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Parker J, O’Brien C, Hawrelak J, Gersh FL. Polycystic Ovary Syndrome: An Evolutionary Adaptation to Lifestyle and the Environment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031336. [PMID: 35162359 PMCID: PMC8835454 DOI: 10.3390/ijerph19031336] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023]
Abstract
Polycystic ovary syndrome (PCOS) is increasingly recognized as a complex metabolic disorder that manifests in genetically susceptible women following a range of negative exposures to nutritional and environmental factors related to contemporary lifestyle. The hypothesis that PCOS phenotypes are derived from a mismatch between ancient genetic survival mechanisms and modern lifestyle practices is supported by a diversity of research findings. The proposed evolutionary model of the pathogenesis of PCOS incorporates evidence related to evolutionary theory, genetic studies, in utero developmental epigenetic programming, transgenerational inheritance, metabolic features including insulin resistance, obesity and the apparent paradox of lean phenotypes, reproductive effects and subfertility, the impact of the microbiome and dysbiosis, endocrine-disrupting chemical exposure, and the influence of lifestyle factors such as poor-quality diet and physical inactivity. Based on these premises, the diverse lines of research are synthesized into a composite evolutionary model of the pathogenesis of PCOS. It is hoped that this model will assist clinicians and patients to understand the importance of lifestyle interventions in the prevention and management of PCOS and provide a conceptual framework for future research. It is appreciated that this theory represents a synthesis of the current evidence and that it is expected to evolve and change over time.
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Affiliation(s)
- Jim Parker
- School of Medicine, University of Wollongong, Wollongong 2500, Australia
- Correspondence:
| | - Claire O’Brien
- Faculty of Science and Technology, University of Canberra, Bruce 2617, Australia;
| | - Jason Hawrelak
- College of Health and Medicine, University of Tasmania, Hobart 7005, Australia;
| | - Felice L. Gersh
- College of Medicine, University of Arizona, Tucson, AZ 85004, USA;
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2
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Muotri AR. "Archealization" of human brain organoids. Neuropsychopharmacology 2022; 47:401-402. [PMID: 34389807 PMCID: PMC8616917 DOI: 10.1038/s41386-021-01133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Alysson R. Muotri
- grid.266100.30000 0001 2107 4242Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Archealization Center (ArchC), Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, Stem Cell Program, Institute for Genomic Medicine, University of California San Diego, La Jolla, CA USA
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3
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Chiang CWK. The Opportunities and Challenges of Integrating Population Histories Into Genetic Studies for Diverse Populations: A Motivating Example From Native Hawaiians. Front Genet 2021; 12:643883. [PMID: 34646295 PMCID: PMC8503554 DOI: 10.3389/fgene.2021.643883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
There is a well-recognized need to include diverse populations in genetic studies, but several obstacles continue to be prohibitive, including (but are not limited to) the difficulty of recruiting individuals from diverse populations in large numbers and the lack of representation in available genomic references. These obstacles notwithstanding, studying multiple diverse populations would provide informative, population-specific insights. Using Native Hawaiians as an example of an understudied population with a unique evolutionary history, I will argue that by developing key genomic resources and integrating evolutionary thinking into genetic epidemiology, we will have the opportunity to efficiently advance our knowledge of the genetic risk factors, ameliorate health disparity, and improve healthcare in this underserved population.
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Affiliation(s)
- Charleston W K Chiang
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, United States
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4
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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: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [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
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.252890.40000 0001 2111 2894Department of Computer Science, Baylor University, Waco, TX USA
| | - Abin Abraham
- grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN USA
| | - Abigail L. LaBella
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Patrick Abbot
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Antonis Rokas
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - John A. Capra
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA ,grid.266102.10000 0001 2297 6811Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA USA
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5
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Liu L, Sanderford MD, Patel R, Chandrashekar P, Gibson G, Kumar S. Biological relevance of computationally predicted pathogenicity of noncoding variants. Nat Commun 2019; 10:330. [PMID: 30659175 PMCID: PMC6338804 DOI: 10.1038/s41467-018-08270-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 12/19/2018] [Indexed: 11/15/2022] Open
Abstract
Computational prediction of the phenotypic propensities of noncoding single nucleotide variants typically combines annotation of genomic, functional and evolutionary attributes into a single score. Here, we evaluate if the claimed excellent accuracies of these predictions translate into high rates of success in addressing questions important in biological research, such as fine mapping causal variants, distinguishing pathogenic allele(s) at a given position, and prioritizing variants for genetic risk assessment. A significant disconnect is found to exist between the statistical modelling and biological performance of predictive approaches. We discuss fundamental reasons underlying these deficiencies and suggest that future improvements of computational predictions need to address confounding of allelic, positional and regional effects as well as imbalance of the proportion of true positive variants in candidate lists. Researchers can make use of a variety of computational tools to prioritize genetic variants and predict their pathogenicity. Here, the authors evaluate the performance of six of these tools in three typical biological tasks and find generally low concordance of predictions and experimental confirmation.
