemisphere malformations are shaped by both genetic and non-genetic factors, producing distinct phenotype distributions in different inbred genetic backgrounds. In genetic mapping studies, we identify four additive modifier loci (Amzn1-4) and seven synthetically interacting loci (Smzn1.1-3.1) that together explain approximately one-third of the phenotypic variance. Strain-specific sequence polymorphism and expression data provide a reduced list of functional variant candidate genes at each modifier locus. Environmental covariates add only modest explanatory power, suggesting an additional stochastic component. These results provide a comprehensive analysis of sources of phenotype variation in a model of hindbrain malformation.
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Affiliation(s)
- Wendy A Alcaraz
- Biomedical Sciences Graduate Program,, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0644, USA
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Bloss CS, Pawlikowska L, Schork NJ. Contemporary human genetic strategies in aging research. Ageing Res Rev 2011; 10:191-200. [PMID: 20709627 DOI: 10.1016/j.arr.2010.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 07/22/2010] [Accepted: 07/28/2010] [Indexed: 12/11/2022]
Abstract
Human aging is a complex, multifactorial process influenced by a number of genetic and non-genetic factors. This article first reviews genetic strategies for human aging research and considers the advantages and disadvantages of each. We then discuss the issue of phenotypic definition for genetic studies of aging, including longevity/life span, as well as disease-free survival and other endophenotypes. Finally, we argue that extensions of this area of research, including incorporation of gene×environment interactions, multivariate phenotypes, integration of functional genomic annotations, and exploitation of orthology - many of which are already initiated and ongoing - are critical to advancing this field.
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Stein CM, Baker AR. Tuberculosis as a complex trait: impact of genetic epidemiological study design. Mamm Genome 2010; 22:91-9. [PMID: 21104256 DOI: 10.1007/s00335-010-9301-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 11/03/2010] [Indexed: 12/29/2022]
Abstract
Several studies have suggested a role for human genetic risk factors in the susceptibility to developing tuberculosis (TB). However, results of these studies have been inconsistent, and one potential reason for these inconsistencies is variation in aspects of study design. Specifically, phenotype definitions and population genetic factors have varied dramatically. Since TB is a complex trait, there are many challenges in designing studies to assess appropriately human genetic risk factors for the development of TB as opposed to the acquisition of latent M. tuberculosis infection. In this review we summarize these important study design differences, with illustrations from the TB genetics literature. We cite specific examples of studies of the NRAMP1 (SLC11A1) gene and present Fisher's combined p values for different stratifications of these studies to further illustrate the impact of study design differences. Finally, we provide suggestions for the design of future genetic epidemiological studies of TB.
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Affiliation(s)
- Catherine M Stein
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Wolstein Research Building, Room 1316, 2103 Cornell Rd., Cleveland, OH, 44106, USA,
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18
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Association of genetic profiles to Crohn’s disease by linear combinations of single nucleotide polymorphisms. Artif Intell Med 2009; 46:131-8. [DOI: 10.1016/j.artmed.2008.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Revised: 07/21/2008] [Accepted: 07/21/2008] [Indexed: 10/21/2022]
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19
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van Nas A, Guhathakurta D, Wang SS, Yehya N, Horvath S, Zhang B, Ingram-Drake L, Chaudhuri G, Schadt EE, Drake TA, Arnold AP, Lusis AJ. Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology 2009; 150:1235-49. [PMID: 18974276 PMCID: PMC2654741 DOI: 10.1210/en.2008-0563] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We previously used high-density expression arrays to interrogate a genetic cross between strains C3H/HeJ and C57BL/6J and observed thousands of differences in gene expression between sexes. We now report analyses of the molecular basis of these sex differences and of the effects of sex on gene expression networks. We analyzed liver gene expression of hormone-treated gonadectomized mice as well as XX male and XY female mice. Differences in gene expression resulted in large part from acute effects of gonadal hormones acting in adulthood, and the effects of sex chromosomes, apart from hormones, were modest. We also determined whether there are sex differences in the organization of gene expression networks in adipose, liver, skeletal muscle, and brain tissue. Although coexpression networks of highly correlated genes were largely conserved between sexes, some exhibited striking sex dependence. We observed strong body fat and lipid correlations with sex-specific modules in adipose and liver as well as a sexually dimorphic network enriched for genes affected by gonadal hormones. Finally, our analyses identified chromosomal loci regulating sexually dimorphic networks. This study indicates that gonadal hormones play a strong role in sex differences in gene expression. In addition, it results in the identification of sex-specific gene coexpression networks related to genetic and metabolic traits.
