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Mazahir F, Alam MI, Yadav AK. Development of nanomedicines for the treatment of Alzheimer's disease: Raison d'être, strategies, challenges and regulatory aspects. Ageing Res Rev 2024; 98:102318. [PMID: 38705362 DOI: 10.1016/j.arr.2024.102318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/04/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disorder characterized by progressive loss of memory. Presently, AD is challenging to treat with current drug therapy as their delivery to the brain is restricted by the presence of the blood-brain barrier. Nanomedicines, due to their size, high surface volume ratio, and ease of tailoring drug release characteristics, showed their potential to treat AD. The nanotechnology-based formulations for brain targeting are expected to enter the market in the near future. So, regulatory frameworks are required to ensure the quality, safety, and effectiveness of the nanomedicines to treat AD. In this review, we discuss different strategies, in-vitro blood-brain permeation models, in-vivo permeation assessment, and regulatory aspects for the development of nanomedicine to treat AD.
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Affiliation(s)
- Farhan Mazahir
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Raebareli, India
| | - Md Imtiyaz Alam
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Raebareli, India
| | - Awesh Kumar Yadav
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Raebareli, India.
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2
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Djurišić M. Immune receptors and aging brain. Biosci Rep 2024; 44:BSR20222267. [PMID: 38299364 PMCID: PMC10866841 DOI: 10.1042/bsr20222267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 02/02/2024] Open
Abstract
Aging brings about a myriad of degenerative processes throughout the body. A decrease in cognitive abilities is one of the hallmark phenotypes of aging, underpinned by neuroinflammation and neurodegeneration occurring in the brain. This review focuses on the role of different immune receptors expressed in cells of the central and peripheral nervous systems. We will discuss how immune receptors in the brain act as sentinels and effectors of the age-dependent shift in ligand composition. Within this 'old-age-ligand soup,' some immune receptors contribute directly to excessive synaptic weakening from within the neuronal compartment, while others amplify the damaging inflammatory environment in the brain. Ultimately, chronic inflammation sets up a positive feedback loop that increases the impact of immune ligand-receptor interactions in the brain, leading to permanent synaptic and neuronal loss.
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Affiliation(s)
- Maja Djurišić
- Departments of Biology, Neurobiology, and Bio-X, Stanford University, Stanford, CA 94305, U.S.A
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3
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Batista AF, Khan KA, Papavergi MT, Lemere CA. The Importance of Complement-Mediated Immune Signaling in Alzheimer's Disease Pathogenesis. Int J Mol Sci 2024; 25:817. [PMID: 38255891 PMCID: PMC10815224 DOI: 10.3390/ijms25020817] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/05/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
As an essential component of our innate immune system, the complement system is responsible for our defense against pathogens. The complement cascade has complex roles in the central nervous system (CNS), most of what we know about it stems from its role in brain development. However, in recent years, numerous reports have implicated the classical complement cascade in both brain development and decline. More specifically, complement dysfunction has been implicated in neurodegenerative disorders, such as Alzheimer's disease (AD), which is the most common form of dementia. Synapse loss is one of the main pathological hallmarks of AD and correlates with memory impairment. Throughout the course of AD progression, synapses are tagged with complement proteins and are consequently removed by microglia that express complement receptors. Notably, astrocytes are also capable of secreting signals that induce the expression of complement proteins in the CNS. Both astrocytes and microglia are implicated in neuroinflammation, another hallmark of AD pathogenesis. In this review, we provide an overview of previously known and newly established roles for the complement cascade in the CNS and we explore how complement interactions with microglia, astrocytes, and other risk factors such as TREM2 and ApoE4 modulate the processes of neurodegeneration in both amyloid and tau models of AD.
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Affiliation(s)
- André F. Batista
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.F.B.); (K.A.K.); (M.-T.P.)
| | - Khyrul A. Khan
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.F.B.); (K.A.K.); (M.-T.P.)
| | - Maria-Tzousi Papavergi
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.F.B.); (K.A.K.); (M.-T.P.)
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Cynthia A. Lemere
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.F.B.); (K.A.K.); (M.-T.P.)
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4
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Karachanak-Yankova S, Serbezov D, Mihaylova M, Nikolova D, Balabanski L, Damyanova V, Antonova O, Staneva R, Ganev M, Spasova V, Rukova B, Nesheva D, Josifovska S, Stancheva M, Belejanska D, Petrova M, Mehrabian S, Traykov L, Hadjidekova S, Toncheva D. Detection of pathogenic variants in Alzheimer’s disease related genes in Bulgarian patients by pooled whole-exome sequencing. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2022.2155572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Sena Karachanak-Yankova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
- Department of Genetics, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | - Dimitar Serbezov
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Marta Mihaylova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Dragomira Nikolova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | | | - Vera Damyanova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Olga Antonova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Mihail Ganev
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Victoria Spasova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Blaga Rukova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Slavica Josifovska
- Department of Molecular Biology, Genetics and Microbiology, Faculty of Natural Sciences and Mathematics, ‘Ss. Cyril and Methodius’ University, Skopje, North Macedonia
| | - Mikaela Stancheva
- Department of Genetics, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | - Diana Belejanska
- Department of Neurology, University Hospital ‘Alexandrovska’, Sofia, Bulgaria
| | - Mariya Petrova
- Department of Neurology, University Hospital ‘Alexandrovska’, Sofia, Bulgaria
| | - Shima Mehrabian
- Department of Neurology, University Hospital ‘Alexandrovska’, Sofia, Bulgaria
| | - Latchezar Traykov
- Department of Neurology, University Hospital ‘Alexandrovska’, Sofia, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
- Bulgarian Academy of Sciences, Sofia, Bulgaria
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5
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Lee WP, Wang H, Dombroski B, Cheng PL, Tucci A, Si YQ, Farrell J, Tzeng JY, Leung YY, Malamon J, Wang LS, Vardarajan B, Farrer L, Schellenberg G. Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects. RESEARCH SQUARE 2023:rs.3.rs-3353179. [PMID: 37886469 PMCID: PMC10602095 DOI: 10.21203/rs.3.rs-3353179/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: 10/28/2023]
Abstract
Structural variations (SVs) are important contributors to the genetics of human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due to challenges in accurately detecting SVs. We analyzed whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (N = 16,905) and identified 400,234 (168,223 high-quality) SVs. Laboratory validation yielded a sensitivity of 82% (85% for high-quality). We found a significant burden of deletions and duplications in AD cases, particularly for singletons and homozygous events. On AD genes, we observed the ultra-rare SVs associated with the disease, including protein-altering SVs in ABCA7, APP, PLCG2, and SORL1. Twenty-one SVs are in linkage disequilibrium (LD) with known AD-risk variants, exemplified by a 5k deletion in complete LD with rs143080277 in NCK2. We also identified 16 SVs associated with AD and 13 SVs linked to AD-related pathological/cognitive endophenotypes. This study highlights the pivotal role of SVs in shaping our understanding of AD genetics.