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Affiliation(s)
- Li Liu
- College of Health Solutions, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Maxwell D Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Ravi Patel
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Pramod Chandrashekar
- College of Health Solutions, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Greg Gibson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA. .,Department of Biology, Temple University, Philadelphia, PA, USA.
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6
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Sato DX, Kawata M. Positive and balancing selection on SLC18A1 gene associated with psychiatric disorders and human-unique personality traits. Evol Lett 2018; 2:499-510. [PMID: 30283697 PMCID: PMC6145502 DOI: 10.1002/evl3.81] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/07/2018] [Accepted: 07/30/2018] [Indexed: 12/15/2022] Open
Abstract
Maintenance of genetic variants susceptible to psychiatric disorders is one of the intriguing evolutionary enigmas. The present study detects three psychiatric disorder‐relevant genes (CLSTN2, FAT1, and SLC18A1) that have been under positive selection during the human evolution. In particular, SLC18A1 (vesicular monoamine transporter 1; VMAT1) gene has a human‐unique variant (rs1390938, Thr136Ile), which is associated with bipolar disorders and/or the anxiety‐related personality traits. 136Ile shows relatively high (20–61%) frequency in non‐African populations, and Tajima's D reports a significant peak around the Thr136Ile site, suggesting that this polymorphism has been positively maintained by balancing selection in non‐African populations. Moreover, Coalescent simulations predict that 136Ile originated around 100,000 years ago, the time being generally associated with the Out‐of‐Africa migration of modern humans. Our study sheds new light on a gene in monoamine pathway as a strong candidate contributing to human‐unique psychological traits.
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Affiliation(s)
- Daiki X Sato
- Graduate School of Life Sciences, Tohoku University Sendai 980-8578 Japan
| | - Masakado Kawata
- Graduate School of Life Sciences, Tohoku University Sendai 980-8578 Japan
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Spataro N, Rodríguez JA, Navarro A, Bosch E. Properties of human disease genes and the role of genes linked to Mendelian disorders in complex disease aetiology. Hum Mol Genet 2017; 26:489-500. [PMID: 28053046 PMCID: PMC5409085 DOI: 10.1093/hmg/ddw405] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 11/10/2016] [Accepted: 11/23/2016] [Indexed: 01/19/2023] Open
Abstract
Do genes presenting variation that has been linked to human disease have different biological properties than genes that have never been related to disease? What is the relationship between disease and fitness? Are the evolutionary pressures that affect genes linked to Mendelian diseases the same to those acting on genes whose variation contributes to complex disorders? The answers to these questions could shed light on the architecture of human genetic disorders and may have relevant implications when designing mapping strategies in future genetic studies. Here we show that, relative to non-disease genes, human disease (HD) genes have specific evolutionary profiles and protein network properties. Additionally, our results indicate that the mutation-selection balance renders an insufficient account of the evolutionary history of some HD genes and that adaptive selection could also contribute to shape their genetic architecture. Notably, several biological features of HD genes depend on the type of pathology (complex or Mendelian) with which they are related. For example, genes harbouring both causal variants for Mendelian disorders and risk factors for complex disease traits (Complex-Mendelian genes), tend to present higher functional relevance in the protein network and higher expression levels than genes associated only with complex disorders. Moreover, risk variants in Complex-Mendelian genes tend to present higher odds ratios than those on genes associated with the same complex disorders but with no link to Mendelian diseases. Taken together, our results suggest that genetic variation at genes linked to Mendelian disorders plays an important role in driving susceptibility to complex disease.
