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Oveisgharan S, Yu L, de Paiva Lopes K, Tasaki S, Wang Y, Menon V, Schneider JA, Seyfried NT, Bennett DA. Proteins linking APOE ɛ4 with Alzheimer's disease. Alzheimers Dement 2024. [PMID: 38856164 DOI: 10.1002/alz.13867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/29/2024] [Accepted: 04/08/2024] [Indexed: 06/11/2024]
Abstract
INTRODUCTION The ɛ4 allele of the apolipoprotein E gene (APOE ɛ4) is the strongest genetic risk factor for Alzheimer's disease (AD), but the mechanisms connecting APOE ɛ4 to AD are not clear. METHODS Participants (n = 596) were from two clinical-pathological studies. Tissues from dorsolateral prefrontal cortex were examined to identify 8425 proteins. Post mortem pathological assessment used immunohistochemistry to obtain amyloid beta (Aβ) load and tau tangle density. RESULTS In separate models, APOE ɛ4 was associated with 18 proteins, which were associated with Aβ and tau tangles. Examining the proteins in a single model identified Netrin-1 and secreted frizzled-related protein 1 (SFRP1) as the two proteins linking APOE ɛ4 with Aβ with the largest effect sizes and Netrin-1 and testican-3 linking APOE ɛ4 with tau tangles. DISCUSSION We identified Netrin-1, SFRP1, and testican-3 as the most promising proteins that link APOE ɛ4 with Aβ and tau tangles. HIGHLIGHTS Of 8425 proteins extracted from prefrontal cortex, 18 were related to APOE ɛ4. The 18 proteins were also related to amyloid beta (Aβ) and tau. The 18 proteins were more related to APOE ɛ4 than other AD genetic risk variants. Netrin-1 and secreted frizzled-related protein 1 were the two most promising proteins linking APOE ɛ4 with Aβ. Netrin-1 and testican-3 were two most promising proteins linking APOE ɛ4 with tau.
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Affiliation(s)
- Shahram Oveisgharan
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
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Malamon JS, Farrell JJ, Xia LC, Dombroski BA, Das RG, Way J, Kuzma AB, Valladares O, Leung YY, Scanlon AJ, Lopez IAB, Brehony J, Worley KC, Zhang NR, Wang LS, Farrer LA, Schellenberg GD, Lee WP, Vardarajan BN. A comparative study of structural variant calling in WGS from Alzheimer's disease families. Life Sci Alliance 2024; 7:e202302181. [PMID: 38418088 PMCID: PMC10902710 DOI: 10.26508/lsa.202302181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
Detecting structural variants (SVs) in whole-genome sequencing poses significant challenges. We present a protocol for variant calling, merging, genotyping, sensitivity analysis, and laboratory validation for generating a high-quality SV call set in whole-genome sequencing from the Alzheimer's Disease Sequencing Project comprising 578 individuals from 111 families. Employing two complementary pipelines, Scalpel and Parliament, for SV/indel calling, we assessed sensitivity through sample replicates (N = 9) with in silico variant spike-ins. We developed a novel metric, D-score, to evaluate caller specificity for deletions. The accuracy of deletions was evaluated by Sanger sequencing. We generated a high-quality call set of 152,301 deletions of diverse sizes. Sanger sequencing validated 114 of 146 detected deletions (78.1%). Scalpel excelled in accuracy for deletions ≤100 bp, whereas Parliament was optimal for deletions >900 bp. Overall, 83.0% and 72.5% of calls by Scalpel and Parliament were validated, respectively, including all 11 deletions called by both Parliament and Scalpel between 101 and 900 bp. Our flexible protocol successfully generated a high-quality deletion call set and a truth set of Sanger sequencing-validated deletions with precise breakpoints spanning 1-17,000 bp.
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Affiliation(s)
- John S Malamon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - John J Farrell
- Biomedical Genetics Section, Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Li Charlie Xia
- https://ror.org/03mtd9a03 Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rueben G Das
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jessica Way
- Broad Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda B Kuzma
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Otto Valladares
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison J Scanlon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Irving Antonio Barrera Lopez
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jack Brehony
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kim C Worley
- https://ror.org/02pttbw34 Human Genome Sequencing Center, and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nancy R Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lindsay A Farrer
- Biomedical Genetics Section, Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA, USA
- Departments of Neurology and Ophthalmology, Boston University School of Medicine, Boston University, Boston, MA, USA
- Departments of Epidemiology and Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Badri N Vardarajan
- https://ror.org/01esghr10 Gertrude H. Sergievsky Center and Taub Institute of Aging Brain, Department of Neurology, Columbia University Medical Center, New York, NY, USA
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de Vries LE, Huitinga I, Kessels HW, Swaab DF, Verhaagen J. The concept of resilience to Alzheimer's Disease: current definitions and cellular and molecular mechanisms. Mol Neurodegener 2024; 19:33. [PMID: 38589893 PMCID: PMC11003087 DOI: 10.1186/s13024-024-00719-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Some individuals are able to maintain their cognitive abilities despite the presence of significant Alzheimer's Disease (AD) neuropathological changes. This discrepancy between cognition and pathology has been labeled as resilience and has evolved into a widely debated concept. External factors such as cognitive stimulation are associated with resilience to AD, but the exact cellular and molecular underpinnings are not completely understood. In this review, we discuss the current definitions used in the field, highlight the translational approaches used to investigate resilience to AD and summarize the underlying cellular and molecular substrates of resilience that have been derived from human and animal studies, which have received more and more attention in the last few years. From these studies the picture emerges that resilient individuals are different from AD patients in terms of specific pathological species and their cellular reaction to AD pathology, which possibly helps to maintain cognition up to a certain tipping point. Studying these rare resilient individuals can be of great importance as it could pave the way to novel therapeutic avenues for AD.
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Affiliation(s)
- Luuk E de Vries
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands.
| | - Inge Huitinga
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - Helmut W Kessels
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Dick F Swaab
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, Netherlands
| | - Joost Verhaagen
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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Cai M, Zheng Q, Chen Y, Liu S, Zhu H, Bai B. Insights from the neural guidance factor Netrin-1 into neurodegeneration and other diseases. Front Mol Neurosci 2024; 17:1379726. [PMID: 38638604 PMCID: PMC11024333 DOI: 10.3389/fnmol.2024.1379726] [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: 01/31/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Netrin-1 was initially discovered as a neuronal growth cue for axonal guidance, and its functions have later been identified in inflammation, tumorigenesis, neurodegeneration, and other disorders. We have recently found its alterations in the brains with Alzheimer's disease, which might provide important clues to the mechanisms of some unique pathologies. To provide better understanding of this promising molecule, we here summarize research progresses in genetics, pathology, biochemistry, cell biology and other studies of Netrin-1 about its mechanistic roles and biomarker potentials with an emphasis on clinical neurodegenerative disorders in order to expand understanding of this promising molecular player in human diseases.
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Affiliation(s)
- Minqi Cai
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, Jiangsu, China
| | - Qian Zheng
- Health Management Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Yiqiang Chen
- Center for Precision Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Siyuan Liu
- Center for Precision Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Huimin Zhu
- Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Bing Bai
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, Jiangsu, China
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Zhang T, Kim BM, Lee TH. Death-associated protein kinase 1 as a therapeutic target for Alzheimer's disease. Transl Neurodegener 2024; 13:4. [PMID: 38195518 PMCID: PMC10775678 DOI: 10.1186/s40035-023-00395-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024] Open
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia in the elderly and represents a major clinical challenge in the ageing society. Neuropathological hallmarks of AD include neurofibrillary tangles composed of hyperphosphorylated tau, senile plaques derived from the deposition of amyloid-β (Aβ) peptides, brain atrophy induced by neuronal loss, and synaptic dysfunctions. Death-associated protein kinase 1 (DAPK1) is ubiquitously expressed in the central nervous system. Dysregulation of DAPK1 has been shown to contribute to various neurological diseases including AD, ischemic stroke and Parkinson's disease (PD). We have established an upstream effect of DAPK1 on Aβ and tau pathologies and neuronal apoptosis through kinase-mediated protein phosphorylation, supporting a causal role of DAPK1 in the pathophysiology of AD. In this review, we summarize current knowledge about how DAPK1 is involved in various AD pathological changes including tau hyperphosphorylation, Aβ deposition, neuronal cell death and synaptic degeneration. The underlying molecular mechanisms of DAPK1 dysregulation in AD are discussed. We also review the recent progress regarding the development of novel DAPK1 modulators and their potential applications in AD intervention. These findings substantiate DAPK1 as a novel therapeutic target for the development of multifunctional disease-modifying treatments for AD and other neurological disorders.
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Affiliation(s)
- Tao Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Byeong Mo Kim
- Research Center for New Drug Development, AgingTarget Inc., 10F Ace Cheonggye Tower, 53, Seonggogae-Ro, Uiwang-Si, 16006, Gyeonggi-Do, Korea.
| | - Tae Ho Lee
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, 1 Xuefu North Road, Fuzhou, 350122, Fujian, China.
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Area-Gomez E, Schon EA. Towards a Unitary Hypothesis of Alzheimer's Disease Pathogenesis. J Alzheimers Dis 2024; 98:1243-1275. [PMID: 38578892 DOI: 10.3233/jad-231318] [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] [Indexed: 04/07/2024]
Abstract
The "amyloid cascade" hypothesis of Alzheimer's disease (AD) pathogenesis invokes the accumulation in the brain of plaques (containing the amyloid-β protein precursor [AβPP] cleavage product amyloid-β [Aβ]) and tangles (containing hyperphosphorylated tau) as drivers of pathogenesis. However, the poor track record of clinical trials based on this hypothesis suggests that the accumulation of these peptides is not the only cause of AD. Here, an alternative hypothesis is proposed in which the AβPP cleavage product C99, not Aβ, is the main culprit, via its role as a regulator of cholesterol metabolism. C99, which is a cholesterol sensor, promotes the formation of mitochondria-associated endoplasmic reticulum (ER) membranes (MAM), a cholesterol-rich lipid raft-like subdomain of the ER that communicates, both physically and biochemically, with mitochondria. We propose that in early-onset AD (EOAD), MAM-localized C99 is elevated above normal levels, resulting in increased transport of cholesterol from the plasma membrane to membranes of intracellular organelles, such as ER/endosomes, thereby upregulating MAM function and driving pathology. By the same token, late-onset AD (LOAD) is triggered by any genetic variant that increases the accumulation of intracellular cholesterol that, in turn, boosts the levels of C99 and again upregulates MAM function. Thus, the functional cause of AD is upregulated MAM function that, in turn, causes the hallmark disease phenotypes, including the plaques and tangles. Accordingly, the MAM hypothesis invokes two key interrelated elements, C99 and cholesterol, that converge at the MAM to drive AD pathogenesis. From this perspective, AD is, at bottom, a lipid disorder.
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Affiliation(s)
- Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY, USA
- Centro de Investigaciones Biológicas "Margarita Salas", Spanish National Research Council, Madrid, Spain
| | - Eric A Schon
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Genetics and Development>, Columbia University, New York, NY, USA
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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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8
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Rapti G. Regulation of axon pathfinding by astroglia across genetic model organisms. Front Cell Neurosci 2023; 17:1241957. [PMID: 37941606 PMCID: PMC10628440 DOI: 10.3389/fncel.2023.1241957] [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: 06/18/2023] [Accepted: 09/07/2023] [Indexed: 11/10/2023] Open
Abstract
Glia and neurons are intimately associated throughout bilaterian nervous systems, and were early proposed to interact for patterning circuit assembly. The investigations of circuit formation progressed from early hypotheses of intermediate guideposts and a "glia blueprint", to recent genetic and cell manipulations, and visualizations in vivo. An array of molecular factors are implicated in axon pathfinding but their number appears small relatively to circuit complexity. Comprehending this circuit complexity requires to identify unknown factors and dissect molecular topographies. Glia contribute to both aspects and certain studies provide molecular and functional insights into these contributions. Here, I survey glial roles in guiding axon navigation in vivo, emphasizing analogies, differences and open questions across major genetic models. I highlight studies pioneering the topic, and dissect recent findings that further advance our current molecular understanding. Circuits of the vertebrate forebrain, visual system and neural tube in zebrafish, mouse and chick, the Drosophila ventral cord and the C. elegans brain-like neuropil emerge as major contexts to study glial cell functions in axon navigation. I present astroglial cell types in these models, and their molecular and cellular interactions that drive axon guidance. I underline shared principles across models, conceptual or technical complications, and open questions that await investigation. Glia of the radial-astrocyte lineage, emerge as regulators of axon pathfinding, often employing common molecular factors across models. Yet this survey also highlights different involvements of glia in embryonic navigation or pioneer axon pathfinding, and unknowns in the molecular underpinnings of glial cell functions. Future cellular and molecular investigations should complete the comprehensive view of glial roles in circuit assembly.
