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Liu M, Khasiyev F, Sariya S, Spagnolo‐Allende A, Sanchez DL, Andrews H, Yang Q, Beiser A, Qiao Y, Thomas EA, Romero JR, Rundek T, Brickman AM, Manly JJ, Elkind MSV, Seshadri S, Chen C, Hilal S, Wasserman BA, Tosto G, Fornage M, Gutierrez J. Chromosome 10q24.32 Variants Associate With Brain Arterial Diameters in Diverse Populations: A Genome-Wide Association Study. J Am Heart Assoc 2023; 12:e030935. [PMID: 38038215 PMCID: PMC10727334 DOI: 10.1161/jaha.123.030935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Brain arterial diameters (BADs) are novel imaging biomarkers of cerebrovascular disease, cognitive decline, and dementia. Traditional vascular risk factors have been associated with BADs, but whether there may be genetic determinants of BADs is unknown. METHODS AND RESULTS The authors studied 4150 participants from 6 geographically diverse population-based cohorts (40% European, 14% African, 22% Hispanic, 24% Asian ancestries). Brain arterial diameters for 13 segments were measured and averaged to obtain a global measure of BADs as well as the posterior and anterior circulations. A genome-wide association study revealed 14 variants at one locus associated with global BAD at genome-wide significance (P<5×10-8) (top single-nucleotide polymorphism, rs7921574; β=0.06 [P=1.54×10-8]). This locus mapped to an intron of CNNM2. A trans-ancestry genome-wide association study meta-analysis identified 2 more loci at NT5C2 (rs10748839; P=2.54×10-8) and AS3MT (rs10786721; P=4.97×10-8), associated with global BAD. In addition, 2 single-nucleotide polymorphisms colocalized with expression of CNNM2 (rs7897654; β=0.12 [P=6.17×10-7]) and AL356608.1 (rs10786719; β=-0.17 [P=6.60×10-6]) in brain tissue. For the posterior BAD, 2 variants at one locus mapped to an intron of TCF25 were identified (top single-nucleotide polymorphism, rs35994878; β=0.11 [P=2.94×10-8]). For the anterior BAD, one locus at ADAP1 was identified in trans-ancestry genome-wide association analysis (rs34217249; P=3.11×10-8). CONCLUSIONS The current study reveals 3 novel risk loci (CNNM2, NT5C2, and AS3MT) associated with BADs. These findings may help elucidate the mechanism by which BADs may influence cerebrovascular health.
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Affiliation(s)
- Minghua Liu
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Farid Khasiyev
- Department of NeurologySaint Louis University School of MedicineSt. LouisMOUSA
| | - Sanjeev Sariya
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Antonio Spagnolo‐Allende
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Danurys L Sanchez
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Howard Andrews
- Biostatistics Department, Mailman School of Public HealthColumbia UniversityNew YorkNYUSA
| | - Qiong Yang
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Alexa Beiser
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Ye Qiao
- Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Emy A Thomas
- Brown Foundation Institute of Molecular Medicine, McGovern Medical SchoolThe University of Texas Health Science Center at HoustonHoustonTXUSA
| | | | - Tatjana Rundek
- Department of NeurologyUniversity of Miami Miller School of MedicineMiamiFLUSA
- Department of Public Health SciencesUniversity of Miami Miller School of MedicineMiamiFLUSA
- Evelyn F. McKnight Brain InstituteUniversity of Miami Miller School of MedicineMiamiFLUSA
| | - Adam M Brickman
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Jennifer J Manly
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Mitchell SV Elkind
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Department of Epidemiology, Mailman School of Public HealthColumbia UniversityNew YorkNYUSA
| | - Sudha Seshadri
- Department of NeurologyBoston University School of MedicineBostonMAUSA
- The Glenn Biggs Institute for Alzheimer’s and Neurodegenerative DiseasesUniversity of Texas Health Sciences CenterSan AntonioTXUSA
| | - Christopher Chen
- Memory Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Saima Hilal
- Memory Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Bruce A Wasserman
- Johns Hopkins University School of MedicineBaltimoreMDUSA
- University of Maryland School of MedicineBaltimoreMDUSA
| | - Giuseppe Tosto
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical SchoolThe University of Texas Health Science Center at HoustonHoustonTXUSA
- Human Genetics Center, School of Public HealthThe University of Texas Health Science Center at HoustonHoustonTXUSA
| | - Jose Gutierrez
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
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Rajabli F, Tosto G, Hamilton-Nelson KL, Kunkle BW, Vardarajan BN, Naj A, Whitehead PG, Gardner OK, Bush WS, Sariya S, Mayeux RP, Farrer LA, Cuccaro ML, Vance JM, Griswold AJ, Schellenberg GD, Haines JL, Byrd GS, Reitz C, Beecham GW, Pericak-Vance MA, Martin ER. Admixture mapping identifies novel Alzheimer's disease risk regions in African Americans. Alzheimers Dement 2023; 19:2538-2548. [PMID: 36539198 PMCID: PMC10272044 DOI: 10.1002/alz.12865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND This study used admixture mapping to prioritize the genetic regions associated with Alzheimer's disease (AD) in African American (AA) individuals, followed by ancestry-aware regression analysis to fine-map the prioritized regions. METHODS We analyzed 10,271 individuals from 17 different AA datasets. We performed admixture mapping and meta-analyzed the results. We then used regression analysis, adjusting for local ancestry main effects and interactions with genotype, to refine the regions identified from admixture mapping. Finally, we leveraged in silico annotation and differential gene expression data to prioritize AD-related variants and genes. RESULTS Admixture mapping identified two genome-wide significant loci on chromosomes 17p13.2 (p = 2.2 × 10-5 ) and 18q21.33 (p = 1.2 × 10-5 ). Our fine mapping of the chromosome 17p13.2 and 18q21.33 regions revealed several interesting genes such as the MINK1, KIF1C, and BCL2. DISCUSSION Our ancestry-aware regression approach showed that AA individuals have a lower risk of AD if they inherited African ancestry admixture block at the 17p13.2 locus. HIGHLIGHTS We identified two genome-wide significant admixture mapping signals: on chromosomes 17p13.2 and 18q21.33, which are novel in African American (AA) populations. Our ancestry-aware regression approach showed that AA individuals have a lower risk of Alzheimer's disease (AD) if they inherited African ancestry admixture block at the 17p13.2 locus. We found that the overall proportion of African ancestry does not differ between the cases and controls that suggest African genetic ancestry alone is not likely to explain the AD prevalence difference between AA and non-Hispanic White populations.
