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Katsumata Y, Fardo DW, Shade LMP, Nelson PT. LATE-NC risk alleles (in TMEM106B, GRN, and ABCC9 genes) among persons with African ancestry. J Neuropathol Exp Neurol 2023; 82:760-768. [PMID: 37528055 PMCID: PMC10440720 DOI: 10.1093/jnen/nlad059] [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] [Indexed: 08/03/2023] Open
Abstract
Limbic-predominant age-related TDP-43 encephalopathy (LATE) affects approximately one-third of older individuals and is associated with cognitive impairment. However, there is a highly incomplete understanding of the genetic determinants of LATE neuropathologic changes (LATE-NC) in diverse populations. The defining neuropathologic feature of LATE-NC is TDP-43 proteinopathy, often with comorbid hippocampal sclerosis (HS). In terms of genetic risk factors, LATE-NC and/or HS are associated with single nucleotide variants (SNVs) in 3 genes-TMEM106B (rs1990622), GRN (rs5848), and ABCC9 (rs1914361 and rs701478). We evaluated these 3 genes in convenience samples of individuals of African ancestry. The allele frequencies of the LATE-associated alleles were significantly different between persons of primarily African (versus European) ancestry: In persons of African ancestry, the risk-associated alleles for TMEM106B and ABCC9 were less frequent, whereas the risk allele in GRN was more frequent. We performed an exploratory analysis of data from African-American subjects processed by the Alzheimer's Disease Genomics Consortium, with a subset of African-American participants (n = 166) having corroborating neuropathologic data through the National Alzheimer's Coordinating Center (NACC). In this limited-size sample, the ABCC9/rs1914361 SNV was associated with HS pathology. More work is required concerning the genetic factors influencing non-Alzheimer disease pathology such as LATE-NC in diverse cohorts.
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Affiliation(s)
- Yuriko Katsumata
- University of Kentucky Sanders-Brown Center on Aging, Lexington, Kentucky, USA
- University of Kentucky Department of Biostatistics, Lexington, Kentucky, USA
| | - David W Fardo
- University of Kentucky Sanders-Brown Center on Aging, Lexington, Kentucky, USA
- University of Kentucky Department of Biostatistics, Lexington, Kentucky, USA
| | - Lincoln M P Shade
- University of Kentucky Department of Biostatistics, Lexington, Kentucky, USA
| | - Peter T Nelson
- University of Kentucky Sanders-Brown Center on Aging, Lexington, Kentucky, USA
- University of Kentucky Department of Pathology and Laboratory Medicine, Lexington, Kentucky, USA
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2
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Soo CC, Brandenburg JT, Nebel A, Tollman S, Berkman L, Ramsay M, Choudhury A. Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community. Commun Biol 2023; 6:328. [PMID: 36973338 PMCID: PMC10043003 DOI: 10.1038/s42003-023-04636-1] [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: 10/18/2021] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Cognitive function is an indicator for global physical and mental health, and cognitive impairment has been associated with poorer life outcomes and earlier mortality. A standard cognition test, adapted to a rural-dwelling African community, and the Oxford Cognition Screen-Plus were used to capture cognitive performance as five continuous traits (total cognition score, verbal episodic memory, executive function, language, and visuospatial ability) for 2,246 adults in this population of South Africans. A novel common variant, rs73485231, reached genome-wide significance for association with episodic memory using data for ~14 million markers imputed from the H3Africa genotyping array data. Window-based replication of previously implicated variants and regions of interest support the discovery of African-specific associated variants despite the small population size and low allele frequency. This African genome-wide association study identifies suggestive associations with general cognition and domain-specific cognitive pathways and lays the groundwork for further genomic studies on cognition in Africa.
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Affiliation(s)
- Cassandra C Soo
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Almut Nebel
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lisa Berkman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, MA, USA
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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3
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The APOE locus is linked to decline in general cognitive function: 20-years follow-up in the Doetinchem Cohort Study. Transl Psychiatry 2022; 12:496. [PMID: 36446774 PMCID: PMC9708640 DOI: 10.1038/s41398-022-02258-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Cognitive decline is part of the normal aging process. However, some people experience a more rapid decline than others due to environmental and genetic factors. Numerous single nucleotide polymorphisms (SNPs) have been linked to cognitive function, but only a few to cognitive decline. To understand whether cognitive function and cognitive decline are driven by the same mechanisms, we investigated whether 433 SNPs previously linked to cognitive function and 2 SNPs previously linked to cognitive decline are associated with both general cognitive functioning at baseline and general cognitive decline up to 20-years follow-up in the Doetinchem Cohort Study (DCS). The DCS is a longitudinal population-based study that enrolled men and women aged 20-59 years between 1987-1991, with follow-up examinations every 5 years. We used data of rounds 2-6 (1993-2017, n = 2559). General cognitive function was assessed using four cognition tests measuring memory, speed, fluency and flexibility. With these test scores, standardized residuals (adjusted for sex, age and examination round) were calculated for each cognition test at each round and subsequently combined into one general cognitive function measure using principal component analyses. None of the 435 previously identified variants were associated with baseline general cognitive function in the DCS. But rs429358-C, a coding apolipoprotein E (APOE) SNP and one of the variants previously associated with cognitive decline, was associated with general cognitive decline in our study as well (p-value = 1 × 10-5, Beta = -0.013). These findings suggest that decline of general cognitive function is influenced by other mechanisms than those that are involved in the regulation of general cognitive function.
