1
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August I, Gagneux P, Semendeferi K, Marchetto MC. Evolution of Human Susceptibility to Alzheimer's Disease: A Review of Hypotheses and Comparative Evidence. Evol Anthropol 2025; 34:e22054. [PMID: 39806778 DOI: 10.1002/evan.22054] [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: 08/24/2024] [Revised: 12/11/2024] [Accepted: 01/02/2025] [Indexed: 01/16/2025]
Abstract
Primates rely on memory to navigate both physical and social environments and in humans, loss of memory function leads to devastating consequences. Alzheimer's disease (AD) is a neurodegenerative disease which begins by impacting memory functioning and is ultimately fatal. AD is common across human populations and its prevalence is predicted to rise with increases in the aging population. Despite this, the full AD phenotype has not been observed in any other nonhuman primate species. While a significant amount of research has been devoted to understanding the immediate mechanisms involved in AD pathogenesis in humans, less research has focused on why humans are particularly vulnerable to neurodegenerative diseases like AD. Here we explore hypotheses on the evolution of distinct human susceptibility to AD and place these in the context of findings from comparative neuroanatomical and molecular studies and discuss recent evidence for evolutionary changes protective against AD in the primate lineage.
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Affiliation(s)
- Isabel August
- Department of Anthropology, University of California San Diego, La Jolla, California, USA
| | - Pascal Gagneux
- Department of Anthropology, University of California San Diego, La Jolla, California, USA
- Department of Pathology, University of California San Diego, La Jolla, California, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California, USA
| | - Katerina Semendeferi
- Department of Anthropology, University of California San Diego, La Jolla, California, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California, USA
| | - Maria Carolina Marchetto
- Department of Anthropology, University of California San Diego, La Jolla, California, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California, USA
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2
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Brassington L, Arner AM, Watowich MM, Damstedt J, Ng KS, Lim YAL, Venkataraman VV, Wallace IJ, Kraft TS, Lea AJ. Integrating the Thrifty Genotype and Evolutionary Mismatch Hypotheses to understand variation in cardiometabolic disease risk. Evol Med Public Health 2024; 12:214-226. [PMID: 39484023 PMCID: PMC11525211 DOI: 10.1093/emph/eoae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/18/2024] [Indexed: 11/03/2024] Open
Abstract
More than 60 years ago, James Neel proposed the Thrifty Genotype Hypothesis to explain the widespread prevalence of type 2 diabetes in Western, industrial contexts. This hypothesis posits that variants linked to conservative energy usage and increased fat deposition would have been favored throughout human evolution due to the advantages they could provide during periods of resource limitation. However, in industrial environments, these variants instead produce an increased risk of obesity, metabolic syndrome, type 2 diabetes, and related health issues. This hypothesis has been popular and impactful, with thousands of citations, many ongoing debates, and several spin-off theories in biomedicine, evolutionary biology, and anthropology. However, despite great attention, the applicability and utility of the Thrifty Genotype Hypothesis (TGH) to modern human health remains, in our opinion, unresolved. To move research in this area forward, we first discuss the original formulation of the TGH and its critiques. Second, we trace the TGH to updated hypotheses that are currently at the forefront of the evolutionary medicine literature-namely, the Evolutionary Mismatch Hypothesis. Third, we lay out empirical predictions for updated hypotheses and evaluate them against the current literature. Finally, we discuss study designs that could be fruitful for filling current knowledge gaps; here, we focus on partnerships with subsistence-level groups undergoing lifestyle transitions, and we present data from an ongoing study with the Orang Asli of Malaysia to illustrate this point. Overall, we hope this synthesis will guide new empirical research aimed at understanding how the human evolutionary past interacts with our modern environments to influence cardiometabolic health.
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Affiliation(s)
- Layla Brassington
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Audrey M Arner
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Marina M Watowich
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Jane Damstedt
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Kee Seong Ng
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Yvonne A L Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Vivek V Venkataraman
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Ian J Wallace
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas S Kraft
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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3
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Long E, Zhang J. Evidence for the role of selection for reproductively advantageous alleles in human aging. SCIENCE ADVANCES 2023; 9:eadh4990. [PMID: 38064565 PMCID: PMC10708185 DOI: 10.1126/sciadv.adh4990] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023]
Abstract
The antagonistic pleiotropy hypothesis posits that natural selection for pleiotropic mutations that confer earlier or more reproduction but impair the post-reproductive life causes aging. This hypothesis of the evolutionary origin of aging is supported by case studies but lacks unambiguous genomic evidence. Here, we genomically test this hypothesis using the genotypes, reproductive phenotypes, and death registry of 276,406 U.K. Biobank participants. We observe a strong, negative genetic correlation between reproductive traits and life span. Individuals with higher polygenetic scores for reproduction (PGSR) have lower survivorships to age 76 (SV76), and PGSR increased over birth cohorts from 1940 to 1969. Similar trends are seen from individual genetic variants examined. The antagonistically pleiotropic variants are often associated with cis-regulatory effects across multiple tissues or on multiple target genes. These and other findings support the antagonistic pleiotropy hypothesis of aging in humans and point to potential molecular mechanisms of the reproduction-life-span antagonistic pleiotropy.
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Affiliation(s)
- Erping Long
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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4
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Sun KY, Bai X, Chen S, Bao S, Kapoor M, Zhang C, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Gioia AD, Rajagopal V, Lopez A, Varela JR, Alegre J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Regeneron Genetics Center, RGC-ME Cohort Partners, Cantor M, Thornton T, Kang HM, Overton J, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalog of protein-coding variation in 985,830 individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539329. [PMID: 37214792 PMCID: PMC10197621 DOI: 10.1101/2023.05.09.539329] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Adam Locke
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | - Jesus Alegre
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Roberto Tapia-Conyer
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Pablo Kuri-Morales
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jason Torres
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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5
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Zhu Z, Chen X, Zhang S, Yu R, Qi C, Cheng L, Zhang X. Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective. Hum Genet 2023; 142:1543-1560. [PMID: 37755483 DOI: 10.1007/s00439-023-02602-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023]
Abstract
Comprehending the molecular basis of quantitative genetic variation is a principal goal for complex diseases or traits. Molecular quantitative trait loci (molQTLs) have made it possible to investigate the effects of genetic variants hiding behind large-scale omics data. A deeper understanding of molQTL is urgently required in light of the multi-dimensionalization of omics data to more fully elucidate the pertinent biological mechanisms. Herein, we reviewed molQTLs with the corresponding resource from the omics perspective and further discussed the integrative strategy of GWAS-molQTL to infer their causal effects. Subsequently, we described the opportunities and challenges encountered by molQTL. The case studies showed that molQTL is essential for complex diseases and traits, whether single- or multi-omics QTLs. Overall, we highlighted the functional significance of genetic variants to employ the discovery of molQTL in complex diseases and traits.
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Affiliation(s)
- Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xinyu Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Rui Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Changlu Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China.
| | - Xue Zhang
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
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6
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Lea AJ, Clark AG, Dahl AW, Devinsky O, Garcia AR, Golden CD, Kamau J, Kraft TS, Lim YAL, Martins DJ, Mogoi D, Pajukanta P, Perry GH, Pontzer H, Trumble BC, Urlacher SS, Venkataraman VV, Wallace IJ, Gurven M, Lieberman DE, Ayroles JF. Applying an evolutionary mismatch framework to understand disease susceptibility. PLoS Biol 2023; 21:e3002311. [PMID: 37695771 PMCID: PMC10513379 DOI: 10.1371/journal.pbio.3002311] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/21/2023] [Indexed: 09/13/2023] Open
Abstract
Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.