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Affiliation(s)
- Farid Rajabli
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Giuseppe Tosto
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Kara L. Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Badri N. Vardarajan
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Adam Naj
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PE, USA
| | - Patrice G. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Olivia K. Gardner
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William S. Bush
- Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sanjeev Sariya
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Richard P. Mayeux
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jeffrey M. Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PE, USA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Goldie S. Byrd
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC, USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
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Liu CM, Aziz M, Park DE, Wu Z, Stegger M, Li M, Wang Y, Schmidlin K, Johnson TJ, Koch BJ, Hungate BA, Nordstrom L, Gauld L, Weaver B, Rolland D, Statham S, Hall B, Sariya S, Davis GS, Keim PS, Johnson JR, Price LB. Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections. One Health 2023; 16:100518. [PMID: 37363239 PMCID: PMC10288061 DOI: 10.1016/j.onehlt.2023.100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
A one-health perspective may provide new and actionable information about Escherichia coli transmission. E. coli colonizes a broad range of vertebrates, including humans and food-production animals, and is a leading cause of bladder, kidney, and bloodstream infections in humans. Substantial evidence supports foodborne transmission of pathogenic E. coli strains from food animals to humans. However, the relative contribution of foodborne zoonotic E. coli (FZEC) to the human extraintestinal disease burden and the distinguishing characteristics of such strains remain undefined. Using a comparative genomic analysis of a large collection of contemporaneous, geographically-matched clinical and meat-source E. coli isolates (n = 3111), we identified 17 source-associated mobile genetic elements - predominantly plasmids and bacteriophages - and integrated them into a novel Bayesian latent class model to predict the origins of clinical E. coli isolates. We estimated that approximately 8 % of human extraintestinal E. coli infections (mostly urinary tract infections) in our study population were caused by FZEC. FZEC strains were equally likely to cause symptomatic disease as non-FZEC strains. Two FZEC lineages, ST131-H22 and ST58, appeared to have particularly high virulence potential. Our findings imply that FZEC strains collectively cause more urinary tract infections than does any single non-E. coli uropathogenic species (e.g., Klebsiella pneumoniae). Our novel approach can be applied in other settings to identify the highest-risk FZEC strains, determine their sources, and inform new one-health strategies to decrease the heavy public health burden imposed by extraintestinal E. coli infections.
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Affiliation(s)
- Cindy M. Liu
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
| | - Maliha Aziz
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Daniel E. Park
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Michigan Institute for Data Science (MIDAS), University of Michigan, 500 Church Street, Suite 600, Ann Arbor, MI 48109, USA
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Mengbing Li
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Yashan Wang
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Kara Schmidlin
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Ave, St Paul, MN 55108, USA
| | - Benjamin J. Koch
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Lora Nordstrom
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Lori Gauld
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Brett Weaver
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Diana Rolland
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Sally Statham
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sanjeev Sariya
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Gregg S. Davis
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - James R. Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN 55417, USA
| | - Lance B. Price
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
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4
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Liu M, Khasiyev F, Sariya S, Spagnolo-Allende A, Sanchez DL, Andrews H, Yang Q, Beiser A, Qiao Y, Thomas EA, Romero JR, Rundek T, Brickman AM, Manly JJ, Elkind MSV, Seshadri S, Chen C, Sacco RL, Hilal S, Wasserman BA, Tosto G, Fornage M, Gutierrez J. Chromosome 10q24.32 Variants Associate with Brain Arterial Diameters in Diverse Populations: A Genome-Wide Association Study. medRxiv 2023:2023.01.31.23285251. [PMID: 36778463 PMCID: PMC9915818 DOI: 10.1101/2023.01.31.23285251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background Brain arterial diameters are novel imaging biomarkers of cerebrovascular disease, cognitive decline and dementia. Traditional vascular risk factors have been associated with brain arterial diameters but whether there may be genetic determinants of brain arterial diameters is unknown. Results We studied 4150 participants from six geographically diverse population-based cohorts (40% European, 14% African, 22% Hispanic, 24% Asian ancestries). We measured brain arterial diameters for 13 segments and averaged them to obtain a global measure of brain arterial diameters as well as the posterior and anterior circulations. A genome-wide association study (GWAS) revealed 14 variants at one locus associated with global brain arterial diameter at genome-wide significance (P<5×10-8) (top SNP, rs7921574; β =0.06, P=1.54×10-8). This locus mapped to an intron of CNNM2. A trans-ancestry GWAS meta-analysis identified two more loci at NT5C2 (rs10748839; P=2.54×10-8) and at AS3MT (rs10786721; P=4.97×10-8), associated with global brain arterial diameter. In addition, two SNPs co-localized with expression of CNNM2 (rs7897654, β=0.12, P=6.17×10-7) and AL356608.1 (rs10786719, β =-0.17, P=6.60×10-6) in brain tissue. For the posterior brain arterial diameter, two variants at one locus mapped to an intron of TCF25 were identified (top SNP, rs35994878; β =0.11, P=2.94×10-8). For the anterior brain arterial diameter, one locus at ADAP1 was identified in trans-ancestry genome-wide association analysis (rs34217249; P=3.11×10-8). Conclusion Our study reveals three novel risk loci (CNNM2, NT5C2 and AS3MT) associated with brain arterial diameters. Our finding may elucidate the mechanisms by which brain arterial diameters influence the risk of stroke and dementia.
