1
|
Bhattarai P, Gunasekaran TI, Belloy ME, Reyes-Dumeyer D, Jülich D, Tayran H, Yilmaz E, Flaherty D, Turgutalp B, Sukumar G, Alba C, McGrath EM, Hupalo DN, Bacikova D, Le Guen Y, Lantigua R, Medrano M, Rivera D, Recio P, Nuriel T, Ertekin-Taner N, Teich AF, Dickson DW, Holley S, Greicius M, Dalgard CL, Zody M, Mayeux R, Kizil C, Vardarajan BN. Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer's disease. Acta Neuropathol 2024; 147:70. [PMID: 38598053 PMCID: PMC11006751 DOI: 10.1007/s00401-024-02721-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The risk of developing Alzheimer's disease (AD) significantly increases in individuals carrying the APOEε4 allele. Elderly cognitively healthy individuals with APOEε4 also exist, suggesting the presence of cellular mechanisms that counteract the pathological effects of APOEε4; however, these mechanisms are unknown. We hypothesized that APOEε4 carriers without dementia might carry genetic variations that could protect them from developing APOEε4-mediated AD pathology. To test this, we leveraged whole-genome sequencing (WGS) data in the National Institute on Aging Alzheimer's Disease Family Based Study (NIA-AD FBS), Washington Heights/Inwood Columbia Aging Project (WHICAP), and Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) cohorts and identified potentially protective variants segregating exclusively among unaffected APOEε4 carriers. In homozygous unaffected carriers above 70 years old, we identified 510 rare coding variants. Pathway analysis of the genes harboring these variants showed significant enrichment in extracellular matrix (ECM)-related processes, suggesting protective effects of functional modifications in ECM proteins. We prioritized two genes that were highly represented in the ECM-related gene ontology terms, (FN1) and collagen type VI alpha 2 chain (COL6A2) and are known to be expressed at the blood-brain barrier (BBB), for postmortem validation and in vivo functional studies. An independent analysis in a large cohort of 7185 APOEε4 homozygous carriers found that rs140926439 variant in FN1 was protective of AD (OR = 0.29; 95% CI [0.11, 0.78], P = 0.014) and delayed age at onset of disease by 3.37 years (95% CI [0.42, 6.32], P = 0.025). The FN1 and COL6A2 protein levels were increased at the BBB in APOEε4 carriers with AD. Brain expression of cognitively unaffected homozygous APOEε4 carriers had significantly lower FN1 deposition and less reactive gliosis compared to homozygous APOEε4 carriers with AD, suggesting that FN1 might be a downstream driver of APOEε4-mediated AD-related pathology and cognitive decline. To validate our findings, we used zebrafish models with loss-of-function (LOF) mutations in fn1b-the ortholog for human FN1. We found that fibronectin LOF reduced gliosis, enhanced gliovascular remodeling, and potentiated the microglial response, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF. Our study suggests that vascular deposition of FN1 is related to the pathogenicity of APOEε4, and LOF variants in FN1 may reduce APOEε4-related AD risk, providing novel clues to potential therapeutic interventions targeting the ECM to mitigate AD risk.
Collapse
Affiliation(s)
- Prabesh Bhattarai
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Tamil Iniyan Gunasekaran
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Dolly Reyes-Dumeyer
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Dörthe Jülich
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Hüseyin Tayran
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Elanur Yilmaz
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Delaney Flaherty
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Bengisu Turgutalp
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Gauthaman Sukumar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Camille Alba
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Elisa Martinez McGrath
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Daniel N Hupalo
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Dagmar Bacikova
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Rafael Lantigua
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Medicine, College of Physicians and Surgeons, Columbia University New York, New York, USA
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra, 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
| | - Patricia Recio
- Department of Neurology, CEDIMAT, Plaza de la Salud, Santo Domingo, Dominican Republic
| | - Tal Nuriel
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Andrew F Teich
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Scott Holley
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Michael Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- The American Genome Center, Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Michael Zody
- New York Genome Center, New York, NY, 10013, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY, 10032, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 W 168th St., New York, NY, 10032, USA
| | - Caghan Kizil
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA.
