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Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. Neurobiol Aging 2023; 131:182-195. [PMID: 37677864 PMCID: PMC10538380 DOI: 10.1016/j.neurobiolaging.2023.07.007] [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: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 09/09/2023]
Abstract
A missense variant in the tetratricopeptide repeat domain 3 (TTC3) gene (rs377155188, p.S1038C, NM_003316.4:c 0.3113C>G) was found to segregate with disease in a multigenerational family with late-onset Alzheimer's disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing, and the resulting isogenic pair of iPSC lines was differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3-dimensional morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant.
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Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carolina L Duarte
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mayra J Laverde-Paz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shaina A Simon
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek J Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Amanda T Miyares
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; JJ Vance Memorial Summer Internship in Biological and Computational Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina M Carney
- Mental Health & Behavioral Science Service, Bruce W. Carter VA Medical Center, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
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Myllykangas L. Alzheimer's disease with a CADASIL twist - neuropathological examination proves its value in clarifying the genetics behind familial dementia. J Neurol Sci 2023; 452:120769. [PMID: 37625337 DOI: 10.1016/j.jns.2023.120769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Affiliation(s)
- Liisa Myllykangas
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki, Finland.
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Korvatska O, Bucks SA, Yoda RA, Nolan A, Dorschner MO, Tsuang D, Jayadev S, Raskind WH, Bird TD. NOTCH3 C201R variant causes cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) that can be confused with early-onset Alzheimer's disease. J Neurol Sci 2023; 452:120763. [PMID: 37598468 PMCID: PMC10863424 DOI: 10.1016/j.jns.2023.120763] [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: 04/23/2023] [Revised: 07/08/2023] [Accepted: 08/05/2023] [Indexed: 08/22/2023]
Abstract
BACKGROUND NOTCH3 is the causative gene for autosomal dominant cerebral arteriopathy with subcortical infarctions and leukoencephalopathy (CADASIL) which is associated with both stroke and dementia. When CADASIL presents primarily as dementia it can be difficult to distinguish from Alzheimer's disease (AD) at both the clinical and neuropathological levels. METHODS We performed exome sequencing of several affected individuals from a large family affected with AD. PCR amplification and direct Sanger sequencing were used to verify variants detected by exome analysis and to screen family members at-risk to carry those variants. Neuropathologic brain evaluation by immunohistochemistry and MRI were performed for the carriers of the NOTCH3 variant. RESULTS In a three-generation family with AD, we found a c.601 T > C p.Cys201Arg variant in the NOTCH3 gene that caused clinical and neuropathological manifestations of CADASIL. These features included earlier onset of dementia accompanied by behavioral abnormalities in the father and son and white matter abnormalities in the asymptomatic grandson. The family is one branch of a large pedigree studied by the Alzheimer's Disease Sequencing Project (ADSP). As part of the ADSP linkage analysis and whole genome sequencing endeavor, an ABCA1 variant, p.Ala937Val, was previously found associated with AD in this pedigree. CONCLUSIONS Our findings, together with other reported pathogenic missense variants of the C201 codon in NOTCH3, support the role of cysteine 201 as a mutation hotspot for CADASIL and highlight the genetic complexity both clinically and pathologically of AD and related dementia.
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Affiliation(s)
- Olena Korvatska
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, USA.
| | - Stephanie A Bucks
- Department of Neurology, University of Washington, Seattle, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Rebecca A Yoda
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Amber Nolan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Michael O Dorschner
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, USA
| | - Debby Tsuang
- Geriatric Research, Education and Clinical Center (GRECC), VA Puget Sound Medical Center, Seattle, USA
| | - Suman Jayadev
- Department of Neurology, University of Washington, Seattle, USA
| | - Wendy H Raskind
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, USA; Geriatric Research, Education and Clinical Center (GRECC), VA Puget Sound Medical Center, Seattle, USA; Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Medical Center, Seattle, USA
| | - Thomas D Bird
- Department of Neurology, University of Washington, Seattle, USA; Geriatric Research, Education and Clinical Center (GRECC), VA Puget Sound Medical Center, Seattle, USA
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Lee WP, Choi SH, Shea MG, Cheng PL, Dombroski BA, Pitsillides AN, Heard-Costa NL, Wang H, Bulekova K, Kuzma AB, Leung YY, Farrell JJ, Lin H, Naj A, Blue EE, Nusetor F, Wang D, Boerwinkle E, Bush WS, Zhang X, De Jager PL, Dupuis J, Farrer LA, Fornage M, Martin E, Pericak-Vance M, Seshadri S, Wijsman EM, Wang LS, Schellenberg GD, Destefano AL, Haines JL, Peloso GM. Association of Common and Rare Variants with Alzheimer's Disease in over 13,000 Diverse Individuals with Whole-Genome Sequencing from the Alzheimer's Disease Sequencing Project. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.01.23294953. [PMID: 37693521 PMCID: PMC10491367 DOI: 10.1101/2023.09.01.23294953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Alzheimer's Disease (AD) is a common disorder of the elderly that is both highly heritable and genetically heterogeneous. Here, we investigated the association between AD and both common variants and aggregates of rare coding and noncoding variants in 13,371 individuals of diverse ancestry with whole genome sequence (WGS) data. Pooled-population analyses identified genetic variants in or near APOE, BIN1, and LINC00320 significantly associated with AD (p < 5×10-8). Population-specific analyses identified a haplotype on chromosome 14 including PSEN1 associated with AD in Hispanics, further supported by aggregate testing of rare coding and noncoding variants in this region. Finally, we observed suggestive associations (p < 5×10-5) of aggregates of rare coding rare variants in ABCA7 among non-Hispanic Whites (p=5.4×10-6), and rare noncoding variants in the promoter of TOMM40 distinct of APOE in pooled-population analyses (p=7.2×10-8). Complementary pooled-population and population-specific analyses offered unique insights into the genetic architecture of AD.