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Affiliation(s)
- Atila van Nas
- Department of Human Genetics, University of California, Los Angeles, California 90095-1679, USA
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20
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Abe K, Klaften M, Narita A, Kimura T, Imai K, Kimura M, Rubio-Aliaga I, Wagner S, Jakob T, Hrabé de Angelis M. Genome-wide search for genes that modulate inflammatory arthritis caused by Ali18 mutation in mice. Mamm Genome 2009; 20:152-61. [PMID: 19238339 DOI: 10.1007/s00335-009-9170-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Accepted: 12/30/2008] [Indexed: 01/17/2023]
Abstract
Many of inflammatory diseases, including inflammatory arthritis, are multifactorial bases. The Ali18 semidominant mutation induced by N-ethyl-N-nitrosourea in the C3HeB/FeJ (C3H) genome causes spontaneous inflammation of peripheral limbs and elevated immunoglobulin E (IgE) levels in mice. Although the Ali18 locus was mapped to a single locus on chromosome 4, the arthritic phenotype of Ali18/+ mice was completely suppressed in F1 hybrid genetic backgrounds. To determine the chromosomal locations of the modifier loci affecting the severity of arthritis, an autosomal genome scan of 22 affected Ali18/+ F2 mice was conducted using C57BL/6J as a partner strain. Interestingly, regions on chromosomes 1 and 3 in C3H showed significant genetic interactions. Moreover, 174 N2 (backcross to Ali18/Ali18) and 267 F2 animals were used for measurement of arthritis scores and plasma IgE levels, and also for genotyping with 153 genome-wide single nucleotide polymorphism (SNP) markers. In N2 populations, two significant trait loci for arthritis scores on chromosomes 1 and 15 were detected. Although no significant scores were detected in F2 mice besides chromosome 4, a suggestive score was detected on chromosome 3. In addition, a two-dimensional genome scan using F2 identified five suggestive scores of chromosomal combinations, chromosomes 1 x 10, 2 x 6, 3 x 4, 4 x 9, and 6 x 15. No significant trait loci affecting IgE levels were detected in both N2 and F2 populations. Identification of the Ali18 modifier genes by further detailed analyses such as congenic strains and expression profiling may dissect molecular complexity in inflammatory diseases.
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Affiliation(s)
- Koichiro Abe
- Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa, 259-1193, Japan.
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21
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Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis. Proc Natl Acad Sci U S A 2008; 105:19910-4. [PMID: 19066216 DOI: 10.1073/pnas.0810388105] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic architecture of complex traits underlying physiology and disease in most organisms remains elusive. We still know little about the number of genes that underlie these traits, the magnitude of their effects, or the extent to which they interact. Chromosome substitution strains (CSSs) enable statistically powerful studies based on testing engineered inbred strains that have single, unique, and nonoverlapping genetic differences, thereby providing measures of phenotypic effects that are attributable to individual chromosomes. Here, we report a study of phenotypic effects and gene interactions for 90 blood, bone, and metabolic traits in a mouse CSS panel and 54 traits in a rat CSS panel. Two key observations emerge about the genetic architecture of these traits. First, the traits tend to be highly polygenic: across the genome, many individual chromosome substitutions each had significant phenotypic effects and, within each of the chromosomes studied, multiple distinct loci were found. Second, strong epistasis was found among the individual chromosomes. Specifically, individual chromosome substitutions often conferred surprisingly large effects (often a substantial fraction of the entire phenotypic difference between the parental strains), with the result that the sum of these individual effects often dramatically exceeded the difference between the parental strains. We suggest that strong, pervasive epistasis may reflect the presence of several phenotypically-buffered physiological states. These results have implications for identification of complex trait genes, developmental and physiological studies of phenotypic variation, and opportunities to engineer phenotypic outcomes in complex biological systems.