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Affiliation(s)
- Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Andrew G. Clark
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, New York, United States of America
| | - Andrew W. Dahl
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Orrin Devinsky
- Department of Neurology, NYU Langone Comprehensive Epilepsy Center, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Angela R. Garcia
- Department of Anthropology, Stanford University, Stanford, California, United States of America
| | - Christopher D. Golden
- Department of Nutrition, Harvard T H Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph Kamau
- One Health Centre, Institute of Primate Research, Karen, Nairobi, Kenya
| | - Thomas S. Kraft
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Yvonne A. L. Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Dino J. Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, New York, United States of America
| | - Donald Mogoi
- Department of Medical Services and Public Health, Ministry of Health Laikipia County, Nanyuki, Kenya
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, United States of America
| | - George H. Perry
- Departments of Anthropology and Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Herman Pontzer
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - Benjamin C. Trumble
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Samuel S. Urlacher
- Department of Anthropology, Baylor University, Waco, Texas, United States of America
| | - Vivek V. Venkataraman
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Ian J. Wallace
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Michael Gurven
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Daniel E. Lieberman
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Julien F. Ayroles
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
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7
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Lea AJ, Clark AG, Dahl AW, Devinsky O, Garcia AR, Golden CD, Kamau J, Kraft TS, Lim YAL, Martins D, Mogoi D, Pajukanta P, Perry G, Pontzer H, Trumble BC, Urlacher SS, Venkataraman VV, Wallace IJ, Gurven M, Lieberman D, Ayroles JF. Evolutionary mismatch and the role of GxE interactions in human disease. ARXIV 2023:arXiv:2301.05255v2. [PMID: 36713247 PMCID: PMC9882586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases that were rare throughout human history but are now common. A key idea from anthropology and evolutionary biology-the evolutionary mismatch hypothesis-seeks to explain this phenomenon. It posits that humans evolved in environments that radically differ from the ones experienced by most people today, and thus traits that were advantageous in past environments may now be "mismatched" and disease-causing. This hypothesis is, at its core, a genetic one: it predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions and have differential health effects in ancestral versus modern environments. Here, we discuss how this concept could be leveraged to uncover the genetic architecture of NCDs in a principled way. Specifically, we advocate for partnering with small-scale, subsistence-level groups that are currently transitioning from environments that are arguably more "matched" with their recent evolutionary history to those that are more "mismatched". These populations provide diverse genetic backgrounds as well as the needed levels and types of environmental variation necessary for mapping GxE interactions in an explicit mismatch framework. Such work would make important contributions to our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and sociocultural contexts.
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Affiliation(s)
- Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Child and Brain Development, Canadian Institute for Advanced Research, Toronto, Canada
| | - Andrew G. Clark
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Andrew W. Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Orrin Devinsky
- Department of Neurology, NYU Langone Medical Center, New York, NY, USA
- Comprehensive Epilepsy Center, NYU Langone Medical Center, New York, NY, USA
| | - Angela R. Garcia
- Center for Evolution and Medicine, Arizona State University, Tempe, United States
| | | | - Joseph Kamau
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Thomas S. Kraft
- Department of Anthropology, University of Utah, Salt Lake City, USA
| | - Yvonne A. L. Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Dino Martins
- Turkana Basin Research Institute, Turkana, Kenya
- Department of Ecology and Evolution, Princeton University, Princeton, NJ, USA
| | - Donald Mogoi
- Director at County Government of Laikipia, Nanyuki, Kenya
| | - Paivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - George Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Herman Pontzer
- Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Benjamin C. Trumble
- School of Human Evolution and Social Change, Arizona State University, Tempe, US
- Center for Evolution and Medicine, Arizona State University, Tempe, United States
| | - Samuel S. Urlacher
- Department of Anthropology, Baylor University, Waco, TX, USA
- Child and Brain Development, Canadian Institute for Advanced Research, Toronto, Canada
| | | | - Ian J. Wallace
- Department of Anthropology, University of New Mexico, Albuquerque, USA
| | - Michael Gurven
- Department of Anthropology, University of California: Santa Barbara, Santa Barbara, CA, USA
| | - Daniel Lieberman
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Julien F. Ayroles
- Department of Ecology and Evolution, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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8
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Abraham A, LaBella AL, Capra JA, Rokas A. Mosaic patterns of selection in genomic regions associated with diverse human traits. PLoS Genet 2022; 18:e1010494. [PMID: 36342969 PMCID: PMC9671423 DOI: 10.1371/journal.pgen.1010494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/17/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
Abstract
Natural selection shapes the genetic architecture of many human traits. However, the prevalence of different modes of selection on genomic regions associated with variation in traits remains poorly understood. To address this, we developed an efficient computational framework to calculate positive and negative enrichment of different evolutionary measures among regions associated with complex traits. We applied the framework to summary statistics from >900 genome-wide association studies (GWASs) and 11 evolutionary measures of sequence constraint, population differentiation, and allele age while accounting for linkage disequilibrium, allele frequency, and other potential confounders. We demonstrate that this framework yields consistent results across GWASs with variable sample sizes, numbers of trait-associated SNPs, and analytical approaches. The resulting evolutionary atlas maps diverse signatures of selection on genomic regions associated with complex human traits on an unprecedented scale. We detected positive enrichment for sequence conservation among trait-associated regions for the majority of traits (>77% of 290 high power GWASs), which included reproductive traits. Many traits also exhibited substantial positive enrichment for population differentiation, especially among hair, skin, and pigmentation traits. In contrast, we detected widespread negative enrichment for signatures of balancing selection (51% of GWASs) and absence of enrichment for evolutionary signals in regions associated with late-onset Alzheimer's disease. These results support a pervasive role for negative selection on regions of the human genome that contribute to variation in complex traits, but also demonstrate that diverse modes of evolution are likely to have shaped trait-associated loci. This atlas of evolutionary signatures across the diversity of available GWASs will enable exploration of the relationship between the genetic architecture and evolutionary processes in the human genome.
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Affiliation(s)
- Abin Abraham
- Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Abigail L. LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina, United States of America
- North Carolina Research Center, Kannapolis, North Carolina, United States of America
| | - John A. Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
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9
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Li J, Abedi V, Zand R. Dissecting Polygenic Etiology of Ischemic Stroke in the Era of Precision Medicine. J Clin Med 2022; 11:jcm11205980. [PMID: 36294301 PMCID: PMC9604604 DOI: 10.3390/jcm11205980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 12/03/2022] Open
Abstract
Ischemic stroke (IS), the leading cause of death and disability worldwide, is caused by many modifiable and non-modifiable risk factors. This complex disease is also known for its multiple etiologies with moderate heritability. Polygenic risk scores (PRSs), which have been used to establish a common genetic basis for IS, may contribute to IS risk stratification for disease/outcome prediction and personalized management. Statistical modeling and machine learning algorithms have contributed significantly to this field. For instance, multiple algorithms have been successfully applied to PRS construction and integration of genetic and non-genetic features for outcome prediction to aid in risk stratification for personalized management and prevention measures. PRS derived from variants with effect size estimated based on the summary statistics of a specific subtype shows a stronger association with the matched subtype. The disruption of the extracellular matrix and amyloidosis account for the pathogenesis of cerebral small vessel disease (CSVD). Pathway-specific PRS analyses confirm known and identify novel etiologies related to IS. Some of these specific PRSs (e.g., derived from endothelial cell apoptosis pathway) individually contribute to post-IS mortality and, together with clinical risk factors, better predict post-IS mortality. In this review, we summarize the genetic basis of IS, emphasizing the application of methodologies and algorithms used to construct PRSs and integrate genetics into risk models.
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Affiliation(s)
- Jiang Li
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA
| | - Vida Abedi
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA
- Correspondence: (V.A.); (R.Z.)
| | - Ramin Zand
- Department of Neurology, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA
- Neuroscience Institute, Geisinger Health System, 100 North Academy Avenue, Danville, PA 17822, USA
- Correspondence: (V.A.); (R.Z.)
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10
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Mc Auley MT. DNA methylation in genes associated with the evolution of ageing and disease: A critical review. Ageing Res Rev 2021; 72:101488. [PMID: 34662746 DOI: 10.1016/j.arr.2021.101488] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022]
Abstract
Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.
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Affiliation(s)
- Mark Tomás Mc Auley
- Faculty of Science and Engineering, University of Chester, Exton Park, Chester CH1 4BJ, UK.
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11
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Abstract
In recognition that evolutionary theory is critical for understanding modern human health, eLife is publishing a special issue on evolutionary medicine to showcase recent research in this growing and increasingly interdisciplinary field.
