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James K, Oluwole OG. Leveraging human-mouse studies to advance the genetics of hearing impairment in Africa. J Gene Med 2024; 26:e3714. [PMID: 38949079 DOI: 10.1002/jgm.3714] [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: 12/09/2023] [Revised: 04/10/2024] [Accepted: 06/02/2024] [Indexed: 07/02/2024] Open
Abstract
Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, in this review, we investigate the potential of using genetic mouse models to identify genetic markers that can disrupt hearing thresholds in mice and then target the hearing-enriched orthologues and loci in humans. Currently, little is known about the real prevalence of genes that cause hearing impairment (HI) in Africa. Pre-screening mouse cell lines to identify orthologues of interest has the potential to improve the genetic diagnosis for HI in Africa to a significant percentage, for example, 10-20%. Furthermore, the functionality of a candidate gene derived from mouse screening with heterogeneous genetic backgrounds and multi-omic approaches can shed light on the molecular, genetic heterogeneity and plausible mode of inheritance of a gene in hearing-impaired individuals especially in the absence of large families to investigate.
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Affiliation(s)
- Kili James
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Oluwafemi G Oluwole
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biomedical Research Centre, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Bae H, Gurinovich A, Karagiannis TT, Song Z, Leshchyk A, Li M, Andersen SL, Arbeev K, Yashin A, Zmuda J, An P, Feitosa M, Giuliani C, Franceschi C, Garagnani P, Mengel-From J, Atzmon G, Barzilai N, Puca A, Schork NJ, Perls TT, Sebastiani P. A Genome-Wide Association Study of 2304 Extreme Longevity Cases Identifies Novel Longevity Variants. Int J Mol Sci 2022; 24:ijms24010116. [PMID: 36613555 PMCID: PMC9820206 DOI: 10.3390/ijms24010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
We performed a genome-wide association study (GWAS) of human extreme longevity (EL), defined as surviving past the 99th survival percentile, by aggregating data from four centenarian studies. The combined data included 2304 EL cases and 5879 controls. The analysis identified a locus in CDKN2B-AS1 (rs6475609, p = 7.13 × 10-8) that almost reached genome-wide significance and four additional loci that were suggestively significant. Among these, a novel rare variant (rs145265196) on chromosome 11 had much higher longevity allele frequencies in cases of Ashkenazi Jewish and Southern Italian ancestry compared to cases of other European ancestries. We also correlated EL-associated SNPs with serum proteins to link our findings to potential biological mechanisms that may be related to EL and are under genetic regulation. The findings from the proteomic analyses suggested that longevity-promoting alleles of significant genetic variants either provided EL cases with more youthful molecular profiles compared to controls or provided some form of protection from other illnesses, such as Alzheimer's disease, and disease progressions.
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Affiliation(s)
- Harold Bae
- Biostatistics Program, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
- Correspondence:
| | - Anastasia Gurinovich
- Center for Quantitative Methods and Data Science, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA 02111, USA
| | - Tanya T. Karagiannis
- Center for Quantitative Methods and Data Science, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA 02111, USA
| | - Zeyuan Song
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Anastasia Leshchyk
- Division of Computational Biomedicine, Boston University, Boston, MA 02215, USA
| | - Mengze Li
- Division of Computational Biomedicine, Boston University, Boston, MA 02215, USA
| | - Stacy L. Andersen
- Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02215, USA
| | - Konstantin Arbeev
- Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Anatoliy Yashin
- Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Joseph Zmuda
- School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ping An
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mary Feitosa
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Department of Applied Mathematics and Laboratory of Systems Medicine of Aging, Lobachevsky University, 603950 Nizhny Novgorod, Russia
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
| | - Jonas Mengel-From
- Department of Public Health, University of Southern Denmark, 5230 Odense, Denmark
| | - Gil Atzmon
- Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10451, USA
| | - Nir Barzilai
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10451, USA
| | - Annibale Puca
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84084 Fisciano, Italy
- Cardiovascular Research Unit, IRCCS MultiMedica, 20099 Milan, Italy
| | - Nicholas J. Schork
- Quantitative Medicine & Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Thomas T. Perls
- Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02215, USA
| | - Paola Sebastiani
- Center for Quantitative Methods and Data Science, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA 02111, USA
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Gurinovich A, Andersen SL, Puca A, Atzmon G, Barzilai N, Sebastiani P. Varying Effects of APOE Alleles on Extreme Longevity in European Ethnicities. J Gerontol A Biol Sci Med Sci 2020; 74:S45-S51. [PMID: 31724059 DOI: 10.1093/gerona/glz179] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Indexed: 12/19/2022] Open
Abstract
APOE is a well-studied gene with multiple effects on aging and longevity. The gene has three alleles: e2, e3, and e4, whose frequencies vary by ethnicity. While the e2 is associated with healthy cognitive aging, the e4 allele is associated with Alzheimer's disease and early mortality and therefore its prevalence among people with extreme longevity (EL) is low. Using the PopCluster algorithm, we identified several ethnically different clusters in which the effect of the e2 and e4 alleles on EL changed substantially. For example, PopCluster discovered a large group of 1,309 subjects enriched of Southern Italian genetic ancestry with weaker protective effect of e2 (odds ratio [OR] = 1.27, p = .14) and weaker damaging effect of e4 (OR = 0.82, p = .31) on the phenotype of EL compared to other European ethnicities. Further analysis of this cluster suggests that the odds for EL in carriers of the e4 allele with Southern Italian genetic ancestry differ depending on whether they live in the United States (OR = 0.29, p = .009) or Italy (OR = 1.21, p = .38). PopCluster also found clusters enriched of subjects with Danish ancestry with varying effect of e2 on EL. The country of residence (Denmark or United States) appears to change the odds for EL in the e2 carriers.
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Affiliation(s)
- Anastasia Gurinovich
- Bioinformatics Program, Boston University, Massachusetts.,Department of Biostatistics, Boston University School of Public Health, Massachusetts
| | | | - Annibale Puca
- Department of Medicine and Surgery, University of Salerno, Fisciano, SA, Italy.,Cardiovascular Research Unit, IRCCS MultiMedica, Sesto San Giovanni, MI, Italy
| | - Gil Atzmon
- Faculty of Natural Science, University of Haifa, Israel.,Albert Einstein College of Medicine, Bronx, New York
| | - Nir Barzilai
- Albert Einstein College of Medicine, Bronx, New York
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Massachusetts
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Cui Y, Zhang F, Ma P, Fan L, Ning C, Zhang Q, Zhang W, Wang L, Robbeets M. Bioarchaeological perspective on the expansion of Transeurasian languages in Neolithic Amur River basin. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e15. [PMID: 37588356 PMCID: PMC10427477 DOI: 10.1017/ehs.2020.16] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Owing to the development of sequencing technology, paleogenomics has become an important source of information on human migration and admixture, complementing findings from archaeology and linguistics. In this study, we retrieved the whole genome and Y chromosome lineage from late Neolithic Honghe individuals in the Middle Amur region in order to provide a bioarchaeological perspective on the origin and expansion of Transeurasian languages in the Amur River basin. Our genetic analysis reveals that the population of the Amur River basin has a stable and continuous genetic structure from the Mesolithic Age up to date. Integrating linguistic and archaeological evidence, we support the hypothesis that the expansion of the Transeurasian language system in the Amur River basin is related to the agricultural development and expansion of the southern Hongshan culture. The spread of agricultural technology resulted in the addition of millet cultivation to the original subsistence mode of fishing and hunting. It played a vital role in the expansion of the population of the region, which in its turn has contributed to the spread of language.
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Affiliation(s)
- Yinqiu Cui
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun130012, China
- School of Life Sciences, Jilin University, Changchun130012, China
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun130012, China
| | - Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun130012, China
| | - Linyuan Fan
- School of Life Sciences, Jilin University, Changchun130012, China
| | - Chao Ning
- School of Life Sciences, Jilin University, Changchun130012, China
- Eurasia3angle, Max Planck Institute for the Science of Human History, JenaD-07745, Germany
| | - Quanchao Zhang
- School of Archaeology, Jilin University, Changchun130012, China
| | - Wei Zhang
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin150008, P. R. China
| | - Lixin Wang
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun130012, China
| | - Martine Robbeets
- Eurasia3angle, Max Planck Institute for the Science of Human History, JenaD-07745, Germany
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