101
|
Bueichekú E, Diez I, Kim CM, Becker JA, Koops EA, Kwong K, Papp KV, Salat DH, Bennett DA, Rentz DM, Sperling RA, Johnson KA, Sepulcre J, Jacobs HIL. Spatiotemporal patterns of locus coeruleus integrity predict cortical tau and cognition. NATURE AGING 2024; 4:625-637. [PMID: 38664576 PMCID: PMC11108787 DOI: 10.1038/s43587-024-00626-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Autopsy studies indicated that the locus coeruleus (LC) accumulates hyperphosphorylated tau before allocortical regions in Alzheimer's disease. By combining in vivo longitudinal magnetic resonance imaging measures of LC integrity, tau positron emission tomography imaging and cognition with autopsy data and transcriptomic information, we examined whether LC changes precede allocortical tau deposition and whether specific genetic features underlie LC's selective vulnerability to tau. We found that LC integrity changes preceded medial temporal lobe tau accumulation, and together these processes were associated with lower cognitive performance. Common gene expression profiles between LC-medial temporal lobe-limbic regions map to biological functions in protein transport regulation. These findings advance our understanding of the spatiotemporal patterns of initial tau spreading from the LC and LC's selective vulnerability to Alzheimer's disease pathology. LC integrity measures can be a promising indicator for identifying the time window when individuals are at risk of disease progression and underscore the importance of interventions mitigating initial tau spread.
Collapse
Affiliation(s)
- Elisenda Bueichekú
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ibai Diez
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Chan-Mi Kim
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - John Alex Becker
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Kenneth Kwong
- Harvard Medical School, Boston, MA, USA
- The Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn V Papp
- Harvard Medical School, Boston, MA, USA
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - David H Salat
- Harvard Medical School, Boston, MA, USA
- The Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Neuroimaging Research for Veterans Center, VA Boston Healthcare System, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Dorene M Rentz
- Harvard Medical School, Boston, MA, USA
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Reisa A Sperling
- Harvard Medical School, Boston, MA, USA
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Keith A Johnson
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Jorge Sepulcre
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- The Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Radiology, Yale PET Center, Yale Medical School, Yale University, New Haven, CT, USA.
| | - Heidi I L Jacobs
- Harvard Medical School, Boston, MA, USA.
- The Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA.
- Faculty of Health, Medicine and Life Sciences, School for Mental Health and Neuroscience, Alzheimer Centre Limburg, Maastricht University, Maastricht, Netherlands.
| |
Collapse
|
102
|
Oveisgharan S, Wang T, Barnes LL, Schneider JA, Bennett DA, Buchman AS. The time course of motor and cognitive decline in older adults and their associations with brain pathologies: a multicohort study. THE LANCET. HEALTHY LONGEVITY 2024; 5:e336-e345. [PMID: 38582095 PMCID: PMC11129202 DOI: 10.1016/s2666-7568(24)00033-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Many studies have reported that impaired gait precedes cognitive impairment in older people. We aimed to characterise the time course of cognitive and motor decline in older individuals and the association of these declines with the pathologies of Alzheimer's disease and related dementias. METHODS This multicohort study used data from three community-based cohort studies (Religious Orders Study, Rush Memory and Aging Project, and Minority Aging Research Study, all in the USA). The inclusion criteria for all three cohorts were no clinical dementia at the time of enrolment and consent to annual clinical assessments. Eligible participants consented to post-mortem brain donation and had post-mortem pathological assessments and three or more repeated annual measures of cognition and motor functions. Clinical and post-mortem data were analysed using functional mixed-effects models. Global cognition was based on 19 neuropsychological tests, a hand strength score was based on grip and pinch strength, and a gait score was based on the number of steps and time to walk 8 feet and turn 360°. Brain pathologies of Alzheimer's disease and related dementias were assessed at autopsy. FINDINGS From 1994 to 2022, there were 1570 eligible cohort participants aged 65 years or older, 1303 of whom had cognitive and motor measurements and were included in the analysis. Mean age at death was 90·3 years (SD 6·3), 905 (69%) participants were female, and 398 (31%) were male. Median follow-up time was 9 years (IQR 5-11). On average, cognition was stable from 25 to 15 years before death, when cognition began to decline. By contrast, gait function and hand strength declined during the entire study. The combinations of pathologies of Alzheimer's disease and related dementias associated with cognitive and motor decline and their onsets of associations varied; only tau tangles, Parkinson's disease pathology, and macroinfarcts were associated with decline of all three phenotypes. Tau tangles were significantly associated with cognitive decline, gait function decline, and hand function decline (p<0·0001 for each); however, the association with cognitive decline persisted for more than 11 years before death, but the association with hand strength only began 3·57 years before death and the association with gait began 3·49 years before death. By contrast, the association of macroinfarcts with declining gait function began 9·25 years before death (p<0·0001) compared with 6·65 years before death (p=0·0005) for cognitive decline and 2·66 years before death (p=0·024) for decline in hand strength. INTERPRETATION Our findings suggest that average motor decline in older adults precedes cognitive decline. Macroinfarcts but not tau tangles are associated with declining gait function that precedes cognitive decline. This suggests the need for further studies to test if gait impairment is a clinical proxy for preclinical vascular cognitive impairment. FUNDING National Institutes of Health.
Collapse
Affiliation(s)
- Shahram Oveisgharan
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| | - Tianhao Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA; Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA; Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| |
Collapse
|
103
|
Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs: improved discovery of DNA methylation associations with complex traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590171. [PMID: 38746367 PMCID: PMC11092597 DOI: 10.1101/2024.05.01.590171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We have developed the regional principal components (rPCs) method, a novel approach for summarizing gene-level methylation. rPCs address the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease (AD). In contrast to traditional averaging, rPCs leverage principal components analysis to capture complex methylation patterns across gene regions. Our method demonstrated a 54% improvement in sensitivity over averaging in simulations, offering a robust framework for identifying subtle epigenetic variations. Applying rPCs to the AD brain methylation data in ROSMAP, combined with cell type deconvolution, we uncovered 838 differentially methylated genes associated with neuritic plaque burden-significantly outperforming conventional methods. Integrating methylation quantitative trait loci (meQTL) with genome-wide association studies (GWAS) identified 17 genes with potential causal roles in AD, including MS4A4A and PICALM. Our approach is available in the Bioconductor package regionalpcs, opening avenues for research and facilitating a deeper understanding of the epigenetic landscape in complex diseases.
Collapse
Affiliation(s)
- Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Olivier Gevaert
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael D Greicius
- Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | | |
Collapse
|
104
|
Ward D, Flint J, Littlejohns T, Foote I, Canevelli M, Wallace L, Gordon E, Llewellyn D, Ranson J, Hubbard R, Rockwood K, Stolz E. Frailty trajectories preceding dementia: an individual-level analysis of four cohort studies in the United States and United Kingdom. RESEARCH SQUARE 2024:rs.3.rs-4314795. [PMID: 38746437 PMCID: PMC11092835 DOI: 10.21203/rs.3.rs-4314795/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Frailty may represent a modifiable risk factor for dementia, but the direction of that association remains uncertain. We investigated frailty trajectories in the years preceding dementia onset using data from 23,672 participants (242,760 person-years of follow-up, 2,906 cases of incident dementia) across four cohort studies in the United States and United Kingdom. Bayesian non-linear models revealed accelerations in frailty trajectories 4-9 years before incident dementia. Among participants whose time between frailty measurement and incident dementia exceeded that prodromal period, frailty remained positively associated with dementia risk (adjusted hazard ratios ranged from 1.20 [95% confidence interval, CI = 1.15-1.26] to 1.43 [95% CI = 1.14-1.81]). This observational evidence suggests that frailty increases dementia risk independently of any reverse causality. These findings indicate that frailty measurements can be used to identify high-risk population groups for preferential enrolment into clinical trials for dementia prevention and treatment. Frailty itself may represent a useful upstream target for behavioural and societal approaches to dementia prevention.
Collapse
|
105
|
Kim Y, Jeong M, Koh IG, Kim C, Lee H, Kim JH, Yurko R, Kim IB, Park J, Werling DM, Sanders SJ, An JY. CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.15.24305828. [PMID: 38699372 PMCID: PMC11065022 DOI: 10.1101/2024.04.15.24305828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Variants in cis-regulatory elements link the noncoding genome to human brain pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS) employs both whole-genome sequencing and user-provided functional data to enhance noncoding variant analysis, with a faster and more efficient execution of the CWAS workflow. Here, we used single-nuclei assay for transposase-accessible chromatin with sequencing to facilitate CWAS-guided noncoding variant analysis at cell-type specific enhancers and promoters. Examining autism spectrum disorder whole-genome sequencing data (n = 7,280), CWAS-Plus identified noncoding de novo variant associations in transcription factor binding sites within conserved loci. Independently, in Alzheimer's disease whole-genome sequencing data (n = 1,087), CWAS-Plus detected rare noncoding variant associations in microglia-specific regulatory elements. These findings highlight CWAS-Plus's utility in genomic disorders and scalability for processing large-scale whole-genome sequencing data and in multiple-testing corrections. CWAS-Plus and its user manual are available at https://github.com/joonan-lab/cwas/ and https://cwas-plus.readthedocs.io/en/latest/, respectively.
Collapse
Affiliation(s)
- Yujin Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Minwoo Jeong
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - In Gyeong Koh
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Chanhee Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Hyeji Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Ronald Yurko
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Il Bin Kim
- Department of Psychiatry, CHA Gangnam Medical Center, CHA University School of Medicine, Seoul, 06135, Republic of Korea
| | - Jeongbin Park
- School of Biomedical Convergence Engineering, Pusan National University, Busan, 50612, Republic of Korea
| | - Donna M. Werling
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Stephan J. Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| |
Collapse
|
106
|
Reeder HT, Lee KH, Haneuse S. Characterizing quantile-varying covariate effects under the accelerated failure time model. Biostatistics 2024; 25:449-467. [PMID: 36610077 PMCID: PMC11484523 DOI: 10.1093/biostatistics/kxac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023] Open
Abstract
An important task in survival analysis is choosing a structure for the relationship between covariates of interest and the time-to-event outcome. For example, the accelerated failure time (AFT) model structures each covariate effect as a constant multiplicative shift in the outcome distribution across all survival quantiles. Though parsimonious, this structure cannot detect or capture effects that differ across quantiles of the distribution, a limitation that is analogous to only permitting proportional hazards in the Cox model. To address this, we propose a general framework for quantile-varying multiplicative effects under the AFT model. Specifically, we embed flexible regression structures within the AFT model and derive a novel formula for interpretable effects on the quantile scale. A regression standardization scheme based on the g-formula is proposed to enable the estimation of both covariate-conditional and marginal effects for an exposure of interest. We implement a user-friendly Bayesian approach for the estimation and quantification of uncertainty while accounting for left truncation and complex censoring. We emphasize the intuitive interpretation of this model through numerical and graphical tools and illustrate its performance through simulation and application to a study of Alzheimer's disease and dementia.
Collapse
Affiliation(s)
- Harrison T Reeder
- Biostatistics, Massachusetts General Hospital, 50 Staniford Street, Suite 560, Boston, MA 02114, USA and Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Kyu Ha Lee
- Departments of Nutrition, Epidemiology, and Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
| | - Sebastien Haneuse
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
| |
Collapse
|
107
|
Haq I, Ngo JC, Roy N, Pan RL, Nawsheen N, Chiu R, Zhang Y, Fujita M, Soni RK, Wu X, Bennett DA, Menon V, Olah M, Sher F. An integrated toolkit for human microglia functional genomics. Stem Cell Res Ther 2024; 15:104. [PMID: 38600587 PMCID: PMC11005142 DOI: 10.1186/s13287-024-03700-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Microglia, the brain's resident immune cells, play vital roles in brain development, and disorders like Alzheimer's disease (AD). Human iPSC-derived microglia (iMG) provide a promising model to study these processes. However, existing iMG generation protocols face challenges, such as prolonged differentiation time, lack of detailed characterization, and limited gene function investigation via CRISPR-Cas9. METHODS Our integrated toolkit for in-vitro microglia functional genomics optimizes iPSC differentiation into iMG through a streamlined two-step, 20-day process, producing iMG with a normal karyotype. We confirmed the iMG's authenticity and quality through single-cell RNA sequencing, chromatin accessibility profiles (ATAC-Seq), proteomics and functional tests. The toolkit also incorporates a drug-dependent CRISPR-ON/OFF system for temporally controlled gene expression. Further, we facilitate the use of multi-omic data by providing online searchable platform that compares new iMG profiles to human primary microglia: https://sherlab.shinyapps.io/IPSC-derived-Microglia/ . RESULTS Our method generates iMG that closely align with human primary microglia in terms of transcriptomic, proteomic, and chromatin accessibility profiles. Functionally, these iMG exhibit Ca2 + transients, cytokine driven migration, immune responses to inflammatory signals, and active phagocytosis of CNS related substrates including synaptosomes, amyloid beta and myelin. Significantly, the toolkit facilitates repeated iMG harvesting, essential for large-scale experiments like CRISPR-Cas9 screens. The standalone ATAC-Seq profiles of our iMG closely resemble primary microglia, positioning them as ideal tools to study AD-associated single nucleotide variants (SNV) especially in the genome regulatory regions. CONCLUSIONS Our advanced two-step protocol rapidly and efficiently produces authentic iMG. With features like the CRISPR-ON/OFF system and a comprehensive multi-omic data platform, our toolkit equips researchers for robust microglial functional genomic studies. By facilitating detailed SNV investigation and offering a sustainable cell harvest mechanism, the toolkit heralds significant progress in neurodegenerative disease drug research and therapeutic advancement.