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Affiliation(s)
- George H Perry
- Departments of Anthropology and Biology, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, United States
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12
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Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. The influence of evolutionary history on human health and disease. Nat Rev Genet 2021; 22:269-283. [PMID: 33408383 PMCID: PMC7787134 DOI: 10.1038/s41576-020-00305-9] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2020] [Indexed: 01/29/2023]
Abstract
Nearly all genetic variants that influence disease risk have human-specific origins; however, the systems they influence have ancient roots that often trace back to evolutionary events long before the origin of humans. Here, we review how advances in our understanding of the genetic architectures of diseases, recent human evolution and deep evolutionary history can help explain how and why humans in modern environments become ill. Human populations exhibit differences in the prevalence of many common and rare genetic diseases. These differences are largely the result of the diverse environmental, cultural, demographic and genetic histories of modern human populations. Synthesizing our growing knowledge of evolutionary history with genetic medicine, while accounting for environmental and social factors, will help to achieve the promise of personalized genomics and realize the potential hidden in an individual's DNA sequence to guide clinical decisions. In short, precision medicine is fundamentally evolutionary medicine, and integration of evolutionary perspectives into the clinic will support the realization of its full potential.
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Affiliation(s)
- Mary Lauren Benton
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Computer Science, Baylor University, Waco, TX, USA
| | - Abin Abraham
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, USA
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Antonis Rokas
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - John A Capra
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
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13
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Tseng CC, Wong MC, Liao WT, Chen CJ, Lee SC, Yen JH, Chang SJ. Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases. Int J Mol Sci 2021; 22:ijms22084187. [PMID: 33919522 PMCID: PMC8073710 DOI: 10.3390/ijms22084187] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Variants of transcription factor binding sites (TFBSs) constitute an important part of the human genome. Current evidence demonstrates close links between nucleotides within TFBSs and gene expression. There are multiple pathways through which genomic sequences located in TFBSs regulate gene expression, and recent genome-wide association studies have shown the biological significance of TFBS variation in human phenotypes. However, numerous challenges remain in the study of TFBS polymorphisms. This article aims to cover the current state of understanding as regards the genomic features of TFBSs and TFBS variants; the mechanisms through which TFBS variants regulate gene expression; the approaches to studying the effects of nucleotide changes that create or disrupt TFBSs; the challenges faced in studies of TFBS sequence variations; the effects of natural selection on collections of TFBSs; in addition to the insights gained from the study of TFBS alleles related to gout, its associated comorbidities (increased body mass index, chronic kidney disease, diabetes, dyslipidemia, coronary artery disease, ischemic heart disease, hypertension, hyperuricemia, osteoporosis, and prostate cancer), and the treatment responses of patients.
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Affiliation(s)
- Chia-Chun Tseng
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Man-Chun Wong
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
| | - Chung-Jen Chen
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 80145, Taiwan;
| | - Su-Chen Lee
- Laboratory Diagnosis of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Jeng-Hsien Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu 30010, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung 81148, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
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Li J, Chaudhary DP, Khan A, Griessenauer C, Carey DJ, Zand R, Abedi V. Polygenic Risk Scores Augment Stroke Subtyping. NEUROLOGY-GENETICS 2021; 7:e560. [PMID: 33709033 PMCID: PMC7943221 DOI: 10.1212/nxg.0000000000000560] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022]
Abstract
Objective To determine whether the polygenic risk score (PRS) derived from MEGASTROKE is associated with ischemic stroke (IS) and its subtypes in an independent tertiary health care system and to identify the PRS derived from gene sets of known biological pathways associated with IS. Methods Controls (n = 19,806/7,484, age ≥69/79 years) and cases (n = 1,184/951 for discovery/replication) of acute IS with European ancestry and clinical risk factors were identified by leveraging the Geisinger Electronic Health Record and chart review confirmation. All Geisinger MyCode patients with age ≥69/79 years and without any stroke-related diagnostic codes were included as low risk control. Genetic heritability and genetic correlation between Geisinger and MEGASTROKE (EUR) were calculated using the summary statistics of the genome-wide association study by linkage disequilibrium score regression. All PRS for any stroke (AS), any ischemic stroke (AIS), large artery stroke (LAS), cardioembolic stroke (CES), and small vessel stroke (SVS) were constructed by PRSice-2. Results A moderate heritability (10%–20%) for Geisinger sample as well as the genetic correlation between MEGASTROKE and the Geisinger cohort was identified. Variation of all 5 PRS significantly explained some of the phenotypic variations of Geisinger IS, and the R2 increased by raising the cutoff for the age of controls. PRSLAS, PRSCES, and PRSSVS derived from low-frequency common variants provided the best fit for modeling (R2 = 0.015 for PRSLAS). Gene sets analyses highlighted the association of PRS with Gene Ontology terms (vascular endothelial growth factor, amyloid precursor protein, and atherosclerosis). The PRSLAS, PRSCES, and PRSSVS explained the most variance of the corresponding subtypes of Geisinger IS suggesting shared etiologies and corroborated Geisinger TOAST subtyping. Conclusions We provide the first evidence that PRSs derived from MEGASTROKE have value in identifying shared etiologies and determining stroke subtypes.
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Affiliation(s)
- Jiang Li
- Department of Molecular and Functional Genomics (J.L., D.J.C., V.A.), Weis Center for Research, Geisinger Health System; Neuroscience Institute (D.P.C., A.K., C.G., R.Z.), Geisinger Health System, Danville, PA; Biocomplexity Institute (V.A.), Virginia Tech, Blacksburg, VA; and Research Institute of Neurointervention (C.G.), Paracelsus Medical University, Salzburg, Austria
| | - Durgesh P Chaudhary
- Department of Molecular and Functional Genomics (J.L., D.J.C., V.A.), Weis Center for Research, Geisinger Health System; Neuroscience Institute (D.P.C., A.K., C.G., R.Z.), Geisinger Health System, Danville, PA; Biocomplexity Institute (V.A.), Virginia Tech, Blacksburg, VA; and Research Institute of Neurointervention (C.G.), Paracelsus Medical University, Salzburg, Austria
| | - Ayesha Khan
- Department of Molecular and Functional Genomics (J.L., D.J.C., V.A.), Weis Center for Research, Geisinger Health System; Neuroscience Institute (D.P.C., A.K., C.G., R.Z.), Geisinger Health System, Danville, PA; Biocomplexity Institute (V.A.), Virginia Tech, Blacksburg, VA; and Research Institute of Neurointervention (C.G.), Paracelsus Medical University, Salzburg, Austria
| | - Christoph Griessenauer
- Department of Molecular and Functional Genomics (J.L., D.J.C., V.A.), Weis Center for Research, Geisinger Health System; Neuroscience Institute (D.P.C., A.K., C.G., R.Z.), Geisinger Health System, Danville, PA; Biocomplexity Institute (V.A.), Virginia Tech, Blacksburg, VA; and Research Institute of Neurointervention (C.G.), Paracelsus Medical University, Salzburg, Austria
| | - David J Carey
- Department of Molecular and Functional Genomics (J.L., D.J.C., V.A.), Weis Center for Research, Geisinger Health System; Neuroscience Institute (D.P.C., A.K., C.G., R.Z.), Geisinger Health System, Danville, PA; Biocomplexity Institute (V.A.), Virginia Tech, Blacksburg, VA; and Research Institute of Neurointervention (C.G.), Paracelsus Medical University, Salzburg, Austria
| | - Ramin Zand
- Department of Molecular and Functional Genomics (J.L., D.J.C., V.A.), Weis Center for Research, Geisinger Health System; Neuroscience Institute (D.P.C., A.K., C.G., R.Z.), Geisinger Health System, Danville, PA; Biocomplexity Institute (V.A.), Virginia Tech, Blacksburg, VA; and Research Institute of Neurointervention (C.G.), Paracelsus Medical University, Salzburg, Austria
| | - Vida Abedi
- Department of Molecular and Functional Genomics (J.L., D.J.C., V.A.), Weis Center for Research, Geisinger Health System; Neuroscience Institute (D.P.C., A.K., C.G., R.Z.), Geisinger Health System, Danville, PA; Biocomplexity Institute (V.A.), Virginia Tech, Blacksburg, VA; and Research Institute of Neurointervention (C.G.), Paracelsus Medical University, Salzburg, Austria
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15
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Monnahan PJ, Colicchio J, Fishman L, Macdonald SJ, Kelly JK. Predicting evolutionary change at the DNA level in a natural Mimulus population. PLoS Genet 2021; 17:e1008945. [PMID: 33439857 PMCID: PMC7837469 DOI: 10.1371/journal.pgen.1008945] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 01/26/2021] [Accepted: 10/26/2020] [Indexed: 12/03/2022] Open
Abstract
Evolution by natural selection occurs when the frequencies of genetic variants change because individuals differ in Darwinian fitness components such as survival or reproductive success. Differential fitness has been demonstrated in field studies of many organisms, but it remains unclear how well we can quantitatively predict allele frequency changes from fitness measurements. Here, we characterize natural selection on millions of Single Nucleotide Polymorphisms (SNPs) across the genome of the annual plant Mimulus guttatus. We use fitness estimates to calibrate population genetic models that effectively predict allele frequency changes into the next generation. Hundreds of SNPs experienced "male selection" in 2013 with one allele at each SNP elevated in frequency among successful male gametes relative to the entire population of adults. In the following generation, allele frequencies at these SNPs consistently shifted in the predicted direction. A second year of study revealed that SNPs had effects on both viability and reproductive success with pervasive trade-offs between fitness components. SNPs favored by male selection were, on average, detrimental to survival. These trade-offs (antagonistic pleiotropy and temporal fluctuations in fitness) may be essential to the long-term maintenance of alleles. Despite the challenges of measuring selection in the wild, the strong correlation between predicted and observed allele frequency changes suggests that population genetic models have a much greater role to play in forward-time prediction of evolutionary change.