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Affiliation(s)
- Georgia Rapti
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Rome, Italy
- Interdisciplinary Center of Neurosciences, Heidelberg University, Heidelberg, Germany
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Huang J, Wang Y, Stein TD, Ang TFA, Zhu Y, Tao Q, Lunetta KL, Mez J, Au R, Farrer LA, Qiu WQ, Zhang X. The impact of blood MCP-1 levels on Alzheimer's disease with genetic variation of UNC5C and NAV3 loci. RESEARCH SQUARE 2023:rs.3.rs-3376348. [PMID: 37841863 PMCID: PMC10571626 DOI: 10.21203/rs.3.rs-3376348/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: 10/17/2023]
Abstract
Background Previous study shows that monocyte chemoattractant protein-1 (MCP-1), which is implicated in the peripheral proinflammatory cascade and blood-brain barrier (BBB) disruption, modulates the genetic risks of AD in established AD loci. Methods In this study, we hypothesized that blood MCP-1 impacts the AD risk of genetic variants beyond known AD loci. We thus performed a genome-wide association study (GWAS) using the logistic regression via generalized estimating equations (GEE) and the Cox proportional-hazards models to examine the interactive effects between single nucleotide polymorphisms (SNPs) and blood MCP-1 level on AD in three cohorts: the Framingham Heart Study (FHS), Alzheimer's Disease Neuroimaging Initiative (ADNI) and Religious Orders Study/Memory and Aging Project (ROSMAP). Results We identified SNPs in two genes, neuron navigator 3 (NAV3, also named Unc-53 Homolog 3, rs696468) (p < 7.55×10- 9) and Unc-5 Netrin Receptor C (UNC5C rs72659964) (p < 1.07×10- 8) that showed an association between increasing levels of blood MCP-1 and AD. Elevating blood MCP-1 concentrations increased AD risk and AD pathology in genotypes of NAV3 (rs696468-CC) and UNC5C (rs72659964-AT + TT), but did not influence the other counterpart genotypes of these variants. Conclusions NAV3 and UNC5C are homologs and may increase AD risk through dysregulating the functions of neurite outgrowth and guidance. Overall, the association of risk alleles of NAV3 and UNC5C with AD is enhanced by peripheral MCP-1 level, suggesting that lowering the level of blood MCP-1 may reduce the risk of developing AD for people with these genotypes.
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Affiliation(s)
- Jinghan Huang
- Boston University Chobanian & Avedisian School of Medicine
| | - Yixuan Wang
- Boston University Chobanian & Avedisian School of Medicine
| | - Thor D Stein
- Boston University Chobanian & Avedisian School of Medicine
| | | | - Yibo Zhu
- Boston University Chobanian & Avedisian School of Medicine
| | - Qiushan Tao
- Boston University Chobanian & Avedisian School of Medicine
| | | | - Jesse Mez
- Boston University Chobanian & Avedisian School of Medicine
| | - Rhoda Au
- Boston University Chobanian & Avedisian School of Medicine
| | | | - Wei Qiao Qiu
- Boston University Chobanian & Avedisian School of Medicine
| | - Xiaoling Zhang
- Boston University Chobanian & Avedisian School of Medicine
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10
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Arbeev KG, Ukraintseva S, Bagley O, Duan H, Wu D, Akushevich I, Stallard E, Kulminski A, Christensen K, Feitosa MF, O’Connell JR, Parker D, Whitson H, Yashin AI. Interactions between genes involved in physiological dysregulation and axon guidance: role in Alzheimer's disease. Front Genet 2023; 14:1236509. [PMID: 37719713 PMCID: PMC10500346 DOI: 10.3389/fgene.2023.1236509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
Dysregulation of physiological processes may contribute to Alzheimer's disease (AD) development. We previously found that an increase in the level of physiological dysregulation (PD) in the aging body is associated with declining resilience and robustness to major diseases. Also, our genome-wide association study found that genes associated with the age-related increase in PD frequently represented pathways implicated in axon guidance and synaptic function, which in turn were linked to AD and related traits (e.g., amyloid, tau, neurodegeneration) in the literature. Here, we tested the hypothesis that genes involved in PD and axon guidance/synapse function may jointly influence onset of AD. We assessed the impact of interactions between SNPs in such genes on AD onset in the Long Life Family Study and sought to replicate the findings in the Health and Retirement Study. We found significant interactions between SNPs in the UNC5C and CNTN6, and PLXNA4 and EPHB2 genes that influenced AD onset in both datasets. Associations with individual SNPs were not statistically significant. Our findings, thus, support a major role of genetic interactions in the heterogeneity of AD and suggest the joint contribution of genes involved in PD and axon guidance/synapse function (essential for the maintenance of complex neural networks) to AD development.
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Affiliation(s)
- Konstantin G. Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Svetlana Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Olivia Bagley
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Hongzhe Duan
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Deqing Wu
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Igor Akushevich
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Eric Stallard
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Alexander Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Kaare Christensen
- Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Jeffrey R. O’Connell
- Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Daniel Parker
- Duke Center for the Study of Aging and Human Development, Duke University, Durham, NC, United States
| | - Heather Whitson
- Duke Center for the Study of Aging and Human Development, Duke University, Durham, NC, United States
- Durham VA Geriatrics Research Education and Clinical Center, Durham, NC, United States
| | - Anatoliy I. Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, United States
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11
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Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C. Extended genome-wide association study employing the African Genome Resources Panel identifies novel susceptibility loci for Alzheimer's Disease in individuals of African ancestry. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.29.23294774. [PMID: 37693582 PMCID: PMC10491365 DOI: 10.1101/2023.08.29.23294774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Despite a two-fold increased risk, individuals of African ancestry have been significantly underrepresented in Alzheimer's Disease (AD) genomics efforts. METHODS GWAS of 2,903 AD cases and 6,265 cognitive controls of African ancestry. Within-dataset results were meta-analyzed, followed by gene-based and pathway analyses, and analysis of RNAseq and whole-genome sequencing data. RESULTS A novel AD risk locus was identified in MPDZ on chromosome 9p23 (rs141610415, MAF=.002, P =3.68×10 -9 ). Two additional novel common and nine novel rare loci approached genome-wide significance at P <9×10 -7 . Comparison of association and LD patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 ( ASCL1 ), suggesting that the association is modulated by regional origin of local African ancestry. DISCUSSION Increased sample sizes and sample sets from Africa covering as much African genetic diversity as possible will be critical to identify additional disease-associated loci and improve deconvolution of local genetic ancestry effects.
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12
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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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13
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Kim SH, Nichols KD, Anderson EN, Liu Y, Ramesh N, Jia W, Kuerbis CJ, Scalf M, Smith LM, Pandey UB, Tibbetts RS. Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2. eLife 2023; 12:e84382. [PMID: 37039476 PMCID: PMC10147378 DOI: 10.7554/elife.84382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
Mutations in the ubiquitin (Ub) chaperone Ubiquilin 2 (UBQLN2) cause X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) through unknown mechanisms. Here, we show that aggregation-prone, ALS-associated mutants of UBQLN2 (UBQLN2ALS) trigger heat stress-dependent neurodegeneration in Drosophila. A genetic modifier screen implicated endolysosomal and axon guidance genes, including the netrin receptor, Unc-5, as key modulators of UBQLN2 toxicity. Reduced gene dosage of Unc-5 or its coreceptor Dcc/frazzled diminished neurodegenerative phenotypes, including motor dysfunction, neuromuscular junction defects, and shortened lifespan, in flies expressing UBQLN2ALS alleles. Induced pluripotent stem cells (iPSCs) harboring UBQLN2ALS knockin mutations exhibited lysosomal defects while inducible motor neurons (iMNs) expressing UBQLN2ALS alleles exhibited cytosolic UBQLN2 inclusions, reduced neurite complexity, and growth cone defects that were partially reversed by silencing of UNC5B and DCC. The combined findings suggest that altered growth cone dynamics are a conserved pathomechanism in UBQLN2-associated ALS/FTD.
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Affiliation(s)
- Sang Hwa Kim
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Kye D Nichols
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Yining Liu
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Nandini Ramesh
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Weiyan Jia
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Connor J Kuerbis
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Randal S Tibbetts
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
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14
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Díaz MM, Tsenkina Y, Arizanovska D, Mehlen P, Liebl DJ. DCC/netrin-1 regulates cell death in oligodendrocytes after brain injury. Cell Death Differ 2023; 30:397-406. [PMID: 36456775 PMCID: PMC9950151 DOI: 10.1038/s41418-022-01091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Hallmark pathological features of brain trauma are axonal degeneration and demyelination because myelin-producing oligodendrocytes (OLs) are particularly vulnerable to injury-induced death signals. To reveal mechanisms responsible for this OL loss, we examined a novel class of "death receptors" called dependence receptors (DepRs). DepRs initiate pro-death signals in the absence of their respective ligand(s), yet little is known about their role after injury. Here, we investigated whether the deleted in colorectal cancer (DCC) DepR contributes to OL loss after brain injury. We found that administration of its netrin-1 ligand is sufficient to block OL cell death. We also show that upon acute injury, DCC is upregulated while netrin-1 is downregulated in perilesional tissues. Moreover, after genetically silencing pro-death activity using DCCD1290N mutant mice, we observed greater OL survival, greater myelin integrity, and improved motor function. Our findings uncover a novel role for the netrin-1/DCC pathway in regulating OL loss in the traumatically injured brain.
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Affiliation(s)
- Madelen M Díaz
- The Miami Project to Cure Paralysis, Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yanina Tsenkina
- The Miami Project to Cure Paralysis, Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Dena Arizanovska
- The Miami Project to Cure Paralysis, Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université de Lyon1, Lyon, France.
| | - Daniel J Liebl
- The Miami Project to Cure Paralysis, Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, FL, USA.
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15
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Aerqin Q, Wang ZT, Wu KM, He XY, Dong Q, Yu JT. Omics-based biomarkers discovery for Alzheimer's disease. Cell Mol Life Sci 2022; 79:585. [PMID: 36348101 DOI: 10.1007/s00018-022-04614-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorders presenting with the pathological hallmarks of amyloid plaques and tau tangles. Over the past few years, great efforts have been made to explore reliable biomarkers of AD. High-throughput omics are a technology driven by multiple levels of unbiased data to detect the complex etiology of AD, and it provides us with new opportunities to better understand the pathophysiology of AD and thereby identify potential biomarkers. Through revealing the interaction networks between different molecular levels, the ultimate goal of multi-omics is to improve the diagnosis and treatment of AD. In this review, based on the current AD pathology and the current status of AD diagnostic biomarkers, we summarize how genomics, transcriptomics, proteomics and metabolomics are all conducing to the discovery of reliable AD biomarkers that could be developed and used in clinical AD management.