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Jepsen KJ, Hu B, Tommasini SM, Courtland HW, Price C, Cordova M, Nadeau JH. Phenotypic integration of skeletal traits during growth buffers genetic variants affecting the slenderness of femora in inbred mouse strains. Mamm Genome 2008; 20:21-33. [PMID: 19082857 DOI: 10.1007/s00335-008-9158-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Accepted: 11/12/2008] [Indexed: 10/21/2022]
Abstract
Compensatory interactions among adult skeletal traits are critical for establishing strength but complicate the search for fracture susceptibility genes by allowing many genetic variants to exist in a population without loss of function. A better understanding of how these interactions arise during growth will provide new insight into genotype-phenotype relationships and the biological controls that establish skeletal strength. We tested the hypothesis that genetic variants affecting growth in width relative to growth in length (slenderness) are coordinated with movement of the inner bone surface and matrix mineralization to match stiffness with weight-bearing loads during postnatal growth. Midshaft femoral morphology and tissue-mineral density were quantified at ages of 1 day and at 4, 8, and 16 weeks for a panel of 20 female AXB/BXA recombinant inbred mouse strains. Path Analyses revealed significant compensatory interactions among outer-surface expansion rate, inner-surface expansion rate, and tissue-mineral density during postnatal growth, indicating that genetic variants affecting bone slenderness were buffered mechanically by the precise regulation of bone surface movements and matrix mineralization. Importantly, the covariation between morphology and mineralization resulted from a heritable constraint limiting the amount of tissue that could be used to construct a functional femur. The functional interactions during growth explained 56-99% of the variability in adult traits and mechanical properties. These functional interactions provide quantitative expectations of how genetic or environmental variants affecting one trait should be compensated by changes in other traits. Variants that impair this process or that cannot be fully compensated are expected to alter skeletal growth leading to underdesigned (weak) or overdesigned (bulky) structures.
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Affiliation(s)
- Karl J Jepsen
- Leni and Peter W. May Department of Orthopaedics, Mount Sinai School of Medicine, New York, NY 10029, USA.
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23
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Willcox BJ, Willcox DC, Ferrucci L. Secrets of healthy aging and longevity from exceptional survivors around the globe: lessons from octogenarians to supercentenarians. J Gerontol A Biol Sci Med Sci 2008; 63:1181-5. [PMID: 19038832 PMCID: PMC4986604 DOI: 10.1093/gerona/63.11.1181] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bradley J Willcox
- Pacific Health Research Institute, Geriatrics, 846 South Hotel St., Suite 201, Honolulu, HI 96813 USA.