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Affiliation(s)
- Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Jack Colicchio
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Minnesota, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - John K. Kelly
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
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16
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Wu X, Lin X, Li Q, Wang Z, Zhang N, Tian M, Wang X, Deng H, Tan H. Identification of novel SNPs associated with coronary artery disease and birth weight using a pleiotropic cFDR method. Aging (Albany NY) 2020; 13:3618-3644. [PMID: 33411684 PMCID: PMC7906162 DOI: 10.18632/aging.202322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/11/2020] [Indexed: 11/30/2022]
Abstract
Objectives: Clinical and epidemiological findings indicate an association between coronary artery disease (CAD) and low birth weight (BW). However, the mechanisms underlying this relationship are largely unknown. Here, we aimed to identify novel single-nucleotide polymorphisms (SNPs) associated with CAD, BW, and their shared pleiotropic loci, and to detect the potential causal relationship between CAD and BW. Methods: We first applied a genetic pleiotropic conditional false discovery rate (cFDR) method to two independent genome-wide association studies (GWAS) summary statistics of CAD and BW to estimate the pleiotropic enrichment between them. Then, bi-directional Mendelian randomization (MR) analyses were performed to clarify the causal association between these two traits. Results: By incorporating related traits into a conditional analysis framework, we observed the significant pleiotropic enrichment between CAD and BW. By applying the cFDR level of 0.05, 109 variants were detected for CAD, 203 for BW, and 26 pleiotropic variants for both traits. We identified 11 CAD- and/or BW-associated SNPs that showed more than three of the metabolic quantitative trait loci (metaQTL), protein QTL (pQTL), methylation QTL (meQTL), or expression QTL (eQTL) effects. The pleiotropic SNP rs10774625, located at ATXN2, showed metaQTL, pQTL, meQTL, and eQTL effects simultaneously. Using the bi-directional MR approach, we found a negative association from BW to CAD (odds ratio [OR] = 0.68, 95% confidence interval [CI]: 0.59 to 0.80, p = 1.57× 10-6). Conclusion: We identified several pleiotropic loci between CAD and BW by leveraging GWAS results of related phenotypes and identified a potential causal relationship from BW to CAD. Our findings provide novel insights into the shared biological mechanisms and overlapping genetic heritability between CAD and BW.
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Affiliation(s)
- Xinrui Wu
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Xu Lin
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Qi Li
- Xiangxi Center for Disease Prevention and Control, Jishou 416000, China
| | - Zun Wang
- Xiangya Nursing School, Central South University, Changsha 410013, China
| | - Na Zhang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Mengyuan Tian
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Xiaolei Wang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Hongwen Deng
- School of Basic Medical Science, Central South University, Changsha 410013, China.,Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hongzhuan Tan
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
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Gallo JE, Ochoa JE, Warren HR, Misas E, Correa MM, Gallo-Villegas JA, Bedoya G, Aristizábal D, McEwen JG, Caulfield MJ, Parati G, Clay OK. Hypertension and the roles of the 9p21.3 risk locus: Classic findings and new association data. Int J Cardiol Hypertens 2020; 7:100050. [PMID: 33330845 PMCID: PMC7491459 DOI: 10.1016/j.ijchy.2020.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The band 9p21.3 contains an established genomic risk zone for cardiovascular disease (CVD). Since the initial 2007 Wellcome Trust Case Control Consortium study (WTCCC), the increased CVD risk associated with 9p21.3 has been confirmed by multiple studies in different continents. However, many years later there was still no confirmed report of a corresponding association of 9p21.3 with hypertension, a major CV risk factor, nor with blood pressure (BP). THEORY In this contribution, we review the bipartite haplotype structure of the 9p21.3 risk locus: one block is devoid of protein-coding genes but contains the lead CVD risk SNPs, while the other block contains the first exon and regulatory DNA of the gene for the cell cycle inhibitor p15. We consider how findings from molecular biology offer possibilities of an involvement of p15 in hypertension etiology, with expression of the p15 gene modulated by genetic variation from within the 9p21.3 risk locus. RESULTS We present original results from a Colombian study revealing moderate but persistent association signals for BP and hypertension within the classic 9p21.3 CVD risk locus. These SNPs are mostly confined to a 'hypertension island' that spans less than 60 kb and coincides with the p15 haplotype block. We find confirmation in data originating from much larger, recent European BP studies, albeit with opposite effect directions. CONCLUSION Although more work will be needed to elucidate possible mechanisms, previous findings and new data prompt reconsidering the question of how variation in 9p21.3 might influence hypertension components of cardiovascular risk.
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Key Words
- 1 KG, 1000 Genomes Project
- BP, blood pressure
- Blood pressure levels
- CVD, cardiovascular disease
- DBP, diastolic blood pressure
- EGFR, epidermal growth factor receptor
- GWAS, genome wide association studi(es)
- Genotype-phenotype associations
- Haplotypes
- MAF, minor allele frequency
- RAS, renin angiotensin system
- SBP, systolic blood pressure
- SNP, single nucleotide polymorphism
- TGF-β, transforming growth factor beta
- VSMC, vascular smooth muscle cell(s)
- bp, base pair
- kb, kilobase pair
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Affiliation(s)
- Juan E. Gallo
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan E. Ochoa
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular Neural and Metabolic Sciences, San Luca Hospital, Milan, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Helen R. Warren
- Clinical Pharmacology Department, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- National Institute for Health Research, Barts Cardiovascular Biomedical Research Center, Queen Mary University of London, London, UK
| | - Elizabeth Misas
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | | | | | - Gabriel Bedoya
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Dagnóvar Aristizábal
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- SICOR, Medellín, Colombia
| | - Juan G. McEwen
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Mark J. Caulfield
- Clinical Pharmacology Department, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- National Institute for Health Research, Barts Cardiovascular Biomedical Research Center, Queen Mary University of London, London, UK
| | - Gianfranco Parati
- Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular Neural and Metabolic Sciences, San Luca Hospital, Milan, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Oliver K. Clay
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Translational Microbiology and Emerging Diseases (MICROS), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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19
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LaBella AL, Abraham A, Pichkar Y, Fong SL, Zhang G, Muglia LJ, Abbot P, Rokas A, Capra JA. Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nat Commun 2020; 11:3731. [PMID: 32709900 PMCID: PMC7382462 DOI: 10.1038/s41467-020-17258-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/19/2020] [Indexed: 02/02/2023] Open
Abstract
Currently, there is no comprehensive framework to evaluate the evolutionary forces acting on genomic regions associated with human complex traits and contextualize the relationship between evolution and molecular function. Here, we develop an approach to test for signatures of diverse evolutionary forces on trait-associated genomic regions. We apply our method to regions associated with spontaneous preterm birth (sPTB), a complex disorder of global health concern. We find that sPTB-associated regions harbor diverse evolutionary signatures including conservation, excess population differentiation, accelerated evolution, and balanced polymorphism. Furthermore, we integrate evolutionary context with molecular evidence to hypothesize how these regions contribute to sPTB risk. Finally, we observe enrichment in signatures of diverse evolutionary forces in sPTB-associated regions compared to genomic background. By quantifying multiple evolutionary forces acting on sPTB-associated regions, our approach improves understanding of both functional roles and the mosaic of evolutionary forces acting on loci. Our work provides a blueprint for investigating evolutionary pressures on complex traits.