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Affiliation(s)
- Qiaolifan Aerqin
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zuo-Teng Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Kai-Min Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao-Yu He
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
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16
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Abstract
PURPOSE OF REVIEW This article discusses the spectrum of genetic risk in familial and sporadic forms of early- and late-onset Alzheimer disease (AD). Recent work illuminating the complex genetic architecture of AD is discussed in the context of high and low risk and what is known in different populations. RECENT FINDINGS A small proportion of AD is autosomal dominant familial AD caused by variants in PSEN1, PSEN2, or APP, although more recently described rare genetic changes can also increase risk substantially over the general population, with odds ratios estimated at 2 to 4. APOE remains the strongest genetic risk factor for late-onset AD, and understanding the biology of APOE has yielded mechanistic insights and leads for therapeutic interventions. Genome-wide studies enabled by rapidly developing technologic advances in sequencing have identified numerous risk factors that have a low impact on risk but are widely shared throughout the population and involve a repertoire of cell pathways, again shining light on potential paths to intervention. Population studies aimed at defining and stratifying genetic AD risk have been informative, although they are not yet widely applicable clinically because the studies were not performed in people with diverse ancestry and ethnicity and thus population-wide data are lacking. SUMMARY The value of genetic information to practitioners in the clinic is distinct from information sought by researchers looking to identify novel therapeutic targets. It is possible to envision a future in which genetic stratification joins other biomarkers to facilitate therapeutic choices and inform prognosis. Genetics already has transformed our understanding of AD pathogenesis and will, no doubt, continue to reveal the complexity of brain biology in health and disease.
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17
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Hawksworth J, Fernández E, Gevaert K. A new generation of AD biomarkers: 2019 to 2021. Ageing Res Rev 2022; 79:101654. [PMID: 35636691 DOI: 10.1016/j.arr.2022.101654] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and cases are rising worldwide. The effort to fight this disease is hampered by a lack of disease-modifying treatments and the absence of an early, accurate diagnostic tool. Neuropathology begins years or decades before symptoms occur and, upon onset of symptoms, diagnosis can take a year or more. Such delays postpone treatment and make research into the early stages of the disease difficult. Ideally, clinicians require a minimally invasive test that can detect AD in its early stages, before cognitive symptoms occur. Advances in proteomic technologies have facilitated the study of promising biomarkers of AD. Over the last two years (2019-2021) studies have identified and validated many species which can be measured in cerebrospinal fluid (CSF), plasma, or in both fluids, and which have a high predictive value for AD. We herein discuss proteins which have been highlighted as promising biomarkers of AD in the last two years, and consider implications for future research within the research framework of the amyloid (A), tau (T), neurodegeneration (N) scoring system. We review recently identified species of amyloid and tau which may improve diagnosis when used in combination with current measures such as amyloid-beta-42 (Aβ42), total tau (t-tau) and phosphorylated tau (p-tau). In addition, several proteins have been identified as likely proxies for neurodegeneration, including neurofilament light (NfL), synaptosomal-associated protein 25 (SNAP-25) and neurogranin (NRGN). Finally, proteins originating from diverse processes such as neuroinflammation, lipid transport and mitochondrial dysfunction could aid in both AD diagnosis and patient stratification.
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18
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Jiao B, Xiao X, Yuan Z, Guo L, Liao X, Zhou Y, Zhou L, Wang X, Liu X, Liu H, Jiang Y, Lin Z, Zhu Y, Yang Q, Zhang W, Li J, Shen L. Associations of risk genes with onset age and plasma biomarkers of Alzheimer's disease: a large case-control study in mainland China. Neuropsychopharmacology 2022; 47:1121-1127. [PMID: 35001095 PMCID: PMC8938514 DOI: 10.1038/s41386-021-01258-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/28/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022]
Abstract
Most genetic studies concerning risk genes in Alzheimer's disease (AD) are from Caucasian populations, whereas the data remain limited in the Chinese population. In this study, we systematically explored the relationship between AD and risk genes in mainland China. We sequenced 33 risk genes previously reported to be associated with AD in a total of 3604 individuals in the mainland Chinese population. Common variant (MAF ≥ 0.01) based association analysis and gene-based (MAF < 0.01) association test were performed by PLINK 1.9 and Sequence Kernel Association Test-Optimal, respectively. Polygenic risk score (PRS) was calculated, and receiver operating characteristic curve (AUC) was computed. Plasma Aβ42, Aβ40, total tau (T-tau), and neurofilament light chain (NFL) were tested in a subgroup, and their associations with PRS were conducted using the Spearman correlation test. Six common variants varied significantly between AD patients and cognitively normal controls after the adjustment of age, gender, and APOE ε4 status, including variants in ABCA7 (n = 5) and APOE (n = 1). Among them, four variants were novel and two were reported previously. The AUC of PRS was 0.71. The high PRS was significantly associated with an earlier age at onset (P = 4.30 × 10-4). PRS was correlated with plasma Aβ42, Aβ42/Aβ40 ratio, T-tau, and NFL levels. Gene-based association test revealed that ABCA7 and UNC5C reached statistical significance. The common variants in APOE and ABCA7, as well as rare variants in ABCA7 and UNC5C, may contribute to the etiology of AD. Moreover, the PRS, to some extent, could predict the risk, onset age, and biological changes of AD.
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Affiliation(s)
- Bin Jiao
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China ,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Xuewen Xiao
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Yuan
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lina Guo
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Liao
- grid.216417.70000 0001 0379 7164National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China ,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China ,grid.452223.00000 0004 1757 7615Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yafang Zhou
- grid.216417.70000 0001 0379 7164National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China ,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China ,grid.452223.00000 0004 1757 7615Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Zhou
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Wang
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Liu
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yaling Jiang
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhuojie Lin
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Zhu
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qijie Yang
- grid.452223.00000 0004 1757 7615Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Weiwei Zhang
- grid.216417.70000 0001 0379 7164National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China ,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Jinchen Li
- grid.216417.70000 0001 0379 7164National Clinical Research Center for Geriatric 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. .,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China. .,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, 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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Chen G, Ahn EH, Kang SS, Xia Y, Liu X, Zhang Z, Ye K. UNC5C Receptor Proteolytic Cleavage by Active AEP Promotes Dopaminergic Neuronal Degeneration in Parkinson's Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103396. [PMID: 35023303 PMCID: PMC8895126 DOI: 10.1002/advs.202103396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Netrin-1 is a chemotropic cue mediating axon growth and neural migration in neuronal development, and its receptors deletion in colorectal cancer and UNC5s act as dependence receptors regulating neuronal apoptosis. Asparagine endopeptidase (AEP) is an age-dependent protease that cuts human alpha-synuclein (α-Syn) at N103 and triggers its aggregation and neurotoxicity. In the current study, it is reported that UNC5C receptor is cleaved by AEP in Parkinson's disease (PD) and facilitates dopaminergic neuronal loss. UNC5C is truncated by active AEP in human α-SNCA transgenic mice in an age-dependent manner or induced by neurotoxin rotenone. Moreover, UNC5C is fragmented by AEP in PD brains, inversely correlated with reduced netrin-1 levels. Netrin-1 deprivation in primary cultures induces AEP and caspase-3 activation, triggering UNC5C proteolytic fragmentation and enhancing neuronal loss. Noticeably, blocking UNC5C cleavage by AEP attenuates netrin-1 deprivation-elicited neuronal death and motor disorders in netrin flox/flox mice. Overexpression of AEP-truncated UNC5C intracellular fragment strongly elicits α-Syn aggregation and dopaminergic loss, locomotor deficits in α-SNCA transgenic mice. Hence, the findings demonstrate that netrin-1 reduction and UNC5C truncation by AEP contribute to PD pathogenesis.
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Affiliation(s)
- Guiqin Chen
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGA30322USA
- Department of NeurologyRenmin Hospital of Wuhan UniversityWuhanHubei Province430060China
| | - Eun Hee Ahn
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGA30322USA
| | - Seong Su Kang
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGA30322USA
| | - Yiyuan Xia
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGA30322USA
| | - Xia Liu
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGA30322USA
| | - Zhaohui Zhang
- Department of NeurologyRenmin Hospital of Wuhan UniversityWuhanHubei Province430060China
| | - Keqiang Ye
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGA30322USA
- Faculty of Life and Health SciencesShenzhen Institute of Advanced TechnologyChinese Academy of ScienceShenzhenGuangdong518035China
- The Brain Cognition and Brain Disease Institute (BCBDI)Shenzhen Institute of Advanced TechnologyChinese Academy of ScienceShenzhenGuangdong518035China
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20
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Ju T, Sun L, Fan Y, Wang T, Liu Y, Liu D, Liu T, Zhao C, Wang W, Chi L. Decreased Netrin-1 in Mild Cognitive Impairment and Alzheimer’s Disease Patients. Front Aging Neurosci 2022; 13:762649. [PMID: 35250531 PMCID: PMC8888826 DOI: 10.3389/fnagi.2021.762649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background and Objective Inflammatory mediators are closely associated with the pathogenesis of Alzheimer’s disease (AD) and mild cognitive impairment (MCI). Netrin-1 is an axon guidance protein and despite its capacity to function as a neuroimmune guidance signal, its role in AD or MCI is poorly understood. In addition, the association among netrin-1, cognitive impairment and serum inflammatory cytokines such as interleukin-17 (IL-17) and tumor necrosis (TNF-α) remains unclear. The aim of this study was to determine serum levels of IL-17, TNF-α and netrin-1in a cohort of AD and MCI patients, and to study the relationship between these cytokines and cognitive status, as well as to assess the possible relationships between netrin-1 levels and inflammatory molecules. Methods Serum concentrations of netrin-1, TNF-α and IL-17 were determined in 20 AD patients, 22 MCI patients and 22 healthy controls using an enzyme-linked immunosorbent assay (ELISA). In addition, neuropsychological evaluations and psychometric assessments were performed in all subjects. Results Serum netrin-1 levels were decreased in AD and MCI patients and were positively correlated with Mini Mental State Examination (MMSE) scores. In contrast, serum TNF-α and IL-17 levels were elevated in AD and MCI cohorts and negatively correlated with MMSE scores. Serum netrin-1 levels were inversely related with TNF-α and IL-17 levels in AD, but not MCI, patients. Conclusion Based on the findings reported here, netrin-1 may serve as a marker for the early recognition of dementia and predict cognitive impairment.
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Affiliation(s)
- Ting Ju
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lina Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuwei Fan
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tianhang Wang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanchen Liu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dan Liu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tianyi Liu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chang Zhao
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Intensive Care Unit, Jiangyin People’s Hospital, Wuxi, China
| | - Wenxin Wang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Neurology, Shenzhen Samii Medical Center, Shenzhen, China
| | - Lijun Chi
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Lijun Chi,
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21
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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: 17] [Impact Index Per Article: 8.5] [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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22
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Dickson SP, Hendrix SB, Brown BL, Ridge PG, Nicodemus-Johnson J, Hardy ML, McKeany AM, Booth SB, Fortna RR, Kauwe JSK. GenoRisk: A polygenic risk score for Alzheimer's disease. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2021; 7:e12211. [PMID: 34621978 PMCID: PMC8485054 DOI: 10.1002/trc2.12211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Recent clinical trials are considering inclusion of more than just apolipoprotein E (APOE) ε4 genotype as a way of reducing variability in analysis of outcomes. METHODS Case-control data were used to compare the capacity of age, sex, and 58 Alzheimer's disease (AD)-associated single nucleotide polymorphisms (SNPs) to predict AD status using several statistical models. Model performance was assessed with Brier scores and tenfold cross-validation. Genotype and sex × age estimates from the best performing model were combined with age and intercept estimates from the general population to develop a personalized genetic risk score, termed age, and sex-adjusted GenoRisk. RESULTS The elastic net model that included age, age x sex interaction, allelic APOE terms, and 29 additional SNPs performed the best. This model explained an additional 19% of the heritable risk compared to APOE genotype alone and achieved an area under the curve of 0.747. DISCUSSION GenoRisk could improve the risk assessment of individuals identified for prevention studies.