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Wang H, Dombroski BA, Cheng PL, Tucci A, Si YQ, Farrell JJ, Tzeng JY, Leung YY, Malamon JS, Wang LS, Vardarajan BN, Farrer LA, Schellenberg GD, Lee WP. Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.13.23295505. [PMID: 37745545 PMCID: PMC10516060 DOI: 10.1101/2023.09.13.23295505] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Structural variations (SVs) are important contributors to the genetics of numerous human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due to challenges in accurately detecting SVs. Here, we analyzed whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (ADSP, N=16,905 subjects) and identified 400,234 (168,223 high-quality) SVs. We found a significant burden of deletions and duplications in AD cases (OR=1.05, P=0.03), particularly for singletons (OR=1.12, P=0.0002) and homozygous events (OR=1.10, P<0.0004). On AD genes, the ultra-rare SVs, including protein-altering SVs in ABCA7, APP, PLCG2, and SORL1, were associated with AD (SKAT-O P=0.004). Twenty-one SVs are in linkage disequilibrium (LD) with known AD-risk variants, e.g., a deletion (chr2:105731359-105736864) in complete LD (R2=0.99) with rs143080277 (chr2:105749599) in NCK2. We also identified 16 SVs associated with AD and 13 SVs associated with AD-related pathological/cognitive endophenotypes. Our findings demonstrate the broad impact of SVs on AD genetics.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Po-Liang Cheng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Albert Tucci
- Bioinformatics Research Center, North Carolina State University, NC 27695, USA
| | - Ya-Qin Si
- Bioinformatics Research Center, North Carolina State University, NC 27695, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, MA 02118, USA
| | - Jung-Ying Tzeng
- Bioinformatics Research Center, North Carolina State University, NC 27695, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - John S Malamon
- Department of Surgery, Scholl of Medicine, University of Colorado, CO 80045, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, NY 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, NY 10032, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, MA 02118, USA
- Department of Ophthalmology, Boston University School of Medicine, MA 02118, USA
- Department of Biostatistics, Boston University School of Public Health, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, MA 02118, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
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7
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Cruchaga C, Western D, Timsina J, Wang L, Wang C, Yang C, Ali M, Beric A, Gorijala P, Kohlfeld P, Budde J, Levey A, Morris J, Perrin R, Ruiz A, Marquié M, Boada M, de Rojas I, Rutledge J, Oh H, Wilson E, Guen YL, Alvarez I, Aguilar M, Greicius M, Pastor P, Pulford D, Ibanez L, Wyss-Coray T, Sung YJ, Phillips B. Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and informs causal proteins for Alzheimer's disease. RESEARCH SQUARE 2023:rs.3.rs-2814616. [PMID: 37333337 PMCID: PMC10275048 DOI: 10.21203/rs.3.rs-2814616/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The integration of quantitative trait loci (QTL) with disease genome-wide association studies (GWAS) has proven successful at prioritizing candidate genes at disease-associated loci. QTL mapping has mainly been focused on multi-tissue expression QTL or plasma protein QTL (pQTL). Here we generated the largest-to-date cerebrospinal fluid (CSF) pQTL atlas by analyzing 7,028 proteins in 3,107 samples. We identified 3,373 independent study-wide associations for 1,961 proteins, including 2,448 novel pQTLs of which 1,585 are unique to CSF, demonstrating unique genetic regulation of the CSF proteome. In addition to the established chr6p22.2-21.32 HLA region, we identified pleiotropic regions on chr3q28 near OSTN and chr19q13.32 near APOE that were enriched for neuron-specificity and neurological development. We also integrated this pQTL atlas with the latest Alzheimer's disease (AD) GWAS through PWAS, colocalization and Mendelian Randomization and identified 42 putative causal proteins for AD, 15 of which have drugs available. Finally, we developed a proteomics-based risk score for AD that outperforms genetics-based polygenic risk scores. These findings will be instrumental to further understand the biology and identify causal and druggable proteins for brain and neurological traits.
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Affiliation(s)
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Washington University School of Medicine
| | | | | | | | | | | | - Patsy Kohlfeld
- Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | | | | | | | - Mercè Boada
- Memory Clinic of Fundaciò ACE, Catalan Institute of Applied Neurosciences
| | | | | | | | | | | | - Ignacio Alvarez
- Fundació Docència i Recerca Mútua Terrassa, Terrassa, Barcelona, Spain
| | | | | | - Pau Pastor
- University Hospital Germans Trias i Pujol
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8
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Daskoulidou N, Shaw B, Torvell M, Watkins L, Cope EL, Carpanini SM, Allen ND, Morgan BP. Complement receptor 1 is expressed on brain cells and in the human brain. Glia 2023; 71:1522-1535. [PMID: 36825534 PMCID: PMC10953339 DOI: 10.1002/glia.24355] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023]
Abstract
Genome wide association studies (GWAS) have highlighted the importance of the complement cascade in pathogenesis of Alzheimer's disease (AD). Complement receptor 1 (CR1; CD35) is among the top GWAS hits. The long variant of CR1 is associated with increased risk for AD; however, roles of CR1 in brain health and disease are poorly understood. A critical confounder is that brain expression of CR1 is controversial; failure to demonstrate brain expression has provoked the suggestion that peripherally expressed CR1 influences AD risk. We took a multi-pronged approach to establish whether CR1 is expressed in brain. Expression of CR1 at the protein and mRNA level was assessed in human microglial lines, induced pluripotent stem cell (iPSC)-derived microglia from two sources and brain tissue from AD and control donors. CR1 protein was detected in microglial lines and iPSC-derived microglia expressing different CR1 variants when immunostained with a validated panel of CR1-specific antibodies; cell extracts were positive for CR1 protein and mRNA. CR1 protein was detected in control and AD brains, co-localizing with astrocytes and microglia, and expression was significantly increased in AD compared to controls. CR1 mRNA expression was detected in all AD and control brain samples tested; expression was significantly increased in AD. The data unequivocally demonstrate that the CR1 transcript and protein are expressed in human microglia ex vivo and on microglia and astrocytes in situ in the human brain; the findings support the hypothesis that CR1 variants affect AD risk by directly impacting glial functions.