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Badri N Vardarajan
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA.
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| |
Collapse
|
2
|
Carter RC, Yang Z, Akkaya-Hocagil T, Jacobson SW, Jacobson JL, Dodge NC, Hoyme HE, Zeisel SH, Meintjes EM, Kizil C, Tosto G. Genetic admixture predictors of fetal alcohol spectrum disorders (FASD) in the South African Cape Coloured population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.31.24305130. [PMID: 38633769 PMCID: PMC11023663 DOI: 10.1101/2024.03.31.24305130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Ancestrally admixed populations are underrepresented in genetic studies of complex diseases, which are still dominated by European-descent populations. This is relevant not only from a representation standpoint but also because of admixed populations' unique features, including being enriched for rare variants, for which effect sizes are disproportionately larger than common polymorphisms. Furthermore, results from these populations may be generalizable to other populations. The South African Cape Coloured (SACC) population is genetically admixed, with one of the highest prevalences of fetal alcohol spectrum disorders (FASD) worldwide. We profiled its admixture and examined associations between ancestry profiles and FASD outcomes using two longitudinal birth cohorts ( N =308 mothers, 280 children) designed to examine effects of prenatal alcohol exposure on development. Participants were genotyped via MEGA-ex array to capture common and rare variants. Rare variants were overrepresented in our SACC cohorts, with numerous polymorphisms being monomorphic in other reference populations (e.g., ∼30,000 and ∼221,000 variants in gnomAD European and Asian populations, respectively). The cohorts showed global African (51%; Bantu and San); European (26%; Northern/Western); South Asian (18%); and East Asian (5%; largely Southern regions) ancestries. The cohorts exhibited high rates of homozygosity (6%), with regions of homozygosity harboring more deleterious variants when lying within African local-ancestry genomic segments. Both maternal and child ancestry profiles were associated with FASD risk and altered severity of prenatal alcohol exposure-related cognitive deficits in the child. Our findings indicate that the SACC population may be a valuable asset to identify novel disease-associated genetic loci for FASD and other diseases.
Collapse
|
3
|
Bhattarai P, Gunasekaran TI, Reyes-Dumeyer D, Jülich D, Tayran H, Yilmaz E, Flaherty D, Lantigua R, Medrano M, Rivera D, Recio P, Ertekin-Taner N, Teich AF, Dickson DW, Holley S, Mayeux R, Kizil C, Vardarajan BN. Rare genetic variation in Fibronectin 1 ( FN1 ) protects against APOEe4 in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573895. [PMID: 38260431 PMCID: PMC10802344 DOI: 10.1101/2024.01.02.573895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The risk of developing Alzheimer's disease (AD) significantly increases in individuals carrying the APOEε4 allele. Elderly cognitively healthy individuals with APOEε4 also exist, suggesting the presence of cellular mechanisms that counteract the pathological effects of APOEε4 ; however, these mechanisms are unknown. We hypothesized that APOEε4 carriers without dementia might carry genetic variations that could protect them from developing APOEε4- mediated AD pathology. To test this, we leveraged whole genome sequencing (WGS) data in National Institute on Aging Alzheimer's Disease Family Based Study (NIA-AD FBS), Washington Heights/Inwood Columbia Aging Project (WHICAP), and Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) cohorts and identified potentially protective variants segregating exclusively among unaffected APOEε4 carriers. In homozygous unaffected carriers above 70 years old, we identified 510 rare coding variants. Pathway analysis of the genes harboring these variants showed significant enrichment in extracellular matrix (ECM)-related processes, suggesting protective effects of functional modifications in ECM proteins. We prioritized two genes that were highly represented in the ECM-related gene ontology terms, (FN1) and collagen type VI alpha 2 chain ( COL6A2 ) and are known to be expressed at the blood-brain barrier (BBB), for postmortem validation and in vivo functional studies. The FN1 and COL6A2 protein levels were increased at the BBB in APOEε4 carriers with AD. Brain expression of cognitively unaffected homozygous APOEε4 carriers had significantly lower FN1 deposition and less reactive gliosis compared to homozygous APOEε4 carriers with AD, suggesting that FN1 might be a downstream driver of APOEε4 -mediated AD-related pathology and cognitive decline. To validate our findings, we used zebrafish models with loss-of-function (LOF) mutations in fn1b - the ortholog for human FN1 . We found that fibronectin LOF reduced gliosis, enhanced gliovascular remodeling and potentiated the microglial response, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF. Our study suggests vascular deposition of FN1 is related to the pathogenicity of APOEε4 , LOF variants in FN1 may reduce APOEε4 -related AD risk, providing novel clues to potential therapeutic interventions targeting the ECM to mitigate AD risk.