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Affiliation(s)
- Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Abin Abraham
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Yakov Pichkar
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Sarah L Fong
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, 37235, USA
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- The Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, 45267, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- The Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, 45267, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
- Departments of Biomedical Informatics and Computer Science, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
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20
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Timmers PRHJ, Wilson JF, Joshi PK, Deelen J. Multivariate genomic scan implicates novel loci and haem metabolism in human ageing. Nat Commun 2020; 11:3570. [PMID: 32678081 PMCID: PMC7366647 DOI: 10.1038/s41467-020-17312-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022] Open
Abstract
Ageing phenotypes, such as years lived in good health (healthspan), total years lived (lifespan), and survival until an exceptional old age (longevity), are of interest to us all but require exceptionally large sample sizes to study genetically. Here we combine existing genome-wide association summary statistics for healthspan, parental lifespan, and longevity in a multivariate framework, increasing statistical power, and identify 10 genomic loci which influence all three phenotypes, of which five (near FOXO3, SLC4A7, LINC02513, ZW10, and FGD6) have not been reported previously at genome-wide significance. The majority of these 10 loci are associated with cardiovascular disease and some affect the expression of genes known to change their activity with age. In total, we implicate 78 genes, and find these to be enriched for ageing pathways previously highlighted in model organisms, such as the response to DNA damage, apoptosis, and homeostasis. Finally, we identify a pathway worthy of further study: haem metabolism.
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Affiliation(s)
- Paul R H J Timmers
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - Joris Deelen
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.
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21
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Chignon A, Bon-Baret V, Boulanger MC, Li Z, Argaud D, Bossé Y, Thériault S, Arsenault BJ, Mathieu P. Single-cell expression and Mendelian randomization analyses identify blood genes associated with lifespan and chronic diseases. Commun Biol 2020; 3:206. [PMID: 32358504 PMCID: PMC7195437 DOI: 10.1038/s42003-020-0937-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/10/2020] [Indexed: 12/13/2022] Open
Abstract
The human lifespan is a heritable trait, which is intricately linked to the development of disorders. Here, we show that genetic associations for the parental lifespan are enriched in open chromatin of blood cells. By using blood expression quantitative trait loci (eQTL) derived from 31,684 samples, we identified for the lifespan 125 cis- and 559 trans-regulated expressed genes (eGenes) enriched in adaptive and innate responses. Analysis of blood single-cell expression data showed that eGenes were enriched in dendritic cells (DCs) and the modelling of cell ligand-receptor interactions predicted crosstalk between DCs and a cluster of monocytes with a signature of cytotoxicity. In two-sample Mendelian randomization (MR), we identified 16 blood cis-eGenes causally associated with the lifespan. In MR, the majority of cis-eGene-disorder association pairs had concordant effects with the lifespan. The present work underlined that the lifespan is linked with the immune response and identifies eGenes associated with the lifespan and disorders.
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Affiliation(s)
- Arnaud Chignon
- Laboratory of Cardiovascular Pathobiology, Department of Surgery, Quebec Heart and Lung Institute/Research Center, Laval University, Quebec, QC, Canada
| | - Valentin Bon-Baret
- Laboratory of Cardiovascular Pathobiology, Department of Surgery, Quebec Heart and Lung Institute/Research Center, Laval University, Quebec, QC, Canada
| | - Marie-Chloé Boulanger
- Laboratory of Cardiovascular Pathobiology, Department of Surgery, Quebec Heart and Lung Institute/Research Center, Laval University, Quebec, QC, Canada
| | - Zhonglin Li
- Laboratory of Cardiovascular Pathobiology, Department of Surgery, Quebec Heart and Lung Institute/Research Center, Laval University, Quebec, QC, Canada
| | - Deborah Argaud
- Laboratory of Cardiovascular Pathobiology, Department of Surgery, Quebec Heart and Lung Institute/Research Center, Laval University, Quebec, QC, Canada
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Quebec, QC, Canada
| | - Sébastien Thériault
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec, QC, Canada
| | | | - Patrick Mathieu
- Laboratory of Cardiovascular Pathobiology, Department of Surgery, Quebec Heart and Lung Institute/Research Center, Laval University, Quebec, QC, Canada.
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22
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Williams AC, Hill LJ. The 4 D's of Pellagra and Progress. Int J Tryptophan Res 2020; 13:1178646920910159. [PMID: 32327922 PMCID: PMC7163231 DOI: 10.1177/1178646920910159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Nicotinamide homeostasis is a candidate common denominator to explain smooth transitions, whether demographic, epidemiological or economic. This 'NAD world', dependent on hydrogen-based energy, is not widely recognised as it is neither measured nor viewed from a sufficiently multi-genomic or historical perspective. Reviewing the importance of meat and nicotinamide balances during our co-evolution, recent history suggests that populations only modernise and age well with low fertility on a suitably balanced diet. Imbalances on the low meat side lead to an excess of infectious disease, short lives and boom-bust demographics. On the high side, meat has led to an excess of degenerative, allergic and metabolic disease and low fertility. A 'Goldilocks' diet derived from mixed and sustainable farming (preserving the topsoil) allows for high intellectual capital, height and good health with controlled population growth resulting in economic growth and prosperity. Implementing meat equity worldwide could lead to progress for future generations on 'spaceship' earth by establishing control over population quality, thermostat and biodiversity, if it is not already too late.
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Affiliation(s)
- Adrian C Williams
- Department of Neurology, University
Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lisa J Hill
- School of Biomedical Sciences, Institute
of Clinical Sciences, University of Birmingham, Birmingham, UK
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23
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Genetic hypothesis for the developmental origins of health and disease theory. JOURNAL OF BIO-X RESEARCH 2020. [DOI: 10.1097/jbr.0000000000000056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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24
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Kyriazis M. Ageing Throughout History: The Evolution of Human Lifespan. J Mol Evol 2020; 88:57-65. [PMID: 31197416 DOI: 10.1007/s00239-019-09896-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/06/2019] [Indexed: 12/20/2022]
Abstract
It is not surprising that one of the most complex phenomena in nature is that of ageing. It does not only bear biological interest, but it is also associated with cultural, psychological, social and even philosophical issues. It is therefore to be expected that a great deal of research is being performed in order to study the evolution of ageing and, more specifically, the evolution of human ageing. Historical aspects of this evolution will be discussed. Evidence from a variety of sources shows that the human lifespan is increasing, and may well continue to increase to levels that are difficult to predict. In addition, the most important theories about ageing based on evolutionary principles will be examined. Examples are mutation accumulation, antagonistic pleiotropy and the disposable soma theory. Finally, a section about future evolution of human ageing, based upon newly emerging research, will shed some light and provide speculative-provocative ideas about the future of ageing in humans.
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25
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Abstract
Between the 1930s and 1950s, scientists developed key principles of population genetics to try and explain the aging process. Almost a century later, these aging theories, including antagonistic pleiotropy and mutation accumulation, have been experimentally validated in animals. Although the theories have been much harder to test in humans despite research dating back to the 1970s, recent research is closing this evidence gap. Here we examine the strength of evidence for antagonistic pleiotropy in humans, one of the leading evolutionary explanations for the retention of genetic risk variation for non-communicable diseases. We discuss the analytical tools and types of data that are used to test for patterns of antagonistic pleiotropy and provide a primer of evolutionary theory on types of selection as a guide for understanding this mechanism and how it may manifest in other diseases. We find an abundance of non-experimental evidence for antagonistic pleiotropy in many diseases. In some cases, several studies have independently found corroborating evidence for this mechanism in the same or related sets of diseases including cancer and neurodegenerative diseases. Recent studies also suggest antagonistic pleiotropy may be involved in cardiovascular disease and diabetes. There are also compelling examples of disease risk variants that confer fitness benefits ranging from resistance to other diseases or survival in extreme environments. This provides increasingly strong support for the theory that antagonistic pleiotropic variants have enabled improved fitness but have been traded for higher burden of disease later in life. Future research in this field is required to better understand how this mechanism influences contemporary disease and possible consequences for their treatment.