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Affiliation(s)
| | - Bethany Shaw
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Megan Torvell
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Lewis Watkins
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Emma L. Cope
- School of Biosciences, Cardiff UniversityCardiffUK
| | | | - Nicholas D. Allen
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
- School of Biosciences, Cardiff UniversityCardiffUK
| | - B. Paul Morgan
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
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9
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Lorenzini PA, Gusareva ES, Ghosh AG, Ramli NAB, Preiser PR, Kim HL. Population-specific positive selection on low CR1 expression in malaria-endemic regions. PLoS One 2023; 18:e0280282. [PMID: 36626386 PMCID: PMC9831336 DOI: 10.1371/journal.pone.0280282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/25/2022] [Indexed: 01/11/2023] Open
Abstract
Complement Receptor Type 1 (CR1) is a malaria-associated gene that encodes a transmembrane receptor of erythrocytes and is crucial for malaria parasite invasion. The expression of CR1 contributes to the rosetting of erythrocytes in the brain bloodstream, causing cerebral malaria, the most severe form of the disease. Here, we study the history of adaptation against malaria by analyzing selection signals in the CR1 gene. We used whole-genome sequencing datasets of 907 healthy individuals from malaria-endemic and non-endemic populations. We detected robust positive selection in populations from the hyperendemic regions of East India and Papua New Guinea. Importantly, we identified a new adaptive variant, rs12034598, which is associated with a slower rate of erythrocyte sedimentation and is linked with a variant associated with low levels of CR1 expression. The combination of the variants likely drives natural selection. In addition, we identified a variant rs3886100 under positive selection in West Africans, which is also related to a low level of CR1 expression in the brain. Our study shows the fine-resolution history of positive selection in the CR1 gene and suggests a population-specific history of CR1 adaptation to malaria. Notably, our novel approach using population genomic analyses allows the identification of protective variants that reduce the risk of malaria infection without the need for patient samples or malaria individual medical records. Our findings contribute to understanding of human adaptation against cerebral malaria.
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Affiliation(s)
- Paolo Alberto Lorenzini
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- The GenomeAsia 100K Consortium, Singapore, Singapore
| | - Elena S. Gusareva
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- The GenomeAsia 100K Consortium, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Amit Gourav Ghosh
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- The GenomeAsia 100K Consortium, Singapore, Singapore
| | - Nurul Adilah Binte Ramli
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- The GenomeAsia 100K Consortium, Singapore, Singapore
| | - Peter Rainer Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hie Lim Kim
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- The GenomeAsia 100K Consortium, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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10
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Gao C, Shen X, Tan Y, Chen S. Pathogenesis, therapeutic strategies and biomarker development based on "omics" analysis related to microglia in Alzheimer's disease. J Neuroinflammation 2022; 19:215. [PMID: 36058959 PMCID: PMC9441025 DOI: 10.1186/s12974-022-02580-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/27/2022] [Indexed: 11/10/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease and the most common cause of dementia. Among various pathophysiological aspects, microglia are considered to play important roles in the pathogenesis of AD. Genome wide association studies (GWAS) showed that the majority of AD risk genes are highly or exclusively expressed in microglia, underscoring the critical roles of microglia in AD pathogenesis. Recently, omics technologies have greatly advanced our knowledge of microglia biology in AD. Omics approaches, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics/lipidomics, present remarkable opportunities to delineate the underlying mechanisms, discover novel diagnostic biomarkers, monitor disease progression, and shape therapeutic strategies for diseases. In this review, we summarized research based on microglial "omics" analysis in AD, especially the recent research advances in the identification of AD-associated microglial subsets. This review reinforces the important role of microglia in AD and advances our understanding of the mechanism of microglia in AD pathogenesis. Moreover, we proposed the value of microglia-based omics in the development of therapeutic strategies and biomarkers for AD.
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Affiliation(s)
- Chao Gao
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shen
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuyan Tan
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Shengdi Chen
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Lab for Translational Research of Neurodegenerative Diseases, Shanghai Institute for Advanced Immunochemical Studies (SIAIS), Shanghai Tech University, Shanghai, 201210, China.
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11
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Cheng J, Clayton JS, Acemel RD, Zheng Y, Taylor RL, Keleş S, Franke M, Boackle SA, Harley JB, Quail E, Gómez-Skarmeta JL, Ulgiati D. Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer. Front Immunol 2022; 13:901747. [PMID: 35769482 PMCID: PMC9235356 DOI: 10.3389/fimmu.2022.901747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/05/2022] [Indexed: 12/03/2022] Open
Abstract
The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes with shared functions within the immune system. RCA members, such as complement receptor 2 (CR2), are well-established susceptibility genes in complex autoimmune diseases. Altered expression of RCA genes has been demonstrated at both the functional and genetic level, but the mechanisms underlying their regulation are not fully characterised. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression of CR2 and other genes in this immunomodulatory region. Using 4C, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topologically associated domains (TADs). Interestingly, an inter-TAD boundary was located within the CR1 gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we identified an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2 and CD55) in B cells. We have uncovered novel, long-range mechanisms whereby autoimmune disease susceptibility may be influenced by genetic variants, thus highlighting the important contribution of chromatin topology to gene regulation and complex genetic disease.