Collapse
|
4
|
Tayran H, Yilmaz E, Bhattarai P, Min Y, Wang X, Ma Y, Nelson N, Kassara N, Cosacak MI, Dogru RM, Reyes-Dumeyer D, Reddy JS, Qiao M, Flaherty D, Teich AF, Gunasekaran TI, Yang Z, Tosto G, Vardarajan BN, İş Ö, Ertekin-Taner N, Mayeux R, Kizil C. ABCA7-dependent Neuropeptide-Y signalling is a resilience mechanism required for synaptic integrity in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573893. [PMID: 38260408 PMCID: PMC10802315 DOI: 10.1101/2024.01.02.573893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) remains a complex challenge characterized by cognitive decline and memory loss. Genetic variations have emerged as crucial players in the etiology of AD, enabling hope for a better understanding of the disease mechanisms; yet the specific mechanism of action for those genetic variants remain uncertain. Animal models with reminiscent disease pathology could uncover previously uncharacterized roles of these genes. Using CRISPR/Cas9 gene editing, we generated a knockout model for abca7, orthologous to human ABCA7 - an established AD-risk gene. The abca7 +/- zebrafish showed reduced astroglial proliferation, synaptic density, and microglial abundance in response to amyloid beta 42 (Aβ42). Single-cell transcriptomics revealed abca7 -dependent neuronal and glial cellular crosstalk through neuropeptide Y (NPY) signaling. The abca7 knockout reduced the expression of npy, bdnf and ngfra , which are required for synaptic integrity and astroglial proliferation. With clinical data in humans, we showed reduced NPY in AD correlates with elevated Braak stage, predicted regulatory interaction between NPY and BDNF , identified genetic variants in NPY associated with AD, found segregation of variants in ABCA7, BDNF and NGFR in AD families, and discovered epigenetic changes in the promoter regions of NPY, NGFR and BDNF in humans with specific single nucleotide polymorphisms in ABCA7 . These results suggest that ABCA7-dependent NPY signaling is required for synaptic integrity, the impairment of which generates a risk factor for AD through compromised brain resilience. Abstract Figure
Collapse
|
5
|
Area-Gomez E, Schon EA. Towards a Unitary Hypothesis of Alzheimer's Disease Pathogenesis. J Alzheimers Dis 2024; 98:1243-1275. [PMID: 38578892 DOI: 10.3233/jad-231318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
The "amyloid cascade" hypothesis of Alzheimer's disease (AD) pathogenesis invokes the accumulation in the brain of plaques (containing the amyloid-β protein precursor [AβPP] cleavage product amyloid-β [Aβ]) and tangles (containing hyperphosphorylated tau) as drivers of pathogenesis. However, the poor track record of clinical trials based on this hypothesis suggests that the accumulation of these peptides is not the only cause of AD. Here, an alternative hypothesis is proposed in which the AβPP cleavage product C99, not Aβ, is the main culprit, via its role as a regulator of cholesterol metabolism. C99, which is a cholesterol sensor, promotes the formation of mitochondria-associated endoplasmic reticulum (ER) membranes (MAM), a cholesterol-rich lipid raft-like subdomain of the ER that communicates, both physically and biochemically, with mitochondria. We propose that in early-onset AD (EOAD), MAM-localized C99 is elevated above normal levels, resulting in increased transport of cholesterol from the plasma membrane to membranes of intracellular organelles, such as ER/endosomes, thereby upregulating MAM function and driving pathology. By the same token, late-onset AD (LOAD) is triggered by any genetic variant that increases the accumulation of intracellular cholesterol that, in turn, boosts the levels of C99 and again upregulates MAM function. Thus, the functional cause of AD is upregulated MAM function that, in turn, causes the hallmark disease phenotypes, including the plaques and tangles. Accordingly, the MAM hypothesis invokes two key interrelated elements, C99 and cholesterol, that converge at the MAM to drive AD pathogenesis. From this perspective, AD is, at bottom, a lipid disorder.