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26
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Schooling CM, Johnson GD, Grassman J. Effects of blood lead on coronary artery disease and its risk factors: a Mendelian Randomization study. Sci Rep 2019; 9:15995. [PMID: 31690775 PMCID: PMC6831655 DOI: 10.1038/s41598-019-52482-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/09/2019] [Indexed: 11/09/2022] Open
Abstract
Lead is pervasive, although lead exposure has fallen in response to public health efforts. Observationally, lead is positively associated with cardiovascular disease and hypertension. We used separate-sample instrumental variable analysis with genetic instruments (Mendelian randomization) based on 13 single nucleotide polymorphisms (SNP), from a genome wide association study, strongly (p-value < 5 × 10-6) and independently associated with blood lead. These SNPs were applied to a large extensively genotyped coronary artery disease (CAD) study (cases = <76014, controls = <264785) largely based on CARDIoGRAPMplusC4D 1000 Genomes and the UK Biobank SOFT CAD, to the UK Biobank (n = 361,194) for blood pressure and to the DIAGRAM 1000 genomes diabetes case (n = 26,676)-control (n = 132,532) study. SNP-specific Wald estimates were combined using inverse variance weighting, MR-Egger and MR-PRESSO. Genetically instrumented blood lead was not associated with CAD (odds ratio (OR) 1.01 per effect size of log transformed blood lead, 95% confidence interval (CI) 0.97, 1.05), blood pressure (systolic -0.18 mmHg, 95% CI -0.44 to 0.08 and diastolic -0.03 mmHg, 95% CI -0.09 to 0.15) or diabetes (OR 0.98, 95% CI 0.92 to 1.03) using MR-PRESSO estimates corrected for an outlier SNP (rs550057) from the highly pleiotropic gene ABO. Exogenous lead may have different effects from endogenous lead; nevertheless, this study raises questions about the role of blood lead in CAD.
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Affiliation(s)
- C Mary Schooling
- Graduate School of Public Health and Health Policy, City University of New York, New York, United States. .,School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.
| | - Glen D Johnson
- Graduate School of Public Health and Health Policy, City University of New York, New York, United States
| | - Jean Grassman
- Graduate School of Public Health and Health Policy, City University of New York, New York, United States
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27
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Zhao JV, Luo S, Schooling CM. Sex-specific Mendelian randomization study of genetically predicted insulin and cardiovascular events in the UK Biobank. Commun Biol 2019; 2:332. [PMID: 31508506 PMCID: PMC6728387 DOI: 10.1038/s42003-019-0579-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/08/2019] [Indexed: 01/14/2023] Open
Abstract
Insulin drives growth and reproduction which trade-off against longevity. Genetically predicted insulin, i.e., insulin proxied by genetic variants, is positively associated with ischemic heart disease, but sex differences are unclear, despite different disease rates and reproductive strategies by sex. We used Mendelian randomization in 392,010 white British from the UK Biobank to assess the sex-specific role of genetically predicted insulin in myocardial infarction (MI) (14,442 cases, 77% men), angina (21,939 cases, 65% men) and heart failure (5537 cases, 71% men). Genetically predicted insulin was associated with MI (odds ratio (OR) 4.27 per pmol/L higher insulin, 95% confidence interval (CI) 1.60 to 11.3) and angina (OR 2.93, 1.27 to 6.73) in men, but not women (MI OR 0.80, 95% CI 0.23 to 2.84, angina OR 1.10, 95% CI 0.38 to 3.18). Patterns were similar for insulin resistance and heart failure. Mitigating the effects of insulin might address sexual disparities in health.
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Affiliation(s)
- Jie V. Zhao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shan Luo
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - C. Mary Schooling
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- City University of New York, School of Public Health and Health Policy, New York, NY USA
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28
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Chevalier RL. Evolution, kidney development, and chronic kidney disease. Semin Cell Dev Biol 2019; 91:119-131. [PMID: 29857053 PMCID: PMC6281795 DOI: 10.1016/j.semcdb.2018.05.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/29/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]
Abstract
There is a global epidemic of chronic kidney disease (CKD) characterized by a progressive loss of nephrons, ascribed in large part to a rising incidence of hypertension, metabolic syndrome, and type 2 diabetes mellitus. There is a ten-fold variation in nephron number at birth in the general population, and a 50% overall decrease in nephron number in the last decades of life. The vicious cycle of nephron loss stimulating hypertrophy by remaining nephrons and resulting in glomerulosclerosis has been regarded as maladaptive, and only partially responsive to angiotensin inhibition. Advances over the past century in kidney physiology, genetics, and development have elucidated many aspects of nephron formation, structure and function. Parallel advances have been achieved in evolutionary biology, with the emergence of evolutionary medicine, a discipline that promises to provide new insight into the treatment of chronic disease. This review provides a framework for understanding the origins of contemporary developmental nephrology, and recent progress in evolutionary biology. The establishment of evolutionary developmental biology (evo-devo), ecological developmental biology (eco-devo), and developmental origins of health and disease (DOHaD) followed the discovery of the hox gene family, the recognition of the contribution of cumulative environmental stressors to the changing phenotype over the life cycle, and mechanisms of epigenetic regulation. The maturation of evolutionary medicine has contributed to new investigative approaches to cardiovascular disease, cancer, and infectious disease, and promises the same for CKD. By incorporating these principles, developmental nephrology is ideally positioned to answer important questions regarding the fate of nephrons from embryo through senescence.
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Affiliation(s)
- Robert L Chevalier
- Department of Pediatrics, The University of Virginia, P.O. Box 800386, Charlottesville, VA, United States.
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29
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Muntané G, Farré X, Rodríguez JA, Pegueroles C, Hughes DA, de Magalhães JP, Gabaldón T, Navarro A. Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis. Mol Biol Evol 2019; 35:1990-2004. [PMID: 29788292 PMCID: PMC6063263 DOI: 10.1093/molbev/msy105] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan across primate species. We used two different approaches. First, we searched for parallel amino-acid mutations that co-occur with increases in longevity across the primate linage. Twenty-five such amino-acid variants were identified, several of which have been previously reported by studies with different experimental setups and in different model organisms. The genes harboring these mutations are mainly enriched in functional categories such as wound healing, blood coagulation, and cardiovascular disorders. We demonstrate that these pathways are highly enriched for pleiotropic effects, as predicted by the antagonistic pleiotropy theory of aging. A second approach was focused on changes in rates of protein evolution across the primate phylogeny. Using the phylogenetic generalized least squares, we show that some genes exhibit strong correlations between their evolutionary rates and longevity-associated traits. These include genes in the Sphingosine 1-phosphate pathway, PI3K signaling, and the Thrombin/protease-activated receptor pathway, among other cardiovascular processes. Together, these results shed light into human senescence patterns and underscore the power of comparative genomics to identify pathways related to aging and longevity.
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Affiliation(s)
- Gerard Muntané
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Biomedical Network Research Centre on Mental Health (CIBERSAM), Reus, Spain
| | - Xavier Farré
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Juan Antonio Rodríguez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cinta Pegueroles
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - David A Hughes
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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30
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Schooling CM, Ng JCM. Reproduction and longevity: A Mendelian randomization study of gonadotropin-releasing hormone and ischemic heart disease. SSM Popul Health 2019; 8:100411. [PMID: 31198836 PMCID: PMC6556548 DOI: 10.1016/j.ssmph.2019.100411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/17/2019] [Accepted: 05/12/2019] [Indexed: 01/22/2023] Open
Abstract
Background According to well-established evolutionary biology theory there is a trade-off between reproduction and longevity, implying that upregulating the reproductive axis might drive major diseases. We assessed whether the central driver of reproduction gonadotropin-releasing hormone 1 (GnRH1) had a causal effect on the leading cause of global morbidity and mortality, i.e. ischemic heart disease (IHD). As a contrast we similarly examined the role of GnRH2 because it is more a driver of female sexual behavior. Methods We applied strong (p-value <5 × 10-6) and independent genetic predictors of GnRH1 and GnRH2 to an extensively genotyped IHD case (n = 76,014) - control (n = 264,785) study and combined the genetic variant specific Wald estimates using inverse variance weighting (IVW) with multiplicative random effects, and as a sensitivity analysis used weighted median, MR-Egger and MR-PRESSO estimates, and repeated the analysis only using genome wide significant genetic predictors. Findings GnRH1, predicted by 11 genetic variants, was positively associated with IHD (IVW odds ratio (OR) 1.04 per effect size, 95% confidence interval (CI) 1.01 to 1.08), but GnRH2, predicted by 15 genetic variants, was not (IVW OR 0.98, 95% CI 0.95 to 1.02). Estimates from sensitivity analysis were similar. Interpretation GnRH1 is a potential IHD genetic target. Apart from demonstrating a central tenet of evolutionary biology in humans, our study suggests that existing treatments and environmental factors targeting GnRH1, its drivers or consequences could be re-purposed to prevent and treat IHD. Given, the importance of reproduction to the human species, many such exposures likely exist.