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Affiliation(s)
| | | | - Bruce L Brown
- Department of Psychology Brigham Young University Provo Utah USA
| | - Perry G Ridge
- Department of Biology Brigham Young University-Hawaii Laie Hawaii USA
| | | | | | | | | | | | - John S K Kauwe
- Department of Psychology Brigham Young University Provo Utah USA
- Department of Biology Brigham Young University-Hawaii Laie Hawaii USA
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23
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Bruni AC, Bernardi L, Maletta R. Evolution of genetic testing supports precision medicine for caring Alzheimer's disease patients. Curr Opin Pharmacol 2021; 60:275-280. [PMID: 34487952 DOI: 10.1016/j.coph.2021.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/22/2022]
Abstract
Genetic testing for Alzheimer's disease offers a molecular diagnosis to patients and their relatives and provides information on personal risk, reproductive choices, clinical trial eligibility, and treatment options. In the past, molecular testing was limited to detecting single variations in single genes. Currently, with the advent of next-generation sequencing, simultaneous analysis of more than 100 genes using the same DNA sample is possible. This approach allows the determination of gene mutations, genetic risk factors, genotypes at many pharmacogenomic loci, and the determination of a polygenic risk scores for stratification of risk. This article reviews the diagnostic genetic testing of Alzheimer's disease, from the first molecular approaches to recent advances in NGS, focusing on a precision medicine approach.
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Affiliation(s)
| | - Livia Bernardi
- Regional Neurogenetic Centre, ASP CZ, Lamezia Terme, CZ, Italy
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24
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Zhan L, Li J, Jew B, Sul JH. Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. PLoS Genet 2021; 17:e1009772. [PMID: 34516545 PMCID: PMC8460036 DOI: 10.1371/journal.pgen.1009772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/23/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common type of dementia causing irreversible brain damage to the elderly and presents a major public health challenge. Clinical research and genome-wide association studies have suggested a potential contribution of the endocytic pathway to AD, with an emphasis on common loci. However, the contribution of rare variants in this pathway to AD has not been thoroughly investigated. In this study, we focused on the effect of rare variants on AD by first applying a rare-variant gene-set burden analysis using genes in the endocytic pathway on over 3,000 individuals with European ancestry from three large whole-genome sequencing (WGS) studies. We identified significant associations of rare-variant burden within the endocytic pathway with AD, which were successfully replicated in independent datasets. We further demonstrated that this endocytic rare-variant enrichment is associated with neurofibrillary tangles (NFTs) and age-related phenotypes, increasing the risk of obtaining severer brain damage, earlier age-at-onset, and earlier age-of-death. Next, by aggregating rare variants within each gene, we sought to identify single endocytic genes associated with AD and NFTs. Careful examination using NFTs revealed one significantly associated gene, ANKRD13D. To identify functional associations, we integrated bulk RNA-Seq data from over 600 brain tissues and found two endocytic expression genes (eGenes), HLA-A and SLC26A7, that displayed significant influences on their gene expressions. Differential expressions between AD patients and controls of these three identified genes were further examined by incorporating scRNA-Seq data from 48 post-mortem brain samples and demonstrated distinct expression patterns across cell types. Taken together, our results demonstrated strong rare-variant effect in the endocytic pathway on AD risk and progression and functional effect of gene expression alteration in both bulk and single-cell resolution, which may bring more insight and serve as valuable resources for future AD genetic studies, clinical research, and therapeutic targeting.
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Affiliation(s)
- Lingyu Zhan
- Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jiajin Li
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Brandon Jew
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, California, United States of America
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25
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Satake E, Saulnier PJ, Kobayashi H, Gupta MK, Looker HC, Wilson JM, Md Dom ZI, Ihara K, O’Neil K, Krolewski B, Pipino C, Pavkov ME, Nair V, Bitzer M, Niewczas MA, Kretzler M, Mauer M, Doria A, Najafian B, Kulkarni RN, Duffin KL, Pezzolesi MG, Kahn CR, Nelson RG, Krolewski AS. Comprehensive Search for Novel Circulating miRNAs and Axon Guidance Pathway Proteins Associated with Risk of ESKD in Diabetes. J Am Soc Nephrol 2021; 32:2331-2351. [PMID: 34140396 PMCID: PMC8729832 DOI: 10.1681/asn.2021010105] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/23/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Mechanisms underlying the pro gression of diabetic kidney disease to ESKD are not fully understood. METHODS We performed global microRNA (miRNA) analysis on plasma from two cohorts consisting of 375 individuals with type 1 and type 2 diabetes with late diabetic kidney disease, and targeted proteomics analysis on plasma from four cohorts consisting of 746 individuals with late and early diabetic kidney disease. We examined structural lesions in kidney biopsy specimens from the 105 individuals with early diabetic kidney disease. Human umbilical vein endothelial cells were used to assess the effects of miRNA mimics or inhibitors on regulation of candidate proteins. RESULTS In the late diabetic kidney disease cohorts, we identified 17 circulating miRNAs, represented by four exemplars (miR-1287-5p, miR-197-5p, miR-339-5p, and miR-328-3p), that were strongly associated with 10-year risk of ESKD. These miRNAs targeted proteins in the axon guidance pathway. Circulating levels of six of these proteins-most notably, EFNA4 and EPHA2-were strongly associated with 10-year risk of ESKD in all cohorts. Furthermore, circulating levels of these proteins correlated with severity of structural lesions in kidney biopsy specimens. In contrast, expression levels of genes encoding these proteins had no apparent effects on the lesions. In in vitro experiments, mimics of miR-1287-5p and miR-197-5p and inhibitors of miR-339-5p and miR-328-3p upregulated concentrations of EPHA2 in either cell lysate, supernatant, or both. CONCLUSIONS This study reveals novel mechanisms involved in progression to ESKD and points to the importance of systemic factors in the development of diabetic kidney disease. Some circulating miRNAs and axon guidance pathway proteins represent potential targets for new therapies to prevent and treat this condition.
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Affiliation(s)
- Eiichiro Satake
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Pierre-Jean Saulnier
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona,Poitiers University Hospital, University of Poitiers, Institut National de la Santé et de la Recherche Médicale (INSERM), Clinical Investigation Center CIC1402, Poitiers, France
| | - Hiroki Kobayashi
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Manoj K. Gupta
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Helen C. Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona
| | - Jonathan M. Wilson
- Diabetes and Complication Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Zaipul I. Md Dom
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Katsuhito Ihara
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Kristina O’Neil
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Bozena Krolewski
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Caterina Pipino
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts,Department of Medical, Oral and Biotechnological Sciences, Center for Advanced Studies and Technology (CAST), University G. d’Annunzio, Chieti, Italy
| | - Meda E. Pavkov
- Division of Diabetes Translation, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Viji Nair
- Nephrology/Internal Medicine and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Markus Bitzer
- Nephrology/Internal Medicine and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Monika A. Niewczas
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Matthias Kretzler
- Nephrology/Internal Medicine and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Michael Mauer
- Department of Pediatrics and Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Alessandro Doria
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Behzad Najafian
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Rohit N. Kulkarni
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Kevin L. Duffin
- Diabetes and Complication Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Marcus G. Pezzolesi
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts,Division of Nephrology and Hypertension, University of Utah, Salt Lake City, Utah
| | - C. Ronald Kahn
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Robert G. Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona
| | - Andrzej S. Krolewski
- Research Division, Joslin Diabetes Center, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
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26
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Bai B, Vanderwall D, Li Y, Wang X, Poudel S, Wang H, Dey KK, Chen PC, Yang K, Peng J. Proteomic landscape of Alzheimer's Disease: novel insights into pathogenesis and biomarker discovery. Mol Neurodegener 2021; 16:55. [PMID: 34384464 PMCID: PMC8359598 DOI: 10.1186/s13024-021-00474-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/18/2021] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry-based proteomics empowers deep profiling of proteome and protein posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the advances and limitations in historic and recent AD proteomic research. Complementary to genetic mapping, proteomic studies not only validate canonical amyloid and tau pathways, but also uncover novel components in broad protein networks, such as RNA splicing, development, immunity, membrane transport, lipid metabolism, synaptic function, and mitochondrial activity. Meta-analysis of seven deep datasets reveals 2,698 differentially expressed (DE) proteins in the landscape of AD brain proteome (n = 12,017 proteins/genes), covering 35 reported AD genes and risk loci. The DE proteins contain cellular markers enriched in neurons, microglia, astrocytes, oligodendrocytes, and epithelial cells, supporting the involvement of diverse cell types in AD pathology. We discuss the hypothesized protective or detrimental roles of selected DE proteins, emphasizing top proteins in "amyloidome" (all biomolecules in amyloid plaques) and disease progression. Comprehensive PTM analysis represents another layer of molecular events in AD. In particular, tau PTMs are correlated with disease stages and indicate the heterogeneity of individual AD patients. Moreover, the unprecedented proteomic coverage of biofluids, such as cerebrospinal fluid and serum, procures novel putative AD biomarkers through meta-analysis. Thus, proteomics-driven systems biology presents a new frontier to link genotype, proteotype, and phenotype, accelerating the development of improved AD models and treatment strategies.
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Affiliation(s)
- Bing Bai
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Current address: Center for Precision Medicine, Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu 210008 Nanjing, China
| | - David Vanderwall
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Current address: Department of Biology, University of North Dakota, ND 58202 Grand Forks, USA
| | - Suresh Poudel
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Hong Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Ping-Chung Chen
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Ka Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
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27
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Uddin MS, Kabir MT, Jakaria M, Sobarzo-Sánchez E, Barreto GE, Perveen A, Hafeez A, Bin-Jumah MN, Abdel-Daim MM, Ashraf GM. Exploring the Potential of Neuroproteomics in Alzheimer's Disease. Curr Top Med Chem 2021; 20:2263-2278. [PMID: 32493192 DOI: 10.2174/1568026620666200603112030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/27/2020] [Accepted: 05/08/2020] [Indexed: 12/25/2022]
Abstract
Alzheimer's disease (AD) is progressive brain amyloidosis that damages brain regions associated with memory, thinking, behavioral and social skills. Neuropathologically, AD is characterized by intraneuronal hyperphosphorylated tau inclusions as neurofibrillary tangles (NFTs), and buildup of extracellular amyloid-beta (Aβ) peptide as senile plaques. Several biomarker tests capturing these pathologies have been developed. However, for the full clinical expression of the neurodegenerative events of AD, there exist other central molecular pathways. In terms of understanding the unidentified underlying processes for the progression and development of AD, a complete comprehension of the structure and composition of atypical aggregation of proteins is essential. Presently, to aid the prognosis, diagnosis, detection, and development of drug targets in AD, neuroproteomics is elected as one of the leading essential tools for the efficient exploratory discovery of prospective biomarker candidates estimated to play a crucial role. Therefore, the aim of this review is to present the role of neuroproteomics to analyze the complexity of AD.
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Affiliation(s)
- Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh,Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | | | - Md Jakaria
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Eduardo Sobarzo-Sánchez
- Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile,Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Spain
| | - George E Barreto
- Department of Biological Sciences, University of Limerick, Limerick, Ireland,Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Saharanpur, India
| | - Abdul Hafeez
- Glocal School of Pharmacy, Glocal University, Saharanpur, India
| | - May N Bin-Jumah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11474, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia,Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ghulam M Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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28
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Vélez JI, Samper LA, Arcos-Holzinger M, Espinosa LG, Isaza-Ruget MA, Lopera F, Arcos-Burgos M. A Comprehensive Machine Learning Framework for the Exact Prediction of the Age of Onset in Familial and Sporadic Alzheimer's Disease. Diagnostics (Basel) 2021; 11:887. [PMID: 34067584 PMCID: PMC8156402 DOI: 10.3390/diagnostics11050887] [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: 04/05/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
Machine learning (ML) algorithms are widely used to develop predictive frameworks. Accurate prediction of Alzheimer's disease (AD) age of onset (ADAOO) is crucial to investigate potential treatments, follow-up, and therapeutic interventions. Although genetic and non-genetic factors affecting ADAOO were elucidated by other research groups and ours, the comprehensive and sequential application of ML to provide an exact estimation of the actual ADAOO, instead of a high-confidence-interval ADAOO that may fall, remains to be explored. Here, we assessed the performance of ML algorithms for predicting ADAOO using two AD cohorts with early-onset familial AD and with late-onset sporadic AD, combining genetic and demographic variables. Performance of ML algorithms was assessed using the root mean squared error (RMSE), the R-squared (R2), and the mean absolute error (MAE) with a 10-fold cross-validation procedure. For predicting ADAOO in familial AD, boosting-based ML algorithms performed the best. In the sporadic cohort, boosting-based ML algorithms performed best in the training data set, while regularization methods best performed for unseen data. ML algorithms represent a feasible alternative to accurately predict ADAOO with little human intervention. Future studies may include predicting the speed of cognitive decline in our cohorts using ML.
