Publications by authors named "Charles C White"

62 Publications

Sex-Specific Association of the X Chromosome With Cognitive Change and Tau Pathology in Aging and Alzheimer Disease.

JAMA Neurol 2021 Aug 23. Epub 2021 Aug 23.

Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco.

Importance: The X chromosome represents 5% of the human genome in women and men, and its influence on cognitive aging and Alzheimer disease (AD) is largely unknown.

Objective: To determine whether the X chromosome is associated with sex-specific cognitive change and tau pathology in aging and AD.

Design, Setting, Participants: This study examined differential gene expression profiling of the X chromosome from an RNA sequencing data set of the dorsolateral prefrontal cortex obtained from autopsied, elderly individuals enrolled in the Religious Orders Study and Rush Memory and Aging Project joint cohorts. Samples were collected from the cohort study with enrollment from 1994 to 2017. Data were last analyzed in May 2021.

Main Outcomes And Measures: The main analysis examined whether X chromosome gene expression measured by RNA sequencing of the dorsolateral prefrontal cortex was associated with cognitive change during aging and AD, independent of AD pathology and at the transcriptome-wide level in women and men. Whether X chromosome gene expression was associated with neurofibrillary tangle burden, a measure of tau pathology that influences cognition, in women and men was also explored.

Results: Samples for RNA sequencing of the dorsolateral prefrontal cortex were obtained from 508 individuals (mean [SD] age at death, 88.4 [6.6] years; 315 [62.0%] were female; 197 [38.8%] had clinical diagnosis of AD at death; 293 [58.2%] had pathological diagnosis of AD at death) enrolled in the Religious Orders Study and Rush Memory and Aging Project joint cohorts and were followed up annually for a mean (SD) of 6.3 (3.9) years. X chromosome gene expression (29 genes), adjusted for age at death, education, and AD pathology, was significantly associated with cognitive change at the genome-wide level in women but not men. In the majority of identified X genes (19 genes), increased expression was associated with slower cognitive decline in women. In contrast with cognition, X chromosome gene expression (3 genes), adjusted for age at death and education, was associated with neuropathological tau burden at the genome-wide level in men but not women.

Conclusions And Relevance: In this study, the X chromosome was associated with cognitive trajectories and neuropathological tau burden in aging and AD in a sex-specific manner. This is important because specific X chromosome factors could contribute risk or resilience to biological pathways of aging and AD in women, men, or both.
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http://dx.doi.org/10.1001/jamaneurol.2021.2806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8383157PMC
August 2021

Effects of the Obesity Epidemic on Total Hip and Knee Arthroplasty Demographics.

J Arthroplasty 2021 Sep 22;36(9):3097-3100. Epub 2021 Apr 22.

Department of Orthopaedics, Medical University of South Carolina, Charleston, SC.

Background: Higher body mass index (BMI) is a well-known risk factor for the development of hip and knee osteoarthritis and predicts total hip arthroplasty (THA) and total knee arthroplasty (TKA) at an earlier age. The purpose of this study is to document the nationwide trends in age and obesity in primary THA and TKA throughout the obesity epidemic.

Methods: A retrospective analysis of the National Inpatient Sample database was conducted on patients undergoing primary THA and TKA for primary OA between 2002 and 2017. Analysis of variance and chi-square tests were performed to examine changes in age and obesity percentage over time, respectively. Pearson correlations were used to assess the relationship between patient age, BMI, and year of surgery.

Results: A total of 688,371 THA and 1,556,651 TKA were identified over the sixteen-year period. Between 2002 and 2017, the proportion of obese patients increased for both THA (7.0% to 22.7%, P < .001) and TKA (10.7% to 30.4%, P < .001). Mean age significantly decreased for both THA (66.7 to 65.9 years, P < .001) and TKA (67.6 to 66.8 years; P < .001). Over time, BMI significantly increased (THA: r = 0.221 vs. TKA: r = 0.272) and patient age decreased (THA: r = -0.031 vs. TKA: r = -0.137) for both procedures (P < .001 for all).

Conclusion: THA and TKA patients have become younger and increasingly more obese throughout the obesity epidemic, as obesity rates have tripled over this time period. The current investigation is the first to demonstrate significant trends in both age and obesity in the THA and TKA populations on a national level.

Level Of Evidence: III.
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http://dx.doi.org/10.1016/j.arth.2021.04.017DOI Listing
September 2021

Neuroticism alters the transcriptome of the frontal cortex to contribute to the cognitive decline and onset of Alzheimer's disease.

Transl Psychiatry 2021 02 24;11(1):139. Epub 2021 Feb 24.

Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA.

Accumulating evidence has suggested that the molecular transcriptional mechanism contributes to Alzheimer's disease (AD) and its endophenotypes of cognitive decline and neuropathological traits, β-amyloid (Aβ) and phosphorylated tangles (TAU). However, it is unknown what is the impact of the AD risk factors, personality characteristics assessed by the NEO Five-Factor Inventory, on the human brain's transcriptome. Using postmortem human brain samples from 466 subjects, we found that neuroticism has a significant overall impact on the brain transcriptome (omnibus P = 0.005) but not the other four personality characteristics. Focused on those cognitive decline related gene co-expressed modules, neuroticism has nominally significant associations (P < 0.05) with four neuronal modules, which are more related to PHFtau than Aβ across all eight brain regions. Furthermore, the effect of neuroticism on cognitive decline and AD might be mediated through the expression of module 7 and TAU pathology (P = 0.008). To conclude, neuroticism has a broad impact on the transcriptome of human brains, and its effect on cognitive decline and AD may be mediated through gene transcription programs related to TAU pathology.
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http://dx.doi.org/10.1038/s41398-021-01253-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904919PMC
February 2021

A cortical immune network map identifies distinct microglial transcriptional programs associated with β-amyloid and Tau pathologies.

Transl Psychiatry 2021 01 14;11(1):50. Epub 2021 Jan 14.

Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA.

Microglial dysfunction has been proposed as one of the many cellular mechanisms that can contribute to the development of Alzheimer's disease (AD). Here, using a transcriptional network map of the human frontal cortex, we identify five modules of co-expressed genes related to microglia and assess their role in the neuropathologic features of AD in 540 subjects from two cohort studies of brain aging. Two of these transcriptional programs-modules 113 and 114-relate to the accumulation of β-amyloid, while module 5 relates to tau pathology. We replicate these associations in brain epigenomic data and in two independent datasets. In terms of tau, we propose that module 5, a marker of activated microglia, may lead to tau accumulation and subsequent cognitive decline. We validate our model further by showing that three representative module 5 genes (ACADVL, TRABD, and VASP) encode proteins that are upregulated in activated microglia in AD.
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http://dx.doi.org/10.1038/s41398-020-01175-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7809035PMC
January 2021

Cross-Species Analyses Identify Dlgap2 as a Regulator of Age-Related Cognitive Decline and Alzheimer's Dementia.