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Affiliation(s)
- Minghua Liu
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Farid Khasiyev
- Department of Neurology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Sanjeev Sariya
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Antonio Spagnolo-Allende
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Danurys L Sanchez
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Howard Andrews
- Biostatistics Department, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Qiong Yang
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Alexa Beiser
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Ye Qiao
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emy A Thomas
- Brown Foundation Institute of Molecular Medicine, Mc Govern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jose Rafael Romero
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Tatjana Rundek
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Adam M Brickman
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jennifer J Manly
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mitchell SV Elkind
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- The Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Christopher Chen
- Memory Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ralph L Sacco
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Saima Hilal
- Memory Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bruce A Wasserman
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Giuseppe Tosto
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, Mc Govern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jose Gutierrez
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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5
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Gao Y, Felsky D, Reyes-Dumeyer D, Sariya S, Rentería MA, Ma Y, Klein HU, Cosentino S, De Jager PL, Bennett DA, Brickman AM, Schellenberg GD, Mayeux R, Barral S. Integration of GWAS and brain transcriptomic analyses in a multiethnic sample of 35,245 older adults identifies DCDC2 gene as predictor of episodic memory maintenance. Alzheimers Dement 2022; 18:1797-1811. [PMID: 34873813 PMCID: PMC9170841 DOI: 10.1002/alz.12524] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 01/28/2023]
Abstract
Identifying genes underlying memory function will help characterize cognitively resilient and high-risk declining subpopulations contributing to precision medicine strategies. We estimated episodic memory trajectories in 35,245 ethnically diverse older adults representing eight independent cohorts. We conducted apolipoprotein E (APOE)-stratified genome-wide association study (GWAS) analyses and combined individual cohorts' results via meta-analysis. Three independent transcriptomics datasets were used to further interpret GWAS signals. We identified DCDC2 gene significantly associated with episodic memory (Pmeta = 3.3 x 10-8 ) among non-carriers of APOE ε4 (N = 24,941). Brain transcriptomics revealed an association between episodic memory maintenance and (1) increased dorsolateral prefrontal cortex DCDC2 expression (P = 3.8 x 10-4 ) and (2) lower burden of pathological Alzheimer's disease (AD) hallmarks (paired helical fragment tau P = .003, and amyloid beta load P = .008). Additional transcriptomics results comparing AD and cognitively healthy brain samples showed a downregulation of DCDC2 levels in superior temporal gyrus (P = .007) and inferior frontal gyrus (P = .013). Our work identified DCDC2 gene as a novel predictor of memory maintenance.
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Affiliation(s)
- Yizhe Gao
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction
and Mental Health, Toronto, ON, Canada.,Department of Psychiatry & Institute of Medical
Science, University of Toronto, Toronto, ON, Canada
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Sanjeev Sariya
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA
| | - Miguel Arce Rentería
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Yiyi Ma
- Center for Translational & Computational
Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center,
New York, NY, 10032, USA
| | - Hans-Ulrich Klein
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,Center for Translational & Computational
Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center,
New York, NY, 10032, USA
| | - Stephanie Cosentino
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Philip L. De Jager
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,Center for Translational & Computational
Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center,
New York, NY, 10032, USA.,Cell Circuits Program, Broad Institute, Cambridge, MA,
USA
| | - David A. Bennett
- Rush University Medical Center, Rush Alzheimer’s
Disease Center, Chicago, IL, USA.,Rush University Medical Center, Department of Neurological
Sciences, Chicago, IL, USA
| | - Adam M. Brickman
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine,
University of Pennsylvania, Philadelphia, PA, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Sandra Barral
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | -
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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6
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Lee AJ, Raghavan NS, Bhattarai P, Siddiqui T, Sariya S, Reyes-Dumeyer D, Flowers XE, Cardoso SAL, De Jager PL, Bennett DA, Schneider JA, Menon V, Wang Y, Lantigua RA, Medrano M, Rivera D, Jiménez-Velázquez IZ, Kukull WA, Brickman AM, Manly JJ, Tosto G, Kizil C, Vardarajan BN, Mayeux R. FMNL2 regulates gliovascular interactions and is associated with vascular risk factors and cerebrovascular pathology in Alzheimer's disease. Acta Neuropathol 2022; 144:59-79. [PMID: 35608697 PMCID: PMC9217776 DOI: 10.1007/s00401-022-02431-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) has been associated with cardiovascular and cerebrovascular risk factors (CVRFs) during middle age and later and is frequently accompanied by cerebrovascular pathology at death. An interaction between CVRFs and genetic variants might explain the pathogenesis. Genome-wide, gene by CVRF interaction analyses for AD, in 6568 patients and 8101 controls identified FMNL2 (p = 6.6 × 10-7). A significant increase in FMNL2 expression was observed in the brains of patients with brain infarcts and AD pathology and was associated with amyloid and phosphorylated tau deposition. FMNL2 was also prominent in astroglia in AD among those with cerebrovascular pathology. Amyloid toxicity in zebrafish increased fmnl2a expression in astroglia with detachment of astroglial end feet from blood vessels. Knockdown of fmnl2a prevented gliovascular remodeling, reduced microglial activity and enhanced amyloidosis. APP/PS1dE9 AD mice also displayed increased Fmnl2 expression and reduced the gliovascular contacts independent of the gliotic response. Based on this work, we propose that FMNL2 regulates pathology-dependent plasticity of the blood-brain-barrier by controlling gliovascular interactions and stimulating the clearance of extracellular aggregates. Therefore, in AD cerebrovascular risk factors promote cerebrovascular pathology which in turn, interacts with FMNL2 altering the normal astroglial-vascular mechanisms underlying the clearance of amyloid and tau increasing their deposition in brain.