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Affiliation(s)
- C M Schooling
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Graduate School of Public Health and Health Policy, The City University of New York, New York, USA
| | - Jack C M Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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31
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Abstract
Bromodomain and extra-terminal (BET) inhibitors, acting via epigenetic mechanisms, have been developed recently as potential new treatments for cancer, including prostate cancer, and inflammatory conditions. Some BET inhibitors, such as RVX-208, also raise high-density lipoprotein cholesterol (HDL-C) and apolipoprotein A-1 levels. A recent meta-analysis of three small trials (n = 798) found that RVX-208 protected against major adverse cardiovascular events (MACE), raising the question as to whether this protective effect was an artefact, a chance finding, or mediated by HDL-C, anti-inflammatory pathways, or other factors. Notably, the effect of RVX-208 on MACE was largely driven by revascularizations, but fewer interventions in the treatment arm could have arisen accidently from favorable effects of RVX-208 on HDL-C and C-reactive protein influencing decisions about patient care. A larger (n = 2400) trial of RVX-208, BETonMACE (NCT02586155), with a more restricted definition of MACE, excluding hospitalizations, will shortly provide clarity. A successful BETonMACE trial would raise the question as to whether RVX-208 operates via lipids, inflammation, or other means, because several previous HDL-C modulators and anti-inflammatories have not provided effective means of treating cardiovascular disease and reducing overall mortality. Re-conceptualizing cardiovascular disease within the well-established evolutionary biology theory that growth and specifically reproduction trade-off against longevity might provide a more comprehensive explanation. Drivers of the gonadotropic axis, particularly androgens, suppress both HDL-C and the immune system while promoting ischemic heart disease and stroke. As such, any effects of RVX-208 on cardiovascular disease might be the result of reducing androgens, of which higher HDL-C and reduced inflammation are biomarkers. Notably, several other effective treatments for cardiovascular disease, such as statins and spironolactone, are known anti-androgens. Results of the BETonMACE trial, and corresponding insight about the mechanism of BET inhibitors in cardiovascular disease, are eagerly awaited.
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32
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Zhao JV, Kwok MK, Schooling CM. Effect of glutamate and aspartate on ischemic heart disease, blood pressure, and diabetes: a Mendelian randomization study. Am J Clin Nutr 2019; 109:1197-1206. [PMID: 30949673 DOI: 10.1093/ajcn/nqy362] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Evolutionary biology suggests reproduction trades off against longevity. Genetic selection in favor of fertility and ischemic heart disease (IHD) exists in humans. Observationally, soy protects against IHD. Soy amino acids, glutamate and aspartate, may lower androgens. No large randomized controlled trials testing their health effects exist. OBJECTIVE Using Mendelian randomization, we assessed how genetically predicted glutamate and aspartate affected IHD, blood pressure, and diabetes. METHODS A separate sample instrumental variable analysis with genetic instruments was used to obtain unconfounded estimates using genetic variants strongly (P < 5 × 10(-8)) and solely associated with glutamate or aspartate applied to an IHD case (n ≤76,014)-control (n ≤ 264,785) study (based on a meta-analysis of CARDIoGRAMplusC4D 1000 Genomes, UK Biobank CAD SOFT GWAS and Myocardial Infarction Genetics and CARDIoGRAM Exome), blood pressure from the UK Biobank (n ≤ 361,194), and the DIAbetes Genetics Replication And Meta-analysis diabetes case (n = 26,676)-control (n = 132,532) study. A weighted median and MR-Egger were used for a sensitivity analysis. RESULTS Glutamate was not associated with IHD, blood pressure, or diabetes after correction for multiple comparisons. Aspartate was inversely associated with IHD (odds ratio (OR) 0.92 per log-transformed standard deviation (SD); 95% confidence interval (CI) 0.88, 0.96) and diastolic blood pressure (-0.03; 95% CI -0.04, -0.02) using inverse variance weighting, but not diabetes (OR 1.00; 95% CI 0.91, 1.09). Associations were robust to the sensitivity analysis. CONCLUSIONS Our findings suggest aspartate may play a role in IHD and blood pressure, potentially underlying cardiovascular benefits of soy. Clarifying the mechanisms would be valuable for IHD prevention and for defining a healthy diet.
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Affiliation(s)
- Jie V Zhao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - M K Kwok
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - C Mary Schooling
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,City University of New York, School of Public Health and Health Policy, New York, NY
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33
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Biological insights into multiple birth: genetic findings from UK Biobank. Eur J Hum Genet 2019; 27:970-979. [PMID: 30760885 DOI: 10.1038/s41431-019-0355-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/15/2018] [Accepted: 01/05/2019] [Indexed: 11/08/2022] Open
Abstract
The tendency to conceive spontaneous dizygotic (DZ) twins is a complex trait with important contributions from both environmental factors and genetic disposition. In earlier work, we identified the first two genes as maternal susceptibility loci for DZ twinning. The aim of this study was to identify genetic variants influencing multiple births and to genetically correlate the findings across a broad range of traits. We performed a genome-wide association study (GWAS) in 8962 participants with Caucasian ancestry from UK Biobank who reported being part of a multiple birth, and 409,591 singleton controls. We replicated the association between FSHB, SMAD3 and twinning in the gene-based (but not SNP-based) test, which had been established in previous genome-wide association analyses in mothers with dizygotic twin offspring. Additionally, we report a novel genetic variant associated with multiple birth, rs428022 at 15q23 (p = 2.84 × 10-8) close to two genes: PIAS1 and SKOR1. Finally, we identified meaningful genetic correlations between being part of a multiple birth and other phenotypes (anthropometric traits, health-related traits, and fertility-related measures). The outcomes of this study provide important new insights into the genetic aetiology of multiple births and fertility, and open up novel directions for fertility and reproduction research.
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34
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Byars SG, Voskarides K. Genes that improved fitness also cost modern humans: evidence for genes with antagonistic effects on longevity and disease. EVOLUTION MEDICINE AND PUBLIC HEALTH 2019; 2019:4-6. [PMID: 30799869 PMCID: PMC6379702 DOI: 10.1093/emph/eoz002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/14/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Sean G Byars
- Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
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35
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Austad SN, Hoffman JM. Response to genes that improved fitness also cost modern humans: evidence for genes with antagonistic effects on longevity and disease. Evol Med Public Health 2019; 2019:7-8. [PMID: 30799868 PMCID: PMC6379704 DOI: 10.1093/emph/eoz003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/16/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Steven N Austad
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jessica M Hoffman
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
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36
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Maisano Delser P, Ravnik-Glavač M, Gasparini P, Glavač D, Mezzavilla M. Genetic Landscape of Slovenians: Past Admixture and Natural Selection Pattern. Front Genet 2018; 9:551. [PMID: 30510563 PMCID: PMC6252347 DOI: 10.3389/fgene.2018.00551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
The Slovenian territory played a crucial role in the past serving as gateway for several human migrations. Previous studies used Slovenians as a source population to interpret different demographic events happened in Europe but not much is known about the genetic background and the demographic history of this population. Here, we analyzed genome-wide data from 96 individuals to shed light on the genetic role and history of the Slovenian population. Y chromosome diversity splits into two major haplogroups R1b and R1a with the latter suggesting a genetic contribution from the steppe. Slovenian individuals are more closely related to Northern and Eastern European populations than Southern European populations even though they are geographically closer. This pattern is confirmed by an admixture and clustering analysis. We also identified a single stream of admixture events between the Slovenians with Sardinians and Russians around ∼2630 BCE (2149-3112). Using ancient samples, we found a significant admixture in Slovenians using Yamnaya and the early Neolithic Hungarians as sources, dated around ∼1762 BCE (1099-2426) suggesting a strong contribution from the steppe to the foundation of the observed modern genetic diversity. Finally, we looked for signals of selection in candidate variants and we found significant hits in HERC2 and FADS responsible for blue eye color and synthesis of long-chain unsaturated fatty acids, respectively, when Slovenians were compared to Southern Europeans. While the comparison was done with Eastern Europeans, we identified significant signals in PKD2L1 and IL6R which are genes associated with taste and coronary artery disease, respectively.