Cell Rep 2020 09;32(9):108091

The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, ME 04469, USA. Electronic address:

Genetic mechanisms underlying age-related cognitive decline and dementia remain poorly understood. Here, we take advantage of the Diversity Outbred mouse population to utilize quantitative trait loci mapping and identify Dlgap2 as a positional candidate responsible for modifying working memory decline. To evaluate the translational relevance of this finding, we utilize longitudinal cognitive measures from human patients, RNA expression from post-mortem brain tissue, data from a genome-wide association study (GWAS) of Alzheimer's dementia (AD), and GWAS results in African Americans. We find an association between Dlgap2 and AD phenotypes at the variant, gene and protein expression, and methylation levels. Lower cortical DLGAP2 expression is observed in AD and is associated with more plaques and tangles at autopsy and faster cognitive decline. Results will inform future studies aimed at investigating the cross-species role of Dlgap2 in regulating cognitive decline and highlight the benefit of using genetically diverse mice to prioritize novel candidates.
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http://dx.doi.org/10.1016/j.celrep.2020.108091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7502175PMC
September 2020

A second X chromosome contributes to resilience in a mouse model of Alzheimer's disease.

Sci Transl Med 2020 08;12(558)

Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.

A major sex difference in Alzheimer's disease (AD) is that men with the disease die earlier than do women. In aging and preclinical AD, men also show more cognitive deficits. Here, we show that the X chromosome affects AD-related vulnerability in mice expressing the human amyloid precursor protein (hAPP), a model of AD. XY-hAPP mice genetically modified to develop testicles or ovaries showed worse mortality and deficits than did XX-hAPP mice with either gonad, indicating a sex chromosome effect. To dissect whether the absence of a second X chromosome or the presence of a Y chromosome conferred a disadvantage on male mice, we varied sex chromosome dosage. With or without a Y chromosome, hAPP mice with one X chromosome showed worse mortality and deficits than did those with two X chromosomes. Thus, adding a second X chromosome conferred resilience to XY males and XO females. In addition, the Y chromosome, its sex-determining region Y gene (), or testicular development modified mortality in hAPP mice with one X chromosome such that XY males with testicles survived longer than did XY or XO females with ovaries. Furthermore, a second X chromosome conferred resilience potentially through the candidate gene , which does not undergo X-linked inactivation. In humans, genetic variation in was linked to higher brain expression and associated with less cognitive decline in aging and preclinical AD, suggesting its relevance to human brain health. Our study suggests a potential role for sex chromosomes in modulating disease vulnerability related to AD.
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http://dx.doi.org/10.1126/scitranslmed.aaz5677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8409261PMC
August 2020

Association of social network structure and physical function in patients with multiple sclerosis.

Neurology 2020 09 7;95(11):e1565-e1574. Epub 2020 Aug 7.

From the Multiple Sclerosis Center and the Center for Translational & Computational Neuroimmunology, Department of Neurology (S.N.L., C.S.R., C.N., L.S., K.O., V.M.L., L.L., R.S.F., W.S.V., P.L.D.J.), and The Taub Institute for Alzheimer's Disease Research (P.L.D.J.), Columbia University Irving Medical Center, New York, NY; Department of Neurology (A.D.), Brigham and Women's Hospital, Harvard Medical School; Network Science Institute (A.D.), Northeastern University, Boston; Broad Institute (C.C.W., Z.X., P.L.D.J.), Cell Circuits Program, Cambridge, MA; and Department of Neurology (S.V., B.B., R.H., Z.X.), University of Pittsburgh, PA.

Objective: To test the association between physical function and the social environment in multiple sclerosis (MS), we quantified personal social networks.

Methods: In this cross-sectional study, we analyzed data from 2 academic MS centers, with center 1 serving as a discovery group and center 2 as the extension group. We performed a meta-analysis of the centers to extend the analysis. We used responses from a questionnaire to map the structure and health habits of participants' social networks as well as the NIH Patient-Reported Outcomes Measurement Information System (PROMIS) physical function scale (0-100, mean 50 for US general population) as the primary outcome. We applied multivariable models to test the association between network metrics and physical function.

Results: The discovery cohort included 263 patients with MS: 81% were women, 96% non-Hispanic European, 78% had relapsing MS, average age was 50 (12.4) years, and mean disease duration was 17 (12.3) years. The extension group included 163 patients, who were younger, more racially diverse, and less physically disabled, and had shorter disease duration. In the meta-analysis, higher network constraint, a measure of tightly bound networks, was associated with worse physical function (β = -0.163 ± 0.047, < 0.001), while larger network effective size, a measure of clustered groups in the network, correlated with better physical function (β = 0.134 ± 0.046, = 0.003).

Conclusions: Our study highlights personal networks as an important environmental factor associated with physical function in MS. Patients with close-knit networks had worse function than those with more open networks. Longitudinal studies are warranted to evaluate a causal relationship between network structure and physical impairment.
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http://dx.doi.org/10.1212/WNL.0000000000010460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7713741PMC
September 2020

Genetics of Gene Expression in the Aging Human Brain Reveal TDP-43 Proteinopathy Pathophysiology.

Neuron 2020 08 10;107(3):496-508.e6. Epub 2020 Jun 10.

The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA. Electronic address:

Here, we perform a genome-wide screen for variants that regulate the expression of gene co-expression modules in the aging human brain; we discover and replicate such variants in the TMEM106B and RBFOX1 loci. The TMEM106B haplotype is known to influence the accumulation of TAR DNA-binding protein 43 kDa (TDP-43) proteinopathy, and the haplotype's large-scale transcriptomic effects include the dysregulation of lysosomal genes and alterations in synaptic gene splicing that are also seen in the pathophysiology of TDP-43 proteinopathy. Further, a variant near GRN, another TDP-43 proteinopathy susceptibility gene, shows concordant effects with the TMEM106B haplotype. Leveraging neuropathology data from the same participants, we also show that TMEM106B and APOE-amyloid-β effects converge to alter myelination and lysosomal gene expression, which then contributes to TDP-43 accumulation. These results advance our mechanistic understanding of the TMEM106B TDP-43 risk haplotype and uncover a transcriptional program that mediates the converging effects of APOE-amyloid-β and TMEM106B on TDP-43 aggregation in older adults.
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http://dx.doi.org/10.1016/j.neuron.2020.05.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7416464PMC
August 2020

Genetic architecture of subcortical brain structures in 38,851 individuals.

Nat Genet 2019 11 21;51(11):1624-1636. Epub 2019 Oct 21.

Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.

Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease.
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http://dx.doi.org/10.1038/s41588-019-0511-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055269PMC
November 2019

CpG-related SNPs in the MS4A region have a dose-dependent effect on risk of late-onset Alzheimer disease.

Aging Cell 2019 08 29;18(4):e12964. Epub 2019 May 29.

Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.