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24
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Glasscock E, Noebels JL. When a disease gene is not really a disease gene. FUTURE NEUROLOGY 2008. [DOI: 10.2217/14796708.3.2.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Edward Glasscock
- Baylor College of Medicine, Department of Neurology, One Baylor Plaza, Houston, TX 77030, USA
| | - Jeffrey L Noebels
- Baylor College of Medicine, Department of Neurology, Department of Neuroscience & Department of Molecular & Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
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25
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van Loo KMJ, Martens GJM. Identification of genetic and epigenetic variations in a rat model for neurodevelopmental disorders. Behav Genet 2008; 37:697-705. [PMID: 17899354 PMCID: PMC2039802 DOI: 10.1007/s10519-007-9164-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 07/23/2007] [Indexed: 11/17/2022]
Abstract
A combination of genetic variations, epimutations and environmental factors may be involved in the etiology of complex neurodevelopmental disorders like schizophrenia. To study such disorders, we use apomorphine-unsusceptible (APO-UNSUS) Wistar rats and their phenotypic counterpart apomorphine-susceptible (APO-SUS) rats that display a complex phenotype remarkably similar to that of schizophrenic patients. As the molecular basis of the APO-SUS/UNSUS rat model, we recently identified a genomic rearrangement of the Aph-1b gene. Here, we discovered between the two rat lines differences other than the Aph-1b gene defect, including a remarkable cluster of genetic variations, two variants corresponding to topoisomerase II-based recombination hot spots and an epigenetic (DNA methylation) difference in cerebellum and (hypo)thalamic but not hippocampal genomic DNA. Furthermore, genetic variations were found to correlate with the degree of apomorphine susceptibility in unselected Wistar rats. Together, the results show that a number of genetic and epigenetic differences exist between the APO-SUS and -UNSUS rat genomes, raising the possibility that in addition to the Aph-1b gene defect the newly identified variations may also contribute to the complex APO-SUS phenotype.
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Affiliation(s)
- Karen M. J. van Loo
- Department of Molecular Animal Physiology, Nijmegen Center for Molecular Life Sciences (NCMLS) & Institute for Neuroscience, Faculty of Science, Radboud University Nijmegen, 282 RT, Geert Grooteplein Zuid 28, Nijmegen, 6525 GA The Netherlands
| | - Gerard J. M. Martens
- Department of Molecular Animal Physiology, Nijmegen Center for Molecular Life Sciences (NCMLS) & Institute for Neuroscience, Faculty of Science, Radboud University Nijmegen, 282 RT, Geert Grooteplein Zuid 28, Nijmegen, 6525 GA The Netherlands
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26
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Abstract
Functional studies can be utilized to give importance/relevance to clinical associations. Once a clinical genetic or pharmacogenetic association is found, molecular studies can be utilized to explore the mechanism for the association. By employing cells in culture or transgenic mice modified with specific variant genes or sequence polymorphisms of interest, pathophysiological processes and response to pharmacological agents may be tested under conditions that are not approachable in human patients. These mechanistic studies may be particularly important when it comes to pharmacogenetic associations by providing significant, clinically relevant insights into the variable responses patients show to drug therapy.
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27
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Glasscock E, Qian J, Yoo JW, Noebels JL. Masking epilepsy by combining two epilepsy genes. Nat Neurosci 2007; 10:1554-8. [PMID: 17982453 DOI: 10.1038/nn1999] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Accepted: 09/24/2007] [Indexed: 11/09/2022]
Abstract
Inherited errors in ion channel genes comprise the largest subset of monogenic causes of idiopathic epilepsy, and pathogenic variants contribute to genetic risk in the complex inheritance of this common disorder. We generated a digenic mouse model of human idiopathic epilepsy by combining two epilepsy-associated ion channel mutations with mutually opposing excitability defects and overlapping subcellular localization. We found that increasing membrane excitability by removing Shaker-like K(+) channels, which are encoded by the Kcna1 gene, masked the absence epilepsy caused by a P/Q-type Ca(2+) channelopathy due to a missense mutation in the Cacna1a gene. Conversely, decreasing network excitability by impairing Cacna1a Ca(2+)-channel function attenuated limbic seizures and sudden death in Kcna1-null mice. We also identified intermediate excitability phenotypes at the network and axonal levels. Protective interactions between pathogenic ion channel variants may markedly alter the clinical expression of epilepsy, highlighting the need for comprehensive profiling of this candidate gene set to improve the accuracy of genetic risk assessment of this complex disease.