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4
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Chung JY, Jung HU, Kim DJ, Baek EJ, Kim HK, Kang JO, Lim JE, Oh B. Identification of five genetic variants with differential effects on obesity-related traits based on age. Front Genet 2022; 13:970657. [PMID: 36276968 PMCID: PMC9585212 DOI: 10.3389/fgene.2022.970657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Obesity is a major public health concern, and its prevalence generally increases with age. As the number of elderly people is increasing in the aging population, the age-dependent increase in obesity has raised interest in the underlying mechanism. To understand the genetic basis of age-related increase in obesity, we identified genetic variants showing age-dependent differential effects on obesity. We conducted stratified analyses between young and old groups using genome-wide association studies of 355,335 United Kingom Biobank participants for five obesity-related phenotypes, including body mass index, body fat percentage, waist-hip ratio, waist circumference, and hip circumference. Using t-statistic, we identified five significant lead single nucleotide polymorphisms: rs2258461 with body mass index, rs9861311 and rs429358 with body fat percentage, rs2870099 with waist-hip ratio, and rs145500243 with waist circumference. Among these single nucleotide polymorphisms, rs429358, located in APOE gene was associated with diverse age-related diseases, such as Alzheimer’s disease, coronary artery disease, age-related degenerative macular diseases, and cognitive decline. The C allele of rs429358 gradually decreases body fat percentage as one grows older in the range of 40–69 years. In conclusion, we identified five genetic variants with differential effects on obesity-related phenotypes based on age using a stratified analysis between young and old groups, which may help to elucidate the mechanisms by which age influences the development of obesity.
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Affiliation(s)
- Ju Yeon Chung
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Hae-Un Jung
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Dong Jun Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Eun Ju Baek
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Han Kyul Kim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Ji-One Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Ji Eun Lim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
- *Correspondence: Ji Eun Lim, ; Bermseok Oh,
| | - Bermseok Oh
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
- *Correspondence: Ji Eun Lim, ; Bermseok Oh,
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5
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Cognitive Capacity Genome-Wide Polygenic Scores Identify Individuals with Slower Cognitive Decline in Aging. Genes (Basel) 2022; 13:genes13081320. [PMID: 35893057 PMCID: PMC9331374 DOI: 10.3390/genes13081320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/23/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
The genetic protective factors for cognitive decline in aging remain unknown. Predicting an individual’s rate of cognitive decline—or with better cognitive resilience—using genetics will allow personalized intervention for cognitive enhancement and the optimal selection of target samples in clinical trials. Here, using genome-wide polygenic scores (GPS) of cognitive capacity as the genomic indicators for variations of human intelligence, we analyzed the 18-year records of cognitive and behavioral data of 8511 European-ancestry adults from the Wisconsin Longitudinal Study (WLS), specifically focusing on the cognitive assessments that were repeatedly administered to the participants with their average ages of 64.5 and 71.5. We identified a significant interaction effect between age and cognitive capacity GPS, which indicated that a higher cognitive capacity GPS significantly correlated with a slower cognitive decline in the domain of immediate memory recall (β = 1.86 × 10−1, p-value = 1.79 × 10−3). The additional phenome-wide analyses identified several associations between cognitive capacity GPSs and cognitive/behavioral phenotypes, such as similarities task (β = 1.36, 95% CI = (1.22, 1.51), p-value = 3.59 × 10−74), number series task (β = 0.94, 95% CI = (0.85, 1.04), p-value = 2.55 × 10−78), IQ scores (β = 1.42, 95% CI = (1.32, 1.51), p-value = 7.74 × 10−179), high school classrank (β = 1.86, 95% CI = (1.69, 2.02), p-value = 3.07 × 10−101), Openness from the BIG 5 personality factor (p-value = 2.19 × 10−14, β = 0.57, 95% CI = (0.42, 0.71)), and leisure activity of reading books (β = 0.50, 95% CI = (0.40, 0.60), p-value = 2.03 × 10−21), attending cultural events, such as concerts, plays, or museums (β = 0.60, 95% CI = (0.49, 0.72), p-value = 2.06 × 10−23), and watching TV (β = −0.48, 95% CI = (−0.59, −0.37), p-value = 4.16 × 10−18). As the first phenome-wide analysis of cognitive and behavioral phenotypes, this study presents the novel genetic protective effects of cognitive ability on the decline of memory recall in an aging population.
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Machlovi SI, Neuner SM, Hemmer BM, Khan R, Liu Y, Huang M, Zhu JD, Castellano JM, Cai D, Marcora E, Goate AM. APOE4 confers transcriptomic and functional alterations to primary mouse microglia. Neurobiol Dis 2022; 164:105615. [PMID: 35031484 PMCID: PMC8934202 DOI: 10.1016/j.nbd.2022.105615] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 12/09/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Common genetic variants in more than forty loci modulate risk for Alzheimer's disease (AD). AD risk alleles are enriched within enhancers active in myeloid cells, suggesting that microglia, the brain-resident macrophages, may play a key role in the etiology of AD. A major genetic risk factor for AD is Apolipoprotein E (APOE) genotype, with the ε4/ε4 (E4) genotype increasing risk for AD by approximately 15 fold compared to the most common ε3/ε3 (E3) genotype. However, the impact of APOE genotype on microglial function has not been thoroughly investigated. To address this, we cultured primary microglia from mice in which both alleles of the mouse Apoe gene have been humanized to encode either human APOE ε3 or APOE ε4. Relative to E3 microglia, E4 microglia exhibit altered morphology, increased endolysosomal mass, increased cytokine/chemokine production, and increased lipid and lipid droplet accumulation at baseline. These changes were accompanied by decreased translation and increased phosphorylation of eIF2ɑ and eIF2ɑ-kinases that participate in the integrated stress response, suggesting that E4 genotype leads to elevated levels of cellular stress in microglia relative to E3 genotype. Using live-cell imaging and flow cytometry, we also show that E4 microglia exhibited increased phagocytic uptake of myelin and other substrates compared to E3 microglia. While transcriptomic profiling of myelin-challenged microglia revealed a largely overlapping response profile across genotypes, differential enrichment of genes in interferon signaling, extracellular matrix and translation-related pathways was identified in E4 versus E3 microglia both at baseline and following myelin challenge. Together, our results suggest E4 genotype confers several important functional alterations to microglia even prior to myelin challenge, providing insight into the molecular and cellular mechanisms by which APOE4 may increase risk for AD.