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Affiliation(s)
- Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Seung Hoan Choi
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Margaret G Shea
- Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, MA, USA
| | - Po-Liang Cheng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Nancy L Heard-Costa
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katia Bulekova
- Research Computing Services, Information Services & Technology, Boston University, Boston, MA, USA
| | - Amanda B Kuzma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John J Farrell
- Biomedical Genetics, Department of Medicine, Boston University Medical School, Boston, MA, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Adam Naj
- Department of Biostatistics, Epidemiology, and Informatics, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth E Blue
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Frederick Nusetor
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Dongyu Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Xiaoling Zhang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Biomedical Genetics, Department of Medicine, Boston University Medical School, Boston, MA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - Lindsay A Farrer
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Biomedical Genetics, Department of Medicine, Boston University Medical School, Boston, MA, USA
- Department of Ophthalmology, Department of Medicine, Boston University Medical School, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eden Martin
- John P Hussman Institute for Human Genomics, Miami, FL, USA
- John T Macdonald Department of Human Genetics, Miami, FL, USA
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret Pericak-Vance
- John P Hussman Institute for Human Genomics, Miami, FL, USA
- John T Macdonald Department of Human Genetics, Miami, FL, USA
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
| | - Ellen M Wijsman
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anita L Destefano
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
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Miao J, Ma H, Yang Y, Liao Y, Lin C, Zheng J, Yu M, Lan J. Microglia in Alzheimer's disease: pathogenesis, mechanisms, and therapeutic potentials. Front Aging Neurosci 2023; 15:1201982. [PMID: 37396657 PMCID: PMC10309009 DOI: 10.3389/fnagi.2023.1201982] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by protein aggregation in the brain. Recent studies have revealed the critical role of microglia in AD pathogenesis. This review provides a comprehensive summary of the current understanding of microglial involvement in AD, focusing on genetic determinants, phenotypic state, phagocytic capacity, neuroinflammatory response, and impact on synaptic plasticity and neuronal regulation. Furthermore, recent developments in drug discovery targeting microglia in AD are reviewed, highlighting potential avenues for therapeutic intervention. This review emphasizes the essential role of microglia in AD and provides insights into potential treatments.
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Affiliation(s)
- Jifei Miao
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Haixia Ma
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yang Yang
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yuanpin Liao
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Cui Lin
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Juanxia Zheng
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Muli Yu
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Jiao Lan
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
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Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542316. [PMID: 37292815 PMCID: PMC10246004 DOI: 10.1101/2023.05.25.542316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A missense variant in the tetratricopeptide repeat domain 3 ( TTC3 ) gene (rs377155188, p.S1038C, NM_003316.4:c.3113C>G) was found to segregate with disease in a multigenerational family with late onset Alzheimer's disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing and the resulting isogenic pair of iPSC lines were differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3D morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant. Highlights The AD risk variant TTC3 p.S1038C reduces the expression levels of TTC3 The variant modifies the expression of AD specific genes BACE1 , INPP5F , and UNC5C Neurons with the variant are enriched for genes in the PI3K-Akt pathwayiPSC-derived neurons with the alteration have increased neurite length and branchingThe variant interferes with actin cytoskeleton and is ameliorated by Cytochalasin D.