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Affiliation(s)
- Annie J Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Neha S Raghavan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Prabesh Bhattarai
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Tatzberg 41, 01307, Dresden, Germany
| | - Tohid Siddiqui
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Tatzberg 41, 01307, Dresden, Germany
| | - Sanjeev Sariya
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Xena E Flowers
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Sarah A L Cardoso
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Philip L De Jager
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Vilas Menon
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Rafael A Lantigua
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, 630 West 168th Street, New York, NY, 10032, USA
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra (PUCMM), Santiago, Dominican Republic
| | - Diones Rivera
- Department of Neurology, CEDIMAT, Plaza de la Salud, Santo Domingo, Dominican Republic
- School of Medicine, Universidad Pedro Henriquez Urena (UNPHU), Santo Domingo, Dominican Republic
| | - Ivonne Z Jiménez-Velázquez
- Department of Medicine, Medical Sciences Campus, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, 00936, USA
| | - Walter A Kukull
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, 98195, USA
| | - Adam M Brickman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Jennifer J Manly
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Caghan Kizil
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Tatzberg 41, 01307, Dresden, Germany
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA.
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA.
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA.
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY, 10032, USA.
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7
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Kizil C, Sariya S, Kim YA, Rajabli F, Martin E, Reyes-Dumeyer D, Vardarajan B, Maldonado A, Haines JL, Mayeux R, Jiménez-Velázquez IZ, Santa-Maria I, Tosto G. Admixture Mapping of Alzheimer's disease in Caribbean Hispanics identifies a new locus on 22q13.1. Mol Psychiatry 2022; 27:2813-2820. [PMID: 35365809 PMCID: PMC9167722 DOI: 10.1038/s41380-022-01526-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 11/09/2022]
Abstract
Late-onset Alzheimer's disease (LOAD) is significantly more frequent in Hispanics than in non-Hispanic Whites. Ancestry may explain these differences across ethnic groups. To this end, we studied a large cohort of Caribbean Hispanics (CH, N = 8813) and tested the association between Local Ancestry (LA) and LOAD ("admixture mapping") to identify LOAD-associated ancestral blocks, separately for ancestral components (European [EUR], African [AFR], Native American[NA]) and jointly (AFR + NA). Ancestral blocks significant after permutation were fine-mapped employing multi-ethnic whole-exome sequencing (WES) to identify rare variants associated with LOAD (SKAT-O) and replicated in the UK Biobank WES dataset. Candidate genes were validated studying (A) protein expression in human LOAD and control brains; (B) two animal AD models, Drosophila and Zebrafish. In the joint AFR + NA model, we identified four significant ancestral blocks located on chromosomes 1 (p value = 8.94E-05), 6 (p value = 8.63E-05), 21 (p value = 4.64E-05) and 22 (p value = 1.77E-05). Fine-mapping prioritized the GCAT gene on chromosome 22 (SKAT-O p value = 3.45E-05) and replicated in the UK Biobank (SKAT-O p value = 0.05). In LOAD brains, a decrease of 28% in GCAT protein expression was observed (p value = 0.038), and GCAT knockdown in Amyloid-β42 Drosophila exacerbated rough eye phenotype (68% increase, p value = 4.84E-09). In zebrafish, gcat expression increased after acute amyloidosis (34%, p value = 0.0049), and decreased upon anti-inflammatory Interleukin-4 (39%, p value = 2.3E-05). Admixture mapping uncovered genomic regions harboring new LOAD-associated loci that might explain the observed different frequency of LOAD across ethnic groups. Our results suggest that the inflammation-related activity of GCAT is a response to amyloid toxicity, and reduced GCAT expression exacerbates AD pathology.
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Affiliation(s)
- Caghan Kizil
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Tatzberg 41, 01307, Dresden, Germany
| | - Sanjeev Sariya
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Yoon A Kim
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Eden Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Aleyda Maldonado
- Department of Medicine, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, 00936, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, 630 West 168th Street, New York, NY, 10032, USA
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY, 10032, USA
| | - Ivonne Z Jiménez-Velázquez
- Department of Medicine, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, 00936, USA
| | - Ismael Santa-Maria
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West168 th Street, New York, NY, 10032, USA.
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, 10032, USA.
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA.