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Affiliation(s)
- Saima I Machlovi
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah M Neuner
- Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brittany M Hemmer
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Riana Khan
- Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiyuan Liu
- Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Min Huang
- James J Peters VA Medical Center, Research & Development, Bronx, NY, USA; Department of Neurology, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey D Zhu
- Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph M Castellano
- Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Department of Neurology, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dongming Cai
- Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; James J Peters VA Medical Center, Research & Development, Bronx, NY, USA; Department of Neurology, New York, NY, USA; Alzheimer Disease Research Center, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's Disease, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Department of Neurology, New York, NY, USA; Alzheimer Disease Research Center, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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7
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Chino B, Zegarra-Valdivia J, de Frutos-Lucas J, Paredes-Manrique C, Custodio N. Impact of Sociodemographic Features and Lifestyle on Cognitive Performance of Peruvian Adults. J Alzheimers Dis 2022; 90:599-608. [PMID: 36155510 PMCID: PMC9697037 DOI: 10.3233/jad-220428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Cognitive impairment and dementia may result from a combination of modifiable and nonmodifiable risk and protective factors, such as the environment, educational attainment, time devoted to cognitively stimulating activities, and physical activity. OBJECTIVE This study aimed to investigate the mediating role of sociodemographic characteristics and lifestyle factors in the years of education and cognitive performance in Peruvian adults. METHODS This cross-sectional study included 1,478 subjects assessed by Addenbrooke's Cognitive Examination Revised (ACE-R). Using mediation models, we evaluated the mediation role of parents' educational level, reading time (RT), and physical activity time (PAT) in the years of education (IYE) and cognitive performance. RESULTS People who reported having lived in an urban area during their childhood are estimated to have, on average, 2.085 years more formal education than those who lived in rural areas. In addition, 49% of cognitive performance scores are explained by the mediation effect of reading and physical activity time in the IYE. This implies that higher levels of education, mediated by RT and PAT per week, are 1.596 units associated with higher scores on the ACE-R. CONCLUSION Despite the fact that nonmodifiable factors (i.e., childhood residence area, parents' educational level) seem to exert an effect on older adults' cognition, their influence is mediated by other factors that are indeed modifiable (i.e., reading time, physical activity engagement). In this sense, lifestyle changes could help prevent or decrease the risk of cognitive impairment and reduce the disease's impact on vulnerable environments in Latin American and Caribbean countries.
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Affiliation(s)
- Brenda Chino
- Center for Cognitive and Computational Neuroscience, Complutense University of Madrid, Madrid, Spain
- Institute of Neuroscience INc, Universidad Autónoma de Barcelona, Spain
- Universidad Nacional de San Agustín de Arequipa, Perú
| | - Jonathan Zegarra-Valdivia
- Universidad Señor de Sipán, Chiclayo, Perú
- Global Brain Health Institute, University of California, San Francisco, CA, USA
- Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Jaisalmer de Frutos-Lucas
- Center for Cognitive and Computational Neuroscience, Complutense University of Madrid, Madrid, Spain
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Departamento de Psicología, Facultad de Ciencias de la Vida y la Naturaleza, Universidad Antonio de Nebrija, Spain
| | | | - Nilton Custodio
- Instituto Peruano de Neurociencias, Lima, Perú
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Perú
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8
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O'Connell KS, Shadrin A, Bahrami S, Smeland OB, Bettella F, Frei O, Krull F, Askeland RB, Walters GB, Davíðsdóttir K, Haraldsdóttir GS, Guðmundsson ÓÓ, Stefánsson H, Fan CC, Steen NE, Reichborn-Kjennerud T, Dale AM, Stefánsson K, Djurovic S, Andreassen OA. Identification of genetic overlap and novel risk loci for attention-deficit/hyperactivity disorder and bipolar disorder. Mol Psychiatry 2021; 26:4055-4065. [PMID: 31792363 DOI: 10.1038/s41380-019-0613-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/07/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Differential diagnosis between childhood onset attention-deficit/hyperactivity disorder (ADHD) and bipolar disorder (BD) remains a challenge, mainly due to overlapping symptoms and high rates of comorbidity. Despite this, genetic correlation reported for these disorders is low and non-significant. Here we aimed to better characterize the genetic architecture of these disorders utilizing recent large genome-wide association studies (GWAS). We analyzed independent GWAS summary statistics for ADHD (19,099 cases and 34,194 controls) and BD (20,352 cases and 31,358 controls) applying the conditional/conjunctional false discovery rate (condFDR/conjFDR) statistical framework that increases the power to detect novel phenotype-specific and shared loci by leveraging the combined power of two GWAS. We observed cross-trait polygenic enrichment for ADHD conditioned on associations with BD, and vice versa. Leveraging this enrichment, we identified 19 novel ADHD risk loci and 40 novel BD risk loci at condFDR <0.05. Further, we identified five loci jointly associated with ADHD and BD (conjFDR < 0.05). Interestingly, these five loci show concordant directions of effect for ADHD and BD. These results highlight a shared underlying genetic risk for ADHD and BD which may help to explain the high comorbidity rates and difficulties in differentiating between ADHD and BD in the clinic. Improving our understanding of the underlying genetic architecture of these disorders may aid in the development of novel stratification tools to help reduce these diagnostic difficulties.