CpG-related single nucleotide polymorphisms (CGS) have the potential to perturb DNA methylation; however, their effects on Alzheimer disease (AD) risk have not been evaluated systematically. We conducted a genome-wide association study using a sliding-window approach to measure the combined effects of CGSes on AD risk in a discovery sample of 24 European ancestry cohorts (12,181 cases, 12,601 controls) from the Alzheimer's Disease Genetics Consortium (ADGC) and replication sample of seven European ancestry cohorts (7,554 cases, 27,382 controls) from the International Genomics of Alzheimer's Project (IGAP). The potential functional relevance of significant associations was evaluated by analysis of methylation and expression levels in brain tissue of the Religious Orders Study and the Rush Memory and Aging Project (ROSMAP), and in whole blood of Framingham Heart Study participants (FHS). Genome-wide significant (p < 5 × 10 ) associations were identified with 171 1.0 kb-length windows spanning 932 kb in the APOE region (top p < 2.2 × 10 ), five windows at BIN1 (top p = 1.3 × 10 ), two windows at MS4A6A (top p = 2.7 × 10 ), two windows near MS4A4A (top p = 6.4 × 10 ), and one window at PICALM (p = 6.3 × 10 ). The total number of CGS-derived CpG dinucleotides in the window near MS4A4A was associated with AD risk (p = 2.67 × 10 ), brain DNA methylation (p = 2.15 × 10 ), and gene expression in brain (p = 0.03) and blood (p = 2.53 × 10 ). Pathway analysis of the genes responsive to changes in the methylation quantitative trait locus signal at MS4A4A (cg14750746) showed an enrichment of methyltransferase functions. We confirm the importance of CGS in AD and the potential for creating a functional CpG dosage-derived genetic score to predict AD risk.
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http://dx.doi.org/10.1111/acel.12964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612647PMC
August 2019

An UNC5C Allele Predicts Cognitive Decline and Hippocampal Atrophy in Clinically Normal Older Adults.

J Alzheimers Dis 2019 ;68(3):1161-1170

Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.

Background: The UNC5C rs3846455G allele has been linked to poor cognitive resilience against age-related neuropathologies, but this association remains to be replicated, and the allele's effect on hippocampal neurodegeneration needs to be examined.

Objective: To further validate the association between rs3846455G and faster cognitive decline, especially among cognitively normal older adults, and to assess whether rs3846455G predicts accelerated hippocampal volume loss in older adults.

Methods: We assessed participants in the Harvard Aging Brain Study (HABS), a longitudinal cohort study of older adults who were clinically normal at baseline. To avoid bias from population admixture, analyses were limited to participants of European descent with longitudinal neuroimaging data (n = 174). Linear mixed effect models were used to examine the effect of rs3846455G on longitudinal change of the Preclinical Alzheimer Cognitive Composite (PACC) and MRI-measured bilateral hippocampal volume, adjusting for baseline amyloid-β (Aβ) measured by the cortical Pittsburgh Compound B PET distributed volume ratio. We also tested whether hippocampal atrophy mediates the association between rs3846455G and greater PACC decline through a mediation analysis.

Results: rs3846455G was associated with greater PACC decline (β= -0.087/year, 95% CI -0.169 to -0.005, p = 0.039) after controlling for baseline Aβ. Further, rs3846455G predicted accelerated hippocampal atrophy after controlling for baseline Aβ (β= -57.3 mm3/year, 95% CI -102.8 to -11.9, p = 0.014). The association between rs3846455G and greater PACC decline was partially mediated by accelerated hippocampal atrophy (mediated effect (relative scale) = -0.014, 95% CI -0.032 to -6.0×10-4, p = 0.039).

Conclusion: UNC5C rs3846455G predicts greater cognitive decline and accelerated hippocampal atrophy in clinically normal older adults.
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http://dx.doi.org/10.3233/JAD-180788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6571137PMC
August 2020

Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing.

Nat Genet 2019 03 28;51(3):414-430. Epub 2019 Feb 28.

Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades-Universitat Internacional de Catalunya, Barcelona, Spain.

Risk for late-onset Alzheimer's disease (LOAD), the most prevalent dementia, is partially driven by genetics. To identify LOAD risk loci, we performed a large genome-wide association meta-analysis of clinically diagnosed LOAD (94,437 individuals). We confirm 20 previous LOAD risk loci and identify five new genome-wide loci (IQCK, ACE, ADAM10, ADAMTS1, and WWOX), two of which (ADAM10, ACE) were identified in a recent genome-wide association (GWAS)-by-familial-proxy of Alzheimer's or dementia. Fine-mapping of the human leukocyte antigen (HLA) region confirms the neurological and immune-mediated disease haplotype HLA-DR15 as a risk factor for LOAD. Pathway analysis implicates immunity, lipid metabolism, tau binding proteins, and amyloid precursor protein (APP) metabolism, showing that genetic variants affecting APP and Aβ processing are associated not only with early-onset autosomal dominant Alzheimer's disease but also with LOAD. Analyses of risk genes and pathways show enrichment for rare variants (P = 1.32 × 10), indicating that additional rare variants remain to be identified. We also identify important genetic correlations between LOAD and traits such as family history of dementia and education.
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http://dx.doi.org/10.1038/s41588-019-0358-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463297PMC
March 2019

A scalable online tool for quantitative social network assessment reveals potentially modifiable social environmental risks.

Nat Commun 2018 09 26;9(1):3930. Epub 2018 Sep 26.

Broad Institute, Program in Medical and Population Genetics, Cambridge, 02142, MA, USA.

Social networks are conduits of support, information, and health behavior flows. Existing measures of social networks used in clinical research are typically summative scales of social support or artificially truncated networks of ≤ 5 people. Here, we introduce a quantitative social network assessment tool on a secure open-source web platform, readily deployable in large-scale clinical studies. The tool maps an individual's personal network, including specific persons, their relationships to each other, and their health habits. To demonstrate utility, we used the tool to measure the social networks of 1493 persons at risk of multiple sclerosis. We examined each person's social network in relation to self-reported neurological disability. We found that the characteristics of persons surrounding the participant, such as negative health behaviors, were strongly associated with the individual's functional disability. This quantitative assessment reveals the key elements of individuals' social environments that could be targeted in clinical trials.
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http://dx.doi.org/10.1038/s41467-018-06408-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158181PMC
September 2018

Evaluation of TDP-43 proteinopathy and hippocampal sclerosis in relation to APOE ε4 haplotype status: a community-based cohort study.

Lancet Neurol 2018 09 6;17(9):773-781. Epub 2018 Aug 6.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA. Electronic address:

Background: Transactive response DNA-binding protein of 43 kDa (TDP-43) proteinopathy in older adults frequently coexists with Alzheimer's disease pathology and hippocampal sclerosis. It is unclear whether there is a link between APOE ε4 and TDP-43 proteinopathy, and the role of APOE ε4 in the association of TDP-43 proteinopathy with hippocampal sclerosis remains to be examined. We investigated the relationships of TDP-43 proteinopathy and hippocampal sclerosis with APOE ε4.