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Affiliation(s)
- Jessica Cheng
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Joshua S. Clayton
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Rafael D. Acemel
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States,Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States
| | - Rhonda L. Taylor
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Martin Franke
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Susan A. Boackle
- Department of Medicine, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States,US Department of Veterans Affairs Medical Centre, US Department of Veterans Affairs, Cincinnati, OH, United States
| | - Elizabeth Quail
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Daniela Ulgiati
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia,*Correspondence: Daniela Ulgiati,
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12
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Zhu XC, Liu L, Dai WZ, Ma T. Crry silencing alleviates Alzheimer's disease injury by regulating neuroinflammatory cytokines and the complement system. Neural Regen Res 2022; 17:1841-1849. [PMID: 35017447 PMCID: PMC8820699 DOI: 10.4103/1673-5374.332160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Complement component (3b/4b) receptor 1 (CR1) expression is positively related to the abundance of phosphorylated microtubule-associated protein tau (tau), and CR1 expression is associated with susceptibility to Alzheimer’s disease. However, the exact role of CR1 in tau protein-associated neurodegenerative diseases is unknown. In this study, we show that the mouse Cr1-related protein Y (Crry) gene, Crry, is localized to microglia. We also found that Crry protein expression in the hippocampus and cortex was significantly elevated in P301S mice (a mouse model widely used for investigating tau pathology) compared with that in wild-type mice. Tau protein phosphorylation (at serine 202, threonine 205, threonine 231, and serine 262) and expression of the major tau kinases glycogen synthase kinase-3 beta and cyclin-dependent-like kinase 5 were greater in P301S mice than in wild-type mice. Crry silencing by lentivirus-transfected short hairpin RNA led to greatly reduced tau phosphorylation and glycogen synthase kinase-3 beta and cyclin-dependent-like kinase 5 activity. Crry silencing reduced neuronal apoptosis and rescued cognitive impairment of P301S mice. Crry silencing also reduced the levels of the neuroinflammatory factors interleukin-1 beta, tumor necrosis factor alpha, and interleukin-6 and the complement components complement 3 and complement component 3b. Our results suggest that Crry silencing in the P301S mouse model reduces tau protein phosphorylation by reducing the levels of neuroinflammation and complement components, thereby improving cognitive function.
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Affiliation(s)
- Xi-Chen Zhu
- Department of Neurology, Wuxi No. 2 People's Hospital of Nanjing Medical University; Department of Neurology, Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu Province, China
| | - Lu Liu
- Department of Neurology, Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Wen-Zhuo Dai
- Department of Neurology, Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Tao Ma
- Department of Neurology, Wuxi No. 2 People's Hospital of Nanjing Medical University; Department of Neurology, Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu Province, China
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13
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Torvell M, Carpanini SM, Daskoulidou N, Byrne RAJ, Sims R, Morgan BP. Genetic Insights into the Impact of Complement in Alzheimer's Disease. Genes (Basel) 2021; 12:1990. [PMID: 34946939 PMCID: PMC8702080 DOI: 10.3390/genes12121990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Abstract
The presence of complement activation products at sites of pathology in post-mortem Alzheimer's disease (AD) brains is well known. Recent evidence from genome-wide association studies (GWAS), combined with the demonstration that complement activation is pivotal in synapse loss in AD, strongly implicates complement in disease aetiology. Genetic variations in complement genes are widespread. While most variants individually have only minor effects on complement homeostasis, the combined effects of variants in multiple complement genes, referred to as the "complotype", can have major effects. In some diseases, the complotype highlights specific parts of the complement pathway involved in disease, thereby pointing towards a mechanism; however, this is not the case with AD. Here we review the complement GWAS hits; CR1 encoding complement receptor 1 (CR1), CLU encoding clusterin, and a suggestive association of C1S encoding the enzyme C1s, and discuss difficulties in attributing the AD association in these genes to complement function. A better understanding of complement genetics in AD might facilitate predictive genetic screening tests and enable the development of simple diagnostic tools and guide the future use of anti-complement drugs, of which several are currently in development for central nervous system disorders.
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Affiliation(s)
- Megan Torvell
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK; (M.T.); (S.M.C.); (N.D.); (R.A.J.B.)
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Sarah M. Carpanini
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK; (M.T.); (S.M.C.); (N.D.); (R.A.J.B.)
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Nikoleta Daskoulidou
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK; (M.T.); (S.M.C.); (N.D.); (R.A.J.B.)
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Robert A. J. Byrne
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK; (M.T.); (S.M.C.); (N.D.); (R.A.J.B.)
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK;
| | - B. Paul Morgan
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK; (M.T.); (S.M.C.); (N.D.); (R.A.J.B.)
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
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14
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Lu L, Yao QY, Ruan SS, Hu JW, Long WJ, Dai WZ, Ma T, Zhu XC. Explore the role of CR1 genetic variants in late-onset Alzheimer's disease susceptibility. Psychiatr Genet 2021; 31:216-229. [PMID: 34347684 DOI: 10.1097/ypg.0000000000000291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Complement component (3b/4b) receptor 1 (CR1) is an interesting candidate gene which has a close connection with Alzheimer's disease, and its polymorphisms have been reported to link to the late-onset Alzheimer's disease (LOAD) susceptibility. However, the findings of these related studies are inconsistent. Objective To explore the effect of CR1 genetic variants in LOAD susceptibility. MethodsWe searched relevant studies for the period up to 1 November 2020. And odds ratios (ORs) and their 95% confidence intervals (CIs) were utilized to assess the strength of the association. In addition, we carried out a case-control association study to assess their genetic association. RESULTS Finally, a total of 30 articles with 30108 LOAD cases and 37895 controls were included. Significant allele frequency between LOAD patients and controls was observed in rs3818361 and rs6656401 (rs3818361, T vs. C: OR,1.18; 95% CI, 1.13-1.23; rs6656401, A vs. G: OR, 1.23; 95% CI, 1.10-1.36). Moreover, these results remain significant in subgroup of rs3818361 in Asia or America (OR,1.26; 95% CI,1.06-1.45; OR, 1.18; 95% CI, 1.13-1.24, respectively) and rs6656401 in Europe (OR = 1.26; 95% CI, 1.09-1.42). In addition, the two single nucleotide polymorphisms were proved to significantly increase LOAD risk in the overall population under the dominant model (OR = 1.12; 95% CI, 1.02-1.21; OR = 1.18, 95% CI, 1.15-1.22, respectively). Our case-control study showed that the distribution of rs6656401 genotype was significant (P = 0.000; OR, 6.889; 95% CI, 2.709-17.520), suggesting the A allele of rs6656401 is the risk allele. CONCLUSION These available data indicate that rs6656401 in CR1 is significant to increase LOAD risk.
