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Hermansen M, Nygaard M, Tan Q, Jeune B, Semkovska M, Christensen K, Thinggaard M, Mengel-From J. Cognitively high-performing oldest old individuals are physically active and have strong motor skills-A study of the Danish 1905 and 1915 birth cohorts. Arch Gerontol Geriatr 2024; 122:105398. [PMID: 38460266 DOI: 10.1016/j.archger.2024.105398] [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: 01/16/2024] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/11/2024]
Abstract
Preserving cognitive function with age or super-aging greatly contributes to successful aging. Super-aging nonagenarians born in Denmark in either year 1905 or 1915 were classified as Cognitively High-Performing Oldest Old individuals with a five item cognitive composite score, equivalent to or better than mean middle-aged subjects. Cognitively high-performers were more physically active and had a better physical performance on e.g., Activity of Daily Living (p-value < 0.01), gait speed (p-value < 0.01) and grip strength (p-value < 0.05) compared with age-matched peers. Cognitive high-performing was also linked to lower depression symptomatology. When comparing super-agers with semi super-agers classified by Mini Mental State Examination > 27, super-agers were still more physically active and had a better physical performance (p-value < 0.05). Results suggests that physical activity is a lifestyle factor strongly associated with both semi and full cognitive super-aging.
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Affiliation(s)
- Maja Hermansen
- The Danish Twin Registry and Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Marianne Nygaard
- The Danish Twin Registry and Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Qihua Tan
- The Danish Twin Registry and Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark; Department of Biochemistry, Odense University Hospital, Denmark
| | - Bernard Jeune
- The Danish Twin Registry and Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Maria Semkovska
- Department of Psychology, University of Southern Denmark, Odense, Denmark
| | - Kaare Christensen
- The Danish Twin Registry and Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Biochemistry, Odense University Hospital, Denmark
| | - Mikael Thinggaard
- The Danish Twin Registry and Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jonas Mengel-From
- The Danish Twin Registry and Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
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Moore A, Ritchie MD. Cross-phenotype associations between Alzheimer's Disease and its comorbidities may provide clues to progression. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2024; 2024:623-631. [PMID: 38827078 PMCID: PMC11141840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease worldwide, with one in nine people over the age of 65 living with the disease in 2023. In this study, we used a phenome wide association study (PheWAS) approach to identify cross-phenotype between previously identified genetic associations for AD and electronic health record (EHR) diagnoses from the UK Biobank (UKBB) (n=361,194 of European ancestry) and the eMERGE Network (n=105,108 of diverse ancestry). Based on 497 previously identified AD-associated variants from the Alzheimer's Disease Variant Portal (ADVP), we found significant associations primarily in immune and cardiac related diseases in our PheWAS. Replicating variants have widespread impacts on immune genes in diverse tissue types. This study demonstrates the potential of using the PheWAS strategy to improve our understanding of AD progression as well as identify potential drug repurposing opportunities for new treatment and disease prevention strategies.
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Affiliation(s)
- Anni Moore
- Genomics and Computational Biology Group, University of Pennsylvania, Philadelphia, PA
| | - Marylyn D Ritchie
- Genomics and Computational Biology Group, University of Pennsylvania, Philadelphia, PA
- Institute of Biomedical Informatics, University of Pennsylvania, Philadelphia, PA
- Division of Informatics, DBEI, Perelman School of Medicine., University of Pennsylvania, Philadelphia, PA
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3
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Jaye S, Sandau US, Saugstad JA. Clathrin mediated endocytosis in Alzheimer's disease: cell type specific involvement in amyloid beta pathology. Front Aging Neurosci 2024; 16:1378576. [PMID: 38694257 PMCID: PMC11061891 DOI: 10.3389/fnagi.2024.1378576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
This review provides a comprehensive examination of the role of clathrin-mediated endocytosis (CME) in Alzheimer's disease (AD) pathogenesis, emphasizing its impact across various cellular contexts beyond neuronal dysfunction. In neurons, dysregulated CME contributes to synaptic dysfunction, amyloid beta (Aβ) processing, and Tau pathology, highlighting its involvement in early AD pathogenesis. Furthermore, CME alterations extend to non-neuronal cell types, including astrocytes and microglia, which play crucial roles in Aβ clearance and neuroinflammation. Dysregulated CME in these cells underscores its broader implications in AD pathophysiology. Despite significant progress, further research is needed to elucidate the precise mechanisms underlying CME dysregulation in AD and its therapeutic implications. Overall, understanding the complex interplay between CME and AD across diverse cell types holds promise for identifying novel therapeutic targets and interventions.
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Affiliation(s)
| | | | - Julie A. Saugstad
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, United States
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Zhang C, Liu Y, Zeng L, Luo X, Fan G, Shi H, Shen J. Combined associations of cognitive impairment and psychological resilience with all-cause mortality in community-dwelling older adults. J Affect Disord 2024; 351:962-970. [PMID: 38346647 DOI: 10.1016/j.jad.2024.02.015] [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: 09/28/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Cognitive impairment and psychological resilience are closely related in older adults, but their combined effect on mortality has not been reported. Using a nationally representative sample from the Chinese Longitudinal Healthy Longevity Study, this study examined the interactions between cognitive impairment and psychological resilience and their associations with overall survival. METHODS A total of 32,349 community-dwelling older adults (86.85 ± 11.16 years, 56.06 % female) were enrolled in 1998, 2000, 2002, 2005, 2008, 2011, and 2014; all participants were followed until 2018. Cognitive function and psychological resilience were assessed using the Mini-Mental State Examination (MMSE) and the 7-item psychological resilience questionnaire (PRQ), respectively. Illiterate subjects with an MMSE score <18, or literate subjects with an MMSE score <24 were defined as having cognitive impairment. Cox proportional risk regressions were used to analyze the association of cognitive impairment and psychological resilience with all-cause mortality. RESULTS After 146,993.52 person-years of follow-up, 23,349 older adults died. Both MMSE and PRQ scores (as continuous variables) were negatively associated with mortality risk after adjusting for all covariates. The hazard ratio (HR) of all-cause mortality for cognitive impairment was not significantly moderated by levels of psychological resilience (P-interaction = 0.094). In joint analyses, participants with combined cognitive impairment and low resilience (by the median of PRQ: < 25 points) had the highest risk of mortality (adjusted-HR: 1.56, 95%CI: 1.48-1.61), which was higher than that of patients with either condition alone. There was a significant additive interaction effect of cognitive impairment and low resilience on all-cause mortality (relative excess risk due to interaction: 0.11, 95 % CI: 0.09-0.13), and 7 % of the overall mortality risk was attributable to their synergistic effect. CONCLUSIONS Cognitive impairment and low resilience are synergistically associated with increased risk of all-cause mortality in community-dwelling older adults. The potential mechanisms underlying this combined effect warrant further exploration.
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Affiliation(s)
- Chi Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Ye Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Lvtao Zeng
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Xuanmei Luo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Guoqing Fan
- Department of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hong Shi
- Department of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
| | - Ji Shen
- Department of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
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Kikuchi M, Miyashita A, Hara N, Kasuga K, Saito Y, Murayama S, Kakita A, Akatsu H, Ozaki K, Niida S, Kuwano R, Iwatsubo T, Nakaya A, Ikeuchi T. Polygenic effects on the risk of Alzheimer's disease in the Japanese population. Alzheimers Res Ther 2024; 16:45. [PMID: 38414085 PMCID: PMC10898021 DOI: 10.1186/s13195-024-01414-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] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/11/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Polygenic effects have been proposed to account for some disease phenotypes; these effects are calculated as a polygenic risk score (PRS). This score is correlated with Alzheimer's disease (AD)-related phenotypes, such as biomarker abnormalities and brain atrophy, and is associated with conversion from mild cognitive impairment (MCI) to AD. However, the AD PRS has been examined mainly in Europeans, and owing to differences in genetic structure and lifestyle, it is unclear whether the same relationships between the PRS and AD-related phenotypes exist in non-European populations. In this study, we calculated and evaluated the AD PRS in Japanese individuals using genome-wide association study (GWAS) statistics from Europeans. METHODS In this study, we calculated the AD PRS in 504 Japanese participants (145 cognitively unimpaired (CU) participants, 220 participants with late mild cognitive impairment (MCI), and 139 patients with mild AD dementia) enrolled in the Japanese Alzheimer's Disease Neuroimaging Initiative (J-ADNI) project. In order to evaluate the clinical value of this score, we (1) determined the polygenic effects on AD in the J-ADNI and validated it using two independent cohorts (a Japanese neuropathology (NP) cohort (n = 565) and the North American ADNI (NA-ADNI) cohort (n = 617)), (2) examined the AD-related phenotypes associated with the PRS, and (3) tested whether the PRS helps predict the conversion of MCI to AD. RESULTS The PRS using 131 SNPs had an effect independent of APOE. The PRS differentiated between CU participants and AD patients with an area under the curve (AUC) of 0.755 when combined with the APOE variants. Similar AUC was obtained when PRS calculated by the NP and NA-ADNI cohorts was applied. In MCI patients, the PRS was associated with cerebrospinal fluid phosphorylated-tau levels (β estimate = 0.235, p value = 0.026). MCI with a high PRS showed a significantly increased conversion to AD in APOE ε4 noncarriers with a hazard rate of 2.22. In addition, we also developed a PRS model adjusted for LD and observed similar results. CONCLUSIONS We showed that the AD PRS is useful in the Japanese population, whose genetic structure is different from that of the European population. These findings suggest that the polygenicity of AD is partially common across ethnic differences.