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Affiliation(s)
- Kevin S O'Connell
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
| | - Alexey Shadrin
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Shahram Bahrami
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Olav B Smeland
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Francesco Bettella
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Oleksandr Frei
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Florian Krull
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Ragna B Askeland
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
| | - G Bragi Walters
- deCODE genetics/Amgen, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Katrín Davíðsdóttir
- The Centre for Child Development and Behaviour, Capital Area Primary Health Care, Reykjavik, Iceland
| | - Gyða S Haraldsdóttir
- The Centre for Child Development and Behaviour, Capital Area Primary Health Care, Reykjavik, Iceland
| | - Ólafur Ó Guðmundsson
- deCODE genetics/Amgen, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland.,Department of Child and Adolescent Psychiatry, National University Hospital, Reykjavik, Iceland
| | | | - Chun C Fan
- Department of Radiology, University of California, San Diego, La Jolla, CA, 92093, USA.,Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Nils Eiel Steen
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Ted Reichborn-Kjennerud
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anders M Dale
- Department of Radiology, University of California, San Diego, La Jolla, CA, 92093, USA.,Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.,Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kári Stefánsson
- deCODE genetics/Amgen, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole A Andreassen
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway. .,Departments of Neurology and Psychiatry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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9
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Chen SD, Li HQ, Shen XN, Li JQ, Xu W, Huang YY, Tan L, Dong Q, Yu JT. Genome-Wide Association Study Identifies SLAMF1 Affecting the Rate of Memory Decline. J Alzheimers Dis 2021; 74:139-149. [PMID: 31985465 DOI: 10.3233/jad-191214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND As cognitive function declines with age, identifying factors affecting the trajectory of cognitive decline is an indispensable step toward developing intervention strategies to improve the quality of the elderly life. OBJECTIVE We performed a genome-wide association study (GWAS) focusing on memory function to explore single nucleotide polymorphisms (SNPs) associated with the rate of memory decline. METHODS Seven hundred and nine eligible non-Hispanic Caucasians from the Alzheimer's Disease Neuroimaging Initiative (ADNI) were included for analysis after quality control. GWAS was performed with linear regression. We subsequently tested whether the associations remained significant in subgroup analysis and also examined the impact of SNPs on the longitudinal changes in other neuropsychological measures and amyloid pathology. RESULTS We identified rs13374761-A in SLAMF1 gene associated with less memory decline (MAF = 0.071, β= 0.0103, p = 4.14×10-8). Subgroup analysis showed stability of results across groups with different diagnosis at baseline. Rs13374761-A also had protective effects on global cognition (p = 0.024), episodic memory (p = 0.024), and semantic memory (p = 0.042), and exerts protection against a decrease in CSF Aβ42 concentration (p = 0.0463) and an increase in Aβ loading in cerebral cortex (p = 0.00666) among minor allele carriers. CONCLUSION A novel variant in gene SLAMF1 affects the rate of memory decline in the aged population. Given the protective effect of this variant, SLAMF1 should be further investigated as a potential preventive and therapeutic target for monitoring cognition trajectories.
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Affiliation(s)
- Shi-Dong Chen
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hong-Qi Li
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xue-Ning Shen
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jie-Qiong Li
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wei Xu
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Yu-Yuan Huang
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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10
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Deters KD, Napolioni V, Sperling RA, Greicius MD, Mayeux R, Hohman T, Mormino EC. Amyloid PET Imaging in Self-Identified Non-Hispanic Black Participants of the Anti-Amyloid in Asymptomatic Alzheimer's Disease (A4) Study. Neurology 2021; 96:e1491-e1500. [PMID: 33568538 DOI: 10.1212/wnl.0000000000011599] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/07/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To examine whether amyloid PET in cognitively normal (CN) individuals screened for the Anti-Amyloid in Asymptomatic Alzheimer's Disease (A4) study differed across self-identified non-Hispanic White and Black (NHW and NHB) groups. METHODS We examined 3,689 NHW and 144 NHB participants who passed initial screening for the A4 study and underwent amyloid PET. The effect of race on amyloid PET was examined using logistic (dichotomous groups) and linear (continuous values) regression controlling for age, sex, and number of APOE ε4 and APOE ε2 alleles. Associations between amyloid and genetically determined ancestry (reflecting African, South Asian, East Asian, American, and European populations) were tested within the NHB group. Potential interactions with APOE were assessed. RESULTS NHB participants had lower rates of amyloid positivity and lower continuous amyloid levels compared to NHW participants. This race effect on amyloid was strongest in the APOE ε4 group. Within NHB participants, those with a lower percentage of African ancestry had higher amyloid. A greater proportion of NHB participants did not pass initial screening compared to NHW participants, suggesting potential sources of bias related to race in the A4 PET data. CONCLUSION Reduced amyloid was observed in self-identified NHB participants who passed initial eligibility criteria for the A4 study. This work stresses the importance of investigating AD biomarkers in ancestrally diverse samples as well as the need for careful consideration regarding study eligibility criteria in AD prevention trials.