Collapse
Affiliation(s)
- Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY, USA
- Centro de Investigaciones Biológicas "Margarita Salas", Spanish National Research Council, Madrid, Spain
| | - Eric A Schon
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Genetics and Development>, Columbia University, New York, NY, USA
| |
Collapse
|
6
|
Cullina S, Wojcik GL, Shemirani R, Klarin D, Gorman BR, Sorokin EP, Gignoux CR, Belbin GM, Pyarajan S, Asgari S, Tsao PS, Damrauer SM, Abul-Husn NS, Kenny EE. Admixture mapping of peripheral artery disease in a Dominican population reveals a putative risk locus on 2q35. Front Genet 2023; 14:1181167. [PMID: 37600667 PMCID: PMC10432698 DOI: 10.3389/fgene.2023.1181167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Peripheral artery disease (PAD) is a form of atherosclerotic cardiovascular disease, affecting ∼8 million Americans, and is known to have racial and ethnic disparities. PAD has been reported to have a significantly higher prevalence in African Americans (AAs) compared to non-Hispanic European Americans (EAs). Hispanic/Latinos (HLs) have been reported to have lower or similar rates of PAD compared to EAs, despite having a paradoxically high burden of PAD risk factors; however, recent work suggests prevalence may differ between sub-groups. Here, we examined a large cohort of diverse adults in the BioMe biobank in New York City. We observed the prevalence of PAD at 1.7% in EAs vs. 8.5% and 9.4% in AAs and HLs, respectively, and among HL sub-groups, the prevalence was found at 11.4% and 11.5% in Puerto Rican and Dominican populations, respectively. Follow-up analysis that adjusted for common risk factors demonstrated that Dominicans had the highest increased risk for PAD relative to EAs [OR = 3.15 (95% CI 2.33-4.25), p < 6.44 × 10-14]. To investigate whether genetic factors may explain this increased risk, we performed admixture mapping by testing the association between local ancestry and PAD in Dominican BioMe participants (N = 1,813) separately from European, African, and Native American (NAT) continental ancestry tracts. The top association with PAD was an NAT ancestry tract at chromosome 2q35 [OR = 1.96 (SE = 0.16), p < 2.75 × 10-05) with 22.6% vs. 12.9% PAD prevalence in heterozygous NAT tract carriers versus non-carriers, respectively. Fine-mapping at this locus implicated tag SNP rs78529201 located within a long intergenic non-coding RNA (lincRNA) LINC00607, a gene expression regulator of key genes related to thrombosis and extracellular remodeling of endothelial cells, suggesting a putative link of the 2q35 locus to PAD etiology. Efforts to reproduce the signal in other Hispanic cohorts were unsuccessful. In summary, we showed how leveraging health system data helped understand nuances of PAD risk across HL sub-groups and admixture mapping approaches elucidated a putative risk locus in a Dominican population.