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Affiliation(s)
- Masataka Kikuchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, 6-2-3 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
- Department of Medical Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan.
| | - Akinori Miyashita
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Niigata, 951-8585, Japan
| | - Norikazu Hara
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Niigata, 951-8585, Japan
| | - Kensaku Kasuga
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Niigata, 951-8585, Japan
| | - Yuko Saito
- Brain Bank for Aging Research (Department of Neuropathology), Tokyo Metropolitan Institute of Geriatrics and Gerontology, Tokyo, Japan
| | - Shigeo Murayama
- Brain Bank for Aging Research (Department of Neuropathology), Tokyo Metropolitan Institute of Geriatrics and Gerontology, Tokyo, Japan
- Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Osaka, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroyasu Akatsu
- Department of General Medicine & General Internal Medicine, Nagoya City University Graduate School of Medicine, Nagoya, Japan
| | - Kouichi Ozaki
- Medical Genome Center, National Center for Geriatrics and Gerontology, Research Institute, Aichi, Japan
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Shumpei Niida
- Core Facility Administration, National Center for Geriatrics and Gerontology, Research Institute, Aichi, Japan
| | - Ryozo Kuwano
- Social Welfare Corporation Asahigawaso, Asahigawaso Research Institute, Okayama, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akihiro Nakaya
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, 6-2-3 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Niigata, 951-8585, Japan.
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Bai Q, Sun D, Zeng Y, Zhu J, Zhang C, Zhang X, Chen L, Zhou X, Ye L, Tang Y, Liu Y, Morozova-Roche LA. Effect of Proinflammatory S100A9 Protein on Migration and Proliferation of Microglial Cells. J Mol Neurosci 2023; 73:983-995. [PMID: 37947991 DOI: 10.1007/s12031-023-02168-1] [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: 05/19/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial disease affecting aging population worldwide. Neuroinflammation became a focus of research as one of the major pathologic processes relating to the disease onset and progression. Proinflammatory S100A9 is the central culprit in the amyloid-neuroinflammatory cascade implicated in AD and other neurodegenerative diseases. We studied the effect of S100A9 on microglial BV-2 cell proliferation and migration. The responses of BV-2 cells to S100A9 stimulation were monitored in real-time using live cell microscopy, transcriptome sequencing, immunofluorescence staining, western blot analysis, and ELISA. We observed that a low dose of S100A9 promotes migration and proliferation of BV-2 cells. However, acute inflammatory condition (i.e., high S100A9 doses) causes diminished cell viability; it is uncovered that S100A9 activates TLR-4 and TLR-7 signaling pathways, leading to TNF-α and IL-6 expression, which affect BV-2 cell migration and proliferation in a concentration-dependent manner. Interestingly, the effects of S100A9 are not only inhibited by TNF-α and IL-6 antibodies. The addition of amyloid-β (Aβ) 1-40 peptide resumes the capacities of BV-2 cells to the level of low S100A9 concentrations. Based on these results, we conclude that in contrast to the beneficial effects of low S100A9 dose, high S100A9 concentration leads to impaired mobility and proliferation of immune cells, reflecting neurotoxicity at acute inflammatory conditions. However, the formation of Aβ plaques may be a natural mechanism that rescues cells from the proinflammatory and cytotoxic effects of S100A9, especially considering that inflammation is one of the primary causes of AD.
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Affiliation(s)
- Qiao Bai
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Dan Sun
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, Shaanxi, China
| | - Yang Zeng
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jie Zhu
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, Shaanxi, China
| | - Ce Zhang
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, Shaanxi, China
| | - Xiaoyin Zhang
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Li Chen
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Xin Zhou
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Liu Ye
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Yong Tang
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Yonggang Liu
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China.
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Yang HS, Teng L, Kang D, Menon V, Ge T, Finucane HK, Schultz AP, Properzi M, Klein HU, Chibnik LB, Schneider JA, Bennett DA, Hohman TJ, Mayeux RP, Johnson KA, De Jager PL, Sperling RA. Cell-type-specific Alzheimer's disease polygenic risk scores are associated with distinct disease processes in Alzheimer's disease. Nat Commun 2023; 14:7659. [PMID: 38036535 PMCID: PMC10689816 DOI: 10.1038/s41467-023-43132-2] [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: 05/22/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Many of the Alzheimer's disease (AD) risk genes are specifically expressed in microglia and astrocytes, but how and when the genetic risk localizing to these cell types contributes to AD pathophysiology remains unclear. Here, we derive cell-type-specific AD polygenic risk scores (ADPRS) from two extensively characterized datasets and uncover the impact of cell-type-specific genetic risk on AD endophenotypes. In an autopsy dataset spanning all stages of AD (n = 1457), the astrocytic ADPRS affected diffuse and neuritic plaques (amyloid-β), while microglial ADPRS affected neuritic plaques, microglial activation, neurofibrillary tangles (tau), and cognitive decline. In an independent neuroimaging dataset of cognitively unimpaired elderly (n = 2921), astrocytic ADPRS was associated with amyloid-β, and microglial ADPRS was associated with amyloid-β and tau, connecting cell-type-specific genetic risk with AD pathology even before symptom onset. Together, our study provides human genetic evidence implicating multiple glial cell types in AD pathophysiology, starting from the preclinical stage.
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Affiliation(s)
- Hyun-Sik Yang
- 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.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ling Teng
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Kang
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Tian Ge
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Hilary K Finucane
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron P Schultz
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael Properzi
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Lori B Chibnik
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Richard P Mayeux
- Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Keith A Johnson
- 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
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Reisa A Sperling
- 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
- Harvard Medical School, Boston, MA, USA
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8
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Moore A, Ritchie MD. Cross-phenotype associations between Alzheimer's Disease and its comorbidities may provide clues to progression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.06.23297993. [PMID: 37986758 PMCID: PMC10659497 DOI: 10.1101/2023.11.06.23297993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease worldwide, with one in nine people over the age of 65 living with the disease in 2023. In this study, we used a phenome wide association study (PheWAS) approach to identify cross-phenotype associations between previously identified genetic AD and for electronic health record (EHR) diagnoses from the UK Biobank (UKBB) (n=361,194 of European ancestry) and the eMERGE Network (n=105,108 of diverse ancestry). Based on 497 previously identified AD-associated variants from the Alzheimer's Disease Variant Portal (ADVP), we found significant associations primarily in immune and cardiac related diseases in our PheWAS. Replicating variants have widespread impacts on immune genes in diverse tissue types. This study demonstrates the potential of using the PheWAS strategy to improve our understanding of AD progression as well as identify potential drug repurposing opportunities for new treatment and disease prevention strategies.
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Affiliation(s)
- Anni Moore
- Genomics and Computational Biology Group, University of Pennsylvania, Philadelphia, PA
| | - Marylyn D Ritchie
- Genomics and Computational Biology Group, University of Pennsylvania, Philadelphia, PA
- Institute of Biomedical Informatics, University of Pennsylvania, Philadelphia, PA; Division of Informatics, DBEI, Perelman School of Medicine., University of Pennsylvania, Philadelphia, PA
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9
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Jury-Garfe N, You Y, Martínez P, Redding-Ochoa J, Karahan H, Johnson TS, Zhang J, Kim J, Troncoso JC, Lasagna-Reeves CA. Enhanced microglial dynamics and paucity of tau seeding in the amyloid plaque microenvironment contributes to cognitive resilience in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550884. [PMID: 37546928 PMCID: PMC10402121 DOI: 10.1101/2023.07.27.550884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Asymptomatic Alzheimer's disease (AsymAD) describes the status of subjects with preserved cognition but with identifiable Alzheimer's disease (AD) brain pathology (i.e. Aβ-amyloid deposits, neuritic plaques, and neurofibrillary tangles) at autopsy. In this study, we investigated the postmortem brains of a cohort of AsymAD cases to gain insight into the underlying mechanisms of resilience to AD pathology and cognitive decline. Our results showed that AsymAD cases exhibit an enrichment of core plaques and decreased filamentous plaque accumulation, as well as an increase in microglia surrounding this last type. In AsymAD cases we found less pathological tau aggregation in dystrophic neurites compared to AD and tau seeding activity comparable to healthy control subjects. We used spatial transcriptomics to further characterize the plaque niche and found autophagy, endocytosis, and phagocytosis within the top upregulated pathways in the AsymAD plaque niche, but not in AD. Furthermore, we found ARP2, an actin-based motility protein crucial to initiate the formation of new actin filaments, increased within microglia in the proximity of amyloid plaques in AsymAD. Our findings support that the amyloid-plaque microenvironment in AsymAD cases is characterized by microglia with highly efficient actin-based cell motility mechanisms and decreased tau seeding compared to AD. These two mechanisms can potentially provide protection against the toxic cascade initiated by Aβ that preserves brain health and slows down the progression of AD pathology.