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Affiliation(s)
- Kacie D Deters
- From the Department of Neurology and Neurological Sciences (K.D.D., V.N., M.D.G., E.C.M.), Stanford University School of Medicine, Palo Alto, CA; Department of Neurology (R.A.S.), Brigham and Women's Hospital, Massachusetts General Hospital, Boston; Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, and The Institute for Genomic Medicine (R.M.), Columbia University Medical Center and The New York Presbyterian Hospital, New York; and Vanderbilt Memory and Alzheimer's Center and Vanderbilt Genetics Institute (T.H.), Nashville, TN.
| | - Valerio Napolioni
- From the Department of Neurology and Neurological Sciences (K.D.D., V.N., M.D.G., E.C.M.), Stanford University School of Medicine, Palo Alto, CA; Department of Neurology (R.A.S.), Brigham and Women's Hospital, Massachusetts General Hospital, Boston; Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, and The Institute for Genomic Medicine (R.M.), Columbia University Medical Center and The New York Presbyterian Hospital, New York; and Vanderbilt Memory and Alzheimer's Center and Vanderbilt Genetics Institute (T.H.), Nashville, TN
| | - Reisa A Sperling
- From the Department of Neurology and Neurological Sciences (K.D.D., V.N., M.D.G., E.C.M.), Stanford University School of Medicine, Palo Alto, CA; Department of Neurology (R.A.S.), Brigham and Women's Hospital, Massachusetts General Hospital, Boston; Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, and The Institute for Genomic Medicine (R.M.), Columbia University Medical Center and The New York Presbyterian Hospital, New York; and Vanderbilt Memory and Alzheimer's Center and Vanderbilt Genetics Institute (T.H.), Nashville, TN
| | - Michael D Greicius
- From the Department of Neurology and Neurological Sciences (K.D.D., V.N., M.D.G., E.C.M.), Stanford University School of Medicine, Palo Alto, CA; Department of Neurology (R.A.S.), Brigham and Women's Hospital, Massachusetts General Hospital, Boston; Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, and The Institute for Genomic Medicine (R.M.), Columbia University Medical Center and The New York Presbyterian Hospital, New York; and Vanderbilt Memory and Alzheimer's Center and Vanderbilt Genetics Institute (T.H.), Nashville, TN
| | - Richard Mayeux
- From the Department of Neurology and Neurological Sciences (K.D.D., V.N., M.D.G., E.C.M.), Stanford University School of Medicine, Palo Alto, CA; Department of Neurology (R.A.S.), Brigham and Women's Hospital, Massachusetts General Hospital, Boston; Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, and The Institute for Genomic Medicine (R.M.), Columbia University Medical Center and The New York Presbyterian Hospital, New York; and Vanderbilt Memory and Alzheimer's Center and Vanderbilt Genetics Institute (T.H.), Nashville, TN
| | - Timothy Hohman
- From the Department of Neurology and Neurological Sciences (K.D.D., V.N., M.D.G., E.C.M.), Stanford University School of Medicine, Palo Alto, CA; Department of Neurology (R.A.S.), Brigham and Women's Hospital, Massachusetts General Hospital, Boston; Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, and The Institute for Genomic Medicine (R.M.), Columbia University Medical Center and The New York Presbyterian Hospital, New York; and Vanderbilt Memory and Alzheimer's Center and Vanderbilt Genetics Institute (T.H.), Nashville, TN
| | - Elizabeth C Mormino
- From the Department of Neurology and Neurological Sciences (K.D.D., V.N., M.D.G., E.C.M.), Stanford University School of Medicine, Palo Alto, CA; Department of Neurology (R.A.S.), Brigham and Women's Hospital, Massachusetts General Hospital, Boston; Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, and The Institute for Genomic Medicine (R.M.), Columbia University Medical Center and The New York Presbyterian Hospital, New York; and Vanderbilt Memory and Alzheimer's Center and Vanderbilt Genetics Institute (T.H.), Nashville, TN
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11
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Andrews SJ, McFall GP, Booth A, Dixon RA, Anstey KJ. Association of Alzheimer's Disease Genetic Risk Loci with Cognitive Performance and Decline: A Systematic Review. J Alzheimers Dis 2020; 69:1109-1136. [PMID: 31156182 DOI: 10.3233/jad-190342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The association of Apolipoprotein E (APOE) with late-onset Alzheimer's disease (LOAD) and cognitive endophenotypes of aging has been widely investigated. There is increasing interest in evaluating the association of other LOAD risk loci with cognitive performance and decline. The results of these studies have been inconsistent and inconclusive. We conducted a systematic review of studies investigating the association of non-APOE LOAD risk loci with cognitive performance in older adults. Studies published from January 2009 to April 2018 were identified through a PubMed database search using keywords and by scanning reference lists. Studies were included if they were either cross-sectional or longitudinal in design, included at least one genome-wide significant LOAD risk loci or a genetic risk score, and had one objective measure of cognition. Quality assessment of the studies was conducted using the quality of genetic studies (Q-Genie) tool. Of 2,466 studies reviewed, 49 met inclusion criteria. Fifteen percent of the associations between non-APOE LOAD risk loci and cognition were significant. However, these associations were not replicated across studies, and the majority were rendered non-significant when adjusting for multiple testing. One-third of the studies included genetic risk scores, and these were typically significant only when APOE was included. The findings of this systematic review do not support a consistent association between individual non-APOE LOAD risk and cognitive performance or decline. However, evidence suggests that aggregate LOAD genetic risk exerts deleterious effects on decline in episodic memory and global cognition.
