1
|
Hudgins AD, Zhou S, Arey RN, Rosenfeld MG, Murphy CT, Suh Y. A systems biology-based identification and in vivo functional screening of Alzheimer's disease risk genes reveal modulators of memory function. Neuron 2024; 112:2112-2129.e4. [PMID: 38692279 PMCID: PMC11223975 DOI: 10.1016/j.neuron.2024.04.009] [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: 07/16/2022] [Revised: 10/18/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
Genome-wide association studies (GWASs) have uncovered over 75 genomic loci associated with risk for late-onset Alzheimer's disease (LOAD), but identification of the underlying causal genes remains challenging. Studies of induced pluripotent stem cell (iPSC)-derived neurons from LOAD patients have demonstrated the existence of neuronal cell-intrinsic functional defects. Here, we searched for genetic contributions to neuronal dysfunction in LOAD using an integrative systems approach that incorporated multi-evidence-based gene mapping and network-analysis-based prioritization. A systematic perturbation screening of candidate risk genes in Caenorhabditis elegans (C. elegans) revealed that neuronal knockdown of the LOAD risk gene orthologs vha-10 (ATP6V1G2), cmd-1 (CALM3), amph-1 (BIN1), ephx-1 (NGEF), and pho-5 (ACP2) alters short-/intermediate-term memory function, the cognitive domain affected earliest during LOAD progression. These results highlight the impact of LOAD risk genes on evolutionarily conserved memory function, as mediated through neuronal endosomal dysfunction, and identify new targets for further mechanistic interrogation.
Collapse
Affiliation(s)
- Adam D Hudgins
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shiyi Zhou
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Rachel N Arey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael G Rosenfeld
- Department of Medicine, School of Medicine, University of California, La Jolla, CA, USA; Howard Hughes Medical Institute, University of California, La Jolla, CA, USA
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; LSI Genomics, Princeton University, Princeton, NJ, USA.
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
2
|
Nicolas G. Lessons from genetic studies in Alzheimer disease. Rev Neurol (Paris) 2024; 180:368-377. [PMID: 38429159 DOI: 10.1016/j.neurol.2023.12.006] [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: 11/22/2023] [Accepted: 12/27/2023] [Indexed: 03/03/2024]
Abstract
Research on Alzheimer disease (AD) genetics has provided critical advances to the knowledge of AD pathophysiological mechanisms. The etiology of AD can be divided into monogenic (autosomal dominant inheritance) and complex (multifactorial determinism). In monogenic AD, recent advances mainly concern mutation-associated mechanisms, presymptomatic clinical studies, and the search for modifiers of ages of onset that are still ongoing. In complex AD, genetic factors can be further categorized into three classes: (i) the APOE-ɛ4 and ɛ2 common alleles that represent a category by themselves as they are both common and with a strong impact on AD risk; (ii) common variants with a modest effect, identified in genome-wide association studies (GWAS); and (iii) rare variants with a moderate-to-strong effect, identified in case-control sequencing studies. Regarding APOE, odds ratios, available in multiple ethnicities, can now be converted into penetrance curves, although such curves remain to be performed in diverse ethnicities. In addition, advances in the understanding of mechanisms have been recently reported and rare APOE variants add to the complexity. In the GWAS category, novel loci have been discovered thanks to larger studies, doubling the number of hits as compared to the previous reference meta-analysis. However, such modest risk factors cannot be used in the clinic, neither individually, nor in genetic risk scores. In the category of rare variants, two novel genes, ABCA1 and ATP8B4 now add to the three main ones, TREM2, SORL1, and ABCA7. The study of such rare variants suggests oligogenic inheritance in some families, as also suggested by digenic penetrance curves for SORL1 loss-of-function variants with APOE-ɛ4. Cumulate frequencies of definite (so-called) rare risk factors are 2.3% to 3.6% (depending on thresholds on odds ratios) in control databases and many more remain to be classified and identified, showing how important these risk factors may be as part of the complex determinism of AD. A better understanding of these rare risk factors and their combined effects on each other, with common variants, and with environmental factors, should allow for a prediction of AD risk and, eventually, preventive medicine. Taken together, most genetic determinants of AD, in monogenic and in complex forms, point toward the aggregation of Aβ as a pivotal triggering factor, such that targeting it may be efficient as prevention in at-risk individuals. The role of neuroinflammation, microglia, and Tau pathology modulation are important sources of research for disease modification.
Collapse
Affiliation(s)
- G Nicolas
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Genetics and CNRMAJ, 76000 Rouen, France.
| |
Collapse
|
3
|
Nicolas G, Zaréa A, Lacour M, Quenez O, Rousseau S, Richard AC, Bonnevalle A, Schramm C, Olaso R, Sandron F, Boland A, Deleuze JF, Andriuta D, Anthony P, Auriacombe S, Balageas AC, Ballan G, Barbay M, Béjot Y, Belliard S, Benaiteau M, Bennys K, Bombois S, Boutoleau-Bretonnière C, Branger P, Carlier J, Cartz-Piver L, Cassagnaud P, Ceccaldi MP, Chauviré V, Chen Y, Cogez J, Cognat E, Contegal-Callier F, Corneille L, Couratier P, Cretin B, Crinquette C, Dauriat B, Dautricourt S, de la Sayette V, de Liège A, Deffond D, Demurger F, Deramecourt V, Derollez C, Dionet E, Doco Fenzy M, Dumurgier J, Dutray A, Etcharry-Bouyx F, Formaglio M, Gabelle A, Gainche-Salmon A, Godefroy O, Graber M, Gregoire C, Grimaldi S, Gueniat J, Gueriot C, Guillet-Pichon V, Haffen S, Hanta CR, Hardy C, Hautecloque G, Heitz C, Hourregue C, Jonveaux T, Jurici S, Koric L, Krolak-Salmon P, Lagarde J, Lanoiselée HM, Laurens B, Le Ber I, Le Guyader G, Leblanc A, Lebouvier T, Levy R, Lippi A, Mackowiak MA, Magnin E, Marelli C, Martinaud O, Maureille A, Migliaccio R, Milongo-Rigal E, Mohr S, Mollion H, Morin A, Nivelle J, Noiray C, Olivieri P, Paquet C, Pariente J, Pasquier F, Perron A, Philippi N, Planche V, Pouclet-Courtemanche H, Rafiq M, Rollin-Sillaire A, Roué-Jagot C, Saracino D, Sarazin M, Sauvée M, Sellal F, Teichmann M, Thauvin C, Thomas Q, Tisserand C, Turpinat C, Van Damme L, Vercruysse O, Villain N, Wagemann N, Charbonnier C, Wallon D. Assessment of Mendelian and risk-factor genes in Alzheimer disease: A prospective nationwide clinical utility study and recommendations for genetic screening. Genet Med 2024; 26:101082. [PMID: 38281098 DOI: 10.1016/j.gim.2024.101082] [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: 07/11/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/29/2024] Open
Abstract
PURPOSE To assess the likely pathogenic/pathogenic (LP/P) variants rates in Mendelian dementia genes and the moderate-to-strong risk factors rates in patients with Alzheimer disease (AD). METHODS We included 700 patients in a prospective study and performed exome sequencing. A panel of 28 Mendelian and 6 risk-factor genes was interpreted and returned to patients. We built a framework for risk variant interpretation and risk gradation and assessed the detection rates among early-onset AD (EOAD, age of onset (AOO) ≤65 years, n = 608) depending on AOO and pedigree structure and late-onset AD (66 < AOO < 75, n = 92). RESULTS Twenty-one patients carried a LP/P variant in a Mendelian gene (all with EOAD, 3.4%), 20 of 21 affected APP, PSEN1, or PSEN2. LP/P variant detection rates in EOAD ranged from 1.7% to 11.6% based on AOO and pedigree structure. Risk factors were found in 69.5% of the remaining 679 patients, including 83 (12.2%) being heterozygotes for rare risk variants, in decreasing order of frequency, in TREM2, ABCA7, ATP8B4, SORL1, and ABCA1, including 5 heterozygotes for multiple rare risk variants, suggesting non-monogenic inheritance, even in some autosomal-dominant-like pedigrees. CONCLUSION We suggest that genetic screening should be proposed to all EOAD patients and should no longer be prioritized based on pedigree structure.
Collapse
Affiliation(s)
- Gaël Nicolas
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Genetics and CNRMAJ, F-76000 Rouen, France.