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Affiliation(s)
- Nur Jury-Garfe
- Stark Neuroscience Research Institute, Indiana University, Indianapolis, USA
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yanwen You
- Stark Neuroscience Research Institute, Indiana University, Indianapolis, USA
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Pablo Martínez
- Stark Neuroscience Research Institute, Indiana University, Indianapolis, USA
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Javier Redding-Ochoa
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Hande Karahan
- Stark Neuroscience Research Institute, Indiana University, Indianapolis, USA
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, USA
| | - Travis S. Johnson
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, USA
| | - Jie Zhang
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jungsu Kim
- Stark Neuroscience Research Institute, Indiana University, Indianapolis, USA
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, USA
| | - Juan C. Troncoso
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Cristian A. Lasagna-Reeves
- Stark Neuroscience Research Institute, Indiana University, Indianapolis, USA
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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Li X, Fernandes BS, Liu A, Lu Y, Chen J, Zhao Z, Dai Y. Genetically-regulated pathway-polygenic risk score (GRPa-PRS): A risk stratification method to identify genetically regulated pathways in polygenic diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.19.23291621. [PMID: 37425929 PMCID: PMC10327215 DOI: 10.1101/2023.06.19.23291621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Background Alzheimer's disease (AD) is a common neurodegenerative disease in the elderly population, with genetic factors playing an important role. A considerable proportion of elderly people carry a high genetic AD risk but evade AD. On the other hand, some individuals with a low risk for AD eventually develop AD. We hypothesized that unknown counterfactors might be involved in reversing the polygenic risk scores (PRS) prediction, which might provide insights into AD pathogenesis, prevention, and early clinical intervention. Methods We built a novel computational framework to identify genetically-regulated pathways (GRPa) using PRS-based stratification for each cohort. We curated two AD cohorts with genotyping data; the discovery and the replication dataset include 2722 and 2492 individuals, respectively. First, we calculated the optimized PRS model based on the three latest AD GWAS summary statistics for each cohort. Then, we sub-grouped the individuals by their PRS and clinical diagnosis into groups such as cognitively normal (CN) with high PRS for AD (resilient group), AD cases with low PRS (susceptible group), and AD/CNs participants with similar PRS backgrounds. Lastly, we imputed the individual genetically-regulated expression (GReX) and identified the differential GRPas between subgroups with gene-set enrichment analysis and gene-set variational analysis in 2 models with and without the effect of APOE. Results For each subgroup, we conducted the same procedures in both the discovery and replication datasets across three PRS models for comparison. In Model 1 with the APOE region, we identified well-known AD-related pathways, including amyloid-beta clearance, tau protein binding, and astrocytes response to oxidative stress. In Model 2 without the APOE region, synapse function, microglia function, histidine metabolism, and thiolester hydrolase activity were significant, suggesting that they are pathways independent of the effect of APOE. Finally, our GRPa-PRS method reduces the false discovery rate in detecting differential pathways compared to another variants-based pathway PRS method. Conclusions We developed a framework, GRPa-PRS, to systematically explore the differential GRPas among individuals stratified by their estimated PRS. The GReX-level comparison among those groups unveiled new insights into the pathways associated with AD risk and resilience. Our framework can be extended to other polygenic complex diseases.
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Affiliation(s)
- Xiaoyang Li
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Brisa S. Fernandes
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Andi Liu
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yimei Lu
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Jingchun Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Alsaqati M, Thomas RS, Kidd EJ. Upregulation of endocytic protein expression in the Alzheimer's disease male human brain. AGING BRAIN 2023; 4:100084. [PMID: 37449017 PMCID: PMC10336166 DOI: 10.1016/j.nbas.2023.100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Amyloid-beta (Aβ) is produced from amyloid precursor protein (APP) primarily after APP is internalised by endocytosis and clathrin-mediated endocytic processes are altered in Alzheimer's disease (AD). There is also evidence that cholesterol and flotillin affect APP endocytosis. We hypothesised that endocytic protein expression would be altered in the brains of people with AD compared to non-diseased subjects which could be linked to increased Aβ generation. We compared protein expression in frontal cortex samples from men with AD compared to age-matched, non-diseased controls. Soluble and insoluble Aβ40 and Aβ42, the soluble Aβ42/Aβ40 ratio, βCTF, BACE1, presenilin-1 and the ratio of phosphorylated:total GSK3β were significantly increased while the insoluble Aβ42:Aβ40 ratio was significantly decreased in AD brains. Total and phosphorylated tau were markedly increased in AD brains. Significant increases in clathrin, AP2, PICALM isoform 4, Rab-5 and caveolin-1 and 2 were seen in AD brains but BIN1 was decreased. However, using immunohistochemistry, caveolin-1 and 2 were decreased. The results obtained here suggest an overall increase in endocytosis in the AD brain, explaining, at least in part, the increased production of Aβ during AD.
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Affiliation(s)
| | | | - Emma J. Kidd
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3NB, UK
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12
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Yang HS, Teng L, Kang D, Menon V, Ge T, Finucane HK, Schultz AP, Properzi M, Klein HU, Chibnik LB, Schneider JA, Bennett DA, Hohman TJ, Mayeux RP, Johnson KA, De Jager PL, Sperling RA. Cell-type-specific Alzheimer's disease polygenic risk scores are associated with distinct disease processes in Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.01.23290850. [PMID: 37333223 PMCID: PMC10274993 DOI: 10.1101/2023.06.01.23290850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Alzheimer's disease (AD) heritability is enriched in glial genes, but how and when cell-type-specific genetic risk contributes to AD remains unclear. Here, we derive cell-type-specific AD polygenic risk scores (ADPRS) from two extensively characterized datasets. In an autopsy dataset spanning all stages of AD (n=1,457), astrocytic (Ast) ADPRS was associated with both diffuse and neuritic Aβ plaques, while microglial (Mic) ADPRS was associated with neuritic Aβ plaques, microglial activation, tau, and cognitive decline. Causal modeling analyses further clarified these relationships. In an independent neuroimaging dataset of cognitively unimpaired elderly (n=2,921), Ast-ADPRS were associated with Aβ, and Mic-ADPRS was associated with Aβ and tau, showing a consistent pattern with the autopsy dataset. Oligodendrocytic and excitatory neuronal ADPRSs were associated with tau, but only in the autopsy dataset including symptomatic AD cases. Together, our study provides human genetic evidence implicating multiple glial cell types in AD pathophysiology, starting from the preclinical stage.
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Affiliation(s)
- Hyun-Sik Yang
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ling Teng
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Daniel Kang
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Tian Ge
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Hilary K. Finucane
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron P. Schultz
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA
| | - Michael Properzi
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Hans-Ulrich Klein
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lori B. Chibnik
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Julie A. Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Timothy J. Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Richard P. Mayeux
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Keith A. Johnson
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Philip L. De Jager
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Reisa A. Sperling
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA
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Schork NJ, Elman JA. Pathway-specific polygenic risk scores correlate with clinical status and Alzheimer's-related biomarkers. RESEARCH SQUARE 2023:rs.3.rs-2583037. [PMID: 36909609 PMCID: PMC10002839 DOI: 10.21203/rs.3.rs-2583037/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Background: APOE is the largest genetic risk factor for sporadic Alzheimer's disease (AD), but there is a substantial polygenic component as well. Polygenic risk scores (PRS) can summarize small effects across the genome but may obscure differential risk associated with different molecular processes and pathways. Variability at the genetic level may contribute to the extensive phenotypic heterogeneity of Alzheimer's disease (AD). Here, we examine polygenic risk impacting specific pathways associated with AD and examined its relationship with clinical status and AD biomarkers of amyloid, tau, and neurodegeneration (A/T/N). Methods: A total of 1,411 participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI) with genotyping data were included. Sets of variants identified from a pathway analysis of AD GWAS summary statistics were combined into clusters based on their assigned pathway. We constructed pathway-specific PRSs for each participant and tested their associations with diagnostic status (AD vs cognitively normal), abnormal levels of amyloid and ptau (positive vs negative), and hippocampal volume. The APOE region was excluded from all PRSs, and analyses controlled for APOE -ε4 carrier status. Results: Thirteen pathway clusters were identified relating to categories such as immune response, amyloid precursor processing, protein localization, lipid transport and binding, tyrosine kinase, and endocytosis. Eight pathway-specific PRSs were significantly associated with AD dementia diagnosis. Amyloid-positivity was associated with endocytosis and fibril formation, response misfolded protein, and regulation protein tyrosine PRSs. Ptau positivity and hippocampal volume were both related to protein localization and mitophagy PRS, and ptau positivity was additionally associated with an immune signaling PRS. A global AD PRS showed stronger associations with diagnosis and all biomarkers compared to pathway PRSs, suggesting a strong synergistic effect of all loci contributing to the global AD PRS. Conclusions: Pathway PRS may contribute to understanding separable disease processes, but do not appear to add significant power for predictive purposes. These findings demonstrate that, although genetic risk for AD is widely distributed, AD-phenotypes may be preferentially associated with risk in specific pathways. Defining genetic risk along multiple dimensions at the individual level may help clarify the etiological heterogeneity in AD.