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Affiliation(s)
- Edward Glasscock
- Department of Neurology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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28
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Abstract
"Inborn errors of metabolism," first recognized 100 years ago by Garrod, were seen as transforming evidence for chemical and biological individuality. Phenylketonuria (PKU), a Mendelian autosomal recessive phenotype, was identified in 1934 by Asbjörn Fölling. It is a disease with impaired postnatal cognitive development resulting from a neurotoxic effect of hyperphenylalaninemia (HPA). Its metabolic phenotype is accountable to multifactorial origins both in nurture, where the normal nutritional experience introduces L-phenylalanine, and in nature, where mutations (>500 alleles) occur in the phenylalanine hydroxylase gene (PAH) on chromosome 12q23.2 encoding the L-phenylalanine hydroxylase enzyme (EC 1.14.16.1). The PAH enzyme converts phenylalanine to tyrosine in the presence of molecular oxygen and catalytic amounts of tetrahydrobiopterin (BH4), its nonprotein cofactor. PKU is among the first of the human genetic diseases to enter, through newborn screening, the domain of public health, and to show a treatment effect. This effect caused a paradigm shift in attitudes about genetic disease. The PKU story contains many messages, including: a framework on which to appreciate the complexity of PKU in which phenotype reflects both locus-specific and genomic components; what the human PAH gene tells us about human population genetics and evolution of modern humans; and how our interest in PKU is served by a locus-specific mutation database (http://www.pahdb.mcgill.ca; last accessed 20 March 2007). The individual Mendelian PKU phenotype has no "simple" or single explanation; every patient has her/his own complex PKU phenotype and will be treated accordingly. Knowledge about PKU reveals genomic components of both disease and health.
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Affiliation(s)
- Charles R Scriver
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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29
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Tomita Y, Ikeda M, Mutoh H, Inada T, Iwata N, Ozaki N, Honda H. Association study between Apolipoprotein L and schizophrenia by exhaustive and rule-based combination analysis for identification of multilocus interactions. J Biosci Bioeng 2007; 103:303-10. [PMID: 17502270 DOI: 10.1263/jbb.103.303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 12/28/2006] [Indexed: 01/17/2023]
Abstract
Several single marker association and haplotypic analyses have been performed to identify susceptible genes for various common diseases, but these approaches using candidate genes did not provide accurate and consistent evidence in each analysis. This inconsistency is partly due to the fact that the common diseases are caused by complex interactions among various genetic factors. Therefore, in this study, to evaluate exhaustive genotype or allele combinations, we applied the binomial and random permutation test (BRP) proposed by Tomita et al. [IPSJ Digital Courier, 2, 691-709 (2006)] for the association analysis between an Apolipoprotein L gene cluster and schizophrenia. Using the seven selected representative single nucleotide polymorphisms (SNPs) based on the results of linkage disequilibrium evaluation, we analyzed 845 schizophrenic patients and 707 healthy controls, and investigated the validation of risk and protective factors with two randomly divided data sets. A comparative study of a method for analyzing the interactions was performed by conventional methods. Even if all the tested methods were used for analysis, the risk factor with a high significance was not commonly selected from both independent data sets. However, the significant interactions for the protective factor against disease development were commonly obtained from both data sets by BRP analysis. In conclusion, although it is considered that the causality of schizophrenia is too complex to identify a susceptible interaction using a small sample size, it was suggested that the healthy controls tend to have the same combination of certain alleles or genotypes for protection from disease development when BRP as a new exhaustive combination analytical method was used.