| | - Aline Zaréa
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Neurology and CNRMAJ, F-76000 Rouen, France
| | - Morgane Lacour
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Neurology and CNRMAJ, F-76000 Rouen, France
| | - Olivier Quenez
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Genetics and CNRMAJ, F-76000 Rouen, France
| | - Stéphane Rousseau
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Genetics and CNRMAJ, F-76000 Rouen, France
| | - Anne-Claire Richard
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Genetics and CNRMAJ, F-76000 Rouen, France
| | - Antoine Bonnevalle
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Genetics and CNRMAJ, F-76000 Rouen, France; Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Neurology and CNRMAJ, F-76000 Rouen, France
| | - Catherine Schramm
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Genetics and CNRMAJ, F-76000 Rouen, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Florian Sandron
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Daniela Andriuta
- Service de Neurologie CHU Amiens et Laboratoire de Neurosciences Fonctionnelles et Pathologies, Université de Picardie Jules Verne, Amiens, France
| | - Pierre Anthony
- Department of Neurology, Hôpitaux Civils de Colmar, F-68000 Colmar, France
| | - Sophie Auriacombe
- Univ. Bordeaux, CNRS UMR 5293, Institut des Maladies Neurodégénératives, Bordeaux, France
| | | | | | - Mélanie Barbay
- Service de Neurologie CHU Amiens et Laboratoire de Neurosciences Fonctionnelles et Pathologies, Université de Picardie Jules Verne, Amiens, France
| | - Yannick Béjot
- Department of Neurology, University Hospital of Dijon, University of Burgundy, Dijon, France
| | - Serge Belliard
- Unité de recherche 1077 INSERM-EPHE-UNICAEN Neuropsychologie & Imagerie de la Mémoire Humaine (NIMH), Caen, France; Centre Mémoire Ressources et Recherche Haute Bretagne, CHU Rennes, Rennes, France
| | - Marie Benaiteau
- Neurology Department, Hôpital Pierre-Paul Riquet, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Karim Bennys
- Memory Ressources Research Center, Department of Neurology, University Hospital of Montpellier, Montpellier, France
| | - Stéphanie Bombois
- Sorbonne Université, INSERM U1127, CNRS 7235, Institut du Cerveau - ICM, Paris, France; AP-HP Sorbonne Université, Pitié-Salpêtrière Hospital, Department of Neurology, Institute of Memory and Alzheimer's Disease, Paris, France
| | | | - Pierre Branger
- Department of Neurology, Caen University Hospital, Caen, France
| | - Jasmine Carlier
- Neurology Department, Hôpital Pierre-Paul Riquet, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Leslie Cartz-Piver
- Memory Ressources Research Center, Department of Neurology, University Hospital of Limoges, France Inserm U1094, IRD U270, EPIMACT, Université of Limoges, Limoges, France
| | | | - Mathieu-Pierre Ceccaldi
- Institute of Neurophysiopathology UMR 7051 Aix Marseille Université & Assistance Publique de Marseille, Marseille, France
| | - Valérie Chauviré
- CMRR, CRMR Neurogénétique, Service de Neurologie, CHU d'ANGERS, Angers, France
| | - Yaohua Chen
- Univ Lille, CHU Lille, Inserm 1172, Memory center, CNRMAJ, LiCEND, Labex DistAlz 59000 Lille, France
| | - Julien Cogez
- Department of Neurology, Caen University Hospital, Caen, France
| | - Emmanuel Cognat
- Cognitive Neurology Center, AP-HP.Nord, Site Lariboisière Fernand-Widal, Paris, France; Université Paris Cité, UMR-S 1144, INSERM, Paris, France
| | | | - Léa Corneille
- Institute of Neurophysiopathology UMR 7051 Aix Marseille Université & Assistance Publique de Marseille, Marseille, France
| | | | - Benjamin Cretin
- CMRR d'Alsace, Service de Neurologie, CHU Strasbourg, Strasbourg, France
| | | | - Benjamin Dauriat
- Service de Génétique Médicale, Hopital Mère-Enfant, CHU Limoges, Limoges, France
| | - Sophie Dautricourt
- CMRR Lyon, Department of Neurology, University Hospital of Lyon, Hospices Civils de Lyon, Lyon, France
| | - Vincent de la Sayette
- Department of Neurology, Caen University Hospital, Caen, France; Normandie UNIV, UNICAEN, PSL Research University, EPHE, INSERM, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Caen, France
| | - Astrid de Liège
- Service de Neurologie, APHP, Hôpital Avicenne, Université Sorbonne Paris Nord, Bobigny, France
| | - Didier Deffond
- CMRR Clermont-Ferrand, Service de Neurologie, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Vincent Deramecourt
- Univ Lille, CHU Lille, Inserm 1172, Memory center, CNRMAJ, LiCEND, Labex DistAlz 59000 Lille, France
| | | | - Elsa Dionet
- CMRR Clermont-Ferrand, Service de Neurologie, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Martine Doco Fenzy
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France; CHU Nantes, Service de Génétique, Nantes, France; CHU Reims, Service de Génétique, Reims, France
| | - Julien Dumurgier
- Cognitive Neurology Center, AP-HP.Nord, Site Lariboisière Fernand-Widal, Paris, France; Université Paris Cité, UMR-S 1144, INSERM, Paris, France
| | - Anaïs Dutray
- Service de Neurologie, Centre Hospitalier Perpignan, Perpignan, France
| | | | - Maïté Formaglio
- CMRR Lyon, Department of Neurology, University Hospital of Lyon, Hospices Civils de Lyon, Lyon, France
| | - Audrey Gabelle
- Memory Ressources Research Center, Department of Neurology, University Hospital of Montpellier, Montpellier, France
| | - Anne Gainche-Salmon
- Centre Mémoire Ressources et Recherche Haute Bretagne, CHU Rennes, Rennes, France
| | - Olivier Godefroy
- Service de Neurologie CHU Amiens et Laboratoire de Neurosciences Fonctionnelles et Pathologies, Université de Picardie Jules Verne, Amiens, France
| | - Mathilde Graber
- Centre mémoire ressources et recherche, CHU Dijon, Dijon, France
| | - Chloé Gregoire
- CHU de Bordeaux, Pôle de Neurosciences Cliniques, Centre Mémoire de Ressources et de Recherche, Bordeaux, France
| | - Stephan Grimaldi
- Institute of Neurophysiopathology UMR 7051 Aix Marseille Université & Assistance Publique de Marseille, Marseille, France
| | - Julien Gueniat
- Centre mémoire ressources et recherche, CHU Dijon, Dijon, France
| | - Claude Gueriot
- Institute of Neurophysiopathology UMR 7051 Aix Marseille Université & Assistance Publique de Marseille, Marseille, France
| | | | - Sophie Haffen
- Centre mémoire Recherche Ressources, Service de Neurologie, CHU Besançon, Besançon, France
| | - Cezara-Roxana Hanta
- Centre Mémoire Ressources et Recherche Haute Bretagne, CHU Rennes, Rennes, France
| | - Clémence Hardy
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Neurology and CNRMAJ, F-76000 Rouen, France
| | | | - Camille Heitz
- Institut du cerveau Trocadero, Paris, France; Neurology Department, Hôpital Universitaire de Nîmes, Nîmes, France
| | - Claire Hourregue
- Cognitive Neurology Center, AP-HP.Nord, Site Lariboisière Fernand-Widal, Paris, France
| | - Thérèse Jonveaux
- Centre Mémoire de Ressources et de Recherche de Lorraine Service de Neurologie CHRU Nancy, Nancy, France; Laboratoire 2LPN EA 7489 Université de Lorraine, Nancy, France
| | - Snejana Jurici
- Consultation Mémoire, Service de Gériatrie, Centre Hospitalier Perpignan, Perpignan, France
| | - Lejla Koric
- Institute of Neurophysiopathology UMR 7051 Aix Marseille Université & Assistance Publique de Marseille, Marseille, France; Aix-Marseille Univ, UMR 7249, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Pierre Krolak-Salmon
- CMRR Lyon, Department of Neurology, University Hospital of Lyon, Hospices Civils de Lyon, Lyon, France
| | - Julien Lagarde
- Department of Neurology of Memory and Language, GHU Paris Psychiatrie & Neurosciences, Hôpital Sainte Anne, F-75014, Paris, France; Université Paris-Cité, F-75006 Paris, France; Université Paris-Saclay, BioMaps, Service Hospitalier Frédéric Joliot CEA, CNRS, Inserm, F-91401, Orsay, France
| | | | - Brice Laurens
- CHU de Bordeaux, Pôle de Neurosciences Cliniques, Centre Mémoire de Ressources et de Recherche, Bordeaux, France
| | - Isabelle Le Ber
- Sorbonne Université, INSERM U1127, CNRS 7235, Institut du Cerveau - ICM, Paris, France; AP-HP Sorbonne Université, Pitié-Salpêtrière Hospital, Department of Neurology, Institute of Memory and Alzheimer's Disease, Paris, France
| | | | - Amélie Leblanc
- Consultations neurologiques, HIA Clermont-Tonnerre, Brest, France; Service de neurologie, CHU Cavale-Blanche, Brest, France
| | - Thibaud Lebouvier
- Univ Lille, CHU Lille, Inserm 1172, Memory center, CNRMAJ, LiCEND, Labex DistAlz 59000 Lille, France
| | - Richard Levy
- Sorbonne Université, INSERM U1127, CNRS 7235, Institut du Cerveau - ICM, Paris, France; AP-HP Sorbonne Université, Pitié-Salpêtrière Hospital, Department of Neurology, Institute of Memory and Alzheimer's Disease, Paris, France
| | - Anaïs Lippi
- Service de Neurologie, Hopital Gui de Chauliac, CHU de Montpellier, Montpellier, France
| | | | - Eloi Magnin
- Laboratoire de neuroscience, Université de Franche-Comté UFC et Service de Neurologie, CMRR, CHU Besançon, Besançon, France
| | - Cecilia Marelli
- Service de Neurologie, Hopital Gui de Chauliac, CHU de Montpellier, Montpellier, France
| | - Olivier Martinaud
- Department of Neurology, Caen University Hospital, Caen, France; Normandie UNIV, UNICAEN, PSL Research University, EPHE, INSERM, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Caen, France
| | | | - Raffaella Migliaccio
- Sorbonne Université, INSERM U1127, CNRS 7235, Institut du Cerveau - ICM, Paris, France; AP-HP Sorbonne Université, Pitié-Salpêtrière Hospital, Department of Neurology, Institute of Memory and Alzheimer's Disease, Paris, France
| | - Emilie Milongo-Rigal
- Neurology Department, Hôpital Pierre-Paul Riquet, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Sophie Mohr
- Centre mémoire ressources et recherche, CHU Dijon, Dijon, France
| | - Hélène Mollion
- CMRR Lyon, Department of Neurology, University Hospital of Lyon, Hospices Civils de Lyon, Lyon, France
| | - Alexandre Morin
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Neurology and CNRMAJ, F-76000 Rouen, France; Département de Psychiatrie, Centre Hospitalier du Rouvray, Université de Rouen, 76000, Sotteville-lès-Rouen, France
| | | | - Camille Noiray
- Department of Neurology of Memory and Language, GHU Paris Psychiatrie & Neurosciences, Hôpital Sainte Anne, F-75014, Paris, France; Université Paris-Cité, F-75006 Paris, France; Université Paris-Saclay, BioMaps, Service Hospitalier Frédéric Joliot CEA, CNRS, Inserm, F-91401, Orsay, France
| | - Pauline Olivieri
- Department of Neurology of Memory and Language, GHU Paris Psychiatrie & Neurosciences, Hôpital Sainte Anne, F-75014, Paris, France; Université Paris-Cité, F-75006 Paris, France; Université Paris-Saclay, BioMaps, Service Hospitalier Frédéric Joliot CEA, CNRS, Inserm, F-91401, Orsay, France
| | - Claire Paquet
- Cognitive Neurology Center, AP-HP.Nord, Site Lariboisière Fernand-Widal, Paris, France; Université Paris Cité, UMR-S 1144, INSERM, Paris, France
| | - Jérémie Pariente
- Neurology Department, Hôpital Pierre-Paul Riquet, Centre Hospitalier Universitaire de Toulouse, Toulouse, France; Toulouse NeuroImaging Center (ToNIC), INSERM-University of Toulouse Paul Sabatier, Toulouse, France
| | - Florence Pasquier
- Univ Lille, CHU Lille, Inserm 1172, Memory center, CNRMAJ, LiCEND, Labex DistAlz 59000 Lille, France
| | - Alexandre Perron
- Department of Neurology, Hôpitaux Civils de Colmar, F-68000 Colmar, France
| | - Nathalie Philippi
- CMRR d'Alsace, Service de Neurologie, CHU Strasbourg, Strasbourg, France
| | - Vincent Planche
- Univ. Bordeaux, CNRS UMR 5293, Institut des Maladies Neurodégénératives, Bordeaux, France; CHU de Bordeaux, Pôle de Neurosciences Cliniques, Centre Mémoire de Ressources et de Recherche, Bordeaux, France
| | | | - Marie Rafiq
- Neurology Department, Hôpital Pierre-Paul Riquet, Centre Hospitalier Universitaire de Toulouse, Toulouse, France; Toulouse NeuroImaging Center (ToNIC), INSERM-University of Toulouse Paul Sabatier, Toulouse, France
| | | | - Carole Roué-Jagot
- Department of Neurology of Memory and Language, GHU Paris Psychiatrie & Neurosciences, Hôpital Sainte Anne, F-75014, Paris, France; Université Paris-Cité, F-75006 Paris, France; Université Paris-Saclay, BioMaps, Service Hospitalier Frédéric Joliot CEA, CNRS, Inserm, F-91401, Orsay, France
| | - Dario Saracino
- Sorbonne Université, INSERM U1127, CNRS 7235, Institut du Cerveau - ICM, Paris, France; AP-HP Sorbonne Université, Pitié-Salpêtrière Hospital, Department of Neurology, Institute of Memory and Alzheimer's Disease, Paris, France
| | - Marie Sarazin
- Department of Neurology of Memory and Language, GHU Paris Psychiatrie & Neurosciences, Hôpital Sainte Anne, F-75014, Paris, France; Université Paris-Cité, F-75006 Paris, France; Université Paris-Saclay, BioMaps, Service Hospitalier Frédéric Joliot CEA, CNRS, Inserm, F-91401, Orsay, France
| | - Mathilde Sauvée
- Centre Mémoire de Ressources et de Recherche, Pôle PReNeLe, CHU Grenoble Alpes CS 10226, 38043 Grenoble Cedex 9, France; Unité de recherche mixte Université Grenoble Alpes/Université Savoie Montblanc, CNRS UMR 5115, Laboratoire de Psychologie et Neurocognition (LPNC), 38000 Grenoble, France
| | - François Sellal
- Department of Neurology, Hôpitaux Civils de Colmar, F-68000 Colmar, France; University of Strasbourg, Medicine Faculty, INSERM, U-1118, Strasbourg, France
| | - Marc Teichmann
- AP-HP Sorbonne Université, Pitié-Salpêtrière Hospital, Department of Neurology, Institute of Memory and Alzheimer's Disease, Paris, France
| | - Christel Thauvin
- Genetics Center, University Hospital of Dijon, University of Burgundy, Dijon, France
| | - Quentin Thomas
- Department of Neurology, University Hospital of Dijon, University of Burgundy, Dijon, France; Genetics Center, University Hospital of Dijon, University of Burgundy, Dijon, France
| | - Camille Tisserand
- Neurology Department, Hôpital Pierre-Paul Riquet, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Cédric Turpinat
- Service de Neurologie, Hopital Gui de Chauliac, CHU de Montpellier, Montpellier, France
| | - Laurène Van Damme
- Service de Neurologie, Centre Hospitalier Perpignan, Perpignan, France
| | | | - Nicolas Villain
- Sorbonne Université, INSERM U1127, CNRS 7235, Institut du Cerveau - ICM, Paris, France; AP-HP Sorbonne Université, Pitié-Salpêtrière Hospital, Department of Neurology, Institute of Memory and Alzheimer's Disease, Paris, France
| | | | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Biostatistics and CNRMAJ, F-76000 Rouen, France
| | - David Wallon
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Neurology and CNRMAJ, F-76000 Rouen, France
| |
Collapse
|
4
|
Nicolas G. Recent advances in Alzheimer disease genetics. Curr Opin Neurol 2024; 37:154-165. [PMID: 38235704 DOI: 10.1097/wco.0000000000001242] [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: 01/19/2024]
Abstract
PURPOSE OF REVIEW Genetics studies provide important insights into Alzheimer disease (AD) etiology and mechanisms. Critical advances have been made recently, mainly thanks to the access to novel techniques and larger studies. RECENT FINDINGS In monogenic AD, progress has been made with a better understanding of the mechanisms associated with pathogenic variants and the input of clinical studies in presymptomatic individuals. In complex AD, increasing sample sizes in both DNA chip-based (genome-wide association studies, GWAS) and exome/genome sequencing case-control studies unveiled novel common and rare risk factors, while the understanding of their combined effect starts to suggest the existence of rare families with oligogenic inheritance of early-onset, nonmonogenic, AD. SUMMARY Most genetic risk factors with a known consequence designate the aggregation of the Aβ peptide as a core etiological factor in complex AD thus confirming that the research based on monogenic AD - where the amyloid cascade seems more straightforward - is relevant to complex AD as well. Novel mechanistic insights and risk factor studies unveiling novel factors and attempting to combine the effect of common and rare variants will offer promising perspectives for future AD prevention, at least regarding early-onset AD, and probably in case of later onset as well.