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Affiliation(s)
- Nino Spataro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juan Antonio Rodríguez
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- National Institute for Bioinformatics (INB), Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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8
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Neural plasticity and network remodeling: From concepts to pathology. Neuroscience 2017; 344:326-345. [PMID: 28069532 DOI: 10.1016/j.neuroscience.2016.12.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 11/22/2022]
Abstract
Neuroplasticity has been subject to a great deal of research in the last century. Recently, significant emphasis has been placed on the global effect of localized plastic changes throughout the central nervous system, and on how these changes integrate in a pathological context. Specifically, alterations of network functionality have been described in various pathological contexts to which corresponding structural alterations have been proposed. However, considering the amount of literature and the different pathological contexts, an integration of this information is still lacking. In this paper we will review the concepts of neural plasticity as well as their repercussions on network remodeling and provide a possible explanation to how these two concepts relate to each other. We will further examine how alterations in different pathological contexts may relate to each other and will discuss the concept of plasticity diseases, its models and implications.
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9
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Assaf ZJ, Petrov DA, Blundell JR. Obstruction of adaptation in diploids by recessive, strongly deleterious alleles. Proc Natl Acad Sci U S A 2015; 112:E2658-66. [PMID: 25941393 PMCID: PMC4443376 DOI: 10.1073/pnas.1424949112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recessive deleterious mutations are common, causing many genetic disorders in humans and producing inbreeding depression in the majority of sexually reproducing diploids. The abundance of recessive deleterious mutations in natural populations suggests they are likely to be present on a chromosome when a new adaptive mutation occurs, yet the dynamics of recessive deleterious hitchhikers and their impact on adaptation remains poorly understood. Here we model how a recessive deleterious mutation impacts the fate of a genetically linked dominant beneficial mutation. The frequency trajectory of the adaptive mutation in this case is dramatically altered and results in what we have termed a "staggered sweep." It is named for its three-phased trajectory: (i) Initially, the two linked mutations have a selective advantage while rare and will increase in frequency together, then (ii), at higher frequencies, the recessive hitchhiker is exposed to selection and can cause a balanced state via heterozygote advantage (the staggered phase), and (iii) finally, if recombination unlinks the two mutations, then the beneficial mutation can complete the sweep to fixation. Using both analytics and simulations, we show that strongly deleterious recessive mutations can substantially decrease the probability of fixation for nearby beneficial mutations, thus creating zones in the genome where adaptation is suppressed. These mutations can also significantly prolong the number of generations a beneficial mutation takes to sweep to fixation, and cause the genomic signature of selection to resemble that of soft or partial sweeps. We show that recessive deleterious variation could impact adaptation in humans and Drosophila.
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Affiliation(s)
| | | | - Jamie R Blundell
- Biology, and Applied Physics, Stanford University, Stanford, CA 94305
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10
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Ogawa LM, Vallender EJ. Evolutionary conservation in genes underlying human psychiatric disorders. Front Hum Neurosci 2014; 8:283. [PMID: 24834046 PMCID: PMC4018557 DOI: 10.3389/fnhum.2014.00283] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/16/2014] [Indexed: 01/07/2023] Open
Abstract
Many psychiatric diseases observed in humans have tenuous or absent analogs in other species. Most notable among these are schizophrenia and autism. One hypothesis has posited that these diseases have arisen as a consequence of human brain evolution, for example, that the same processes that led to advances in cognition, language, and executive function also resulted in novel diseases in humans when dysfunctional. Here, the molecular evolution of the protein-coding regions of genes associated with these and other psychiatric disorders are compared among species. Genes associated with psychiatric disorders are drawn from the literature and orthologous sequences are collected from eleven primate species (human, chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, baboon, marmoset, squirrel monkey, and galago) and 34 non-primate mammalian species. Evolutionary parameters, including dN/dS, are calculated for each gene and compared between disease classes and among species, focusing on humans and primates compared to other mammals, and on large-brained taxa (cetaceans, rhinoceros, walrus, bear, and elephant) compared to their small-brained sister species. Evidence of differential selection in humans to the exclusion of non-human primates was absent, however elevated dN/dS was detected in catarrhines as a whole, as well as in cetaceans, possibly as part of a more general trend. Although this may suggest that protein changes associated with schizophrenia and autism are not a cost of the higher brain function found in humans, it may also point to insufficiencies in the study of these diseases including incomplete or inaccurate gene association lists and/or a greater role of regulatory changes or copy number variation. Through this work a better understanding of the molecular evolution of the human brain, the pathophysiology of disease, and the genetic basis of human psychiatric disease is gained.
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Affiliation(s)
- Lisa M Ogawa
- Division of Neuroscience, New England Primate Research Center, Harvard Medical School Southborough, MA, USA
| | - Eric J Vallender
- Division of Neuroscience, New England Primate Research Center, Harvard Medical School Southborough, MA, USA
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