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Affiliation(s)
- Yasuyuki Tomita
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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30
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Brighina L, Okubadejo NU, Schneider NK, Lesnick TG, de Andrade M, Cunningham JM, Farrer MJ, Lincoln SJ, Rocca WA, Maraganore DM. Beta-synuclein gene variants and Parkinson's disease: a preliminary case-control study. Neurosci Lett 2007; 420:229-34. [PMID: 17556099 PMCID: PMC1978171 DOI: 10.1016/j.neulet.2007.05.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 03/30/2007] [Accepted: 05/05/2007] [Indexed: 12/11/2022]
Abstract
Aggregation and fibrillization of the alpha-synuclein protein, which is the main component of Lewy bodies, may represent important processes in the pathogenesis of Parkinson's disease (PD). Several in vivo and in vitro studies suggest that beta-synuclein may be a natural negative regulator of alpha-synuclein aggregation and fibrillization. The goal of the present study was to investigate the association of two polymorphisms (rs35035889 and rs1352303) in the beta-synuclein (SNCB) gene with PD. Our case-control study included a total of 370 case-unaffected sibling pairs and 168 case-unrelated control pairs (538 pairs total). The subjects were recruited from an ongoing study of the molecular epidemiology of PD in the Upper Midwest (USA). We employed a liberalization of the sibling transmission disequilibrium test to study the main effects of the gene variants for subjects overall and for strata defined by age at study, gender, ethnicity, clinical diagnostic certainty, dementia, and family history of PD (adjusted for age at study and gender as appropriate). The analyses were conducted for each SNCB variant separately, and also for two-locus haplotypes using score tests. Neither of the SNCB SNPs examined were associated with PD overall or in strata, and haplotype analyses were negative as well. However, one of the two SNPs (rs1352303) was associated with a delayed age at onset of PD in women. The results of this preliminary study suggest that the SNCB locus, though not a susceptibility gene for PD, might modify the age at onset of PD.
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Affiliation(s)
- Laura Brighina
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Njide U. Okubadejo
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Nicole K. Schneider
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Timothy G. Lesnick
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Julie M. Cunningham
- Department of Laboratory Medicine, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Matthew J. Farrer
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL USA
| | - Sarah J. Lincoln
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL USA
| | - Walter A. Rocca
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN USA
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Demetrius M. Maraganore
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN USA
- *Corresponding author. Department of Neurology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905. Tel.: 507 538 1038; fax: 507 284 3665. E-mail address: (D. Maraganore)
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32
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Abstract
SUMMARY
Functional genomics research using Fundulus heteroclitus has focused on variation among individuals because of the evolutionary importance and value of Fundulus in explaining the human condition (why individual humans are different and are affected differently by stress,disease and drugs). Among different populations and species of Fundulus, there are evolutionarily adaptive differences in gene expression. This natural variation in gene expression seems to affect cardiac metabolism because up to 81% of the variation in glucose utilization observed in isolated heart ventricles is related to specific patterns of gene expression. The surprising result from this research is that among different groups of individuals, the expression of mRNA from different metabolic pathways explains substrate-specific metabolism. For example, variation in oxidative phosphorylation mRNAs explains glucose metabolism for one group of individuals but expression of glucose metabolism genes explains this metabolism in a different group of individuals. This variation among individuals has important implications for studies using inbred strains:conclusions based on one individual or one strain will not necessarily reflect a generalized conclusion for a population or species. Finally, there are surprisingly strong positive and negative correlations among metabolic genes,both within and between pathways. These data suggest that measures of mRNA expression are meaningful, yet there is a complexity in how gene expression is related to physiological processes.
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Affiliation(s)
- Douglas L Crawford
- Rosenstiel School of Marine and Atmospheric Sciences, Marine Biology and Fisheries, 4600 Rickenbacker Causeway, Miami, FL 33149, USA.