Collapse
Affiliation(s)
- Imdadul Haq
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Jason C Ngo
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Nainika Roy
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Richard L Pan
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Nadiya Nawsheen
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Rebecca Chiu
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Neuroimmunology Core, Center for Translational & Computational Neuroimmunology, Division of Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Ya Zhang
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Neuroimmunology Core, Center for Translational & Computational Neuroimmunology, Division of Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Rajesh K Soni
- Proteomics Core, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Xuebing Wu
- Department of Medicine, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Marta Olah
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Falak Sher
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
| |
Collapse
|
108
|
Oveisgharan S, Grodstein F, Evia AM, James BD, Capuano AW, Chen Y, Arfanakis K, Schneider JA, Bennett DA. Association of Age-Related Neuropathologic Findings at Autopsy With a Claims-Based Epilepsy Diagnosis in Older Adults. Neurology 2024; 102:e209172. [PMID: 38478792 PMCID: PMC11383919 DOI: 10.1212/wnl.0000000000209172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/08/2023] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Epilepsy is 1 of the 3 most common neurologic diseases of older adults, but few studies have examined its underlying pathologies in older age. We examined the associations of age-related brain pathologies with epilepsy in older persons. METHODS Clinical and pathologic data came from 2 ongoing clinical pathologic cohort studies of community-dwelling older adults. Epilepsy was ascertained using Medicare fee-for-service Parts A and B claims data that were linked to data from the cohort studies. The postmortem pathologic assessment collected indices of 9 pathologies including Alzheimer disease, hippocampal sclerosis, macroinfarcts, and cerebral amyloid angiopathy. The fixed brain hemisphere was imaged using 3T MRI scanners before the pathologic assessments in a subgroup of participants. RESULTS The participants (n = 1,369) were on average 89.3 (6.6) years at death, and 67.0% were women. Epilepsy was identified in 58 (4.2%) participants. Cerebral amyloid angiopathy (odds ratio [OR] = 2.21, 95% CI 1.24-3.95, p = 0.007) and cortical macroinfarcts (OR = 2.74, 95% CI 1.42-5.28, p = 0.003) were associated with a higher odds of epilepsy. Of note, hippocampal sclerosis and Alzheimer disease pathology were not associated with epilepsy (both p's > 0.25), although hippocampal sclerosis was not common and thus hard to examine with the modest number of epilepsy cases here. In 673 participants with MRI data, the association of cerebral amyloid angiopathy and cortical macroinfarcts with epilepsy did not change after controlling for cortical gray matter atrophy, which was independently associated with a higher odds of epilepsy (OR = 1.06, 95% CI 1.02-1.10, p = 0.003). By contrast, hippocampal volume was not associated with epilepsy. DISCUSSION Cerebrovascular pathologies and cortical atrophy were associated with epilepsy in older persons.
Collapse
Affiliation(s)
- Shahram Oveisgharan
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Francine Grodstein
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Arnold M Evia
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Bryan D James
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Ana W Capuano
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Yi Chen
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Konstantinos Arfanakis
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Julie A Schneider
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - David A Bennett
- From the Rush Alzheimer's Disease Center (S.O., F.G., A.M.E., B.D.J., A.W.C., Y.C., K.A., J.A.S., D.A.B.); Department of Neurological Sciences (S.O., A.W.C., J.A.S., D.A.B.); Department of Internal Medicine (F.G., B.D.J., Y.C.); Department of Diagnostic Radiology and Nuclear Medicine (A.M.E., K.A.), Rush University Medical Center; Department of Biomedical Engineering (K.A.), Illinois Institute of Technology; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| |
Collapse
|
109
|
Buchman AS, Yu L, Klein HU, Zammit AR, Oveisgharan S, Nag S, Tickotsky N, Levy H, Seyfried N, Morgenstern D, Levin Y, Schnaider Beeri M, Bennett DA. Glycoproteome-Wide Discovery of Cortical Glycoproteins That May Provide Cognitive Resilience in Older Adults. Neurology 2024; 102:e209223. [PMID: 38502899 DOI: 10.1212/wnl.0000000000209223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/05/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Molecular omics studies have identified proteins related to cognitive resilience but unrelated to Alzheimer disease and Alzheimer disease-related dementia (AD/ADRD) pathologies. Posttranslational modifications of proteins with glycans can modify protein function. In this study, we identified glycopeptiforms associated with cognitive resilience. METHODS We studied brains from adults with annual cognitive testing with postmortem indices of 10 AD/ADRD pathologies and proteome-wide data from dorsal lateral prefrontal cortex (DLPFC). We quantified 11, 012 glycopeptiforms from DLPFC using liquid chromatography with tandem mass spectrometry. We used linear mixed-effects models to identify glycopeptiforms associated with cognitive decline correcting for multiple comparisons (p < 5 × 10-6). Then, we regressed out the effect of AD/ADRD pathologies to identify glycopeptiforms that may provide cognitive resilience. RESULTS We studied 366 brains, average age at death 89 years, and 70% female with no cognitive impairment = 152, mild cognitive impairment = 93, and AD = 121 cognitive status at death. In models adjusting for age, sex and education, 11 glycopeptiforms were associated with cognitive decline. In further modeling, 8 of these glycopeptiforms remained associated with cognitive decline after adjusting for AD/ADRD pathologies: NPTX2a (Est., 0.030, SE, 0.005, p = 1 × 10-4); NPTX2b (Est.,0.019, SE, 0.005, p = 2 × 10-4) NECTIN1(Est., 0.029, SE, 0.009, p = 9 × 10-4), NPTX2c (Est., 0.015, SE, 0.004, p = 9 × 10-4), HSPB1 (Est., -0.021, SE, 0.006, p = 2 × 10-4), PLTP (Est., -0.027, SE, 0.009, p = 4.2 × 10-3), NAGK (Est., -0.027, SE, 0.008, p = 1.4 × 10-3), and VAT1 (Est., -0.020, SE, 0.006, p = 1.1 × 10-3). Higher levels of 4 resilience glycopeptiforms derived through glycosylation were associated with slower decline and higher levels of 4 derived through glycation were related to faster decline. Together, these 8 glycopeptiforms accounted for an additional 6% of cognitive decline over the 33% accounted for the 10 brain pathologies and demographics. All 8 resilience glycopeptiforms remained associated with cognitive decline after adjustments for the expression level of their corresponding protein. Exploratory gene ontology suggested that molecular mechanisms of glycopeptiforms associated with cognitive decline may involve metabolic pathways including pyruvate and NADH pathways and highlighted the importance of molecular mechanisms involved in glucose metabolism. DISCUSSION Glycopeptiforms in aging brains may provide cognitive resilience. Targeting these glycopeptiforms may lead to therapies that maintain cognition through resilience.
Collapse
Affiliation(s)
- Aron S Buchman
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Lei Yu
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Hans-Ulrich Klein
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Andrea R Zammit
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Shahram Oveisgharan
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Sukriti Nag
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Nili Tickotsky
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Hila Levy
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Nicholas Seyfried
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - David Morgenstern
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Yishai Levin
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - Michal Schnaider Beeri
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| | - David A Bennett
- From the Rush Alzheimer's Disease Center (A.S.B., L.Y., A.R.Z., S.O., S.N., D.A.B.); Department of Neurological Sciences (A.S.B., L.Y., S.O., D.A.B.), Rush University Medical Center, Chicago, IL; Center for Translational and Computational Neuroimmunology (H.-U.K.), Department of Neurology, Columbia University Medical Center, New York; Department of Pathology (Neuropathology) (S.N.), Rush University Medical Center, Chicago, IL; Katz Institute for Nanoscale Science and Technology Ben Gurion University (N.T.), Beer Sheva; The de Botton Institute for Protein Profiling (H.L., D.M., Y.L.), Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel; Department of Neurology (N.S.), Emory University School of Medicine; Department of Biochemistry (N.S.), Emory University, Atlanta, GA; and Department of Neurology (M.S.B.), Rutgers Robert Wood Johnson Medical School and Rutgers Brain Health Institute, NJ
| |
Collapse
|
110
|
de Vries LE, Huitinga I, Kessels HW, Swaab DF, Verhaagen J. The concept of resilience to Alzheimer's Disease: current definitions and cellular and molecular mechanisms. Mol Neurodegener 2024; 19:33. [PMID: 38589893 PMCID: PMC11003087 DOI: 10.1186/s13024-024-00719-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Some individuals are able to maintain their cognitive abilities despite the presence of significant Alzheimer's Disease (AD) neuropathological changes. This discrepancy between cognition and pathology has been labeled as resilience and has evolved into a widely debated concept. External factors such as cognitive stimulation are associated with resilience to AD, but the exact cellular and molecular underpinnings are not completely understood. In this review, we discuss the current definitions used in the field, highlight the translational approaches used to investigate resilience to AD and summarize the underlying cellular and molecular substrates of resilience that have been derived from human and animal studies, which have received more and more attention in the last few years. From these studies the picture emerges that resilient individuals are different from AD patients in terms of specific pathological species and their cellular reaction to AD pathology, which possibly helps to maintain cognition up to a certain tipping point. Studying these rare resilient individuals can be of great importance as it could pave the way to novel therapeutic avenues for AD.
Collapse
Affiliation(s)
- Luuk E de Vries
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands.
| | - Inge Huitinga
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - Helmut W Kessels
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Dick F Swaab
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, Netherlands
| | - Joost Verhaagen
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| |
Collapse
|
111
|
Maden SK, Huuki-Myers LA, Kwon SH, Collado-Torres L, Maynard KR, Hicks SC. lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588105. [PMID: 38617294 PMCID: PMC11014536 DOI: 10.1101/2024.04.04.588105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Relative cell type fraction estimates in bulk RNA-sequencing data are important to control for cell composition differences across heterogenous tissue samples. Current computational tools estimate relative RNA abundances rather than cell type proportions in tissues with varying cell sizes, leading to biased estimates. We present lute, a computational tool to accurately deconvolute cell types with varying sizes. Our software wraps existing deconvolution algorithms in a standardized framework. Using simulated and real datasets, we demonstrate how lute adjusts for differences in cell sizes to improve the accuracy of cell composition. Software is available from https://bioconductor.org/packages/lute.
Collapse
Affiliation(s)
- Sean K. Maden
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Louise A. Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Kristen R. Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| |
Collapse
|
112
|
Arvanitakis Z, Capuano AW, Tong H, Mehta RI, Anokye-Danso F, Bennett DA, Arnold SE, Ahima RS. Associations of Serum Insulin and Related Measures With Neuropathology and Cognition in Older Persons With and Without Diabetes. Ann Neurol 2024; 95:665-676. [PMID: 38379184 PMCID: PMC11023784 DOI: 10.1002/ana.26882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/23/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024]
Abstract
OBJECTIVE To examine associations of serum insulin and related measures with neuropathology and cognition in older persons. METHODS We studied 192 older persons (96 with diabetes and 96 without, matched by sex and balanced by age-at-death, education, and postmortem interval) from a community-based, clinical-pathologic study of aging, with annual evaluations including neuropsychological testing (summarized into global cognition and 5 cognitive domains) and postmortem autopsy. We assessed serum insulin, glucose, leptin, adiponectin, hemoglobin A1C, advanced glycation-end products (AGEs), and receptors for advanced glycation-end products, and calculated the Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) and adiponectin-to-leptin ratio. Using adjusted regression analyses, we examined the associations of serum measures with neuropathology of cerebrovascular disease and Alzheimer's disease, and with the level of cognition proximate-to-death. RESULTS Higher HOMA-IR was associated with the presence of brain infarcts and specifically microinfarcts, and higher HOMA-IR and leptin were each associated with subcortical infarcts. Further, higher leptin levels and lower adiponectin-to-leptin ratios were associated with the presence of moderate-to-severe atherosclerosis. Serum insulin and related measures were not associated with the level of Alzheimer's disease pathology, as assessed by global, as well as amyloid burden or tau tangle density scores. Regarding cognitive outcomes, higher insulin and leptin levels, and lower adiponectin and receptors for advanced glycation-end products levels, respectively, were each associated with lower levels of global cognition. INTERPRETATION Peripheral insulin resistance indicated by HOMA-IR and related serum measures was associated with a greater burden of cerebrovascular neuropathology and lower cognition. ANN NEUROL 2024;95:665-676.
Collapse
Affiliation(s)
- Zoe Arvanitakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - Ana W Capuano
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - Han Tong
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - Rupal I Mehta
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - Frederick Anokye-Danso
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - Steven E Arnold
- Alzheimer's Clinical and Translational Research Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Rexford S Ahima
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD
| |
Collapse
|
113
|
Kumar P, Goettemoeller AM, Espinosa-Garcia C, Tobin BR, Tfaily A, Nelson RS, Natu A, Dammer EB, Santiago JV, Malepati S, Cheng L, Xiao H, Duong DD, Seyfried NT, Wood LB, Rowan MJM, Rangaraju S. Native-state proteomics of Parvalbumin interneurons identifies unique molecular signatures and vulnerabilities to early Alzheimer's pathology. Nat Commun 2024; 15:2823. [PMID: 38561349 PMCID: PMC10985119 DOI: 10.1038/s41467-024-47028-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Dysfunction in fast-spiking parvalbumin interneurons (PV-INs) may represent an early pathophysiological perturbation in Alzheimer's Disease (AD). Defining early proteomic alterations in PV-INs can provide key biological and translationally-relevant insights. We used cell-type-specific in-vivo biotinylation of proteins (CIBOP) coupled with mass spectrometry to obtain native-state PV-IN proteomes. PV-IN proteomic signatures include high metabolic and translational activity, with over-representation of AD-risk and cognitive resilience-related proteins. In bulk proteomes, PV-IN proteins were associated with cognitive decline in humans, and with progressive neuropathology in humans and the 5xFAD mouse model of Aβ pathology. PV-IN CIBOP in early stages of Aβ pathology revealed signatures of increased mitochondria and metabolism, synaptic and cytoskeletal disruption and decreased mTOR signaling, not apparent in whole-brain proteomes. Furthermore, we demonstrated pre-synaptic defects in PV-to-excitatory neurotransmission, validating our proteomic findings. Overall, in this study we present native-state proteomes of PV-INs, revealing molecular insights into their unique roles in cognitive resiliency and AD pathogenesis.
