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Dallmeier JD, Gober R, Vontell RT, Barreda A, Dorfsman DA, Davis DA, Sun X, Brzostowicki D, Bennett I, Garamszegi SP, Wander CM, Cohen T, Scott WK. Corpora amylacea negatively correlate with hippocampal tau pathology in Alzheimer's disease. Front Neurosci 2024; 18:1286924. [PMID: 38486969 PMCID: PMC10937356 DOI: 10.3389/fnins.2024.1286924] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/19/2024] [Indexed: 03/17/2024] Open
Abstract
Introduction Severity and distribution of aggregated tau and neurofibrillary tangles (NFT) are strongly correlated with the clinical presentation of Alzheimer's disease (AD). Clearance of aggregated tau could decrease the rate of NFT formation and delay AD onset. Recent studies implicate corpora amylacea (CA) as a regulator of onset or accumulation of tau pathology. Normally, CA clear brain waste products by amassing cellular debris, which are then extruded into the cerebrospinal fluid to be phagocytosed. The proper functioning of CA may slow progression of AD-associated NFT pathology, and this relationship may be influenced by amount and distribution of phospho-tau (pTau) produced, age, sex, and genetic risk. Objective The goal of this study was to determine if CA size and number are associated with hippocampal location and local pTau severity while accounting for variations in age, sex, and genetic risk. Methods Postmortem brain hippocampal tissue sections from 40 AD and 38 unaffected donors were immunohistochemically stained with AT8 (pTau) and counter stained with periodic acid Schiff (PAS). Stained sections of the CA1 and CA3 regions of the hippocampus were analyzed. The percent area occupied (%AO) of CA, pTau, and NFT was calculated. Pairwise comparisons and regression modeling were used to analyze the influence of age, pTau %AO, and genetic risk on %AO by CA in each region, separately in donors with AD and unaffected donors. Results CA %AO was significantly higher in the CA3 region compared to CA1 in both groups. A significant negative correlation of CA %AO with both pTau %AO and neurofibrillary tangle %AO in the CA3 region of AD brain donors was found. Regression analysis in the CA3 region revealed a significant negative association between CA with both pTau and age. Conclusion We found an increase of CA in the CA3 region, compared to CA1 region, in AD and unaffected donors. This may suggest that the CA3 region is a hub for waste removal. Additionally, the negative correlation between %AO by CA and NFT in the CA3 region of the hippocampus in donors with AD suggests CA could play a role in AD pathologic progression by influencing tau clearance.
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Affiliation(s)
- Julian D. Dallmeier
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ryan Gober
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Regina T. Vontell
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Neurology, Evelyn F. McKnight Brain Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ayled Barreda
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - David A. Davis
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Neurology, Evelyn F. McKnight Brain Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Xiaoyan Sun
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Neurology, Evelyn F. McKnight Brain Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Daniel Brzostowicki
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Illiana Bennett
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Susanna P. Garamszegi
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Connor M. Wander
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Todd Cohen
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - William K. Scott
- Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
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Main LR, Song YE, Lynn A, Laux RA, Miskimen KL, Osterman MD, Cuccaro ML, Ogrocki PK, Lerner AJ, Vance JM, Fuzzell MD, Fuzzell SL, Hochstetler SD, Dorfsman DA, Caywood LJ, Prough MB, Adams LD, Clouse JE, Herington SD, Scott WK, Pericak-Vance MA, Haines JL. Genetic analysis of cognitive preservation in the midwestern Amish reveals a novel locus on chromosome 2. medRxiv 2023:2023.12.13.23299932. [PMID: 38168325 PMCID: PMC10760262 DOI: 10.1101/2023.12.13.23299932] [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: 01/05/2024]
Abstract
INTRODUCTION Alzheimer disease (AD) remains a debilitating condition with limited treatments and additional therapeutic targets needed. Identifying AD protective genetic loci may identify new targets and accelerate identification of therapeutic treatments. We examined a founder population to identify loci associated with cognitive preservation into advanced age. METHODS Genome-wide association and linkage analyses were performed on 946 examined and sampled Amish individuals, aged 76-95, who were either cognitively unimpaired (CU) or impaired (CI). RESULTS 12 SNPs demonstrated suggestive association (P≤5×10-4) with cognitive preservation. Genetic linkage analyses identified >100 significant (LOD≥3.3) SNPs, some which overlapped with the association results. Only one locus on chromosome 2 retained significance across multiple analyses. DISCUSSION A novel significant result for cognitive preservation on chromosome 2 includes the genes LRRTM4 and CTNNA2. Additionally, the lead SNP, rs1402906, impacts the POU3F2 transcription factor binding affinity, which regulates LRRTM4 and CTNNA2.
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Affiliation(s)
- Leighanne R Main
- Departments of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Renee A Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Kristy L Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Michael D Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Michael L Cuccaro
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Paula K Ogrocki
- Department of Neurology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Neurology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Alan J Lerner
- Department of Neurology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Neurology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Jeffery M Vance
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - M Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Sarada L Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Sherri D Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Daniel A Dorfsman
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Laura J Caywood
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Michael B Prough
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Larry D Adams
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Jason E Clouse
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Sharlene D Herington
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - William K Scott
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Margaret A Pericak-Vance
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Jonathan L Haines
- Departments of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
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Osterman MD, Song YE, Lynn A, Miskimen K, Adams LD, Laux RA, Caywood LJ, Prough MB, Clouse JE, Herington SD, Slifer SH, Fuzzell SL, Hochstetler SD, Main LR, Dorfsman DA, Zaman AF, Ogrocki P, Lerner AJ, Vance JM, Cuccaro ML, Scott WK, Pericak-Vance MA, Haines JL. Founder population-specific weights yield improvements in performance of polygenic risk scores for Alzheimer disease in the Midwestern Amish. HGG Adv 2023; 4:100241. [PMID: 37742071 PMCID: PMC10565871 DOI: 10.1016/j.xhgg.2023.100241] [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] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/16/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023] Open
Abstract
Alzheimer disease (AD) is the most common type of dementia and is estimated to affect 6 million Americans. Risk for AD is multifactorial, including both genetic and environmental risk factors. AD genomic research has generally focused on identification of risk variants. Using this information, polygenic risk scores (PRSs) can be calculated to quantify an individual's relative disease risk due to genetic factors. The Amish are a founder population descended from German and Swiss Anabaptist immigrants. They experienced a genetic bottleneck after arrival in the United States, making their genetic architecture different from the broader European ancestry population. Prior work has demonstrated the lack of transferability of PRSs across populations. Here, we compared the performance of PRSs derived from genome-wide association studies (GWASs) of Amish individuals to those derived from a large European ancestry GWAS. Participants were screened for cognitive impairment with further evaluation for AD. Genotype data were imputed after collection via Illumina genotyping arrays. The Amish individuals were split into two groups based on the primary site of recruitment. For each group, GWAS was conducted with account for relatedness and adjustment for covariates. PRSs were then calculated using weights from the other Amish group. PRS models were evaluated with and without covariates. The Amish-derived PRSs distinguished between dementia status better than the European-derived PRS in our Amish populations and demonstrated performance improvements despite a smaller training sample size. This work highlighted considerations for AD PRS usage in populations that cannot be adequately described by basic race/ethnicity or ancestry classifications.
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Affiliation(s)
- Michael D Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Renee A Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Laura J Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael B Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason E Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sharlene D Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sarada L Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sherri D Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Leighanne R Main
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Daniel A Dorfsman
- 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
| | - Andrew F Zaman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Paula Ogrocki
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alan J Lerner
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffery M Vance
- 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
| | - Michael L Cuccaro
- 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
| | - William K Scott
- 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
| | - Margaret A Pericak-Vance
- 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
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
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4
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Prough MB, Zaman A, Caywood LJ, Clouse JE, Herington SD, Slifer SH, Dorfsman DA, Adams LA, Laux RA, Song YE, Lynn A, Fuzzell D, Fuzzell SL, Miller SD, Miskimen K, Main LR, Osterman MD, Ogrocki P, Lerner AJ, Vance JM, Haines JL, Scott WK, Pericak-Vance M, Cuccaro ML. Visuospatial and Verbal Memory Differences in Amish Individuals With Alzheimer Disease and Related Dementias. Alzheimer Dis Assoc Disord 2023; 37:195-199. [PMID: 37561946 PMCID: PMC10529392 DOI: 10.1097/wad.0000000000000570] [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] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/13/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Verbal and visuospatial memory impairments are common to Alzheimer disease and Related Dementias (ADRD), but the patterns of decline in these domains may reflect genetic and lifestyle influences. The latter may be pertinent to populations such as the Amish who have unique lifestyle experiences. METHODS Our data set included 420 Amish and 401 CERAD individuals. Sex-adjusted, age-adjusted, and education-adjusted Z-scores were calculated for the recall portions of the Constructional Praxis Delay (CPD) and Word List Delay (WLD). ANOVAs were then used to examine the main and interaction effects of cohort (Amish, CERAD), cognitive status (case, control), and sex on CPD and WLD Z-scores. RESULTS The Amish performed better on the CPD than the CERAD cohort. In addition, the difference between cases and controls on the CPD and WLD were smaller in the Amish and Amish female cases performed better on the WLD than the CERAD female cases. DISCUSSION The Amish performed better on the CPD task, and ADRD-related declines in CPD and WLD were less severe in the Amish. In addition, Amish females with ADRD may have preferential preservation of WLD. This study provides evidence that the Amish exhibit distinct patterns of verbal and visuospatial memory loss associated with aging and ADRD.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Reneé A Laux
- Department of Population and Quantitative Health Sciences
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences
| | - Denise Fuzzell
- Department of Population and Quantitative Health Sciences
| | | | | | | | - Leighanne R Main
- Department of Genetics and Genome Sciences
- Cleveland Institute for Computational Biology, Case Western Reserve University
| | - Michael D Osterman
- Department of Population and Quantitative Health Sciences
- Cleveland Institute for Computational Biology, Case Western Reserve University
| | - Paula Ogrocki
- Department of Neurology, Case Western Reserve University School of Medicine
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Alan J Lerner
- Department of Neurology, Case Western Reserve University School of Medicine
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences
- Cleveland Institute for Computational Biology, Case Western Reserve University
| | - William K Scott
- John P. Hussman Institute for Human Genomics
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
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5
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Zaman A, Caywood L, Prough M, Clouse J, Harrington S, Adams L, Fuzzell D, Fuzzell S, Laux R, Hochstetler SD, Ogrocki P, Lerner A, Vance JM, Haines JL, Scott WK, Pericak-Vance MA, Cuccaro ML. Psychometric Approaches to Defining Cognitive Phenotypes in the Old Order Amish. Int J Geriatr Psychiatry 2023; 38:e5903. [PMID: 36929524 DOI: 10.1002/gps.5903] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/11/2023] [Indexed: 03/18/2023]
Abstract
OBJECTIVE Memory and cognitive problems are central to the diagnosis of Alzheimer's disease (AD). Psychometric approaches to defining phenotypes can aid in identify genetic variants associated with AD. However, these approaches have mostly been limited to affected individuals. Defining phenotypes of both affected and unaffected individuals may help identify genetic variants associated with both AD and healthy aging. This study compares psychometric methods for developing cognitive phenotypes that are more granular than clinical classifications. METHODS 682 older Old Order Amish individuals were included in the analysis. Adjusted Z-scores of cognitive tests were used to create four models including 1) global threshold scores or 2) memory threshold scores, and 3) global clusters and 4) memory clusters. An ordinal regression examined the coherence of the models with clinical classifications [cognitively impaired (CI), mildly impaired (MI), cognitively unimpaired (CU)], APOE-e4, sex, and age. An ANOVA examined the best model phenotypes for differences in clinical classification, APOE-e4, domain Z-scores (memory, language, executive function, and processing speed), sex, and age. RESULTS The memory cluster identified four phenotypes and had the best fit (χ2 = 491.66). Individuals in the worse performing phenotypes were more likely to be classified as CI or MI and to have APOE-e4. Additionally, all four phenotypes performed significantly differently from one another on the domains of memory, language, and executive functioning. CONCLUSIONS Memory cluster stratification identified the cognitive phenotypes that best aligned with clinical classifications, APOE-e4, and cognitive performance We predict these phenotypes will prove useful in searching for protective genetic variants. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew Zaman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Laura Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sharlene Harrington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Sarada Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Renee Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Sherri D Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Paula Ogrocki
- Department of Neurology, Case Western Reserve University, Cleveland, OH, USA
| | - Alan Lerner
- Department of Neurology, Case Western Reserve University, Cleveland, OH, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
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6
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Ciesielski TH, Zhang X, Tacconelli A, Lutsar I, de Cabre VM, Roilides E, Ciccacci C, Borgiani P, Scott WK, Williams SM, Sirugo G. Late-onset neonatal sepsis: genetic differences by sex and involvement of the NOTCH pathway. Pediatr Res 2023; 93:1085-1095. [PMID: 35835848 DOI: 10.1038/s41390-022-02114-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/10/2022] [Accepted: 04/27/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Late-Onset Neonatal Sepsis (LOS) is a rare condition, involving widespread infection, immune disruption, organ dysfunction, and often death. Because exposure to pathogens is not completely preventable, identifying susceptibility factors is critical to characterizing the pathophysiology and developing interventions. Prior studies demonstrated both genetics and infant sex influence susceptibility. Our study was designed to identify LOS associated genetic variants. METHODS We performed an exploratory genome wide association study (GWAS) with 224 LOS cases and 273 controls from six European countries. LOS was defined as sepsis presenting from 3 to 90 days of age; diagnosis was established by clinical criteria consensus guidelines. We tested for association with both autosomal and X-chromosome variants in the total sample and in sex-stratified analyses. RESULTS In total, 71 SNPs associated with neonatal sepsis at p < 1 × 10-4 in at least one analysis. Most importantly, sex-stratified analyses revealed associations with multiple SNPs (28 in males and 16 in females), but no variants from single-sex analyses associated with sepsis in the other sex. Pathway analyses showed NOTCH signaling is over-represented among genes linked to these SNPS. CONCLUSION Our results indicate genetic susceptibility to LOS is sexually dimorphic and corroborate that NOTCH signaling plays a role in determining risk. IMPACT Genes associate with late onset neonatal sepsis. Notch pathway genes are overrepresented in associations with sepsis. Genes associating with sepsis do not overlap between males and females. Sexual dimorphism can lead to sex specific treatment of sepsis.