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8
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Liu M, Sariya S, Khasiyev F, Tosto G, Dueker ND, Cheung YK, Wright CB, Sacco RL, Rundek T, Elkind MS, Gutierrez J. Genetic determinants of intracranial large artery stenosis in the northern Manhattan study. J Neurol Sci 2022; 436:120218. [PMID: 35259553 PMCID: PMC9018518 DOI: 10.1016/j.jns.2022.120218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/01/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Intracranial stenosis is one of the most common causes of stroke worldwide. Several single nucleotide polymorphisms have been associated with intracranial atherosclerosis, which is inferred to be the most common underlying cause of intracranial large artery stenosis (ILAS). We previously reviewed known genetic variants related to ILAS in predominantly Asian cohorts, but their prevalence and role in ILAS among western multiethnic populations are uncertain. METHODS We leveraged existing imaging and genetic data from the Northern Manhattan Study, a multiethnic prospective cohort study. Based on literature review, we selected adiponectin Q (ADIPOQ) rs2241767 and rs182052, ring finger protein 213 (RNF213) rs112735431, apolipoprotein E (APOE) rs429358, phosphodiesterase 4D (PDE4D) rs2910829, lipoprotein lipase (LPL) rs320, and aldosterone synthase (CYP11B2) rs1799998 variants as candidates to explore. We defined ILAS as luminal stenosis >50% in any intracranial large artery using time-of-flight magnetic resonance angiography (MRA). RESULTS We included 1109 participants (mean age 70 ± 9 years, 70% Hispanic, 60% women) in this study. ILAS was identified in 81 (7%) NOMAS participants. Logistic regression analyses adjusted for age, sex, principal components, and vascular risk factors showed ILAS prevalence associated with CYP11B2 rs1799998 under the dominant model (OR = 0.56, 95%CI: 0.35-0.89) and LPL rs320 heterozygote genotype (OR = 1.68, 95%CI: 1.05-2.71). The genotype distributions of ADIPOQ rs2241767 and rs182052, APOE rs429358 and CYP11B2 rs1799998 variants were significantly different among non-Hispanic white and Black, and Hispanic groups. When participants were further stratified by race/ethnicity, the estimates were consistent for CYP11B2 rs1799998 across race/ethnic groups but not for LPL rs320. CONCLUSION The CYP11B2 rs1799998 variant may be a protective genetic factor for ILAS across race/ethnic groups, but the risk of ILAS associated with LPL rs320 varies by race/ethnic group. Further functional studies may help elucidate the role that these variants play in the pathophysiology of ILAS.
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9
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Liu M, Khasiyev F, Wasserman BA, Qiao Y, Thomas EA, Elkind MS, Sacco RL, Rundek T, Tosto G, Sariya S, Hilal S, Seshadri S, Romero JR, Yang Q, Fornage M, Gutierrez J. Abstract WP205: Trans-ethnic Genome-wide Association Studies Meta-analysis Of Large Brain Arterial Diameters Identifies Two Novel Genetic Loci. Stroke 2022. [DOI: 10.1161/str.53.suppl_1.wp205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction:
Larger brain arterial diameters, which may be a consequence of connective tissue disorders or hypertension, are associated with mortality, cognitive decline and risk of dementia. Whether there may be genetic determinants of large brain arterial diameters is unknown, but identifying such traits may shed light into possible mechanistic links between large brain arterial diameters and the observed outcomes.
Methods:
We studied 3654 participants from four ethnically diverse population-based cohorts: The Atherosclerosis Risk in Communities study (n=1565: 74.3% white, 25.7% black), The Northern Manhattan Study (n=1092: 13.8% white, 16.6% black, 69.6% Hispanic), Epidemiology of Dementia in Singapore (n=647: 31.7% Chinese, 35.7% Malay, 32.6% Indian), and Memory Clinic Cohort in Singapore (n=350: 84.9% Chinese, 7.8% Malay, 7.3% Indian). We measured brain arterial diameters for 13 segments and normalized the averaged diameter per participant to obtain global brain arterial diameter as dependent variable. Genome-wide association studies (GWAS) was performed in each study using linear regression, adjusted for sex, age, head size, number of missing arteries and population substructure. Meta-analysis of association statistics was performed using the METAL to generate combined trait-specific effect estimates. We also performed trans-ethnic meta-regression by MR-MEGA to account for the heterogeneity in allelic effect that is correlated with ancestry.
Results:
Genome-wide significant (P<5x10
-8
) associations were observed for global brain arterial diameter with three SNPs: rs7921574(P=1.2x10
-8
) mapping to an intron of CNNM2; rs2075858(P=2.47x10
-8
) and rs2075857 (P=2.37x10
-8
) mapping to introns of MUC5B. MR-MEGA analysis showed suggestive evidence of association (P=5.05x10
-8
) for rs7921574. These loci comprise genes involved in response to magnesium transport, neuronal transmission, hypertension, mucociliary clearance and host defense.
Conclusion:
Our study reveals two novel risk loci for large brain arterial diameters. We have begun to replicate these associations and to identify functional causal variants in independent studies. Identifying these loci may help us to elucidate underlying disease mechanisms.