Collapse
Affiliation(s)
- Prateek Kumar
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Annie M Goettemoeller
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Neuroscience Graduate Program, Laney Graduate School, Emory University, Atlanta, USA
| | - Claudia Espinosa-Garcia
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Brendan R Tobin
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Ali Tfaily
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ruth S Nelson
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Aditya Natu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric B Dammer
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Juliet V Santiago
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Neuroscience Graduate Program, Laney Graduate School, Emory University, Atlanta, USA
| | - Sneha Malepati
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lihong Cheng
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
| | - Hailian Xiao
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
| | - Duc D Duong
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Levi B Wood
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
- School of Chemical and Biological Engineering, GeoInsrgia titute of Technology, Atlanta, GA, 30322, USA
| | - Matthew J M Rowan
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA.
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA.
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA.
| |
Collapse
|
114
|
Biesbroek JM, Coenen M, DeCarli C, Fletcher EM, Maillard PM, Barkhof F, Barnes J, Benke T, Chen CPLH, Dal‐Bianco P, Dewenter A, Duering M, Enzinger C, Ewers M, Exalto LG, Franzmeier N, Hilal S, Hofer E, Koek HL, Maier AB, McCreary CR, Papma JM, Paterson RW, Pijnenburg YAL, Rubinski A, Schmidt R, Schott JM, Slattery CF, Smith EE, Sudre CH, Steketee RME, Teunissen CE, van den Berg E, van der Flier WM, Venketasubramanian N, Venkatraghavan V, Vernooij MW, Wolters FJ, Xin X, Kuijf HJ, Biessels GJ. Amyloid pathology and vascular risk are associated with distinct patterns of cerebral white matter hyperintensities: A multicenter study in 3132 memory clinic patients. Alzheimers Dement 2024; 20:2980-2989. [PMID: 38477469 PMCID: PMC11032573 DOI: 10.1002/alz.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 03/14/2024]
Abstract
INTRODUCTION White matter hyperintensities (WMH) are associated with key dementia etiologies, in particular arteriolosclerosis and amyloid pathology. We aimed to identify WMH locations associated with vascular risk or cerebral amyloid-β1-42 (Aβ42)-positive status. METHODS Individual patient data (n = 3,132; mean age 71.5 ± 9 years; 49.3% female) from 11 memory clinic cohorts were harmonized. WMH volumes in 28 regions were related to a vascular risk compound score (VRCS) and Aß42 status (based on cerebrospinal fluid or amyloid positron emission tomography), correcting for age, sex, study site, and total WMH volume. RESULTS VRCS was associated with WMH in anterior/superior corona radiata (B = 0.034/0.038, p < 0.001), external capsule (B = 0.052, p < 0.001), and middle cerebellar peduncle (B = 0.067, p < 0.001), and Aß42-positive status with WMH in posterior thalamic radiation (B = 0.097, p < 0.001) and splenium (B = 0.103, p < 0.001). DISCUSSION Vascular risk factors and Aß42 pathology have distinct signature WMH patterns. This regional vulnerability may incite future studies into how arteriolosclerosis and Aß42 pathology affect the brain's white matter. HIGHLIGHTS Key dementia etiologies may be associated with specific patterns of white matter hyperintensities (WMH). We related WMH locations to vascular risk and cerebral Aβ42 status in 11 memory clinic cohorts. Aβ42 positive status was associated with posterior WMH in splenium and posterior thalamic radiation. Vascular risk was associated with anterior and infratentorial WMH. Amyloid pathology and vascular risk have distinct signature WMH patterns.
Collapse
|
115
|
Katsumata Y, Fardo DW, Shade LMP, Wu X, Karanth SD, Hohman TJ, Schneider JA, Bennett DA, Farfel JM, Gauthreaux K, Mock C, Kukull WA, Abner EL, Nelson PT. Genetic associations with dementia-related proteinopathy: Application of item response theory. Alzheimers Dement 2024; 20:2906-2921. [PMID: 38460116 PMCID: PMC11032554 DOI: 10.1002/alz.13741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 03/11/2024]
Abstract
INTRODUCTION Although dementia-related proteinopathy has a strong negative impact on public health, and is highly heritable, understanding of the related genetic architecture is incomplete. METHODS We applied multidimensional generalized partial credit modeling (GPCM) to test genetic associations with dementia-related proteinopathies. Data were analyzed to identify candidate single nucleotide variants for the following proteinopathies: Aβ, tau, α-synuclein, and TDP-43. RESULTS Final included data comprised 966 participants with neuropathologic and WGS data. Three continuous latent outcomes were constructed, corresponding to TDP-43-, Aβ/Tau-, and α-synuclein-related neuropathology endophenotype scores. This approach helped validate known genotype/phenotype associations: for example, TMEM106B and GRN were risk alleles for TDP-43 pathology; and GBA for α-synuclein/Lewy bodies. Novel suggestive proteinopathy-linked alleles were also discovered, including several (SDHAF1, TMEM68, and ARHGEF28) with colocalization analyses and/or high degrees of biologic credibility. DISCUSSION A novel methodology using GPCM enabled insights into gene candidates for driving misfolded proteinopathies. HIGHLIGHTS Latent factor scores for proteinopathies were estimated using a generalized partial credit model. The three latent continuous scores corresponded well with proteinopathy severity. Novel genes associated with proteinopathies were identified. Several genes had high degrees of biologic credibility for dementia risk factors.
Collapse
Affiliation(s)
- Yuriko Katsumata
- Department of BiostatisticsUniversity of KentuckyLexingtonKentuckyUSA
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
| | - David W. Fardo
- Department of BiostatisticsUniversity of KentuckyLexingtonKentuckyUSA
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
| | | | - Xian Wu
- Department of BiostatisticsUniversity of KentuckyLexingtonKentuckyUSA
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
| | - Shama D. Karanth
- Department of SurgeryCollege of MedicineUniversity of FloridaGainesvilleFloridaUSA
- UF Health Cancer CenterUniversity of FloridaGainesvilleFloridaUSA
| | - Timothy J. Hohman
- Vanderbilt Memory and Alzheimer's CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Julie A. Schneider
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - David A. Bennett
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Jose M. Farfel
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Kathryn Gauthreaux
- National Alzheimer's Coordinating CenterDepartment of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Charles Mock
- National Alzheimer's Coordinating CenterDepartment of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Walter A. Kukull
- National Alzheimer's Coordinating CenterDepartment of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Erin L. Abner
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
- Department of Epidemiology and Environmental HealthUniversity of KentuckyLexingtonKentuckyUSA
| | - Peter T. Nelson
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKentuckyUSA
- Department of PathologyDivision of NeuropathologyUniversity of KentuckyLexingtonKentuckyUSA
| |
Collapse
|
116
|
Fujita M, Gao Z, Zeng L, McCabe C, White CC, Ng B, Green GS, Rozenblatt-Rosen O, Phillips D, Amir-Zilberstein L, Lee H, Pearse RV, Khan A, Vardarajan BN, Kiryluk K, Ye CJ, Klein HU, Wang G, Regev A, Habib N, Schneider JA, Wang Y, Young-Pearse T, Mostafavi S, Bennett DA, Menon V, De Jager PL. Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nat Genet 2024; 56:605-614. [PMID: 38514782 DOI: 10.1038/s41588-024-01685-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
The relationship between genetic variation and gene expression in brain cell types and subtypes remains understudied. Here, we generated single-nucleus RNA sequencing data from the neocortex of 424 individuals of advanced age; we assessed the effect of genetic variants on RNA expression in cis (cis-expression quantitative trait loci) for seven cell types and 64 cell subtypes using 1.5 million transcriptomes. This effort identified 10,004 eGenes at the cell type level and 8,099 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer's disease pathology, after adjusting for APOEε4, providing mechanistic insights into both pathologies. Furthermore, only a TMEM106B variant affects the proportion of cell subtypes. Integration of these results with genome-wide association studies highlighted the targeted cell type and probable causal gene within Alzheimer's disease, schizophrenia, educational attainment and Parkinson's disease loci.
Collapse
Affiliation(s)
- Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Zongmei Gao
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lu Zeng
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles C White
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Bernard Ng
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Gilad Sahar Green
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Atlas Khan
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gao Wang
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Naomi Habib
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Tracy Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara Mostafavi
- Department of Statistics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
117
|
Ceylan B, Düz E, Çakir T. Personalized Protein-Protein Interaction Networks Towards Unraveling the Molecular Mechanisms of Alzheimer's Disease. Mol Neurobiol 2024; 61:2120-2135. [PMID: 37855983 DOI: 10.1007/s12035-023-03690-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
Alzheimer's disease (AD) is a highly heterogenous neurodegenerative disease, and several omic-based datasets were generated in the last decade from the patients with the disease. However, the vast majority of studies evaluate these datasets in bulk by considering all the patients as a single group, which obscures the molecular differences resulting from the heterogeneous nature of the disease. In this study, we adopted a personalized approach and analyzed the transcriptome data from 403 patients individually by mapping the data on a human protein-protein interaction network. Patient-specific subnetworks were discovered and analyzed in terms of the genes in the subnetworks, enriched functional terms, and known AD genes. We identified several affected pathways that could not be captured by the bulk comparison. We also showed that our personalized findings point to patterns of alterations consistent with the recently suggested AD subtypes.
Collapse
Affiliation(s)
- Betül Ceylan
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Elif Düz
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Tunahan Çakir
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
| |
Collapse
|
118
|
Qiu X, Robert AL, McAlaine K, Quan L, Mangano J, Weisskopf MG. Early-life participation in cognitively stimulating activities and risk of depression and anxiety in late life. Psychol Med 2024; 54:962-970. [PMID: 37706289 PMCID: PMC10937330 DOI: 10.1017/s0033291723002702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
BACKGROUND Early-life stressful experiences are associated with increased risk of adverse psychological outcomes in later life. However, much less is known about associations between early-life positive experiences, such as participation in cognitively stimulating activities, and late-life mental health. We investigated whether greater engagement in cognitively stimulating activities in early life is associated with lower risk of depression and anxiety in late life. METHODS We surveyed former participants of the St. Louis Baby Tooth study, between 22 June 2021 and 25 March 2022 to collect information on participants' current depression/anxiety symptoms and their early-life activities (N = 2187 responded). A composite activity score was created to represent the early-life activity level by averaging the frequency of self-reported participation in common cognitively stimulating activities in participants' early life (age 6, 12, 18), each rated on a 1 (least frequent) to 5 (most frequent) point scale. Depression/anxiety symptoms were measured by Patient Health Questionnaire (PHQ-9) and Generalized Anxiety Disorder Screener (GAD-7). We used logistic regressions to estimate odds ratios (OR) and 95% confidence intervals (CI) of outcome risk associated with frequency of early-life activity. RESULTS Each one-point increase in the early-life composite cognitive activity score was associated with an OR of 0.54 (95% CI 0.38-0.77) for late-life depression and an OR of 0.94 (95% CI 0.61-1.43) for late-life anxiety, adjusting for age, sex, race, parental education, childhood family structure, and socioeconomic status. CONCLUSIONS More frequent participation in cognitively stimulating activities during early life was associated with reduced risk of late-life depression.
Collapse
Affiliation(s)
- Xinye Qiu
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Andrea L. Robert
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Kaleigh McAlaine
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Luwei Quan
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Joseph Mangano
- Metals and Metal Mixtures, Cognitive Aging, Remediation and Exposure Sources (MEMCARE) Harvard Radiation and Public Health Project, Inc
| | - Marc G. Weisskopf
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| |
Collapse
|
119
|
Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585576. [PMID: 38562822 PMCID: PMC10983939 DOI: 10.1101/2024.03.18.585576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
Collapse
Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Opthalmology, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Inc., Chicago, IL, 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA, 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Michael Margolis
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Manman Shi
- Tempus Labs, Inc., Chicago, IL, 60654, USA
| | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT, 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT, 06520, USA
| |
Collapse
|
120
|
Adewale Q, Khan AF, Bennett DA, Iturria-Medina Y. Single-nucleus RNA velocity reveals critical synaptic and cell-cycle dysregulations in neuropathologically confirmed Alzheimer's disease. Sci Rep 2024; 14:7269. [PMID: 38538816 PMCID: PMC10973452 DOI: 10.1038/s41598-024-57918-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024] Open
Abstract
Typical differential single-nucleus gene expression (snRNA-seq) analyses in Alzheimer's disease (AD) provide fixed snapshots of cellular alterations, making the accurate detection of temporal cell changes challenging. To characterize the dynamic cellular and transcriptomic differences in AD neuropathology, we apply the novel concept of RNA velocity to the study of single-nucleus RNA from the cortex of 60 subjects with varied levels of AD pathology. RNA velocity captures the rate of change of gene expression by comparing intronic and exonic sequence counts. We performed differential analyses to find the significant genes driving both cell type-specific RNA velocity and expression differences in AD, extensively compared these two transcriptomic metrics, and clarified their associations with multiple neuropathologic traits. The results were cross-validated in an independent dataset. Comparison of AD pathology-associated RNA velocity with parallel gene expression differences reveals sets of genes and molecular pathways that underlie the dynamic and static regimes of cell type-specific dysregulations underlying the disease. Differential RNA velocity and its linked progressive neuropathology point to significant dysregulations in synaptic organization and cell development across cell types. Notably, most of the genes underlying this synaptic dysregulation showed increased RNA velocity in AD subjects compared to controls. Accelerated cell changes were also observed in the AD subjects, suggesting that the precocious depletion of precursor cell pools might be associated with neurodegeneration. Overall, this study uncovers active molecular drivers of the spatiotemporal alterations in AD and offers novel insights towards gene- and cell-centric therapeutic strategies accounting for dynamic cell perturbations and synaptic disruptions.