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Affiliation(s)
- Timothy H Ciesielski
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Mary Ann Swetland Center for Environmental Health at Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Xueyi Zhang
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Irja Lutsar
- Department of Microbiology, School of Medicine, University of Tartu, Tartu, Estonia
| | | | - Emmanuel Roilides
- Laboratory of Infectious Diseases, 3rd Department of Paediatrics, School of Medicine, Aristotle University, Thessaloniki, Greece
| | - Cinzia Ciccacci
- Dipartimento di Biomedicina e Prevenzione, Facolta' di Medicina e Chirurgia, Universita' di Tor Vergata, Rome, Italy
- Unicamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Paola Borgiani
- Dipartimento di Biomedicina e Prevenzione, Facolta' di Medicina e Chirurgia, Universita' di Tor Vergata, Rome, Italy
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | | | - Scott M Williams
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA.
- 10900 Euclid Ave, Cleveland Institute for Computational Biology, Cleveland, USA.
| | - Giorgio Sirugo
- Institute of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Division of Translational Medicine and Human Genetics, Perelman SPerelman School of Medicine, University of Pennsylvaniachool of Medicine, University of Pennsylvania, Philadelphia, USA.
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7
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Ramos J, Caywood LJ, Prough MB, Clouse JE, Herington SD, Slifer SH, Fuzzell MD, Fuzzell SL, Hochstetler SD, Miskimen KL, Main LR, Osterman MD, Zaman AF, Whitehead PL, Adams LD, Laux RA, Song YE, Foroud TM, Mayeux RP, George-Hyslop PS, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Pericak-Vance MA, Scott WK. Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets. Alzheimers Dement 2023; 19:611-620. [PMID: 35490390 PMCID: PMC9622429 DOI: 10.1002/alz.12686] [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] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/08/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Studies of cognitive impairment (CI) in Amish communities have identified sibships containing CI and cognitively unimpaired (CU) individuals. We hypothesize that CU individuals may carry protective alleles delaying age at onset (AAO) of CI. METHODS A total of 1522 individuals screened for CI were genotyped. The outcome studied was AAO for CI individuals or age at last normal exam for CU individuals. Cox mixed-effects models examined association between age and single nucleotide variants (SNVs). RESULTS Three SNVs were significantly associated (P < 5 × 10-8 ) with AAO on chromosomes 6 (rs14538074; hazard ratio [HR] = 3.35), 9 (rs534551495; HR = 2.82), and 17 (rs146729640; HR = 6.38). The chromosome 17 association was replicated in the independent National Institute on Aging Genetics Initiative for Late-Onset Alzheimer's Disease dataset. DISCUSSION The replicated genome-wide significant association with AAO on chromosome 17 is located in the SHISA6 gene, which is involved in post-synaptic transmission in the hippocampus and is a biologically plausible candidate gene for Alzheimer's disease.
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Affiliation(s)
- Jairo Ramos
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M. Denise Fuzzell
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sarada L. Fuzzell
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | | | - Leighanne R. Main
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Michael D. Osterman
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Andrew F. Zaman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Renee A. Laux
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yeunjoo E. Song
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Tatiana M. Foroud
- Indiana Alzheimer’s Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard P. Mayeux
- Taub Institute on Alzheimer’s Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
| | | | - Paula K. Ogrocki
- University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Alan J. Lerner
- University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jeffery M. Vance
- 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
| | - Michael L. Cuccaro
- 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
| | - Jonathan L. Haines
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Margaret A. Pericak-Vance
- 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
| | - William K. Scott
- 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
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8
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Main LR, Song YE, Laux RA, Miskimen KL, Cuccaro ML, Ogrocki PK, Lerner AJ, Vance JM, Fuzzell MD, Fuzzell SL, Hochstetler SD, Osterman MD, Lynn A, Dorfsman DA, Caywood LJ, Prough MB, Adams LD, Clouse JE, Herington SD, Scott WK, Pericak‐Vance MA, Haines JL. Detecting genetic loci for preservation of cognition in the Midwestern United States Amish. Alzheimers Dement 2022. [DOI: 10.1002/alz.061554] [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: 12/24/2022]
Affiliation(s)
- Leighanne R. Main
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Paula K. Ogrocki
- Brain Health and Memory Center, University Hospital Cleveland OH USA
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Alan J. Lerner
- Brain Health and Memory Center, University Hospital Cleveland OH USA
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sherri D. Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, 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
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
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9
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Godrich D, Martin ER, Schellenberg G, Pericak‐Vance MA, Cuccaro M, Scott WK, Kukull W, Montine T, Beecham GW. Neuropathological lesions and their contribution to dementia and cognitive impairment in a heterogeneous clinical population. Alzheimers Dement 2022; 18:2403-2412. [PMID: 35142102 PMCID: PMC9360193 DOI: 10.1002/alz.12516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/07/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Alzheimer disease (AD) and related dementias are characterized by damage caused by neuropathological lesions in the brain. These include AD lesions (plaques and tangles) and non-AD lesions such as vascular injury or Lewy bodies. We report here an assessment of lesion association to dementia in a large clinic-based population. METHODS We identified 5272 individuals with neuropathological data from the National Alzheimer's Coordinating Center. Individual lesions, as well as a neuropathological composite score (NPCS) were tested for association with dementia, and both functional and neurocognitive impairment using regression models. RESULTS Most individuals exhibited mixed pathologies, especially AD lesions in combination with non-AD lesions. All lesion types were associated with one or more clinical outcomes; most even while controlling for AD pathology. The NPCS was also associated with clinical outcomes. DISCUSSION These data suggest mixed-type pathologies are extremely common in a clinic-based population and may contribute to dementia and cognitive impairment.
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Affiliation(s)
- Dana Godrich
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Eden R. Martin
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Gerard Schellenberg
- Penn Neurodegeneration Genomics CenterDepartment of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Margaret A. Pericak‐Vance
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Michael Cuccaro
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - William K. Scott
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Walter Kukull
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Thomas Montine
- Department of PathologyStanford UniversityStanfordCaliforniaUSA
| | - Gary W. Beecham
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
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10
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Osterman MD, Song YE, Wheeler NR, Laux RA, Adams LD, Caywood LJ, Prough MB, Clouse JE, Herington SD, Slifer SH, Lynn A, Bartlett J, Fuzzell MD, Fuzzell SL, Hochstetler SD, Miskimen KL, Main LR, Dorfsman DA, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Bush WS, Scott WK, Pericak‐Vance MA, Haines JL. Assessing a Network‐Specific Polygenic Risk Score for Alzheimer’s Disease in the Midwestern Amish and Across Diverse Ancestries. Alzheimers Dement 2022. [DOI: 10.1002/alz.067210] [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: 12/24/2022]
Affiliation(s)
- Michael D. Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | | | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Larry D. Adams
- University of Miami Miller School of Medicine Miami FL USA
| | | | | | | | | | | | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | | | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | | | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Leighanne R. Main
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | | | - Paula K. Ogrocki
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | | | | | - William S. Bush
- Case Western Reserve University School of Medicine Cleveland OH USA
| | | | | | - Jonathan L. Haines
- Case Western Reserve University School of Medicine, Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology Cleveland OH USA
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11
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Dallmeier J, Vontell RT, Davis DA, Gober R, Barreda A, Garamszergi S, Sun X, Wander C, Cohen TJ, Scott WK. Negative Correlation of Corpora Amylacea with pTau in the Hippocampus of People with AD. Alzheimers Dement 2022. [DOI: 10.1002/alz.067662] [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: 12/24/2022]
Affiliation(s)
| | | | - David A. Davis
- University of Miami Miller School of Medicine Miami FL USA
| | - Ryan Gober
- University of Miami Miller School of Medicine Miami FL USA
| | - Ayled Barreda
- University of Miami Miller School of Medicine Miami FL USA
| | | | - Xiaoyan Sun
- Neurology Department, University of Miami Miller School of Medicine Miami FL USA
| | | | | | - William K. Scott
- University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
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12
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Godrich D, Pasteris J, Martin ER, Schellenberg GD, Pericak‐Vance MA, Cuccaro ML, Scott WK, Kukull WA, Montine TJ, Beecham GW. Alzheimer Disease candidate variants are associated with cerebral amyloid angiopathy. Alzheimers Dement 2022. [DOI: 10.1002/alz.067799] [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: 12/24/2022]
Affiliation(s)
- Dana Godrich
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami Miami FL USA
| | - Jeremy Pasteris
- John P. Hussman Institute for Human Genomics, 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
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Walter A. Kukull
- National Alzheimer's Coordinating Center, University of Washington Seattle WA USA
| | | | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
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13
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Dorfsman DA, Prough MB, Caywood LJ, Clouse JE, Herington SD, Slifer SH, Adams LD, Laux RA, Song YE, Lynn A, Fuzzell MD, Fuzzell SL, Hochstetler SD, Miskimen KL, Main LR, Osterman MD, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Pericak‐Vance MA, Scott WK. Association of mitochondrial haplogroups and cognitive impairment in the Amish. Alzheimers Dement 2022. [DOI: 10.1002/alz.067658] [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: 12/24/2022]
Affiliation(s)
- Daniel A. Dorfsman
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sherri D. Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Leighanne R. Main
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Paula K. Ogrocki
- University Hospitals Cleveland Medical Center Cleveland OH USA
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Alan J. Lerner
- University Hospitals Cleveland Medical Center Cleveland OH USA
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Michael L. Cuccaro
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Margaret A. Pericak‐Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - William K. Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
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14
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Prough MB, Caywood LJ, Clouse JE, Herington SD, Slifer SH, Dorfsman DA, Adams LD, Laux RA, Song YE, Lynn A, Fuzzell MD, Fuzzell SL, Miller SD, Miskimen KL, Main LR, Osterman MD, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Scott WK, Pericak‐Vance MA. Plasma pTau181 is associated with impaired cognition in the Old Order Amish and adds additional information beyond the known genetic risk factors for AD. Alzheimers Dement 2022. [DOI: 10.1002/alz.067752] [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: 12/24/2022]
Affiliation(s)
- Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Leighanne R. Main
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Paula K. Ogrocki
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Jeffery M. Vance
- 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 Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
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Hopfner F, Tietz AK, Ruf VC, Ross OA, Koga S, Dickson D, Aguzzi A, Attems J, Beach T, Beller A, Cheshire WP, van Deerlin V, Desplats P, Deuschl G, Duyckaerts C, Ellinghaus D, Evsyukov V, Flanagan ME, Franke A, Frosch MP, Gearing M, Gelpi E, van Gerpen JA, Ghetti B, Glass JD, Grinberg LT, Halliday G, Helbig I, Höllerhage M, Huitinga I, Irwin DJ, Keene DC, Kovacs GG, Lee EB, Levin J, Martí MJ, Mackenzie I, McKeith I, Mclean C, Mollenhauer B, Neumann M, Newell KL, Pantelyat A, Pendziwiat M, Peters A, Porcel LM, Rabano A, Matěj R, Rajput A, Rajput A, Reimann R, Scott WK, Seeley W, Selvackadunco S, Simuni T, Stadelmann C, Svenningsson P, Thomas A, Trenkwalder C, Troakes C, Trojanowski JQ, Uitti RJ, White CL, Wszolek ZK, Xie T, Ximelis T, Justo Y, Müller U, Schellenberg GD, Herms J, Kuhlenbäumer G, Höglinger G. Common Variants Near ZIC1 and ZIC4 in Autopsy-Confirmed Multiple System Atrophy. Mov Disord 2022; 37:2110-2121. [PMID: 35997131 PMCID: PMC10052809 DOI: 10.1002/mds.29164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 01/24/2022] [Revised: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Multiple System Atrophy is a rare neurodegenerative disease with alpha-synuclein aggregation in glial cytoplasmic inclusions and either predominant olivopontocerebellar atrophy or striatonigral degeneration, leading to dysautonomia, parkinsonism, and cerebellar ataxia. One prior genome-wide association study in mainly clinically diagnosed patients with Multiple System Atrophy failed to identify genetic variants predisposing for the disease. OBJECTIVE Since the clinical diagnosis of Multiple System Atrophy yields a high rate of misdiagnosis when compared to the neuropathological gold standard, we studied only autopsy-confirmed cases. METHODS We studied common genetic variations in Multiple System Atrophy cases (N = 731) and controls (N = 2898). RESULTS The most strongly disease-associated markers were rs16859966 on chromosome 3, rs7013955 on chromosome 8, and rs116607983 on chromosome 4 with P-values below 5 × 10-6 , all of which were supported by at least one additional genotyped and several imputed single nucleotide polymorphisms. The genes closest to the chromosome 3 locus are ZIC1 and ZIC4 encoding the zinc finger proteins of cerebellum 1 and 4 (ZIC1 and ZIC4). INTERPRETATION Since mutations of ZIC1 and ZIC4 and paraneoplastic autoantibodies directed against ZIC4 are associated with severe cerebellar dysfunction, we conducted immunohistochemical analyses in brain tissue of the frontal cortex and the cerebellum from 24 Multiple System Atrophy patients. Strong immunohistochemical expression of ZIC4 was detected in a subset of neurons of the dentate nucleus in all healthy controls and in patients with striatonigral degeneration, whereas ZIC4-immunoreactive neurons were significantly reduced inpatients with olivopontocerebellar atrophy. These findings point to a potential ZIC4-mediated vulnerability of neurons in Multiple System Atrophy. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Anja K. Tietz
- Department of Neurology, Kiel University, Kiel, Germany
| | - Viktoria C. Ruf
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, Munich, Germany
| | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida, USA
| | - Shunsuke Koga
- 6Department of Neuroscience (Neuropathology), Mayo Clinic, Jacksonville, Florida, USA
| | - Dennis Dickson
- 6Department of Neuroscience (Neuropathology), Mayo Clinic, Jacksonville, Florida, USA
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zürich, Zürich, Switzerland
| | - Johannes Attems
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | | | - Vivianna van Deerlin
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paula Desplats