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Affiliation(s)
- Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Metka Ravnik-Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Massimo Mezzavilla
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
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Fox M. 'Evolutionary medicine' perspectives on Alzheimer's Disease: Review and new directions. Ageing Res Rev 2018; 47:140-148. [PMID: 30059789 PMCID: PMC6195455 DOI: 10.1016/j.arr.2018.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
Evolution by natural selection eliminates maladaptive traits from a species, and yet Alzheimer's Disease (AD) persists with rapidly increasing prevalence globally. This apparent paradox begs an explanation within the framework of evolutionary sciences. Here, I summarize and critique previously proposed theories to explain human susceptibility to AD, grouped into 8 distinct hypotheses based on the concepts of novel extension of the lifespan; lack of selective pressure during the post-reproductive phase; antagonistic pleiotropy; rapid brain evolution; delayed neuropathy by selection for grandmothering; novel alleles selected to delay neuropathy; by-product of selection against cardiovascular disease; and thrifty genotype. Subsequently, I describe a new hypothesis inspired by the concept of mismatched environments. Many of the factors that enhance AD risk today may have been absent or functioned differently before the modern era, potentially making AD a less common affliction for age-matched individuals before industrialization and for the majority of human history. Future research is needed to further explore whether changes in environments and lifestyles across human history moderate risk factors and susceptibility to AD.
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Affiliation(s)
- Molly Fox
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, 90095, USA; Department of Anthropology, University of California Los Angeles, Los Angeles, CA, 90095, USA.
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Schooling CM, Luo S, Au Yeung SL, Thompson DJ, Karthikeyan S, Bolton TR, Mason AM, Ingelsson E, Burgess S. Genetic predictors of testosterone and their associations with cardiovascular disease and risk factors: A Mendelian randomization investigation. Int J Cardiol 2018; 267:171-176. [PMID: 29804699 PMCID: PMC6024225 DOI: 10.1016/j.ijcard.2018.05.051] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 04/02/2018] [Accepted: 05/15/2018] [Indexed: 11/17/2022]
Abstract
BACKGROUND Testosterone supplementation has been linked to increased cardiovascular disease risk in some observational studies. The causal role of testosterone can be investigated using a Mendelian randomization approach. METHODS AND RESULTS We assessed genetic associations of variants in two gene regions (SHBG and JMJD1C) with several cardiovascular risk factors (lipids, adiponectin, blood pressure, anthropometric traits) plus male pattern baldness, including control outcomes and potential mediators. We assessed genetic associations with coronary artery disease (CAD) risk in the CARDIoGRAMplusC4D consortium (171,191 individuals including 60,801 cases), and associations with CAD and ischaemic stroke risk in the UK Biobank (367,643 individuals including 25,352 CAD cases and 3650 ischaemic stroke cases). Genetic predictors of increased serum testosterone were associated with lipids, blood pressure, and height. There was some evidence of an association with risk of CAD (SHBG gene region: odds ratio (OR) 0.95 per 1 unit increase in log-transformed testosterone [95% confidence interval: 0.81-1.12, p = 0.55]; JMJD1C gene region: OR 1.24 [1.01-1.51, p = 0.04]) and ischaemic stroke both overall (SHBG: OR 1.05 [0.64, 1.73, p = 0.83]; JMJD1C: OR 2.52 [1.33, 4.77, p = 0.005]) and in men. However, associations with some control outcomes were in the opposite direction to that expected. CONCLUSIONS Sex hormone-related mechanisms appear to be relevant to cardiovascular risk factors and for stroke (particularly for men). However, the extent that these findings are specifically informative about endogenous testosterone or testosterone supplementation is unclear. These findings underline a fundamental limitation for the use of Mendelian randomization where biological knowledge about the function of genetic variants is uncertain.
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Affiliation(s)
- C Mary Schooling
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region; School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Shan Luo
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Shiu Lun Au Yeung
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Savita Karthikeyan
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Thomas R Bolton
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Amy M Mason
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Erik Ingelsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Stephen Burgess
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, Cambridgeshire, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge, Cambridgeshire, UK; Homerton College, University of Cambridge, Cambridge, Cambridgeshire, UK.
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Abstract
Between the 1930s and 50s, evolutionary biologists developed a successful theory of why organisms age, firmly rooted in population genetic principles. By the 1980s the evolution of aging had a secure experimental basis. Since the force of selection declines with age, aging evolves due to mutation accumulation or a benefit to fitness early in life. Here we review major insights and challenges that have emerged over the last 35 years: selection does not always necessarily decline with age; higher extrinsic (i.e., environmentally caused) mortality does not always accelerate aging; conserved pathways control aging rate; senescence patterns are more diverse than previously thought; aging is not universal; trade-offs involving lifespan can be 'broken'; aging might be 'druggable'; and human life expectancy continues to rise but compressing late-life morbidity remains a pressing challenge.
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Affiliation(s)
- Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Linda Partridge
- Max Planck Institute for Biology of Aging, Joseph-Stelzmann-Strasse 9b, D-50931, Cologne, Germany.
- Institute for Healthy Aging and GEE, University College London, Darwin Building, Gower Street, London, WC1E6BT, UK.
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40
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Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning. Methods 2018; 145:41-50. [DOI: 10.1016/j.ymeth.2018.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/10/2018] [Accepted: 06/01/2018] [Indexed: 12/20/2022] Open
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Kodali HP, Pavilonis BT, Schooling CM. Effects of copper and zinc on ischemic heart disease and myocardial infarction: a Mendelian randomization study. Am J Clin Nutr 2018; 108:237-242. [PMID: 29982268 DOI: 10.1093/ajcn/nqy129] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/22/2018] [Indexed: 11/14/2022] Open
Abstract
Background Despite great progress in prevention and control, ischemic heart disease (IHD) remains a leading cause of global morbidity and mortality. Diet plays a key role in IHD, but a comprehensive delineation of the role of dietary factors in IHD is not yet quite complete. Objective The aim of this study was to test the long-standing hypothesis that copper is protective and zinc harmful in IHD. Design We used separate-sample instrumental variable analysis with genetic instruments (Mendelian randomization). We obtained single nucleotide polymorphisms (SNPs) from a genome wide association study, strongly (P value < 5 × 10-8) and independently associated with erythrocyte copper and zinc. We applied these genetic predictors of copper and zinc to the largest, most extensively genotyped IHD case (n ≤ 76014)-control (n ≤ 264785) study, based largely on CARDIoGRAMplusC4D 1000 Genomes and the UK Biobank SOFT CAD, to obtain SNP-specific Wald estimates for the effects of copper and zinc on IHD, which were combined through the use of inverse variance weighting. Sensitivity analysis included use of the MR-Egger method, and reanalysis including SNPs independently associated with erythrocyte copper and zinc at P value < 5 × 10-6. Results Genetically instrumented copper was negatively associated with IHD (OR: 0.94; 95% CI: 0.90, 0.98). Genetically instrumented zinc was positively associated with IHD (OR: 1.06; 95% CI: 1.02, 1.11). Sensitivity analysis via MR-Egger gave no indication of unknown pleiotropy; less strongly associated SNPs gave similar results for copper. Conclusion Genetic validation of a long-standing hypothesis suggests that further investigation of the effects, particularly of copper, on IHD may provide a practical means of reducing the leading cause of mortality and morbidity.
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Affiliation(s)
- Hanish P Kodali
- CUNY Graduate School of Public Health and Health Policy, New York, NY
| | - Brian T Pavilonis
- CUNY Graduate School of Public Health and Health Policy, New York, NY
| | - C Mary Schooling
- CUNY Graduate School of Public Health and Health Policy, New York, NY.,School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Corbett S, Courtiol A, Lummaa V, Moorad J, Stearns S. The transition to modernity and chronic disease: mismatch and natural selection. Nat Rev Genet 2018; 19:419-430. [DOI: 10.1038/s41576-018-0012-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Stearns SC. Outstanding research opportunities at the interface of evolution and medicine. Nat Ecol Evol 2017; 2:3-4. [PMID: 29180708 DOI: 10.1038/s41559-017-0409-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephen C Stearns
- Department of Ecology and Evolutionary Biology, Yale University, Box 208106, New Haven, CT, 06520, USA.
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Schooling CM. Insights From the Positive Association of Height With Incident Venous Thromboembolism. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.117.001911. [PMID: 28874397 DOI: 10.1161/circgenetics.117.001911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- C Mary Schooling
- From the School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China and City University of New York Graduate School of Public Health and Health Policy.
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