Collapse
Affiliation(s)
- Quadri Adewale
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada
| | - Ahmed F Khan
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Yasser Iturria-Medina
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada.
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada.
| |
Collapse
|
121
|
Morgan GR, Carlyle BC. Interrogation of the human cortical peptidome uncovers cell-type specific signatures of cognitive resilience against Alzheimer's disease. Sci Rep 2024; 14:7161. [PMID: 38531951 DOI: 10.1038/s41598-024-57104-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
Alzheimer's disease (AD) is characterised by age-related cognitive decline. Brain accumulation of amyloid-β plaques and tau tangles is required for a neuropathological AD diagnosis, yet up to one-third of AD-pathology positive community-dwelling elderly adults experience no symptoms of cognitive decline during life. Conversely, some exhibit chronic cognitive impairment in absence of measurable neuropathology, prompting interest into cognitive resilience-retained cognition despite significant neuropathology-and cognitive frailty-impaired cognition despite low neuropathology. Synapse loss is widespread within the AD-dementia, but not AD-resilient, brain. Recent evidence points towards critical roles for synaptic proteins, such as neurosecretory VGF, in cognitive resilience. However, VGF and related proteins often signal as peptide derivatives. Here, nontryptic peptidomic mass spectrometry was performed on 102 post-mortem cortical samples from individuals across cognitive and neuropathological spectra. Neuropeptide signalling proteoforms derived from VGF, somatostatin (SST) and protachykinin-1 (TAC1) showed higher abundance in AD-resilient than AD-dementia brain, whereas signalling proteoforms of cholecystokinin (CCK) and chromogranin (CHG) A/B and multiple cytoskeletal molecules were enriched in frail vs control brain. Integrating our data with publicly available single nuclear RNA sequencing (snRNA-seq) showed enrichment of cognition-related genes in defined cell-types with established links to cognitive resilience, including SST interneurons and excitatory intratelencephalic cells.
Collapse
Affiliation(s)
- G R Morgan
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, OX1 3QU, UK
| | - B C Carlyle
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, OX1 3QU, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
| |
Collapse
|
122
|
Dressman D, Tasaki S, Yu L, Schneider J, Bennett DA, Elyaman W, Vardarajan B. Polygenic risk associated with Alzheimer's disease and other traits influences genes involved in T cell signaling and activation. Front Immunol 2024; 15:1337831. [PMID: 38590520 PMCID: PMC10999606 DOI: 10.3389/fimmu.2024.1337831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction T cells, known for their ability to respond to an enormous variety of pathogens and other insults, are increasingly recognized as important mediators of pathology in neurodegeneration and other diseases. T cell gene expression phenotypes can be regulated by disease-associated genetic variants. Many complex diseases are better represented by polygenic risk than by individual variants. Methods We first compute a polygenic risk score (PRS) for Alzheimer's disease (AD) using genomic sequencing data from a cohort of Alzheimer's disease (AD) patients and age-matched controls, and validate the AD PRS against clinical metrics in our cohort. We then calculate the PRS for several autoimmune disease, neurological disorder, and immune function traits, and correlate these PRSs with T cell gene expression data from our cohort. We compare PRS-associated genes across traits and four T cell subtypes. Results Several genes and biological pathways associated with the PRS for these traits relate to key T cell functions. The PRS-associated gene signature generally correlates positively for traits within a particular category (autoimmune disease, neurological disease, immune function) with the exception of stroke. The trait-associated gene expression signature for autoimmune disease traits was polarized towards CD4+ T cell subtypes. Discussion Our findings show that polygenic risk for complex disease and immune function traits can have varying effects on T cell gene expression trends. Several PRS-associated genes are potential candidates for therapeutic modulation in T cells, and could be tested in in vitro applications using cells from patients bearing high or low polygenic risk for AD or other conditions.
Collapse
Affiliation(s)
- Dallin Dressman
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Shinya Tasaki
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Lei Yu
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Julie Schneider
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
- Department of Pathology, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Wassim Elyaman
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Badri Vardarajan
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
- College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, The Gertrude H. Sergievsky Center, New York, NY, United States
| |
Collapse
|
123
|
Leventhal MJ, Zanella CA, Kang B, Peng J, Gritsch D, Liao Z, Bukhari H, Wang T, Pao PC, Danquah S, Benetatos J, Nehme R, Farhi S, Tsai LH, Dong X, Scherzer CR, Feany MB, Fraenkel E. A systems-biology approach connects aging mechanisms with Alzheimer's disease pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585262. [PMID: 38559190 PMCID: PMC10980014 DOI: 10.1101/2024.03.17.585262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Age is the strongest risk factor for developing Alzheimer's disease, the most common neurodegenerative disorder. However, the mechanisms connecting advancing age to neurodegeneration in Alzheimer's disease are incompletely understood. We conducted an unbiased, genome-scale, forward genetic screen for age-associated neurodegeneration in Drosophila to identify the underlying biological processes required for maintenance of aging neurons. To connect genetic screen hits to Alzheimer's disease pathways, we measured proteomics, phosphoproteomics, and metabolomics in Drosophila models of Alzheimer's disease. We further identified Alzheimer's disease human genetic variants that modify expression in disease-vulnerable neurons. Through multi-omic, multi-species network integration of these data, we identified relationships between screen hits and tau-mediated neurotoxicity. Furthermore, we computationally and experimentally identified relationships between screen hits and DNA damage in Drosophila and human iPSC-derived neural progenitor cells. Our work identifies candidate pathways that could be targeted to attenuate the effects of age on neurodegeneration and Alzheimer's disease.
Collapse
Affiliation(s)
- Matthew J Leventhal
- MIT Ph.D. Program in Computational and Systems Biology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Camila A Zanella
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Byunguk Kang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Jiajie Peng
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - David Gritsch
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhixiang Liao
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Hassan Bukhari
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Tao Wang
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Present address: School of Computer Science, Northwestern Polytechnical University, Xi’an, China
| | - Ping-Chieh Pao
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Serwah Danquah
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joseph Benetatos
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ralda Nehme
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samouil Farhi
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Li-Huei Tsai
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xianjun Dong
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Clemens R Scherzer
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Present address: Stephen and Denise Adams Center of Yale School of Medicine, CT, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Ernest Fraenkel
- MIT Ph.D. Program in Computational and Systems Biology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Lead contact
| |
Collapse
|
124
|
Brand YE, Kluge F, Palmerini L, Paraschiv-Ionescu A, Becker C, Cereatti A, Maetzler W, Sharrack B, Vereijken B, Yarnall AJ, Rochester L, Del Din S, Muller A, Buchman AS, Hausdorff JM, Perlman O. Automated Gait Detection in Older Adults during Daily-Living using Self-Supervised Learning of Wrist-Worn Accelerometer Data: Development and Validation of ElderNet. RESEARCH SQUARE 2024:rs.3.rs-4102403. [PMID: 38559043 PMCID: PMC10980143 DOI: 10.21203/rs.3.rs-4102403/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Progressive gait impairment is common in aging adults. Remote phenotyping of gait during daily living has the potential to quantify gait alterations and evaluate the effects of interventions that may prevent disability in the aging population. Here, we developed ElderNet, a self-supervised learning model for gait detection from wrist-worn accelerometer data. Validation involved two diverse cohorts, including over 1,000 participants without gait labels, as well as 83 participants with labeled data: older adults with Parkinson's disease, proximal femoral fracture, chronic obstructive pulmonary disease, congestive heart failure, and healthy adults. ElderNet presented high accuracy (96.43 ± 2.27), specificity (98.87 ± 2.15), recall (82.32 ± 11.37), precision (86.69 ± 17.61), and F1 score (82.92 ± 13.39). The suggested method yielded superior performance compared to two state-of-the-art gait detection algorithms, with improved accuracy and F1 score (p < 0.05). In an initial evaluation of construct validity, ElderNet identified differences in estimated daily walking durations across cohorts with different clinical characteristics, such as mobility disability (p < 0.001) and parkinsonism (p < 0.001). The proposed self-supervised gait detection method has the potential to serve as a valuable tool for remote phenotyping of gait function during daily living in aging adults.
Collapse
|
125
|
Bejarano L, Kauzlaric A, Lamprou E, Lourenco J, Fournier N, Ballabio M, Colotti R, Maas R, Galland S, Massara M, Soukup K, Lilja J, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms. Cancer Cell 2024; 42:378-395.e10. [PMID: 38242126 DOI: 10.1016/j.ccell.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/11/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Brain metastasis (BrM) is a common malignancy, predominantly originating from lung, melanoma, and breast cancers. The vasculature is a key component of the BrM tumor microenvironment with critical roles in regulating metastatic seeding and progression. However, the heterogeneity of the major BrM vascular components, namely endothelial and mural cells, is still poorly understood. We perform single-cell and bulk RNA-sequencing of sorted vascular cell types and detect multiple subtypes enriched specifically in BrM compared to non-tumor brain, including previously unrecognized immune regulatory subtypes. We integrate the human data with mouse models, creating a platform to interrogate vascular targets for the treatment of BrM. We find that the CD276 immune checkpoint molecule is significantly upregulated in the BrM vasculature, and anti-CD276 blocking antibodies prolonged survival in preclinical trials. This study provides important insights into the complex interactions between the vasculature, immune cells, and cancer cells, with translational relevance for designing therapeutic interventions.
Collapse
Affiliation(s)
- Leire Bejarano
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Annamaria Kauzlaric
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eleni Lamprou
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Joao Lourenco
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nadine Fournier
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michelle Ballabio
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Roberto Colotti
- In Vivo Imaging Facility (IVIF), University of Lausanne, Lausanne, Switzerland
| | - Roeltje Maas
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Sabine Galland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Matteo Massara
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Klara Soukup
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Johanna Lilja
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Jean-Philippe Brouland
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Andreas F Hottinger
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Roy T Daniel
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Monika E Hegi
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Johanna A Joyce
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
| |
Collapse
|
126
|
Lu Y, Xu K, Kang B, Pierce BL, Yang F, Chen LS. An integrative multi-context Mendelian randomization method for identifying risk genes across human tissues. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.04.24303731. [PMID: 38496462 PMCID: PMC10942526 DOI: 10.1101/2024.03.04.24303731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Mendelian randomization (MR) provides valuable assessments of the causal effect of exposure on outcome, yet the application of conventional MR methods for mapping risk genes encounters new challenges. One of the issues is the limited availability of expression quantitative trait loci (eQTLs) as instrumental variables (IVs), hampering the estimation of sparse causal effects. Additionally, the often context/tissue-specific eQTL effects challenge the MR assumption of consistent IV effects across eQTL and GWAS data. To address these challenges, we propose a multi-context multivariable integrative MR framework, mintMR, for mapping expression and molecular traits as joint exposures. It models the effects of molecular exposures across multiple tissues in each gene region, while simultaneously estimating across multiple gene regions. It uses eQTLs with consistent effects across more than one tissue type as IVs, improving IV consistency. A major innovation of mintMR involves employing multi-view learning methods to collectively model latent indicators of disease relevance across multiple tissues, molecular traits, and gene regions. The multi-view learning captures the major patterns of disease-relevance and uses these patterns to update the estimated tissue relevance probabilities. The proposed mintMR iterates between performing a multi-tissue MR for each gene region and joint learning the disease-relevant tissue probabilities across gene regions, improving the estimation of sparse effects across genes. We apply mintMR to evaluate the causal effects of gene expression and DNA methylation for 35 complex traits using multi-tissue QTLs as IVs. The proposed mintMR controls genome-wide inflation and offers new insights into disease mechanisms.
Collapse
|
127
|
Kelley CM, Maloney B, Beck JS, Ginsberg SD, Liang W, Lahiri DK, Mufson EJ, Counts SE. Micro-RNA profiles of pathology and resilience in posterior cingulate cortex of cognitively intact elders. Brain Commun 2024; 6:fcae082. [PMID: 38572270 PMCID: PMC10988646 DOI: 10.1093/braincomms/fcae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/22/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
The posterior cingulate cortex (PCC) is a key hub of the default mode network underlying autobiographical memory retrieval, which falters early in the progression of Alzheimer's disease (AD). We recently performed RNA sequencing of post-mortem PCC tissue samples from 26 elderly Rush Religious Orders Study participants who came to autopsy with an ante-mortem diagnosis of no cognitive impairment but who collectively displayed a range of Braak I-IV neurofibrillary tangle stages. Notably, cognitively unimpaired subjects displaying high Braak stages may represent cognitive resilience to AD pathology. Transcriptomic data revealed elevated synaptic and ATP-related gene expression in Braak Stages III/IV compared with Stages I/II, suggesting these pathways may be related to PCC resilience. We also mined expression profiles for small non-coding micro-RNAs (miRNAs), which regulate mRNA stability and may represent an underexplored potential mechanism of resilience through the fine-tuning of gene expression within complex cellular networks. Twelve miRNAs were identified as differentially expressed between Braak Stages I/II and III/IV. However, the extent to which the levels of all identified miRNAs were associated with subject demographics, neuropsychological test performance and/or neuropathological diagnostic criteria within this cohort was not explored. Here, we report that a total of 667 miRNAs are significantly associated (rho > 0.38, P < 0.05) with subject variables. There were significant positive correlations between miRNA expression levels and age, perceptual orientation and perceptual speed. By contrast, higher miRNA levels correlated negatively with semantic and episodic memory. Higher expression of 15 miRNAs associated with lower Braak Stages I-II and 47 miRNAs were associated with higher Braak Stages III-IV, suggesting additional mechanistic influences of PCC miRNA expression with resilience. Pathway analysis showed enrichment for miRNAs operating in pathways related to lysine degradation and fatty acid synthesis and metabolism. Finally, we demonstrated that the 12 resilience-related miRNAs differentially expressed in Braak Stages I/II versus Braak Stages III/IV were predicted to regulate mRNAs related to amyloid processing, tau and inflammation. In summary, we demonstrate a dynamic state wherein differential PCC miRNA levels are associated with cognitive performance and post-mortem neuropathological AD diagnostic criteria in cognitively intact elders. We posit these relationships may inform miRNA transcriptional alterations within the PCC relevant to potential early protective (resilience) or pathogenic (pre-clinical or prodromal) responses to disease pathogenesis and thus may be therapeutic targets.