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Affiliation(s)
- Jorge I. Vélez
- Department of Industrial Engineering, Universidad del Norte, Barranquilla 081007, Colombia
| | - Luiggi A. Samper
- Department of Public Health, Universidad del Norte, Barranquilla 081007, Colombia;
| | - Mauricio Arcos-Holzinger
- Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Lady G. Espinosa
- INPAC Research Group, Fundación Universitaria Sanitas, Bogotá 111321, Colombia; (L.G.E.); (M.A.I.-R.)
| | - Mario A. Isaza-Ruget
- INPAC Research Group, Fundación Universitaria Sanitas, Bogotá 111321, Colombia; (L.G.E.); (M.A.I.-R.)
| | - Francisco Lopera
- Neuroscience Research Group, University of Antioquia, Medellín 050010, Colombia;
| | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
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29
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Abstract
tRNA-derived small RNA (tsRNA) is a novel class of non-coding RNA that is usually produced from tRNA following endonuclease cleavage which occurs under stress conditions. There are two types of tsRNAs: tRNA-derived fragments (tRFs) and stress-induced tRNA halves (tiRNAs), which differ in their cleavage position. Many studies have demonstrated that tsRNAs are involved in various physiological and pathological processes apart from cancer and gene expression. In this review, we briefly described the biogenesis, classification, and characteristics of tsRNAs and summarized the current research progress of tsRNAs in metabolic diseases, senescence, reproduction, stress, and organ injury, and finally put forward some problems to be solved.
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Affiliation(s)
- Qiyu Pan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
| | - Tingting Han
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
| | - Guoping Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
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30
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Chen G, Kang SS, Wang Z, Ahn EH, Xia Y, Liu X, Sandoval IM, Manfredsson FP, Zhang Z, Ye K. Netrin-1 receptor UNC5C cleavage by active δ-secretase enhances neurodegeneration, promoting Alzheimer's disease pathologies. SCIENCE ADVANCES 2021; 7:7/16/eabe4499. [PMID: 33863723 PMCID: PMC8051868 DOI: 10.1126/sciadv.abe4499] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/26/2021] [Indexed: 05/22/2023]
Abstract
Netrin-1, a family member of laminin-related secreted proteins, mediates axon guidance and cell migration during neural development. T835M mutation in netrin receptor UNC5C predisposes to the late-onset Alzheimer's disease (AD) and increases neuronal cell death. However, it remains unclear how this receptor is molecularly regulated in AD. Here, we show that δ-secretase selectively cleaves UNC5C and escalates its proapoptotic activity, facilitating neurodegeneration in AD. Netrin deficiency activates δ-secretase that specifically cuts UNC5C at N467 and N547 residues and enhances subsequent caspase-3 activation, additively augmenting neuronal cell death. Blockade of δ-secretase cleavage of UNC5C diminishes T835M mutant's proapoptotic activity. Viral expression of δ-secretase-truncated UNC5C fragments into APP/PS1 mice strongly accelerates AD pathologies, impairing learning and memory. Conversely, deletion of UNC5C from netrin-1-depleted mice attenuates AD pathologies and rescues cognitive disorders. Hence, δ-secretase truncates UNC5C and elevates its neurotoxicity, contributing to AD pathogenesis.
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Affiliation(s)
- Guiqin Chen
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Seong Su Kang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhihao Wang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eun Hee Ahn
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yiyuan Xia
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xia Liu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ivette M Sandoval
- Parkinson's Disease Research Unit, Department of Neurobiology, Barrow Neurological Institute, 350 West Thomas Road, Phoenix, AZ 85013, USA
| | - Fredric P Manfredsson
- Parkinson's Disease Research Unit, Department of Neurobiology, Barrow Neurological Institute, 350 West Thomas Road, Phoenix, AZ 85013, USA
| | - Zhaohui Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China.
| | - Keqiang Ye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
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31
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Patel D, Zhang X, Farrell JJ, Lunetta KL, Farrer LA. Set-Based Rare Variant Expression Quantitative Trait Loci in Blood and Brain from Alzheimer Disease Study Participants. Genes (Basel) 2021; 12:419. [PMID: 33804025 PMCID: PMC7999141 DOI: 10.3390/genes12030419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Because studies of rare variant effects on gene expression have limited power, we investigated set-based methods to identify rare expression quantitative trait loci (eQTL) related to Alzheimer disease (AD). Gene-level and pathway-level cis rare-eQTL mapping was performed genome-wide using gene expression data derived from blood donated by 713 Alzheimer's Disease Neuroimaging Initiative participants and from brain tissues donated by 475 Religious Orders Study/Memory and Aging Project participants. The association of gene or pathway expression with a set of all cis potentially regulatory low-frequency and rare variants within 1 Mb of genes was evaluated using SKAT-O. A total of 65 genes expressed in the brain were significant targets for rare expression single nucleotide polymorphisms (eSNPs) among which 17% (11/65) included established AD genes HLA-DRB1 and HLA-DRB5. In the blood, 307 genes were significant targets for rare eSNPs. In the blood and the brain, GNMT, LDHC, RBPMS2, DUS2, and HP were targets for significant eSNPs. Pathway enrichment analysis revealed significant pathways in the brain (n = 9) and blood (n = 16). Pathways for apoptosis signaling, cholecystokinin receptor (CCKR) signaling, and inflammation mediated by chemokine and cytokine signaling were common to both tissues. Significant rare eQTLs in inflammation pathways included five genes in the blood (ALOX5AP, CXCR2, FPR2, GRB2, IFNAR1) that were previously linked to AD. This study identified several significant gene- and pathway-level rare eQTLs, which further confirmed the importance of the immune system and inflammation in AD and highlighted the advantages of using a set-based eQTL approach for evaluating the effect of low-frequency and rare variants on gene expression.
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Affiliation(s)
- Devanshi Patel
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA;
| | - Lindsay A. Farrer
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA;
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
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32
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Hoogmartens J, Cacace R, Van Broeckhoven C. Insight into the genetic etiology of Alzheimer's disease: A comprehensive review of the role of rare variants. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12155. [PMID: 33665345 PMCID: PMC7896636 DOI: 10.1002/dad2.12155] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
Early-onset Alzheimer's disease (EOAD) is generally known as a dominant disease due to highly penetrant pathogenic mutations in the amyloid precursor protein, presenilin 1 and 2. However, they explain only a fraction of EOAD patients (5% to 10%). Furthermore, only 10% to 15% of EOAD families present with clear autosomal dominant inheritance. Studies showed that only 35% to 60% of EOAD patients have at least one affected first-degree relative. Parent-offspring concordance in EOAD was estimated to be <10%, indicating that full penetrant dominant alleles are not the sole players in EOAD. We aim to summarize current knowledge of rare variants underlying familial and seemingly sporadic Alzheimer's disease (AD) patients. Genetic findings indicate that in addition to the amyloid beta pathway, other pathways are of importance in AD pathophysiology. We discuss the difficulties in interpreting the influence of rare variants on disease onset and we underline the value of carefully selected ethnicity-matched cohorts in AD genetic research.
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Affiliation(s)
- Julie Hoogmartens
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Rita Cacace
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain DiseasesVIB Center for Molecular NeurologyAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
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33
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Macedo A, Gómez C, Rebelo MÂ, Poza J, Gomes I, Martins S, Maturana-Candelas A, Pablo VGD, Durães L, Sousa P, Figueruelo M, Rodríguez M, Pita C, Arenas M, Álvarez L, Hornero R, Lopes AM, Pinto N. Risk Variants in Three Alzheimer's Disease Genes Show Association with EEG Endophenotypes. J Alzheimers Dis 2021; 80:209-223. [PMID: 33522999 PMCID: PMC8075394 DOI: 10.3233/jad-200963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background: Dementia due to Alzheimer’s disease (AD) is a complex neurodegenerative disorder, which much of heritability remains unexplained. At the clinical level, one of the most common physiological alterations is the slowing of oscillatory brain activity, measurable by electroencephalography (EEG). Relative power (RP) at the conventional frequency bands (i.e., delta, theta, alpha, beta-1, and beta-2) can be considered as AD endophenotypes. Objective: The aim of this work is to analyze the association between sixteen genes previously related with AD: APOE, PICALM, CLU, BCHE, CETP, CR1, SLC6A3, GRIN2
β, SORL1, TOMM40, GSK3
β, UNC5C, OPRD1, NAV2, HOMER2, and IL1RAP, and the slowing of the brain activity, assessed by means of RP at the aforementioned frequency bands. Methods: An Iberian cohort of 45 elderly controls, 45 individuals with mild cognitive impairment, and 109 AD patients in the three stages of the disease was considered. Genomic information and brain activity of each subject were analyzed. Results: The slowing of brain activity was observed in carriers of risk alleles in IL1RAP (rs10212109, rs9823517, rs4687150), UNC5C (rs17024131), and NAV2 (rs1425227, rs862785) genes, regardless of the disease status and situation towards the strongest risk factors: age, sex, and APOE ɛ4 presence. Conclusion: Endophenotypes reduce the complexity of the general phenotype and genetic variants with a major effect on those specific traits may be then identified. The found associations in this work are novel and may contribute to the comprehension of AD pathogenesis, each with a different biological role, and influencing multiple factors involved in brain physiology.
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Affiliation(s)
- Ana Macedo
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,JTA: The Data Scientists, Porto, Portugal
| | - Carlos Gómez
- Grupo de Ingeniería Biomédica, Universidad de Valladolid, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Miguel Ângelo Rebelo
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Jesús Poza
- Grupo de Ingeniería Biomédica, Universidad de Valladolid, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain.,Instituto de Investigación en Matemáticas (IMUVA), Universidad de Valladolid, Valladolid, Spain
| | - Iva Gomes
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Martins
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | | | | | - Luis Durães
- Associação Portuguesa de Familiares e Amigos de Doentes de Alzheimer, Lavra, Portugal
| | - Patrícia Sousa
- Associação Portuguesa de Familiares e Amigos de Doentes de Alzheimer, Lavra, Portugal
| | - Manuel Figueruelo
- Asociación de Familiares y Amigos de Enfermos de Alzheimer y otras demencias de Zamora, Zamora, Spain
| | - María Rodríguez
- Asociación de Familiares y Amigos de Enfermos de Alzheimer y otras demencias de Zamora, Zamora, Spain
| | - Carmen Pita
- Asociación de Familiares y Amigos de Enfermos de Alzheimer y otras demencias de Zamora, Zamora, Spain
| | - Miguel Arenas
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,CINBIO (Biomedical Research Center), University of Vigo, Vigo, Spain.,Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Luis Álvarez
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Adeneas, Valencia, Spain
| | - Roberto Hornero
- Grupo de Ingeniería Biomédica, Universidad de Valladolid, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain.,Instituto de Investigación en Matemáticas (IMUVA), Universidad de Valladolid, Valladolid, Spain
| | - Alexandra M Lopes
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Nádia Pinto
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Centro de Matemática da Universidade do Porto, Porto, Portugal
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34
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Yamagishi S, Bando Y, Sato K. Involvement of Netrins and Their Receptors in Neuronal Migration in the Cerebral Cortex. Front Cell Dev Biol 2021; 8:590009. [PMID: 33520982 PMCID: PMC7843923 DOI: 10.3389/fcell.2020.590009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/23/2020] [Indexed: 12/17/2022] Open
Abstract
In mammals, excitatory cortical neurons develop from the proliferative epithelium and progenitor cells in the ventricular zone and subventricular zone, and migrate radially to the cortical plate, whereas inhibitory GABAergic interneurons are born in the ganglionic eminence and migrate tangentially. The migration of newly born cortical neurons is tightly regulated by both extracellular and intracellular signaling to ensure proper positioning and projections. Non-cell-autonomous extracellular molecules, such as growth factors, axon guidance molecules, extracellular matrix, and other ligands, play a role in cortical migration, either by acting as attractants or repellents. In this article, we review the guidance molecules that act as cell-cell recognition molecules for the regulation of neuronal migration, with a focus on netrin family proteins, their receptors, and related molecules, including neogenin, repulsive guidance molecules (RGMs), Down syndrome cell adhesion molecule (DSCAM), fibronectin leucine-rich repeat transmembrane proteins (FLRTs), and draxin. Netrin proteins induce attractive and repulsive signals depending on their receptors. For example, binding of netrin-1 to deleted in colorectal cancer (DCC), possibly together with Unc5, repels migrating GABAergic neurons from the ventricular zone of the ganglionic eminence, whereas binding to α3β1 integrin promotes cortical interneuron migration. Human genetic disorders associated with these and related guidance molecules, such as congenital mirror movements, schizophrenia, and bipolar disorder, are also discussed.