- Department of Neurosciences, School of Medicine University of California San Diego, La Jolla, California, USA
- Department of Pathology, School of Medicine University of California San Diego, La Jolla, California, USA
| | | | - Charles Duyckaerts
- Institut du Cerveau, UMR 7225, Sorbonne Université, Paris Brain Institute-ICM, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Inserm U1127 DMU Neurosciences, Paris, France
- Brainbank NeuroCEB Neuropathology Network: Plateforme de Ressources Biologiques, Hôpital de La Pitié-Salpêtrière, Bâtiment Roger Baillet, Paris Cedex, France
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Margaret Ellen Flanagan
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthew P. Frosch
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marla Gearing
- Departments of Pathology and Laboratory Medicine and Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ellen Gelpi
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
- Medical University of Vienna, Austrian Reference Center for Human Prion Diseases (OERPE), Vienna, Austria
| | | | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - Lea T. Grinberg
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Global Health Institute, University of California, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, California, USA
- Department of Pathology, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Glenda Halliday
- The University of Sydney, School of Medical Sciences, and Brain & Mind Centre, Sydney, New South Wales, Australia
| | - Ingo Helbig
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Inge Huitinga
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands
- Brain Plasticity Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - David John Irwin
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Dirk C. Keene
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Gabor G. Kovacs
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
- Department of Laboratory Medicine and Pathobiology and Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program and Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
| | - Edward B. Lee
- Department of Pathology and Laboratory Medicine, Translational Neuropathology Research Laboratory Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Johannes Levin
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maria J. Martí
- Parkinson’s Disease and Movement Disorders Unit, Department of Neurology, Hospital Clinic of Barcelona, Barcelona, Spain
- Institut de Neurociències, Maeztu Center, University of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigacion Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Ian Mackenzie
- Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ian McKeith
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catriona Mclean
- Department of Anatomical Pathology, Alfred Health, Melbourne, Victoria, Australia
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurology, University Medical Center Goettingen, Gottingen, Germany
| | - Manuela Neumann
- Molecular Neuropathology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Tübingen, Germany
- Department of Neuropathology, University Hospital of Tübingen, Tübingen, Germany
| | - Kathy L. Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Alex Pantelyat
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Children’s Hospital, University Medical Center Schleswig-Holstein, University of Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Alberto Rabano
- Neuropathology Department, CIEN Foundation, Alzheimer’s Centre Queen Sofía Foundation, Madrid, Spain
| | - Radoslav Matěj
- Department of Pathology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, 3rd Faculty of Medicine, Charles University, Thomayer University Hospital, Prague, Czech Republic
| | - Alex Rajput
- Division of Neurology, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ali Rajput
- Saskatchewan Movement Disorders Program, Saskatchewan Health Authority/University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Regina Reimann
- Institute of Neuropathology, University Hospital Zürich, Zürich, Switzerland
| | - William K. Scott
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - William Seeley
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Global Health Institute, University of California, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, California, USA
| | - Sashika Selvackadunco
- Basic and Clinical Neuroscience Department, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Tanya Simuni
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christine Stadelmann
- Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Per Svenningsson
- Section of Neurology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Alan Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurosurgery, University Medical Center Goettingen, Goettingen, Germany
| | - Claire Troakes
- Basic and Clinical Neuroscience Department, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - John Q. Trojanowski
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ryan J. Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA
| | - Charles L. White
- Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Tao Xie
- Department of Neurology, University of Chicago Medicine, Chicago, Illinois, USA
| | - Teresa Ximelis
- Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Yebenes Justo
- Neurological Tissue Bank, Biobanc-Hospital Clínic-IDIBAPS, Barcelona, Spain
- Servicio de Neurología, Hospital Ramón y Cajal de Madrid, Madrid, Spain
| | | | - Ulrich Müller
- Institute of Human Genetics, JLU-Gießen, Giessen, Germany
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jochen Herms
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, Munich, Germany
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Günter Höglinger
- Department of Neurology Hannover Medical School, Hannover, Germany
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
- Zentrum für Systemische Neurowissenschaften, Hannover, Germany
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16
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Wander CM, Tsujimoto THM, Ervin JF, Wang C, Maranto SM, Bhat V, Dallmeier JD, Wang SHJ, Lin FC, Scott WK, Holtzman DM, Cohen TJ. Corpora amylacea are associated with tau burden and cognitive status in Alzheimer's disease. Acta Neuropathol Commun 2022; 10:110. [PMID: 35941704 PMCID: PMC9361643 DOI: 10.1186/s40478-022-01409-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/16/2022] [Indexed: 02/04/2023] Open
Abstract
Corpora amylacea (CA) and their murine analogs, periodic acid Schiff (PAS) granules, are age-related, carbohydrate-rich structures that serve as waste repositories for aggregated proteins, damaged cellular organelles, and other cellular debris. The structure, morphology, and suspected functions of CA in the brain imply disease relevance. Despite this, the link between CA and age-related neurodegenerative diseases, particularly Alzheimer's disease (AD), remains poorly defined. We performed a neuropathological analysis of mouse PAS granules and human CA and correlated these findings with AD progression. Increased PAS granule density was observed in symptomatic tau transgenic mice and APOE knock-in mice. Using a cohort of postmortem AD brain samples, we examined CA in cognitively normal and dementia patients across Braak stages with varying APOE status. We identified a Braak-stage dependent bimodal distribution of CA in the dentate gyrus, with CA accumulating and peaking by Braak stages II-III, then steadily declining with increasing tau burden. Refined analysis revealed an association of CA levels with both cognition and APOE status. Finally, tau was detected in whole CA present in human patient cerebrospinal fluid, highlighting CA-tau as a plausible prodromal AD biomarker. Our study connects hallmarks of the aging brain with the emergence of AD pathology and suggests that CA may act as a compensatory factor that becomes depleted with advancing tau burden.
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Affiliation(s)
- Connor M. Wander
- grid.10698.360000000122483208Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Pharmacology, University of North Carolina, Chapel Hill, NC USA
| | | | - John F. Ervin
- grid.26009.3d0000 0004 1936 7961Bryan Brain Bank, Department of Neurology, Duke University School of Medicine, Durham, NC USA
| | - Chanung Wang
- grid.4367.60000 0001 2355 7002Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO USA
| | - Spencer M. Maranto
- grid.10698.360000000122483208Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Vanya Bhat
- grid.10698.360000000122483208Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Julian D. Dallmeier
- grid.26790.3a0000 0004 1936 8606Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL USA
| | - Shih-Hsiu Jerry Wang
- grid.26009.3d0000 0004 1936 7961Bryan Brain Bank, Department of Neurology, Duke University School of Medicine, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Department of Pathology, Duke University School of Medicine, Durham, NC USA
| | - Feng-Chang Lin
- grid.410711.20000 0001 1034 1720Department of Biostatistics, University of North Carolina, Chapel Hill, NC USA
| | - William K. Scott
- grid.26790.3a0000 0004 1936 8606Brain Endowment Bank, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL USA ,grid.26790.3a0000 0004 1936 8606Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL USA
| | - David M. Holtzman
- grid.4367.60000 0001 2355 7002Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO USA
| | - Todd J. Cohen
- grid.10698.360000000122483208Department of Neurology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC USA
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17
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Waksmunski AR, Miskimen K, Song YE, Grunin M, Laux R, Fuzzell D, Fuzzell S, Adams LD, Caywood L, Prough M, Stambolian D, Scott WK, Pericak-Vance MA, Haines JL. Consequences of a Rare Complement Factor H Variant for Age-Related Macular Degeneration in the Amish. Invest Ophthalmol Vis Sci 2022; 63:8. [PMID: 35930268 PMCID: PMC9363678 DOI: 10.1167/iovs.63.9.8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Genetic variants in the complement factor H gene (CFH) have been consistently implicated in age-related macular degeneration (AMD) risk. However, their functional effects are not fully characterized. We previously identified a rare, AMD-associated variant in CFH (P503A, rs570523689) in 19 Amish individuals, but its functional consequences were not investigated. Methods We performed genotyping for CFH P503A in 1326 Amish individuals to identify additional risk allele carriers. We examined differences for age at AMD diagnosis between carriers and noncarriers. In blood samples from risk allele carriers and noncarriers, we quantified (i) CFH RNA expression, (ii) CFH protein expression, and (iii) C-reactive protein (CRP) expression. Potential changes to the CFH protein structure were interrogated computationally with Phyre2 and Chimera software programs. Results We identified 39 additional carriers from Amish communities in Ohio and Indiana. On average, carriers were younger than noncarriers at AMD diagnosis, but this difference was not significant. CFH transcript and protein levels in blood samples from Amish carriers and noncarriers were also not significantly different. CRP levels were also comparable in plasma samples from carriers and noncarriers. Computational protein modeling showed slight changes in the CFH protein conformation that were predicted to alter interactions between the CFH 503 residue and other neighboring residues. Conclusions In total, we have identified 58 risk allele carriers for CFH P503A in the Ohio and Indiana Amish. Although we did not detect significant differences in age at AMD diagnosis or expression levels of CFH in blood samples from carriers and noncarriers, we observed modest structural changes to the CFH protein through in silico modeling. Based on our functional and computational observations, we hypothesize that CFH P503A may affect CFH binding or function rather than expression, which would require additional research to confirm.
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Affiliation(s)
- Andrea R Waksmunski
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Michelle Grunin
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Renee Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Sarada Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Laura Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Michael Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Jonathan L Haines
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
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18
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Osterman MD, Song YE, Adams LD, Laux RA, Caywood LJ, Prough MB, Clouse JE, Herington SD, Slifer SH, Lynn A, Fuzzell MD, Fuzzell SL, Hochstetler SD, Miskimen K, Main LR, Dorfsman DA, Ogrocki P, Lerner AJ, Ramos J, Vance JM, Cuccaro ML, Scott WK, Pericak-Vance MA, Haines JL. The genetic architecture of Alzheimer disease risk in the Ohio and Indiana Amish. HGG Adv 2022; 3:100114. [PMID: 35599847 PMCID: PMC9114685 DOI: 10.1016/j.xhgg.2022.100114] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/22/2022] [Indexed: 11/26/2022] Open
Abstract
Alzheimer disease (AD) is the most common type of dementia and is currently estimated to affect 6.2 million Americans. It ranks as the sixth leading cause of death in the United States, and the proportion of deaths due to AD has been increasing since 2000, while the proportion of many other leading causes of deaths have decreased or remained constant. The risk for AD is multifactorial, including genetic and environmental risk factors. Although APOE ε4 remains the largest genetic risk factor for AD, more than 26 other loci have been associated with AD risk. Here, we recruited Amish adults from Ohio and Indiana to investigate AD risk and protective genetic effects. As a founder population that typically practices endogamy, variants that are rare in the general population may be of a higher frequency in the Amish population. Since the Amish have a slightly lower incidence and later age of onset of disease, they represent an excellent and unique population for research on protective genetic variants. We compared AD risk in the Amish and to a non-Amish population through APOE genotype, a non-APOE genetic risk score of genome-wide significant variants, and a non-APOE polygenic risk score considering all of the variants. Our results highlight the lesser relative impact of APOE and differing genetic architecture of AD risk in the Amish compared to a non-Amish, general European ancestry population.
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Affiliation(s)
- Michael D. Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sherri D. Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Leighanne R. Main
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Paula Ogrocki
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alan J. Lerner
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jairo Ramos
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
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19
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Osterman MD, Song YE, Nittala M, Sadda SR, Scott WK, Stambolian D, Pericak-Vance MA, Haines JL. Genomewide Association Study of Retinal Traits in the Amish Reveals Loci Influencing Drusen Development and Link to Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci 2022; 63:17. [PMID: 35857289 PMCID: PMC9315071 DOI: 10.1167/iovs.63.8.17] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Purpose The purpose of this study was to identify genetic risk loci for retinal traits, including drusen, in an Amish study population and compare these risk loci to known risk loci of age-related macular degeneration (AMD). Methods Participants were recruited from Amish communities in Ohio, Indiana, and Pennsylvania. Each participant underwent a basic health history, ophthalmologic examination, and genotyping. A genomewide association analysis (GWAS) was conducted for the presence and quantity of each of three retinal traits: geographic atrophy, drusen area, and drusen volume. The findings were compared to results from a prior large GWAS of predominantly European-ancestry individuals. Further, a genetic risk score for AMD was used to predict the presence and quantity of the retinal traits. Results After quality control, 1074 participants were included in analyses. Six single nucleotide polymorphisms (SNPs) met criteria for genomewide significance and 48 were suggestively associated across three retinal traits. The significant SNPs were not highly correlated with known risk SNPs for AMD. A genetic risk score for AMD provided significant predictive value of the retinal traits. Conclusions We identified potential novel genetic risk loci for AMD in a midwestern Amish study population. Additionally, we determined that there is a clear link between the genetic risk of AMD and drusen. Further study, including longitudinal data collection, may improve our ability to define this connection and improve understanding of the biological risk factors underlying drusen development.