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Affiliation(s)
- Liu Lu
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Qing-Yu Yao
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Sha-Sha Ruan
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Jia-Wei Hu
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Wen-Jun Long
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Wen-Zhuo Dai
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Tao Ma
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
- Department of Neurology, The WuXi NO.2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
| | - Xi-Chen Zhu
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
- Department of Neurology, The WuXi NO.2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
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15
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Liang X, Wu H, Colt M, Guo X, Pluimer B, Zeng J, Dong S, Zhao Z. Microglia and its Genetics in Alzheimer's Disease. Curr Alzheimer Res 2021; 18:676-688. [PMID: 34749609 DOI: 10.2174/1567205018666211105140732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 12/27/2022]
Abstract
Alzheimer's Disease (AD) is the most prevalent form of dementia across the world. While its discovery and pathological manifestations are centered on protein aggregations of amyloid- beta (Aβ) and hyperphosphorylated tau protein, neuroinflammation has emerged in the last decade as a main component of the disease in terms of both pathogenesis and progression. As the main innate immune cell type in the central nervous system (CNS), microglia play a very important role in regulating neuroinflammation, which occurs commonly in neurodegenerative conditions, including AD. Under inflammatory response, microglia undergo morphological changes and status transition from homeostatic to activated forms. Different microglia subtypes displaying distinct genetic profiles have been identified in AD, and these signatures often link to AD risk genes identified from the genome-wide association studies (GWAS), such as APOE and TREM2. Furthermore, many AD risk genes are highly enriched in microglia and specifically influence the functions of microglia in pathogenesis, e.g. releasing inflammatory cytokines and clearing Aβ. Therefore, building up a landscape of these risk genes in microglia, based on current preclinical studies and in the context of their pathogenic or protective effects, would largely help us to understand the complex etiology of AD and provide new insight into the unmet need for effective treatment.
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Affiliation(s)
- Xinyan Liang
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033,United States
| | - Haijian Wu
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033,United States
| | - Mark Colt
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033,United States
| | - Xinying Guo
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033,United States
| | - Brock Pluimer
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033,United States
| | - Jianxiong Zeng
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033,United States
| | - Shupeng Dong
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033,United States
| | - Zhen Zhao
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033,United States
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16
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Behl T, Sehgal A, Grover M, Singh S, Sharma N, Bhatia S, Al-Harrasi A, Aleya L, Bungau S. Uncurtaining the pivotal role of ABC transporters in diabetes mellitus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:41533-41551. [PMID: 34085197 DOI: 10.1007/s11356-021-14675-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
The metabolic disorders are the edge points for the initiation of various diseases. These disorders comprised of several diseases including diabetes, obesity, and cardiovascular complications. Worldwide, the prevalence of these disorders is increasing day by day. The world's population is at higher threat of developing metabolic disease, especially diabetes. Therefore, there is an impregnable necessity of searching for a newer therapeutic target to reduce the burden of these disorders. Diabetes mellitus (DM) is marked with the dysregulated insulin secretion and resistance. The lipid and glucose transporters portray a pivotal role in the metabolism and transport of both of these. The excess production of lipid and glucose and decreased clearance of these leads to the emergence of DM. The ATP-binding cassette transporters (ABCT) are important for the metabolism of glucose and lipid. Various studies suggest the key involvement of ABCT in the pathologic process of different diseases. In addition, the involvement of other pathways, including IGF signaling, P13-Akt/PKC/MAPK signaling, and GLP-1 via regulation of ABCT, may help develop new treatment strategies to cope with insulin resistance dysregulated glucose metabolism, key features in DM.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Madhuri Grover
- BS Anangpuria Institute of Pharmacy, Faridabad, Haryana, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Saurabh Bhatia
- Amity Institute of Pharmacy, Amity University, Gurugram, Haryana, India
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa, Oman
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Simona Bungau
- Department of Pharmacy, Faculty of Pharmacy, University of Oradea, Oradea, Romania
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17
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The contribution of CNVs to the most common aging-related neurodegenerative diseases. Aging Clin Exp Res 2021; 33:1187-1195. [PMID: 32026430 DOI: 10.1007/s40520-020-01485-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
Alzheimer and Parkinson's diseases are neurodegenerative aging-related pathological conditions, mainly caused by the interplay of genetic and non-genetic factors and whose incidence rate is going to drastically increase given the growing life expectancy. To address these complex multifactorial traits, a systems biology strategy is needed to highlight genotype-phenotype correlations as well as overlapping gene signatures. Copy number variants (CNVs) are structural chromosomal imbalances that can have pathogenic nature causing or contributing to the disease onset or progression. Moreover, neurons affected by CNVs have been found to decline in number depending on age in healthy controls and may be selectively vulnerable to aging-related cell-death. In this review, we aim to update the reader on the role of these variations in the pathogenesis of Alzheimer and Parkinson diseases. To widen the comprehension of pathogenic mechanisms underlying them, we discuss variations detected from blood or brain specimens, as well as overlapped signatures between the two pathologies.