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Affiliation(s)
- Shea J Andrews
- Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - G Peggy McFall
- Department of Psychology, University of Alberta, Edmonton, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Andrew Booth
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Roger A Dixon
- Department of Psychology, University of Alberta, Edmonton, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Kaarin J Anstey
- UNSW Ageing Futures Institute, University of New South Wales, Australia.,School of Psychology, University of New South Wales, Australia.,Neuroscience Research Australia, Australia
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12
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Dunn AR, Hadad N, Neuner SM, Zhang JG, Philip VM, Dumitrescu L, Hohman TJ, Herskowitz JH, O’Connell KMS, Kaczorowski CC. Identifying Mechanisms of Normal Cognitive Aging Using a Novel Mouse Genetic Reference Panel. Front Cell Dev Biol 2020; 8:562662. [PMID: 33042997 PMCID: PMC7517308 DOI: 10.3389/fcell.2020.562662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022] Open
Abstract
Developing strategies to maintain cognitive health is critical to quality of life during aging. The basis of healthy cognitive aging is poorly understood; thus, it is difficult to predict who will have normal cognition later in life. Individuals may have higher baseline functioning (cognitive reserve) and others may maintain or even improve with age (cognitive resilience). Understanding the mechanisms underlying cognitive reserve and resilience may hold the key to new therapeutic strategies for maintaining cognitive health. However, reserve and resilience have been inconsistently defined in human studies. Additionally, our understanding of the molecular and cellular bases of these phenomena is poor, compounded by a lack of longitudinal molecular and cognitive data that fully capture the dynamic trajectories of cognitive aging. Here, we used a genetically diverse mouse population (B6-BXDs) to characterize individual differences in cognitive abilities in adulthood and investigate evidence of cognitive reserve and/or resilience in middle-aged mice. We tested cognitive function at two ages (6 months and 14 months) using y-maze and contextual fear conditioning. We observed heritable variation in performance on these traits (h 2 RIx̄ = 0.51-0.74), suggesting moderate to strong genetic control depending on the cognitive domain. Due to the polygenetic nature of cognitive function, we did not find QTLs significantly associated with y-maze, contextual fear acquisition (CFA) or memory, or decline in cognitive function at the genome-wide level. To more precisely interrogate the molecular regulation of variation in these traits, we employed RNA-seq and identified gene networks related to transcription/translation, cellular metabolism, and neuronal function that were associated with working memory, contextual fear memory, and cognitive decline. Using this method, we nominate the Trio gene as a modulator of working memory ability. Finally, we propose a conceptual framework for identifying strains exhibiting cognitive reserve and/or resilience to assess whether these traits can be observed in middle-aged B6-BXDs. Though we found that earlier cognitive reserve evident early in life protects against cognitive impairment later in life, cognitive performance and age-related decline fell along a continuum, with no clear genotypes emerging as exemplars of exceptional reserve or resilience - leading to recommendations for future use of aging mouse populations to understand the nature of cognitive reserve and resilience.
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Affiliation(s)
- Amy R. Dunn
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Niran Hadad
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Sarah M. Neuner
- The Jackson Laboratory, Bar Harbor, ME, United States
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Ji-Gang Zhang
- The Jackson Laboratory, Bar Harbor, ME, United States
| | | | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer’s Center and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Timothy J. Hohman
- Vanderbilt Memory and Alzheimer’s Center and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jeremy H. Herskowitz
- Center for Neurodegeneration and Experimental Therapeutics and Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
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13
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Gouveia MH, Cesar CC, Santolalla ML, Anna HPS, Scliar MO, Leal TP, Araújo NM, Soares-Souza GB, Magalhães WCS, Mata IF, Ferri CP, Castro-Costa E, Mbulaiteye SM, Tishkoff SA, Shriner D, Rotimi CN, Tarazona-Santos E, Lima-Costa MF. Genetics of cognitive trajectory in Brazilians: 15 years of follow-up from the Bambuí-Epigen Cohort Study of Aging. Sci Rep 2019; 9:18085. [PMID: 31792241 PMCID: PMC6889148 DOI: 10.1038/s41598-019-53988-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/07/2019] [Indexed: 01/11/2023] Open
Abstract
Age-related cognitive decline (ACD) is the gradual process of decreasing of cognitive function over age. Most genetic risk factors for ACD have been identified in European populations and there are no reports in admixed Latin American individuals. We performed admixture mapping, genome-wide association analysis (GWAS), and fine-mapping to examine genetic factors associated with 15-year cognitive trajectory in 1,407 Brazilian older adults, comprising 14,956 Mini-Mental State Examination measures. Participants were enrolled as part of the Bambuí-Epigen Cohort Study of Aging. Our admixture mapping analysis identified a genomic region (3p24.2) in which increased Native American ancestry was significantly associated with faster ACD. Fine-mapping of this region identified a single nucleotide polymorphism (SNP) rs142380904 (β = -0.044, SE = 0.01, p = 7.5 × 10-5) associated with ACD. In addition, our GWAS identified 24 associated SNPs, most in genes previously reported to influence cognitive function. The top six associated SNPs accounted for 18.5% of the ACD variance in our data. Furthermore, our longitudinal study replicated previous GWAS hits for cognitive decline and Alzheimer's disease. Our 15-year longitudinal study identified both ancestry-specific and cosmopolitan genetic variants associated with ACD in Brazilians, highlighting the need for more trans-ancestry genomic studies, especially in underrepresented ethnic groups.