Collapse
Affiliation(s)
- Sinead Cullina
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ruhollah Shemirani
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Derek Klarin
- VA Palo Alto Healthcare System, Palo Alto, CA, United States
- Division of Vascular Surgery, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Bryan R. Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, United States
- Booz Allen Hamilton, McLean, VA, United States
| | - Elena P. Sorokin
- Department of Genetics, Stanford University, Stanford, CA, United States
| | - Christopher R. Gignoux
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Colorado Center for Personalized Medicine, Aurora, CO, United States
| | - Gillian M. Belbin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Brigham Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Samira Asgari
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Philip S. Tsao
- VA Palo Alto Healthcare System, Palo Alto, CA, United States
| | - Scott M. Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
7
|
Horimoto AR, Boyken LA, Blue EE, Grinde KE, Nafikov RA, Sohi HK, Nato AQ, Bis JC, Brusco LI, Morelli L, Ramirez A, Dalmasso MC, Temple S, Satizabal C, Browning SR, Seshadri S, Wijsman EM, Thornton TA. Admixture mapping implicates 13q33.3 as ancestry-of-origin locus for Alzheimer disease in Hispanic and Latino populations. HGG ADVANCES 2023; 4:100207. [PMID: 37333771 PMCID: PMC10276158 DOI: 10.1016/j.xhgg.2023.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
Alzheimer disease (AD) is the most common form of senile dementia, with high incidence late in life in many populations including Caribbean Hispanic (CH) populations. Such admixed populations, descended from more than one ancestral population, can present challenges for genetic studies, including limited sample sizes and unique analytical constraints. Therefore, CH populations and other admixed populations have not been well represented in studies of AD, and much of the genetic variation contributing to AD risk in these populations remains unknown. Here, we conduct genome-wide analysis of AD in multiplex CH families from the Alzheimer Disease Sequencing Project (ADSP). We developed, validated, and applied an implementation of a logistic mixed model for admixture mapping with binary traits that leverages genetic ancestry to identify ancestry-of-origin loci contributing to AD. We identified three loci on chromosome 13q33.3 associated with reduced risk of AD, where associations were driven by Native American (NAM) ancestry. This AD admixture mapping signal spans the FAM155A, ABHD13, TNFSF13B, LIG4, and MYO16 genes and was supported by evidence for association in an independent sample from the Alzheimer's Genetics in Argentina-Alzheimer Argentina consortium (AGA-ALZAR) study with considerable NAM ancestry. We also provide evidence of NAM haplotypes and key variants within 13q33.3 that segregate with AD in the ADSP whole-genome sequencing data. Interestingly, the widely used genome-wide association study approach failed to identify associations in this region. Our findings underscore the potential of leveraging genetic ancestry diversity in recently admixed populations to improve genetic mapping, in this case for AD-relevant loci.
Collapse
Affiliation(s)
| | - Lisa A. Boyken
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth E. Blue
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Kelsey E. Grinde
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Department of Mathematics, Statistics and Computer Science, Macalester College, Saint Paul, MN 55105, USA
| | - Rafael A. Nafikov
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Harkirat K. Sohi
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Biomedical and Health Informatics Program, University of Washington, Seattle, WA 98195, USA
| | - Alejandro Q. Nato
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Luis I. Brusco
- CENECON - Center of Behavioural Neurology and Neuropsychiatry, School of Medicine, University of Buenos Aires, C1121A6B Buenos Aires, Argentina
| | - Laura Morelli
- Laboratory of Brain Aging and Neurodegeneration-Fundación Instituto Leloir-IIBBA- National Scientific and Technical Research Council (CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Argentina
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) University of Cologne, 50674 Cologne, Germany
- Department of Psychiatry, UT Health San Antonio, San Antonio, TX 78229, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Maria Carolina Dalmasso
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
- Neurosciences and Complex Systems Unit (EnyS), CONICET, Hospital El Cruce, National University A. Jauretche (UNAJ), B1888AAE Florencio Varela, Argentina
| | - Seth Temple
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Claudia Satizabal
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas, San Antonio, TX 78229, USA
- Department of Neurology, University of Texas, San Antonio, TX 78229, USA
| | - Sharon R. Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sudha Seshadri
- Department of Neurology, University of Texas, San Antonio, TX 78229, USA
| | - Ellen M. Wijsman
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics/Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
8
|
Siddiqui T, Cosacak MI, Popova S, Bhattarai P, Yilmaz E, Lee AJ, Min Y, Wang X, Allen M, İş Ö, Atasavum ZT, Rodriguez-Muela N, Vardarajan BN, Flaherty D, Teich AF, Santa-Maria I, Freudenberg U, Werner C, Tosto G, Mayeux R, Ertekin-Taner N, Kizil C. Nerve growth factor receptor (Ngfr) induces neurogenic plasticity by suppressing reactive astroglial Lcn2/Slc22a17 signaling in Alzheimer's disease. NPJ Regen Med 2023; 8:33. [PMID: 37429840 DOI: 10.1038/s41536-023-00311-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