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Affiliation(s)
- Minghua Liu
- Dept of Neurology, Columbia Univ, New York City, NY
| | | | | | - Ye Qiao
- JOHNS HOPKINS UNIVERISITY, Baltimore, MD
| | | | | | | | | | - Giuseppe Tosto
- Taub Institute for Rsch on Alzheimer's Disease and the Aging Brain, Columbia Univ, New York City, NY
| | - Sanjeev Sariya
- Taub Institute for Rsch on Alzheimer's Disease and the Aging Brain, Columbia Univ, New York City, NY
| | - Saima Hilal
- National Univ of Singapore, Singapore, Singapore
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10
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Sariya S, Felsky D, Lali R, Reyes‐Dumeyer D, Lantigua RA, Brickman AM, Manly JJ, Vardarajan BN, Jiménez‐Velázquez IZ, Pare G, Mayeux R, Tosto G. Polygenic risk score for Alzheimer’s disease in Caribbean Hispanics. Alzheimers Dement 2021. [DOI: 10.1002/alz.055031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sanjeev Sariya
- Columbia University Irving Medical Center New York NY USA
| | - Daniel Felsky
- Centre for Addiction and Mental Health Toronto ON Canada
| | - Ricky Lali
- Department of Pathology and Molecular Medicine McMaster University Hamilton ON Canada
| | | | | | | | | | - Badri N. Vardarajan
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain Columbia University New York NY USA
| | | | - Guillaume Pare
- Department of Pathology and Molecular Medicine McMaster University Hamilton ON Canada
| | - Richard Mayeux
- Columbia University Irving Medical Center New York NY USA
| | - Giuseppe Tosto
- Columbia University Irving Medical Center New York NY USA
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11
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Siddiqui T, Bhattarai P, Popova S, Cosacak MI, Sariya S, Zhang Y, Mayeux R, Tosto G, Kizil C. KYNA/Ahr Signaling Suppresses Neural Stem Cell Plasticity and Neurogenesis in Adult Zebrafish Model of Alzheimer's Disease. Cells 2021; 10:2748. [PMID: 34685728 PMCID: PMC8534484 DOI: 10.3390/cells10102748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Neurogenesis decreases in Alzheimer's disease (AD) patients, suggesting that restoring the normal neurogenic response could be a disease modifying intervention. To study the mechanisms of pathology-induced neuro-regeneration in vertebrate brains, zebrafish is an excellent model due to its extensive neural regeneration capacity. Here, we report that Kynurenic acid (KYNA), a metabolite of the amino acid tryptophan, negatively regulates neural stem cell (NSC) plasticity in adult zebrafish brain through its receptor, aryl hydrocarbon receptor 2 (Ahr2). The production of KYNA is suppressed after amyloid-toxicity through reduction of the levels of Kynurenine amino transferase 2 (KAT2), the key enzyme producing KYNA. NSC proliferation is enhanced by an antagonist for Ahr2 and is reduced with Ahr2 agonists or KYNA. A subset of Ahr2-expressing zebrafish NSCs do not express other regulatory receptors such as il4r or ngfra, indicating that ahr2-positive NSCs constitute a new subset of neural progenitors that are responsive to amyloid-toxicity. By performing transcriptome-wide association studies (TWAS) in three late onset Alzheimer disease (LOAD) brain autopsy cohorts, we also found that several genes that are components of KYNA metabolism or AHR signaling are differentially expressed in LOAD, suggesting a strong link between KYNA/Ahr2 signaling axis to neurogenesis in LOAD.
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Affiliation(s)
- Tohid Siddiqui
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany; (T.S.); (P.B.); (S.P.); (M.I.C.)
| | - Prabesh Bhattarai
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany; (T.S.); (P.B.); (S.P.); (M.I.C.)
| | - Stanislava Popova
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany; (T.S.); (P.B.); (S.P.); (M.I.C.)
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany; (T.S.); (P.B.); (S.P.); (M.I.C.)
| | - Sanjeev Sariya
- The Department of Neurology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA; (S.S.); (R.M.); (G.T.)
| | - Yixin Zhang
- B-CUBE, Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307 Dresden, Germany;
| | - Richard Mayeux
- The Department of Neurology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA; (S.S.); (R.M.); (G.T.)
| | - Giuseppe Tosto
- The Department of Neurology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA; (S.S.); (R.M.); (G.T.)
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany; (T.S.); (P.B.); (S.P.); (M.I.C.)
- The Department of Neurology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA; (S.S.); (R.M.); (G.T.)
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12
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Sariya S, Felsky D, Reyes-Dumeyer D, Lali R, Lantigua RA, Vardarajan B, Jiménez-Velázquez IZ, Haines JL, Shellenberg GD, Pericak-Vance MA, Paré G, Mayeux R, Tosto G. Polygenic Risk Score for Alzheimer's Disease in Caribbean Hispanics. Ann Neurol 2021; 90:366-376. [PMID: 34038570 PMCID: PMC8435026 DOI: 10.1002/ana.26131] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Polygenic risk scores (PRSs) assess the individual genetic propensity to a condition by combining sparse information scattered across genetic loci, often displaying small effect sizes. Most PRSs are constructed in European-ancestry populations, limiting their use in other ethnicities. Here we constructed and validated a PRS for late-onset Alzheimer's Disease (LOAD) in Caribbean Hispanics (CH). METHODS We used a CH discovery (n = 4,312) and independent validation sample (n = 1,850) to construct an ancestry-specific PRS ("CH-PRS") and evaluated its performance alone and with other predictors using the area under curve (AUC) and logistic regression (strength of association with LOAD and statistical significance). We tested if CH-PRS predicted conversion to LOAD in a subsample with longitudinal data (n = 1,239). We also tested the CH-PRS in an independent replication CH cohort (n = 200) and brain autopsy cohort (n = 33). Finally, we tested the effect of ancestry on PRS by using European and African American discovery cohorts to construct alternative PRSs ("EUR-PRS", "AA-PRS"). RESULTS The full model (LOAD ~ CH-PRS + sex + age + APOE-ɛ4), achieved an AUC = 74% (ORCH-PRS = 1.51 95%CI = 1.36-1.68), raising to >75% in APOE-ɛ4 non-carriers. CH-PRS alone achieved an AUC = 72% in the autopsy cohort, raising to AUC = 83% in full model. Higher CH-PRS was significantly associated with clinical LOAD in the replication CH cohort (OR = 1.61, 95%CI = 1.19-2.17) and significantly predicted conversion to LOAD (HR = 1.93, CI = 1.70-2.20) in the longitudinal subsample. EUR-PRS and AA-PRS reached lower prediction accuracy (AUC = 58% and 53%, respectively). INTERPRETATION Enriching diversity in genetic studies is critical to provide an effective PRS in profiling LOAD risk across populations. ANN NEUROL 2021;90:366-376.