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Affiliation(s)
- Mateus H Gouveia
- Fundação Oswaldo Cruz, Instituto de Pesquisas René Rachou, Belo Horizonte, Brazil.
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
| | - Cibele C Cesar
- Universidade Federal de Minas Gerais, Faculdade de Ciências Econômicas, Belo Horizonte, Brazil
| | - Meddly L Santolalla
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Hanaisa P Sant Anna
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Marilia O Scliar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Thiago P Leal
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Nathalia M Araújo
- Fundação Oswaldo Cruz, Instituto de Pesquisas René Rachou, Belo Horizonte, Brazil
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Giordano B Soares-Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Wagner C S Magalhães
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Núcleo de Ensino e Pesquisa - NEP, Instituto Mário Penna, Rua Gentios, Terceiro Andar, Belo Horizonte, Minas Gerais, 3052, Brazil
| | - Ignacio F Mata
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Cleusa P Ferri
- Universidade Federal de São Paulo, Department of Psychiatry, São Paulo, Brazil
| | - Erico Castro-Costa
- Fundação Oswaldo Cruz, Instituto de Pesquisas René Rachou, Belo Horizonte, Brazil
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
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14
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Saul MC, Philip VM, Reinholdt LG, Chesler EJ. High-Diversity Mouse Populations for Complex Traits. Trends Genet 2019; 35:501-514. [PMID: 31133439 DOI: 10.1016/j.tig.2019.04.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/21/2022]
Abstract
Contemporary mouse genetic reference populations are a powerful platform to discover complex disease mechanisms. Advanced high-diversity mouse populations include the Collaborative Cross (CC) strains, Diversity Outbred (DO) stock, and their isogenic founder strains. When used in systems genetics and integrative genomics analyses, these populations efficiently harnesses known genetic variation for precise and contextualized identification of complex disease mechanisms. Extensive genetic, genomic, and phenotypic data are already available for these high-diversity mouse populations and a growing suite of data analysis tools have been developed to support research on diverse mice. This integrated resource can be used to discover and evaluate disease mechanisms relevant across species.
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Affiliation(s)
- Michael C Saul
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Vivek M Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
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- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA; UNC Chapel Hill, Chapel Hill, NC, USA; SUNY Binghamton, Binghamton, NY, USA; Pittsburgh University, Pittsburgh, PA, USA
| | - Elissa J Chesler
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA.
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15
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Stepler KE, Robinson RAS. The Potential of ‘Omics to Link Lipid Metabolism and Genetic and Comorbidity Risk Factors of Alzheimer’s Disease in African Americans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:1-28. [DOI: 10.1007/978-3-030-05542-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Neuner SM, Heuer SE, Huentelman MJ, O'Connell KMS, Kaczorowski CC. Harnessing Genetic Complexity to Enhance Translatability of Alzheimer's Disease Mouse Models: A Path toward Precision Medicine. Neuron 2018; 101:399-411.e5. [PMID: 30595332 DOI: 10.1016/j.neuron.2018.11.040] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/02/2018] [Accepted: 11/20/2018] [Indexed: 01/15/2023]
Abstract
An individual's genetic makeup plays a large role in determining susceptibility to Alzheimer's disease (AD) but has largely been ignored in preclinical studies. To test the hypothesis that incorporating genetic diversity into mouse models of AD would improve translational potential, we combined a well-established mouse model of AD with a genetically diverse reference panel to generate mice that harbor identical high-risk human mutations but differ across the remainder of their genome. We first show that genetic variation profoundly modifies the impact of human AD mutations on both cognitive and pathological phenotypes. We then validate this complex AD model by demonstrating high degrees of genetic, transcriptomic, and phenotypic overlap with human AD. Overall, work here both introduces a novel AD mouse population as an innovative and reproducible resource for the study of mechanisms underlying AD and provides evidence that preclinical models incorporating genetic diversity may better translate to human disease.
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Affiliation(s)
- Sarah M Neuner
- The Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA; The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Sarah E Heuer
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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17
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Brewster P, Barnes L, Haan M, Johnson JK, Manly JJ, Nápoles AM, Whitmer RA, Carvajal-Carmona L, Early D, Farias S, Mayeda ER, Melrose R, Meyer OL, Zeki Al Hazzouri A, Hinton L, Mungas D. Progress and future challenges in aging and diversity research in the United States. Alzheimers Dement 2018; 15:995-1003. [PMID: 30240574 DOI: 10.1016/j.jalz.2018.07.221] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 05/18/2018] [Accepted: 07/31/2018] [Indexed: 12/31/2022]
Abstract
In 2016, the UC Davis Latino Aging Research Resource Center and UC Davis Alzheimer's Disease Center brought together experts from across the country to consolidate current knowledge and identify future directions in aging and diversity research. This report disseminates the research priorities that emerged from this conference, building on an earlier Gerontological Society of America preconference. We review key racial/ethnic differences in cognitive aging and dementia and identify current knowledge gaps in the field. We advocate for a systems-level framework for future research whereby environmental, sociocultural, behavioral, neuropathological, genetic, and psychometric levels of analysis are examined together to identify pathways and mechanisms that influence disparities. We then discuss steps to increase the recruitment and retention of racial/ethnic minorities in aging studies, as none of the recommendations will be possible without strong collaboration between racial/ethnic minority communities and researchers. This approach is consistent with the National Institute on Aging Health Disparities Research Framework.