Collapse
Affiliation(s)
- Gaël Nicolas
- Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Department of Genetics and CNRMAJ, F-76000 Rouen, France
| |
Collapse
|
5
|
Bøgh N, Sørensen CB, Alstrup AKO, Hansen ESS, Andersen OM, Laustsen C. Mice and minipigs with compromised expression of the Alzheimer's disease gene SORL1 show cerebral metabolic disturbances on hyperpolarized [1- 13C]pyruvate and sodium MRI. Brain Commun 2024; 6:fcae114. [PMID: 38650831 PMCID: PMC11034025 DOI: 10.1093/braincomms/fcae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/24/2024] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
The sortilin-related receptor 1 (SORL1) gene, encoding the cellular endosomal sorting-related receptor with A-type repeats (SORLA), is now established as a causal gene for Alzheimer's disease. As the latest addition to the list of causal genes, the pathophysiological effects and biomarker potential of SORL1 variants remain relatively undiscovered. Metabolic dysfunction is, however, well described in patients with Alzheimer's disease and is used as an imaging biomarker in clinical diagnosis settings. To understand the metabolic consequences of loss-of-function SORL1 mutations, we applied two metabolic MRI technologies, sodium (23Na) MRI and MRI with hyperpolarized [1-13C]pyruvate, in minipigs and mice with compromised expression of SORL1. At the age analysed here, both animal models display no conventional imaging evidence of neurodegeneration but show biochemical signs of elevated amyloid production, thus representing the early preclinical disease. With hyperpolarized MRI, the exchange from [1-13C]pyruvate to [1-13C]lactate and 13C-bicarbonate was decreased by 32 and 23%, respectively, in the cerebrum of SORL1-haploinsufficient minipigs. A robust 11% decrease in the sodium content was observed with 23Na-MRI in the same minipigs. Comparably, the brain sodium concentration gradually decreased from control to SORL1 haploinsufficient (-11%) to SORL1 knockout mice (-23%), suggesting a gene dose dependence in the metabolic dysfunction. The present study highlights that metabolic MRI technologies are sensitive to the functional, metabolic consequences of Alzheimer's disease and Alzheimer's disease-linked genotypes. Further, the study suggests a potential avenue of research into the mechanisms of metabolic alterations by SORL1 mutations and their potential role in neurodegeneration.
Collapse
Affiliation(s)
- Nikolaj Bøgh
- Department of Clinical Medicine, The MR Research Centre, Aarhus University, 8200 Aarhus, Denmark
- A&E, Gødstrup Hospital, 7400 Herning, Denmark
| | | | - Aage K O Alstrup
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark
- Department of Nuclear Medicine and PET-Centre, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Esben S S Hansen
- Department of Clinical Medicine, The MR Research Centre, Aarhus University, 8200 Aarhus, Denmark
| | - Olav M Andersen
- Department of Biomedicine, Aarhus University, 8200 Aarhus, Denmark
| | - Christoffer Laustsen
- Department of Clinical Medicine, The MR Research Centre, Aarhus University, 8200 Aarhus, Denmark
| |
Collapse
|
6
|
Habicher J, Sanvido I, Bühler A, Sartori S, Piccoli G, Carl M. The Risk Genes for Neuropsychiatric Disorders negr1 and opcml Are Expressed throughout Zebrafish Brain Development. Genes (Basel) 2024; 15:363. [PMID: 38540422 PMCID: PMC10969947 DOI: 10.3390/genes15030363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 06/14/2024] Open
Abstract
The immunoglobulin LAMP/OBCAM/NTM (IgLON) family of cell adhesion molecules comprises five members known for their involvement in establishing neural circuit connectivity, fine-tuning, and maintenance. Mutations in IgLON genes result in alterations in these processes and can lead to neuropsychiatric disorders. The two IgLON family members NEGR1 and OPCML share common links with several of them, such as schizophrenia, autism, and major depressive disorder. However, the onset and the underlying molecular mechanisms have remained largely unresolved, hampering progress in developing therapies. NEGR1 and OPCML are evolutionarily conserved in teleosts like the zebrafish (Danio rerio), which is excellently suited for disease modelling and large-scale screening for disease-ameliorating compounds. To explore the potential applicability of zebrafish for extending our knowledge on NEGR1- and OPCML-linked disorders and to develop new therapeutic strategies, we investigated the spatio-temporal expression of the two genes during early stages of development. negr1 and opcml are expressed maternally and subsequently in partially distinct domains of conserved brain regions. Other areas of expression in zebrafish have not been reported in mammals to date. Our results indicate that NEGR1 and OPCML may play roles in neural circuit development and function at stages earlier than previously anticipated. A detailed functional analysis of the two genes based on our findings could contribute to understanding the mechanistic basis of related psychiatric disorders.
Collapse
Affiliation(s)
- Judith Habicher
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| | - Ilaria Sanvido
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| | - Anja Bühler
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, 89081 Ulm, Germany
| | - Samuele Sartori
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| | - Giovanni Piccoli
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| | - Matthias Carl
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| |
Collapse
|
7
|
Mušálková D, Přistoupilová A, Jedličková I, Hartmannová H, Trešlová H, Nosková L, Hodaňová K, Bittmanová P, Stránecký V, Jiřička V, Langmajerová M, Woodbury‐Smith M, Zarrei M, Trost B, Scherer SW, Bleyer AJ, Vevera J, Kmoch S. Increased burden of rare protein-truncating variants in constrained, brain-specific and synaptic genes in extremely impulsively violent males with antisocial personality disorder. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12882. [PMID: 38359179 PMCID: PMC10869132 DOI: 10.1111/gbb.12882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/17/2024]
Abstract
The genetic correlates of extreme impulsive violence are poorly understood, and there have been few studies that have characterized a large group of affected individuals both clinically and genetically. We performed whole exome sequencing (WES) in 290 males with the life-course-persistent, extremely impulsively violent form of antisocial personality disorder (APD) and analyzed the spectrum of rare protein-truncating variants (rPTVs). Comparisons were made with 314 male controls and publicly available genotype data. Functional annotation tools were used for biological interpretation. Participants were significantly more likely to harbor rPTVs in genes that are intolerant to loss-of-function variants (odds ratio [OR] 2.06; p < 0.001), specifically expressed in brain (OR 2.80; p = 0.036) and enriched for those involved in neurotransmitter transport and synaptic processes. In 60 individuals (20%), we identified rPTVs that we classified as clinically relevant based on their clinical associations, biological function and gene expression patterns. Of these, 37 individuals harbored rPTVs in 23 genes that are associated with a monogenic neurological disorder, and 23 individuals harbored rPTVs in 20 genes reportedly intolerant to loss-of-function variants. The analysis presents evidence in support of a model where presence of either one or several private, functionally relevant mutations contribute significantly to individual risk of life-course-persistent APD and reveals multiple individuals who could be affected by clinically unrecognized neuropsychiatric Mendelian disease. Thus, Mendelian diseases and increased rPTV burden may represent important factors for the development of extremely impulsive violent life-course-persistent forms of APD irrespective of their clinical presentation.