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Affiliation(s)
- Satoru Yamagishi
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuki Bando
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kohji Sato
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
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35
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Kim YW, Al‐Ramahi I, Koire A, Wilson SJ, Konecki DM, Mota S, Soleimani S, Botas J, Lichtarge O. Harnessing the paradoxical phenotypes of APOE ɛ2 and APOE ɛ4 to identify genetic modifiers in Alzheimer's disease. Alzheimers Dement 2020; 17:831-846. [PMID: 33576571 PMCID: PMC8247413 DOI: 10.1002/alz.12240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 10/22/2020] [Indexed: 01/05/2023]
Abstract
The strongest genetic risk factor for idiopathic late‐onset Alzheimer's disease (LOAD) is apolipoprotein E (APOE) ɛ4, while the APOE ɛ2 allele is protective. However, there are paradoxical APOE ɛ4 carriers who remain disease‐free and APOE ɛ2 carriers with LOAD. We compared exomes of healthy APOE ɛ4 carriers and APOE ɛ2 Alzheimer's disease (AD) patients, prioritizing coding variants based on their predicted functional impact, and identified 216 genes with differential mutational load between these two populations. These candidate genes were significantly dysregulated in LOAD brains, and many modulated tau‐ or β42‐induced neurodegeneration in Drosophila. Variants in these genes were associated with AD risk, even in APOE ɛ3 homozygotes, showing robust predictive power for risk stratification. Network analyses revealed involvement of candidate genes in brain cell type‐specific pathways including synaptic biology, dendritic spine pruning and inflammation. These potential modifiers of LOAD may constitute novel biomarkers, provide potential therapeutic intervention avenues, and support applying this approach as larger whole exome sequencing cohorts become available.
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Affiliation(s)
- Young Won Kim
- Program in Integrative Molecular and Biomedical SciencesBaylor College of MedicineHoustonTexasUSA
| | - Ismael Al‐Ramahi
- Jan and Dan Duncan Neurological Research InstituteHoustonTexasUSA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Amanda Koire
- Graduate Program in Quantitative and Computational BiosciencesBaylor College of MedicineHoustonTexasUSA
- Medical Scientist Training ProgramBaylor College of MedicineHoustonTexasUSA
| | - Stephen J. Wilson
- Biochemistry and Molecular BiologyBaylor College of MedicineHoustonTexasUSA
| | - Daniel M. Konecki
- Graduate Program in Quantitative and Computational BiosciencesBaylor College of MedicineHoustonTexasUSA
| | - Samantha Mota
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Shirin Soleimani
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Juan Botas
- Jan and Dan Duncan Neurological Research InstituteHoustonTexasUSA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Graduate Program in Quantitative and Computational BiosciencesBaylor College of MedicineHoustonTexasUSA
| | - Olivier Lichtarge
- Program in Integrative Molecular and Biomedical SciencesBaylor College of MedicineHoustonTexasUSA
- Jan and Dan Duncan Neurological Research InstituteHoustonTexasUSA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Graduate Program in Quantitative and Computational BiosciencesBaylor College of MedicineHoustonTexasUSA
- Medical Scientist Training ProgramBaylor College of MedicineHoustonTexasUSA
- Biochemistry and Molecular BiologyBaylor College of MedicineHoustonTexasUSA
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36
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Yang HS, Chhatwal JP, Xu J, White CC, Hanseeuw B, Rabin JS, Papp KV, Buckley RF, Schultz AP, Properzi MJ, Gatchel JR, Amariglio RE, Donovan NJ, Mormino EC, Hedden T, Marshall GA, Rentz DM, Johnson KA, De Jager PL, Sperling RA. An UNC5C Allele Predicts Cognitive Decline and Hippocampal Atrophy in Clinically Normal Older Adults. J Alzheimers Dis 2020; 68:1161-1170. [PMID: 30883345 DOI: 10.3233/jad-180788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The UNC5C rs3846455G allele has been linked to poor cognitive resilience against age-related neuropathologies, but this association remains to be replicated, and the allele's effect on hippocampal neurodegeneration needs to be examined. OBJECTIVE To further validate the association between rs3846455G and faster cognitive decline, especially among cognitively normal older adults, and to assess whether rs3846455G predicts accelerated hippocampal volume loss in older adults. METHODS We assessed participants in the Harvard Aging Brain Study (HABS), a longitudinal cohort study of older adults who were clinically normal at baseline. To avoid bias from population admixture, analyses were limited to participants of European descent with longitudinal neuroimaging data (n = 174). Linear mixed effect models were used to examine the effect of rs3846455G on longitudinal change of the Preclinical Alzheimer Cognitive Composite (PACC) and MRI-measured bilateral hippocampal volume, adjusting for baseline amyloid-β (Aβ) measured by the cortical Pittsburgh Compound B PET distributed volume ratio. We also tested whether hippocampal atrophy mediates the association between rs3846455G and greater PACC decline through a mediation analysis. RESULTS rs3846455G was associated with greater PACC decline (β= -0.087/year, 95% CI -0.169 to -0.005, p = 0.039) after controlling for baseline Aβ. Further, rs3846455G predicted accelerated hippocampal atrophy after controlling for baseline Aβ (β= -57.3 mm3/year, 95% CI -102.8 to -11.9, p = 0.014). The association between rs3846455G and greater PACC decline was partially mediated by accelerated hippocampal atrophy (mediated effect (relative scale) = -0.014, 95% CI -0.032 to -6.0×10-4, p = 0.039). CONCLUSION UNC5C rs3846455G predicts greater cognitive decline and accelerated hippocampal atrophy in clinically normal older adults.
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Affiliation(s)
- Hyun-Sik Yang
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MAs, USA
| | - Jasmeer P Chhatwal
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jishu Xu
- Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MAs, USA
| | - Charles C White
- Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MAs, USA
| | - Bernard Hanseeuw
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Neurology, Cliniques Universitaires Saint-Luc, Institute of Neurosciences, Université Catholique de Louvain, Brussels, Belgium
| | - Jennifer S Rabin
- Harvard Medical School, Boston, MA, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn V Papp
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Rachel F Buckley
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Florey Institutes of Neuroscience and Mental Health, Melbourne, VIC, Australia.,Melbourne School of Psychological Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Aaron P Schultz
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael J Properzi
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Jennifer R Gatchel
- Harvard Medical School, Boston, MA, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.,Division of Geriatric Psychiatry, McLean Hospital, Belmont, MA, USA.,Gerontology Research Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Rebecca E Amariglio
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Nancy J Donovan
- Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.,Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth C Mormino
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Trey Hedden
- Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Gad A Marshall
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Dorene M Rentz
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Keith A Johnson
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Philip L De Jager
- Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MAs, USA.,Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
| | - Reisa A Sperling
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Center for Alzheimer Research and Treatment, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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37
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Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Cantwell L, Charbonnier C, Chung J, Crane PK, Cruchaga C, Cupples LA, Dartigues JF, Debette S, Deleuze JF, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, Ikram MA, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimäki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, Pericak-Vance MA, Perola M, Psaty BM, Quenez O, Rajabli F, Redon R, Reitz C, Remes AM, Salomaa V, Sarnowski C, Schmidt H, Schmidt M, Schmidt R, Soininen H, Thornton TA, Tosto G, Tzourio C, van der Lee SJ, van Duijn CM, Valladares O, Vardarajan B, Wang LS, Wang W, Wijsman E, Wilson RK, Witten D, Worley KC, Zhang X, Bellenguez C, Lambert JC, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, Destefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj AC, Fornage M, Farrer LA. Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry 2020; 25:1859-1875. [PMID: 30108311 PMCID: PMC6375806 DOI: 10.1038/s41380-018-0112-7] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/01/2018] [Accepted: 05/14/2018] [Indexed: 12/21/2022]
Abstract
The Alzheimer's Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls were Caribbean Hispanic (CH). An age-, sex- and APOE based risk score and family history were used to select cases most likely to harbor novel AD risk variants and controls least likely to develop AD by age 85 years. We tested ~1.5 million single nucleotide variants (SNVs) and 50,000 insertion-deletion polymorphisms (indels) for association to AD, using multiple models considering individual variants as well as gene-based tests aggregating rare, predicted functional, and loss of function variants. Sixteen single variants and 19 genes that met criteria for significant or suggestive associations after multiple-testing correction were evaluated for replication in four independent samples; three with whole exome sequencing (2,778 cases, 7,262 controls) and one with genome-wide genotyping imputed to the Haplotype Reference Consortium panel (9,343 cases, 11,527 controls). The top findings in the discovery sample were also followed-up in the ADSP whole-genome sequenced family-based dataset (197 members of 42 EA families and 501 members of 157 CH families). We identified novel and predicted functional genetic variants in genes previously associated with AD. We also detected associations in three novel genes: IGHG3 (p = 9.8 × 10-7), an immunoglobulin gene whose antibodies interact with β-amyloid, a long non-coding RNA AC099552.4 (p = 1.2 × 10-7), and a zinc-finger protein ZNF655 (gene-based p = 5.0 × 10-6). The latter two suggest an important role for transcriptional regulation in AD pathogenesis.
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Affiliation(s)
- Joshua C Bis
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
| | - Xueqiu Jian
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Yuning Chen
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William S Bush
- Case Western Reserve University, Cleveland Heights, OH, USA
| | - William J Salerno
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Lancour
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Yiyi Ma
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Alan E Renton
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Yi Zhao
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Liming Qu
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shahzad Ahmad
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - Najaf Amin
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Philippe Amouyel
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- Institut Pasteur de Lille, Lille, France
- University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dominique Campion
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
- Department of Research, Centre Hospitalier du Rouvray, Sotteville-lès-, Rouen, France
| | - Laura Cantwell
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Camille Charbonnier
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Paul K Crane
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - L Adrienne Cupples
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Jean-François Dartigues
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
| | - Stéphanie Debette
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
- Department of Neurology and Institute for Neurodegenerative Diseases, Bordeaux University Hospital, Memory Clinic, F-33000, Bordeaux, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, Direction de le Recherche Fondamentale, CEA, Evry, France
| | - Lucinda Fulton
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | | | | | - Richard A Gibbs
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alison Goate
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Grenier-Boley
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Seppo Helisalmi
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Daniel P Howrigan
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - M Arfan Ikram
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jan Konrad
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Amanda Kuzma
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Honghuang Lin
- Department of Medicine (Computational Biomedicine), Boston University School of Medicine, Boston, MA, USA
| | - Kari Mattila
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | - Donna M Muzny
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Waleed Nasser
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin Neale
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kwangsik Nho
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gaël Nicolas
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Devanshi Patel
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
- University of Tartu, Estonian Genome Center, Tartu, Estonia
| | - Bruce M Psaty
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Olivier Quenez
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Richard Redon
- Inserm, CNRS, Univ. Nantes, CHU Nantes, l'institut du thorax, Nantes, France
| | | | - Anne M Remes
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
- Unit of Clinical Neuroscience, Neurology, University of Oulu and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Chloe Sarnowski
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Helena Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Michael Schmidt
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Hilkka Soininen
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | | | | | - Christophe Tzourio
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
| | | | | | - Otto Valladares
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Li-San Wang
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Weixin Wang
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ellen Wijsman
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Daniela Witten
- Department of Statistics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kim C Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaoling Zhang
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Celine Bellenguez
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Jean-Charles Lambert
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kathryn L Lunetta
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Anita L Destefano
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Josée Dupuis
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Sudha Seshadri
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Adam C Naj
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lindsay A Farrer
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA.