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Affiliation(s)
- Michael D Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland Ohio, United States.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland Ohio, United States
| | - Muneeswar Nittala
- Doheny Imaging Reading Center, Doheny Eye Institute, Los Angeles, California, United States
| | - SriniVas R Sadda
- Doheny Imaging Reading Center, Doheny Eye Institute, Los Angeles, California, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Dwight Stambolian
- Ophthalmology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland Ohio, United States.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
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20
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Scott WK. Two Decades of Progress "Toward a National PTSD Brain Bank," on the Occasion of Dr. Matthew J. Friedman's Retirement. Psychiatry 2022; 85:187-191. [PMID: 35588479 DOI: 10.1080/00332747.2022.2068934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Scott WK, Ramos J, Slifer SH, Caywood LJ, Prough MB, Clouse JE, Dorfsman DA, Herington SD, Fuzzell MD, Fuzzell SL, Sewell JL, Miller SD, Osterman MD, Main LR, Miskimen KL, Lynn A, Whitehead PL, Adams LD, Laux RA, Song YE, Foroud TM, Mayeux R, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Pericak‐Vance MA. Association of a locus on chromosome 17 with earlier age at onset of cognitive impairment in a familial Amish dataset. Alzheimers Dement 2021. [DOI: 10.1002/alz.056288] [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: 11/10/2022]
Affiliation(s)
- William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jairo Ramos
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Leighanne R Main
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
| | | | - Richard Mayeux
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain Columbia University New York NY USA
| | - Paula K. Ogrocki
- Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
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22
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Griswold AJ, Rajabli F, Garcia‐Serje C, Hamilton‐Nelson KL, Adams LD, Tejada S, Mena PR, Starks TD, Whitehead PL, Silva‐Vergara C, Cuccaro ML, Martinez I, Illanes‐Manrique M, Cornejo‐Olivas MR, Laux RA, Caywood LJ, Reitz C, Beecham GW, Byrd GS, Feliciano‐Astacio BE, Scott WK, Haines JL, Vance JM, Pericak‐Vance MA. Assessment of AD‐related plasma biomarkers in diverse ancestral populations. Alzheimers Dement 2021. [DOI: 10.1002/alz.056258] [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: 11/08/2022]
Affiliation(s)
- Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Catherine Garcia‐Serje
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Sergio Tejada
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Pedro Ramon Mena
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Takiyah D. Starks
- Maya Angelou Center for Health Equity (MACHE) / Wake Forest School of Medicine Winston Salem NC USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | | | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | | | | | | | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | | | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Goldie S. Byrd
- Maya Angelou Center for Health Equity (MACHE) / Wake Forest School of Medicine Winston Salem NC USA
| | | | - William K. Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
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23
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Godrich D, Richeson P, Schellenberg GD, Scott WK, Montine TJ, Beecham GW. Neuropathologic lesions and comorbidity in Alzheimer disease and related dementias in a heterogeneous clinical population. Alzheimers Dement 2021. [DOI: 10.1002/alz.056249] [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: 11/11/2022]
Affiliation(s)
| | | | | | - William K. Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | | | - Gary W. Beecham
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
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24
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Prough MB, Caywood LJ, Clouse JE, Herington SD, Slifer SH, Dorfsman DA, Adams LD, Laux RA, Song YE, Lynn A, Fuzzell MD, Fuzzell SL, Sewell JL, Miller SD, Miskimen KL, Main LR, Osterman MD, Ogrocki PK, Lerner AJ, Ramos J, Vance JM, Cuccaro ML, Haines JL, Scott WK, Pericak‐Vance MA. Preferential preservation of constructional praxis delayed recall compared to word list delayed recall in the Amish. Alzheimers Dement 2021. [DOI: 10.1002/alz.056386] [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: 11/10/2022]
Affiliation(s)
- Michael B. Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Leighanne R Main
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Paula K. Ogrocki
- Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Jairo Ramos
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
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25
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Main LR, Song YE, Laux RA, Miskimen KL, Cuccaro ML, Ogrocki PK, Lerner AJ, Vance JM, Fuzzell MD, Fuzzell SL, Sewell JL, Caywood LJ, Prough MB, Adams LD, Clouse JE, Herington SD, Scott WK, Pericak‐Vance MA, Haines JL. Genome‐wide association for protective variants in Alzheimer’s disease in the Midwestern Amish. Alzheimers Dement 2021. [DOI: 10.1002/alz.056363] [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: 11/08/2022]
Affiliation(s)
- Leighanne R Main
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | - Alan J. Lerner
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
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26
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Stein CM, Benchek P, Bartlett J, Igo RP, Sobota RS, Chervenak K, Mayanja-Kizza H, von Reyn CF, Lahey T, Bush WS, Boom WH, Scott WK, Marsit C, Sirugo G, Williams SM. Methylome-wide Analysis Reveals Epigenetic Marks Associated With Resistance to Tuberculosis in Human Immunodeficiency Virus-Infected Individuals From East Africa. J Infect Dis 2021; 224:695-704. [PMID: 33400784 DOI: 10.1093/infdis/jiaa785] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/04/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the most deadly infectious disease globally and is highly prevalent in the developing world. For individuals infected with both Mycobacterium tuberculosis (Mtb) and human immunodeficiency virus (HIV), the risk of active TB is 10% or more annually. Previously, we identified in a genome-wide association study (GWAS) a region on chromosome 5 associated with resistance to TB, which included epigenetic marks that could influence gene regulation. We hypothesized that HIV-infected individuals exposed to Mtb who remain disease free carry epigenetic changes that strongly protect them from active TB. METHODS We conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania and integrated data from our GWAS. RESULTS We identified 3 regions of interest that included markers that were differentially methylated between TB cases and controls with latent TB infection: chromosome 1 (RNF220, P = 4 × 10-5), chromosome 2 (between COPS8 and COL6A3, P = 2.7 × 10-5), and chromosome 5 (CEP72, P = 1.3 × 10-5). These methylation results co-localized with associated single-nucleotide polymorphisms (SNPs), methylation QTLs, and methylation × SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. CONCLUSIONS Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.
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Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Division of Infectious Disease and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Penelope Benchek
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jacquelaine Bartlett
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rafal S Sobota
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Keith Chervenak
- Division of Infectious Disease and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Harriet Mayanja-Kizza
- Department of Medicine and Mulago Hospital, School of Medicine, Makerere University, Kampala, Uganda
| | - C Fordham von Reyn
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Timothy Lahey
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - W Henry Boom
- Division of Infectious Disease and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Carmen Marsit
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Giorgio Sirugo
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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27
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Lai D, Alipanahi B, Fontanillas P, Schwantes-An TH, Aasly J, Alcalay RN, Beecham GW, Berg D, Bressman S, Brice A, Brockman K, Clark L, Cookson M, Das S, Van Deerlin V, Follett J, Farrer MJ, Trinh J, Gasser T, Goldwurm S, Gustavsson E, Klein C, Lang AE, Langston JW, Latourelle J, Lynch T, Marder K, Marras C, Martin ER, McLean CY, Mejia-Santana H, Molho E, Myers RH, Nuytemans K, Ozelius L, Payami H, Raymond D, Rogaeva E, Rogers MP, Ross OA, Samii A, Saunders-Pullman R, Schüle B, Schulte C, Scott WK, Tanner C, Tolosa E, Tomkins JE, Vilas D, Trojanowski JQ, Uitti R, Vance JM, Visanji NP, Wszolek ZK, Zabetian CP, Mirelman A, Giladi N, Orr Urtreger A, Cannon P, Fiske B, Foroud T. Genomewide Association Studies of LRRK2 Modifiers of Parkinson's Disease. Ann Neurol 2021; 90:76-88. [PMID: 33938021 PMCID: PMC8252519 DOI: 10.1002/ana.26094] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 02/03/2023]
Abstract
Objective The aim of this study was to search for genes/variants that modify the effect of LRRK2 mutations in terms of penetrance and age‐at‐onset of Parkinson's disease. Methods We performed the first genomewide association study of penetrance and age‐at‐onset of Parkinson's disease in LRRK2 mutation carriers (776 cases and 1,103 non‐cases at their last evaluation). Cox proportional hazard models and linear mixed models were used to identify modifiers of penetrance and age‐at‐onset of LRRK2 mutations, respectively. We also investigated whether a polygenic risk score derived from a published genomewide association study of Parkinson's disease was able to explain variability in penetrance and age‐at‐onset in LRRK2 mutation carriers. Results A variant located in the intronic region of CORO1C on chromosome 12 (rs77395454; p value = 2.5E‐08, beta = 1.27, SE = 0.23, risk allele: C) met genomewide significance for the penetrance model. Co‐immunoprecipitation analyses of LRRK2 and CORO1C supported an interaction between these 2 proteins. A region on chromosome 3, within a previously reported linkage peak for Parkinson's disease susceptibility, showed suggestive associations in both models (penetrance top variant: p value = 1.1E‐07; age‐at‐onset top variant: p value = 9.3E‐07). A polygenic risk score derived from publicly available Parkinson's disease summary statistics was a significant predictor of penetrance, but not of age‐at‐onset. Interpretation This study suggests that variants within or near CORO1C may modify the penetrance of LRRK2 mutations. In addition, common Parkinson's disease associated variants collectively increase the penetrance of LRRK2 mutations. ANN NEUROL 2021;90:82–94
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Affiliation(s)
- Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | | | | | - Tae-Hwi Schwantes-An
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Jan Aasly
- Department of Neurology, St. Olavs Hospital, Trondheim, Norway
| | - Roy N Alcalay
- Department of Neurology, Columbia University, New York, NY
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts-University of Kiel, Kiel, Germany.,Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Susan Bressman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM), AP-HP, Inserm, CNRS, University Hospital Pitié-Salpêtrière, Paris, France
| | - Kathrin Brockman
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Lorraine Clark
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Mark Cookson
- Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda, MD
| | | | - Vivianna Van Deerlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jordan Follett
- Laboratory of Neurogenetics and Neuroscience, Fixel Institute for Neurological Diseases, McKnight Brain Institute, L5-101D, UF Clinical and Translational Science Institute, University of Florida, Gainesville, FL
| | - Matthew J Farrer
- Laboratory of Neurogenetics and Neuroscience, Fixel Institute for Neurological Diseases, McKnight Brain Institute, L5-101D, UF Clinical and Translational Science Institute, University of Florida, Gainesville, FL
| | - Joanne Trinh
- Institute of Neurogenetics, University of Luebeck, Luebeck, Germany
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | | | - Emil Gustavsson
- Centre for Applied Neurogenetics, University of British Columbia, Vancouver, Canada
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, Luebeck, Germany
| | - Anthony E Lang
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, Canada
| | - J William Langston
- Departments of Neurology, Neuroscience, and Pathology, Stanford University School of Medicine, Stanford, CA
| | | | - Timothy Lynch
- Dublin Neurological Institute at the Mater Misericordiae University Hospital, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Karen Marder
- Department of Neurology and Psychiatry, Taub Institute and Sergievsky Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Connie Marras
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, Canada
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Cory Y McLean
- 23andMe, Inc., Sunnyvale, CA.,Google LLC, Cambridge, MA
| | | | - Eric Molho
- Department of Neurology, Albany Medical College, Albany, NY
| | | | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Laurie Ozelius
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL
| | - Deborah Raymond
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Neurology, University of Toronto, Toronto, Canada
| | - Michael P Rogers
- Department of General Surgery, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Owen A Ross
- Departments of Neuroscience and Clinical Genomics, Mayo Clinic, Jacksonville, FL.,School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Ali Samii
- VA Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, WA
| | | | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Claudia Schulte
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - William K Scott
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Caroline Tanner
- University of California, San Francisco Veterans Affairs Health Care System, San Francisco, CA
| | - Eduardo Tolosa
- Parkinson Disease and Movement Disorders Unit, Hospital Clínic Universitari, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | | | - Dolores Vilas
- Parkinson Disease and Movement Disorders Unit, Hospital Clínic Universitari, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | -
- 23andMe, Inc., Sunnyvale, CA
| | - Ryan Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, FL
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Naomi P Visanji
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, Canada
| | | | - Cyrus P Zabetian
- VA Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, WA
| | - Anat Mirelman
- Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Nir Giladi
- Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Avi Orr Urtreger
- Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | | | - Brian Fiske
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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28
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Myers HF, Fair AM, Villalta F, Walz K, Beech BM, Scott WK, Haas DW. Transdisciplinary Perspectives on Precision Medicine. Health Equity 2021; 5:288-298. [PMID: 34036211 PMCID: PMC8139256 DOI: 10.1089/heq.2020.0131] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2021] [Indexed: 01/11/2023] Open
Abstract
Purpose: The Precision Medicine Health Disparities Collaborative fosters collaboration between researchers with diverse backgrounds in precision medicine and health disparities research, to include training at the interface between genomics and health disparities. Understanding how perceptions about precision medicine differ by background may inform activities to better understand such differences. Methods: We conducted a cross-sectional survey of Center members and beyond. Data were collected on categories of educational background, current activities, and level of agreement with 20 statements related to genomics and health disparities. Respondents categorized their background and activities as social/behavioral, genetics, both, or neither. Fisher's exact test was used to assess levels of agreement in response to each statement. Statistically significant associations were further analyzed using ordinal logistic regression adjusting for age, self-identified race/ethnicity, and gender. Results: Of 130 respondents, 50 (38%) identified educational backgrounds and current activities as social-behavioral or genomic 55 (42%). Respondents differed by educational background on the statement Lifestyle and other life experiences influence how genes impact disease risk (p=0.0009). Respondents also differed by current activities on the statement Reducing disparities in access to health care will make precision medicine more effective (p=0.0008), and on Racism and discrimination make me concerned about how genetic test results will be used (p=0.0011). Conclusions: Respondents who differed on prior education and current activities, whether social behavioral science or human genomics, were associated with different perceptions regarding precision medicine and health disparities. These results identify potential barriers and opportunities to strengthen transdisciplinary collaboration.