Methods: We used data from two community-based cohort studies of ageing and dementia: the Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP). A battery of cognitive tests examining multiple cognitive domains is given to ROS-MAP participants each year, and a measure of annual global cognitive function for each participant is derived by averaging Z scores of these tests. The final clinical diagnosis is assigned after death by a neurologist using all available clinical data without access to post-mortem pathology. Amyloid-β, paired helical filament tau, Lewy bodies, TDP-43, and hippocampal sclerosis were microscopically evaluated in the midbrain, medial temporal, and neocortical regions that capture the progression of each neuropathology. TDP-43 proteinopathy topographic stage was recorded as an ordinal variable, and TDP-43 burden was defined by averaging a semi-quantitative six-point scale across six brain regions. The relationships among APOE ε4, TDP-43 proteinopathy, and hippocampal sclerosis were tested with regression models controlled for sex and age at death, and they were further explored with a mediation analysis using the quasi-Bayesian Monte Carlo method.

Findings: ROS began data collection in 1994, and MAP began data collection in 1997. The data included in this study were analysed from Jan 16, 2017, to July 12, 2017. When analysis began in January, 2017, a total of 1059 ROS-MAP participants who were deceased had APOE genotype and complete pathological measures for amyloid-β, paired helical filament tau, and TDP-43 proteinopathy stage. After excluding 15 participants with other pathological diagnoses, 1044 participants, 1042 of whom also had measures of Lewy body pathology, were included in this study (470 from ROS and 574 from MAP). APOE ε4 count was associated with higher TDP-43 proteinopathy stage (odds ratio [OR] 2·0, 95% CI 1·6-2·6; p=1·9 × 10) and TDP-43 burden (0·40, 0·28-0·52; p=1·2 × 10). Amyloid-β, paired helical filament tau, or Lewy body pathology did not fully explain this association. APOE ε4 increased the odds of hippocampal sclerosis (OR 2·1, 95% CI 1·4-3·0; p=1·7 × 10); this effect was largely mediated by TDP-43 burden (mediated effect p<1·0 × 10) but not directly by APOE ε4 (direct effect p=0·40). APOE ε4 was associated with worse global cognition proximate to death even after adjusting for amyloid-β and paired helical filament tau (estimated effect -0·18, 95% CI -0·31 to -0·04; p=0·010), but this association was attenuated by additionally adjusting for TDP-43 burden (-0·09, -0·22 to 0·04; p=0·18).

Interpretation: APOE ε4 seems to increase TDP-43 burden, and this effect in turn was associated with higher odds of hippocampal sclerosis, a pathology potentially downstream of TDP-43 proteinopathy. TDP-43 proteinopathy contributes to the detrimental effect of APOE ε4 on late-life cognition through mechanisms independent of Alzheimer's disease pathology, and future research should consider that TDP-43 proteinopathy might be an integral component of APOE-related neurodegeneration.

Funding: US National Institute on Aging and Alzheimer's Association.
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http://dx.doi.org/10.1016/S1474-4422(18)30251-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6154505PMC
September 2018

A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research.

Sci Data 2018 08 7;5:180142. Epub 2018 Aug 7.

Rush Alzehimer Disease Center, RUSH University, 600 South Paulina Street, Chicago IL 60612, USA.

We initiated the systematic profiling of the dorsolateral prefrontal cortex obtained from a subset of autopsied individuals enrolled in the Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP), which are jointly designed prospective studies of aging and dementia with detailed, longitudinal cognitive phenotyping during life and a quantitative, structured neuropathologic examination after death. They include over 3,322 subjects. Here, we outline the first generation of data including genome-wide genotypes (n=2,090), whole genome sequencing (n=1,179), DNA methylation (n=740), chromatin immunoprecipitation with sequencing using an anti-Histone 3 Lysine 9 acetylation (H3K9Ac) antibody (n=712), RNA sequencing (n=638), and miRNA profile (n=702). Generation of other omic data including ATACseq, proteomic and metabolomics profiles is ongoing. Thanks to its prospective design and recruitment of older, non-demented individuals, these data can be repurposed to investigate a large number of syndromic and quantitative neuroscience phenotypes. The many subjects that are cognitively non-impaired at death also offer insights into the biology of the human brain in older non-impaired individuals.
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http://dx.doi.org/10.1038/sdata.2018.142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6080491PMC
August 2018

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease.

Nat Neurosci 2018 06 25;21(6):811-819. Epub 2018 May 25.

Broad Institute, Cambridge, MA, USA.

There is a need for new therapeutic targets with which to prevent Alzheimer's disease (AD), a major contributor to aging-related cognitive decline. Here we report the construction and validation of a molecular network of the aging human frontal cortex. Using RNA sequence data from 478 individuals, we first build a molecular network using modules of coexpressed genes and then relate these modules to AD and its neuropathologic and cognitive endophenotypes. We confirm these associations in two independent AD datasets. We also illustrate the use of the network in prioritizing amyloid- and cognition-associated genes for in vitro validation in human neurons and astrocytes. These analyses based on unique cohorts enable us to resolve the role of distinct cortical modules that have a direct effect on the accumulation of AD pathology from those that have a direct effect on cognitive decline, exemplifying a network approach to complex diseases.
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http://dx.doi.org/10.1038/s41593-018-0154-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599633PMC
June 2018

A Bayesian Framework for Generalized Linear Mixed Modeling Identifies New Candidate Loci for Late-Onset Alzheimer's Disease.

Genetics 2018 05 5;209(1):51-64. Epub 2018 Mar 5.

The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609

Recent technical and methodological advances have greatly enhanced genome-wide association studies (GWAS). The advent of low-cost, whole-genome sequencing facilitates high-resolution variant identification, and the development of linear mixed models (LMM) allows improved identification of putatively causal variants. While essential for correcting false positive associations due to sample relatedness and population stratification, LMMs have commonly been restricted to quantitative variables. However, phenotypic traits in association studies are often categorical, coded as binary case-control or ordered variables describing disease stages. To address these issues, we have devised a method for genomic association studies that implements a generalized LMM (GLMM) in a Bayesian framework, called Bayes-GLMM has four major features: (1) support of categorical, binary, and quantitative variables; (2) cohesive integration of previous GWAS results for related traits; (3) correction for sample relatedness by mixed modeling; and (4) model estimation by both Markov chain Monte Carlo sampling and maximal likelihood estimation. We applied Bayes-GLMM to the whole-genome sequencing cohort of the Alzheimer's Disease Sequencing Project. This study contains 570 individuals from 111 families, each with Alzheimer's disease diagnosed at one of four confidence levels. Using Bayes-GLMM we identified four variants in three loci significantly associated with Alzheimer's disease. Two variants, rs140233081 and rs149372995, lie between and The coded proteins are localized to the glial-vascular unit, and transcript levels are associated with Alzheimer's disease-related neuropathology. In summary, this work provides implementation of a flexible, generalized mixed-model approach in a Bayesian framework for association studies.
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http://dx.doi.org/10.1534/genetics.117.300673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937180PMC
May 2018

A transcriptomic atlas of aged human microglia.