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA.
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PCDH7 interacts with GluN1 and regulates dendritic spine morphology and synaptic function. Sci Rep 2020; 10:10951. [PMID: 32616769 PMCID: PMC7331671 DOI: 10.1038/s41598-020-67831-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/12/2020] [Indexed: 01/28/2023] Open
Abstract
The N-terminal domain (NTD) of the GluN1 subunit (GluN1-NTD) is important for NMDA receptor structure and function, but the interacting proteins of the GluN1-NTD are not well understood. Starting with an unbiased screen of ~ 1,500 transmembrane proteins using the purified GluN1-NTD protein as a bait, we identify Protocadherin 7 (PCDH7) as a potential interacting protein. PCDH7 is highly expressed in the brain and has been linked to CNS disorders, including epilepsy. Using primary neurons and brain slice cultures, we find that overexpression and knockdown of PCDH7 induce opposing morphological changes of dendritic structures. We also find that PCDH7 overexpression reduces synaptic NMDA receptor currents. These data show that PCDH7 can regulate dendritic spine morphology and synaptic function, possibly via interaction with the GluN1 subunit.
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39
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Vegeto E, Villa A, Della Torre S, Crippa V, Rusmini P, Cristofani R, Galbiati M, Maggi A, Poletti A. The Role of Sex and Sex Hormones in Neurodegenerative Diseases. Endocr Rev 2020; 41:5572525. [PMID: 31544208 PMCID: PMC7156855 DOI: 10.1210/endrev/bnz005] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
Neurodegenerative diseases (NDs) are a wide class of disorders of the central nervous system (CNS) with unknown etiology. Several factors were hypothesized to be involved in the pathogenesis of these diseases, including genetic and environmental factors. Many of these diseases show a sex prevalence and sex steroids were shown to have a role in the progression of specific forms of neurodegeneration. Estrogens were reported to be neuroprotective through their action on cognate nuclear and membrane receptors, while adverse effects of male hormones have been described on neuronal cells, although some data also suggest neuroprotective activities. The response of the CNS to sex steroids is a complex and integrated process that depends on (i) the type and amount of the cognate steroid receptor and (ii) the target cell type-either neurons, glia, or microglia. Moreover, the levels of sex steroids in the CNS fluctuate due to gonadal activities and to local metabolism and synthesis. Importantly, biochemical processes involved in the pathogenesis of NDs are increasingly being recognized as different between the two sexes and as influenced by sex steroids. The aim of this review is to present current state-of-the-art understanding on the potential role of sex steroids and their receptors on the onset and progression of major neurodegenerative disorders, namely, Alzheimer's disease, Parkinson's diseases, amyotrophic lateral sclerosis, and the peculiar motoneuron disease spinal and bulbar muscular atrophy, in which hormonal therapy is potentially useful as disease modifier.
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Affiliation(s)
- Elisabetta Vegeto
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Scienze Farmaceutiche (DiSFarm), Università degli Studi di Milano, Italy
| | - Alessandro Villa
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Scienze della Salute (DiSS), Università degli Studi di Milano, Italy
| | - Sara Della Torre
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Scienze Farmaceutiche (DiSFarm), Università degli Studi di Milano, Italy
| | - Valeria Crippa
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Eccellenza di Scienze Farmacologiche e Biomolecolari (DiSFeB), Università degli Studi di Milano, Italy
| | - Paola Rusmini
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Eccellenza di Scienze Farmacologiche e Biomolecolari (DiSFeB), Università degli Studi di Milano, Italy
| | - Riccardo Cristofani
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Eccellenza di Scienze Farmacologiche e Biomolecolari (DiSFeB), Università degli Studi di Milano, Italy
| | - Mariarita Galbiati
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Eccellenza di Scienze Farmacologiche e Biomolecolari (DiSFeB), Università degli Studi di Milano, Italy
| | - Adriana Maggi
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Scienze Farmaceutiche (DiSFarm), Università degli Studi di Milano, Italy
| | - Angelo Poletti
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Italy.,Dipartimento di Eccellenza di Scienze Farmacologiche e Biomolecolari (DiSFeB), Università degli Studi di Milano, Italy
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40
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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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41
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The Genetics of Alzheimer's Disease in the Chinese Population. Int J Mol Sci 2020; 21:ijms21072381. [PMID: 32235595 PMCID: PMC7178026 DOI: 10.3390/ijms21072381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/22/2020] [Accepted: 03/27/2020] [Indexed: 12/30/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease characterized by progressive cognitive dysfunction and behavioral impairment. In China, the number of AD patients is growing rapidly, which poses a considerable burden on society and families. In recent years, through the advancement of genome-wide association studies, second-generation gene sequencing technology, and their application in AD genetic research, more genetic loci associated with the risk for AD have been discovered, including KCNJ15, TREM2, and GCH1, which provides new ideas for the etiology and treatment of AD. This review summarizes three early-onset AD causative genes (APP, PSEN1, and PSEN2) and some late-onset AD susceptibility genes and their mutation sites newly discovered in China, and briefly introduces the potential mechanisms of these genetic susceptibilities in the pathogenesis of AD, which would help in understanding the genetic mechanisms underlying this devastating disease.
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42
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Bai B, Wang X, Li Y, Chen PC, Yu K, Dey KK, Yarbro JM, Han X, Lutz BM, Rao S, Jiao Y, Sifford JM, Han J, Wang M, Tan H, Shaw TI, Cho JH, Zhou S, Wang H, Niu M, Mancieri A, Messler KA, Sun X, Wu Z, Pagala V, High AA, Bi W, Zhang H, Chi H, Haroutunian V, Zhang B, Beach TG, Yu G, Peng J. Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression. Neuron 2020; 105:975-991.e7. [PMID: 31926610 PMCID: PMC7318843 DOI: 10.1016/j.neuron.2019.12.015] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/11/2019] [Accepted: 12/10/2019] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) displays a long asymptomatic stage before dementia. We characterize AD stage-associated molecular networks by profiling 14,513 proteins and 34,173 phosphosites in the human brain with mass spectrometry, highlighting 173 protein changes in 17 pathways. The altered proteins are validated in two independent cohorts, showing partial RNA dependency. Comparisons of brain tissue and cerebrospinal fluid proteomes reveal biomarker candidates. Combining with 5xFAD mouse analysis, we determine 15 Aβ-correlated proteins (e.g., MDK, NTN1, SMOC1, SLIT2, and HTRA1). 5xFAD shows a proteomic signature similar to symptomatic AD but exhibits activation of autophagy and interferon response and lacks human-specific deleterious events, such as downregulation of neurotrophic factors and synaptic proteins. Multi-omics integration prioritizes AD-related molecules and pathways, including amyloid cascade, inflammation, complement, WNT signaling, TGF-β and BMP signaling, lipid metabolism, iron homeostasis, and membrane transport. Some Aβ-correlated proteins are colocalized with amyloid plaques. Thus, the multilayer omics approach identifies protein networks during AD progression.
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Affiliation(s)
- Bing Bai
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ping-Chung Chen
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jay M Yarbro
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Xian Han
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Brianna M Lutz
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shuquan Rao
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yun Jiao
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeffrey M Sifford
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jonghee Han
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Minghui Wang
- Departments of Psychiatry and Neuroscience, The Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Timothy I Shaw
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hong Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mingming Niu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ariana Mancieri
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kaitlynn A Messler
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaojun Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Bi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hui Zhang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, The Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences and Department of Pharmacological Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Gang Yu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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43
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Glasgow SD, Ruthazer ES, Kennedy TE. Guiding synaptic plasticity: Novel roles for netrin-1 in synaptic plasticity and memory formation in the adult brain. J Physiol 2020; 599:493-505. [PMID: 32017127 DOI: 10.1113/jp278704] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
Adult neural plasticity engages mechanisms that change synapse structure and function, yet many of the underlying events bear a striking similarity to processes that occur during the initial establishment of neural circuits during development. It is a long-standing hypothesis that the molecular mechanisms critical for neural development may also regulate synaptic plasticity related to learning and memory in adults. Netrins were initially described as chemoattractant guidance cues that direct cell and axon migration during embryonic development, yet they continue to be expressed by neurons in the adult brain. Recent findings have identified roles for netrin-1 in synaptogenesis during postnatal maturation, and in synaptic plasticity in the adult mammalian brain, regulating AMPA glutamate receptor trafficking at excitatory synapses. These findings provide an example of a conserved developmental guidance cue that is expressed by neurons in the adult brain and functions as a key regulator of activity-dependent synaptic plasticity. Notably, in humans, genetic polymorphisms in netrin-1 and its receptors have been linked to neurodevelopmental and neurodegenerative disorders. The molecular mechanisms associated with the synaptic function of netrin-1 therefore present new therapeutic targets for neuropathologies associated with memory dysfunction. Here, we summarize recent findings that link netrin-1 signalling to synaptic plasticity, and discuss the implications of these discoveries for the neurobiological basis of memory consolidation.
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Affiliation(s)
- Stephen D Glasgow
- Department of Neurology & Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Edward S Ruthazer
- Department of Neurology & Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Timothy E Kennedy
- Department of Neurology & Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, H3A 2B4, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
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44
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Sims R, Hill M, Williams J. The multiplex model of the genetics of Alzheimer's disease. Nat Neurosci 2020; 23:311-322. [PMID: 32112059 DOI: 10.1038/s41593-020-0599-5] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/24/2020] [Indexed: 12/25/2022]
Abstract
Genes play a strong role in Alzheimer's disease (AD), with late-onset AD showing heritability of 58-79% and early-onset AD showing over 90%. Genetic association provides a robust platform to build our understanding of the etiology of this complex disease. Over 50 loci are now implicated for AD, suggesting that AD is a disease of multiple components, as supported by pathway analyses (immunity, endocytosis, cholesterol transport, ubiquitination, amyloid-β and tau processing). Over 50% of late-onset AD heritability has been captured, allowing researchers to calculate the accumulation of AD genetic risk through polygenic risk scores. A polygenic risk score predicts disease with up to 90% accuracy and is an exciting tool in our research armory that could allow selection of those with high polygenic risk scores for clinical trials and precision medicine. It could also allow cellular modelling of the combined risk. Here we propose the multiplex model as a new perspective from which to understand AD. The multiplex model reflects the combination of some, or all, of these model components (genetic and environmental), in a tissue-specific manner, to trigger or sustain a disease cascade, which ultimately results in the cell and synaptic loss observed in AD.
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Affiliation(s)
- Rebecca Sims
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Matthew Hill
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
- UK Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Julie Williams
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
- UK Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
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45
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Liao X, Cai F, Sun Z, Zhang Y, Wang J, Jiao B, Guo J, Li J, Liu X, Guo L, Zhou Y, Wang J, Yan X, Jiang H, Xia K, Li J, Tang B, Shen L, Song W. Identification of Alzheimer's disease-associated rare coding variants in the ECE2 gene. JCI Insight 2020; 5:135119. [PMID: 32102983 DOI: 10.1172/jci.insight.135119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/29/2020] [Indexed: 11/17/2022] Open
Abstract
Accumulation of amyloid β protein (Aβ) due to increased generation and/or impaired degradation plays an important role in Alzheimer's disease (AD) pathogenesis. In this report, we describe the identification of rare coding mutations in the endothelin-converting enzyme 2 (ECE2) gene in 1 late-onset AD family, and additional case-control cohort analysis indicates ECE2 variants associated with the risk of developing AD. The 2 mutations (R186C and F751S) located in the peptidase domain in the ECE2 protein were found to severely impair the enzymatic activity of ECE2 in Aβ degradation. We further evaluated the effect of the R186C mutation in mutant APP-knockin mice. Overexpression of wild-type ECE2 in the hippocampus reduced amyloid load and plaque formation, and improved learning and memory deficits in the AD model mice. However, the effect was abolished by the R186C mutation in ECE2. Taken together, the results demonstrated that ECE2 peptidase mutations contribute to AD pathogenesis by impairing Aβ degradation, and overexpression of ECE2 alleviates AD phenotypes. This study indicates that ECE2 is a risk gene for AD development and pharmacological activation of ECE2 could be a promising strategy for AD treatment.