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Affiliation(s)
- Hector F. Myers
- Department of Medicine, Health & Society, Department of Psychology, and Department of African American & Diaspora Studies, Vanderbilt University, Nashville, Tennessee, USA
| | - Alecia M. Fair
- Department of Medicine, Division of Geriatric Medicine, Vanderbilt University Medical Center, Meharry-Vanderbilt Alliance, Nashville, Tennessee, USA
| | - Fernando Villalta
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
| | - Katherina Walz
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Bettina M. Beech
- Department of Health Systems and Population Health Sciences, University of Houston, College of Medicine, Houston, Texas, USA
| | - William K. Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - David W. Haas
- Department of Medicine, Division of Geriatric Medicine, Vanderbilt University Medical Center, Meharry-Vanderbilt Alliance, Nashville, Tennessee, USA.,Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA.,*Address correspondence to: David W. Haas, MD, Department of Microbiology, Immunology, and Physiology, Vanderbilt University Medical Center, Meharry Medical College, Vanderbilt HealthOne Hundred Oaks, 719 Thompson Lane, Suite 47183, Nashville, TN 37204, USA,
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29
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Griswold AJ, Celis K, Bussies PL, Rajabli F, Whitehead PL, Hamilton-Nelson KL, Beecham GW, Dykxhoorn DM, Nuytemans K, Wang L, Gardner OK, Dorfsman DA, Bigio EH, Mesulam MM, Weintraub S, Geula C, Gearing M, McGrath-Martinez E, Dalgard CL, Scott WK, Haines JL, Pericak-Vance MA, Young JI, Vance JM. Increased APOE ε4 expression is associated with the difference in Alzheimer's disease risk from diverse ancestral backgrounds. Alzheimers Dement 2021; 17:1179-1188. [PMID: 33522086 DOI: 10.1002/alz.12287] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 06/02/2020] [Revised: 12/02/2020] [Accepted: 12/06/2020] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Apolipoprotein E (APOE) ε4 confers less risk for Alzheimer's disease (AD) in carriers with African local genomic ancestry (ALA) than APOE ε4 carriers with European local ancestry (ELA). Cell type specific transcriptional variation between the two local ancestries (LAs) could contribute to this disease risk differences. METHODS Single-nucleus RNA sequencing was performed on frozen frontal cortex of homozygous APOE ε4/ε4 AD patients: seven with ELA, four with ALA. RESULTS A total of 60,908 nuclei were sequenced. Within the LA region (chr19:44-46Mb), APOE was the gene most differentially expressed, with ELA carriers having significantly more expression (overall P < 1.8E-317 ) in 24 of 32 cell clusters. The transcriptome of one astrocyte cluster, with high APOE ε4 expression and specific to ELA, is suggestive of A1 reactive astrocytes. DISCUSSION AD patients with ELA expressed significantly greater levels of APOE than ALA APOE ε4 carriers. These differences in APOE expression could contribute to the reduced risk for AD seen in African APOE ε4 carriers.
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Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Katrina Celis
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Parker L Bussies
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Olivia K Gardner
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Daniel A Dorfsman
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Eileen H Bigio
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Marek Marsel Mesulam
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sandra Weintraub
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Changiz Geula
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Marla Gearing
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, Georgia, USA
| | - Elisa McGrath-Martinez
- The American Genome Center, Uniformed Services University, Bethesda, Maryland, USA.,Collaborative Health Initiative Research Program, Henry Jackson Foundation, Bethesda, Maryland, USA
| | - Clifton L Dalgard
- Collaborative Health Initiative Research Program, Henry Jackson Foundation, Bethesda, Maryland, USA.,Department of Anatomy Physiology & Genetics, Uniformed Services University, Bethesda, Maryland, USA
| | - William K Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
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30
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Ramos J, Chowdhury AR, Caywood LJ, Prough M, Denise Fuzzell M, Fuzzell S, Miskimen K, Whitehead PL, Adams LD, Laux R, Song Y, Ogrocki P, Lerner AJ, Vance JM, Haines JL, Scott WK, Pericak-Vance MA, Cuccaro ML. Lower Levels of Education Are Associated with Cognitive Impairment in the Old Order Amish. J Alzheimers Dis 2020; 79:451-458. [PMID: 33285633 DOI: 10.3233/jad-200909] [Citation(s) in RCA: 4] [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] [Indexed: 01/12/2023]
Abstract
BACKGROUND Lower education has been reported to be associated with dementia. However, many studies have been done in settings where 12 years of formal education is the standard. Formal schooling in the Old Order Amish communities (OOA) ends at 8th grade which, along with their genetic homogeneity, makes it an interesting population to study the effect of education on cognitive impairment. OBJECTIVE The objective of this study was to examine the association of education with cognitive function in individuals from the OOA. We hypothesized that small differences in educational attainment at lower levels of formal education were associated with risk for cognitive impairment. METHODS Data of 2,426 individuals from the OOA aged 54-99 were analyzed. The Modified Mini-Mental State Examination (3MS-R) was used to classify participants as CI or normal. Individuals were classified into three education categories: <8, 8, and >8 years of education. To measure the association of education with cognitive status, a logistic regression model was performed adding age and sex as covariates. RESULTS Our results showed that individuals who attained lowest levels of education (<8 and 8) had a higher probability of becoming cognitvely impaired compared with people attending >8 years (OR = 2.96 and 1.85). CONCLUSION Even within a setting of low levels of formal education, small differences in educational attainment can still be associated with the risk of cognitive impairment. Given the homogeneity of the OOA, these results are less likely to be biased by differences in socioeconomic backgrounds.
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Affiliation(s)
- Jairo Ramos
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Aneesa R Chowdhury
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Laura J Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M Denise Fuzzell
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sarada Fuzzell
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kristy Miskimen
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Renee Laux
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yeunjoo Song
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Paula Ogrocki
- University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Alan J Lerner
- University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jeffery M Vance
- 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
| | - Jonathan L Haines
- Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - William K Scott
- 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
| | - Margaret A Pericak-Vance
- 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
| | - Michael L Cuccaro
- 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
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31
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Celis K, Griswold AJ, Bussies P, Rajabli F, Whitehead PL, Hamilton‐Nelson KL, Beecham GW, Dykxhoorn DM, Nuytemans K, Wang L, Gardner OK, Dorfsman D, Bigio EH, Mesulam M, Weintraub S, Geula C, Gearing M, Dalgard C, Mcgrath‐Martinez E, Scott WK, Haines JL, Pericak‐Vance MA, Young J, Vance JM. Increased
APOE‐e4
expression is associated with reactive A1 astrocytes and may confer the difference in Alzheimer disease risk from different ancestral backgrounds. Alzheimers Dement 2020. [DOI: 10.1002/alz.045415] [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)
- Katrina Celis
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Anthony J. Griswold
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Parker Bussies
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Gary W. Beecham
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Karen Nuytemans
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | | | - Olivia K. Gardner
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | | | | | | | | | | | | | | | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | | | - Juan Young
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
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32
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Vontell RT, Davis DA, Barreda A, Blennow K, Zetterberg H, Gultekin SH, DeKosky S, Scott WK, Sun X. Reduction of neurogranin immunostaining in the hippocampus of post‐mortem brain of Alzheimer’s disease. Alzheimers Dement 2020. [DOI: 10.1002/alz.040707] [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: 11/11/2022]
Affiliation(s)
| | | | | | - Kaj Blennow
- Institute of Neuroscience and Physiology the Sahlgrenska Academy at the University of Gothenburg Gothenburg Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology the Sahlgrenska Academy at the University of Gothenburg Gothenburg Sweden
| | | | | | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Xiaoyan Sun
- University of Miami Miller School of Medicine Miami FL USA
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33
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Song YE, Miskimen K, Laux RA, Fuzzell MD, Fuzzell SL, Sewell JL, Miller SD, Adams LD, Caywood LJ, Prough M, Close JE, Herington SD, Slifer SH, Ramos J, Vance JM, Cuccaro ML, Ogrocki PK, Lerner AJ, Scott WK, Pericak‐Vance MA, Haines JL. Longitudinal assessment of cognitive decline in the Amish. Alzheimers Dement 2020. [DOI: 10.1002/alz.043440] [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: 11/08/2022]
Affiliation(s)
- Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Close
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jairo Ramos
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | | | - Alan J. Lerner
- Brain Health and Memory Center University Hospital Cleveland OH USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
- Case Western Reserve University School of Medicine Cleveland OH USA
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34
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Ramos J, Jaworski J, Adams LD, Laux RA, Caywood LJ, Prough M, Clouse JE, Herington SD, Slifer SH, Fuzzell MD, Fuzzell SL, Sewell JL, Miller SD, Song YE, Miskimen K, Main LR, Ogrocki P, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Pericak‐Vance MA, Scott WK. Joint linkage and association mapping of preserved cognition in the old‐order Amish. Alzheimers Dement 2020. [DOI: 10.1002/alz.046416] [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: 11/12/2022]
Affiliation(s)
- Jairo Ramos
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - James Jaworski
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | | | - Paula Ogrocki
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Case Western Reserve University School of Medicine Cleveland OH USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | | | | | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
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Nuytemans K, Rajabli F, Bussies PL, Celis K, Scott WK, Singer C, Luca CC, Vinuela A, Pericak-Vance MA, Vance JM. Novel Variants in LRRK2 and GBA Identified in Latino Parkinson Disease Cohort Enriched for Caribbean Origin. Front Neurol 2020; 11:573733. [PMID: 33281709 PMCID: PMC7689018 DOI: 10.3389/fneur.2020.573733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/17/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022] Open
Abstract
Background: The Latino population is greatly understudied in biomedical research, including genetics. Very little information is available on presence of known variants originally identified in non-Hispanic white patients or novel variants in the Latino population. The Latino population is admixed, with contributions of European, African, and Amerindian ancestries. Therefore, the ancestry surrounding a gene (local ancestry, LA) can be any of the three contributing ancestries and thus can determine the presence or risk effect of variants detected. Methods: We sequenced the major exons and exons of reported Latino-specific variants in GBA and LRRK2 and performed genome-wide genotyping for LA assessments in 79 Latino Parkinson disease (PD) patients, of which ~80% identified as Caribbean Latino. Results: We observed five carriers of LRRK2 p.G2019S, one GBA p.T408M, and three GBA p.N409S on European as well as three GBA p.L13R on African LA backgrounds. Previous Latino variant GBA p.K237E was not observed in this dataset. A novel highly conserved and predicted damaging variant LRRK2 p.D734N was identified in two unrelated individuals with African LA. Additionally, we identified rare, functional variants LRRK2 p.P1480L and GBA p.S310G in one individual each heterozygous for European/Amerindian LA. Discussion: Additional functional analysis will be needed to determine the pathogenicity of the novel variants in PD. However, the identification of novel disease variants in the Latino cohort potentially contributing to PD supports to importance of inclusion of Latinos in genetics research to provide insight in PD genetics in Latinos specifically as well as other populations with the same ancestral contributions.
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Affiliation(s)
- Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Parker L Bussies
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Katrina Celis
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Carlos Singer
- Division of Parkinson's Disease and Movement Disorders, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Corneliu C Luca
- Division of Parkinson's Disease and Movement Disorders, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Angel Vinuela
- Movement Disorders Group, Manatí Medical Center, Neurosciences Institute, Manatí, Puerto Rico
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Jeff M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, United States
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Fan BJ, Bailey JC, Igo RP, Kang JH, Boumenna T, Brilliant MH, Budenz DL, Fingert JH, Gaasterland T, Gaasterland D, Hauser MA, Kraft P, Lee RK, Lichter PR, Liu Y, Moroi SE, Myers JS, Pericak-Vance MA, Realini A, Rhee DJ, Richards JE, Ritch R, Schuman JS, Scott WK, Singh K, Sit AJ, Vollrath D, Weinreb RN, Wollstein G, Zack DJ, Haines JL, Pasquale LR, Wiggs JL. Association of a Primary Open-Angle Glaucoma Genetic Risk Score With Earlier Age at Diagnosis. JAMA Ophthalmol 2019; 137:1190-1194. [PMID: 31436842 DOI: 10.1001/jamaophthalmol.2019.3109] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Genetic variants associated with primary open-angle glaucoma (POAG) are known to influence disease risk. However, the clinical effect of associated variants individually or in aggregate is not known. Genetic risk scores (GRS) examine the cumulative genetic load by combining individual genetic variants into a single measure, which is assumed to have a larger effect and increased power to detect relevant disease-related associations. Objective To investigate if a GRS that comprised 12 POAG genetic risk variants is associated with age at disease diagnosis. Design, Setting, and Participants A cross-sectional study included individuals with POAG and controls from the Glaucoma Genes and Environment (GLAUGEN) study and the National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) study. A GRS was formulated using 12 variants known to be associated with POAG, and the alleles associated with increasing risk of POAG were aligned in the case-control sets. In case-only analyses, the association of the GRS with age at diagnosis was analyzed as an estimate of disease onset. Results from cohort-specific analyses were combined with meta-analysis. Data collection started in August 2012 for the NEIGHBOR cohort and in July 2008 for the GLAUGEN cohort and were analyzed starting in March 2018. Main Outcomes and Measures Association of a 12 single-nucleotide polymorphism POAG GRS with age at diagnosis in individuals with POAG using linear regression. Results The GLAUGEN study included 976 individuals with POAG and 1140 controls. The NEIGHBOR study included 2132 individuals with POAG and 2290 controls. For individuals with POAG, the mean (SD) age at diagnosis was 63.6 (9.8) years in the GLAUGEN cohort and 66.0 (13.7) years in the NEIGHBOR cohort. For controls, the mean (SD) age at enrollment was 65.5 (9.2) years in the GLAUGEN cohort and 68.9 (11.4) years in the NEIGHBOR cohort. All study participants were European white. The GRS was strongly associated with POAG risk in case-control analysis (odds ratio per 1-point increase in score = 1.24; 95% CI, 1.21-1.27; P = 3.4 × 10-66). In case-only analyses, each higher GRS unit was associated with a 0.36-year earlier age at diagnosis (β = -0.36; 95% CI, -0.56 to -0.16; P = 4.0 × 10-4). Individuals in the top 5% of the GRS had a mean (SD) age at diagnosis of 5.2 (12.8) years earlier than those in the bottom 5% GRS (61.4 [12.7] vs 66.6 [12.9] years; P = 5.0 × 10-4). Conclusions and Relevance A higher dose of POAG risk alleles was associated with an earlier age at glaucoma diagnosis. On average, individuals with POAG with the highest GRS had 5.2-year earlier age at diagnosis of disease. These results suggest that a GRS that comprised genetic variants associated with POAG could help identify patients with risk of earlier disease onset impacting screening and therapeutic strategies.