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Reyes‐Dumeyer D, Faber K, Vardarajan B, Goate A, Renton A, Chao M, Boeve B, Cruchaga C, Pericak‐Vance M, Haines JL, Rosenberg R, Tsuang D, Sweet RA, Bennett DA, Wilson RS, Foroud T, Mayeux R. The National Institute on Aging Late-Onset Alzheimer's Disease Family Based Study: A resource for genetic discovery. Alzheimers Dement 2022; 18:1889-1897. [PMID: 34978149 PMCID: PMC9250549 DOI: 10.1002/alz.12514] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/02/2023]
Abstract
INTRODUCTION The National Institute on Aging Late-Onset Alzheimer's Disease Family Based Study (NIA-LOAD FBS) was established to study the genetic etiology of Alzheimer's disease (AD). METHODS Recruitment focused on families with two living affected siblings and a third first-degree relative similar in age with or without dementia. Uniform assessments were completed, DNA was obtained, as was neuropathology, when possible. Apolipoprotein E (APOE) genotypes, genome-wide single nucleotide polymorphism (SNP) arrays, and sequencing was completed in most families. RESULTS APOE genotype modified the age-at-onset in many large families. Novel variants and known variants associated with early- and late-onset AD and frontotemporal dementia were identified supporting an international effort to solve AD genetics. DISCUSSION The NIA-LOAD FBS is the largest collection of familial AD worldwide, and data or samples have been included in 123 publications addressing the genetic etiology of AD. Genetic heterogeneity and variability in the age-at-onset provides opportunities to investigate the complexity of familial AD.
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Affiliation(s)
- Dolly Reyes‐Dumeyer
- Department of NeurologyTaub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University in the City of New YorkNew YorkNew YorkUSA
| | - Kelley Faber
- Department of Medical and Molecular GeneticsNational Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD)Indiana University School of MedicineIndianapolisIndianaUSA
| | - Badri Vardarajan
- Department of NeurologyTaub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University in the City of New YorkNew YorkNew YorkUSA
| | - Alison Goate
- Department of Genetics & Genomic SciencesRonald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Alan Renton
- Department of Genetics & Genomic SciencesRonald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Michael Chao
- Department of Genetics & Genomic SciencesRonald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Brad Boeve
- Department of NeurologyMayo ClinicRochesterMinnesotaUSA
| | - Carlos Cruchaga
- Department of PsychiatryWashington University in St. LouisSt. LouisMissouriUSA
| | - Margaret Pericak‐Vance
- John P. Hussman Institute for Human GenomicsDr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of MedicineMiamiFloridaUSA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Sciences and Cleveland Institute for Computational BiologyCase Western Reserve UniversityClevelandOhioUSA
| | - Roger Rosenberg
- Department of NeurologyUniversity of Texas Southwestern Medical Center at DallasDallasTexasUSA
| | - Debby Tsuang
- GRECC VA Puget SoundDepartment of Psychiatry and Behavioral SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Robert A. Sweet
- Departments of Psychiatry and NeurologyUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Robert S. Wilson
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Tatiana Foroud
- Department of Medical and Molecular GeneticsNational Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD)Indiana University School of MedicineIndianapolisIndianaUSA
| | - Richard Mayeux
- Department of NeurologyTaub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University in the City of New YorkNew YorkNew YorkUSA
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Abstract
The brain, as one of the most lipid-rich organs, heavily relies on lipid transport and distribution to maintain homeostasis and neuronal function. Lipid transport mediated by lipoprotein particles, which are complex structures composed of apolipoproteins and lipids, has been thoroughly characterized in the periphery. Although lipoproteins in the central nervous system (CNS) were reported over half a century ago, the identification of APOE4 as the strongest genetic risk factor for Alzheimer's disease has accelerated investigation of the biology and pathobiology of lipoproteins in the CNS. This review provides an overview of the different components of lipoprotein particles, in particular apolipoproteins, and their involvements in both physiological functions and pathological mechanisms in the CNS.
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Affiliation(s)
| | - Yuka A Martens
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA;
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA;
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Bossaerts L, Cacace R, Van Broeckhoven C. The role of ATP-binding cassette subfamily A in the etiology of Alzheimer's disease. Mol Neurodegener 2022; 17:31. [PMID: 35477481 PMCID: PMC9044696 DOI: 10.1186/s13024-022-00536-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Abstract
Background Alzheimer’s disease (AD) is the leading cause of dementia, clinically characterized by memory deficits and progressive cognitive decline. Despite decades of research effective therapies are lacking, and a large part of the genetic heritability remains unidentified. ABCA7 and ABCA1, members of the ATP-binding cassette subfamily A (ABCA), were identified as AD risk genes in genome-wide association studies. Nevertheless, genetic and/or functional studies propose a link between AD and two other members of the ABCA subclass, i.e., ABCA2 and ABCA5. Main body Changes in expression or dysfunction of these transporters were found to increase amyloid β levels. This might be related to the common role of ABCA transporters in cellular cholesterol homeostasis, for which a prominent role in AD development has been suggested. In this review, we provide a comprehensive overview and discussion on the contribution of the ABCA subfamily to the etiopathogenesis of AD. Conclusions A better understanding of the function and identification of disease-associated genetic variants in ABCA transporters can contribute to the development of novel therapeutic strategies for AD.
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Affiliation(s)
- Liene Bossaerts
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium. .,Department of Biomedical Sciences, University of Antwerp - CDE, Universiteitsplein 1, B-2610, Antwerp, Belgium.