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14
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I F. The unique neuropathological vulnerability of the human brain to aging. Ageing Res Rev 2023; 87:101916. [PMID: 36990284 DOI: 10.1016/j.arr.2023.101916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Alzheimer's disease (AD)-related neurofibrillary tangles (NFT), argyrophilic grain disease (AGD), aging-related tau astrogliopathy (ARTAG), limbic predominant TDP-43 proteinopathy (LATE), and amygdala-predominant Lewy body disease (LBD) are proteinopathies that, together with hippocampal sclerosis, progressively appear in the elderly affecting from 50% to 99% of individuals aged 80 years, depending on the disease. These disorders usually converge on the same subject and associate with additive cognitive impairment. Abnormal Tau, TDP-43, and α-synuclein pathologies progress following a pattern consistent with an active cell-to-cell transmission and abnormal protein processing in the host cell. However, cell vulnerability and transmission pathways are specific for each disorder, albeit abnormal proteins may co-localize in particular neurons. All these alterations are unique or highly prevalent in humans. They all affect, at first, the archicortex and paleocortex to extend at later stages to the neocortex and other regions of the telencephalon. These observations show that the phylogenetically oldest areas of the human cerebral cortex and amygdala are not designed to cope with the lifespan of actual humans. New strategies aimed at reducing the functional overload of the human telencephalon, including optimization of dream repair mechanisms and implementation of artificial circuit devices to surrogate specific brain functions, appear promising.
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Affiliation(s)
- Ferrer I
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain; Emeritus Researcher of the Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain; Biomedical Research Network of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain; Institute of Neurosciences, University of Barcelona, Barcelona, Spain; Hospitalet de Llobregat, Barcelona, Spain.
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15
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Frankowska N, Bryl E, Fulop T, Witkowski JM. Longevity, Centenarians and Modified Cellular Proteodynamics. Int J Mol Sci 2023; 24:ijms24032888. [PMID: 36769212 PMCID: PMC9918038 DOI: 10.3390/ijms24032888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
We have shown before that at least one intracellular proteolytic system seems to be at least as abundant in the peripheral blood lymphocytes of centenarians as in the same cells of young individuals (with the cells of the elderly population showing a significant dip compared to both young and centenarian cohorts). Despite scarce published data, in this review, we tried to answer the question how do different types of cells of longevous people-nonagenarians to (semi)supercentenarians-maintain the quality and quantity of their structural and functional proteins? Specifically, we asked if more robust proteodynamics participate in longevity. We hypothesized that at least some factors controlling the maintenance of cellular proteomes in centenarians will remain at the "young" level (just performing better than in the average elderly). In our quest, we considered multiple aspects of cellular protein maintenance (proteodynamics), including the quality of transcribed DNA, its epigenetic changes, fidelity and quantitative features of transcription of both mRNA and noncoding RNAs, the process of translation, posttranslational modifications leading to maturation and functionalization of nascent proteins, and, finally, multiple facets of the process of elimination of misfolded, aggregated, and otherwise dysfunctional proteins (autophagy). We also included the status of mitochondria, especially production of ATP necessary for protein synthesis and maintenance. We found that with the exception of the latter and of chaperone function, practically all of the considered aspects did show better performance in centenarians than in the average elderly, and most of them approached the levels/activities seen in the cells of young individuals.
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Affiliation(s)
- Natalia Frankowska
- Department of Physiopathology, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Ewa Bryl
- Department of Pathology and Experimental Rheumatology, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Tamas Fulop
- Research Center on Aging, Geriatric Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Jacek M. Witkowski
- Department of Physiopathology, Medical University of Gdansk, 80-211 Gdansk, Poland
- Correspondence: ; Tel.: +48-58-349-1510
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16
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Schork NJ, Elman JA. Pathway-Specific Polygenic Risk Scores Correlate with Clinical Status and Alzheimer's Disease-Related Biomarkers. J Alzheimers Dis 2023; 95:915-929. [PMID: 37661888 PMCID: PMC10697039 DOI: 10.3233/jad-230548] [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: 09/05/2023]
Abstract
BACKGROUND APOE is the largest genetic risk factor for Alzheimer's disease (AD), but there is a substantial polygenic component. Polygenic risk scores (PRS) can summarize small effects across the genome but may obscure differential risk across molecular processes and pathways that contribute to heterogeneity of disease presentation. OBJECTIVE We examined polygenic risk impacting specific AD-associated pathways and its relationship with clinical status and biomarkers of amyloid, tau, and neurodegeneration (A/T/N). METHODS We analyzed data from 1,411 participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI). We applied pathway analysis and clustering to identify AD-associated "pathway clusters" and construct pathway-specific PRSs (excluding the APOE region). We tested associations with diagnostic status, abnormal levels of amyloid and ptau, and hippocampal volume. RESULTS Thirteen pathway clusters were identified, and eight pathway-specific PRSs were significantly associated with AD diagnosis. Amyloid-positivity was associated with endocytosis and fibril formation, response misfolded protein, and regulation protein tyrosine PRSs. Ptau positivity and hippocampal volume were both related to protein localization and mitophagy PRS, and ptau-positivity was also associated with an immune signaling PRS. A global AD PRS showed stronger associations with diagnosis and all biomarkers compared to pathway PRSs. CONCLUSIONS Pathway PRS may contribute to understanding separable disease processes, but do not add significant power for predictive purposes. These findings demonstrate that AD-phenotypes may be preferentially associated with risk in specific pathways, and defining genetic risk along multiple dimensions may clarify etiological heterogeneity in AD. This approach to delineate pathway-specific PRS can be used to study other complex diseases.
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Affiliation(s)
- Nicholas J. Schork
- The Translational Genomics Research Institute, Quantitative Medicine and Systems Biology, Phoenix, AZ, USA
- Department of Psychiatry University of California, San Diego, La Jolla, CA, USA
| | - Jeremy A. Elman
- Department of Psychiatry University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
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Baker E, Leonenko G, Schmidt KM, Hill M, Myers AJ, Shoai M, de Rojas I, Tesi N, Holstege H, van der Flier WM, Pijnenburg YAL, Ruiz A, Hardy J, van der Lee S, Escott-Price V. What does heritability of Alzheimer's disease represent? PLoS One 2023; 18:e0281440. [PMID: 37115753 PMCID: PMC10146480 DOI: 10.1371/journal.pone.0281440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/24/2023] [Indexed: 04/29/2023] Open
Abstract
INTRODUCTION Both late-onset Alzheimer's disease (AD) and ageing have a strong genetic component. In each case, many associated variants have been discovered, but how much missing heritability remains to be discovered is debated. Variability in the estimation of SNP-based heritability could explain the differences in reported heritability. METHODS We compute heritability in five large independent cohorts (N = 7,396, 1,566, 803, 12,528 and 3,963) to determine whether a consensus for the AD heritability estimate can be reached. These cohorts vary by sample size, age of cases and controls and phenotype definition. We compute heritability a) for all SNPs, b) excluding APOE region, c) excluding both APOE and genome-wide association study hit regions, and d) SNPs overlapping a microglia gene-set. RESULTS SNP-based heritability of late onset Alzheimer's disease is between 38 and 66% when age and genetic disease architecture are correctly accounted for. The heritability estimates decrease by 12% [SD = 8%] on average when the APOE region is excluded and an additional 1% [SD = 3%] when genome-wide significant regions were removed. A microglia gene-set explains 69-84% of our estimates of SNP-based heritability using only 3% of total SNPs in all cohorts. CONCLUSION The heritability of neurodegenerative disorders cannot be represented as a single number, because it is dependent on the ages of cases and controls. Genome-wide association studies pick up a large proportion of total AD heritability when age and genetic architecture are correctly accounted for. Around 13% of SNP-based heritability can be explained by known genetic loci and the remaining heritability likely resides around microglial related genes.