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Affiliation(s)
- Bao Jian Fan
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear, Boston
| | - Jessica Cooke Bailey
- Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Rob P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Tahani Boumenna
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear, Boston
| | | | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill
| | - John H Fingert
- Department of Ophthalmology, University of Iowa, College of Medicine, Iowa City.,Department of Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City
| | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego
| | | | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina.,Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Peter Kraft
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Paul R Lichter
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia
| | - Syoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor
| | | | | | - Anthony Realini
- Department of Ophthalmology, WVU Eye Institute, Morgantown, West Virginia
| | - Douglas J Rhee
- Department of Ophthalmology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York
| | - Joel S Schuman
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, New York
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, California
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - Douglas Vollrath
- Department of Genetics, Stanford University, Palo Alto, California
| | - Robert N Weinreb
- Department of Ophthalmology, Hamilton Glaucoma Center and Shiley Eye Institute, University of California at San Diego, La Jolla
| | - Gadi Wollstein
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, New York
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Jonathan L Haines
- Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine, Mount Sinai Hospital, New York
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear, Boston
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Nuytemans K, Manrique CP, Uhlenberg A, Scott WK, Cuccaro ML, Luca CC, Singer C, Vance JM. Motivations for Participation in Parkinson Disease Genetic Research Among Hispanics versus Non-Hispanics. Front Genet 2019; 10:658. [PMID: 31379924 PMCID: PMC6646686 DOI: 10.3389/fgene.2019.00658] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/21/2019] [Indexed: 11/13/2022] Open
Abstract
Involvement of participants from different racial and ethnic groups in genomic research is vital to reducing health disparities in the precision medicine era. Racial and ethnically diverse populations are underrepresented in current genomic research, creating bias in result interpretation. Limited information is available to support motivations or barriers of these groups to participate in genomic research for late-onset, neurodegenerative disorders. To evaluate willingness for research participation, we compared motivations for participation in genetic studies among 113 Parkinson disease (PD) patients and 49 caregivers visiting the Movement Disorders clinic at the University of Miami. Hispanics and non-Hispanics were equally motivated to participate in genetic research for PD. However, Hispanic patients were less likely to be influenced by the promise of scientific advancements (N = 0.01). This lack of scientific interest, but not other motivations, was found to be likely confounded by lower levels of obtained education (N = 0.001). Overall, these results suggest that underrepresentation of Hispanics in genetic research may be partly due to reduced invitations to these studies.
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Affiliation(s)
- Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Clara P Manrique
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Aaron Uhlenberg
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Corneliu C Luca
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Carlos Singer
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, United States
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Ramos J, Caywood LJ, Prough M, Fuzzell MD, Fuzzell S, Miskimen K, Whitehead PL, Adams LD, Laux R, Song Y, Ogrocki P, Lerner AJ, Vance JM, Scott WK, Pericak-Vance MA, Cuccaro ML. P3-140: PROTECTIVE EFFECT OF EDUCATION ON COGNITIVE FUNCTION IN THE OLD ORDER AMISH. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.3168] [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: 11/29/2022]
Affiliation(s)
- Jairo Ramos
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | | | - Michael Prough
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | - M. Denise Fuzzell
- Case Western Reserve University School of Medicine; Cleveland OH USA
| | - Sarada Fuzzell
- Case Western Reserve University School of Medicine; Cleveland OH USA
| | - Kristy Miskimen
- Case Western Reserve University School of Medicine; Cleveland OH USA
| | | | - Larry D. Adams
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | - Renee Laux
- Case Western Reserve University School of Medicine; Cleveland OH USA
| | - Yeunjoo Song
- Case Western Reserve University School of Medicine; Cleveland OH USA
| | - Paula Ogrocki
- University Hospitals Cleveland Medical Center; Cleveland OH USA
| | - Alan J. Lerner
- Case Western Reserve University School of Medicine; Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics; University of Miami Miller School of Medicine; Miami FL USA
| | - Margaret A. Pericak-Vance
- 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
| | - Michael L. Cuccaro
- 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
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Young JI, Sivasankaran SK, Wang L, Ali A, Mehta A, Davis DA, Dykxhoorn DM, Petito CK, Beecham GW, Martin ER, Mash DC, Pericak-Vance M, Scott WK, Montine TJ, Vance JM. Genome-wide brain DNA methylation analysis suggests epigenetic reprogramming in Parkinson disease. Neurol Genet 2019; 5:e342. [PMID: 31403079 PMCID: PMC6659138 DOI: 10.1212/nxg.0000000000000342] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/09/2019] [Indexed: 12/13/2022]
Abstract
Objective Given the known strong relationship of DNA methylation with environmental exposure, we investigated whether brain regions affected in Parkinson disease (PD) were differentially methylated between PD cases and controls. Methods DNA chip arrays were used to perform a genome-wide screen of DNA methylation on the dorsal motor nucleus of the vagus (DMV), substantia nigra (SN), and cingulate gyrus (CG) of pathologically confirmed PD cases and controls selected using the criteria of Beecham et al. Analysis examined differentially methylated regions (DMRs) between cases and controls for each brain area. RNA sequencing and pathway analysis were also performed for each brain area. Results Thirty-eight PD cases and 41 controls were included in the analysis. Methylation studies revealed 234 significant DMR in the DMV, 44 in the SN, and 141 in the CG between cases and controls (Sidak p < 0.05). Pathway analysis of these genes showed significant enrichment for the Wnt signaling pathway (FDR < 0.01). Conclusions Our data suggest that significant DNA methylation changes exist between cases and controls in PD, especially in the DMV, one of the areas affected earliest in PD. The etiology of these methylation changes is not yet known, but the predominance of methylation changes occurring in the DMV supports the hypothesis that vagus nerve function, perhaps involving the gastrointestinal system, is important in PD pathogenesis. These data also give independent support that genes involved in Wnt signaling are a likely factor in the neurodegenerative processes of PD.
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Affiliation(s)
- Juan I Young
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Sathesh K Sivasankaran
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Lily Wang
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Aleena Ali
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Arpit Mehta
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - David A Davis
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Carol K Petito
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Deborah C Mash
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - William K Scott
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Thomas J Montine
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
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Mitchell SL, Uppal K, Williamson SM, Liu K, Burgess LG, Tran V, Umfress AC, Jarrell KL, Cooke Bailey JN, Agarwal A, Pericak-Vance M, Haines JL, Scott WK, Jones DP, Brantley MA. The Carnitine Shuttle Pathway is Altered in Patients With Neovascular Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci 2019; 59:4978-4985. [PMID: 30326066 PMCID: PMC6188466 DOI: 10.1167/iovs.18-25137] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Purpose To identify metabolites and metabolic pathways altered in neovascular age-related macular degeneration (NVAMD). Methods We performed metabolomics analysis using high-resolution C18 liquid chromatography-mass spectrometry on plasma samples from 100 NVAMD patients and 192 controls. Data for mass/charge ratio ranging from 85 to 850 were captured, and metabolic features were extracted using xMSanalyzer. Nested feature selection was used to identify metabolites that discriminated between NVAMD patients and controls. Pathway analysis was performed with Mummichog 2.0. Hierarchical clustering was used to examine the relationship between the discriminating metabolites and NVAMD patients and controls. Results Of the 10,917 metabolic features analyzed, a set of 159 was identified that distinguished NVAMD patients from controls (area under the curve of 0.83). Of these features, 39 were annotated with confidence and included multiple carnitine metabolites. Pathway analysis revealed that the carnitine shuttle pathway was significantly altered in NVAMD patients (P = 0.0001). Tandem mass spectrometry confirmed the molecular identity of five carnitine shuttle pathway acylcarnitine intermediates that were increased in NVAMD patients. Hierarchical cluster analysis revealed that 51% of the NVAMD patients had similar metabolic profiles, whereas the remaining 49% displayed greater variability in their metabolic profiles. Conclusions Multiple long-chain acylcarnitines that are part of the carnitine shuttle pathway were significantly increased in NVAMD patients compared to controls, suggesting that fatty acid metabolism may be involved in NVAMD pathophysiology. Cluster analysis suggested that clinically indistinguishable NVAMD patients can be separated into distinct subgroups based on metabolic profiles.
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Affiliation(s)
- Sabrina L Mitchell
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Karan Uppal
- Department of Medicine, Emory University Medical Center, Atlanta, Georgia, United States
| | - Samantha M Williamson
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Ken Liu
- Department of Medicine, Emory University Medical Center, Atlanta, Georgia, United States
| | - L Goodwin Burgess
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - ViLinh Tran
- Department of Medicine, Emory University Medical Center, Atlanta, Georgia, United States
| | - Allison C Umfress
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Kelli L Jarrell
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
| | - Anita Agarwal
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Dean P Jones
- Department of Medicine, Emory University Medical Center, Atlanta, Georgia, United States
| | - Milam A Brantley
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
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41
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Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu NY, Chuang LS, Carmi S, Villaverde N, Li X, Rivas M, Levine AP, Bao X, Labrias PR, Haritunians T, Ruane D, Gettler K, Chen E, Li D, Schiff ER, Pontikos N, Barzilai N, Brant SR, Bressman S, Cheifetz AS, Clark LN, Daly MJ, Desnick RJ, Duerr RH, Katz S, Lencz T, Myers RH, Ostrer H, Ozelius L, Payami H, Peter Y, Rioux JD, Segal AW, Scott WK, Silverberg MS, Vance JM, Ubarretxena-Belandia I, Foroud T, Atzmon G, Pe'er I, Ioannou Y, McGovern DPB, Yue Z, Schadt EE, Cho JH, Peter I. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Sci Transl Med 2019; 10:10/423/eaai7795. [PMID: 29321258 DOI: 10.1126/scitranslmed.aai7795] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 03/31/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022]
Abstract
Crohn's disease (CD), a form of inflammatory bowel disease, has a higher prevalence in Ashkenazi Jewish than in non-Jewish European populations. To define the role of nonsynonymous mutations, we performed exome sequencing of Ashkenazi Jewish patients with CD, followed by array-based genotyping and association analysis in 2066 CD cases and 3633 healthy controls. We detected association signals in the LRRK2 gene that conferred risk for CD (N2081D variant, P = 9.5 × 10-10) or protection from CD (N551K variant, tagging R1398H-associated haplotype, P = 3.3 × 10-8). These variants affected CD age of onset, disease location, LRRK2 activity, and autophagy. Bayesian network analysis of CD patient intestinal tissue further implicated LRRK2 in CD pathogenesis. Analysis of the extended LRRK2 locus in 24,570 CD cases, patients with Parkinson's disease (PD), and healthy controls revealed extensive pleiotropy, with shared genetic effects between CD and PD in both Ashkenazi Jewish and non-Jewish cohorts. The LRRK2 N2081D CD risk allele is located in the same kinase domain as G2019S, a mutation that is the major genetic cause of familial and sporadic PD. Like the G2019S mutation, the N2081D variant was associated with increased kinase activity, whereas neither N551K nor R1398H variants on the protective haplotype altered kinase activity. We also confirmed that R1398H, but not N551K, increased guanosine triphosphate binding and hydrolyzing enzyme (GTPase) activity, thereby deactivating LRRK2. The presence of shared LRRK2 alleles in CD and PD provides refined insight into disease mechanisms and may have major implications for the treatment of these two seemingly unrelated diseases.