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18
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Artificial intelligence and leukocyte epigenomics: Evaluation and prediction of late-onset Alzheimer's disease. PLoS One 2021; 16:e0248375. [PMID: 33788842 PMCID: PMC8011726 DOI: 10.1371/journal.pone.0248375] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
We evaluated the utility of leucocyte epigenomic-biomarkers for Alzheimer’s Disease (AD) detection and elucidates its molecular pathogeneses. Genome-wide DNA methylation analysis was performed using the Infinium MethylationEPIC BeadChip array in 24 late-onset AD (LOAD) and 24 cognitively healthy subjects. Data were analyzed using six Artificial Intelligence (AI) methodologies including Deep Learning (DL) followed by Ingenuity Pathway Analysis (IPA) was used for AD prediction. We identified 152 significantly (FDR p<0.05) differentially methylated intragenic CpGs in 171 distinct genes in AD patients compared to controls. All AI platforms accurately predicted AD with AUCs ≥0.93 using 283,143 intragenic and 244,246 intergenic/extragenic CpGs. DL had an AUC = 0.99 using intragenic CpGs, with both sensitivity and specificity being 97%. High AD prediction was also achieved using intergenic/extragenic CpG sites (DL significance value being AUC = 0.99 with 97% sensitivity and specificity). Epigenetically altered genes included CR1L & CTSV (abnormal morphology of cerebral cortex), S1PR1 (CNS inflammation), and LTB4R (inflammatory response). These genes have been previously linked with AD and dementia. The differentially methylated genes CTSV & PRMT5 (ventricular hypertrophy and dilation) are linked to cardiovascular disease and of interest given the known association between impaired cerebral blood flow, cardiovascular disease, and AD. We report a novel, minimally invasive approach using peripheral blood leucocyte epigenomics, and AI analysis to detect AD and elucidate its pathogenesis.
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19
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Carpanini SM, Harwood JC, Baker E, Torvell M, Sims R, Williams J, Morgan BP. The Impact of Complement Genes on the Risk of Late-Onset Alzheimer's Disease. Genes (Basel) 2021; 12:443. [PMID: 33804666 PMCID: PMC8003605 DOI: 10.3390/genes12030443] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD), the most common cause of dementia, and a huge global health challenge, is a neurodegenerative disease of uncertain aetiology. To deliver effective diagnostics and therapeutics, understanding the molecular basis of the disease is essential. Contemporary large genome-wide association studies (GWAS) have identified over seventy novel genetic susceptibility loci for LOAD. Most are implicated in microglial or inflammatory pathways, bringing inflammation to the fore as a candidate pathological pathway. Among the most significant GWAS hits are three complement genes: CLU, encoding the fluid-phase complement inhibitor clusterin; CR1 encoding complement receptor 1 (CR1); and recently, C1S encoding the complement enzyme C1s. Complement activation is a critical driver of inflammation; changes in complement genes may impact risk by altering the inflammatory status in the brain. To assess complement gene association with LOAD risk, we manually created a comprehensive complement gene list and tested these in gene-set analysis with LOAD summary statistics. We confirmed associations of CLU and CR1 genes with LOAD but showed no significant associations for the complement gene-set when excluding CLU and CR1. No significant association with other complement genes, including C1S, was seen in the IGAP dataset; however, these may emerge from larger datasets.
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Affiliation(s)
- Sarah M. Carpanini
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
- Division of Infection and Immunity, School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - Janet C. Harwood
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, CF24 4HQ, UK; (J.C.H.); (R.S.)
| | - Emily Baker
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
| | - Megan Torvell
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
- Division of Infection and Immunity, School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | | | - Rebecca Sims
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, CF24 4HQ, UK; (J.C.H.); (R.S.)
| | - Julie Williams
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
| | - B. Paul Morgan
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
- Division of Infection and Immunity, School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
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20
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de Boer ECW, van Mourik AG, Jongerius I. Therapeutic Lessons to be Learned From the Role of Complement Regulators as Double-Edged Sword in Health and Disease. Front Immunol 2020; 11:578069. [PMID: 33362763 PMCID: PMC7758290 DOI: 10.3389/fimmu.2020.578069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
The complement system is an important part of the innate immune system, providing a strong defense against pathogens and removing apoptotic cells and immune complexes. Due to its strength, it is important that healthy human cells are protected against damage induced by the complement system. To be protected from complement, each cell type relies on a specific combination of both soluble and membrane-bound regulators. Their importance is indicated by the amount of pathologies associated with abnormalities in these complement regulators. Here, we will discuss the current knowledge on complement regulatory protein polymorphisms and expression levels together with their link to disease. These diseases often result in red blood cell destruction or occur in the eye, kidney or brain, which are tissues known for aberrant complement activity or regulation. In addition, complement regulators have also been associated with different types of cancer, although their mechanisms here have not been elucidated yet. In most of these pathologies, treatments are limited and do not prevent the complement system from attacking host cells, but rather fight the consequences of the complement-mediated damage, using for example blood transfusions in anemic patients. Currently only few drugs targeting the complement system are used in the clinic. With further demand for therapeutics rising linked to the wide range of complement-mediated disease we should broaden our horizon towards treatments that can actually protect the host cells against complement. Here, we will discuss the latest insights on how complement regulators can benefit therapeutics. Such therapeutics are currently being developed extensively, and can be categorized into full-length complement regulators, engineered complement system regulators and antibodies targeting complement regulators. In conclusion, this review provides an overview of the complement regulatory proteins and their links to disease, together with their potential in the development of novel therapeutics.
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Affiliation(s)
- Esther C W de Boer
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Anouk G van Mourik
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Ilse Jongerius
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands
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21
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Liccardo D, Marzano F, Carraturo F, Guida M, Femminella GD, Bencivenga L, Agrimi J, Addonizio A, Melino I, Valletta A, Rengo C, Ferrara N, Rengo G, Cannavo A. Potential Bidirectional Relationship Between Periodontitis and Alzheimer's Disease. Front Physiol 2020; 11:683. [PMID: 32719612 PMCID: PMC7348667 DOI: 10.3389/fphys.2020.00683] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease (AD) is the most prevalent form of dementia in the elderly population, representing a global public health priority. Despite a large improvement in understanding the pathogenesis of AD, the etiology of this disorder remains still unclear, and no current treatment is able to prevent, slow, or stop its progression. Thus, there is a keen interest in the identification and modification of the risk factors and novel molecular mechanisms associated with the development and progression of AD. In this context, it is worth noting that several findings support the existence of a direct link between neuronal and non-neuronal inflammation/infection and AD progression. Importantly, recent studies are now supporting the existence of a direct relationship between periodontitis, a chronic inflammatory oral disease, and AD. The mechanisms underlying the association remain to be fully elucidated, however, it is generally accepted, although not confirmed, that oral pathogens can penetrate the bloodstream, inducing a low-grade systemic inflammation that negatively affects brain function. Indeed, a recent report demonstrated that oral pathogens and their toxic proteins infect the brain of AD patients. For instance, when AD progresses from the early to the more advanced stages, patients could no longer be able to adequately adhere to proper oral hygiene practices, thus leading to oral dysbiosis that, in turn, fuels infection, such as periodontitis. Therefore, in this review, we will provide an update on the emerging (preclinical and clinical) evidence that supports the relationship existing between periodontitis and AD. More in detail, we will discuss data attesting that periodontitis and AD share common risk factors and a similar hyper-inflammatory phenotype.