Nat Commun 2018 02 7;9(1):539. Epub 2018 Feb 7.

Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York City, NY, 10032, USA.

With a rapidly aging global human population, finding a cure for late onset neurodegenerative diseases has become an urgent enterprise. However, these efforts are hindered by the lack of understanding of what constitutes the phenotype of aged human microglia-the cell type that has been strongly implicated by genetic studies in the pathogenesis of age-related neurodegenerative disease. Here, we establish the set of genes that is preferentially expressed by microglia in the aged human brain. This HuMi_Aged gene set captures a unique phenotype, which we confirm at the protein level. Furthermore, we find this gene set to be enriched in susceptibility genes for Alzheimer's disease and multiple sclerosis, to be increased with advancing age, and to be reduced by the protective APOEε2 haplotype. APOEε4 has no effect. These findings confirm the existence of an aging-related microglial phenotype in the aged human brain and its involvement in the pathological processes associated with brain aging.
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http://dx.doi.org/10.1038/s41467-018-02926-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803269PMC
February 2018

A human microglia-like cellular model for assessing the effects of neurodegenerative disease gene variants.

Sci Transl Med 2017 Dec;9(421)

Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.

Microglia are emerging as a key cell type in neurodegenerative diseases, yet human microglia are challenging to study in vitro. We developed an in vitro cell model system composed of human monocyte-derived microglia-like (MDMi) cells that recapitulated key aspects of microglia phenotype and function. We then used this model system to perform an expression quantitative trait locus (eQTL) study examining 94 genes from loci associated with Alzheimer's disease, Parkinson's disease, and multiple sclerosis. We found six loci (, , , , , and ) in which the risk haplotype drives the association with both disease susceptibility and altered expression of a nearby gene (cis-eQTL). In the and loci, the cis-eQTL was found in the MDMi cells but not in human peripheral blood monocytes, suggesting that differentiation of monocytes into microglia-like cells led to the acquisition of a cellular state that could reveal the functional consequences of certain genetic variants. We further validated the effect of risk haplotypes at the protein level for and , and we confirmed that the risk haplotype altered phagocytosis by the MDMi cells. We propose that increased gene expression by MDMi cells could be a functional outcome of , a single-nucleotide polymorphism in the locus that is associated with Parkinson's disease.
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http://dx.doi.org/10.1126/scitranslmed.aai7635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945290PMC
December 2017

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome.

Nat Neurosci 2017 Oct 4;20(10):1418-1426. Epub 2017 Sep 4.

Broad Institute, Cambridge, Massachusetts, USA.

We report a multi-omic resource generated by applying quantitative trait locus (xQTL) analyses to RNA sequence, DNA methylation and histone acetylation data from the dorsolateral prefrontal cortex of 411 older adults who have all three data types. We identify SNPs significantly associated with gene expression, DNA methylation and histone modification levels. Many of these SNPs influence multiple molecular features, and we demonstrate that SNP effects on RNA expression are fully mediated by epigenetic features in 9% of these loci. Further, we illustrate the utility of our new resource, xQTL Serve, by using it to prioritize the cell type(s) most affected by an xQTL. We also reanalyze published genome wide association studies using an xQTL-weighted analysis approach and identify 18 new schizophrenia and 2 new bipolar susceptibility variants, which is more than double the number of loci that can be discovered with a larger blood-based expression eQTL resource.
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http://dx.doi.org/10.1038/nn.4632DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5785926PMC
October 2017

variants are associated with cerebral amyloid angiopathy.

Neurol Genet 2017 Aug 18;3(4):e176. Epub 2017 Jul 18.

Departments of Neurology and Psychiatry (H.-S.Y., C.C.W., H.-U.K., P.L.D.J.), Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences; Department of Neurology (H.-S.Y.), Center for Alzheimer Research and Treatment, Brigham and Women's Hospital; Harvard Medical School (H.-S.Y., H.-U.K.); Harvard T.H. Chan School of Public Health (L.B.C.), Boston; Program in Medical and Population Genetics (H.-S.Y., C.C.W., L.B.C., H.-U.K., P.L.D.J.), Broad Institute, Cambridge, MA; Rush Alzheimer's Disease Center (J.A.S., D.A.B.) and Department of Neurological Sciences (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL; and Department of Neurology (P.L.D.J.), Center for Translational & Systems Neuroimmunology, Columbia University Medical Center, New York, NY.

Objective: To determine whether common genetic variants in , a recently identified late-onset Alzheimer disease (LOAD) dementia susceptibility gene, are associated with AD susceptibility or AD-related clinical/pathologic phenotypes.

Methods: We used data from deceased individuals of European descent who participated in the Religious Orders Study or the Rush Memory and Aging Project (n = 1,288). We examined whether there were associations between single nucleotide polymorphisms (SNPs) within ±100 kb of the gene and a diagnosis of AD dementia, global cognitive decline, a pathologic diagnosis of AD, β-amyloid load, neuritic plaque count, diffuse plaque count, paired helical filament tau density, neurofibrillary tangle count, and cerebral amyloid angiopathy (CAA) score. We also evaluated the relation of the CAA-associated variant and dorsolateral prefrontal cortex (DLPFC) RNA expression. Secondary analyses were performed to examine the interaction of the CAA-associated SNP and known genetic risk factors of CAA as well as the association of the SNP with other cerebrovascular pathologies.

Results: A set of SNPs tagged by rs28660566 was associated with a higher CAA score ( = 2.3 × 10): each additional rs28660566 allele was associated with a 0.60 point higher CAA score, which is equivalent to approximately 75% of the higher CAA score associated with each allele of ε4. rs28660566 was weakly associated with lower expression in the human DLPFC ( = 0.036). Moreover, rs28660566 had a synergistic interaction with ε4 on their association with higher CAA severity ( = 0.027) and was associated with more severe arteriolosclerosis ( = 0.0065).

Conclusions: Targeted analysis of the region uncovered a set of SNPs associated with CAA.
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http://dx.doi.org/10.1212/NXG.0000000000000176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515600PMC
August 2017

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease.

Nat Genet 2017 09 17;49(9):1373-1384. Epub 2017 Jul 17.

Boston University School of Medicine, Boston, Massachusetts, USA.

We identified rare coding variants associated with Alzheimer's disease in a three-stage case-control study of 85,133 subjects. In stage 1, we genotyped 34,174 samples using a whole-exome microarray. In stage 2, we tested associated variants (P < 1 × 10) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, we used an additional 14,997 samples to test the most significant stage 2 associations (P < 5 × 10) using imputed genotypes. We observed three new genome-wide significant nonsynonymous variants associated with Alzheimer's disease: a protective variant in PLCG2 (rs72824905: p.Pro522Arg, P = 5.38 × 10, odds ratio (OR) = 0.68, minor allele frequency (MAF) = 0.0059, MAF = 0.0093), a risk variant in ABI3 (rs616338: p.Ser209Phe, P = 4.56 × 10, OR = 1.43, MAF = 0.011, MAF = 0.008), and a new genome-wide significant variant in TREM2 (rs143332484: p.Arg62His, P = 1.55 × 10, OR = 1.67, MAF = 0.0143, MAF = 0.0089), a known susceptibility gene for Alzheimer's disease. These protein-altering changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified risk genes in Alzheimer's disease. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to the development of Alzheimer's disease.
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http://dx.doi.org/10.1038/ng.3916DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669039PMC
September 2017

Loss of Cardioprotective Effects at the Locus as a Result of Gene-Smoking Interactions.