Collapse
Affiliation(s)
- Christy M Kelley
- Department of Translational Neuroscience and Neurology, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
| | - Bryan Maloney
- Departments of Psychiatry and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - John S Beck
- Departments of Translational Neuroscience and Family Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
| | - Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA
- Departments of Psychiatry, Neuroscience & Physiology, and the NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Winnie Liang
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Debomoy K Lahiri
- Departments of Psychiatry and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elliott J Mufson
- Department of Translational Neuroscience and Neurology, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
| | - Scott E Counts
- Departments of Translational Neuroscience and Family Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
| |
Collapse
|
128
|
Panitch R, Sahelijo N, Hu J, Nho K, Bennett DA, Lunetta KL, Au R, Stein TD, Farrer LA, Jun GR. APOE genotype-specific methylation patterns are linked to Alzheimer disease pathology and estrogen response. Transl Psychiatry 2024; 14:129. [PMID: 38424036 PMCID: PMC10904829 DOI: 10.1038/s41398-024-02834-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
The joint effects of APOE genotype and DNA methylation on Alzheimer disease (AD) risk is relatively unknown. We conducted genome-wide methylation analyses using 2,021 samples in blood (91 AD cases, 329 mild cognitive impairment, 1,391 controls) and 697 samples in brain (417 AD cases, 280 controls). We identified differentially methylated levels in AD compared to controls in an APOE genotype-specific manner at 25 cytosine-phosphate-guanine (CpG) sites in brain and 36 CpG sites in blood. Additionally, we identified seven CpG sites in the APOE region containing TOMM40, APOE, and APOC1 genes with P < 5 × 10-8 between APOE ε4 carriers and non-carriers in brain or blood. In brain, the most significant CpG site hypomethylated in ε4 carriers compared to non-carriers was from the TOMM40 in the total sample, while most of the evidence was derived from AD cases. However, the CpG site was not significantly modulating expression of these three genes in brain. Three CpG sites from the APOE were hypermethylated in APOE ε4 carriers in brain or blood compared in ε4 non-carriers and nominally significant with APOE expression in brain. Three CpG sites from the APOC1 were hypermethylated in blood, which one of the 3 CpG sites significantly lowered APOC1 expression in blood using all subjects or ε4 non-carriers. Co-methylation network analysis in blood and brain detected eight methylation networks associated with AD and APOE ε4 status. Five of the eight networks included genes containing network CpGs that were significantly enriched for estradiol perturbation, where four of the five networks were enriched for the estrogen response pathway. Our findings provide further evidence of the role of APOE genotype on methylation levels associated with AD, especially linked to estrogen response pathway.
Collapse
Affiliation(s)
- Rebecca Panitch
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Nathan Sahelijo
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Junming Hu
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences and Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison Street, Suite 1000, Chicago, IL, 60612, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA
| | - Rhoda Au
- Department of Anatomy & Neurobiology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Department of Epidemiology, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA
| | - Thor D Stein
- Department of Pathology & Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- VA Bedford Healthcare System, Bedford, MA, 01730, USA
- VA Boston Healthcare Center, Boston, MA, 02130, USA
| | - Lindsay A Farrer
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Epidemiology, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
| | - Gyungah R Jun
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
| |
Collapse
|
129
|
Ortlund E, Chen CY, Maner-Smith K, Khadka M, Ahn J, Gulbin X, Ivanova A, Dammer E, Seyfried N, Bennett D, Hajjar I. Integrative brain omics approach reveals key role for sn-1 lysophosphatidylethanolamine in Alzheimer's dementia. RESEARCH SQUARE 2024:rs.3.rs-3973736. [PMID: 38464293 PMCID: PMC10925467 DOI: 10.21203/rs.3.rs-3973736/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The biology of individual lipid species and their relevance in Alzheimer's disease (AD) remains incompletely understood. We utilized non-targeted mass spectrometry to examine brain lipids variations across 316 post-mortem brains from participants in the Religious Orders Study (ROS) or Rush Memory and Aging Project (MAP) cohorts classified as either control, asymptomatic AD (AAD), or symptomatic AD (SAD) and integrated the lipidomics data with untargeted proteomic characterization on the same individuals. Lipid enrichment analysis and analysis of variance identified significantly lower abundance of lysophosphatidylethanolamine (LPE) and lysophosphatidylcholine (LPC) species in SAD than controls or AAD. Lipid-protein co-expression network analyses revealed that lipid modules consisting of LPE and LPC exhibited a significant association to protein modules associated with MAPK/metabolism, post-synaptic density, and Cell-ECM interaction pathways and were associated with better antemortem cognition and with neuropathological changes seen in AD. Particularly, LPE 22:6 [sn-1] levels are significantly decreased across AD cases (SAD) and show the most influence on protein changes compared to other lysophospholipid species. LPE 22:6 may be a lipid signature for AD and could be leveraged as potential therapeutic or dietary targets for AD.
Collapse
|
130
|
Agrawal S, Leurgans SE, Barnes LL, Dams-O’Connor K, Mez J, Bennett DA, Schneider JA. Chronic traumatic encephalopathy and aging-related tau astrogliopathy in community-dwelling older persons with and without moderate-to-severe traumatic brain injury. J Neuropathol Exp Neurol 2024; 83:181-193. [PMID: 38300796 PMCID: PMC10880068 DOI: 10.1093/jnen/nlae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
This study examined the frequency of chronic traumatic encephalopathy-neuropathologic change (CTE-NC) and aging-related tau astrogliopathy (ARTAG) in community-dwelling older adults and tested the hypothesis that these tau pathologies are associated with a history of moderate-to-severe traumatic brain injury (msTBI), defined as a TBI with loss of consciousness >30 minutes. We evaluated CTE-NC, ARTAG, and Alzheimer disease pathologies in 94 participants with msTBI and 94 participants without TBI matched by age, sex, education, and dementia status TBI from the Rush community-based cohorts. Six (3%) of brains showed the pathognomonic lesion of CTE-NC; only 3 of these had a history of msTBI. In contrast, ARTAG was common in older brains (gray matter ARTAG = 77%; white matter ARTAG = 54%; subpial ARTAG = 51%); there were no differences in severity, type, or distribution of ARTAG pathology with respect to history of msTBI. Furthermore, those with msTBI did not have higher levels of PHF-tau tangles density but had higher levels of amyloid-β load (Estimate = 0.339, SE = 0.164, p = 0.040). These findings suggest that CTE-NC is infrequent while ARTAG is common in the community and that both pathologies are unrelated to msTBI. The association of msTBI with amyloid-β, rather than with tauopathies suggests differential mechanisms of neurodegeneration in msTBI.
Collapse
Affiliation(s)
- Sonal Agrawal
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Sue E Leurgans
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Lisa L Barnes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Kristen Dams-O’Connor
- Department of Rehabilitation and Human Performance, Mt Sinai School of Medicine, New York, New York, USA
- Department of Neurology, Mt Sinai School of Medicine, New York, New York, USA
| | - Jesse Mez
- Boston University Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Boston University Chronic Traumatic Encephalopathy Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - David A Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Julie A Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| |
Collapse
|
131
|
Mamais A, Sanyal A, Fajfer A, Zykoski CG, Guldin M, Riley-DiPaolo A, Subrahmanian N, Gibbs W, Lin S, LaVoie MJ. The LRRK2 kinase substrates RAB8a and RAB10 contribute complementary but distinct disease-relevant phenotypes in human neurons. Stem Cell Reports 2024; 19:163-173. [PMID: 38307024 PMCID: PMC10874859 DOI: 10.1016/j.stemcr.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 02/04/2024] Open
Abstract
Mutations in the LRRK2 gene cause familial Parkinson's disease presenting with pleomorphic neuropathology that can involve α-synuclein or tau accumulation. LRRK2 mutations are thought to converge upon a pathogenic increase in LRRK2 kinase activity. A subset of small RAB GTPases has been identified as LRRK2 substrates, with LRRK2-dependent phosphorylation resulting in RAB inactivation. We used CRISPR-Cas9 genome editing to generate a novel series of isogenic iPSC lines deficient in the two most well-validated LRRK2 substrates, RAB8a and RAB10, from deeply phenotyped healthy control lines. Thorough characterization of NGN2-induced neurons revealed opposing effects of RAB8a and RAB10 deficiency on lysosomal pH and Golgi organization, with isolated effects of RAB8a and RAB10 ablation on α-synuclein and tau, respectively. Our data demonstrate largely antagonistic effects of genetic RAB8a or RAB10 inactivation, which provide discrete insight into the pathologic features of their biochemical inactivation by pathogenic LRRK2 mutation in human disease.
Collapse
Affiliation(s)
- Adamantios Mamais
- Center for Translational Research in Neurodegenerative Disease and Fixel Institute for Neurologic Diseases, Department of Neurology, University of Florida, Gainesville, FL, USA
| | - Anwesha Sanyal
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Austin Fajfer
- Center for Translational Research in Neurodegenerative Disease and Fixel Institute for Neurologic Diseases, Department of Neurology, University of Florida, Gainesville, FL, USA
| | - Catherine G Zykoski
- Center for Translational Research in Neurodegenerative Disease and Fixel Institute for Neurologic Diseases, Department of Neurology, University of Florida, Gainesville, FL, USA
| | - Michael Guldin
- Center for Translational Research in Neurodegenerative Disease and Fixel Institute for Neurologic Diseases, Department of Neurology, University of Florida, Gainesville, FL, USA
| | | | - Nitya Subrahmanian
- Center for Translational Research in Neurodegenerative Disease and Fixel Institute for Neurologic Diseases, Department of Neurology, University of Florida, Gainesville, FL, USA
| | - Whitney Gibbs
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven Lin
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew J LaVoie
- Center for Translational Research in Neurodegenerative Disease and Fixel Institute for Neurologic Diseases, Department of Neurology, University of Florida, Gainesville, FL, USA; Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
| |
Collapse
|
132
|
Rybnicek J, Chen Y, Milic M, Tio ES, McLaurin J, Hohman TJ, De Jager PL, Schneider JA, Wang Y, Bennett DA, Tripathy S, Felsky D, Lambe EK. CHRNA5 links chandelier cells to severity of amyloid pathology in aging and Alzheimer's disease. Transl Psychiatry 2024; 14:83. [PMID: 38331937 PMCID: PMC10853183 DOI: 10.1038/s41398-024-02785-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Changes in high-affinity nicotinic acetylcholine receptors are intricately connected to neuropathology in Alzheimer's Disease (AD). Protective and cognitive-enhancing roles for the nicotinic α5 subunit have been identified, but this gene has not been closely examined in the context of human aging and dementia. Therefore, we investigate the nicotinic α5 gene CHRNA5 and the impact of relevant single nucleotide polymorphisms (SNPs) in prefrontal cortex from 922 individuals with matched genotypic and post-mortem RNA sequencing in the Religious Orders Study and Memory and Aging Project (ROS/MAP). We find that a genotype robustly linked to increased expression of CHRNA5 (rs1979905A2) predicts significantly reduced cortical β-amyloid load. Intriguingly, co-expression analysis suggests CHRNA5 has a distinct cellular expression profile compared to other nicotinic receptor genes. Consistent with this prediction, single nucleus RNA sequencing from 22 individuals reveals CHRNA5 expression is disproportionately elevated in chandelier neurons, a distinct subtype of inhibitory neuron known for its role in excitatory/inhibitory (E/I) balance. We show that chandelier neurons are enriched in amyloid-binding proteins compared to basket cells, the other major subtype of PVALB-positive interneurons. Consistent with the hypothesis that nicotinic receptors in chandelier cells normally protect against β-amyloid, cell-type proportion analysis from 549 individuals reveals these neurons show amyloid-associated vulnerability only in individuals with impaired function/trafficking of nicotinic α5-containing receptors due to homozygosity of the missense CHRNA5 SNP (rs16969968A2). Taken together, these findings suggest that CHRNA5 and its nicotinic α5 subunit exert a neuroprotective role in aging and Alzheimer's disease centered on chandelier interneurons.