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Affiliation(s)
- Emily Baker
- Division of Neuroscience and Mental Health, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Ganna Leonenko
- Division of Neuroscience and Mental Health, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | | | - Matthew Hill
- Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Amanda J Myers
- Department of Cell Biology, Miller School of Medicine, University of Miami, Coral Gables, FL, United States of America
| | - Maryam Shoai
- Institute of Neurology, University College London, London, United Kingdom
| | - Itziar de Rojas
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Niccoló Tesi
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Henne Holstege
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
| | - Wiesje M van der Flier
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
| | - Agustin Ruiz
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - John Hardy
- Institute of Neurology, University College London, London, United Kingdom
| | - Sven van der Lee
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
| | - Valentina Escott-Price
- Division of Neuroscience and Mental Health, School of Medicine, Cardiff University, Cardiff, United Kingdom
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Zhuang J, Tian J, Xiong X, Li T, Chen Z, Chen R, Chen J, Li X. Associating brain imaging phenotypes and genetic risk factors via a hypergraph based netNMF method. Front Aging Neurosci 2023; 15:1052783. [PMID: 36936501 PMCID: PMC10017840 DOI: 10.3389/fnagi.2023.1052783] [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: 09/24/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023] Open
Abstract
Abstract Alzheimer's disease (AD) is a severe neurodegenerative disease for which there is currently no effective treatment. Mild cognitive impairment (MCI) is an early disease that may progress to AD. The effective diagnosis of AD and MCI in the early stage has important clinical significance. Methods To this end, this paper proposed a hypergraph-based netNMF (HG-netNMF) algorithm for integrating structural magnetic resonance imaging (sMRI) of AD and MCI with corresponding gene expression profiles. Results Hypergraph regularization assumes that regions of interest (ROIs) and genes were located on a non-linear low-dimensional manifold and can capture the inherent prevalence of two modalities of data and mined high-order correlation features of the two data. Further, this paper used the HG-netNMF algorithm to construct a brain structure connection network and a protein interaction network (PPI) with potential role relationships, mine the risk (ROI) and key genes of both, and conduct a series of bioinformatics analyses. Conclusion Finally, this paper used the risk ROI and key genes of the AD and MCI groups to construct diagnostic models. The AUC of the AD group and MCI group were 0.8 and 0.797, respectively.
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Affiliation(s)
- Junli Zhuang
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jinping Tian
- Faculty of Medicine, Jianghan University, Wuhan, China
| | - Xiaoxing Xiong
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Xiaoxing Xiong,
| | - Taihan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- Taihan Li,
| | - Zhengwei Chen
- Department of Radiology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Rong Chen
- Department of Radiology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Jun Chen
- Department of Radiology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Xiang Li
- School of Health, Wuhan University, Wuhan, China
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Xu Y, Vasiljevic E, Deming YK, Jonaitis EM, Koscik RL, Van Hulle CA, Lu Q, Carboni M, Kollmorgen G, Wild N, Carlsson CM, Johnson SC, Zetterberg H, Blennow K, Engelman CD. Effect of Pathway-Specific Polygenic Risk Scores for Alzheimer's Disease (AD) on Rate of Change in Cognitive Function and AD-Related Biomarkers Among Asymptomatic Individuals. J Alzheimers Dis 2023; 94:1587-1605. [PMID: 37482996 PMCID: PMC10468904 DOI: 10.3233/jad-230097] [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: 07/25/2023]
Abstract
BACKGROUND Genetic scores for late-onset Alzheimer's disease (LOAD) have been associated with preclinical cognitive decline and biomarker variations. Compared with an overall polygenic risk score (PRS), a pathway-specific PRS (p-PRS) may be more appropriate in predicting a specific biomarker or cognitive component underlying LOAD pathology earlier in the lifespan. OBJECTIVE In this study, we leveraged longitudinal data from the Wisconsin Registry for Alzheimer's Prevention and explored changing patterns in cognition and biomarkers at various age points along six biological pathways. METHODS PRS and p-PRSs with and without APOE were constructed separately based on the significant SNPs associated with LOAD in a recent genome-wide association study meta-analysis and compared to APOE alone. We used a linear mixed-effects model to assess the association between PRS/p-PRSs and cognitive trajectories among 1,175 individuals. We also applied the model to the outcomes of cerebrospinal fluid biomarkers in a subset. Replication analyses were performed in an independent sample. RESULTS We found p-PRSs and the overall PRS can predict preclinical changes in cognition and biomarkers. The effects of PRS/p-PRSs on rate of change in cognition, amyloid-β, and tau outcomes are dependent on age and appear earlier in the lifespan when APOE is included in these risk scores compared to when APOE is excluded. CONCLUSION In addition to APOE, the p-PRSs can predict age-dependent changes in amyloid-β, tau, and cognition. Once validated, they could be used to identify individuals with an elevated genetic risk of accumulating amyloid-β and tau, long before the onset of clinical symptoms.
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Affiliation(s)
- Yuexuan Xu
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
| | - Eva Vasiljevic
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
- Center for Demography of Health and Aging, University of Wisconsin-Madison, WI, USA
| | - Yuetiva K. Deming
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
- Wisconsin Alzheimer’s Institute, University of Wisconsin-Madison, WI, USA
| | - Erin M. Jonaitis
- Wisconsin Alzheimer’s Institute, University of Wisconsin-Madison, WI, USA
| | - Rebecca L. Koscik
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
- Wisconsin Alzheimer’s Institute, University of Wisconsin-Madison, WI, USA
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin-Madison, WI, USA
| | - Carol A. Van Hulle
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin-Madison, WI, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
| | | | | | | | - Cynthia M. Carlsson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin-Madison, WI, USA
- Geriatric Research Education and Clinical Center, Wm. S. Middleton Memorial VA Hospital, Madison, WI, USA
| | - Sterling C. Johnson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin-Madison, WI, USA
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- UK Dementia Research Institute at UCL, London, UK
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Corinne D. Engelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, WI, USA
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20
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Tomassen J, den Braber A, van der Lee SJ, Reus LM, Konijnenberg E, Carter SF, Yaqub M, van Berckel BN, Collij LE, Boomsma DI, de Geus EJ, Scheltens P, Herholz K, Tijms BM, Visser PJ. Amyloid-β and APOE genotype predict memory decline in cognitively unimpaired older individuals independently of Alzheimer's disease polygenic risk score. BMC Neurol 2022; 22:484. [PMID: 36522743 PMCID: PMC9753236 DOI: 10.1186/s12883-022-02925-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND What combination of risk factors for Alzheimer's disease (AD) are most predictive of cognitive decline in cognitively unimpaired individuals remains largely unclear. We studied associations between APOE genotype, AD-Polygenic Risk Scores (AD-PRS), amyloid-β pathology and decline in cognitive functioning over time in a large sample of cognitively unimpaired older individuals. METHODS We included 276 cognitively unimpaired older individuals (75 ± 10 years, 63% female) from the EMIF-AD PreclinAD cohort. An AD-PRS was calculated including 83 genome-wide significant variants. The APOE gene was not included in the PRS and was analyzed separately. Baseline amyloid-β status was assessed by visual read of [18F]flutemetamol-PET standardized uptake value images. At baseline and follow-up (2.0 ± 0.4 years), the cognitive domains of memory, attention, executive function, and language were measured. We used generalized estimating equations corrected for age, sex and center to examine associations between APOE genotype and AD-PRS with amyloid-β status. Linear mixed models corrected for age, sex, center and education were used to examine associations between APOE genotype, AD-PRS and amyloid-β status, and their interaction on changes in cognitive functioning over time. RESULTS Fifty-two participants (19%) had abnormal amyloid-β, and 84 participants (31%) carried at least one APOE ε4 allele. APOE genotype and AD-PRS were both associated with abnormal amyloid-β status. Increasingly more risk-full APOE genotype, a high AD-PRS and an abnormal amyloid-β status were associated with steeper decline in memory functioning in separate models (all p ≤ 0.02). A model including 4-way interaction term (APOE×AD-PRS×amyloid-β×time) was not significant. When modelled together, both APOE genotype and AD-PRS predicted steeper decline in memory functioning (APOE β(SE)=-0.05(0.02); AD-PRS β(SE)=-0.04(0.01)). Additionally, when modelled together, both amyloid-β status and AD-PRS predicted a steeper decline in memory functioning (amyloid-β β(SE)=-0.07(0.04); AD-PRS β(SE)=-0.04(0.01)). Modelling both APOE genotype and amyloid-β status, we observed an interaction, in which APOE genotype was related to steeper decline in memory and language functioning in amyloid-β abnormal individuals only (β(SE)=-0.13(0.06); β(SE)=-0.22(0.07), respectively). CONCLUSION Our results suggest that APOE genotype is related to steeper decline in memory and language functioning in individuals with abnormal amyloid-β only. Furthermore, independent of amyloid-β status other genetic risk variants contribute to memory decline in initially cognitively unimpaired older individuals.