Neurogenesis, crucial for brain resilience, is reduced in Alzheimer's disease (AD) that induces astroglial reactivity at the expense of the pro-neurogenic potential, and restoring neurogenesis could counteract neurodegenerative pathology. However, the molecular mechanisms promoting pro-neurogenic astroglial fate despite AD pathology are unknown. In this study, we used APP/PS1dE9 mouse model and induced Nerve growth factor receptor (Ngfr) expression in the hippocampus. Ngfr, which promotes neurogenic fate of astroglia during the amyloid pathology-induced neuroregeneration in zebrafish brain, stimulated proliferative and neurogenic outcomes. Histological analyses of the changes in proliferation and neurogenesis, single-cell transcriptomics, spatial proteomics, and functional knockdown studies showed that the induced expression of Ngfr reduced the reactive astrocyte marker Lipocalin-2 (Lcn2), which we found was sufficient to reduce neurogenesis in astroglia. Anti-neurogenic effects of Lcn2 was mediated by Slc22a17, blockage of which recapitulated the pro-neurogenicity by Ngfr. Long-term Ngfr expression reduced amyloid plaques and Tau phosphorylation. Postmortem human AD hippocampi and 3D human astroglial cultures showed elevated LCN2 levels correlate with reactive gliosis and reduced neurogenesis. Comparing transcriptional changes in mouse, zebrafish, and human AD brains for cell intrinsic differential gene expression and weighted gene co-expression networks revealed common altered downstream effectors of NGFR signaling, such as PFKP, which can enhance proliferation and neurogenesis in vitro when blocked. Our study suggests that the reactive non-neurogenic astroglia in AD can be coaxed to a pro-neurogenic fate and AD pathology can be alleviated with Ngfr. We suggest that enhancing pro-neurogenic astroglial fate may have therapeutic ramifications in AD.
Collapse
Affiliation(s)
- Tohid Siddiqui
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
| | - Stanislava Popova
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
- Neuron D GmbH, Tatzberg 47, 01307, Dresden, Germany
| | - Prabesh Bhattarai
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Elanur Yilmaz
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Annie J Lee
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 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
| | - Yuhao Min
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Özkan İş
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Zeynep Tansu Atasavum
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
| | - Natalia Rodriguez-Muela
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
| | - Badri N Vardarajan
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 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
| | - Delaney Flaherty
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Andrew F Teich
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Ismael Santa-Maria
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Edificio E, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Uwe Freudenberg
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Str. 6, D-01069, Dresden, Germany
| | - Carsten Werner
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Str. 6, D-01069, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, D-01307, Dresden, Germany
| | - Giuseppe Tosto
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 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
| | - Richard Mayeux
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 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 Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY, 10032, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany.
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| |
Collapse
|
9
|
Reitz C, Pericak-Vance MA, Foroud T, Mayeux R. A global view of the genetic basis of Alzheimer disease. Nat Rev Neurol 2023; 19:261-277. [PMID: 37024647 PMCID: PMC10686263 DOI: 10.1038/s41582-023-00789-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
The risk of Alzheimer disease (AD) increases with age, family history and informative genetic variants. Sadly, there is still no cure or means of prevention. As in other complex diseases, uncovering genetic causes of AD could identify underlying pathological mechanisms and lead to potential treatments. Rare, autosomal dominant forms of AD occur in middle age as a result of highly penetrant genetic mutations, but the most common form of AD occurs later in life. Large-scale, genome-wide analyses indicate that 70 or more genes or loci contribute to AD. One of the major factors limiting progress is that most genetic data have been obtained from non-Hispanic white individuals in Europe and North America, preventing the development of personalized approaches to AD in individuals of other ethnicities. Fortunately, emerging genetic data from other regions - including Africa, Asia, India and South America - are now providing information on the disease from a broader range of ethnicities. Here, we summarize the current knowledge on AD genetics in populations across the world. We predominantly focus on replicated genetic discoveries but also include studies in ethnic groups where replication might not be feasible. We attempt to identify gaps that need to be addressed to achieve a complete picture of the genetic and molecular factors that drive AD in individuals across the globe.