Collapse
Affiliation(s)
- Jonas Rybnicek
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Yuxiao Chen
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Milos Milic
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Earvin S Tio
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - JoAnne McLaurin
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie A Schneider
- Department of Pathology, Rush University, Chicago, IL, USA
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - Yanling Wang
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - David A Bennett
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - Shreejoy Tripathy
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Evelyn K Lambe
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
- Department of OBGYN, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
133
|
Kapasi A, Capuano AW, Lamar M, Leurgans SE, Evia AM, Bennett DA, Arfanakis K, Schneider JA. Atherosclerosis and Hippocampal Volumes in Older Adults: The Role of Age and Blood Pressure. J Am Heart Assoc 2024; 13:e031551. [PMID: 38240240 PMCID: PMC11056126 DOI: 10.1161/jaha.123.031551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Lower hippocampal volume is associated with late-life cognitive decline and is an important, but nonspecific marker for clinical Alzheimer's dementia. Cerebrovascular disease may also be associated with hippocampal volume. Here we study the role of intracranial large vessel disease (atherosclerosis) in association with hippocampal volume and the potential role of age, average late-life blood pressure across all visits, and other factors (sex, apolipoprotein ε4 [APOE ε4], and diabetes). METHODS AND RESULTS Data came from 765 community-based older people (91 years old on average at death; 72% women), from 2 ongoing clinical-pathologic cohort studies. Participants completed baseline assessment, annual standardized blood pressure measurements, vascular risk assessment for diabetes, and blood draws to determine APOE genotype, and at death, brains were removed and underwent ex vivo magnetic resonance imaging and neuropathologic evaluation for atherosclerosis pathology and other cerebrovascular and neurodegenerative pathologies. Linear regression models examined the association of atherosclerosis and hippocampal to hemisphere volume ratio and whether age at death, blood pressure, and other factors modified associations. In linear regression models adjusted for demographics and neurodegenerative and other cerebrovascular pathologies, atherosclerosis severity was associated with a lower hippocampal to hemisphere volume ratio. In separate models, we found the effect of atherosclerosis on the ratio of hippocampal to hemisphere volume was attenuated among advanced age at death or having higher systolic blood pressure (interaction terms P≤0.03). We did not find confounding or interactions with sex, diabetes, or APOE ε4. CONCLUSIONS Atherosclerosis severity is associated with lower hippocampal volume, independent of neurodegenerative and other cerebrovascular pathologies. Higher systolic blood pressures and advanced age attenuate associations.
Collapse
Affiliation(s)
- Alifiya Kapasi
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
- Department of Pathology (Neuropathology)Rush University Medical CenterChicagoIL
| | - Ana W. Capuano
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
- Department of Neurological SciencesRush University Medical CenterChicagoIL
| | - Melissa Lamar
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
- Department of Psychiatry and Behavioral SciencesRush University Medical CenterChicagoIL
| | - Sue E. Leurgans
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
- Department of Neurological SciencesRush University Medical CenterChicagoIL
| | - Arnold M. Evia
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
| | - David A. Bennett
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
- Department of Neurological SciencesRush University Medical CenterChicagoIL
| | - Konstantinos Arfanakis
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
- Department of Biomedical EngineeringIllinois Institute of TechnologyChicagoIL
- Department of Diagnostic RadiologyRush University Medical CenterChicagoIL
| | - Julie A. Schneider
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
- Department of Pathology (Neuropathology)Rush University Medical CenterChicagoIL
- Department of Neurological SciencesRush University Medical CenterChicagoIL
| |
Collapse
|
134
|
Xu X, Wang H, Bennett DA, Zhang QY, Meng XY, Zhang HY. Characterization of brain resilience in Alzheimer's disease using polygenic risk scores and further improvement by integrating mitochondria-associated loci. J Adv Res 2024; 56:113-124. [PMID: 36921896 PMCID: PMC10834825 DOI: 10.1016/j.jare.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
INTRODUCTION Identification of high-risk people for Alzheimer's disease (AD) is critical for prognosis and early management. Longitudinal epidemiologic studies have observed heterogeneity in the brain and cognitive aging. Brain resilience was described as above-expected cognitive function. The "resilience" framework has been shown to correlate with individual characteristics such as genetic factors and age. Besides, accumulative evidence has confirmed the association of mitochondria with the pathogenesis of AD. However, it is challenging to assess resilience through genetic metrics, in particular incorporating mitochondria-associated loci. OBJECTIVES In this paper, we first demonstrated that polygenic risk scores (PRS) could characterize individuals' resilience levels. Then, we indicated that mitochondria-associated loci could improve the performance of PRSs, providing more reliable measurements for the prevention and diagnosis of AD. METHODS The discovery (N = 1,550) and independent validation samples (N = 2,090) were used to construct nine types of PRSs containing mitochondria-related loci (PRSMT) from both biological and statistical aspects and combined them with known AD risk loci derived from genome-wide association studies (GWAS).Individuals' levels of brain resilience were comprehensively measured by linear regression models using eight pathological characteristics. RESULTS It was found that PRSs could characterize brain resilience levels (e.g., Pearson correlation test Pmin = 7.96×10-9). Moreover, the performance of PRS models could be efficiently improved by incorporating a small number of mitochondria-related loci (e.g., Pearson correlation test P improved from 1.41×10-3 to 6.09×10-6). PRSs' ability to characterize brain resilience was validated. More importantly, by incorporating some mitochondria-related loci, the performance of PRSs in measuring brain resilience could be significantly improved. CONCLUSION Our findings imply that mitochondria may play an important role in brain resilience, and targeting mitochondria may open a new door to AD prevention and therapy.
Collapse
Affiliation(s)
- Xuan Xu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang-Yu Meng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; College of Basic Medical Sciences, Medical School, Hubei Minzu University, Enshi 445000, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
135
|
Breen C, Papale LA, Clark LR, Bergmann PE, Madrid A, Asthana S, Johnson SC, Keleş S, Alisch RS, Hogan KJ. Whole genome methylation sequencing in blood identifies extensive differential DNA methylation in late-onset dementia due to Alzheimer's disease. Alzheimers Dement 2024; 20:1050-1062. [PMID: 37856321 PMCID: PMC10916976 DOI: 10.1002/alz.13514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/17/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
INTRODUCTION DNA microarray-based studies report differentially methylated positions (DMPs) in blood between late-onset dementia due to Alzheimer's disease (AD) and cognitively unimpaired individuals, but interrogate < 4% of the genome. METHODS We used whole genome methylation sequencing (WGMS) to quantify DNA methylation levels at 25,409,826 CpG loci in 281 blood samples from 108 AD and 173 cognitively unimpaired individuals. RESULTS WGMS identified 28,038 DMPs throughout the human methylome, including 2707 differentially methylated genes (e.g., SORCS3, GABA, and PICALM) encoding proteins in biological pathways relevant to AD such as synaptic membrane, cation channel complex, and glutamatergic synapse. One hundred seventy-three differentially methylated blood-specific enhancers interact with the promoters of 95 genes that are differentially expressed in blood from persons with and without AD. DISCUSSION WGMS identifies differentially methylated CpGs in known and newly detected genes and enhancers in blood from persons with and without AD. HIGHLIGHTS Whole genome DNA methylation levels were quantified in blood from persons with and without Alzheimer's disease (AD). Twenty-eight thousand thirty-eight differentially methylated positions (DMPs) were identified. Two thousand seven hundred seven genes comprise DMPs. Forty-eight of 75 independent genetic risk loci for AD have DMPs. One thousand five hundred sixty-eight blood-specific enhancers comprise DMPs, 173 of which interact with the promoters of 95 genes that are differentially expressed in blood from persons with and without AD.
Collapse
Affiliation(s)
- Coleman Breen
- Department of StatisticsUniversity of Wisconsin, Medical Sciences CenterMadisonWisconsinUSA
| | - Ligia A. Papale
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Lindsay R. Clark
- Wisconsin Alzheimer's Disease Research CenterUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
| | - Phillip E. Bergmann
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Andy Madrid
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sanjay Asthana
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sterling C. Johnson
- Wisconsin Alzheimer's Disease Research CenterUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sündüz Keleş
- Department of StatisticsUniversity of Wisconsin, Medical Sciences CenterMadisonWisconsinUSA
- Department of Biostatistics and Medical InformaticsUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Reid S. Alisch
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Kirk J. Hogan
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Department of AnesthesiologyUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| |
Collapse
|
136
|
Evans P, Nagai T, Konkashbaev A, Zhou D, Knapik EW, Gamazon ER. Transcriptome-Wide Association Studies (TWAS): Methodologies, Applications, and Challenges. Curr Protoc 2024; 4:e981. [PMID: 38314955 PMCID: PMC10846672 DOI: 10.1002/cpz1.981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Transcriptome-wide association study (TWAS) methodologies aim to identify genetic effects on phenotypes through the mediation of gene transcription. In TWAS, in silico models of gene expression are trained as functions of genetic variants and then applied to genome-wide association study (GWAS) data. This post-GWAS analysis identifies gene-trait associations with high interpretability, enabling follow-up functional genomics studies and the development of genetics-anchored resources. We provide an overview of commonly used TWAS approaches, their advantages and limitations, and some widely used applications. © 2024 Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Patrick Evans
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Taylor Nagai
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anuar Konkashbaev
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan Zhou
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ela W Knapik
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eric R Gamazon
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| |
Collapse
|
137
|
Buchman AS. Untangling a taxonomy of living from the science of the continuum of life. Curr Opin Behav Sci 2024; 55:101345. [PMID: 38223539 PMCID: PMC10783655 DOI: 10.1016/j.cobeha.2023.101345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Medical innovation and technologic advances enrich daily living and occur within our normative worlds, that are socially constructed. These advances confront society with critical questions about the nature of human life, laying bare the inadequacies of extant norms and boundaries. Yet, society has been unable to develop consensus about when life ends. Scientific studies highlight that life is best characterized by continua without natural boundaries. Thus, scientific information alone cannot be employed to justify the socially constructed health categories required for setting norms and boundaries. An iterative process that integrates a broad range of non-scientific data with advancing scientific information is needed to facilitate consensus for updating social norms and boundaries. This can lead to a new taxonomy of living across the measurable continuum of life and align our normative worlds with the dizzying pace of medical innovation and advances in technologies transforming the world in which we live.
Collapse
Affiliation(s)
- Aron S Buchman
- Rush Alzheimer's Disease Center, Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| |
Collapse
|
138
|
Gui J, Meng L, Huang D, Wang L, Yang X, Ding R, Han Z, Cheng L, Jiang L. Identification of novel proteins for sleep apnea by integrating genome-wide association data and human brain proteomes. Sleep Med 2024; 114:92-99. [PMID: 38160582 DOI: 10.1016/j.sleep.2023.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Sleep apnea is regarded as a significant global public health issue. The relationship between sleep apnea and nervous system diseases is intricate, yet the precise mechanism remains unclear. METHODS In this study, we conducted a comprehensive analysis integrating the human brain proteome and transcriptome with sleep apnea genome-wide association study (GWAS), employing genome-wide association study (PWAS), transcriptome-wide association study (TWAS), Mendelian randomization (MR), and colocalization analysis to identify brain proteins associated with sleep apnea. RESULTS The discovery PWAS identified six genes (CNNM2, XRCC6, C3orf18, CSDC2, SQRDL, and DGUOK) whose altered protein abundances in the brain were found to be associated with sleep apnea. The independent confirmatory PWAS successfully replicated four out of these six genes (CNNM2, C3orf18, CSDC2, and SQRDL). The transcriptome level TWAS analysis further confirmed two out of the four genes (C3orf18 and CSDC2). The subsequent two-sample Mendelian randomization provided compelling causal evidence supporting the association of C3orf18, CSDC2, CNNM2, and SQRDL with sleep apnea. The co-localization analysis further supported the association between CSDC2 and sleep apnea (posterior probability of hypothesis 4 = 0.75). CONCLUSIONS In summary, the integration of brain proteomic and transcriptomic data provided multifaceted evidence supporting causal relationships between four specific brain proteins (CSDC2, C3orf18, CNNM2, and SQRDL) and sleep apnea. Our findings provide new insights into the molecular basis of sleep apnea in the brain, promising to advance understanding of its pathogenesis in future research.
Collapse
Affiliation(s)
- Jianxiong Gui
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Linxue Meng
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Dishu Huang
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Lingman Wang
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Xiaoyue Yang
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Ran Ding
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Ziyao Han
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Li Cheng
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Li Jiang
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China.
| |
Collapse
|
139
|
Zammit AR, Yu L, Buchman AS, Lange-Maia BS, Bennett DA, Grodstein F. A prospective study of the association of cognitive and motor function with odds of life space constriction in older adults. J Am Geriatr Soc 2024; 72:390-398. [PMID: 37905593 PMCID: PMC10926217 DOI: 10.1111/jgs.18640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/22/2023] [Accepted: 10/01/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Many studies indicate that smaller life space is related to worse cognitive and motor function. It is plausible that cognitive and motor function also predict life space constriction, thus long-term, prospective studies are needed of cognitive and motor function as predictors of life space. METHODS A total of 1246 participants of the Rush Memory and Aging Project, who reported initial maximal life space and at least one follow-up assessment were included in this prospective study, with up to 19 years follow-up. The outcome of interest was the Modified version of the Life Space Questionnaire; which we categorized into large (beyond community), medium (neighborhood/community), and small (home/yard) life space. Participants also had detailed composite measures of global cognition and motor function as predictors and available at the first life space assessment. Life space transitions over one-year periods were modeled using multistate Markov modeling, including confounders and both predictors simultaneously. RESULTS Better cognitive and motor function were broadly associated with lower odds of life space constriction (Cognitive: Large ➔ medium: OR = 0.91, 95% CI 0.83-1.00; Large ➔ small: OR = 0.85, 95% CI 0.74-0.97; Medium ➔ small: OR = 1.01, 95% CI 0.82-1.22. Motor: large ➔ medium: OR = 0.76, 95% CI 0.69-0.83; large ➔ small: OR = 0.58, 95% CI 0.51-0.67; medium ➔ small: OR = 0.71, 95% CI = 0.57-0.87). CONCLUSIONS Combined with previous literature that life space predicts function, these results support the notion of complex inter-relations of cognitive function, motor function, and life space.