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10
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Bossaerts L, Hendrickx Van de Craen E, Cacace R, Asselbergh B, Van Broeckhoven C. Rare missense mutations in ABCA7 might increase Alzheimer's disease risk by plasma membrane exclusion. Acta Neuropathol Commun 2022; 10:43. [PMID: 35361255 PMCID: PMC8973822 DOI: 10.1186/s40478-022-01346-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/11/2022] [Indexed: 11/10/2022] Open
Abstract
The adenosine triphosphate-binding cassette subfamily A member 7 gene (ABCA7) is associated with Alzheimer's disease (AD) in large genome-wide association studies. Targeted sequencing of ABCA7 suggests a role for rare premature termination codon (PTC) mutations in AD, with haploinsufficiency through nonsense-mediated mRNA decay as a plausible pathogenic mechanism. Since other classes of rare variants in ABCA7 are poorly understood, we investigated the contribution and pathogenicity of rare missense, indel and splice variants in ABCA7 in Belgian AD patient and control cohorts. We identified 8.36% rare variants in the patient cohort versus 6.05% in the control cohort. For 10 missense mutations identified in the Belgian cohort we analyzed the pathogenetic effect on protein localization in vitro using immunocytochemistry. Our results demonstrate that rare ABCA7 missense mutations can contribute to AD by inducing protein mislocalization, resulting in a lack of functional protein at the plasma membrane. In one pedigree, a mislocalization-inducing missense mutation in ABCA7 (p.G1820S) co-segregated with AD in an autosomal dominant inheritance pattern. Brain autopsy of six patient missense mutation carriers showed typical AD neuropathological characteristics including cerebral amyloid angiopathy type 1. Also, among the rare ABCA7 missense mutations, we observed mutations that affect amino acid residues that are conserved in ABCA1 and ABCA4, of which some correspond to established ABCA1 or ABCA4 disease-causing mutations involved in Tangier or Stargardt disease.
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11
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Khani M, Gibbons E, Bras J, Guerreiro R. Challenge accepted: uncovering the role of rare genetic variants in Alzheimer's disease. Mol Neurodegener 2022; 17:3. [PMID: 35000612 PMCID: PMC8744312 DOI: 10.1186/s13024-021-00505-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
The search for rare variants in Alzheimer's disease (AD) is usually deemed a high-risk - high-reward situation. The challenges associated with this endeavor are real. Still, the application of genome-wide technologies to large numbers of cases and controls or to small, well-characterized families has started to be fruitful.Rare variants associated with AD have been shown to increase risk or cause disease, but also to protect against the development of AD. All of these can potentially be targeted for the development of new drugs.Multiple independent studies have now shown associations of rare variants in NOTCH3, TREM2, SORL1, ABCA7, BIN1, CLU, NCK2, AKAP9, UNC5C, PLCG2, and ABI3 with AD and suggested that they may influence disease via multiple mechanisms. These genes have reported functions in the immune system, lipid metabolism, synaptic plasticity, and apoptosis. However, the main pathway emerging from the collective of genes harboring rare variants associated with AD is the Aβ pathway. Associations of rare variants in dozens of other genes have also been proposed, but have not yet been replicated in independent studies. Replication of this type of findings is one of the challenges associated with studying rare variants in complex diseases, such as AD. In this review, we discuss some of these primary challenges as well as possible solutions.Integrative approaches, the availability of large datasets and databases, and the development of new analytical methodologies will continue to produce new genes harboring rare variability impacting AD. In the future, more extensive and more diverse genetic studies, as well as studies of deeply characterized families, will enhance our understanding of disease pathogenesis and put us on the correct path for the development of successful drugs.
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Affiliation(s)
- Marzieh Khani
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Elizabeth Gibbons
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave. N.E., Grand Rapids, Michigan 49503-2518 USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave. N.E., Grand Rapids, Michigan 49503-2518 USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave. N.E., Grand Rapids, Michigan 49503-2518 USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI USA
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12
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Ai R, Jin X, Tang B, Yang G, Niu Z, Fang EF. Aging and Alzheimer’s Disease. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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13
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Xue D, Bush WS, Renton AE, Marcora EA, Bis JC, Kunkle BW, Boerwinkle E, DeStefano AL, Farrer L, Goate A, Mayeux R, Pericak‐Vance M, Schellenberg G, Seshadri S, Wijsman E, Haines JL, Blue EE. Large-scale sequencing studies expand the known genetic architecture of Alzheimer's disease. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12255. [PMID: 35005195 PMCID: PMC8720139 DOI: 10.1002/dad2.12255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Genes implicated by genome-wide association studies and family-based studies of Alzheimer's disease (AD) are largely discordant. We hypothesized that genes identified by sequencing studies like the Alzheimer's Disease Sequencing Project (ADSP) may bridge this gap and highlight shared biological mechanisms. METHODS We performed structured literature review of genes prioritized by ADSP studies, genes underlying familial dementias, and genes nominated by genome-wide association studies. Gene set enrichment analyses of each list identified enriched pathways. RESULTS The genes prioritized by the ADSP, familial dementia studies, and genome-wide association studies minimally overlapped. Each gene set identified dozens of enriched pathways, several of which were shared (e.g., regulation of amyloid beta clearance). DISCUSSION Alternative study designs provide unique insights into AD genetics. Shared pathways enriched by different genes highlight their relevance to AD pathogenesis, while the patterns of pathway enrichment unique to each gene set provide additional targets for functional studies.