Circulation 2017 Jun 1;135(24):2336-2353. Epub 2017 May 1.

From Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia (D.S., W.Z.); Center for Non-Communicable Diseases, Karachi, Pakistan (D.S., A.R., P.M.F., PROMIS); Department of Public Health and Primary Care, University of Cambridge, United Kingdom (R.Y., W.K.H., EPIC-CVD); Department of Cardiovascular Sciences, University of Leicester, United Kingdom (C.P.N., N.J.S.); Cardiology Division, Department of Medicine, Vanderbilt University, Nashville, TN (J.F.F., K.O.); Division of Cardiovascular Medicine, Radcliffe Department of Medicine & Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom (A.G., M.F.); The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY (R.D.); Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY (R.D.); Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Canada (A.F.R.S., R.M.); Institute for Genetic Medicine and Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles (J.H., H.A.); Department of Epidemiology and Biostatistics, Imperial College London, United Kingdom (W.Z., J.C.C., J.K.); Department of Cardiology, Ealing Hospital NHS Trust, Middlesex, United Kingdom (W.Z., J.C.C.); Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden (R.J.S.); Helsinki University Central Hospital HUCH Heart and Lung Center, Helsinki, Uusimaa, Finland (J.S.); Cardiology Division, Department of Medicine and the Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY (R.C.B., M.P.R.); William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (S.K., E.M., P.D.); Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands (S.S., A.D.); Department of Dietetics-Nutrition, Harokopio University, Athens, Greece (E.M., G.D.); National Institute for Health and Welfare, Helsinki, Finland (K.K., A.J., V.S., K.K., M.P.); MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, United Kingdom (J.H.Z., R.S.); INSERM, UMRS1138, Centre de Recherche des Cordeliers, Paris, France (D.G., N.W.); Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC (S.H.S.); Icelandic Heart Association, Kopavogur, Iceland (A.V.S., V.G.); Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, United Kingdom (N.v.Z., C.N.A.P.); Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC (A.J.C., D.W.B.); Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Germany (C.W., J.E.); DZHK (German Research Center for Cardiovascular Research) partner site Hamburg-Lübeck-Kiel, Germany (C.W., J.E.); Deutsches Herzzentrum München, Technische Universität München, Germany (T.K., L.Z., H.S.); Klinikum rechts der Isar, München, Germany (T.K.); DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Germany (L.Z., H.S.); Department of Genetics, Washington University School of Medicine, St. Louis, MO (M.A.P., M.F.F.); Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston (A.G.); Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA (A.G.); Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Sweden (L.L.); Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (N.L.P.); Department of Biostatistics Boston University School of Public Health Framingham Heart Study, MA (C.C.W.); Faculty of Medicine, University of Iceland, Reykjavik (A.V.S., V.G.); University of Helsinki, Institute for Molecular Medicine, Finland (FIMM) (A.J., M.P.); Department of Medicine, Mannheim Medical Faculty, Heidelberg University, Germany (M.E.K.); Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds, United Kingdom (A.S.H.); Synlab Academy, Synlab Services GmbH, Mannheim, Germany and Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Austria (W.M.); National Heart, Lung, and Blood Institute and the Framingham Heart Study, National Institutes of Health, Bethesda, MD (C.O'D.); Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden (E.I.); Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (E.I.); Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden (U.D.F.); Lebanese American University, School of Medicine, Beirut (P.Z.); Department of Health Sciences, University of Leicester, United Kingdom (J.R.T.); Imperial College Healthcare NHS Trust, London, United Kingdom (J.C.C., J.K.); Cardiovascular Science, National Heart and Lung Institute, Imperial College London, United Kingdom (J.K.); Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia (P.D.); deCODE Genetics, Sturlugata 8, IS-101 Reykjavik, Iceland (G.T., K.S.); University of Iceland, School of Medicine, Reykjavik, Iceland (G.T., K.S.); Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge (S.K.); Cardiovascular Research Center, Massachusetts General Hospital, Boston (S.K.); Center for Human Genetic Research, Massachusetts General Hospital, Boston (S.K.); Department of Medicine, Harvard Medical School, Boston, MA (S.K.); Department of Genetics, University of Pennsylvania, Philadelphia (D.J.R.); and Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.T.N., D.J.R.).

Background: Common diseases such as coronary heart disease (CHD) are complex in etiology. The interaction of genetic susceptibility with lifestyle factors may play a prominent role. However, gene-lifestyle interactions for CHD have been difficult to identify. Here, we investigate interaction of smoking behavior, a potent lifestyle factor, with genotypes that have been shown to associate with CHD risk.

Methods: We analyzed data on 60 919 CHD cases and 80 243 controls from 29 studies for gene-smoking interactions for genetic variants at 45 loci previously reported to be associated with CHD risk. We also studied 5 loci associated with smoking behavior. Study-specific gene-smoking interaction effects were calculated and pooled using fixed-effects meta-analyses. Interaction analyses were declared to be significant at a value of <1.0×10 (Bonferroni correction for 50 tests).

Results: We identified novel gene-smoking interaction for a variant upstream of the gene. Every T allele of rs7178051 was associated with lower CHD risk by 12% in never-smokers (=1.3×10) in comparison with 5% in ever-smokers (=2.5×10), translating to a 60% loss of CHD protection conferred by this allelic variation in people who smoked tobacco (interaction value=8.7×10). The protective T allele at rs7178051 was also associated with reduced expression in human aortic endothelial cells and lymphoblastoid cell lines. Exposure of human coronary artery smooth muscle cells to cigarette smoke extract led to induction of CONCLUSIONS: Allelic variation at rs7178051 that associates with reduced expression confers stronger CHD protection in never-smokers than in ever-smokers. Increased vascular expression may contribute to the loss of CHD protection in smokers.
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http://dx.doi.org/10.1161/CIRCULATIONAHA.116.022069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5612779PMC
June 2017

Identification of genes associated with dissociation of cognitive performance and neuropathological burden: Multistep analysis of genetic, epigenetic, and transcriptional data.

PLoS Med 2017 04 25;14(4):e1002287. Epub 2017 Apr 25.

Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.

Introduction: The molecular underpinnings of the dissociation of cognitive performance and neuropathological burden are poorly understood, and there are currently no known genetic or epigenetic determinants of the dissociation.