Collapse
Affiliation(s)
- Andrea R. Zammit
- Rush Alzheimer’s Disease Center, Rush University
Medical Center, Chicago, IL 60612, USA
- Department of Psychiatry and Behavioral Sciences, Rush
University Medical Center, Chicago, IL 60612, USA
| | - Lei Yu
- Rush Alzheimer’s Disease Center, Rush University
Medical Center, Chicago, IL 60612, USA
- Department of Neurological Sciences, Rush University
Medical Center, Chicago, IL 60612, USA
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University
Medical Center, Chicago, IL 60612, USA
- Department of Neurological Sciences, Rush University
Medical Center, Chicago, IL 60612, USA
| | - Brittney S. Lange-Maia
- Rush Alzheimer’s Disease Center, Rush University
Medical Center, Chicago, IL 60612, USA
- Department of Family and Preventive Medicine, Rush
University Medical Center, Chicago, IL 60612
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University
Medical Center, Chicago, IL 60612, USA
- Department of Neurological Sciences, Rush University
Medical Center, Chicago, IL 60612, USA
| | - Francine Grodstein
- Rush Alzheimer’s Disease Center, Rush University
Medical Center, Chicago, IL 60612, USA
- Department of Internal Medicine, Rush University Medical
Center, Chicago, IL 60612, USA
| |
Collapse
|
140
|
Su C, Zhang J, Zhao H. Estimating cell-type-specific gene co-expression networks from bulk gene expression data with an application to Alzheimer's disease. J Am Stat Assoc 2024; 119:811-824. [PMID: 39280354 PMCID: PMC11394578 DOI: 10.1080/01621459.2023.2297467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 12/13/2023] [Indexed: 09/18/2024]
Abstract
Inferring and characterizing gene co-expression networks has led to important insights on the molecular mechanisms of complex diseases. Most co-expression analyses to date have been performed on gene expression data collected from bulk tissues with different cell type compositions across samples. As a result, the co-expression estimates only offer an aggregated view of the underlying gene regulations and can be confounded by heterogeneity in cell type compositions, failing to reveal gene coordination that may be distinct across different cell types. In this paper, we introduce a flexible framework for estimating cell-type-specific gene co-expression networks from bulk sample data, without making specific assumptions on the distributions of gene expression profiles in different cell types. We develop a novel sparse least squares estimator, referred to as CSNet, that is efficient to implement and has good theoretical properties. Using CSNet, we analyzed the bulk gene expression data from a cohort study on Alzheimer's disease and identified previously unknown cell-type-specific co-expressions among Alzheimer's disease risk genes, suggesting cell-type-specific disease mechanisms.
Collapse
Affiliation(s)
- Chang Su
- Department of Biostatistics and Bioinformatics, Emory University
- Department of Biostatistics, Yale University
| | - Jingfei Zhang
- Information Systems and Operations Management, Emory University
| | - Hongyu Zhao
- Department of Biostatistics, Yale University
| |
Collapse
|
141
|
Roussos P, Kosoy R, Fullard J, Bendl J, Kleopoulos S, Shao Z, Argyriou S, Mathur D, Vicari J, Ma Y, Humphrey J, Brophy E, Raj T, Katsel P, Voloudakis G, Lee D, Bennett D, Haroutunian V, Hoffman G. Alzheimer's disease transcriptional landscape in ex-vivo human microglia. RESEARCH SQUARE 2024:rs.3.rs-3851590. [PMID: 38343831 PMCID: PMC10854306 DOI: 10.21203/rs.3.rs-3851590/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Microglia are resident immune cells of the brain and are implicated in the etiology of Alzheimer's Disease (AD) and other diseases. Yet the cellular and molecular processes regulating their function throughout the course of the disease are poorly understood. Here, we present the transcriptional landscape of primary microglia from 189 human postmortem brains, including 58 healthy aging individuals and 131 with a range of disease phenotypes, including 63 patients representing the full spectrum of clinical and pathological severity of AD. We identified transcriptional changes associated with multiple AD phenotypes, capturing the severity of dementia and neuropathological lesions. Transcript-level analyses identified additional genes with heterogeneous isoform usage and AD phenotypes. We identified changes in gene-gene coordination in AD, dysregulation of co-expression modules, and disease subtypes with distinct gene expression. Taken together, these data further our understanding of the key role of microglia in AD biology and nominate candidates for therapeutic intervention.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yixuan Ma
- Icahn School of Medicine at Mount Sinai
| | | | | | | | | | | | | | | | | | | |
Collapse
|
142
|
Cha Y, Kagalwala MN, Ross J. Navigating the Frontiers of Machine Learning in Neurodegenerative Disease Therapeutics. Pharmaceuticals (Basel) 2024; 17:158. [PMID: 38399373 PMCID: PMC10891920 DOI: 10.3390/ph17020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Recent advances in machine learning hold tremendous potential for enhancing the way we develop new medicines. Over the years, machine learning has been adopted in nearly all facets of drug discovery, including patient stratification, lead discovery, biomarker development, and clinical trial design. In this review, we will discuss the latest developments linking machine learning and CNS drug discovery. While machine learning has aided our understanding of chronic diseases like Alzheimer's disease and Parkinson's disease, only modest effective therapies currently exist. We highlight promising new efforts led by academia and emerging biotech companies to leverage machine learning for exploring new therapies. These approaches aim to not only accelerate drug development but to improve the detection and treatment of neurodegenerative diseases.
Collapse
Affiliation(s)
| | | | - Jermaine Ross
- Alleo Labs, San Francisco, CA 94105, USA; (Y.C.); (M.N.K.)
| |
Collapse
|
143
|
Arnold M, Buyukozkan M, Doraiswamy PM, Nho K, Wu T, Gudnason V, Launer LJ, Wang-Sattler R, Adamski J, De Jager PL, Ertekin-Taner N, Bennett DA, Saykin AJ, Peters A, Suhre K, Kaddurah-Daouk R, Kastenmüller G, Krumsiek J. Individual bioenergetic capacity as a potential source of resilience to Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.23.23297820. [PMID: 38313266 PMCID: PMC10836119 DOI: 10.1101/2024.01.23.23297820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Impaired glucose uptake in the brain is one of the earliest presymptomatic manifestations of Alzheimer's disease (AD). The absence of symptoms for extended periods of time suggests that compensatory metabolic mechanisms can provide resilience. Here, we introduce the concept of a systemic 'bioenergetic capacity' as the innate ability to maintain energy homeostasis under pathological conditions, potentially serving as such a compensatory mechanism. We argue that fasting blood acylcarnitine profiles provide an approximate peripheral measure for this capacity that mirrors bioenergetic dysregulation in the brain. Using unsupervised subgroup identification, we show that fasting serum acylcarnitine profiles of participants from the AD Neuroimaging Initiative yields bioenergetically distinct subgroups with significant differences in AD biomarker profiles and cognitive function. To assess the potential clinical relevance of this finding, we examined factors that may offer diagnostic and therapeutic opportunities. First, we identified a genotype affecting the bioenergetic capacity which was linked to succinylcarnitine metabolism and significantly modulated the rate of future cognitive decline. Second, a potentially modifiable influence of beta-oxidation efficiency seemed to decelerate bioenergetic aging and disease progression. Our findings, which are supported by data from more than 9,000 individuals, suggest that interventions tailored to enhance energetic health and to slow bioenergetic aging could mitigate the risk of symptomatic AD, especially in individuals with specific mitochondrial genotypes.
Collapse
Affiliation(s)
- Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mustafa Buyukozkan
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - P. Murali Doraiswamy
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences and Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tong Wu
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Vilmundur Gudnason
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Kopavogur, Iceland
| | - Lenore J. Launer
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Bethesda, Maryland
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Taub Institute, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | | | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences and Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; IBE, Medical Faculty, Ludwig-Maximilians-Universität, Munich, Germany; German Center for Diabetes Research (DZD e.V.), Munich, Germany; German Center for Cardiovascular Disease (DZHK e.V.), Munich Heart Alliance, Munich, Germany
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jan Krumsiek
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
144
|
Yang J, Liu X, Oveisgharan S, Zammit AR, Nag S, Bennett DA, Buchman AS. Inferring Alzheimer's disease pathologic traits from clinical measures in living adults. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.05.08.23289668. [PMID: 37214885 PMCID: PMC10197717 DOI: 10.1101/2023.05.08.23289668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Alzheimer's disease neuropathologic changes (AD-NC) are important for identify people with high risk for AD dementia (ADD) and subtyping ADD. Objective Develop imputation models based on clinical measures to infer AD-NC. Methods We used penalized generalized linear regression to train imputation models for four AD-NC traits (amyloid-β, tangles, global AD pathology, and pathologic AD) in Rush Memory and Aging Project decedents, using clinical measures at the last visit prior to death as predictors. We validated these models by inferring AD-NC traits with clinical measures at the last visit prior to death for independent Religious Orders Study (ROS) decedents. We inferred baseline AD-NC traits for all ROS participants at study entry, and then tested if inferred AD-NC traits at study entry predicted incident ADD and postmortem pathologic AD. Results Inferred AD-NC traits at the last visit prior to death were related to postmortem measures with R2=(0.188,0.316,0.262) respectively for amyloid-β, tangles, and global AD pathology, and prediction Area Under the receiver operating characteristic Curve (AUC) 0.765 for pathologic AD. Inferred baseline levels of all four AD-NC traits predicted ADD. The strongest prediction was obtained by the inferred baseline probabilities of pathologic AD with AUC=(0.919,0.896) for predicting the development of ADD in 3 and 5 years from baseline. The inferred baseline levels of all four AD-NC traits significantly discriminated pathologic AD profiled eight years later with p-values<1.4 × 10-10. Conclusion Inferred AD-NC traits based on clinical measures may provide effective AD biomarkers that can estimate the burden of AD-NC traits in aging adults.
Collapse
Affiliation(s)
- Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Atlanta, GA, 30322, USA
| | - Xizhu Liu
- Department of Biostatistics, Yale University School of Public Health, 60 College St, New Haven, CT, 06510, USA
| | - Shahram Oveisgharan
- Rush Alzheimer’s Disease Center, Rush University Medicine Center, 1620 W Harrison St, Chicago, IL, 60612, USA
| | - Andrea R. Zammit
- Rush Alzheimer’s Disease Center, Rush University Medicine Center, 1620 W Harrison St, Chicago, IL, 60612, USA
| | - Sukriti Nag
- Rush Alzheimer’s Disease Center, Rush University Medicine Center, 1620 W Harrison St, Chicago, IL, 60612, USA
| | - David A Bennett
- Rush Alzheimer’s Disease Center, Rush University Medicine Center, 1620 W Harrison St, Chicago, IL, 60612, USA
| | - Aron S Buchman
- Rush Alzheimer’s Disease Center, Rush University Medicine Center, 1620 W Harrison St, Chicago, IL, 60612, USA
| |
Collapse
|
145
|
Bartosch AMW, Youth EHH, Hansen S, Wu Y, Buchanan HM, Kaufman ME, Xiao H, Koo SY, Ashok A, Sivakumar S, Soni RK, Dumitrescu LC, Lam TG, Ropri AS, Lee AJ, Klein HU, Vardarajan BN, Bennett DA, Young-Pearse TL, De Jager PL, Hohman TJ, Sproul AA, Teich AF. ZCCHC17 Modulates Neuronal RNA Splicing and Supports Cognitive Resilience in Alzheimer's Disease. J Neurosci 2024; 44:e2324222023. [PMID: 38050142 PMCID: PMC10860597 DOI: 10.1523/jneurosci.2324-22.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 09/22/2023] [Accepted: 11/07/2023] [Indexed: 12/06/2023] Open
Abstract
ZCCHC17 is a putative master regulator of synaptic gene dysfunction in Alzheimer's disease (AD), and ZCCHC17 protein declines early in AD brain tissue, before significant gliosis or neuronal loss. Here, we investigate the function of ZCCHC17 and its role in AD pathogenesis using data from human autopsy tissue (consisting of males and females) and female human cell lines. Co-immunoprecipitation (co-IP) of ZCCHC17 followed by mass spectrometry analysis in human iPSC-derived neurons reveals that ZCCHC17's binding partners are enriched for RNA-splicing proteins. ZCCHC17 knockdown results in widespread RNA-splicing changes that significantly overlap with splicing changes found in AD brain tissue, with synaptic genes commonly affected. ZCCHC17 expression correlates with cognitive resilience in AD patients, and we uncover an APOE4-dependent negative correlation of ZCCHC17 expression with tangle burden. Furthermore, a majority of ZCCHC17 interactors also co-IP with known tau interactors, and we find a significant overlap between alternatively spliced genes in ZCCHC17 knockdown and tau overexpression neurons. These results demonstrate ZCCHC17's role in neuronal RNA processing and its interaction with pathology and cognitive resilience in AD, and suggest that the maintenance of ZCCHC17 function may be a therapeutic strategy for preserving cognitive function in the setting of AD pathology.
Collapse
Affiliation(s)
- Anne Marie W Bartosch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Elliot H H Youth
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Shania Hansen
- Department of Neurology, Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Yiyang Wu
- Department of Neurology, Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Heather M Buchanan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Maria E Kaufman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Harrison Xiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - So Yeon Koo
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Archana Ashok
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Sharanya Sivakumar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, New York 10032
| | - Logan C Dumitrescu
- Department of Neurology, Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Tiffany G Lam
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Ali S Ropri
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Annie J Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| | - Hans-Ulrich Klein
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612
| | - Tracy L Young-Pearse
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138
| | - Philip L De Jager
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Andrew A Sproul
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Andrew F Teich
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| |
Collapse
|
146
|
Shi JJ, Mao CY, Guo YZ, Fan Y, Hao XY, Li SJ, Tian J, Hu ZW, Li MJ, Li JD, Ma DR, Guo MN, Zuo CY, Liang YY, Xu YM, Yang J, Shi CH. Joint analysis of proteome, transcriptome, and multi-trait analysis to identify novel Parkinson's disease risk genes. Aging (Albany NY) 2024; 16:1555-1580. [PMID: 38240717 PMCID: PMC10866412 DOI: 10.18632/aging.205444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024]
Abstract
Genome-wide association studies (GWAS) have identified multiple risk variants for Parkinson's disease (PD). Nevertheless, how the risk variants confer the risk of PD remains largely unknown. We conducted a proteome-wide association study (PWAS) and summary-data-based mendelian randomization (SMR) analysis by integrating PD GWAS with proteome and protein quantitative trait loci (pQTL) data from human brain, plasma and CSF. We also performed a large transcriptome-wide association study (TWAS) and Fine-mapping of causal gene sets (FOCUS), leveraging joint-tissue imputation (JTI) prediction models of 22 tissues to identify and prioritize putatively causal genes. We further conducted PWAS, SMR, TWAS, and FOCUS using a multi-trait analysis of GWAS (MTAG) to identify additional PD risk genes to boost statistical power. In this large-scale study, we identified 16 genes whose genetically regulated protein abundance levels were associated with Parkinson's disease risk. We undertook a large-scale analysis of PD and correlated traits, through TWAS and FOCUS studies, and discovered 26 casual genes related to PD that had not been reported in previous TWAS. 5 genes (CD38, GPNMB, RAB29, TMEM175, TTC19) showed significant associations with PD at both the proteome-wide and transcriptome-wide levels. Our study provides new insights into the etiology and underlying genetic architecture of PD.