Collapse
Affiliation(s)
- Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Petra Bittmanová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Václav Jiřička
- Department of PsychologyPrison Service of the Czech RepublicPragueCzech Republic
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| | - Michaela Langmajerová
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| | - Marc Woodbury‐Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
- Faculty of Medical Sciences, Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Brett Trost
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Molecular Genetics and McLaughlin CentreUniversity of TorontoTorontoOntarioCanada
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
- Section on Nephrology, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Jan Vevera
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
- Department of PsychiatryUniversity Hospital PilsenPilsenCzech Republic
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| |
Collapse
|
8
|
Perković R, Frančić M, Petrović R, Ozretić D, Škara S, Pećin I, Borovečki F. Early-onset Alzheimer's disease due to novel LDLR gene mutation. Acta Neurol Belg 2024; 124:325-327. [PMID: 37382851 DOI: 10.1007/s13760-023-02316-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Affiliation(s)
- Romana Perković
- Department of Neurology, University Hospital Centre Zagreb, Zagreb, Croatia.
| | | | - Ratimir Petrović
- Department of Nuclear Medicine and Radiation Protection, University Hospital Centre Zagreb, Zagreb, Croatia
| | - David Ozretić
- Department of Diagnostic and Interventional Neuroradiology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Stipe Škara
- Department of Neurology, General Hospital Zadar, Zadar, Croatia
| | - Ivan Pećin
- Department of Internal Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Fran Borovečki
- Department of Neurology, University Hospital Centre Zagreb, Zagreb, Croatia
| |
Collapse
|
9
|
Fazeli E, Child DD, Bucks SA, Stovarsky M, Edwards G, Rose SE, Yu CE, Latimer C, Kitago Y, Bird T, Jayadev S, Andersen OM, Young JE. A familial missense variant in the Alzheimer's disease gene SORL1 impairs its maturation and endosomal sorting. Acta Neuropathol 2024; 147:20. [PMID: 38244079 PMCID: PMC10799806 DOI: 10.1007/s00401-023-02670-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/11/2023] [Accepted: 12/16/2023] [Indexed: 01/22/2024]
Abstract
The SORL1 gene has recently emerged as a strong Alzheimer's Disease (AD) risk gene. Over 500 different variants have been identified in the gene and the contribution of individual variants to AD development and progression is still largely unknown. Here, we describe a family consisting of 2 parents and 5 offspring. Both parents were affected with dementia and one had confirmed AD pathology with an age of onset > 75 years. All offspring were affected with AD with ages at onset ranging from 53 years to 74 years. DNA was available from the parent with confirmed AD and 5 offspring. We identified a coding variant, p.(Arg953Cys), in SORL1 in 5 of 6 individuals affected by AD. Notably, variant carriers had severe AD pathology, and the SORL1 variant segregated with TDP-43 pathology (LATE-NC). We further characterized this variant and show that this Arginine substitution occurs at a critical position in the YWTD-domain of the SORL1 translation product, SORL1. Functional studies further show that the p.R953C variant leads to retention of the SORL1 protein in the endoplasmic reticulum which leads to decreased maturation and shedding of the receptor and prevents its normal endosomal trafficking. Together, our analysis suggests that p.R953C is a pathogenic variant of SORL1 and sheds light on mechanisms of how missense SORL1 variants may lead to AD.
Collapse
Affiliation(s)
- Elnaz Fazeli
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark
| | - Daniel D Child
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98109, USA
| | - Stephanie A Bucks
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - Miki Stovarsky
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, 98195, USA
| | - Gabrielle Edwards
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - Shannon E Rose
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98109, USA
| | - Chang-En Yu
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, 98195, USA
- Geriatric Research Education and Clinical Center (GRECC), Veterans Administration Health Care System, Seattle, WA, 98108, USA
| | - Caitlin Latimer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98109, USA
| | - Yu Kitago
- Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Thomas Bird
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, 98195, USA
- Geriatric Research Education and Clinical Center (GRECC), Veterans Administration Health Care System, Seattle, WA, 98108, USA
| | - Suman Jayadev
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA.
| | - Olav M Andersen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark.
| | - Jessica E Young
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98109, USA.
| |
Collapse
|
10
|
Tejeda M, Farrell J, Zhu C, Wetzler L, Lunetta KL, Bush WS, Martin ER, Wang L, Schellenberg GD, Pericak‐Vance MA, Haines JL, Farrer LA, Sherva R. DNA from multiple viral species is associated with Alzheimer's disease risk. Alzheimers Dement 2024; 20:253-265. [PMID: 37578203 PMCID: PMC10840621 DOI: 10.1002/alz.13414] [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: 01/16/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023]
Abstract
INTRODUCTION Multiple infectious agents, including viruses, bacteria, fungi, and protozoa, have been linked to Alzheimer's disease (AD) risk by independent lines of evidence. We explored this association by comparing the frequencies of viral species identified in a large sample of AD cases and controls. METHODS DNA sequence reads that did not align to the human genome in sequences were mapped to viral reference sequences, quantified, and then were tested for association with AD in whole exome sequences (WES) and whole genome sequences (WGS) datasets. RESULTS Several viruses were significant predictors of AD according to the machine learning classifiers. Subsequent regression analyses showed that herpes simplex type 1 (HSV-1) (odds ratio [OR] = 3.71, p = 8.03 × 10-4) and human papillomavirus 71 (HPV-71; OR = 3.56, p = 0.02), were significantly associated with AD after Bonferroni correction. The phylogenetic-related cluster of Herpesviridae was significantly associated with AD in several strata of the data (p < 0.01). DISCUSSION Our results support the hypothesis that viral infection, especially HSV-1, is associated with AD risk.
Collapse
Affiliation(s)
- Marlene Tejeda
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| | - John Farrell
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| | - Congcong Zhu
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| | - Lee Wetzler
- Departments of Medicine Infectious DiseaseBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- Departments of Medicine MicrobiologyBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| | - Kathryn L. Lunetta
- Departments of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
| | - William S. Bush
- Department of Population & Quantitative Health SciencesCleveland Institute for Computational BiologyCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics and Dr John T. MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Li‐San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics and Dr John T. MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health SciencesCleveland Institute for Computational BiologyCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Lindsay A. Farrer
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- Departments of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
- Departments of Medicine Neurologyand Boston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- OphthalmologyBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- Departments of EpidemiologyBoston University School of Public HealthBostonMassachusettsUSA
| | - Richard Sherva
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| |
Collapse
|
11
|
Zhao J, Quan J, Chen W, Xie X. Grid2 interacting protein is a potential biomarker related to immune infiltration in colorectal cancer. Eur J Med Res 2023; 28:511. [PMID: 37964339 PMCID: PMC10644545 DOI: 10.1186/s40001-023-01468-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the three deadliest malignant tumors in the world, posing a severe hazard to human health. Nonetheless, the 5-year survival rate for advanced CRC remains unsatisfactory. Grid2 interacting protein (GRID2IP) is a Purkinje fiber postsynaptic scaffold protein implicated in a number of signal transduction pathways in the nervous system. Previous studies have shown that Grid2 is closely related to the occurrence and prognosis of gastric cancer and many other diseases. Therefore, we aim to identify the relationship between GRID2IP and the occurrence and prognosis of CRC. METHODS Transcriptome data were retrieved from The Cancer Genome Atlas (TCGA) database to analyze the differential expression of GRID2IP in a variety of malignant tumors and then validate it by quantitative real time polymerase chain reaction(Q-PCR) and Western Blot in HT29 and SW480 cells. "DESeq2" package was used to analyze the differentially expressed genes (DEGs) between the high- and low-GRID2IP subgroups. In relation to DEGs, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed. In addition, gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA) were employed to examine DEGs-associated signaling pathways and GRID2IP-associated immune cell infiltration levels. Besides, overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) were compared between the two subgroups using a Kaplan-Meier analysis. In addition, a prognostic model for GRID2IP and clinical characteristics was developed using the univariate Cox regression method. The "pRRophetic" package was applied to predict the drug sensitivity of different subgroups. Moreover, we also performed single-cell analysis of GRID2IP using the TISCH database. RESULTS GRID2IP is upregulated in CRC patients. The rise of GRID2IP inhibits the invasion of tumor-associated immune cells resulting in a lower immune score. In addition, high GRID2IP expression was associated with poor prognosis in different clinical subgroups. Analysis of single cells revealed that GRID2IP was predominantly expressed in immune cells, myofibroblasts, and cancerous cells. In terms of chemotherapy drug sensitivity, the subgroup with high GRID2IP expression was less sensitive to gemcitabine. CONCLUSIONS Our results suggest that rising GRID2IP promotes tumor-associated immune cell infiltration and suggests adverse outcomes in CRC patients, which may be a useful biomarker for determining the prognosis of CRC and a potential target molecule for CRC therapy.
Collapse
Affiliation(s)
- Jiajing Zhao
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Jiazheng Quan
- Marshall Laboratory of Biomedical Engineering, Institute of Biological Therapy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Weilin Chen
- Marshall Laboratory of Biomedical Engineering, Institute of Biological Therapy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China.
| | - Xiaojun Xie
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China.
| |
Collapse
|
12
|
Fazeli E, Child DD, Bucks SA, Stovarsky M, Edwards G, Rose SE, Yu CE, Latimer C, Kitago Y, Bird T, Jayadev S, Andersen OM, Young JE. A familial missense variant in the Alzheimer's Disease gene SORL1 impairs its maturation and endosomal sorting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.01.547348. [PMID: 37461597 PMCID: PMC10349966 DOI: 10.1101/2023.07.01.547348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The SORL1 gene has recently emerged as a strong Alzheimer's Disease (AD) risk gene. Over 500 different variants have been identified in the gene and the contribution of individual variants to AD development and progression is still largely unknown. Here, we describe a family consisting of 2 parents and 5 offspring. Both parents were affected with dementia and one had confirmed AD pathology with an age of onset >75 years. All offspring were affected with AD with ages at onset ranging from 53yrs-74yrs. DNA was available from the parent with confirmed AD and 5 offspring. We identified a coding variant, p.(Arg953Cys), in SORL1 in 5 of 6 individuals affected by AD. Notably, variant carriers had severe AD pathology, and the SORL1 variant segregated with TDP-43 pathology (LATE-NC). We further characterized this variant and show that this Arginine substitution occurs at a critical position in the YWTD-domain of the SORL1 translation product, SORL1. Functional studies further show that the p.R953C variant leads to retention of the SORL1 protein in the endoplasmic reticulum which leads to decreased maturation and shedding of the receptor and prevents its normal endosomal trafficking. Together, our analysis suggests that p.R953C is a pathogenic variant of SORL1 and sheds light on mechanisms of how missense SORL1 variants may lead to AD.
Collapse
Affiliation(s)
- Elnaz Fazeli
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, DK8000 AarhusC, Denmark
| | - Daniel D. Child
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle Washington USA
| | - Stephanie A. Bucks
- Department of Neurology, University of Washington, Seattle Washington USA
| | - Miki Stovarsky
- Department of Medicine, Division of Medical Genetics University of Washington, Seattle Washington USA
| | - Gabrielle Edwards
- Department of Neurology, University of Washington, Seattle Washington USA
| | - Shannon E. Rose
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle Washington USA
| | - Chang-En Yu
- Department of Medicine, Division of Medical Genetics University of Washington, Seattle Washington USA
- Geriatric Research Education and Clinical Center (GRECC), Veterans Administration Health Care System
| | - Caitlin Latimer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle Washington USA
| | - Yu Kitago
- Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115
| | - Thomas Bird
- Department of Neurology, University of Washington, Seattle Washington USA
- Department of Medicine, Division of Medical Genetics University of Washington, Seattle Washington USA
- Geriatric Research Education and Clinical Center (GRECC), Veterans Administration Health Care System
| | - Suman Jayadev
- Department of Neurology, University of Washington, Seattle Washington USA
| | - Olav M. Andersen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, DK8000 AarhusC, Denmark
| | - Jessica E. Young
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle Washington USA
| |
Collapse
|
13
|
Monti G, Vincke C, Lunding M, Jensen AMG, Madsen P, Muyldermans S, Kjolby M, Andersen OM. Epitope mapping of nanobodies binding the Alzheimer's disease receptor SORLA. J Biotechnol 2023; 375:17-27. [PMID: 37634829 DOI: 10.1016/j.jbiotec.2023.08.005] [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: 05/09/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Reduced levels of the Sortilin-related receptor with A-type repeats (SORLA) in different brain regions as well as in the cerebrospinal fluid have been associated with Alzheimer's disease. Methods and reagents to develop reliable detection assays to quantify SORLA and its specific isoforms are therefore much needed. Nanobodies (Nbs) are unique biomolecules derived from the blood of camelids that display advantageous physicochemical and antigen affinity properties, making them attractive tools with great relevance to both diagnostic and therapeutic applications. Here, we purified and characterized eight Nbs that were isolated from the blood of an alpaca immunized with the recombinant extracellular domain of SORLA. The selected Nbs showed high affinity to SORLA in the low nanomolar range as observed by surface plasmon resonance. For mapping of the Nbs' epitopes within the antigen, we transiently transfected HEK293 cells with a panel of SORLA deletion constructs, and developed a protocol of immunostaining by applying fluorescent dye conjugated Nbs. With this method, we showed that the selected Nbs specifically recognize a part of SORLA containing Fibronectin-type III domains, representing promising tools not only for disease clarifying research, but also for translational medicine as candidates for clinical diagnostic purposes.