Methods And Findings: "Residual cognition" was quantified by regressing out the effects of cerebral pathologies and demographic characteristics on global cognitive performance proximate to death. To identify genes influencing residual cognition, we leveraged neuropathological, genetic, epigenetic, and transcriptional data available for deceased participants of the Religious Orders Study (n = 492) and the Rush Memory and Aging Project (n = 487). Given that our sample size was underpowered to detect genome-wide significance, we applied a multistep approach to identify genes influencing residual cognition, based on our prior observation that independent genetic and epigenetic risk factors can converge on the same locus. In the first step (n = 979), we performed a genome-wide association study with a predefined suggestive p < 10-5, and nine independent loci met this threshold in eight distinct chromosomal regions. Three of the six genes within 100 kb of the lead SNP are expressed in the dorsolateral prefrontal cortex (DLPFC): UNC5C, ENC1, and TMEM106B. In the second step, in the subset of participants with DLPFC DNA methylation data (n = 648), we found that residual cognition was related to differential DNA methylation of UNC5C and ENC1 (false discovery rate < 0.05). In the third step, in the subset of participants with DLPFC RNA sequencing data (n = 469), brain transcription levels of UNC5C and ENC1 were evaluated for their association with residual cognition: RNA levels of both UNC5C (estimated effect = -0.40, 95% CI -0.69 to -0.10, p = 0.0089) and ENC1 (estimated effect = 0.0064, 95% CI 0.0033 to 0.0096, p = 5.7 × 10-5) were associated with residual cognition. In secondary analyses, we explored the mechanism of these associations and found that ENC1 may be related to the previously documented effect of depression on cognitive decline, while UNC5C may alter the composition of presynaptic terminals. Of note, the TMEM106B allele identified in the first step as being associated with better residual cognition is in strong linkage disequilibrium with rs1990622A (r2 = 0.66), a previously identified protective allele for TDP-43 proteinopathy. Limitations include the small sample size for the genetic analysis, which was underpowered to detect genome-wide significance, the evaluation being limited to a single cortical region for epigenetic and transcriptomic data, and the use of categorical measures for certain non-amyloid-plaque, non-neurofibrillary-tangle neuropathologies.

Conclusions: Through a multistep analysis of cognitive, neuropathological, genomic, epigenomic, and transcriptomic data, we identified ENC1 and UNC5C as genes with convergent genetic, epigenetic, and transcriptomic evidence supporting a potential role in the dissociation of cognition and neuropathology in an aging population, and we expanded our understanding of the TMEM106B haplotype that is protective against TDP-43 proteinopathy.
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http://dx.doi.org/10.1371/journal.pmed.1002287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404753PMC
April 2017

Assessment of Early Evidence of Multiple Sclerosis in a Prospective Study of Asymptomatic High-Risk Family Members.

JAMA Neurol 2017 03;74(3):293-300

Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland.

Importance: Subclinical inflammatory demyelination and neurodegeneration often precede symptom onset in multiple sclerosis (MS).

Objective: To investigate the prevalence of brain magnetic resonance imaging (MRI) and subclinical abnormalities among asymptomatic individuals at risk for MS.

Design, Setting, And Participants: The Genes and Environment in Multiple Sclerosis (GEMS) project is a prospective cohort study of first-degree relatives of people with MS. Each participant's risk for MS was assessed using a weighted score (Genetic and Environmental Risk Score for Multiple Sclerosis Susceptibility [GERSMS]) comprising an individual's genetic burden and environmental exposures. The study dates were August 2012 to July 2015.

Main Outcomes And Measures: Participants in the top and bottom 10% of the risk distribution underwent standard and quantitative neurological examination, including disability status, visual, cognitive, motor, and sensory testing, as well as qualitative and quantitative neuroimaging with 3-T brain MRI and optical coherence tomography.

Results: This study included 100 participants at risk for MS, with 41 at higher risk (40 women [98%]) and 59 at lower risk (25 women [42%]), at a mean (SD) age of 35.1 (8.7) years. Given the unequal sex distribution between the 2 groups, the analyses were restricted to women (n = 65). When considering all measured outcomes, higher-risk women differed from lower-risk women (P = .01 by omnibus test). Detailed testing with a vibration sensitivity testing device in a subgroup of 47 women showed that higher-risk women exhibited significantly poorer vibration perception in the distal lower extremities (P = .008, adjusting for age, height, and testing date). Furthermore, 5 of 65 women (8%) (4 at higher risk and 1 at lower risk) met the primary neuroimaging outcome of having T2-weighted hyperintense brain lesions consistent with the 2010 McDonald MRI criteria for dissemination in space. A subset of participants harbor many different neuroimaging features associated with MS, including perivenous T2-weighted hyperintense lesions and focal leptomeningeal enhancement, consistent with the hypothesis that these individuals are at higher risk of developing clinical symptoms of MS than the general population.

Conclusions And Relevance: Higher-risk asymptomatic family members of patients with MS are more likely to have early subclinical manifestations of MS. These findings underscore the importance of early detection in high-risk individuals.

Trial Registration: clinicaltrials.gov Identifier: NCT01353547.
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http://dx.doi.org/10.1001/jamaneurol.2016.5056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348267PMC
March 2017

A candidate regulatory variant at the TREM gene cluster associates with decreased Alzheimer's disease risk and increased TREML1 and TREM2 brain gene expression.

Alzheimers Dement 2017 Jun 8;13(6):663-673. Epub 2016 Dec 8.

Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA; Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA. Electronic address:

Introduction: We hypothesized that common Alzheimer's disease (AD)-associated variants within the triggering receptor expressed on myeloid (TREM) gene cluster influence disease through gene expression.

Methods: Expression microarrays on temporal cortex and cerebellum from ∼400 neuropathologically diagnosed subjects and two independent RNAseq replication cohorts were used for expression quantitative trait locus analysis.

Results: A variant within a DNase hypersensitive site 5' of TREM2, rs9357347-C, associates with reduced AD risk and increased TREML1 and TREM2 levels (uncorrected P = 6.3 × 10 and 4.6 × 10, respectively). Meta-analysis on expression quantitative trait locus results from three independent data sets (n = 1006) confirmed these associations (uncorrected P = 3.4 × 10 and 3.5 × 10, Bonferroni-corrected P = 6.7 × 10 and 7.1 × 10, respectively).

Discussion: Our findings point to rs9357347 as a functional regulatory variant that contributes to a protective effect observed at the TREM locus in the International Genomics of Alzheimer's Project genome-wide association study meta-analysis and suggest concomitant increase in TREML1 and TREM2 brain levels as a potential mechanism for protection from AD.
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http://dx.doi.org/10.1016/j.jalz.2016.10.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462884PMC
June 2017

Hormone therapy use and physical quality of life in postmenopausal women with multiple sclerosis.

Neurology 2016 Oct 7;87(14):1457-1463. Epub 2016 Sep 7.