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Affiliation(s)
- Paul Brewster
- Institute on Aging and Lifelong Health, University of Victoria, Victoria, BC, USA.
| | - Lisa Barnes
- Rush Alzheimer's Disease Center and Departments of Neurological Sciences and Behavioral Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Mary Haan
- Department of Epidemiology and Biostatistics, UC San Francisco, San Francisco, CA, USA
| | - Julene K Johnson
- Institute for Health & Aging, UC San Francisco, San Francisco, CA, USA
| | - Jennifer J Manly
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Anna María Nápoles
- Center for Aging in Diverse Communities, UC San Francisco, San Francisco, CA, USA
| | - Rachel A Whitmer
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Luis Carvajal-Carmona
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA, USA
| | - Dawnte Early
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, USA
| | - Sarah Farias
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, USA
| | - Elizabeth Rose Mayeda
- Department of Epidemiology and Biostatistics, UC San Francisco, San Francisco, CA, USA; University of California, Los Angeles Department of Epidemiology, Los Angeles, CA, USA
| | - Rebecca Melrose
- VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Oanh L Meyer
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, USA
| | - Adina Zeki Al Hazzouri
- Division of Epidemiology and Population Health, Department of Public Health Science, University of Miami, Miami, FL, USA
| | - Ladson Hinton
- Department of Psychiatry and Behavioral Sciences, UC Davis School of Medicine, Sacramento, CA, USA
| | - Dan Mungas
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, USA
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18
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Lima-Costa MF, Gouveia MH, Cesar CC, Tarazona-Santos E, Stewart R, Ferri CP, Castro-Costa E. Genomic African and Native American Ancestry and 15-Year Cognitive Trajectory: Bambui Study, Brazil. J Am Geriatr Soc 2018; 66:1956-1962. [PMID: 30221750 DOI: 10.1111/jgs.15504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 12/01/2022]
Abstract
OBJECTIVES To investigate the association between African and Native American genomic ancestry and long-term cognitive trajectories in admixed Brazilians. DESIGN Population-based longitudinal study. SETTING Bambui-Epigen (Brazil) cohort study. PARTICIPANTS Adults aged 60 and older (N=1,215) MEASUREMENTS: Participants were followed from January 1997 to December 2011. Cognitive function was assessed annually using the Mini-Mental State Examination (MMSE), totaling 12,208 measurements. We used linear mixed-effects pattern models to assess MMSE score trajectories. Ancestry was assessed using a genome-wide approach. RESULTS After adjustments for covariates, the highest quintile of African ancestry was associated with poorer baseline cognitive performance (β=-0.73, 95% confidence interval (CI)=-1.36 to -0.11) but not with cognitive trajectory. Educational level modified the baseline association between highest African ancestry and cognitive performance in that the association was observed only in those with very low (<4 years) education (β=-1.13, 95% CI=-2.02 to -0.23). No association was found between Native American ancestry and baseline cognitive function or its trajectory. CONCLUSION Genomic African and Native American ancestry levels had no prognostic value for age-related cognitive decline in this admixed population.
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Affiliation(s)
| | - Mateus H Gouveia
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil.,Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cibele C Cesar
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil.,Faculdade de Ciências Econômicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eduardo Tarazona-Santos
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rob Stewart
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Cleusa P Ferri
- Departamento de Psicobiologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Erico Castro-Costa
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
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19
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Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK. Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression. Am J Hum Genet 2017; 101:686-699. [PMID: 29106824 PMCID: PMC5673624 DOI: 10.1016/j.ajhg.2017.09.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/13/2017] [Indexed: 01/09/2023] Open
Abstract
Previous studies have prioritized trait-relevant cell types by looking for an enrichment of genome-wide association study (GWAS) signal within functional regions. However, these studies are limited in cell resolution by the lack of functional annotations from difficult-to-characterize or rare cell populations. Measurement of single-cell gene expression has become a popular method for characterizing novel cell types, and yet limited work has linked single-cell RNA sequencing (RNA-seq) to phenotypes of interest. To address this deficiency, we present RolyPoly, a regression-based polygenic model that can prioritize trait-relevant cell types and genes from GWAS summary statistics and gene expression data. RolyPoly is designed to use expression data from either bulk tissue or single-cell RNA-seq. In this study, we demonstrated RolyPoly's accuracy through simulation and validated previously known tissue-trait associations. We discovered a significant association between microglia and late-onset Alzheimer disease and an association between schizophrenia and oligodendrocytes and replicating fetal cortical cells. Additionally, RolyPoly computes a trait-relevance score for each gene to reflect the importance of expression specific to a cell type. We found that differentially expressed genes in the prefrontal cortex of individuals with Alzheimer disease were significantly enriched with genes ranked highly by RolyPoly gene scores. Overall, our method represents a powerful framework for understanding the effect of common variants on cell types contributing to complex traits.
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Affiliation(s)
- Diego Calderon
- Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA.
| | - Anand Bhaskar
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - David A Knowles
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - David Golan
- Faculty of Industrial Engineering & Management, Technion, Haifa 3200003, Israel
| | - Towfique Raj
- Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Audrey Q Fu
- Department of Statistical Science, University of Idaho, Moscow, ID 83844, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
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