Collapse
Affiliation(s)
- Giulia Monti
- Department of Biomedicine, Aarhus University, Høegh‑Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Melanie Lunding
- Department of Biomedicine, Aarhus University, Høegh‑Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Anne Mette G Jensen
- Department of Biomedicine, Aarhus University, Høegh‑Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Peder Madsen
- Department of Biomedicine, Aarhus University, Høegh‑Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mads Kjolby
- Department of Biomedicine, Aarhus University, Høegh‑Guldbergs Gade 10, 8000 Aarhus C, Denmark; Department of Clinical Pharmacology and Steno Diabetes Center Aarhus, Aarhus University Hospital, Denmark
| | - Olav M Andersen
- Department of Biomedicine, Aarhus University, Høegh‑Guldbergs Gade 10, 8000 Aarhus C, Denmark.
| |
Collapse
|
14
|
Lee H, Aylward AJ, Pearse RV, Lish AM, Hsieh YC, Augur ZM, Benoit CR, Chou V, Knupp A, Pan C, Goberdhan S, Duong DM, Seyfried NT, Bennett DA, Taga MF, Huynh K, Arnold M, Meikle PJ, De Jager PL, Menon V, Young JE, Young-Pearse TL. Cell-type-specific regulation of APOE and CLU levels in human neurons by the Alzheimer's disease risk gene SORL1. Cell Rep 2023; 42:112994. [PMID: 37611586 PMCID: PMC10568487 DOI: 10.1016/j.celrep.2023.112994] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/04/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
SORL1 is implicated in the pathogenesis of Alzheimer's disease (AD) through genetic studies. To interrogate the roles of SORL1 in human brain cells, SORL1-null induced pluripotent stem cells (iPSCs) were differentiated to neuron, astrocyte, microglial, and endothelial cell fates. Loss of SORL1 leads to alterations in both overlapping and distinct pathways across cell types, with the greatest effects in neurons and astrocytes. SORL1 loss induces a neuron-specific reduction in apolipoprotein E (APOE) and clusterin (CLU) and altered lipid profiles. Analyses of iPSCs derived from a large cohort reveal a neuron-specific association between SORL1, APOE, and CLU levels, a finding validated in postmortem brain. Enhancement of retromer-mediated trafficking rescues tau phenotypes observed in SORL1-null neurons but does not rescue APOE levels. Pathway analyses implicate transforming growth factor β (TGF-β)/SMAD signaling in SORL1 function, and modulating SMAD signaling in neurons alters APOE RNA levels in a SORL1-dependent manner. Taken together, these data provide a mechanistic link between strong genetic risk factors for AD.
Collapse
Affiliation(s)
- Hyo Lee
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aimee J Aylward
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexandra M Lish
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yi-Chen Hsieh
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zachary M Augur
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Courtney R Benoit
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vicky Chou
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Allison Knupp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Cheryl Pan
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Srilakshmi Goberdhan
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Duc M Duong
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, USA
| | | | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Mariko F Taga
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Bundoora, VIC, Australia
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Bundoora, VIC, Australia
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Jessica E Young
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
15
|
Chandy T. Intervention of next-generation sequencing in diagnosis of Alzheimer's disease: challenges and future prospects. Dement Neuropsychol 2023; 17:e20220025. [PMID: 37577182 PMCID: PMC10417152 DOI: 10.1590/1980-5764-dn-2022-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 08/15/2023] Open
Abstract
Clinical diagnosis of several neurodegenerative disorders based on clinical phenotype is challenging due to its heterogeneous nature and overlapping disease manifestations. Therefore, the identification of underlying genetic mechanisms is of paramount importance for better diagnosis and therapeutic regimens. With the emergence of next-generation sequencing, it becomes easier to identify all gene variants in the genome simultaneously, with a system-wide and unbiased approach. Presently various bioinformatics databases are maintained on discovered gene variants and phenotypic indications are available online. Since individuals are unique in their genome, evaluation based on their genetic makeup helps evolve the diagnosis, counselling, and treatment process at the personal level. This article aims to briefly summarize the utilization of next-generation sequencing in deciphering the genetic causes of Alzheimer's disease and address the limitations of whole genome and exome sequencing.
Collapse
Affiliation(s)
- Tijimol Chandy
- MedGenome Labs Pvt. Ltd., Bangalore-560100, Karnataka, India
| |
Collapse
|
16
|
Silvaieh S, König T, Wurm R, Parvizi T, Berger-Sieczkowski E, Goeschl S, Hotzy C, Wagner M, Berutti R, Sammler E, Stögmann E, Zimprich A. Comprehensive genetic screening of early-onset dementia patients in an Austrian cohort-suggesting new disease-contributing genes. Hum Genomics 2023; 17:55. [PMID: 37330543 PMCID: PMC10276391 DOI: 10.1186/s40246-023-00499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 06/19/2023] Open
Abstract
Early-onset dementia (EOD), with symptom onset before age 65, has a strong genetic burden. Due to genetic and clinical overlaps between different types of dementia, whole-exome sequencing (WES) has emerged as an appropriate screening method for diagnostic testing and novel gene-finding approaches. We performed WES and C9orf72 repeat testing in 60 well-defined Austrian EOD patients. Seven patients (12%) carried likely disease-causing variants in monogenic genes, PSEN1, MAPT, APP, and GRN. Five patients (8%) were APOE4 homozygote carriers. Definite and possible risk variants were detected in the genes TREM2, SORL1, ABCA7 and TBK1. In an explorative approach, we cross-checked rare gene variants in our cohort with a curated neurodegeneration candidate gene list and identified DCTN1, MAPK8IP3, LRRK2, VPS13C and BACE1 as promising candidate genes. Conclusively, 12 cases (20%) carried variants relevant to patient counseling, comparable to previously reported studies, and can thus be considered genetically resolved. Reduced penetrance, oligogenic inheritance and not yet identified high-risk genes might explain the high number of unresolved cases. To address this issue, we provide complete genetic and phenotypic information (uploaded to the European Genome-phenome Archive), enabling other researchers to cross-check variants. Thereby, we hope to increase the chance of independently finding the same gene/variant-hit in other well-defined EOD patient cohorts, thus confirming new genetic risk variants or variant combinations.
Collapse
Affiliation(s)
- Sara Silvaieh
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Theresa König
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Raphael Wurm
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Tandis Parvizi
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Evelyn Berger-Sieczkowski
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Stella Goeschl
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Christoph Hotzy
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Centrum, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Esther Sammler
- Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Elisabeth Stögmann
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria.
| | - Alexander Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
17
|
Miao J, Ma H, Yang Y, Liao Y, Lin C, Zheng J, Yu M, Lan J. Microglia in Alzheimer's disease: pathogenesis, mechanisms, and therapeutic potentials. Front Aging Neurosci 2023; 15:1201982. [PMID: 37396657 PMCID: PMC10309009 DOI: 10.3389/fnagi.2023.1201982] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by protein aggregation in the brain. Recent studies have revealed the critical role of microglia in AD pathogenesis. This review provides a comprehensive summary of the current understanding of microglial involvement in AD, focusing on genetic determinants, phenotypic state, phagocytic capacity, neuroinflammatory response, and impact on synaptic plasticity and neuronal regulation. Furthermore, recent developments in drug discovery targeting microglia in AD are reviewed, highlighting potential avenues for therapeutic intervention. This review emphasizes the essential role of microglia in AD and provides insights into potential treatments.
Collapse
Affiliation(s)
- Jifei Miao
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Haixia Ma
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yang Yang
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yuanpin Liao
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Cui Lin
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Juanxia Zheng
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Muli Yu
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Jiao Lan
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| |
Collapse
|
18
|
Johnson AM, Lukens JR. The innate immune response in tauopathies. Eur J Immunol 2023; 53:e2250266. [PMID: 36932726 PMCID: PMC10247424 DOI: 10.1002/eji.202250266] [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: 01/06/2023] [Revised: 02/23/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
Tauopathies, which include frontotemporal dementia, Alzheimer's disease, and chronic traumatic encephalopathy, are a class of neurological disorders resulting from pathogenic tau aggregates. These aggregates disrupt neuronal health and function leading to the cognitive and physical decline of tauopathy patients. Genome-wide association studies and clinical evidence have brought to light the large role of the immune system in inducing and driving tau-mediated pathology. More specifically, innate immune genes are found to harbor tauopathy risk alleles, and innate immune pathways are upregulated throughout the course of disease. Experimental evidence has expanded on these findings by describing pivotal roles for the innate immune system in the regulation of tau kinases and tau aggregates. In this review, we summarize the literature implicating innate immune pathways as drivers of tauopathy.
Collapse
Affiliation(s)
- Alexis M. Johnson
- Center for Brain Immunology and Glia (BIG), Department of Neuroscience, University of Virginia (UVA), Charlottesville, VA 22908, USA
- Neuroscience Graduate Program, UVA, Charlottesville, VA 22908, USA
- BIG Training Graduate Program, UVA, Charlottesville, VA 22908, USA
| | - John R. Lukens
- Center for Brain Immunology and Glia (BIG), Department of Neuroscience, University of Virginia (UVA), Charlottesville, VA 22908, USA
- Neuroscience Graduate Program, UVA, Charlottesville, VA 22908, USA
- BIG Training Graduate Program, UVA, Charlottesville, VA 22908, USA
| |
Collapse
|
19
|
Young-Pearse TL, Lee H, Hsieh YC, Chou V, Selkoe DJ. Moving beyond amyloid and tau to capture the biological heterogeneity of Alzheimer's disease. Trends Neurosci 2023; 46:426-444. [PMID: 37019812 PMCID: PMC10192069 DOI: 10.1016/j.tins.2023.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Alzheimer's disease (AD) manifests along a spectrum of cognitive deficits and levels of neuropathology. Genetic studies support a heterogeneous disease mechanism, with around 70 associated loci to date, implicating several biological processes that mediate risk for AD. Despite this heterogeneity, most experimental systems for testing new therapeutics are not designed to capture the genetically complex drivers of AD risk. In this review, we first provide an overview of those aspects of AD that are largely stereotyped and those that are heterogeneous, and we review the evidence supporting the concept that different subtypes of AD are important to consider in the design of agents for the prevention and treatment of the disease. We then dive into the multifaceted biological domains implicated to date in AD risk, highlighting studies of the diverse genetic drivers of disease. Finally, we explore recent efforts to identify biological subtypes of AD, with an emphasis on the experimental systems and data sets available to support progress in this area.