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Affiliation(s)
- Jori Tomassen
- grid.12380.380000 0004 1754 9227Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands ,grid.16872.3a0000 0004 0435 165XAlzheimer Center Amsterdam, Neurology, Amsterdam UMC location VUmc, 1007 MB Amsterdam, PO Box 7057, The Netherlands
| | - Anouk den Braber
- grid.12380.380000 0004 1754 9227Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands ,grid.12380.380000 0004 1754 9227Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sven J. van der Lee
- grid.12380.380000 0004 1754 9227Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands ,grid.12380.380000 0004 1754 9227Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
| | - Lianne M. Reus
- grid.12380.380000 0004 1754 9227Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Elles Konijnenberg
- grid.12380.380000 0004 1754 9227Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Stephen F. Carter
- grid.5379.80000000121662407Wolfson Molecular Imaging Centre, Division of Neuroscience and Experimental Psychology, University of Manchester, Manchester, UK ,grid.5335.00000000121885934Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Maqsood Yaqub
- grid.12380.380000 0004 1754 9227Department of Radiology & Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
| | - Bart N.M. van Berckel
- grid.12380.380000 0004 1754 9227Department of Radiology & Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
| | - Lyduine E. Collij
- grid.12380.380000 0004 1754 9227Department of Radiology & Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
| | - Dorret I. Boomsma
- grid.12380.380000 0004 1754 9227Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Eco J.C. de Geus
- grid.12380.380000 0004 1754 9227Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Philip Scheltens
- grid.12380.380000 0004 1754 9227Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Karl Herholz
- grid.5379.80000000121662407Wolfson Molecular Imaging Centre, Division of Neuroscience and Experimental Psychology, University of Manchester, Manchester, UK
| | - Betty M. Tijms
- grid.12380.380000 0004 1754 9227Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Pieter Jelle Visser
- grid.12380.380000 0004 1754 9227Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands ,grid.5012.60000 0001 0481 6099Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands ,grid.4714.60000 0004 1937 0626Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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21
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Upadhya S, Liu H, Luo S, Lutz MW, Chiba-Falek O. Polygenic Risk Score Effectively Predicts Depression Onset in Alzheimer’s Disease Based on Major Depressive Disorder Risk Variants. Front Neurosci 2022; 16:827447. [PMID: 35350557 PMCID: PMC8957806 DOI: 10.3389/fnins.2022.827447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/31/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction Depression is a common, though heterogenous, comorbidity in late-onset Alzheimer’s Disease (LOAD) patients. In addition, individuals with depression are at greater risk to develop LOAD. In previous work, we demonstrated shared genetic etiology between depression and LOAD. Collectively, these previous studies suggested interactions between depression and LOAD. However, the underpinning genetic heterogeneity of depression co-occurrence with LOAD, and the various genetic etiologies predisposing depression in LOAD, are largely unknown. Methods Major Depressive Disorder (MDD) genome-wide association study (GWAS) summary statistics were used to create polygenic risk scores (PRS). The Religious Orders Society and Rush Memory and Aging Project (ROSMAP, n = 1,708) and National Alzheimer’s Coordinating Center (NACC, n = 10,256) datasets served as discovery and validation cohorts, respectively, to assess the PRS performance in predicting depression onset in LOAD patients. Results The PRS showed marginal results in standalone models for predicting depression onset in both ROSMAP (AUC = 0.540) and NACC (AUC = 0.527). Full models, with baseline age, sex, education, and APOEε4 allele count, showed improved prediction of depression onset (ROSMAP AUC: 0.606, NACC AUC: 0.581). In time-to-event analysis, standalone PRS models showed significant effects in ROSMAP (P = 0.0051), but not in NACC cohort. Full models showed significant performance in predicting depression in LOAD for both datasets (P < 0.001 for all). Conclusion This study provided new insights into the genetic factors contributing to depression onset in LOAD and advanced our knowledge of the genetics underlying the heterogeneity of depression in LOAD. The developed PRS accurately predicted LOAD patients with depressive symptoms, thus, has clinical implications including, diagnosis of LOAD patients at high-risk to develop depression for early anti-depressant treatment.
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Affiliation(s)
- Suraj Upadhya
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
| | - Hongliang Liu
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
| | - Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, United States
- *Correspondence: Ornit Chiba-Falek,
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22
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Tesi N, Hulsman M, van der Lee SJ, Jansen IE, Stringa N, van Schoor NM, Scheltens P, van der Flier WM, Huisman M, Reinders MJT, Holstege H. The Effect of Alzheimer's Disease-Associated Genetic Variants on Longevity. Front Genet 2022; 12:748781. [PMID: 34992629 PMCID: PMC8724252 DOI: 10.3389/fgene.2021.748781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/24/2021] [Indexed: 12/22/2022] Open
Abstract
Human longevity is influenced by the genetic risk of age-related diseases. As Alzheimer’s disease (AD) represents a common condition at old age, an interplay between genetic factors affecting AD and longevity is expected. We explored this interplay by studying the prevalence of AD-associated single-nucleotide-polymorphisms (SNPs) in cognitively healthy centenarians, and replicated findings in a parental-longevity GWAS. We found that 28/38 SNPs that increased AD-risk also associated with lower odds of longevity. For each SNP, we express the imbalance between AD- and longevity-risk as an effect-size distribution. Based on these distributions, we grouped the SNPs in three groups: 17 SNPs increased AD-risk more than they decreased longevity-risk, and were enriched for β-amyloid metabolism and immune signaling; 11 variants reported a larger longevity-effect compared to their AD-effect, were enriched for endocytosis/immune-signaling, and were previously associated with other age-related diseases. Unexpectedly, 10 variants associated with an increased risk of AD and higher odds of longevity. Altogether, we show that different AD-associated SNPs have different effects on longevity, including SNPs that may confer general neuro-protective functions against AD and other age-related diseases.
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Affiliation(s)
- Niccolò Tesi
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Alzheimer Centre, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Marc Hulsman
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Alzheimer Centre, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Sven J van der Lee
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Alzheimer Centre, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Iris E Jansen
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU, Amsterdam, Netherlands
| | - Najada Stringa
- Department of Epidemiology and Data Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Natasja M van Schoor
- Department of Epidemiology and Data Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Philip Scheltens
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Wiesje M van der Flier
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Department of Epidemiology and Data Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Martijn Huisman
- Department of Epidemiology and Data Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Henne Holstege
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Alzheimer Centre, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
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23
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Tomassen J, den Braber A, van der Landen SM, Konijnenberg E, Teunissen CE, Vermunt L, de Geus EJC, Boomsma DI, Scheltens P, Tijms BM, Visser PJ. Abnormal cerebrospinal fluid levels of amyloid and tau are associated with cognitive decline over time in cognitively normal older adults: A monozygotic twin study. ALZHEIMER'S & DEMENTIA: TRANSLATIONAL RESEARCH & CLINICAL INTERVENTIONS 2022; 8:e12346. [PMID: 36185992 PMCID: PMC9489168 DOI: 10.1002/trc2.12346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022]
Abstract
Introduction The contribution of genetic and environmental factors to the relation between cerebrospinal fluid (CSF) biomarkers and cognitive decline in preclinical Alzheimer's disease remains unclear. We studied this in initially cognitively normal monozygotic twins. Methods We included 122 cognitively normal monozygotic twins (51 pairs) with a follow‐up of 4.3 ± 0.4 years. We first tested associations of baseline CSF Aβ1‐42/1‐40 ratio, total tau (t‐tau), and 181‐phosphorylated‐tau (p‐tau) status with subsequent cognitive decline using linear mixed models, and then performed twin specific analyses. Results Baseline abnormal amyloid‐β and tau CSF markers predicted steeper decline on memory (p ≤ .003) and language (p ≤ 0.04). Amyloid‐β and p‐tau markers in one twin predicted decline in memory in the co‐twin and tau markers in one twin predicted decline in language in the co‐twin (r range ‐0.26,0.39; p’s ≤ .02). Discussion These results suggest that memory and language decline are early features of AD that are in part determined by the same genetic factors that influence amyloid‐β and tau regulation.