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Affiliation(s)
- Sanjeev Sariya
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | - Ricky Lali
- Population Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Rafael A. Lantigua
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, New York, NY
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | | | - Jonathan L. Haines
- Department of Population & Quantitative Health SciencesCleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH
| | | | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Guillaume Paré
- Population Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, New York, NY
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
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13
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Felsky D, Sariya S, Schneider JA, Bennett DA, Mayeux R, De Jager PL, Tosto G. The Caribbean‐Hispanic Alzheimer’s brain transcriptome reveals ancestry‐specific disease mechanisms. Alzheimers Dement 2020. [DOI: 10.1002/alz.043068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Felsky
- Centre for Addiction and Mental Health Toronto ON Canada
- University of Toronto Toronto ON Canada
| | | | - Julie A. Schneider
- Rush Alzheimer's Disease Center Rush University Medical Center Chicago IL USA
| | - David A. Bennett
- Rush Alzheimer's Disease Center Rush University Medical Center Chicago IL USA
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14
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Sariya S, Rentería MA, Reyes‐Dumeyer D, Arango SM, Obregon AM, Samper‐Ternent R, Wong R, Mayeux R, Barral S, Tosto G. The role of Native American ancestry in Alzheimer’s disease and related dementias. Alzheimers Dement 2020. [DOI: 10.1002/alz.046248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | | | | | - Rebeca Wong
- University of Texas Medical Branch Galveston TX USA
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15
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Gao Y, Vardarajan BN, Reyes‐Dumeyer D, Sariya S, Mayeux R, Tosto G, Barral S. APOE
‐stratified, genome‐wide, gene‐based analysis of episodic memory trajectories in a multi‐ethnic sample of 24,769 elderly. Alzheimers Dement 2020. [DOI: 10.1002/alz.045997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yizhe Gao
- Columbia University Medical Center New York NY USA
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16
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Aziz M, Nicholson AM, Nadimpalli M, Sariya S, Price L, Singh N, Liu C. 1627. Outbreaks of Klebsiella pneumoniae in Special Care Nurseries (SCN) in Jamaica: Role of Whole-Genome Sequencing. Open Forum Infect Dis 2019. [PMCID: PMC6810263 DOI: 10.1093/ofid/ofz360.1491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Klebsiella pneumoniae is a frequent cause of neonatal sepsis and carries a high mortality rate in lower and middle-income countries (LMICs). From March-November 2015, two Jamaican hospitals experienced K. pneumoniae outbreaks in their Special Care Nurseries (SCNs). New admissions to both SCNs were temporarily halted while additional infection control strategies were implemented. 31 babies were infected, of which 15 died. International collaboration was requested to help investigate if the sepsis cases were nosocomial transmission, repeated introductions from the community, or both using whole-genome sequencing
Methods
We sequenced DNA from 19 outbreak isolates (n = 13 from Hospital A, n = 6 from Hospital B) on an Illumina HiSeq2500 instrument and assembled short-reads using SPAdes. We used ResFinder v3.1.0 to screen resistance genes and assigned MLSTs using in-house scripts. To compare the outbreak isolates, we selected a reference genome from among the assembled isolates, aligned raw reads using the Burrows–Wheeler Aligner (BWA), identified SNPs using GATK UnifiedGenotyper, and removed the recombined regions using Gubbins v2.3.4. We further contextualized the 19 outbreak isolates against a global collection of more than 300 K. pneumoniae genomes.
Results
All 13 isolates from Hospital A appeared to be from a single source. All were ST45 and encoded blaCTX-M-15, which confers extended-spectrum β-lactam (ESBL) resistance. Five of 6 isolates from Hospital B appeared to be from a separate, single source. These 5 isolates were ST268 and susceptible to most antibiotics. 1 isolate from Hospital B was ST628, encoded blaCTX-M-15, and grouped separately from other Hospital B outbreak isolates. Hospital A and B outbreak isolates formed independent, unique clades within a global K. pneumoniae collection.
Conclusion
Our findings indicate nosocomial transmission was responsible for both neonatal K. pneumoniae outbreaks, rather than repeat introductions from the community. The main sequence types we detected (ST45 and ST268) are not known pandemic clones and may circulate regionally. Multifaceted infection control measures were implemented for effectively halting outbreaks.
Disclosures
All authors: No reported disclosures.
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Affiliation(s)
- Maliha Aziz
- The George Washington University, Washington, DC
| | | | | | | | - Lance Price
- The George Washington University, Washington, DC
| | - Nalini Singh
- The George Washington University, Washington, DC
| | - Cindy Liu
- The George Washington University, Washington, DC
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17
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Tosto G, Vardarajan B, Sariya S, Brickman AM, Andrews H, Manly JJ, Schupf N, Reyes-Dumeyer D, Lantigua R, Bennett DA, De Jager PL, Mayeux R. Association of Variants in PINX1 and TREM2 With Late-Onset Alzheimer Disease. JAMA Neurol 2019; 76:942-948. [PMID: 31058951 DOI: 10.1001/jamaneurol.2019.1066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Importance Genetic causes of late-onset Alzheimer disease (LOAD) are not completely explained by known genetic loci. Whole-exome and whole-genome sequencing can improve the understanding of the causes of LOAD and provide initial steps required to identify potential therapeutic targets. Objective To identify the genetic loci for LOAD across different ethnic groups. Design, Setting, and Participants This multicenter cohort study was designed to analyze whole-exome sequencing data from a multiethnic cohort using a transethnic gene-kernel association test meta-analysis, adjusted for sex, age, and principal components, to identify genetic variants associated with LOAD. A meta-analysis was conducted on the results of 2 independent studies of whole-exome and whole-genome sequence data from individuals of European ancestry. This group of European American, African American, and Caribbean Hispanic individuals participating in an urban population-based study were the discovery cohort; the additional cohorts included affected individuals and control participants from 2 publicly available data sets. Replication was achieved using independent data sets from Caribbean Hispanic families with multiple family members affected by LOAD and the International Genetics of Alzheimer Project. Main Outcomes and Measures Late-onset Alzheimer disease. Results The discovery cohort included 3595 affected individuals, while the additional cohorts included 5931 individuals with LOAD and 5504 control participants. Of 3916 individuals in the discovery cohort, we included 3595 individuals (1397 with LOAD and 2198 cognitively healthy controls; 2451 [68.2%] women; mean [SD] age, 80.3 [6.83] years). Another 321 individuals (8.2%) were excluded because of non-LOAD diagnosis, age younger than 60 years, missing covariates, duplicate data, or genetic outlier status. Gene-based tests that compared affected individuals (n = 7328) and control participants (n = 7702) and included only rare and uncommon variants annotated as having moderate-high functional effect supported PINX1 (8p23.1) as a locus with gene-wide significance (P = 2.81 × 10-6) after meta-analysis across the 3 studies. The PINX1 finding was replicated using data from the family-based study and the International Genetics of Alzheimer Project. Full meta-analysis of discovery and replication cohorts reached a P value of 6.16 × 10-7 for PINX1 (in 7620 affected individuals vs 7768 control participants). We also identified TREM2 in an annotation model that prioritized highly deleterious variants with a combined annotation dependent depletion greater than 20 (P= 1.0 × 10-7). Conclusions and Relevance This gene-based, transethnic approach identified PINX1, a gene involved in telomere integrity, and TREM2, a gene with a product of an immune receptor found in microglia, as associated with LOAD. Both genes have well-established roles in aging and neurodegeneration.