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Affiliation(s)
- Diane Xue
- Institute for Public Health GeneticsUniversity of WashingtonSeattleWashingtonUSA
| | - William S. Bush
- Department of Population and Quantitative Health Sciences and Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
- Cleveland Institute for Computational BiologyClevelandOhioUSA
| | - Alan E. Renton
- Department of Genetics and Genomic SciencesNash Family Department of Neuroscienceand Ronald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Edoardo A. Marcora
- Department of Genetics and Genomic SciencesNash Family Department of Neuroscienceand Ronald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Joshua C. Bis
- Cardiovascular Health Research UnitDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Brian W. Kunkle
- The John P. Hussman Institute for Human GenomicsUniversity of MiamiMiamiFloridaUSA
- Dr. John T Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | | | - Eric Boerwinkle
- Human Genome Sequencing CenterDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- School of Public HealthUniversity of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Anita L. DeStefano
- Department of BiostatisticsBoston UniversityBostonMassachusettsUSA
- Department of NeurologyBoston UniversityBostonMassachusettsUSA
| | - Lindsay Farrer
- Department of BiostatisticsBoston UniversityBostonMassachusettsUSA
- Department of NeurologyBoston UniversityBostonMassachusettsUSA
- Division of Biomedical GeneticsDepartment of MedicineDepartment of Epidemiologyand Department of OphthalmologyBoston UniversityBostonMassachusettsUSA
| | - Alison Goate
- Department of Genetics and Genomic SciencesNash Family Department of Neuroscienceand Ronald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Genetics and Genomics Sciences and Friedman Brain InstituteMount Sinai School of MedicineNew YorkNew YorkUSA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainGertrude H. Sergievsky CenterDepartment of NeurologyDepartment of Psychiatryand EpidemiologyColumbia UniversityNew YorkNew YorkUSA
| | - Margaret Pericak‐Vance
- The John P. Hussman Institute for Human GenomicsUniversity of MiamiMiamiFloridaUSA
- Dr. John T Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Gerard Schellenberg
- Penn Neurodegeneration Genomics CenterDepartment of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases and Department of NeurologyUniversity of Texas Health Science CenterSan AntonioTexasUSA
| | - Ellen Wijsman
- Institute for Public Health GeneticsUniversity of WashingtonSeattleWashingtonUSA
- Division of Medical GeneticsUniversity of WashingtonSeattleWashingtonUSA
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences and Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
- Cleveland Institute for Computational BiologyClevelandOhioUSA
| | - Elizabeth E. Blue
- Institute for Public Health GeneticsUniversity of WashingtonSeattleWashingtonUSA
- Division of Medical GeneticsUniversity of WashingtonSeattleWashingtonUSA
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14
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Li Y, Laws SM, Miles LA, Wiley JS, Huang X, Masters CL, Gu BJ. Genomics of Alzheimer's disease implicates the innate and adaptive immune systems. Cell Mol Life Sci 2021; 78:7397-7426. [PMID: 34708251 PMCID: PMC11073066 DOI: 10.1007/s00018-021-03986-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/14/2021] [Accepted: 10/16/2021] [Indexed: 02/08/2023]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterised by cognitive impairment, behavioural alteration, and functional decline. Over 130 AD-associated susceptibility loci have been identified by genome-wide association studies (GWAS), while whole genome sequencing (WGS) and whole exome sequencing (WES) studies have identified AD-associated rare variants. These variants are enriched in APOE, TREM2, CR1, CD33, CLU, BIN1, CD2AP, PILRA, SCIMP, PICALM, SORL1, SPI1, RIN3, and more genes. Given that aging is the single largest risk factor for late-onset AD (LOAD), the accumulation of somatic mutations in the brain and blood of AD patients have also been explored. Collectively, these genetic findings implicate the role of innate and adaptive immunity in LOAD pathogenesis and suggest that a systemic failure of cell-mediated amyloid-β (Aβ) clearance contributes to AD onset and progression. AD-associated variants are particularly enriched in myeloid-specific regulatory regions, implying that AD risk variants are likely to perturbate the expression of myeloid-specific AD-associated genes to interfere Aβ clearance. Defective phagocytosis, endocytosis, and autophagy may drive Aβ accumulation, which may be related to naturally-occurring antibodies to Aβ (Nabs-Aβ) produced by adaptive responses. Passive immunisation is providing efficiency in clearing Aβ and slowing cognitive decline, such as aducanumab, donanemab, and lecanemab (ban2401). Causation of AD by impairment of the innate immunity and treatment using the tools of adaptive immunity is emerging as a new paradigm for AD, but immunotherapy that boosts the innate immune functions of myeloid cells is highly expected to modulate disease progression at asymptomatic stage.