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Affiliation(s)
- Jori Tomassen
- Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc Amsterdam The Netherlands
- Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands
| | - Anouk den Braber
- Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc Amsterdam The Netherlands
- Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands
- Department of Biological Psychology Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Sophie M. van der Landen
- Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc Amsterdam The Netherlands
- Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands
| | - Elles Konijnenberg
- Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc Amsterdam The Netherlands
- Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands
| | - Charlotte E. Teunissen
- Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands
- Neurochemistry Laboratory, Department of Clinical Chemistry Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Lisa Vermunt
- Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc Amsterdam The Netherlands
- Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands
- Neurochemistry Laboratory, Department of Clinical Chemistry Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Eco J. C. de Geus
- Department of Biological Psychology Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Philip Scheltens
- Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc Amsterdam The Netherlands
- Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands
| | - Betty M. Tijms
- Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc Amsterdam The Netherlands
- Amsterdam Neuroscience Neurodegeneration Amsterdam The Netherlands
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc Amsterdam The Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience Maastricht University Maastricht The Netherlands
- Department of Neurobiology Division of Neurogeriatrics Karolinska Institutet Care Sciences and Society Stockholm Sweden
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24
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van Bokhoven P, de Wilde A, Vermunt L, Leferink PS, Heetveld S, Cummings J, Scheltens P, Vijverberg EGB. The Alzheimer's disease drug development landscape. Alzheimers Res Ther 2021; 13:186. [PMID: 34763720 PMCID: PMC8582156 DOI: 10.1186/s13195-021-00927-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/28/2021] [Indexed: 01/10/2023]
Abstract
Background Alzheimer’s disease (AD) is a devastating neurodegenerative disease leading to dementia. The field has made significant progress over the last 15 years. AD diagnosis has shifted from syndromal, based on signs and symptoms, to a biomarker construct based on the pathological hallmarks of the disease: amyloid β deposition, pathologic tau, and neurodegeneration. Numerous genetic risk factors for sporadic AD have been identified, providing further insight into the molecular underpinnings of the disease. For the last two decades, however, drug development for AD has been proven to be particularly challenging. Here, we provide a unique overview of the drug development landscape for AD. By comparing preclinical and clinical drug development pipelines, we aim to describe trends and differences regarding target classes and therapeutic modalities in preclinical and clinical development. Methods We analyzed proprietary and public databases and company websites for drugs in preclinical development for AD by the pharmaceutical industry and major clinical trial registries for drugs in clinical development for AD. Drugs were categorized by target class and treatment modality. Results We found a higher proportion of preclinical interventions targeting molecular pathways associated with sporadic AD genetic risk variants, compared to clinical stage interventions. These include apolipoprotein E (ApoE) and lipids, lysosomal/endosomal targets, and proteostasis. Further, we observed a trend suggesting that more traditional therapeutic modalities are developed for these novel targets, while more novel treatment modalities such as gene therapies and enzyme treatments are in development for more traditional targets such as amyloid β and tau. Interestingly, the percentage of amyloid β targeting therapies in preclinical development (19.2%) is even higher than the percentage in clinical development (10.7%), indicating that diversification away from interventions targeting amyloid-beta has not materialized. Inflammation is the second most popular target class in both preclinical and clinical development. Conclusions Our observations show that the AD drug development pipeline is diversifying in terms of targets and treatment modalities, while amyloid-targeting therapies remain a prominent avenue of development as well. To further advance AD drug development, novel companion diagnostics are needed that are directed at disease mechanisms related to genetic risk factors of AD, both for patient stratification and assessment of therapeutic efficacy in clinical trials. Supplementary Information The online version contains supplementary material available at 10.1186/s13195-021-00927-z.
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Affiliation(s)
- Pieter van Bokhoven
- Industry Alliance Office, Amsterdam Neuroscience, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Arno de Wilde
- Life Science Partners (LSP), Amsterdam, The Netherlands
| | - Lisa Vermunt
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.,Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Prisca S Leferink
- Industry Alliance Office, Amsterdam Neuroscience, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Sasja Heetveld
- Industry Alliance Office, Amsterdam Neuroscience, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Jeffrey Cummings
- Chambers-Grundy Center for Transformative Neuroscience, Department of Brain Health, School of Integrated Health Sciences, University of Nevada Las Vegas (UNLV), Las Vegas, NV, USA
| | - Philip Scheltens
- Life Science Partners (LSP), Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Everard G B Vijverberg
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
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25
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Pyun JM, Park YH, Lee KJ, Kim S, Saykin AJ, Nho K. Predictability of polygenic risk score for progression to dementia and its interaction with APOE ε4 in mild cognitive impairment. Transl Neurodegener 2021; 10:32. [PMID: 34465370 PMCID: PMC8406896 DOI: 10.1186/s40035-021-00259-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/14/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The combinatorial effect of multiple genetic factors calculated as a polygenic risk score (PRS) has been studied to predict disease progression to Alzheimer's disease (AD) from mild cognitive impairment (MCI). Previous studies have investigated the performance of PRS in the prediction of disease progression to AD by including and excluding single nucleotide polymorphisms within the region surrounding the APOE gene. These studies may have missed the APOE genotype-specific predictability of PRS for disease progression to AD. METHODS We analyzed 732 MCI from the Alzheimer's Disease Neuroimaging Initiative cohort, including those who progressed to AD within 5 years post-baseline (n = 270) and remained stable as MCI (n = 462). The predictability of PRS including and excluding the APOE region (PRS+APOE and PRS-APOE) on the conversion to AD and its interaction with the APOE ε4 carrier status were assessed using Cox regression analyses. RESULTS PRS+APOE (hazard ratio [HR] 1.468, 95% CI 1.335-1.615) and PRS-APOE (HR 1.293, 95% CI 1.157-1.445) were both associated with a significantly increased risk of MCI progression to dementia. The interaction between PRS+APOE and APOE ε4 carrier status was significant with a P-value of 0.0378. The association of PRSs with the progression risk was stronger in APOE ε4 non-carriers (PRS+APOE: HR 1.710, 95% CI 1.244-2.351; PRS-APOE: HR 1.429, 95% CI 1.182-1.728) than in APOE ε4 carriers (PRS+APOE: HR 1.167, 95% CI 1.005-1.355; PRS-APOE: HR 1.172, 95% CI 1.020-1.346). CONCLUSIONS PRS could predict the conversion of MCI to dementia with a stronger association in APOE ε4 non-carriers than APOE ε4 carriers. This indicates PRS as a potential genetic predictor particularly for MCI with no APOE ε4 alleles.
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Affiliation(s)
- Jung-Min Pyun
- Department of Neurology, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu, Republic of Korea
| | - Young Ho Park
- Department of Neurology, Seoul National University Bundang Hospital and Seoul National University College of Medicine, Seongnam, Republic of Korea.
| | - Keon-Joo Lee
- Department of Neurology, Seoul National University Bundang Hospital and Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University Bundang Hospital and Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA.
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.
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26
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Tesi N, van der Lee SJ, Hulsman M, Jansen IE, Stringa N, van Schoor NM, Scheltens P, van der Flier WM, Huisman M, Reinders MJT, Holstege H. Polygenic Risk Score of Longevity Predicts Longer Survival Across an Age Continuum. J Gerontol A Biol Sci Med Sci 2021; 76:750-759. [PMID: 33216869 PMCID: PMC8087277 DOI: 10.1093/gerona/glaa289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/17/2022] Open
Abstract
Studying the genome of centenarians may give insights into the molecular mechanisms underlying extreme human longevity and the escape of age-related diseases. Here, we set out to construct polygenic risk scores (PRSs) for longevity and to investigate the functions of longevity-associated variants. Using a cohort of centenarians with maintained cognitive health (N = 343), a population-matched cohort of older adults from 5 cohorts (N = 2905), and summary statistics data from genome-wide association studies on parental longevity, we constructed a PRS including 330 variants that significantly discriminated between centenarians and older adults. This PRS was also associated with longer survival in an independent sample of younger individuals (p = .02), leading up to a 4-year difference in survival based on common genetic factors only. We show that this PRS was, in part, able to compensate for the deleterious effect of the APOE-ε4 allele. Using an integrative framework, we annotated the 330 variants included in this PRS by the genes they associate with. We find that they are enriched with genes associated with cellular differentiation, developmental processes, and cellular response to stress. Together, our results indicate that an extended human life span is, in part, the result of a constellation of variants each exerting small advantageous effects on aging-related biological mechanisms that maintain overall health and decrease the risk of age-related diseases.