Collapse
Affiliation(s)
- Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yi-Chen Hsieh
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vicky Chou
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
20
|
Reitz C, Pericak-Vance MA, Foroud T, Mayeux R. A global view of the genetic basis of Alzheimer disease. Nat Rev Neurol 2023; 19:261-277. [PMID: 37024647 PMCID: PMC10686263 DOI: 10.1038/s41582-023-00789-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
The risk of Alzheimer disease (AD) increases with age, family history and informative genetic variants. Sadly, there is still no cure or means of prevention. As in other complex diseases, uncovering genetic causes of AD could identify underlying pathological mechanisms and lead to potential treatments. Rare, autosomal dominant forms of AD occur in middle age as a result of highly penetrant genetic mutations, but the most common form of AD occurs later in life. Large-scale, genome-wide analyses indicate that 70 or more genes or loci contribute to AD. One of the major factors limiting progress is that most genetic data have been obtained from non-Hispanic white individuals in Europe and North America, preventing the development of personalized approaches to AD in individuals of other ethnicities. Fortunately, emerging genetic data from other regions - including Africa, Asia, India and South America - are now providing information on the disease from a broader range of ethnicities. Here, we summarize the current knowledge on AD genetics in populations across the world. We predominantly focus on replicated genetic discoveries but also include studies in ethnic groups where replication might not be feasible. We attempt to identify gaps that need to be addressed to achieve a complete picture of the genetic and molecular factors that drive AD in individuals across the globe.
Collapse
Affiliation(s)
- Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard Mayeux
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.
- Department of Neurology, Columbia University, New York, NY, USA.
- Department of Epidemiology, Columbia University, New York, NY, USA.
| |
Collapse
|
21
|
Pan X, Coban Akdemir ZH, Gao R, Jiang X, Sheynkman GM, Wu E, Huang JH, Sahni N, Yi SS. AD-Syn-Net: systematic identification of Alzheimer's disease-associated mutation and co-mutation vulnerabilities via deep learning. Brief Bioinform 2023; 24:bbad030. [PMID: 36752347 PMCID: PMC10025433 DOI: 10.1093/bib/bbad030] [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: 07/09/2022] [Revised: 12/19/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Alzheimer's disease (AD) is one of the most challenging neurodegenerative diseases because of its complicated and progressive mechanisms, and multiple risk factors. Increasing research evidence demonstrates that genetics may be a key factor responsible for the occurrence of the disease. Although previous reports identified quite a few AD-associated genes, they were mostly limited owing to patient sample size and selection bias. There is a lack of comprehensive research aimed to identify AD-associated risk mutations systematically. To address this challenge, we hereby construct a large-scale AD mutation and co-mutation framework ('AD-Syn-Net'), and propose deep learning models named Deep-SMCI and Deep-CMCI configured with fully connected layers that are capable of predicting cognitive impairment of subjects effectively based on genetic mutation and co-mutation profiles. Next, we apply the customized frameworks to data sets to evaluate the importance scores of the mutations and identified mutation effectors and co-mutation combination vulnerabilities contributing to cognitive impairment. Furthermore, we evaluate the influence of mutation pairs on the network architecture to dissect the genetic organization of AD and identify novel co-mutations that could be responsible for dementia, laying a solid foundation for proposing future targeted therapy for AD precision medicine. Our deep learning model codes are available open access here: https://github.com/Pan-Bio/AD-mutation-effectors.
Collapse
Affiliation(s)
- Xingxin Pan
- Livestrong Cancer Institutes, and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Zeynep H Coban Akdemir
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ruixuan Gao
- Departments of Chemistry and Biological Sciences, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xiaoqian Jiang
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Center for Public Health Genomics, and UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Erxi Wu
- Livestrong Cancer Institutes, and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Surgery, Texas A & M University Health Science Center, College of Medicine, Temple, TX 76508, USA
- Department of Pharmaceutical Sciences, Texas A & M University Health Science Center, College of Pharmacy, College Station, TX 77843, USA
| | - Jason H Huang
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Surgery, Texas A & M University Health Science Center, College of Medicine, Temple, TX 76508, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX 78712, USA
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
22
|
Li X, Xu M, Bi R, Tan LW, Yao YG, Zhang DF. Common and rare variants of EGF increase the genetic risk of Alzheimer's disease as revealed by targeted sequencing of growth factors in Han Chinese. Neurobiol Aging 2023; 123:170-181. [PMID: 36437134 DOI: 10.1016/j.neurobiolaging.2022.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/21/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease with high heritability. Growth factors (GFs) might contribute to the development of AD due to their broad effects on neuronal system. We herein aimed to investigate the role of rare and common variants of GFs in genetic susceptibility of AD. We screened 23 GFs in 6324 individuals using targeted sequencing. A rare-variant-based burden test and common-variant-based single-site association analyses were performed to identify AD-associated GF genes and variants. The burden test showed an enrichment of rare missense variants (p = 6.08 × 10-4) in GF gene-set in AD patients. Among the GFs, EGF showed the strongest signal of enrichment, especially for loss-of-function variants (p = 0.0019). A common variant rs4698800 of EGF showed significant associations with AD risk (p = 3.24 × 10-5, OR = 1.26). The risk allele of rs4698800 was associated with an increased EGF expression, whereas EGF was indeed upregulated in AD brain. These findings suggested EGF as a novel risk gene for AD.
Collapse
Affiliation(s)
- Xiao Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Li-Wen Tan
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
| |
Collapse
|
23
|
Lee H, Aylward AJ, Pearse RV, Hsieh YC, Augur ZM, Benoit CR, Chou V, Knupp A, Pan C, Goberdhan S, Duong DM, Seyfried NT, Bennett DA, Klein HU, De Jager PL, Menon V, Young JE, Young-Pearse TL. Cell-type-specific regulation of APOE levels in human neurons by the Alzheimer's disease risk gene SORL1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530017. [PMID: 36865313 PMCID: PMC9980168 DOI: 10.1101/2023.02.25.530017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
SORL1 is strongly implicated in the pathogenesis of Alzheimer's disease (AD) through human genetic studies that point to an association of reduced SORL1 levels with higher risk for AD. To interrogate the role(s) of SORL1 in human brain cells, SORL1 null iPSCs were generated, followed by differentiation to neuron, astrocyte, microglia, and endothelial cell fates. Loss of SORL1 led to alterations in both overlapping and distinct pathways across cell types, with the greatest effects in neurons and astrocytes. Intriguingly, SORL1 loss led to a dramatic neuron-specific reduction in APOE levels. Further, analyses of iPSCs derived from a human aging cohort revealed a neuron-specific linear correlation between SORL1 and APOE RNA and protein levels, a finding validated in human post-mortem brain. Pathway analysis implicated intracellular transport pathways and TGF- β/SMAD signaling in the function of SORL1 in neurons. In accord, enhancement of retromer-mediated trafficking and autophagy rescued elevated phospho-tau observed in SORL1 null neurons but did not rescue APOE levels, suggesting that these phenotypes are separable. Stimulation and inhibition of SMAD signaling modulated APOE RNA levels in a SORL1-dependent manner. These studies provide a mechanistic link between two of the strongest genetic risk factors for AD.
Collapse
|
24
|
Wright CA, Taylor JW, Cochran M, Lawlor JM, Moyers BA, Amaral MD, Bonnstetter ZT, Carter P, Solomon V, Myers RM, Love MN, Geldmacher DS, Cooper SJ, Roberson ED, Cochran JN. Contributions of rare and common variation to early-onset and atypical dementia risk. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.06.23285383. [PMID: 36798301 PMCID: PMC9934786 DOI: 10.1101/2023.02.06.23285383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
We collected and analyzed genomic sequencing data from individuals with clinician- diagnosed early-onset or atypical dementia. Thirty-two patients were previously described, with sixty-eight newly described in this report. Of those sixty-eight, sixty-two patients reported Caucasian, non-Hispanic ethnicity and six reported as African American, non-Hispanic. Fifty-three percent of patients had a returnable variant. Five patients harbored a pathogenic variant as defined by the American College of Medical Genetics criteria for pathogenicity. A polygenic risk score was calculated for Alzheimer's patients in the total cohort and compared to the scores of a late-onset Alzheimer's cohort and a control set. Patients with early-onset Alzheimer's had higher non- APOE polygenic risk scores than patients with late onset Alzheimer's, supporting the conclusion that both rare and common genetic variation associate with early-onset neurodegenerative disease risk.
Collapse
Affiliation(s)
- Carter A. Wright
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA,University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
| | - Jared W. Taylor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Meagan Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - James M.J. Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Belle A. Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | | | - Princess Carter
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Veronika Solomon
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Marissa Natelson Love
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - David S. Geldmacher
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Erik D. Roberson
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - J. Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA,Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| |
Collapse
|
25
|
Wightman DP, Savage JE, de Leeuw CA, Jansen IE, Posthuma D. Rare variant aggregation in 148,508 exomes identifies genes associated with proxy dementia. Sci Rep 2023; 13:2179. [PMID: 36750708 PMCID: PMC9905079 DOI: 10.1038/s41598-023-29108-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Proxy phenotypes allow for the utilization of genetic data from large population cohorts to analyze late-onset diseases by using parental diagnoses as a proxy for genetic disease risk. Proxy phenotypes based on parental diagnosis status have been used in previous studies to identify common variants associated with Alzheimer's disease. As of yet, proxy phenotypes have not been used to identify genes associated with Alzheimer's disease through rare variants. Here we show that a proxy Alzheimer's disease/dementia phenotype can capture known Alzheimer's disease risk genes through rare variant aggregation. We generated a proxy Alzheimer's disease/dementia phenotype for 148,508 unrelated individuals of European ancestry in the UK biobank in order to perform exome-wide rare variant aggregation analyses to identify genes associated with proxy Alzheimer's disease/dementia. We identified four genes significantly associated with the proxy phenotype, three of which were significantly associated with proxy Alzheimer's disease/dementia in an independent replication cohort consisting of 197,506 unrelated individuals of European ancestry in the UK biobank. All three of the replicated genes have been previously associated with clinically diagnosed Alzheimer's disease (SORL1, TREM2, and TOMM40/APOE). We show that proxy Alzheimer's disease/dementia can be used to identify genes associated with Alzheimer's disease through rare variant aggregation.
Collapse
Affiliation(s)
- Douglas P Wightman
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands.
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands
| | - Iris E Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
26
|
Alkelai A, Greenbaum L, Shohat S, Povysil G, Malakar A, Ren Z, Motelow JE, Schechter T, Draiman B, Chitrit-Raveh E, Hughes D, Jobanputra V, Shifman S, Goldstein DB, Kohn Y. Genetic insights into childhood-onset schizophrenia: The yield of clinical exome sequencing. Schizophr Res 2023; 252:138-145. [PMID: 36645932 DOI: 10.1016/j.schres.2022.12.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 01/15/2023]
Abstract
Childhood-onset schizophrenia (COS) is a rare form of schizophrenia with an onset prior to 13 years of age. Although genetic factors play a role in COS etiology, only a few causal variants have been reported to date. This study presents a diagnostic exome sequencing (ES) in 37 Israeli Jewish families with a proband diagnosed with COS. By implementing a trio/duo ES approach and applying a well-established diagnostic pipeline, we detected clinically significant variants in 7 probands (19 %). These single nucleotide variants and indels were mostly inherited. The implicated genes were ANKRD11, GRIA2, CHD2, CLCN3, CLTC, IGF1R and MICU1. In a secondary analysis that compared COS patients to 4721 healthy controls, we observed that patients had a significant enrichment of rare loss of function (LoF) variants in LoF intolerant genes associated with developmental diseases. Taken together, ES could be considered as a valuable tool in the genetic workup for COS patients.