Collapse
Affiliation(s)
- Jing-Jing Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Cheng-Yuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Ya-Zhou Guo
- School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
| | - Yu Fan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Xiao-Yan Hao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Shuang-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jie Tian
- Zhengzhou Railway Vocational and Technical College, Zhengzhou 450000, Henan, China
| | - Zheng-Wei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Meng-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jia-Di Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Dong-Rui Ma
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Meng-Nan Guo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Chun-Yan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Yuan-Yuan Liang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Yu-Ming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China
| | - Chang-He Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou 450000, Henan, China
| |
Collapse
|
147
|
Zammit AR, Bennett DA, Buchman AS. From theory to practice: translating the concept of cognitive resilience to novel therapeutic targets that maintain cognition in aging adults. Front Aging Neurosci 2024; 15:1303912. [PMID: 38283067 PMCID: PMC10811007 DOI: 10.3389/fnagi.2023.1303912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024] Open
Abstract
While the concept of cognitive resilience is well-established it has not been defined in a way that can be measured. This has been an impediment to studying its underlying biology and to developing instruments for its clinical assessment. This perspective highlights recent work that has quantified the expression of cortical proteins associated with cognitive resilience, thus facilitating studies of its complex underlying biology and the full range of its clinical effects in aging adults. These initial studies provide empirical support for the conceptualization of resilience as a continuum. Like other conventional risk factors, some individuals manifest higher-than-average cognitive resilience and other individuals manifest lower-than-average cognitive resilience. These novel approaches for advancing studies of cognitive resilience can be generalized to other aging phenotypes and can set the stage for the development of clinical tools that might have the potential to measure other mechanisms of resilience in aging adults. These advances also have the potential to catalyze a complementary therapeutic approach that focuses on augmenting resilience via lifestyle changes or therapies targeting its underlying molecular mechanisms to maintain cognition and brain health even in the presence of untreatable stressors like brain pathologies that accumulate in aging adults.
Collapse
Affiliation(s)
- Andrea R. Zammit
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| |
Collapse
|
148
|
Zammit AR, Klein HU, Yu L, Levey AI, Seyfried NT, Wingo AP, Wingo TS, Schneider JA, Bennett DA, Buchman AS. Proteome-wide Analyses Identified Cortical Proteins Associated With Resilience for Varied Cognitive Abilities. Neurology 2024; 102:e207816. [PMID: 38165375 PMCID: PMC10834136 DOI: 10.1212/wnl.0000000000207816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/26/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Prior work suggests that cognitive resilience may contribute to the heterogeneity of cognitive decline. This study examined whether distinct cortical proteins provide resilience for different cognitive abilities. METHODS Participants were from the Religious Orders Study or the Rush Memory and Aging Project who had undergone annual assessments of 5 cognitive abilities and postmortem assessment of 9 Alzheimer disease and related dementia (ADRD) pathologies. Proteome-wide examination of the dorsolateral prefrontal cortex using tandem mass tag and liquid chromatography-mass spectrometry yielded 8,425 high-abundance proteins. We applied linear mixed-effect models to quantify residual cognitive change (cognitive resilience) of 5 cognitive abilities by regressing out cognitive decline related to age, sex, education, and indices of ADRD pathologies. Then we added terms for each of the individual proteins to identify cognitive resilience proteins associated with the different cognitive abilities. RESULTS We included 604 decedents (69% female; mean age at death = 89 years) with proteomic data. A total of 47 cortical proteins that provide cognitive resilience were identified: 22 were associated with specific cognitive abilities, and 25 were common to at least 2 cognitive abilities. NRN1 was the only protein that was associated with more than 2 cognitive abilities (semantic memory: estimate = 0.020, SE = 0.004, p = 2.2 × 10-6; episodic memory: estimate = 0.029, SE = 0.004, p = 5.8 × 10-1; and working memory: estimate = 0.021, SE = 0.004, p = 1.2 × 10-7). Exploratory gene ontology analysis suggested that among top molecular pathways, mitochondrial translation was a molecular mechanism providing resilience in episodic memory, while nuclear-transcribed messenger RNA catabolic processes provided resilience in working memory. DISCUSSION This study identified cortical proteins associated with various cognitive abilities. Differential associations across abilities may reflect distinct underlying biological pathways. These data provide potential high-value targets for further mechanistic and drug discovery studies to develop targeted treatments to prevent loss of cognition.
Collapse
Affiliation(s)
- Andrea R Zammit
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Hans-Ulrich Klein
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Lei Yu
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Allan I Levey
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Nicholas T Seyfried
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Aliza P Wingo
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Thomas S Wingo
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Julie A Schneider
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - David A Bennett
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Aron S Buchman
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| |
Collapse
|
149
|
Zanon Zotin MC, Makkinejad N, Schneider JA, Arfanakis K, Charidimou A, Greenberg SM, van Veluw SJ. Sensitivity and Specificity of the Boston Criteria Version 2.0 for the Diagnosis of Cerebral Amyloid Angiopathy in a Community-Based Sample. Neurology 2024; 102:e207940. [PMID: 38165367 PMCID: PMC10834125 DOI: 10.1212/wnl.0000000000207940] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/27/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND AND OBJECTIVES The Boston criteria are a set of clinical and neuroimaging features that enable accurate diagnosis of cerebral amyloid angiopathy (CAA) without invasive methods such as brain biopsies or autopsy. The last updates to the Boston criteria, named version 2.0, were recently released and incorporated new nonhemorrhagic MRI features. These criteria have been validated in symptomatic samples, with improved diagnostic yield. We set out to investigate the accuracy of the Boston criteria v2.0 for the diagnosis of CAA in a community-based sample. METHODS Participants were recruited from longitudinal clinical-pathologic studies of aging conducted at the Rush Alzheimer's Disease Center in Chicago: the Religious Orders Study and the Rush Memory and Aging Project. Deceased participants with in vivo 3T MRI and detailed pathologic data available were included in the analysis. We compared the diagnostic yield of the current and earlier versions of the Boston criteria in our sample. Among those classified as probable CAA according to the Boston criteria v2.0, we investigated the ability of each neuroimaging marker to distinguish between false-positive and true-positive cases. RESULTS In total, 134 individuals were included in the study (mean age = 82.4 ± 6.0 years; 69.4% F), and 49 of them were considered pathology-proven definite cases with CAA (mean age = 82.9 ± 6.0 years; 63.3% F). The Boston criteria versions 1.0 and 1.5 yielded similar sensitivity (26.5%, both), specificity (90.6% and 89.4%, respectively), and predictive values (negative: 68.1% and 67.9%; positive: 61.9% and 59.1%, respectively). The recently released Boston criteria v2.0 offered higher sensitivity (38.8%) and slightly lower specificity (83.5%). Among those classified as probable CAA (v2.0), pathology-proven true-positive cases had higher numbers of strictly cortical lobar microbleeds compared with false-positive cases (p = 0.004). DISCUSSION Similar to findings from symptomatic samples, the inclusion of nonhemorrhagic neuroimaging markers in the updated Boston criteria offered a 12.3% gain in sensitivity among community-dwelling individuals, at the expense of a 5.9% drop in specificity. In cases with probable CAA, the cortical location of microbleeds may represent a promising distinguishing feature between true-positive and false-positive cases. Despite its improved performance, the diagnostic sensitivity of the updated criteria in a community-based sample remains limited. CLASSIFICATION OF EVIDENCE This study provides Class II evidence that the Boston criteria v2.0 accurately distinguishes people with CAA from those without CAA.
Collapse
Affiliation(s)
- Maria Clara Zanon Zotin
- From the J. Philip Kistler Stroke Research Center (M.C.Z.Z., N.M., A.C., S.M.G., S.J.V.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; Center for Imaging Sciences and Medical Physics (M.C.Z.Z.), Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Brazil; Rush Alzheimer's Disease Center (J.A.S., K.A.), Rush University Medical Center; and Department of Biomedical Engineering (K.A.), Illinois Institute of Technology, Chicago
| | - Nazanin Makkinejad
- From the J. Philip Kistler Stroke Research Center (M.C.Z.Z., N.M., A.C., S.M.G., S.J.V.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; Center for Imaging Sciences and Medical Physics (M.C.Z.Z.), Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Brazil; Rush Alzheimer's Disease Center (J.A.S., K.A.), Rush University Medical Center; and Department of Biomedical Engineering (K.A.), Illinois Institute of Technology, Chicago
| | - Julie A Schneider
- From the J. Philip Kistler Stroke Research Center (M.C.Z.Z., N.M., A.C., S.M.G., S.J.V.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; Center for Imaging Sciences and Medical Physics (M.C.Z.Z.), Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Brazil; Rush Alzheimer's Disease Center (J.A.S., K.A.), Rush University Medical Center; and Department of Biomedical Engineering (K.A.), Illinois Institute of Technology, Chicago
| | - Konstantinos Arfanakis
- From the J. Philip Kistler Stroke Research Center (M.C.Z.Z., N.M., A.C., S.M.G., S.J.V.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; Center for Imaging Sciences and Medical Physics (M.C.Z.Z.), Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Brazil; Rush Alzheimer's Disease Center (J.A.S., K.A.), Rush University Medical Center; and Department of Biomedical Engineering (K.A.), Illinois Institute of Technology, Chicago
| | - Andreas Charidimou
- From the J. Philip Kistler Stroke Research Center (M.C.Z.Z., N.M., A.C., S.M.G., S.J.V.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; Center for Imaging Sciences and Medical Physics (M.C.Z.Z.), Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Brazil; Rush Alzheimer's Disease Center (J.A.S., K.A.), Rush University Medical Center; and Department of Biomedical Engineering (K.A.), Illinois Institute of Technology, Chicago
| | - Steven M Greenberg
- From the J. Philip Kistler Stroke Research Center (M.C.Z.Z., N.M., A.C., S.M.G., S.J.V.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; Center for Imaging Sciences and Medical Physics (M.C.Z.Z.), Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Brazil; Rush Alzheimer's Disease Center (J.A.S., K.A.), Rush University Medical Center; and Department of Biomedical Engineering (K.A.), Illinois Institute of Technology, Chicago
| | - Susanne J van Veluw
- From the J. Philip Kistler Stroke Research Center (M.C.Z.Z., N.M., A.C., S.M.G., S.J.V.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; Center for Imaging Sciences and Medical Physics (M.C.Z.Z.), Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Brazil; Rush Alzheimer's Disease Center (J.A.S., K.A.), Rush University Medical Center; and Department of Biomedical Engineering (K.A.), Illinois Institute of Technology, Chicago
| |
Collapse
|
150
|
Wu D, Bi X, Chow KHM. Identification of female-enriched and disease-associated microglia (FDAMic) contributes to sexual dimorphism in late-onset Alzheimer's disease. J Neuroinflammation 2024; 21:1. [PMID: 38178204 PMCID: PMC10765928 DOI: 10.1186/s12974-023-02987-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Late-onset Alzheimer's disease (LOAD) is the most common form of dementia; it disproportionally affects women in terms of both incidence rates and severity of progression. The cellular and molecular mechanisms underlying this clinical phenomenon remain elusive and ill-defined. METHODS In-depth analyses were performed with multiple human LOAD single-nucleus transcriptome datasets to thoroughly characterize cell populations in the cerebral cortex. ROSMAP bulk human brain tissue transcriptome and DNA methylome datasets were also included for validation. Detailed assessments of microglial cell subpopulations and their relevance to sex-biased changes at the tissue level were performed. Clinical trait associations, cell evolutionary trajectories, and transcription regulon analyses were conducted. RESULTS The relative numbers of functionally defective microglia were aberrantly increased uniquely among affected females. Substratification of the microglia into different subtypes according to their transcriptomic signatures identified a group of female-enriched and disease-associated microglia (FDAMic), the numbers of which were positively associated with disease severity. Phenotypically, these cells exhibit transcriptomic signatures that support active proliferation, MHC class II autoantigen presentation and amyloid-β binding, but they are also likely defective in phagocytosis. FDAMic are likely evolved from female activated response microglia (ARMic) with an APOE4 background and compromised estrogen receptor (ER) signaling that is deemed to be active among most subtypes of microglia. CONCLUSION This study offered important insights at both the cellular and molecular levels into how ER signaling affects microglial heterogeneity and function. FDAMic are associated with more advanced pathologies and severe trends of cognitive decline. Their emergence could, at least in part, explain the phenomenon of greater penetrance of the APOE4 genotype found in females. The biases of FDAMic emergence toward female sex and APOE4 status may also explain why hormone replacement therapy is more effective in APOE4 carriers. The pathologic nature of FDAMic suggests that selective modulations of these cells may help to regain brain neuroimmune homeostasis, serving as a new target for future drug development.
Collapse
Affiliation(s)
- Deng Wu
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, 571199, China
| | - Kim Hei-Man Chow
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.
- Nexus of Rare Neurodegenerative Diseases, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.
| |
Collapse
|