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Affiliation(s)
- Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Sanjeev Sariya
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Adam M Brickman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York
| | - Howard Andrews
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Jennifer J Manly
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Rafael Lantigua
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Medicine, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Phillip L De Jager
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York.,Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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18
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Sariya S, Lee JH, Mayeux R, Vardarajan BN, Reyes-Dumeyer D, Manly JJ, Brickman AM, Lantigua R, Medrano M, Jimenez-Velazquez IZ, Tosto G. Rare Variants Imputation in Admixed Populations: Comparison Across Reference Panels and Bioinformatics Tools. Front Genet 2019; 10:239. [PMID: 31001313 PMCID: PMC6456789 DOI: 10.3389/fgene.2019.00239] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/04/2019] [Indexed: 11/13/2022] Open
Abstract
Background Imputation has become a standard approach in genome-wide association studies (GWAS) to infer in silico untyped markers. Although feasibility for common variants imputation is well established, we aimed to assess rare and ultra-rare variants’ imputation in an admixed Caribbean Hispanic population (CH). Methods We evaluated imputation accuracy in CH (N = 1,000), focusing on rare (0.1% ≤ minor allele frequency (MAF) ≤ 1%) and ultra-rare (MAF < 0.1%) variants. We used two reference panels, the Haplotype Reference Consortium (HRC; N = 27,165) and 1000 Genome Project (1000G phase 3; N = 2,504) and multiple phasing (SHAPEIT, Eagle2) and imputation algorithms (IMPUTE2, MACH-Admix). To assess imputation quality, we reported: (a) high-quality variant counts according to imputation tools’ internal indexes (e.g., IMPUTE2 “Info” ≥ 80%). (b) Wilcoxon Signed-Rank Test comparing imputation quality for genotyped variants that were masked and imputed; (c) Cohen’s kappa coefficient to test agreement between imputed and whole-exome sequencing (WES) variants; (d) imputation of G206A mutation in the PSEN1 (ultra-rare in the general population an more frequent in CH) followed by confirmation genotyping. We also tested ancestry proportion (European, African and Native American) against WES-imputation mismatches in a Poisson regression fashion. Results SHAPEIT2 retrieved higher percentage of imputed high-quality variants than Eagle2 (rare: 51.02% vs. 48.60%; ultra-rare 0.66% vs. 0.65%, Wilcoxon p-value < 0.001). SHAPEIT-IMPUTE2 employing HRC outperformed 1000G (64.50% vs. 59.17%; 1.69% vs. 0.75% for high-quality rare and ultra-rare variants, respectively, Wilcoxon p-value < 0.001). SHAPEIT-IMPUTE2 outperformed MaCH-Admix. Compared to 1000G, HRC-imputation retrieved a higher number of high-quality rare and ultra-rare variants, despite showing lower agreement between imputed and WES variants (e.g., rare: 98.86% for HRC vs. 99.02% for 1000G). High Kappa (K = 0.99) was observed for both reference panels. Twelve G206A mutation carriers were imputed and all validated by confirmation genotyping. African ancestry was associated with higher imputation errors for uncommon and rare variants (p-value < 1e-05). Conclusion Reference panels with larger numbers of haplotypes can improve imputation quality for rare and ultra-rare variants in admixed populations such as CH. Ethnic composition is an important predictor of imputation accuracy, with higher African ancestry associated with poorer imputation accuracy.
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Affiliation(s)
- Sanjeev Sariya
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Joseph H Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Jennifer J Manly
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
| | - Adam M Brickman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
| | - Rafael Lantigua
- Medicine College of Physicians and Surgeons, and The Department of Epidemiology, School of Public Health, Columbia University, New York, NY, United States
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra, Santiago, Dominican Republic
| | - Ivonne Z Jimenez-Velazquez
- Department of Medicine, Geriatrics Program, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
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Sariya S, Vardarajan BN, Barral S, Reitz C, Brickman AM, Manly JJ, Schupf N, Lantigua R, Reyes-Dumeyer D, Tosto G, Mayeux R. P2‐140: GENOME‐WIDE ASSOCIATION STUDY FOR ALZHEIMER'S DISEASE IN A LARGE SAMPLE OF CARIBBEAN HISPANICS. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | | | | | | | - Adam M. Brickman
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNYUSA
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