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Garavito-De Egea G, Domínguez-Vargas A, Vélez JI, Aroca G, Fang L, Navarro-Quiroz E, Espitaleta Z, Del Toro-Camargo K, Martínez-Ariza L, González-Vargas T, García S, Arcos-Burgos M, Egea E. Common interacting genetic variation shapes susceptibility to type 1 diabetes in a Colombian Caribbean community: In search of shared genetic markers. Genes Dis 2024; 11:101058. [PMID: 38510475 PMCID: PMC10951448 DOI: 10.1016/j.gendis.2023.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/27/2023] [Indexed: 03/22/2024] Open
Affiliation(s)
- Gloria Garavito-De Egea
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
| | | | - Jorge I. Vélez
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
| | - Gustavo Aroca
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
- Clínica de la Costa, Grupo de Investigación en Nefrología, Barranquilla, Colombia
| | - Luis Fang
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
| | - Elkin Navarro-Quiroz
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
| | - Zilac Espitaleta
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
- Clínica de la Costa, Grupo de Investigación en Nefrología, Barranquilla, Colombia
| | | | | | | | - Susana García
- Clínica de la Costa, Grupo de Investigación en Nefrología, Barranquilla, Colombia
| | - Mauricio Arcos-Burgos
- Universidad de Antioquia, Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Medellín, Colombia
| | - Eduardo Egea
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
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2
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Cochran JN, Acosta-Uribe J, Esposito BT, Madrigal L, Aguillón D, Giraldo MM, Taylor JW, Bradley J, Fulton-Howard B, Andrews SJ, Acosta-Baena N, Alzate D, Garcia GP, Piedrahita F, Lopez HE, Anderson AG, Rodriguez-Nunez I, Roberts K, Dominantly Inherited Alzheimer Network, Absher D, Myers RM, Beecham GW, Reitz C, Rizzardi LF, Fernandez MV, Goate AM, Cruchaga C, Renton AE, Lopera F, Kosik KS. Genetic associations with age at dementia onset in the PSEN1 E280A Colombian kindred. Alzheimers Dement 2023; 19:3835-3847. [PMID: 36951251 PMCID: PMC10514237 DOI: 10.1002/alz.13021] [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: 10/31/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 03/24/2023]
Abstract
INTRODUCTION Genetic associations with Alzheimer's disease (AD) age at onset (AAO) could reveal genetic variants with therapeutic applications. We present a large Colombian kindred with autosomal dominant AD (ADAD) as a unique opportunity to discover AAO genetic associations. METHODS A genetic association study was conducted to examine ADAD AAO in 340 individuals with the PSEN1 E280A mutation via TOPMed array imputation. Replication was assessed in two ADAD cohorts, one sporadic early-onset AD study and four late-onset AD studies. RESULTS 13 variants had p<1×10-7 or p<1×10-5 with replication including three independent loci with candidate associations with clusterin including near CLU. Other suggestive associations were identified in or near HS3ST1, HSPG2, ACE, LRP1B, TSPAN10, and TSPAN14. DISCUSSION Variants with suggestive associations with AAO were associated with biological processes including clusterin, heparin sulfate, and amyloid processing. The detection of these effects in the presence of a strong mutation for ADAD reinforces their potentially impactful role.
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Affiliation(s)
| | - Juliana Acosta-Uribe
- Neuroscience Research Institute, University of California, Santa Barbara, California, and Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, California, USA
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Bianca T Esposito
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lucia Madrigal
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - David Aguillón
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Margarita M Giraldo
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Jared W Taylor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Joseph Bradley
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Brian Fulton-Howard
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shea J Andrews
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Natalia Acosta-Baena
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Diana Alzate
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Gloria P Garcia
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Francisco Piedrahita
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Hugo E Lopez
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | | | | | - Kevin Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Gary W Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Christiane Reitz
- Department of Epidemiology, Sergievsky Center, Taub Institute for Research on the Aging Brain, Columbia University, New York, New York, USA
| | | | | | - Alison M Goate
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cruchaga
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alan E Renton
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Kenneth S Kosik
- Neuroscience Research Institute, University of California, Santa Barbara, California, and Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, California, USA
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Kelly L, Sharp MM, Thomas I, Brown C, Schrag M, Antunes LV, Solopova E, Martinez-Gonzalez J, Rodríguez C, Carare RO. Targeting lysyl-oxidase (LOX) may facilitate intramural periarterial drainage for the treatment of Alzheimer's disease. CEREBRAL CIRCULATION - COGNITION AND BEHAVIOR 2023; 5:100171. [PMID: 37457664 PMCID: PMC10338210 DOI: 10.1016/j.cccb.2023.100171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Alzheimer's disease is the commonest form of dementia. It is likely that a lack of clearance of amyloid beta (Aβ) results in its accumulation in the parenchyma as Aβ oligomers and insoluble plaques, and within the walls of blood vessels as cerebral amyloid angiopathy (CAA). The drainage of Aβ along the basement membranes of blood vessels as intramural periarterial drainage (IPAD), could be improved if the driving force behind IPAD could be augmented, therefore reducing Aβ accumulation. There are alterations in the composition of the vascular basement membrane in Alzheimer's disease. Lysyl oxidase (LOX) is an enzyme involved in the remodelling of the extracellular matrix and its expression and function is altered in various disease states. The expression of LOX is increased in Alzheimer's disease, but it is unclear whether this is a contributory factor in the impairment of IPAD in Alzheimer's disease. The pharmacological inhibition of LOX may be a strategy to improve IPAD and reduce the accumulation of Aβ in the parenchyma and within the walls of blood vessels.