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Affiliation(s)
- Ken Y Hui
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | | | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Schaffner
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Nicole Villaverde
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xianting Li
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manual Rivas
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Adam P Levine
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Xiuliang Bao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Philippe R Labrias
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Talin Haritunians
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Darren Ruane
- Department of Immunology and Inflammation, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Kyle Gettler
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Genetics, Yale University, New Haven, CT 06520, USA
| | - Ernie Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dalin Li
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Elena R Schiff
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Nikolas Pontikos
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Nir Barzilai
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA.,Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Susan Bressman
- Alan and Barbara Mirken Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Adam S Cheifetz
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark J Daly
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Seymour Katz
- New York University School of Medicine, New York City, NY 10016, USA.,North Shore University-Long Island Jewish Medical Center, Manhasset, NY, USA.,St. Francis Hospital, Roslyn, NY 11576, USA
| | - Todd Lencz
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA 02114, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie Ozelius
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Deparment of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Haydeh Payami
- Departments of Neurology and Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35805, USA
| | - Yakov Peter
- Department of Biology, Touro College, Queens, NY 10033, USA.,Department of Pulmonary Medicine, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10033, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, Quebec H1T1C8, Canada.,Faculté de Médecine, Université de Montréal, Montreal, Quebec H1T1C8, Canada
| | - Anthony W Segal
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - William K Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario M5T3L9, USA.,Department of Medicine, University of Toronto, Toronto, Ontario M5G1X5, Canada
| | - Jeffery M Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gil Atzmon
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Itsik Pe'er
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Yiannis Ioannou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dermot P B McGovern
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zhenyu Yue
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Institute for Genetics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Judy H Cho
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics, Yale University, New Haven, CT 06520, USA.,Section of Gastroenterology and Hepatology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. .,Institute for Genetics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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42
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Scott WK, Medie FM, Ruffin F, Sharma-Kuinkel BK, Cyr DD, Guo S, Dykxhoorn DM, Skov RL, Bruun NE, Dahl A, Lerche CJ, Petersen A, Larsen AR, Lauridsen TK, Johansen HK, Ullum H, Sørensen E, Hassager C, Bundgaard H, Schønheyder HC, Torp-Pedersen C, Østergaard LB, Arpi M, Rosenvinge F, Erikstrup LT, Chehri M, Søgaard P, Andersen PS, Fowler VG. Human genetic variation in GLS2 is associated with development of complicated Staphylococcus aureus bacteremia. PLoS Genet 2018; 14:e1007667. [PMID: 30289878 PMCID: PMC6192642 DOI: 10.1371/journal.pgen.1007667] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 10/17/2018] [Accepted: 08/29/2018] [Indexed: 12/30/2022] Open
Abstract
The role of host genetic variation in the development of complicated Staphylococcus aureus bacteremia (SAB) is poorly understood. We used whole exome sequencing (WES) to examine the cumulative effect of coding variants in each gene on risk of complicated SAB in a discovery sample of 168 SAB cases (84 complicated and 84 uncomplicated, frequency matched by age, sex, and bacterial clonal complex [CC]), and then evaluated the most significantly associated genes in a replication sample of 240 SAB cases (122 complicated and 118 uncomplicated, frequency matched for age, sex, and CC) using targeted sequence capture. In the discovery sample, gene-based analysis using the SKAT-O program identified 334 genes associated with complicated SAB at p<3.5 x 10−3. These, along with eight biologically relevant candidate genes were examined in the replication sample. Gene-based analysis of the 342 genes in the replication sample using SKAT-O identified one gene, GLS2, significantly associated with complicated SAB (p = 1.2 x 10−4) after Bonferroni correction. In Firth-bias corrected logistic regression analysis of individual variants, the strongest association across all 10,931 variants in the replication sample was with rs2657878 in GLS2 (p = 5 x 10−4). This variant is strongly correlated with a missense variant (rs2657879, p = 4.4 x 10−3) in which the minor allele (associated here with complicated SAB) has been previously associated with lower plasma concentration of glutamine. In a microarray-based gene-expression analysis, individuals with SAB exhibited significantly lower expression levels of GLS2 than healthy controls. Similarly, Gls2 expression is lower in response to S. aureus exposure in mouse RAW 264.7 macrophage cells. Compared to wild-type cells, RAW 264.7 cells with Gls2 silenced by CRISPR-Cas9 genome editing have decreased IL1-β transcription and increased nitric oxide production after S. aureus exposure. GLS2 is an interesting candidate gene for complicated SAB due to its role in regulating glutamine metabolism, a key factor in leukocyte activation. Complications from bloodstream infection with Staphylococcus aureus (S. aureus) are important causes of hospitalization, significant illness, and death. The causes of these complications are not well understood, but likely involve genetic factors rendering people more susceptible to such infections, differences in the bacteria that cause the infection, and the interactions between them. We examined the parts of the human genome that code for proteins to find variations that were more common in people with complicated S. aureus bacteremia (SAB), and identified one gene, called GLS2, in which variation is more common in complicated SAB cases than uncomplicated cases. Expression of GLS2 is lower in people with SAB than controls and in mouse white blood cells exposed to S. aureus. GLS2 encodes a protein that regulates the metabolism of glutamine, a regulatory process that activates white blood cells. These cells are very important in the immune response to S. aureus infection, and therefore genetic variants that might influence their growth are important potential genetic risk factors for complicated SAB.
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Affiliation(s)
- William K. Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- * E-mail: (WKS); (PSA); (VGF)
| | - Felix Mba Medie
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, United States of America
| | - Felicia Ruffin
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, United States of America
| | - Batu K. Sharma-Kuinkel
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, United States of America
| | - Derek D. Cyr
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Robert L. Skov
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Niels E. Bruun
- Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Anders Dahl
- Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Denmark
| | - Christian J. Lerche
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Helle Krogh Johansen
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Henrik Ullum
- Department of Clinical Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Christian Hassager
- Department of Cardiology, Rigshospitalet and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Cardiology, Rigshospitalet and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Henrik C. Schønheyder
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Louise Bruun Østergaard
- Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Denmark
- Clinical Institute, Aalborg University, Aalborg, Denmark
| | - Magnus Arpi
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev-Gentofte, Denmark
| | - Flemming Rosenvinge
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Lise T. Erikstrup
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | - Mahtab Chehri
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Peter Søgaard
- Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark
| | - Paal S. Andersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (WKS); (PSA); (VGF)
| | - Vance G. Fowler
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, United States of America
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, United States of America
- * E-mail: (WKS); (PSA); (VGF)
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43
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Bailey JNC, Gharahkhani P, Kang JH, Butkiewicz M, Sullivan DA, Weinreb RN, Aschard H, Allingham RR, Ashley-Koch A, Lee RK, Moroi SE, Brilliant MH, Wollstein G, Schuman JS, Fingert JH, Budenz DL, Realini T, Gaasterland T, Scott WK, Singh K, Sit AJ, Igo RP, Song YE, Hark L, Ritch R, Rhee DJ, Vollrath D, Zack DJ, Medeiros F, Vajaranant TS, Chasman DI, Christen WG, Pericak-Vance MA, Liu Y, Kraft P, Richards JE, Rosner BA, Hauser MA, Craig JE, Burdon KP, Hewitt AW, Mackey DA, Haines JL, MacGregor S, Wiggs JL, Pasquale LR. Testosterone Pathway Genetic Polymorphisms in Relation to Primary Open-Angle Glaucoma: An Analysis in Two Large Datasets. Invest Ophthalmol Vis Sci 2018; 59:629-636. [PMID: 29392307 PMCID: PMC5795896 DOI: 10.1167/iovs.17-22708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Sex hormones may be associated with primary open-angle glaucoma (POAG), although the mechanisms are unclear. We previously observed that gene variants involved with estrogen metabolism were collectively associated with POAG in women but not men; here we assessed gene variants related to testosterone metabolism collectively and POAG risk. Methods We used two datasets: one from the United States (3853 cases and 33,480 controls) and another from Australia (1155 cases and 1992 controls). Both datasets contained densely called genotypes imputed to the 1000 Genomes reference panel. We used pathway- and gene-based approaches with Pathway Analysis by Randomization Incorporating Structure (PARIS) software to assess the overall association between a panel of single nucleotide polymorphisms (SNPs) in testosterone metabolism genes and POAG. In sex-stratified analyses, we evaluated POAG overall and POAG subtypes defined by maximum IOP (high-tension [HTG] or normal tension glaucoma [NTG]). Results In the US dataset, the SNP panel was not associated with POAG (permuted P = 0.77), although there was an association in the Australian sample (permuted P = 0.018). In both datasets, the SNP panel was associated with POAG in men (permuted P ≤ 0.033) and not women (permuted P ≥ 0.42), but in gene-based analyses, there was no consistency on the main genes responsible for these findings. In both datasets, the testosterone pathway association with HTG was significant (permuted P ≤ 0.011), but again, gene-based analyses showed no consistent driver gene associations. Conclusions Collectively, testosterone metabolism pathway SNPs were consistently associated with the high-tension subtype of POAG in two datasets.
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Affiliation(s)
- Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Mariusz Butkiewicz
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - David A Sullivan
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Robert N Weinreb
- Department of Ophthalmology, Hamilton Glaucoma Center and Shiley Eye Institute, University of California at San Diego, La Jolla, California, United States
| | - Hugues Aschard
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States
| | - Gadi Wollstein
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, New York, United States
| | - Joel S Schuman
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, New York, United States
| | - John H Fingert
- Departments of Ophthalmology and Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City, Iowa, United States
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Tony Realini
- Department of Ophthalmology, WVU Eye Institute, Morgantown, West Virginia, United States
| | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, California, United States
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Lisa Hark
- Wills Eye Hospital, Glaucoma Research Center, Philadelphia, Pennsylvania, United States
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York, United States
| | - Douglas J Rhee
- Department of Ophthalmology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Douglas Vollrath
- Department of Genetics, Stanford University, Palo Alto, California, United States
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, United States
| | - Felipe Medeiros
- Department of Ophthalmology, Hamilton Glaucoma Center and Shiley Eye Institute, University of California at San Diego, La Jolla, California, United States
| | - Thasarat S Vajaranant
- Department of Ophthalmology, University of Illinois College of Medicine at Chicago, Chicago, Illinois, United States
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - William G Christen
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Margaret A Pericak-Vance
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Peter Kraft
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Bernard A Rosner
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Kathryn P Burdon
- School of Medicine, Menzies Research Institute of Tasmania, Hobart, Australia
| | - Alex W Hewitt
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - David A Mackey
- School of Medicine, Menzies Research Institute of Tasmania, Hobart, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - Janey L Wiggs
- Department of Ophthalmology, Mass Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Louis R Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States.,Department of Ophthalmology, Mass Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
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Hou L, Kember RL, Roach JC, O'Connell JR, Craig DW, Bucan M, Scott WK, Pericak-Vance M, Haines JL, Crawford MH, Shuldiner AR, McMahon FJ. Author Correction: A population-specific reference panel empowers genetic studies of Anabaptist populations. Sci Rep 2018; 8:6771. [PMID: 29691419 PMCID: PMC5915589 DOI: 10.1038/s41598-018-24604-8] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Liping Hou
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, 20892, USA.
| | - Rachel L Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jared C Roach
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David W Craig
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William K Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Jonathan L Haines
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Michael H Crawford
- Department of Anthropology, University of Kansas, Lawrence, KS, 66045, USA
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, 20892, USA.
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45
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Stein CM, Sausville L, Wejse C, Sobota RS, Zetola NM, Hill PC, Boom WH, Scott WK, Sirugo G, Williams SM. Genomics of human pulmonary tuberculosis: from genes to pathways. Curr Genet Med Rep 2017; 5:149-166. [PMID: 29805915 DOI: 10.1007/s40142-017-0130-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Purpose of review Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major public health threat globally. Several lines of evidence support a role for host genetic factors in resistance/susceptibility to TB disease and MTB infection. However, results across candidate gene and genome-wide association studies (GWAS) are largely inconsistent, so a cohesive genetic model underlying TB risk has not emerged. Recent Findings Despite the difficulties in identifying consistent genetic associations, genetic studies of TB and MTB infection have revealed a few well-documented loci. These well validated genes are presented in this review, but there remains a large gap in how these genes translate into better understanding of TB. To address this, we present a pathway based extension of standard association analyses, seeding the results with the best validated genes from candidate gene and GWAS studies. Summary Several pathways were significantly enriched using pathway analyses that may help to explain population patterns of TB risk. In conclusion, we advocate for novel approaches to the study of host genetic analysis of TB that extend traditional association approaches.
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Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Cleveland, OH.,Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - Lindsay Sausville
- Department of Population and Quantitative Health Sciences, Cleveland, OH
| | - Christian Wejse
- Dept of Infectious Diseases/Center for Global Health, Aarhus University, Aarhus, Denmark
| | - Rafal S Sobota
- The Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, IL
| | - Nicola M Zetola
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA 19104, USA.,Botswana-UPenn Partnership, Gaborone, Botswana.,Department of Medicine, University of Botswana, Gaborone, Botswana
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - William K Scott
- Department of Human Genetics and Genomics, University of Miami School of Medicine, Miami, FL
| | - Giorgio Sirugo
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Cleveland, OH
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Aschard H, Kang JH, Iglesias AI, Hysi P, Cooke Bailey JN, Khawaja AP, Allingham RR, Ashley-Koch A, Lee RK, Moroi SE, Brilliant MH, Wollstein G, Schuman JS, Fingert JH, Budenz DL, Realini T, Gaasterland T, Scott WK, Singh K, Sit AJ, Igo RP, Song YE, Hark L, Ritch R, Rhee DJ, Gulati V, Haven S, Vollrath D, Zack DJ, Medeiros F, Weinreb RN, Cheng CY, Chasman DI, Christen WG, Pericak-Vance MA, Liu Y, Kraft P, Richards JE, Rosner BA, Hauser MA, Klaver CCW, vanDuijn CM, Haines J, Wiggs JL, Pasquale LR. Genetic correlations between intraocular pressure, blood pressure and primary open-angle glaucoma: a multi-cohort analysis. Eur J Hum Genet 2017; 25:1261-1267. [PMID: 28853718 DOI: 10.1038/ejhg.2017.136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 01/30/2023] Open
Abstract
Primary open-angle glaucoma (POAG) is the most common chronic optic neuropathy worldwide. Epidemiological studies show a robust positive relation between intraocular pressure (IOP) and POAG and modest positive association between IOP and blood pressure (BP), while the relation between BP and POAG is controversial. The International Glaucoma Genetics Consortium (n=27 558), the International Consortium on Blood Pressure (n=69 395), and the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database (n=37 333), represent genome-wide data sets for IOP, BP traits and POAG, respectively. We formed genome-wide significant variant panels for IOP and diastolic BP and found a strong relation with POAG (odds ratio and 95% confidence interval: 1.18 (1.14-1.21), P=1.8 × 10-27) for the former trait but no association for the latter (P=0.93). Next, we used linkage disequilibrium (LD) score regression, to provide genome-wide estimates of correlation between traits without the need for additional phenotyping. We also compared our genome-wide estimate of heritability between IOP and BP to an estimate based solely on direct measures of these traits in the Erasmus Rucphen Family (ERF; n=2519) study using Sequential Oligogenic Linkage Analysis Routines (SOLAR). LD score regression revealed high genetic correlation between IOP and POAG (48.5%, P=2.1 × 10-5); however, genetic correlation between IOP and diastolic BP (P=0.86) and between diastolic BP and POAG (P=0.42) were negligible. Using SOLAR in the ERF study, we confirmed the minimal heritability between IOP and diastolic BP (P=0.63). Overall, IOP shares genetic basis with POAG, whereas BP has limited shared genetic correlation with IOP or POAG.