Collapse
Affiliation(s)
- Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard Mayeux
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.
- Department of Neurology, Columbia University, New York, NY, USA.
- Department of Epidemiology, Columbia University, New York, NY, USA.
| |
Collapse
|
10
|
Yang Z, Huaman BC, Reyes-Dumeyer D, Montesinos R, Soto-Añari M, Custodio N, Tosto G. A benchmark study on current GWAS models in admixed populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538299. [PMID: 37163101 PMCID: PMC10168347 DOI: 10.1101/2023.04.27.538299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Objective The performances of popular Genome-wide association study (GWAS) models haven't been examined yet in a consistent manner under the scenario of genetic admixture, which introduces several challenging aspects such as heterogeneity of minor allele frequency (MAF), a wide spectrum of case-control ratio, and varying effect sizes etc. Methods We generated a cohort of synthetic individuals (N=19,234) that simulates 1) a large sample size; 2) two-way admixture [Native American-European ancestry] and 3) a binary phenotype. We then examined the inflation factors produced by three popular GWAS tools: GMMAT, SAIGE, and Tractor. We also computed power calculations under different MAFs, case-control ratios, and varying ancestry percentages. Then, we employed a cohort of Peruvians (N=249) to further examine the performances of the testing models on 1) real genetic data and 2) small sample sizes. Finally, we validated these findings using an independent Peruvian cohort (N=109) included in 1000 Genome project (1000G). Results In the synthetic cohort, SAIGE performed better than GMMAT and Tractor in terms of type-I error rate, especially under severe unbalanced case-control ratio. On the contrary, power analysis identified Tractor as the best method to pinpoint ancestry-specific causal variants, but showed decreased power when no adequate heterogeneity of the true effect sizes was simulated between ancestries. The real Peruvian data showed that Tractor is severely affected by small sample sizes, and produced severely inflated statistics, which we replicated in the 1000G Peruvian cohort. Discussion The current study illustrates the limitations of available GWAS tools under different scenarios of genetic admixture. We urge caution when interpreting results under complex population scenarios.
Collapse
Affiliation(s)
- Zikun Yang
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University. 630 West 168 Street, New York, NY 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University. 630 West 168 Street, New York, NY 10032, USA
| | - Basilio Cieza Huaman
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University. 630 West 168 Street, New York, NY 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University. 630 West 168 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 168 Street, New York, NY 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University. 630 West 168 Street, New York, NY 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital. 710 West 168 Street, New York, NY 10032, USA
| | - Rosa Montesinos
- Unidad de diagnóstico de deterioro cognitivo y prevención de demencia, Instituto Peruano de Neurociencias, Lima, Perú
| | - Marcio Soto-Añari
- Instituto de Neurociencia Cognitiva, Arequipa, Perú
- Laboratorio de Neurociencia, Universidad Católica San Pablo, Arequipa, Perú
| | - Nilton Custodio
- Unidad de diagnóstico de deterioro cognitivo y prevención de demencia, Instituto Peruano de Neurociencias, Lima, Perú
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University. 630 West 168 Street, New York, NY 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University. 630 West 168 Street, New York, NY 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital. 710 West 168 Street, New York, NY 10032, USA
| |
Collapse
|
11
|