Collapse
Affiliation(s)
- Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA; Regeneron Genetics Center, Tarrytown, NY, USA.
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tal Aviv University, Tel Aviv, Israel
| | - Shahar Shohat
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Ayan Malakar
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Joshua E Motelow
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA; Department of Pediatrics, Division of Critical Care and Hospital Medicine, Columbia University Irving Medical Center, New York-Presbyterian Morgan Stanley Children's Hospital of New York, New York, NY, USA
| | - Tanya Schechter
- Department of Child and Adolescent Psychiatry, Jerusalem Mental Health Center, Eitanim Psychiatric Hospital, Israel
| | - Benjamin Draiman
- Department of Child and Adolescent Psychiatry, Jerusalem Mental Health Center, Eitanim Psychiatric Hospital, Israel
| | - Eti Chitrit-Raveh
- Department of Child and Adolescent Psychiatry, Jerusalem Mental Health Center, Eitanim Psychiatric Hospital, Israel
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Yoav Kohn
- Department of Child and Adolescent Psychiatry, Jerusalem Mental Health Center, Eitanim Psychiatric Hospital, Israel; Hadassah-Hebrew University School of Medicine, Jerusalem, Israel
| |
Collapse
|
27
|
Ultra-Rare Variants Identify Biological Pathways and Candidate Genes in the Pathobiology of Non-Syndromic Cleft Palate Only. Biomolecules 2023; 13:biom13020236. [PMID: 36830605 PMCID: PMC9953608 DOI: 10.3390/biom13020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
In recent decades, many efforts have been made to elucidate the genetic causes of non-syndromic cleft palate (nsCPO), a complex congenital disease caused by the interaction of several genetic and environmental factors. Since genome-wide association studies have evidenced a minor contribution of common polymorphisms in nsCPO inheritance, we used whole exome sequencing data to explore the role of ultra-rare variants in this study. In a cohort of 35 nsCPO cases and 38 controls, we performed a gene set enrichment analysis (GSEA) and a hypergeometric test for assessing significant overlap between genes implicated in nsCPO pathobiology and genes enriched in ultra-rare variants in our cohort. GSEA highlighted an enrichment of ultra-rare variants in genes principally belonging to cytoskeletal protein binding pathway (Probability Density Function corrected p-value = 1.57 × 10-4); protein-containing complex binding pathway (p-value = 1.06 × 10-2); cell adhesion molecule binding pathway (p-value = 1.24 × 10-2); ECM-receptor interaction pathway (p-value = 1.69 × 10-2); and in the Integrin signaling pathway (p-value = 1.28 × 10-2). Two genes implicated in nsCPO pathobiology, namely COL2A1 and GLI3, ranked among the genes (n = 34) with nominal enrichment in the ultra-rare variant collapsing analysis (Fisher's exact test p-value < 0.05). These genes were also part of an independent list of genes highly relevant to nsCPO biology (n = 25). Significant overlap between the two sets of genes (hypergeometric test p-value = 5.86 × 10-3) indicated that enriched genes are likely to be implicated in physiological palate development and/or the pathological processes of oral clefting. In conclusion, ultra-rare variants collectively impinge on biological pathways crucial to nsCPO pathobiology and point to candidate genes that may contribute to the individual risk of disease. Sequencing can be an effective approach to identify candidate genes and pathways for nsCPO.
Collapse
|
28
|
Dimerization of the Alzheimer's disease pathogenic receptor SORLA regulates its association with retromer. Proc Natl Acad Sci U S A 2023; 120:e2212180120. [PMID: 36652482 PMCID: PMC9942828 DOI: 10.1073/pnas.2212180120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
SORL1, the gene encoding the large multidomain SORLA protein, has emerged as only the fourth gene that when mutated can by itself cause Alzheimer's disease (AD), and as a gene reliably linked to both the early- and late-onset forms of the disease. SORLA is known to interact with the endosomal trafficking regulatory complex called retromer in regulating the recycling of endosomal cargo, including the amyloid precursor protein (APP) and the glutamate receptor GluA1. Nevertheless, SORLA's precise structural-functional relationship in endosomal recycling tubules remains unknown. Here, we address these outstanding questions by relying on crystallographic and artificial-intelligence evidence to generate a structural model for how SORLA folds and fits into retromer-positive endosomal tubules, where it is found to dimerize via both SORLA's fibronectin-type-III (3Fn)- and VPS10p-domains. Moreover, we identify a SORLA fragment comprising the 3Fn-, transmembrane, and cytoplasmic domains that has the capacity to form a dimer, and to enhance retromer-dependent recycling of APP by decreasing its amyloidogenic processing. Collectively, these observations generate a model for how SORLA dimer (and possibly polymer) formation can function in stabilizing and enhancing retromer function at endosome tubules. These findings can inform investigation of the many AD-associated SORL1 variants for evidence of pathogenicity and can guide discovery of novel drugs for the disease.
Collapse
|
29
|
Rihar N, Krgovic D, Kokalj-Vokač N, Stangler-Herodez S, Zorc M, Dovc P. Identification of potentially pathogenic variants for autism spectrum disorders using gene-burden analysis. PLoS One 2023; 18:e0273957. [PMID: 37167322 PMCID: PMC10174571 DOI: 10.1371/journal.pone.0273957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
Gene- burden analyses have lately become a very successful way for the identification of genes carrying risk variants underlying the analysed disease. This approach is also suitable for complex disorders like autism spectrum disorder (ASD). The gene-burden analysis using Testing Rare Variants with Public Data (TRAPD) software was conducted on whole exome sequencing data of Slovenian patients with ASD to determine potentially novel disease risk variants in known ASD-associated genes as well as in others. To choose the right control group for testing, principal component analysis based on the 1000 Genomes and ASD cohort samples was conducted. The subsequent protein structure and ligand binding analysis usingI-TASSER package were performed to detect changes in protein structure and ligand binding to determine a potential pathogenic consequence of observed mutation. The obtained results demonstrate an association of two variants-p.Glu198Lys (PPP2R5D:c.592G>A) and p.Arg253Gln (PPP2R5D:c.758G>A) with the ASD. Substitution p.Glu198Lys (PPP2R5D:c.592G>A) is a variant, previously described as pathogenic in association with ASD combined with intellectual disability, whereas p.Arg253Gln (PPP2R5D:c.758G>A) has not been described as an ASD-associated pathogenic variant yet. The results indicate that the filtering process was suitable and could be used in the future for detection of novel pathogenic variants when analysing groups of ASD patients.
Collapse
Affiliation(s)
- Nika Rihar
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
| | - Danijela Krgovic
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Maribor Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Nadja Kokalj-Vokač
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Maribor Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Spela Stangler-Herodez
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Maribor Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Minja Zorc
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
| | - Peter Dovc
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
30
|
Vardarajan BN, Reyes‐Dumeyer D, Piriz AL, Lantigua RA, Medrano M, Rivera D, Jiménez‐Velázquez IZ, Martin E, Pericak‐Vance MA, Bush W, Farrer L, Haines JL, Wang L, Leung YY, Schellenberg G, Kukull W, De Jager P, Bennett DA, Schneider JA, Mayeux R. Progranulin mutations in clinical and neuropathological Alzheimer's disease. Alzheimers Dement 2022; 18:2458-2467. [PMID: 35258170 PMCID: PMC9360185 DOI: 10.1002/alz.12567] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/07/2021] [Accepted: 12/10/2021] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Progranulin (GRN) mutations occur in frontotemporal lobar degeneration (FTLD) and in Alzheimer's disease (AD), often with TDP-43 pathology. METHODS We determined the frequency of rs5848 and rare, pathogenic GRN mutations in two autopsy and one family cohort. We compared Braak stage, β-amyloid load, hyperphosphorylated tau (PHFtau) tangle density and TDP-43 pathology in GRN carriers and non-carriers. RESULTS Pathogenic GRN mutations were more frequent in all cohorts compared to the Genome Aggregation Database (gnomAD), but there was no evidence for association with AD. Pathogenic GRN carriers had significantly higher PHFtau tangle density adjusting for age, sex and APOE ε4 genotype. AD patients with rs5848 had higher frequencies of hippocampal sclerosis and TDP-43 deposits. Twenty-two rare, pathogenic GRN variants were observed in the family cohort. DISCUSSION GRN mutations in clinical and neuropathological AD increase the burden of tau-related brain pathology but show no specific association with β-amyloid load or AD.
Collapse
Affiliation(s)
- Badri N. Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- The Gertrude H. Sergievsky CenterCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University and the New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Dolly Reyes‐Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- The Gertrude H. Sergievsky CenterCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University and the New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Angel L. Piriz
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- The Gertrude H. Sergievsky CenterCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Rafael A. Lantigua
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- Department of MedicineCollege of Physicians and SurgeonsColumbia University, and the New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Martin Medrano
- School of MedicinePontificia Universidad Catolica Madre y Maestra (PUCMM)SantiagoDominican Republic
| | - Diones Rivera
- Department of NeurologyCEDIMAT, Plaza de la SaludSanto DomingoDominican Republic
- School of MedicineUniversidad Pedro Henriquez Urena (UNPHU)Santo DomingoDominican Republic
| | | | - Eden Martin
- The John P. Hussman Institute for Human Genomicsand Dr. John T. Macdonald Foundation Department of Human GeneticsMiamiFloridaUSA
| | - Margaret A. Pericak‐Vance
- The John P. Hussman Institute for Human Genomicsand Dr. John T. Macdonald Foundation Department of Human GeneticsMiamiFloridaUSA
| | - William Bush
- Department of Biostatistics and EpidemiologyCase Western Reserve UniversityClevelandOhioUSA
| | - Lindsay Farrer
- Boston University School of MedicineBostonMassachusettsUSA
| | - Jonathan L. Haines
- Department of Biostatistics and EpidemiologyCase Western Reserve UniversityClevelandOhioUSA
| | - Li‐San Wang
- School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Yuk Yee Leung
- School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | | | - Walter Kukull
- Department of EpidemiologySchool of Public HealthUniversity of WashingtonSeattleWashingtonUSA
| | - Philip De Jager
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University and the New York Presbyterian HospitalNew YorkNew YorkUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Julie A. Schneider
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | | | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- The Gertrude H. Sergievsky CenterCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University and the New York Presbyterian HospitalNew YorkNew YorkUSA
- Department of EpidemiologySchool of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Department of PsychiatryCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| |
Collapse
|
31
|
Salasova A, Monti G, Andersen OM, Nykjaer A. Finding memo: versatile interactions of the VPS10p-Domain receptors in Alzheimer’s disease. Mol Neurodegener 2022; 17:74. [PMID: 36397124 PMCID: PMC9673319 DOI: 10.1186/s13024-022-00576-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
The family of VPS10p-Domain (D) receptors comprises five members named SorLA, Sortilin, SorCS1, SorCS2 and SorCS3. While their physiological roles remain incompletely resolved, they have been recognized for their signaling engagements and trafficking abilities, navigating a number of molecules between endosome, Golgi compartments, and the cell surface. Strikingly, recent studies connected all the VPS10p-D receptors to Alzheimer’s disease (AD) development. In addition, they have been also associated with diseases comorbid with AD such as diabetes mellitus and major depressive disorder. This systematic review elaborates on genetic, functional, and mechanistic insights into how dysfunction in VPS10p-D receptors may contribute to AD etiology, AD onset diversity, and AD comorbidities. Starting with their functions in controlling cellular trafficking of amyloid precursor protein and the metabolism of the amyloid beta peptide, we present and exemplify how these receptors, despite being structurally similar, regulate various and distinct cellular events involved in AD. This includes a plethora of signaling crosstalks that impact on neuronal survival, neuronal wiring, neuronal polarity, and synaptic plasticity. Signaling activities of the VPS10p-D receptors are especially linked, but not limited to, the regulation of neuronal fitness and apoptosis via their physical interaction with pro- and mature neurotrophins and their receptors. By compiling the functional versatility of VPS10p-D receptors and their interactions with AD-related pathways, we aim to further propel the AD research towards VPS10p-D receptor family, knowledge that may lead to new diagnostic markers and therapeutic strategies for AD patients.