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Affiliation(s)
- Daniela Liccardo
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Translational Medicine, Temple University, Philadelphia, PA, United States
| | - Federica Marzano
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Marco Guida
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Leonardo Bencivenga
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Jacopo Agrimi
- Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Armida Addonizio
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Imma Melino
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessandra Valletta
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples Federico II, Naples, Italy
| | - Carlo Rengo
- Department of Prosthodontics and Dental Materials, School of Dental Medicine, University of Siena, Siena, Italy
| | - Nicola Ferrara
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Istituti Clinici Scientifici ICS Maugeri - S.p.A.-Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Scientifico di Telese Terme, Telese, Italy
| | - Giuseppe Rengo
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Istituti Clinici Scientifici ICS Maugeri - S.p.A.-Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Scientifico di Telese Terme, Telese, Italy
| | - Alessandro Cannavo
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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22
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Shi L, Winchester LM, Liu BY, Killick R, Ribe EM, Westwood S, Baird AL, Buckley NJ, Hong S, Dobricic V, Kilpert F, Franke A, Kiddle S, Sattlecker M, Dobson R, Cuadrado A, Hye A, Ashton NJ, Morgan AR, Bos I, Vos SJ, ten Kate M, Scheltens P, Vandenberghe R, Gabel S, Meersmans K, Engelborghs S, De Roeck EE, Sleegers K, Frisoni GB, Blin O, Richardson JC, Bordet R, Molinuevo JL, Rami L, Wallin A, Kettunen P, Tsolaki M, Verhey F, Lleó A, Alcolea D, Popp J, Peyratout G, Martinez-Lage P, Tainta M, Johannsen P, Teunissen CE, Freund-Levi Y, Frölich L, Legido-Quigley C, Barkhof F, Blennow K, Rasmussen KL, Nordestgaard BG, Frikke-Schmidt R, Nielsen SF, Soininen H, Vellas B, Kloszewska I, Mecocci P, Zetterberg H, Morgan BP, Streffer J, Visser PJ, Bertram L, Nevado-Holgado AJ, Lovestone S. Dickkopf-1 Overexpression in vitro Nominates Candidate Blood Biomarkers Relating to Alzheimer's Disease Pathology. J Alzheimers Dis 2020; 77:1353-1368. [PMID: 32831200 PMCID: PMC7683080 DOI: 10.3233/jad-200208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Previous studies suggest that Dickkopf-1 (DKK1), an inhibitor of Wnt signaling, plays a role in amyloid-induced toxicity and hence Alzheimer's disease (AD). However, the effect of DKK1 expression on protein expression, and whether such proteins are altered in disease, is unknown. OBJECTIVE We aim to test whether DKK1 induced protein signature obtained in vitro were associated with markers of AD pathology as used in the amyloid/tau/neurodegeneration (ATN) framework as well as with clinical outcomes. METHODS We first overexpressed DKK1 in HEK293A cells and quantified 1,128 proteins in cell lysates using aptamer capture arrays (SomaScan) to obtain a protein signature induced by DKK1. We then used the same assay to measure the DKK1-signature proteins in human plasma in two large cohorts, EMIF (n = 785) and ANM (n = 677). RESULTS We identified a 100-protein signature induced by DKK1 in vitro. Subsets of proteins, along with age and apolipoprotein E ɛ4 genotype distinguished amyloid pathology (A + T-N-, A+T+N-, A+T-N+, and A+T+N+) from no AD pathology (A-T-N-) with an area under the curve of 0.72, 0.81, 0.88, and 0.85, respectively. Furthermore, we found that some signature proteins (e.g., Complement C3 and albumin) were associated with cognitive score and AD diagnosis in both cohorts. CONCLUSIONS Our results add further evidence for a role of DKK regulation of Wnt signaling in AD and suggest that DKK1 induced signature proteins obtained in vitro could reflect theATNframework as well as predict disease severity and progression in vivo.