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Affiliation(s)
- Niccolo' Tesi
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | - Sven J van der Lee
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands.,Department of Clinical Genetics, Amsterdam UMC, The Netherlands
| | - Marc Hulsman
- Delft Bioinformatics Lab, Delft University of Technology, The Netherlands.,Department of Clinical Genetics, Amsterdam UMC, The Netherlands
| | - Iris E Jansen
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands.,Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands
| | - Najada Stringa
- Department of Epidemiology and Biostatistics, Amsterdam UMC, The Netherlands.,Amsterdam Public Health Research Institute, The Netherlands
| | - Natasja M van Schoor
- Department of Epidemiology and Biostatistics, Amsterdam UMC, The Netherlands.,Amsterdam Public Health Research Institute, The Netherlands
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam UMC, The Netherlands
| | - Martijn Huisman
- Department of Epidemiology and Biostatistics, Amsterdam UMC, The Netherlands.,Amsterdam Public Health Research Institute, The Netherlands
| | | | - Henne Holstege
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, The Netherlands.,Department of Clinical Genetics, Amsterdam UMC, The Netherlands
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Mukhopadhyay S, Banerjee D. A Primer on the Evolution of Aducanumab: The First Antibody Approved for Treatment of Alzheimer's Disease. J Alzheimers Dis 2021; 83:1537-1552. [PMID: 34366359 DOI: 10.3233/jad-215065] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia with global burden projected to triple by 2050. It incurs significant biopsychosocial burden worldwide with limited treatment options. Aducanumab is the first monoclonal antibody recently approved by the US-FDA for mild AD through the accelerated approval pathway. It is the first molecule to be approved for AD since 2003 and carries with it a therapeutic promise for the future. As the definition of AD has evolved from a pathological entity to a Clinico-biological construct over the years, the amyloid-β (Aβ) pathway has been increasingly implicated in its pathogenesis. The approval of Aducanumab is based on reduction of the Aβ load in the brain, which forms a surrogate marker for this pathway. The research populace has, however, been globally divided by skepticism and hope regarding this approval. Failure to meet clinical endpoints in the trials, alleged transparency issues, cost-effectiveness, potential adverse effects, need for regular monitoring, and critique of 'amyloid cascade hypothesis' itself are the main caveats concerning the antibody. With this controversy in background, this paper critically looks at antibody research in AD therapeutics, evidence, and evolution of Aducanumab as a drug and the potential clinical implications of its use in future. While the efficacy of this monoclonal antibody in AD stands as a test of time, based on the growing evidence it is vital to rethink and explore alternate pathways of pathogenesis (oxidative stress, neuroinflammation, cholesterol metabolism, vascular factors, etc.) as possible therapeutic targets that may help elucidate the enigma of this complex yet progressive and debilitating neurodegenerative disorder.
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Affiliation(s)
- Sanchari Mukhopadhyay
- Geriatric Unit, Department of Psychiatry, NationalInstitute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Debanjan Banerjee
- Geriatric Unit, Department of Psychiatry, NationalInstitute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
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28
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Tesi N, van der Lee S, Hulsman M, Holstege H, Reinders MJT. snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets. Nucleic Acids Res 2021; 49:W603-W612. [PMID: 34048563 PMCID: PMC8262737 DOI: 10.1093/nar/gkab410] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/19/2021] [Accepted: 05/01/2021] [Indexed: 02/06/2023] Open
Abstract
Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which involves advanced bioinformatic skills. We developed snpXplorer, an easy-to-use web-server application for exploring Single Nucleotide Polymorphisms (SNP) association statistics and to functionally annotate sets of SNPs. snpXplorer can superimpose association statistics from multiple studies, and displays regional information including SNP associations, structural variations, recombination rates, eQTL, linkage disequilibrium patterns, genes and gene-expressions per tissue. By overlaying multiple GWAS studies, snpXplorer can be used to compare levels of association across different traits, which may help the interpretation of variant consequences. Given a list of SNPs, snpXplorer can also be used to perform variant-to-gene mapping and gene-set enrichment analysis to identify molecular pathways that are overrepresented in the list of input SNPs. snpXplorer is freely available at https://snpxplorer.net. Source code, documentation, example files and tutorial videos are available within the Help section of snpXplorer and at https://github.com/TesiNicco/snpXplorer.
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Affiliation(s)
- Niccolo Tesi
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Sven van der Lee
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Marc Hulsman
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Henne Holstege
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
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29
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Improving the Utility of Polygenic Risk Scores as a Biomarker for Alzheimer's Disease. Cells 2021; 10:cells10071627. [PMID: 34209762 PMCID: PMC8305482 DOI: 10.3390/cells10071627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 12/28/2022] Open
Abstract
The treatment of complex and multifactorial diseases constitutes a big challenge in day-to-day clinical practice. As many parameters influence clinical phenotypes, accurate diagnosis and prompt therapeutic management is often difficult. Significant research and investment focuses on state-of-the-art genomic and metagenomic analyses in the burgeoning field of Precision (or Personalized) Medicine with genome-wide-association-studies (GWAS) helping in this direction by linking patient genotypes at specific polymorphic sites (single-nucleotide polymorphisms, SNPs) to the specific phenotype. The generation of polygenic risk scores (PRSs) is a relatively novel statistical method that associates the collective genotypes at many of a person’s SNPs to a trait or disease. As GWAS sample sizes increase, PRSs may become a powerful tool for prevention, early diagnosis and treatment. However, the complexity and multidimensionality of genetic and environmental contributions to phenotypes continue to pose significant challenges for the clinical, broad-scale use of PRSs. To improve the value of PRS measures, we propose a novel pipeline which might better utilize GWAS results and improve the utility of PRS when applied to Alzheimer’s Disease (AD), as a paradigm of multifactorial disease with existing large GWAS datasets that have not yet achieved significant clinical impact. We propose a refined approach for the construction of AD PRS improved by (1), taking into consideration the genetic loci where the SNPs are located, (2) evaluating the post-translational impact of SNPs on coding and non-coding regions by focusing on overlap with open chromatin data and SNPs that are expression quantitative trait loci (QTLs), and (3) scoring and annotating the severity of the associated clinical phenotype into the PRS. Open chromatin and eQTL data need to be carefully selected based on tissue/cell type of origin (e.g., brain, excitatory neurons). Applying such filters to traditional PRS on GWAS studies of complex diseases like AD, can produce a set of SNPs weighted according to our algorithm and a more useful PRS. Our proposed methodology may pave the way for new applications of genomic machine and deep learning pipelines to GWAS datasets in an effort to identify novel clinically useful genetic biomarkers for complex diseases like AD.
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30
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Galvin JE, Kleiman MJ, Chrisphonte S, Cohen I, Disla S, Galvin CB, Greenfield KK, Moore C, Rawn S, Riccio ML, Rosenfeld A, Simon J, Walker M, Tolea MI. The Resilience Index: A Quantifiable Measure of Brain Health and Risk of Cognitive Impairment and Dementia. J Alzheimers Dis 2021; 84:1729-1746. [PMID: 34744081 PMCID: PMC10731582 DOI: 10.3233/jad-215077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND There is increasing interest in lifestyle modification and integrative medicine approaches to treat and/or prevent mild cognitive impairment (MCI) and Alzheimer's disease and related dementias (ADRD). OBJECTIVE To address the need for a quantifiable measure of brain health, we created the Resilience Index (RI). METHODS This cross-sectional study analyzed 241 participants undergoing a comprehensive evaluation including the Clinical Dementia Rating and neuropsychological testing. Six lifestyle factors including physical activity, cognitive activity, social engagements, dietary patterns, mindfulness, and cognitive reserve were combined to derive the RI (possible range of scores: 1-378). Psychometric properties were determined. RESULTS The participants (39 controls, 75 MCI, 127 ADRD) had a mean age of 74.6±9.5 years and a mean education of 15.8±2.6 years. The mean RI score was 138.2±35.6. The RI provided estimates of resilience across participant characteristics, cognitive staging, and ADRD etiologies. The RI showed moderate-to-strong correlations with clinical and cognitive measures and very good discrimination (AUC: 0.836; 95% CI: 0.774-0.897) between individuals with and without cognitive impairment (diagnostic odds ratio = 8.9). Individuals with high RI scores (> 143) had better cognitive, functional, and behavioral ratings than individuals with low RI scores. Within group analyses supported that controls, MCI, and mild ADRD cases with high RI had better cognitive, functional, and global outcomes than those with low RI. CONCLUSION The RI is a brief, easy to administer, score and interpret assessment of brain health that incorporates six modifiable protective factors. Results from the RI could provide clinicians and researchers with a guide to develop personalized prevention plans to support brain health.
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Affiliation(s)
- James E. Galvin
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael J. Kleiman
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Stephanie Chrisphonte
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Iris Cohen
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shanell Disla
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Conor B. Galvin
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Keri K. Greenfield
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Claudia Moore
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan Rawn
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mary Lou Riccio
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Amie Rosenfeld
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Judith Simon
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marcia Walker
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Magdalena I. Tolea
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
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