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Affiliation(s)
- Xinxin Liao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, Vancouver, Canada.,National Clinical Research Center for Geriatric Disorders
| | - Fang Cai
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, Vancouver, Canada
| | - Zhanfang Sun
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders
| | - Yun Zhang
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, Vancouver, Canada
| | - Juelu Wang
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, Vancouver, Canada
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders
| | - Lina Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders
| | - Yafang Zhou
- National Clinical Research Center for Geriatric Disorders
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Kun Xia
- School of Life Sciences, and
| | | | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Weihong Song
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, Vancouver, Canada
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46
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Whelan CD, Mattsson N, Nagle MW, Vijayaraghavan S, Hyde C, Janelidze S, Stomrud E, Lee J, Fitz L, Samad TA, Ramaswamy G, Margolin RA, Malarstig A, Hansson O. Multiplex proteomics identifies novel CSF and plasma biomarkers of early Alzheimer's disease. Acta Neuropathol Commun 2019; 7:169. [PMID: 31694701 PMCID: PMC6836495 DOI: 10.1186/s40478-019-0795-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/24/2019] [Indexed: 12/13/2022] Open
Abstract
To date, the development of disease-modifying therapies for Alzheimer’s disease (AD) has largely focused on the removal of amyloid beta Aβ fragments from the CNS. Proteomic profiling of patient fluids may help identify novel therapeutic targets and biomarkers associated with AD pathology. Here, we applied the Olink™ ProSeek immunoassay to measure 270 CSF and plasma proteins across 415 Aβ- negative cognitively normal individuals (Aβ- CN), 142 Aβ-positive CN (Aβ+ CN), 50 Aβ- mild cognitive impairment (MCI) patients, 75 Aβ+ MCI patients, and 161 Aβ+ AD patients from the Swedish BioFINDER study. A validation cohort included 59 Aβ- CN, 23 Aβ- + CN, 44 Aβ- MCI and 53 Aβ+ MCI. To compare protein concentrations in patients versus controls, we applied multiple linear regressions adjusting for age, gender, medications, smoking and mean subject-level protein concentration, and corrected findings for false discovery rate (FDR, q < 0.05). We identified, and replicated, altered levels of ten CSF proteins in Aβ+ individuals, including CHIT1, SMOC2, MMP-10, LDLR, CD200, EIF4EBP1, ALCAM, RGMB, tPA and STAMBP (− 0.14 < d < 1.16; q < 0.05). We also identified and replicated alterations of six plasma proteins in Aβ+ individuals OSM, MMP-9, HAGH, CD200, AXIN1, and uPA (− 0.77 < d < 1.28; q < 0.05). Multiple analytes associated with cognitive performance and cortical thickness (q < 0.05). Plasma biomarkers could distinguish AD dementia (AUC = 0.94, 95% CI = 0.87–0.98) and prodromal AD (AUC = 0.78, 95% CI = 0.68–0.87) from CN. These findings reemphasize the contributions of immune markers, phospholipids, angiogenic proteins and other biomarkers downstream of, and potentially orthogonal to, Aβ- and tau in AD, and identify candidate biomarkers for earlier detection of neurodegeneration.
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47
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Bradley RA, Shireman J, McFalls C, Choi J, Canfield SG, Dong Y, Liu K, Lisota B, Jones JR, Petersen A, Bhattacharyya A, Palecek SP, Shusta EV, Kendziorski C, Zhang SC. Regionally specified human pluripotent stem cell-derived astrocytes exhibit different molecular signatures and functional properties. Development 2019; 146:dev.170910. [PMID: 31189664 DOI: 10.1242/dev.170910] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/03/2019] [Indexed: 01/10/2023]
Abstract
Astrocytes display diverse morphologies in different regions of the central nervous system. Whether astrocyte diversity is attributable to developmental processes and bears functional consequences, especially in humans, is unknown. RNA-seq of human pluripotent stem cell-derived regional astrocytes revealed distinct transcript profiles, suggesting differential functional properties. This was confirmed by differential calcium signaling as well as effects on neurite growth and blood-brain barrier formation. Distinct transcriptional profiles and functional properties of human astrocytes generated from regionally specified neural progenitors under the same conditions strongly implicate the developmental impact on astrocyte diversity. These findings provide a rationale for renewed examination of regional astrocytes and their role in the pathogenesis of psychiatric and neurological disorders.
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Affiliation(s)
- Robert A Bradley
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA.,Cellular and Molecular Biology Program, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Jack Shireman
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Caya McFalls
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Jeea Choi
- Department of Statistics, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Scott G Canfield
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI 53705, USA.,Department of Cellular and Integrative Physiology, School of Medicine, Indiana University - Terre Haute, IN 47885, USA
| | - Yi Dong
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Katie Liu
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Brianne Lisota
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Jeffery R Jones
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Andrew Petersen
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Anita Bhattacharyya
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI 53705, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI 53792, USA
| | - Su-Chun Zhang
- Department of Neuroscience, Waisman Center, University of Wisconsin - Madison, Madison, WI 53705, USA .,Cellular and Molecular Biology Program, University of Wisconsin - Madison, Madison, WI 53705, USA.,Department of Neuroscience, Department of Neurology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI 53705, USA.,Program in Neuroscience & Behavioral Disorders, Duke-NUS Medical School, Singapore 169857
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48
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Lee WS, Lee WH, Bae YC, Suk K. Axon Guidance Molecules Guiding Neuroinflammation. Exp Neurobiol 2019; 28:311-319. [PMID: 31308791 PMCID: PMC6614065 DOI: 10.5607/en.2019.28.3.311] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/19/2022] Open
Abstract
Axon guidance molecules (AGMs), such as Netrins, Semaphorins, and Ephrins, have long been known to regulate axonal growth in the developing nervous system. Interestingly, the chemotactic properties of AGMs are also important in the postnatal period, such as in the regulation of immune and inflammatory responses. In particular, AGMs play pivotal roles in inflammation of the nervous system, by either stimulating or inhibiting inflammatory responses, depending on specific ligand-receptor combinations. Understanding such regulatory functions of AGMs in neuroinflammation may allow finding new molecular targets to treat neurodegenerative diseases, in which neuroinflammation underlies aetiology and progression.
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Affiliation(s)
- Won Suk Lee
- Department of Pharmacology, School of Medicine, Kyungpook National University, Daegu 41944, Korea.,Brain Science and Engineering Institute, Kyungpook National University, Daegu 41944, Korea
| | - Won-Ha Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Yong Chul Bae
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea
| | - Kyoungho Suk
- Department of Pharmacology, School of Medicine, Kyungpook National University, Daegu 41944, Korea.,Brain Science and Engineering Institute, Kyungpook National University, Daegu 41944, Korea
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49
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Patel D, Mez J, Vardarajan BN, Staley L, Chung J, Zhang X, Farrell JJ, Rynkiewicz MJ, Cannon-Albright LA, Teerlink CC, Stevens J, Corcoran C, Gonzalez Murcia JD, Lopez OL, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg G, Kauwe JSK, Lunetta KL, Farrer LA. Association of Rare Coding Mutations With Alzheimer Disease and Other Dementias Among Adults of European Ancestry. JAMA Netw Open 2019; 2:e191350. [PMID: 30924900 PMCID: PMC6450321 DOI: 10.1001/jamanetworkopen.2019.1350] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/01/2019] [Indexed: 12/26/2022] Open
Abstract
Importance Some of the unexplained heritability of Alzheimer disease (AD) may be due to rare variants whose effects are not captured in genome-wide association studies because very large samples are needed to observe statistically significant associations. Objective To identify genetic variants associated with AD risk using a nonstatistical approach. Design, Setting, and Participants Genetic association study in which rare variants were identified by whole-exome sequencing in unrelated individuals of European ancestry from the Alzheimer's Disease Sequencing Project (ADSP). Data were analyzed between March 2017 and September 2018. Main Outcomes and Measures Minor alleles genome-wide and in 95 genes previously associated with AD, AD-related traits, or other dementias were tabulated and filtered for predicted functional impact and occurrence in participants with AD but not controls. Support for several findings was sought in a whole-exome sequencing data set comprising 19 affected relative pairs from Utah high-risk pedigrees and whole-genome sequencing data sets from the ADSP and Alzheimer's Disease Neuroimaging Initiative. Results Among 5617 participants with AD (3202 [57.0%] women; mean [SD] age, 76.4 [9.3] years) and 4594 controls (2719 [59.0%] women; mean [SD] age, 86.5 [4.5] years), a total of 24 variants with moderate or high functional impact from 19 genes were observed in 10 or more participants with AD but not in controls. These variants included a missense mutation (rs149307620 [p.A284T], n = 10) in NOTCH3, a gene in which coding mutations are associated with cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), that was also identified in 1 participant with AD and 1 participant with mild cognitive impairment in the whole genome sequencing data sets. Four participants with AD carried the TREM2 rs104894002 (p.Q33X) high-impact mutation that, in homozygous form, causes Nasu-Hakola disease, a rare disorder characterized by early-onset dementia and multifocal bone cysts, suggesting an intermediate inheritance model for the mutation. Compared with controls, participants with AD had a significantly higher burden of deleterious rare coding variants in dementia-associated genes (2314 vs 3354 cumulative variants, respectively; P = .006). Conclusions and Relevance Different mutations in the same gene or variable dose of a mutation may be associated with result in distinct dementias. These findings suggest that minor differences in the structure or amount of protein may be associated with in different clinical outcomes. Understanding these genotype-phenotype associations may provide further insight into the pathogenic nature of the mutations, as well as offer clues for developing new therapeutic targets.
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Affiliation(s)
- Devanshi Patel
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
| | - Jesse Mez
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | | | - Lyndsay Staley
- Department of Biology, Brigham Young University, Provo, Utah
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
| | - Michael J. Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Lisa A. Cannon-Albright
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | - Craig C. Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | - Jeffery Stevens
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | | | | | - Oscar L. Lopez
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Richard Mayeux
- Department of Neurology, Columbia University, New York, New York
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia
| | | | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
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50
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Zhang DF, Xu M, Bi R, Yao YG. Genetic Analyses of Alzheimer's Disease in China: Achievements and Perspectives. ACS Chem Neurosci 2019; 10:890-901. [PMID: 30698408 DOI: 10.1021/acschemneuro.8b00435] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Since 2010, the Chinese have become one of the most aged populations in the world, leading to a severe burden of neurodegenerative disorders. Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and has a high genetic heritability. In the past two decades, numerous genetic analyses, from linkage analyses and candidate gene studies to genome-wide association studies (GWASs) and next-generation sequencing studies, have identified dozens of AD susceptibility or causal genes. These studies have provided a comprehensive genetic view and contributed to the understanding of the pathological and molecular mechanisms of the disease. However, most of the recognized AD genetic risk factors have been reported in studies based on European populations or populations of European ancestry, and data about the genetics of AD from other populations has been very limited. As China has the largest AD population in the world and because of the remarkable genetic differences between the East and the West, deciphering the genetic basis and molecular mechanism in Chinese patients with AD may add key points to the full characterization of AD. In this review, we present an overview of the current state of AD genetic research in China, with an emphasis on genome-level studies. We also describe the challenges and opportunities for future advances, especially for in-depth collaborations, brain bank construction, and primate animal modeling. There is an urgent need to promote public awareness and increase our collaborations and data sharing.
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Affiliation(s)
- Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Kunming Institute of Zoology−Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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