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34
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Tomita Y, Nakatochi M, Asano H, Izawa H, Yokota M, Honda H. Investigation of the relationship between sample size and risk factors for complex diseases based on a simulation study. CHEM-BIO INFORMATICS JOURNAL 2007. [DOI: 10.1273/cbij.7.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yasuyuki Tomita
- Department of Biotechnology, School of Engineering, Nagoya University
- Research Fellow of the Japanese Society for the Promotion of Science (JSPS)
| | | | - Hiroyuki Asano
- Department of Cardiology, Nagoya University Graduate School of Medicine
| | - Hideo Izawa
- Department of Cardiology, Nagoya University Graduate School of Medicine
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi-Gakuin University
| | - Hiroyuki Honda
- Department of Biotechnology, School of Engineering, Nagoya University
- MEXT Innovative Research Center for Preventive Medical Engineering, Nagoya University
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35
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Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, Daly MJ, Steinhart AH, Abraham C, Regueiro M, Griffiths A, Dassopoulos T, Bitton A, Yang H, Targan S, Datta LW, Kistner EO, Schumm LP, Lee AT, Gregersen PK, Barmada MM, Rotter JI, Nicolae DL, Cho JH. A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 2006; 314:1461-3. [PMID: 17068223 PMCID: PMC4410764 DOI: 10.1126/science.1135245] [Citation(s) in RCA: 2214] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The inflammatory bowel diseases Crohn's disease and ulcerative colitis are common, chronic disorders that cause abdominal pain, diarrhea, and gastrointestinal bleeding. To identify genetic factors that might contribute to these disorders, we performed a genome-wide association study. We found a highly significant association between Crohn's disease and the IL23R gene on chromosome 1p31, which encodes a subunit of the receptor for the proinflammatory cytokine interleukin-23. An uncommon coding variant (rs11209026, c.1142G>A, p.Arg381Gln) confers strong protection against Crohn's disease, and additional noncoding IL23R variants are independently associated. Replication studies confirmed IL23R associations in independent cohorts of patients with Crohn's disease or ulcerative colitis. These results and previous studies on the proinflammatory role of IL-23 prioritize this signaling pathway as a therapeutic target in inflammatory bowel disease.
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Affiliation(s)
- Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, University of Pittsburgh Medical Center Presbyterian, Mezzanine Level, C-Wing, 200 Lothrop Street, Pittsburgh, PA 15213, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Crabtree A300, 130 Desoto Street, Pittsburgh, PA 15261, USA
| | - Kent D. Taylor
- Medical Genetics Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
- IBD Center, Division of Gastroenterology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Steven R. Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, B136, 1503 East Jefferson Street, Baltimore, MD 21231, USA
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - John D. Rioux
- Université de Montréal and the Montreal Heart Institute, S-6400, 5000 Belanger Street, Montreal, Quebec H1T 1C8, Canada
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Mark S. Silverberg
- Mount Sinai Hospital IBD Centre, University of Toronto, 441–600 University Avenue, Toronto, Ontario M5G 1×5, Canada
| | - Mark J. Daly
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114, USA
| | - A. Hillary Steinhart
- Mount Sinai Hospital IBD Centre, University of Toronto, 441–600 University Avenue, Toronto, Ontario M5G 1×5, Canada
| | - Clara Abraham
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Miguel Regueiro
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, University of Pittsburgh Medical Center Presbyterian, Mezzanine Level, C-Wing, 200 Lothrop Street, Pittsburgh, PA 15213, USA
| | - Anne Griffiths
- Department of Pediatrics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1×8, Canada
| | - Themistocles Dassopoulos
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, B136, 1503 East Jefferson Street, Baltimore, MD 21231, USA
| | - Alain Bitton
- Royal Victoria Hospital, McGill University Health Centre, 687 Pine Avenue West, Montreal, Quebec H3A 1A1, Canada
| | - Huiying Yang
- Medical Genetics Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
- IBD Center, Division of Gastroenterology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Stephan Targan
- IBD Center, Division of Gastroenterology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
- Immunobiology Research Institute, Cedars-Sinai Medical Center, Davis 4063, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Lisa Wu Datta
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, B136, 1503 East Jefferson Street, Baltimore, MD 21231, USA
| | - Emily O. Kistner
- Department of Health Studies, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - L. Philip Schumm
- Department of Health Studies, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Annette T. Lee
- The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA
| | - M. Michael Barmada
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Crabtree A300, 130 Desoto Street, Pittsburgh, PA 15261, USA
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
- IBD Center, Division of Gastroenterology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Dan L. Nicolae
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
- Department of Statistics, University of Chicago, 5734 South University Avenue, Chicago, IL 60637, USA
| | - Judy H. Cho
- IBD Center, Section of Digestive Diseases, Departments of Medicine and Genetics, Yale University, S155A, 300 Cedar Street, New Haven, CT 06519, USA
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