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Affiliation(s)
- Liu Shi
- Department of Psychiatry, University of Oxford, UK
| | | | | | - Richard Killick
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
| | | | | | | | | | - Shengjun Hong
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Fabian Kilpert
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Steven Kiddle
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
- MRC Social, Genetic and Developmental Psychiatry Centre, King’s College London, UK
| | - Martina Sattlecker
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
- MRC Social, Genetic and Developmental Psychiatry Centre, King’s College London, UK
| | - Richard Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Antonio Cuadrado
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria La Paz (IdiPaz), Instituto de Investigaciones Biomédicas Alberto Sols UAM-CSIC, and Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
- ”Victor Babes” National Institute of Pathology, Bucharest, Romania
| | - Abdul Hye
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
| | - Nicholas J. Ashton
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
- NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation, London, UK
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Isabelle Bos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Stephanie J.B. Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Mara ten Kate
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Philip Scheltens
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Silvy Gabel
- University Hospital Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Belgium
| | - Karen Meersmans
- University Hospital Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Belgium
| | - Sebastiaan Engelborghs
- Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology, UZ Brussel, Brussels, Belgium
| | - Ellen E. De Roeck
- Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Belgium
| | - Giovanni B. Frisoni
- University of Geneva, Geneva, Switzerland
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Olivier Blin
- AIX Marseille University, INS, Ap-hm, Marseille, France
| | | | | | - José L. Molinuevo
- Alzheimer’s disease & other cognitive disorders unit, Hospital Clínic, Barcelona, Spain
- BarcelonaBeta Brain Research Center, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lorena Rami
- BarcelonaBeta Brain Research Center, Universitat Pompeu Fabra, Barcelona, Spain
| | - Anders Wallin
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Memory Clinic at Department of Neuropsychiatry, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Petronella Kettunen
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, school of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Makedonia, Greece
| | - Frans Verhey
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Alberto Lleó
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Daniel Alcolea
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Julius Popp
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
- Geriatric Psychiatry, Department of Psychiatry, Geneva University Hospitals, and University of Geneva, Geneva, Switzerland
| | - Gwendoline Peyratout
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | | | - Mikel Tainta
- CITA-Alzheimer Foundation, San Sebastian, Spain
- Organización Sanitaria Integrada Goierri – Alto Urola, Osakidetza, Spain
| | - Peter Johannsen
- Danish Dementia Research Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory, dept of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, the Netherlands
| | - Yvonne Freund-Levi
- School of Medical Sciences, Örebro University, Örebro, Sweden
- Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, Karolinska Institute, Stockholm, Sweden
- Department of Old Age Psychiatry, Psychology and Neuroscience, King’s College London, UK
- Department of Psychiatry, Örebro Universitetssjukhus, Örebro, Sweden
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Zentralinstitut für Seelische Gesundheit, University of Heidelberg, Mannheim, Germany
| | - Cristina Legido-Quigley
- Kings College London, London, UK
- The Systems Medicine Group, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherland
- UCL Institutes of Neurology and Healthcare Engineering, London, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Katrine Laura Rasmussen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Børge Grønne Nordestgaard
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, Frederiksberg, Denmark
| | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sune Fallgaard Nielsen
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Hilkka Soininen
- Neurology / Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Bruno Vellas
- Toulouse Gerontopole University Hospital, Univeriste Paul Sabatier, INSERM U 558, France
| | | | - Patrizia Mecocci
- Section of Gerontology and Geriatrics, Department of Medicine, University of Perugia, Perugia, Italy
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- UK Dementia Research Institute at UCL, London, United Kingdom
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
| | - B. Paul Morgan
- Dementia Research Institute Cardiff, Cardiff University, Cardiff, UK
| | - Johannes Streffer
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- UCB, Braine-l’Alleud, Belgium, formerly Janssen R&D, LLC. Beerse, Belgium at the time of study conduct
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
- Department of Psychology, University of Oslo, Oslo, Norway
| | | | - Simon Lovestone
- Department of Psychiatry, University of Oxford, UK
- Currently at Janssen-Cilag UK, formerly at Department of Psychiatry, University of Oxford, UK at the time of the study conduct
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23
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Ebbert MTW, Jensen TD, Jansen-West K, Sens JP, Reddy JS, Ridge PG, Kauwe JSK, Belzil V, Pregent L, Carrasquillo MM, Keene D, Larson E, Crane P, Asmann YW, Ertekin-Taner N, Younkin SG, Ross OA, Rademakers R, Petrucelli L, Fryer JD. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. Genome Biol 2019; 20:97. [PMID: 31104630 PMCID: PMC6526621 DOI: 10.1186/s13059-019-1707-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/06/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads that we call dark by depth, and others that have ambiguous alignment, called camouflaged. We assess how well long-read or linked-read technologies resolve these regions. RESULTS Based on standard whole-genome Illumina sequencing data, we identify 36,794 dark regions in 6054 gene bodies from pathways important to human health, development, and reproduction. Of these gene bodies, 8.7% are completely dark and 35.2% are ≥ 5% dark. We identify dark regions that are present in protein-coding exons across 748 genes. Linked-read or long-read sequencing technologies from 10x Genomics, PacBio, and Oxford Nanopore Technologies reduce dark protein-coding regions to approximately 50.5%, 35.6%, and 9.6%, respectively. We present an algorithm to resolve most camouflaged regions and apply it to the Alzheimer's Disease Sequencing Project. We rescue a rare ten-nucleotide frameshift deletion in CR1, a top Alzheimer's disease gene, found in disease cases but not in controls. CONCLUSIONS While we could not formally assess the association of the CR1 frameshift mutation with Alzheimer's disease due to insufficient sample-size, we believe it merits investigating in a larger cohort. There remain thousands of potentially important genomic regions overlooked by short-read sequencing that are largely resolved by long-read technologies.
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Affiliation(s)
- Mark T. W. Ebbert
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
| | - Tanner D. Jensen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Jonathon P. Sens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Joseph S. Reddy
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602 USA
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602 USA
| | - Veronique Belzil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Luc Pregent
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA 98195 USA
| | - Eric Larson
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Paul Crane
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Yan W. Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
| | - John D. Fryer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
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24
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Inherited and Acquired Decrease in Complement Receptor 1 (CR1) Density on Red Blood Cells Associated with High Levels of Soluble CR1 in Alzheimer's Disease. Int J Mol Sci 2018; 19:ijms19082175. [PMID: 30044434 PMCID: PMC6121509 DOI: 10.3390/ijms19082175] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/22/2018] [Accepted: 07/23/2018] [Indexed: 12/13/2022] Open
Abstract
The complement receptor 1 (CR1) gene was shown to be involved in Alzheimer's disease (AD). We previously showed that AD is associated with low density of the long CR1 isoform, CR1*2 (S). Here, we correlated phenotype data (CR1 density per erythrocyte (CR1/E), blood soluble CR1 (sCR1)) with genetic data (density/length polymorphisms) in AD patients and healthy controls. CR1/E was enumerated using flow cytometry, while sCR1 was quantified by ELISA. CR1 polymorphisms were assessed using restriction fragment length polymorphism (RFLP), pyrosequencing, and high-resolution melting PCR. In AD patients carrying the H allele (HindIII polymorphism) or the Q allele (Q981H polymorphism), CR1/E was significantly lower when compared with controls carrying the same alleles (p < 0.01), contrary to sCR1, which was significantly higher (p < 0.001). Using multivariate analysis, a reduction of 6.68 units in density was associated with an increase of 1% in methylation of CR1 (estimate -6.68; 95% confidence intervals (CIs) -12.37, -0.99; p = 0.02). Our data show that, in addition to inherited genetic factors, low density of CR1/E is also acquired. The involvement of CR1 in the pathogenesis of AD might be linked to insufficient clearance of amyloid deposits. These findings may open perspectives for new therapeutic strategies in AD.
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