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Affiliation(s)
- Louise Kelly
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom, UK
| | | | | | - Christopher Brown
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom, UK
| | - Matthew Schrag
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee, USA
| | - Lissa Ventura Antunes
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee, USA
| | - Elena Solopova
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee, USA
| | - José Martinez-Gonzalez
- Instituto de Investigaciones Biomédicas de Barcelona (IIBB-CSIC), Barcelona, Spain
- CIBER de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Cristina Rodríguez
- CIBER de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
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4
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Kodam P, Sai Swaroop R, Pradhan SS, Sivaramakrishnan V, Vadrevu R. Integrated multi-omics analysis of Alzheimer's disease shows molecular signatures associated with disease progression and potential therapeutic targets. Sci Rep 2023; 13:3695. [PMID: 36879094 PMCID: PMC9986671 DOI: 10.1038/s41598-023-30892-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by the formation of amyloid plaques implicated in neuronal death. Genetics, age, and sex are the risk factors attributed to AD. Though omics studies have helped to identify pathways associated with AD, an integrated systems analysis with the available data could help to understand mechanisms, potential biomarkers, and therapeutic targets. Analysis of transcriptomic data sets from the GEO database, and proteomic and metabolomic data sets from literature was performed to identify deregulated pathways and commonality analysis identified overlapping pathways among the data sets. The deregulated pathways included those of neurotransmitter synapses, oxidative stress, inflammation, vitamins, complement, and coagulation pathways. Cell type analysis of GEO data sets showed microglia, endothelial, myeloid, and lymphoid cells are affected. Microglia are associated with inflammation and pruning of synapses with implications for memory and cognition. Analysis of the protein-cofactor network of B2, B6, and pantothenate shows metabolic pathways modulated by these vitamins which overlap with the deregulated pathways from the multi-omics analysis. Overall, the integrated analysis identified the molecular signature associated with AD. Treatment with anti-oxidants, B2, B6, and pantothenate in genetically susceptible individuals in the pre-symptomatic stage might help in better management of the disease.
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Affiliation(s)
- Pradeep Kodam
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad, Telangana, 500078, India
| | - R Sai Swaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India.
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad, Telangana, 500078, India.
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Kurkinen M, Fułek M, Fułek K, Beszłej JA, Kurpas D, Leszek J. The Amyloid Cascade Hypothesis in Alzheimer’s Disease: Should We Change Our Thinking? Biomolecules 2023; 13:biom13030453. [PMID: 36979388 PMCID: PMC10046826 DOI: 10.3390/biom13030453] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 03/05/2023] Open
Abstract
Old age increases the risk of Alzheimer’s disease (AD), the most common neurodegenerative disease, a devastating disorder of the human mind and the leading cause of dementia. Worldwide, 50 million people have the disease, and it is estimated that there will be 150 million by 2050. Today, healthcare for AD patients consumes 1% of the global economy. According to the amyloid cascade hypothesis, AD begins in the brain by accumulating and aggregating Aβ peptides and forming β-amyloid fibrils (Aβ42). However, in clinical trials, reducing Aβ peptide production and amyloid formation in the brain did not slow cognitive decline or improve daily life in AD patients. Prevention studies in cognitively unimpaired people at high risk or genetically destined to develop AD also have not slowed cognitive decline. These observations argue against the amyloid hypothesis of AD etiology, its development, and disease mechanisms. Here, we look at other avenues in the research of AD, such as the presenilin hypothesis, synaptic glutamate signaling, and the role of astrocytes and the glutamate transporter EAAT2 in the development of AD.
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Affiliation(s)
| | - Michał Fułek
- Department and Clinic of Internal Medicine, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, 50-556 Wroclaw, Poland
| | - Katarzyna Fułek
- Department and Clinic of Otolaryngology, Head and Neck Surgery, Wroclaw Medical University, 50-556 Wroclaw, Poland
- Correspondence: (K.F.); (J.L.)
| | | | - Donata Kurpas
- Department of Family Medicine, Wroclaw Medical University, 51-141 Wroclaw, Poland
| | - Jerzy Leszek
- Department and Clinic of Psychiatry, Wroclaw Medical University, 50-367 Wroclaw, Poland
- Correspondence: (K.F.); (J.L.)
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Genetics, Functions, and Clinical Impact of Presenilin-1 (PSEN1) Gene. Int J Mol Sci 2022; 23:ijms231810970. [PMID: 36142879 PMCID: PMC9504248 DOI: 10.3390/ijms231810970] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 12/29/2022] Open
Abstract
Presenilin-1 (PSEN1) has been verified as an important causative factor for early onset Alzheimer's disease (EOAD). PSEN1 is a part of γ-secretase, and in addition to amyloid precursor protein (APP) cleavage, it can also affect other processes, such as Notch signaling, β-cadherin processing, and calcium metabolism. Several motifs and residues have been identified in PSEN1, which may play a significant role in γ-secretase mechanisms, such as the WNF, GxGD, and PALP motifs. More than 300 mutations have been described in PSEN1; however, the clinical phenotypes related to these mutations may be diverse. In addition to classical EOAD, patients with PSEN1 mutations regularly present with atypical phenotypic symptoms, such as spasticity, seizures, and visual impairment. In vivo and in vitro studies were performed to verify the effect of PSEN1 mutations on EOAD. The pathogenic nature of PSEN1 mutations can be categorized according to the ACMG-AMP guidelines; however, some mutations could not be categorized because they were detected only in a single case, and their presence could not be confirmed in family members. Genetic modifiers, therefore, may play a critical role in the age of disease onset and clinical phenotypes of PSEN1 mutations. This review introduces the role of PSEN1 in γ-secretase, the clinical phenotypes related to its mutations, and possible significant residues of the protein.
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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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