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Affiliation(s)
- Yihan Li
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
| | - Luke A Miles
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - James S Wiley
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - Xin Huang
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ben J Gu
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia.
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15
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Monk B, Rajkovic A, Petrus S, Rajkovic A, Gaasterland T, Malinow R. A Machine Learning Method to Identify Genetic Variants Potentially Associated With Alzheimer's Disease. Front Genet 2021; 12:647436. [PMID: 34194466 PMCID: PMC8238203 DOI: 10.3389/fgene.2021.647436] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/06/2021] [Indexed: 01/17/2023] Open
Abstract
There is hope that genomic information will assist prediction, treatment, and understanding of Alzheimer's disease (AD). Here, using exome data from ∼10,000 individuals, we explore machine learning neural network (NN) methods to estimate the impact of SNPs (i.e., genetic variants) on AD risk. We develop an NN-based method (netSNP) that identifies hundreds of novel potentially protective or at-risk AD-associated SNPs (along with an effect measure); the majority with frequency under 0.01. For case individuals, the number of "protective" (or "at-risk") netSNP-identified SNPs in their genome correlates positively (or inversely) with their age of AD diagnosis and inversely (or positively) with autopsy neuropathology. The effect measure increases correlations. Simulations suggest our results are not due to genetic linkage, overfitting, or bias introduced by netSNP. These findings suggest that netSNP can identify SNPs associated with AD pathophysiology that may assist with the diagnosis and mechanistic understanding of the disease.
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Affiliation(s)
- Bradley Monk
- Department of Neurosciences, Center for Neural Circuits and Behavior, School of Medicine, University of California, San Diego, San Diego, CA, United States
- Cognitive Science & Psychology IDP, University of California, San Diego, San Diego, CA, United States
| | - Andrei Rajkovic
- Department of Computer Science, Royal Holloway, University of London, Egham, United Kingdom
| | - Semar Petrus
- Institute for Genomic Medicine, Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Aleks Rajkovic
- Department of Pathology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Terry Gaasterland
- Institute for Genomic Medicine, Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Roberto Malinow
- Department of Neurosciences, Center for Neural Circuits and Behavior, School of Medicine, University of California, San Diego, San Diego, CA, United States
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
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16
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Prokopenko D, Morgan SL, Mullin K, Hofmann O, Chapman B, Kirchner R, Amberkar S, Wohlers I, Lange C, Hide W, Bertram L, Tanzi RE. Whole-genome sequencing reveals new Alzheimer's disease-associated rare variants in loci related to synaptic function and neuronal development. Alzheimers Dement 2021; 17:1509-1527. [PMID: 33797837 PMCID: PMC8519060 DOI: 10.1002/alz.12319] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022]
Abstract
Introduction Genome‐wide association studies have led to numerous genetic loci associated with Alzheimer's disease (AD). Whole‐genome sequencing (WGS) now permits genome‐wide analyses to identify rare variants contributing to AD risk. Methods We performed single‐variant and spatial clustering–based testing on rare variants (minor allele frequency [MAF] ≤1%) in a family‐based WGS‐based association study of 2247 subjects from 605 multiplex AD families, followed by replication in 1669 unrelated individuals. Results We identified 13 new AD candidate loci that yielded consistent rare‐variant signals in discovery and replication cohorts (4 from single‐variant, 9 from spatial‐clustering), implicating these genes: FNBP1L, SEL1L, LINC00298, PRKCH, C15ORF41, C2CD3, KIF2A, APC, LHX9, NALCN, CTNNA2, SYTL3, and CLSTN2. Discussion Downstream analyses of these novel loci highlight synaptic function, in contrast to common AD‐associated variants, which implicate innate immunity and amyloid processing. These loci have not been associated previously with AD, emphasizing the ability of WGS to identify AD‐associated rare variants, particularly outside of the exome.