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Affiliation(s)
- Hugues Aschard
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, MA, USA
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adriana I Iglesias
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pirro Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jessica N Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Anthony P Khawaja
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | | | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Gadi Wollstein
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, NY, USA
| | - Joel S Schuman
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, NY, USA
| | - John H Fingert
- Departments of Ophthalmology and Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City, IO, USA
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, USA
| | - Tony Realini
- Department of Ophthalmology, WVU Eye Institute, Morgantown, WV, USA
| | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, CA, USA
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, CA, USA
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, MN, USA
| | - Robert P Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Lisa Hark
- Wills Eye Hospital, Glaucoma Research Center, Philadelphia, PA, USA
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA
| | - Douglas J Rhee
- Department of Ophthalmology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Vikas Gulati
- Department of Ophthalmology &Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shane Haven
- Department of Ophthalmology &Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, MD, USA
| | - Felipe Medeiros
- Department of Ophthalmology, Hamilton Eye Center, University of California at San Diego, San Diego, CA, USA
| | - Robert N Weinreb
- Department of Ophthalmology, Hamilton Eye Center, University of California at San Diego, San Diego, CA, USA
| | - Ching-Yu Cheng
- Singapore National Eye Centre, Singapore Eye Research Institute, Singapore, Singapore.,Ophthalmology &Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - William G Christen
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Yutao Liu
- Department of Cellular Biology &Anatomy, Augusta University, Augusta, GA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, MA, USA
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Bernard A Rosner
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Caroline C W Klaver
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornelia M vanDuijn
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jonathan Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Louis R Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
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Persad PJ, Heid IM, Weeks DE, Baird PN, de Jong EK, Haines JL, Pericak-Vance MA, Scott WK. Joint Analysis of Nuclear and Mitochondrial Variants in Age-Related Macular Degeneration Identifies Novel Loci TRPM1 and ABHD2/RLBP1. Invest Ophthalmol Vis Sci 2017; 58:4027-4038. [PMID: 28813576 PMCID: PMC5559178 DOI: 10.1167/iovs.17-21734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Purpose Presently, 52 independent nuclear single nucleotide polymorphisms (nSNPs) have been associated with age-related macular degeneration (AMD) but their effects do not explain all its variance. Genetic interactions between the nuclear and mitochondrial (mt) genome may unearth additional genetic loci previously unassociated with AMD risk. Methods Joint effects of nSNPs and selected mtSNPs were analyzed by two degree of freedom (2df) joint tests of association in the International AMD Genomics Consortium (IAMDGC) dataset (17,832 controls and 16,144 advanced AMD cases of European ancestry). Subjects were genotyped on the Illumina HumanCoreExome array. After imputation using MINIMAC and the 1000 Genomes Project Phase I reference panel, pairwise linkage disequilibrium pruning, and quality control, 3.9 million nSNPs were analyzed for interaction with mtSNPs chosen based on association in this dataset or publications: A4917G, T5004C, G12771A, and C16069T. Results Novel locus TRPM1 was identified with genome-wide significant joint effects (P < 5.0 × 10−8) of two intronic TRPM1 nSNPs and AMD-associated nonsynonymous MT-ND2 mtSNP A4917G. Stratified analysis by mt allele identified an association only in 4917A (major allele) carriers (P = 4.4 × 10−9, odds ratio [OR] = 0.90, 95% confidence interval [CI] = 0.87–0.93). Intronic and intergenic ABHD2/RLBP1 nSNPs demonstrated genome-wide significant joint effects (2df joint test P values from 1.8 × 10−8 to 4.9 × 10−8) and nominally statistically significant interaction effects with MT-ND5 synonymous mtSNP G12771A. Although a positive association was detected in both strata, the association was stronger in 12771A subjects (P = 0.0020, OR = 2.17, 95% CI = 1.34–3.60). Conclusions These results show that joint tests of main effects and gene–gene interaction reveal associations at some novel loci that were missed when considering main effects alone.
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Affiliation(s)
- Patrice J Persad
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Daniel E Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States.,Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Paul N Baird
- Centre for Eye Research Australia, Department of Surgery (Ophthalmology) University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
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Sobota RS, Stein CM, Kodaman N, Maro I, Wieland-Alter W, Igo RP, Magohe A, Malone LL, Chervenak K, Hall NB, Matee M, Mayanja-Kizza H, Joloba M, Moore JH, Scott WK, Lahey T, Boom WH, von Reyn CF, Williams SM, Sirugo G. A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa. PLoS Genet 2017. [PMID: 28628665 PMCID: PMC5495514 DOI: 10.1371/journal.pgen.1006710] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an “experiment of nature” design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection. Among these individuals, 244 tested were tuberculin skin test (TST) positive either at enrollment or during the >8 year follow up, while 225 were not. We identified a genome-wide significant association between a dominant model of rs877356 and binary TST status in the combined cohort (Odds ratio = 0.2671, p = 1.22x10-8). Association was replicated with similar significance when examining TST induration as a continuous trait. The variant lies in the 5q31.1 region, 57kb downstream from IL9. Two-locus analyses of association of variants near rs877356 showed a haplotype comprised of rs877356 and an IL9 missense variant, rs2069885, had the most significant association (p = 1.59x10-12). We also replicated previously linked loci on chromosomes 2, 5, and 11. IL9 is a cytokine produced by mast cells and TH2 cells during inflammatory responses, providing a possible link between airway inflammation and protection from MTB infection. Our results indicate that studying uninfected, HIV-positive participants with extensive exposure increases the power to detect associations in complex infectious disease. Approximately one-third of the world’s population has been exposed to Mycobacterium tuberculosis, the bacterium that causes tuberculosis. A small number of those infected develop active disease; however, there is a substantial portion of exposed people who do not even show evidence of an immunological response. These people who appear to resist infection, as measured by a negative tuberculin skin test, represent a subpopulation from which we can learn about resistance. We used a genome-wide approach to study the genetic basis of this resistance in unique cohorts of hypervulnerable, HIV-positive individuals from Uganda and Tanzania, in which exposure was virtually assured. We identified one locus that was highly significantly associated and conferred more than 70% protection from infection. The most significant variant, rs8773656, was near IL9 and SLC25A48, and a haplotype including this variant and a missense mutation in IL9 was even more significantly associated with negative skin tests. Although it is impossible based solely on our data to determine the causal variant or genes, IL9 is an attractive candidate as its product has previously been associated with bronchial hyperresponsiveness, thereby providing a possible link between inflammation and protection from Mycobacterium tuberculosis infection.
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Affiliation(s)
- Rafal S. Sobota
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Catherine M. Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Nuri Kodaman
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Isaac Maro
- Tokyo Medical and Dental University, Tokyo, Japan
| | - Wendy Wieland-Alter
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Albert Magohe
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - LaShaunda L. Malone
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, Ohio, United States of America
- Uganda-CWRU Research Collaboration, Kampala, Uganda
| | - Keith Chervenak
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, Ohio, United States of America
- Uganda-CWRU Research Collaboration, Kampala, Uganda
| | - Noemi B. Hall
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mecky Matee
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Harriet Mayanja-Kizza
- Uganda-CWRU Research Collaboration, Kampala, Uganda
- College of Health Sciences Makerere University and Mulago Hospital, Kampala, Uganda
| | - Moses Joloba
- Uganda-CWRU Research Collaboration, Kampala, Uganda
- College of Health Sciences Makerere University and Mulago Hospital, Kampala, Uganda
| | - Jason H. Moore
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Timothy Lahey
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - W. Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - C. Fordham von Reyn
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Scott M. Williams
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
| | - Giorgio Sirugo
- Centro di Ricerca, Ospedale San Pietro Fatebenefratelli, Rome, Italy
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49
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Yan Q, Ahn SH, Medie FM, Sharma-Kuinkel BK, Park LP, Scott WK, Deshmukh H, Tsalik EL, Cyr DD, Woods CW, Yu CHA, Adams C, Qi R, Hansen B, Fowler VG. Candidate genes on murine chromosome 8 are associated with susceptibility to Staphylococcus aureus infection in mice and are involved with Staphylococcus aureus septicemia in humans. PLoS One 2017; 12:e0179033. [PMID: 28594911 PMCID: PMC5464679 DOI: 10.1371/journal.pone.0179033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/23/2017] [Indexed: 02/06/2023] Open
Abstract
We previously showed that chromosome 8 of A/J mice was associated with susceptibility to S. aureus infection. However, the specific genes responsible for this susceptibility are unknown. Chromosome substitution strain 8 (CSS8) mice, which have chromosome 8 from A/J but an otherwise C57BL/6J genome, were used to identify the genetic determinants of susceptibility to S. aureus on chromosome 8. Quantitative trait loci (QTL) mapping of S. aureus-infected N2 backcross mice (F1 [C8A] × C57BL/6J) identified a locus 83180780–88103009 (GRCm38/mm10) on A/J chromosome 8 that was linked to S. aureus susceptibility. All genes on the QTL (n~ 102) were further analyzed by three different strategies: 1) different expression in susceptible (A/J) and resistant (C57BL/6J) mice only in response to S. aureus, 2) consistently different expression in both uninfected and infected states between the two strains, and 3) damaging non-synonymous SNPs in either strain. Eleven candidate genes from the QTL region were significantly differently expressed in patients with S. aureus infection vs healthy human subjects. Four of these 11 genes also exhibited significantly different expression in S. aureus-challenged human neutrophils: Ier2, Crif1, Cd97 and Lyl1. CD97 ligand binding was evaluated within peritoneal neutrophils from A/J and C57BL/6J. CD97 from A/J had stronger CD55 but weaker integrin α5β1 ligand binding as compared with C57BL/6J. Because CD55/CD97 binding regulates immune cell activation and cytokine production, and integrin α5β1 is a membrane receptor for fibronectin, which is also bound by S. aureus, strain-specific differences could contribute to susceptibility to S. aureus. Down-regulation of Crif1 with siRNA was associated with increased host cell apoptosis among both naïve and S. aureus-infected bone marrow-derived macrophages. Specific genes in A/J chromosome 8, including Cd97 and Crif1, may play important roles in host defense against S. aureus.
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Affiliation(s)
- Qin Yan
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sun Hee Ahn
- Department of Biochemistry School of Dentistry, Chonnam National University, Bukgu, Gwangju, Korea
| | - Felix Mba Medie
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Batu K. Sharma-Kuinkel
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Lawrence P. Park
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - William K. Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Hitesh Deshmukh
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Ephraim L. Tsalik
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Emergency Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
| | - Derek D. Cyr
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
| | - Christopher W. Woods
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
- Section on Infectious Diseases, Durham Veteran’s Affairs Medical Center, Durham, North Carolina, United States of America
| | - Chen-Hsin Albert Yu
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Carlton Adams
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Robert Qi
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Brenda Hansen
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Vance G. Fowler
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
- * E-mail:
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Sardell RJ, Persad PJ, Pan SS, Whitehead P, Adams LD, Laux RA, Fortun JA, Brantley MA, Kovach JL, Schwartz SG, Agarwal A, Haines JL, Scott WK, Pericak-Vance MA. Progression Rate From Intermediate to Advanced Age-Related Macular Degeneration Is Correlated With the Number of Risk Alleles at the CFH Locus. Invest Ophthalmol Vis Sci 2017; 57:6107-6115. [PMID: 27832277 PMCID: PMC5104418 DOI: 10.1167/iovs.16-19519] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Progression rate of age-related macular degeneration (AMD) varies substantially, yet its association with genetic variation has not been widely examined. Methods We tested whether progression rate from intermediate AMD to geographic atrophy (GA) or choroidal neovascularization (CNV) was correlated with genotype at seven single nucleotide polymorphisms (SNPs) in the four genes most strongly associated with risk of advanced AMD. Cox proportional hazards survival models examined the association between progression time and SNP genotype while adjusting for age and sex and accounting for variable follow-up time, right censored data, and repeated measures (left and right eyes). Results Progression rate varied with the number of risk alleles at the CFH:rs10737680 but not the CFH:rs1061170 (Y402H) SNP; individuals with two risk alleles progressed faster than those with one allele (hazard ratio [HR] = 1.61, 95% confidence interval [CI] = 1.08-2.40, P < 0.02, n = 547 eyes), although this was not significant after Bonferroni correction. This signal was likely driven by an association at the correlated protective variant, CFH:rs6677604, which tags the CFHR1-3 deletion; individuals with at least one protective allele progressed more slowly. Considering GA and CNV separately showed that the effect of CFH:rs10737680 was stronger for progression to CNV. Conclusions Results support previous findings that AMD progression rate is influenced by CFH, and suggest that variants within CFH may have different effects on risk versus progression. However, since CFH:rs10737680 was not significant after Bonferroni correction and explained only a relatively small portion of variation in progression rate beyond that explained by age, we suggest that additional factors contribute to progression.
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Affiliation(s)
- Rebecca J Sardell
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Patrice J Persad
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Samuel S Pan
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Patrice Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Reneé A Laux
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Jorge A Fortun
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Milam A Brantley
- Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Jaclyn L Kovach
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Stephen G Schwartz
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Anita Agarwal
- Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
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