Cullina S, Wojcik GL, Shemirani R, Klarin D, Gorman BR, Sorokin EP, Gignoux CR, Belbin GM, Pyarajan S, Asgari S, Tsao PS, Damrauer SM, Abul-Husn NS, Kenny EE. Admixture Mapping of Peripheral Artery Disease in a Dominican Population Reveals a Novel Risk Locus on 2q35. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.27.23287788. [PMID: 37034679 PMCID: PMC10081406 DOI: 10.1101/2023.03.27.23287788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Peripheral artery disease (PAD) is a form of atherosclerotic cardiovascular disease, affecting ∼8 million Americans, and is known to have racial and ethnic disparities. PAD has been reported to have significantly higher prevalence in African Americans (AAs) compared to non-Hispanic European Americans (EAs). Hispanic/Latinos (HLs) have been reported to have lower or similar rates of PAD compared to EAs, despite having a paradoxically high burden of PAD risk factors, however recent work suggests prevalence may differ between sub-groups. Here we examined a large cohort of diverse adults in the Bio Me biobank in New York City (NYC). We observed the prevalence of PAD at 1.7% in EAs vs 8.5% and 9.4% in AAs and HLs, respectively; and among HL sub-groups, at 11.4% and 11.5% in Puerto Rican and Dominican populations, respectively. Follow-up analysis that adjusted for common risk factors demonstrated that Dominicans had the highest increased risk for PAD relative to EAs (OR=3.15 (95% CI 2.33-4.25), P <6.44×10 -14 ). To investigate whether genetic factors may explain this increased risk, we performed admixture mapping by testing the association between local ancestry (LA) and PAD in Dominican Bio Me participants (N=1,940) separately for European (EUR), African (AFR) and Native American (NAT) continental ancestry tracts. We identified a NAT ancestry tract at chromosome 2q35 that was significantly associated with PAD (OR=2.05 (95% CI 1.51-2.78), P <4.06×10 -6 ) with 22.5% vs 12.5% PAD prevalence in heterozygous NAT tract carriers versus non-carriers, respectively. Fine-mapping at this locus implicated tag SNP rs78529201 located within a long intergenic non-coding RNA (lincRNA) LINC00607 , a gene expression regulator of key genes related to thrombosis and extracellular remodeling of endothelial cells, suggesting a putative link of the 2q35 locus to PAD etiology. In summary, we showed how leveraging health systems data helped understand nuances of PAD risk across HL sub-groups and admixture mapping approaches elucidated a novel risk locus in a Dominican population.
Collapse
|
12
|
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] [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.
Collapse
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.
| |
Collapse
|
13
|
Single Cell/Nucleus Transcriptomics Comparison in Zebrafish and Humans Reveals Common and Distinct Molecular Responses to Alzheimer’s Disease. Cells 2022; 11:cells11111807. [PMID: 35681503 PMCID: PMC9180693 DOI: 10.3390/cells11111807] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 12/21/2022] Open
Abstract
Neurogenesis is significantly reduced in Alzheimer’s disease (AD) and is a potential therapeutic target. Contrary to humans, a zebrafish can regenerate its diseased brain, and thus is ideal for studying neurogenesis. To compare the AD-related molecular pathways between humans and zebrafish, we compared single cell or nuclear transcriptomic data from a zebrafish amyloid toxicity model and its controls (N = 12) with the datasets of two human adult brains (N = 10 and N = 48 (Microglia)), and one fetal brain (N = 10). Approximately 95.4% of the human and zebrafish cells co-clustered. Within each cell type, we identified differentially expressed genes (DEGs), enriched KEGG pathways, and gene ontology terms. We studied synergistic and non-synergistic DEGs to point at either common or uniquely altered mechanisms across species. Using the top DEGs, a high concordance in gene expression changes between species was observed in neuronal clusters. On the other hand, the molecular pathways affected by AD in zebrafish astroglia differed from humans in favor of the neurogenic pathways. The integration of zebrafish and human transcriptomes shows that the zebrafish can be used as a tool to study the cellular response to amyloid proteinopathies. Uniquely altered pathways in zebrafish could highlight the specific mechanisms underlying neurogenesis, which are absent in humans, and could serve as potential candidates for therapeutic developments.
Collapse
|