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Affiliation(s)
- Dmitry Prokopenko
- Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah L Morgan
- Department of Neuroscience, Sheffield Institute for Translational Neurosciences, University of Sheffield, Sheffield, UK.,Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, Massachusetts, USA
| | - Kristina Mullin
- Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Oliver Hofmann
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Brad Chapman
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Rory Kirchner
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Sandeep Amberkar
- Department of Neuroscience, Sheffield Institute for Translational Neurosciences, University of Sheffield, Sheffield, UK
| | - Inken Wohlers
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Winston Hide
- Harvard Medical School, Boston, Massachusetts, USA.,Department of Neuroscience, Sheffield Institute for Translational Neurosciences, University of Sheffield, Sheffield, UK.,Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, Massachusetts, USA
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany.,Department of Psychology, University of Oslo, Oslo, Norway
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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17
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Ai R, Jin X, Tang B, Yang G, Niu Z, Fang EF. Ageing and Alzheimer’s Disease. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_74-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Mishra R, Li B. The Application of Artificial Intelligence in the Genetic Study of Alzheimer's Disease. Aging Dis 2020; 11:1567-1584. [PMID: 33269107 PMCID: PMC7673858 DOI: 10.14336/ad.2020.0312] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease in which genetic factors contribute approximately 70% of etiological effects. Studies have found many significant genetic and environmental factors, but the pathogenesis of AD is still unclear. With the application of microarray and next-generation sequencing technologies, research using genetic data has shown explosive growth. In addition to conventional statistical methods for the processing of these data, artificial intelligence (AI) technology shows obvious advantages in analyzing such complex projects. This article first briefly reviews the application of AI technology in medicine and the current status of genetic research in AD. Then, a comprehensive review is focused on the application of AI in the genetic research of AD, including the diagnosis and prognosis of AD based on genetic data, the analysis of genetic variation, gene expression profile, gene-gene interaction in AD, and genetic analysis of AD based on a knowledge base. Although many studies have yielded some meaningful results, they are still in a preliminary stage. The main shortcomings include the limitations of the databases, failing to take advantage of AI to conduct a systematic biology analysis of multilevel databases, and lack of a theoretical framework for the analysis results. Finally, we outlook the direction of future development. It is crucial to develop high quality, comprehensive, large sample size, data sharing resources; a multi-level system biology AI analysis strategy is one of the development directions, and computational creativity may play a role in theory model building, verification, and designing new intervention protocols for AD.
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Affiliation(s)
- Rohan Mishra
- Washington Institute for Health Sciences, Arlington, VA 22203, USA
| | - Bin Li
- Washington Institute for Health Sciences, Arlington, VA 22203, USA
- Georgetown University Medical Center, Washington D.C. 20057, USA
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19
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Xiao X, Jiao B, Liao X, Zhang W, Yuan Z, Guo L, Wang X, Zhou L, Liu X, Yan X, Tang B, Shen L. Association of Genes Involved in the Metabolic Pathways of Amyloid-β and Tau Proteins With Sporadic Late-Onset Alzheimer's Disease in the Southern Han Chinese Population. Front Aging Neurosci 2020; 12:584801. [PMID: 33240075 PMCID: PMC7677357 DOI: 10.3389/fnagi.2020.584801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/13/2020] [Indexed: 01/04/2023] Open
Abstract
The genes involved in the metabolic pathways of amyloid-β (Aβ) and tau proteins significantly influence the etiology of Alzheimer's disease (AD). Various studies have explored the associations between some of these genes and AD in the Caucasian population; however, researches regarding these associations remain limited in the Chinese population. To systematically evaluate the associations of these genes with AD, we investigated 19 genes involved in the metabolism of Aβ and tau based on previous studies selected using the PubMed database. This study included 372 patients with sporadic late-onset AD (sLOAD) and 345 cognitively healthy individuals from southern China. The results were replicated in the International Genomics of Alzheimer's Project (IGAP). Protein-protein interactions were determined using the STRING v11 database. We found that a single-nucleotide polymorphism, rs11682128, of BIN1 conferred susceptibility to sLOAD after adjusting for age, sex, and APOE ε4 status and performing the Bonferroni correction {corrected P = 0.000153, odds ratio (OR) [95% confidence interval (CI)] = 1.403 (1.079-1.824)}, which was replicated in the IGAP. Protein-protein interactions indicated that BIN1 was correlated with MAPT. Moreover, rare variants of NEP and FERMT2 (0.0026 < corrected P < 0.05), and the Aβ degradation, tau pathology, and tau phosphatase pathways (0.01 < corrected P < 0.05), were nominally significantly associated with sLOAD. This study suggested that the genes involved in the metabolic pathways of Aβ and tau contributed to the etiology of sLOAD in the southern Han Chinese population.
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Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Xinxin Liao
- Department of Geriatrics Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Weiwei Zhang
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lina Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China
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20
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Prokopenko D, Morgan SL, Mullin K, Hofmann O, Chapman B, Kirchner R, Amberkar S, Wohlers I, Lange C, Hide W, Bertram L, Tanzi RE. Whole-genome sequencing reveals new Alzheimer's disease-associated rare variants in loci related to synaptic function and neuronal development. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.11.03.20225540. [PMID: 33173892 PMCID: PMC7654884 DOI: 10.1101/2020.11.03.20225540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
INTRODUCTION Genome-wide association studies have led to numerous genetic loci associated with Alzheimer's disease (AD). Whole-genome sequencing (WGS) now permit genome-wide analyses to identify rare variants contributing to AD risk. METHODS We performed single-variant and spatial clustering-based testing on rare variants (minor allele frequency ≤1%) in a family-based WGS-based association study of 2,247 subjects from 605 multiplex AD families, followed by replication in 1,669 unrelated individuals. RESULTS We identified 13 new AD candidate loci that yielded consistent rare-variant signals in discovery and replication cohorts (4 from single-variant, 9 from spatial-clustering), implicating these genes: FNBP1L, SEL1L, LINC00298, PRKCH, C15ORF41, C2CD3, KIF2A, APC, LHX9, NALCN, CTNNA2, SYTL3, CLSTN2. DISCUSSION Downstream analyses of these novel loci highlight synaptic function, in contrast to common AD-associated variants, which implicate innate immunity. These loci have not been previously associated with AD, emphasizing the ability of WGS to identify AD-associated rare variants, particularly outside of coding regions.