From the UCSF MS Center (R.B.), Department of Neurology, UCSF, Sandler Neurosciences Center, San Francisco, CA; Ann Romney Center for Neurologic Diseases (C.C.W., T.C., L.C.), Harvard Medical School, Boston, MA; Johns Hopkins Medical Institute (K.C.F.), Department of Neurology and Neuroimmunology, Baltimore, MD; Partners Multiple Sclerosis Center (T.C.), Department of Neurology, Brigham and Women's Hospital, Brookline; Harvard Medical School (T.C., L.C.), Boston; Channing Division of Network Medicine (A.A.), Brigham and Women's Hospital and Harvard Medical School, Boston; and Departments of Nutrition (A.A., K.L.M.) and Epidemiology (L.C., A.A.), Harvard T.H. Chan School of Public Health, Boston, MA.

Objective: To determine the association between hormone therapy (HT) and physical quality of life (QOL) in postmenopausal women with multiple sclerosis (MS).

Methods: We included female participants from the prospective Nurses' Health Study, with a diagnosis of definite or probable MS, who had completed a physical functioning assessment (PF10; subscale of the 36-Item Short-Form Health Survey QOL survey) at a time point between 3 and 10 years after their final menstrual period (early postmenopause). We assessed the association between HT use at this time point (never vs at least 12 months of systemic estrogen with/without progestin) and both PF10 and the 36-Item Short-Form Health Survey Physical Component Scale. We used a linear regression model adjusting for age, MS duration, menopause type and duration, and further for additional covariates (only ancestry was significant).

Results: Among 95 participants meeting all inclusion criteria at their first postmenopausal assessment, 61 reported HT use and 34 reported none. HT users differed from non-HT users in MS duration (p = 0.02) and menopause type (p = 0.01) but no other clinical or demographic characteristics. HT users had average PF10 scores that were 23 points higher than non-HT users (adjusted p = 0.004) and average Physical Component Scale scores that were 9.1 points higher in the 59 women with these available (adjusted p = 0.02). Longer duration of HT use was also associated with higher PF10 scores (p = 0.02, adjusted p = 0.06).

Conclusions: Systemic HT use was associated with better physical QOL in postmenopausal women with MS in this observational study. Further studies are necessary to investigate causality.
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http://dx.doi.org/10.1212/WNL.0000000000003176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075979PMC
October 2016

Trans-pQTL study identifies immune crosstalk between Parkinson and Alzheimer loci.

Neurol Genet 2016 Aug 26;2(4):e90. Epub 2016 Jul 26.

Ann Romney Center for Neurologic Diseases (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Program in Translational NeuroPsychiatric Genomics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Institute for the Neurosciences, Departments of Neurology and Psychiatry, Center for Alzheimer's Research and Treatment (K.A.J., R.A.S.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics (G.C., C.C.W., P.A.W., M.C., J.M.R., L.R.G., N.E.C., K.J.R., L.B.C., P.L.D.J., E.M.B.), Broad Institute, Cambridge, MA; Harvard Medical School (G.C., J.M.R., K.J.R., K.A.J., L.B.C., R.A.S., P.L.D.J., E.M.B.), Boston, MA; Department of Neurology (K.A.J., R.A.S.), Massachusetts General Hospital, Boston; and Rush Alzheimer's Disease Center (J.A.S., D.A.B.), Rush University Medical Center, Chicago, IL.

Objective: Given evidence from genetic studies, we hypothesized that there may be a shared component to the role of myeloid function in Parkinson and Alzheimer disease (PD and AD) and assessed whether PD susceptibility variants influenced protein expression of well-established AD-associated myeloid genes in human monocytes.

Methods: We repurposed data in which AD-related myeloid proteins CD33, TREM1, TREM2, TREML2, TYROBP, and PTK2B were measured by flow cytometry in monocytes from 176 participants of the PhenoGenetic Project (PGP) and Harvard Aging Brain Study. Linear regression was used to identify associations between 24 PD risk variants and protein expression. The 2 cohorts were meta-analyzed in a discovery analysis, and the 4 most strongly suggestive results were validated in an independent cohort of 50 PGP participants.

Results: We discovered and validated an association between the PD risk allele rs12456492(G) in the RIT2 locus and increased CD33 expression (p joint = 3.50 × 10(-5)) and found strongly suggestive evidence that rs11060180(A) in the CCDC62/HIP1R locus decreased PTK2B expression (p joint = 1.12 × 10(-4)). Furthermore, in older individuals, increased CD33 expression on peripheral monocytes was associated with a greater burden of parkinsonism (p = 0.047), particularly bradykinesia (p = 6.64 × 10(-3)).

Conclusions: We find that the rs12456492 PD risk variant affects expression of AD-associated protein CD33 in peripheral monocytes, which suggests that genetic factors for these 2 diseases may converge to influence overlapping innate immune-mediated mechanisms that contribute to neurodegeneration. Furthermore, the effect of the rs12456492(G) PD risk allele on increased CD33 suggests that the inhibition of certain myeloid functions may contribute to PD susceptibility, as is the case for AD.
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http://dx.doi.org/10.1212/NXG.0000000000000090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962525PMC
August 2016

The Role of MAPT Haplotype H2 and Isoform 1N/4R in Parkinsonism of Older Adults.

PLoS One 2016 26;11(7):e0157452. Epub 2016 Jul 26.

Program in Translational Neuropsychiatric Genomics, Departments of Neurology & Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.

Background And Objective: Recently, we have shown that the Parkinson's disease (PD) susceptibility locus MAPT (microtubule associated protein tau) is associated with parkinsonism in older adults without a clinical diagnosis of PD. In this study, we investigated the relationship between parkinsonian signs and MAPT transcripts by assessing the effect of MAPT haplotypes on alternative splicing and expression levels of the most common isoforms in two prospective clinicopathologic studies of aging.

Materials And Methods: using regression analysis, controlling for age, sex, study and neuropathology, we evaluated 976 subjects with clinical, genotyping and brain pathology data for haplotype analysis. For transcript analysis, we obtained MAPT gene and isoform-level expression from the dorsolateral prefrontal cortex for 505 of these subjects.

Results: The MAPT H2 haplotype was associated with lower total MAPT expression (p = 1.2x10-14) and global parkinsonism at both study entry (p = 0.001) and proximate to death (p = 0.050). Specifically, haplotype H2 was primarily associated with bradykinesia in both assessments (p<0.001 and p = 0.008). MAPT total expression was associated with age and decreases linearly with advancing age (p<0.001). Analysing MAPT alternative splicing, the expression of 1N/4R isoform was inversely associated with global parkinsonism (p = 0.008) and bradykinesia (p = 0.008). Diminished 1N/4R isoform expression was also associated with H2 (p = 0.001).

Conclusions: Overall, our results suggest that age and H2 are associated with higher parkinsonism score and decreased total MAPT RNA expression. Additionally, we found that H2 and parkinsonism are associated with altered expression levels of specific isoforms. These findings may contribute to the understanding of the association between MAPT locus and parkinsonism in elderly subjects and in some extent to age-related neurodegenerative diseases.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157452PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961370PMC
July 2017
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