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21
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Griswold AJ, Sivasankaran SK, Van Booven D, Gardner OK, Rajabli F, Whitehead PL, Hamilton-Nelson KL, Adams LD, Scott AM, Hofmann NK, Vance JM, Cuccaro ML, Bush WS, Martin ER, Byrd GS, Haines JL, Pericak-Vance MA, Beecham GW. Immune and Inflammatory Pathways Implicated by Whole Blood Transcriptomic Analysis in a Diverse Ancestry Alzheimer's Disease Cohort. J Alzheimers Dis 2020; 76:1047-1060. [PMID: 32597797 DOI: 10.3233/jad-190855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Significant work has identified genetic variants conferring risk and protection for Alzheimer's disease (AD), but functional effects of these variants is lacking, particularly in under-represented ancestral populations. Expression studies performed in easily accessible tissue, such as whole blood, can recapitulate some transcriptional changes occurring in brain and help to identify mechanisms underlying neurodegenerative processes. OBJECTIVE We aimed to identify transcriptional differences between AD cases and controls in a cohort of diverse ancestry. METHODS We analyzed the protein coding transcriptome using RNA sequencing from peripheral blood collected from 234 African American (AA) (115 AD, 119 controls) and 240 non-Hispanic Whites (NHW) (121 AD, 119 controls). To identify case-control differentially expressed genes and pathways, we performed stratified, joint, and interaction analyses using linear regression models within and across ancestral groups followed by pathway and gene set enrichment analyses. RESULTS Overall, we identified 418 (291 upregulated, 127 downregulated) and 488 genes (352 upregulated, 136 downregulated) differentially expressed in the AA and NHW datasets, respectively, with only 16 genes commonly differentially expressed in both ancestral groups. Joint analyses provided greater power to detect case-control differences and identified 1,102 differentially expressed genes between cases and controls (812 upregulated, 290 downregulated). Interaction analysis identified only 27 genes with different effects in AA compared to NHW. Pathway and gene-set enrichment analyses revealed differences in immune response-related pathways that were enriched across the analyses despite different underlying gene sets. CONCLUSION These results support the hypothesis of converging underlying pathophysiological processes in AD across ancestral groups.
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Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | | | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Olivia K Gardner
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | | | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Aja M Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - William S Bush
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Goldie S Byrd
- Department of Public Health Sciences, Wake Forest University, Winston-Salem, NC, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
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Bellenguez C, Grenier-Boley B, Lambert JC. Genetics of Alzheimer’s disease: where we are, and where we are going. Curr Opin Neurobiol 2020; 61:40-48. [DOI: 10.1016/j.conb.2019.11.024] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
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23
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Adorni MP, Ruscica M, Ferri N, Bernini F, Zimetti F. Proprotein Convertase Subtilisin/Kexin Type 9, Brain Cholesterol Homeostasis and Potential Implication for Alzheimer's Disease. Front Aging Neurosci 2019; 11:120. [PMID: 31178716 PMCID: PMC6538876 DOI: 10.3389/fnagi.2019.00120] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/07/2019] [Indexed: 02/04/2023] Open
Abstract
Alzheimer’s disease (AD) has been associated with dysregulation of brain cholesterol homeostasis. Proprotein convertase subtilisin/kexin type 9 (PCSK9), beyond the known role in the regulation of plasma low-density lipoprotein cholesterol, was first identified in the brain with a potential involvement in brain development and apoptosis. However, its role in the central nervous system (CNS) and in AD pathogenesis is still far from being understood. While in vitro and in vivo evidence led to controversial results, genetic studies apparently did not find an association between PCSK9 loss of function mutations and AD risk or prevalence. In addition, a potential impairment of cognitive performances by the treatment with the PCSK9 inhibitors, alirocumab and evolocumab, have been excluded, although ongoing studies with longer follow-up will provide further insights. PCSK9 is able to affect the expression of neuronal receptors involved in cholesterol homeostasis and neuroinflammation, and higher PCSK9 concentrations have been found in the cerebrospinal fluid (CSF) of AD patients. In this review article, we critically examined the science of PCSK9 with respect to its modulatory role of the mechanisms underlying the pathogenesis of AD. In addition, based on literature data, we made the hypothesis to consider brain PCSK9 as a negative modulator of brain cholesterol homeostasis and neuroinflammation and a potential pharmacological target for treatment.
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Affiliation(s)
- Maria Pia Adorni
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Massimiliano Ruscica
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ferri
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Padova, Italy
| | - Franco Bernini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Francesca Zimetti
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
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