Collapse
|
32
|
A genetically modified minipig model for Alzheimer’s disease with SORL1 haploinsufficiency. Cell Rep Med 2022; 3:100740. [PMID: 36099918 PMCID: PMC9512670 DOI: 10.1016/j.xcrm.2022.100740] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/20/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022]
Abstract
The established causal genes in Alzheimer’s disease (AD), APP, PSEN1, and PSEN2, are functionally characterized using biomarkers, capturing an in vivo profile reflecting the disease’s initial preclinical phase. Mutations in SORL1, encoding the endosome recycling receptor SORLA, are found in 2%–3% of individuals with early-onset AD, and SORL1 haploinsufficiency appears to be causal for AD. To test whether SORL1 can function as an AD causal gene, we use CRISPR-Cas9-based gene editing to develop a model of SORL1 haploinsufficiency in Göttingen minipigs, taking advantage of porcine models for biomarker investigations. SORL1 haploinsufficiency in young adult minipigs is found to phenocopy the preclinical in vivo profile of AD observed with APP, PSEN1, and PSEN2, resulting in elevated levels of β-amyloid (Aβ) and tau preceding amyloid plaque formation and neurodegeneration, as observed in humans. Our study provides functional support for the theory that SORL1 haploinsufficiency leads to endosome cytopathology with biofluid hallmarks of autosomal dominant AD. Minipig model of Alzheimer’s disease by CRISPR knockout of the causal gene SORL1 Young SORL1 het minipigs phenocopy a preclinical CSF biomarker profile of individuals with AD SORL1 haploinsufficiency causes enlarged endosomes similar to neuronal AD pathology A minipig model bridging the translational gap between AD mouse models and affected individuals
Collapse
|
33
|
Tejada Moreno JA, Villegas Lanau A, Madrigal Zapata L, Baena Pineda AY, Velez Hernandez J, Campo Nieto O, Soto Ospina A, Araque Marín P, Rishishwar L, Norris ET, Chande AT, Jordan IK, Bedoya Berrio G. Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PLoS One 2022; 17:e0269955. [PMID: 35905044 PMCID: PMC9337667 DOI: 10.1371/journal.pone.0269955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/31/2022] [Indexed: 11/19/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia in the elderly, affecting over 50 million people worldwide in 2020 and this number will triple to 152 million by 2050. Much of the increase will be in developing countries like Colombia. In familial forms, highly penetrant mutations have been identified in three genes, APP, PSEN1, and PSEN2, supporting a role for amyloid-β peptide. In sporadic forms, more than 30 risk genes involved in the lipid metabolism, the immune system, and synaptic functioning mechanisms. We used whole-exome sequencing (WES) to evaluate a family of 97 members, spanning three generations, with a familiar AD, and without mutations in APP, PSEN1, or PSEN2. We sequenced two affected and one unaffected member with the aim of identifying genetic variants that could explain the presence of the disease in the family and the candidate variants were validated in eleven members. We also built a structural model to try to determine the effect on protein function. WES analysis identified two rare variants in SORL1 and MTHFD1L genes segregating in the family with other potential risk variants in APOE, ABCA7, and CHAT, suggesting an oligogenic inheritance. Additionally, the structural 3D models of SORL1 and MTHFD1L variants shows that these variants produce polarity changes that favor hydrophobic interactions, resulting in local structural changes that could affect the protein function and may contribute to the development of the disease in this family.
Collapse
Affiliation(s)
| | | | | | | | | | - Omer Campo Nieto
- Molecular Genetics Research Group, University of Antioquia, Medellin, Colombia
| | | | - Pedronel Araque Marín
- Research and Innovation Group in Chemical Formulations, EIA University, Medellin, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Emily T. Norris
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Aroon T. Chande
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - I. King Jordan
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | | |
Collapse
|
34
|
Schramm C, Charbonnier C, Zaréa A, Lacour M, Wallon D, Boland A, Deleuze JF, Olaso R, Alarcon F, Campion D, Nuel G, Nicolas G. Penetrance estimation of Alzheimer disease in SORL1 loss-of-function variant carriers using a family-based strategy and stratification by APOE genotypes. Genome Med 2022; 14:69. [PMID: 35761418 PMCID: PMC9238165 DOI: 10.1186/s13073-022-01070-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/08/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Alzheimer disease (AD) is a common complex disorder with a high genetic component. Loss-of-function (LoF) SORL1 variants are one of the strongest AD genetic risk factors. Estimating their age-related penetrance is essential before putative use for genetic counseling or preventive trials. However, relative rarity and co-occurrence with the main AD risk factor, APOE-ε4, make such estimations difficult. METHODS We proposed to estimate the age-related penetrance of SORL1-LoF variants through a survival framework by estimating the conditional instantaneous risk combining (i) a baseline for non-carriers of SORL1-LoF variants, stratified by APOE-ε4, derived from the Rotterdam study (N = 12,255), and (ii) an age-dependent proportional hazard effect for SORL1-LoF variants estimated from 27 extended pedigrees (including 307 relatives ≥ 40 years old, 45 of them having genotyping information) recruited from the French reference center for young Alzheimer patients. We embedded this model into an expectation-maximization algorithm to accommodate for missing genotypes. To correct for ascertainment bias, proband phenotypes were omitted. Then, we assessed if our penetrance curves were concordant with age distributions of APOE-ε4-stratified SORL1-LoF variant carriers detected among sequencing data of 13,007 cases and 10,182 controls from European and American case-control study consortia. RESULTS SORL1-LoF variants penetrance curves reached 100% (95% confidence interval [99-100%]) by age 70 among APOE-ε4ε4 carriers only, compared with 56% [40-72%] and 37% [26-51%] in ε4 heterozygous carriers and ε4 non-carriers, respectively. These estimates were fully consistent with observed age distributions of SORL1-LoF variant carriers in case-control study data. CONCLUSIONS We conclude that SORL1-LoF variants should be interpreted in light of APOE genotypes for future clinical applications.
Collapse
Affiliation(s)
- Catherine Schramm
- Normandie Université, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, FHU-G4 Génomique, 22 boulevard Gambetta - CS 76183, Rouen, F-76000, France
| | - Camille Charbonnier
- Normandie Université, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, FHU-G4 Génomique, 22 boulevard Gambetta - CS 76183, Rouen, F-76000, France
| | - Aline Zaréa
- Normandie Université, UNIROUEN, Inserm U1245, CHU Rouen, Department of Neurology and CNRMAJ, FHU-G4 Génomique, Rouen, F-76000, France
| | - Morgane Lacour
- Normandie Université, UNIROUEN, Inserm U1245, CHU Rouen, Department of Neurology and CNRMAJ, FHU-G4 Génomique, Rouen, F-76000, France
| | - David Wallon
- Normandie Université, UNIROUEN, Inserm U1245, CHU Rouen, Department of Neurology and CNRMAJ, FHU-G4 Génomique, Rouen, F-76000, France
| | | | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Evry, France
| | | | - Flora Alarcon
- MAP5, UMR-CNRS 8145, Paris University, 75270, Paris, France
| | - Dominique Campion
- Normandie Université, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, FHU-G4 Génomique, 22 boulevard Gambetta - CS 76183, Rouen, F-76000, France.,Department of Research, Rouvray Psychiatric Hospital, 76681, Sotteville-Lès-Rouen, France
| | - Grégory Nuel
- LPSM, CNRS 8001, Sorbonne University, 75005, Paris, France
| | - Gaël Nicolas
- Normandie Université, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, FHU-G4 Génomique, 22 boulevard Gambetta - CS 76183, Rouen, F-76000, France.
| |
Collapse
|
35
|
Sirkis DW, Bonham LW, Johnson TP, La Joie R, Yokoyama JS. Dissecting the clinical heterogeneity of early-onset Alzheimer's disease. Mol Psychiatry 2022; 27:2674-2688. [PMID: 35393555 PMCID: PMC9156414 DOI: 10.1038/s41380-022-01531-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/14/2022]
Abstract
Early-onset Alzheimer's disease (EOAD) is a rare but particularly devastating form of AD. Though notable for its high degree of clinical heterogeneity, EOAD is defined by the same neuropathological hallmarks underlying the more common, late-onset form of AD. In this review, we describe the various clinical syndromes associated with EOAD, including the typical amnestic phenotype as well as atypical variants affecting visuospatial, language, executive, behavioral, and motor functions. We go on to highlight advances in fluid biomarker research and describe how molecular, structural, and functional neuroimaging can be used not only to improve EOAD diagnostic acumen but also enhance our understanding of fundamental pathobiological changes occurring years (and even decades) before the onset of symptoms. In addition, we discuss genetic variation underlying EOAD, including pathogenic variants responsible for the well-known mendelian forms of EOAD as well as variants that may increase risk for the much more common forms of EOAD that are either considered to be sporadic or lack a clear autosomal-dominant inheritance pattern. Intriguingly, specific pathogenic variants in PRNP and MAPT-genes which are more commonly associated with other neurodegenerative diseases-may provide unexpectedly important insights into the formation of AD tau pathology. Genetic analysis of the atypical clinical syndromes associated with EOAD will continue to be challenging given their rarity, but integration of fluid biomarker data, multimodal imaging, and various 'omics techniques and their application to the study of large, multicenter cohorts will enable future discoveries of fundamental mechanisms underlying the development of EOAD and its varied clinical presentations.
Collapse
Affiliation(s)
- Daniel W Sirkis
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Luke W Bonham
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Taylor P Johnson
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Renaud La Joie
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, 94158, USA.
| |
Collapse
|
36
|
Abstract
PURPOSE OF REVIEW This article discusses the spectrum of genetic risk in familial and sporadic forms of early- and late-onset Alzheimer disease (AD). Recent work illuminating the complex genetic architecture of AD is discussed in the context of high and low risk and what is known in different populations. RECENT FINDINGS A small proportion of AD is autosomal dominant familial AD caused by variants in PSEN1, PSEN2, or APP, although more recently described rare genetic changes can also increase risk substantially over the general population, with odds ratios estimated at 2 to 4. APOE remains the strongest genetic risk factor for late-onset AD, and understanding the biology of APOE has yielded mechanistic insights and leads for therapeutic interventions. Genome-wide studies enabled by rapidly developing technologic advances in sequencing have identified numerous risk factors that have a low impact on risk but are widely shared throughout the population and involve a repertoire of cell pathways, again shining light on potential paths to intervention. Population studies aimed at defining and stratifying genetic AD risk have been informative, although they are not yet widely applicable clinically because the studies were not performed in people with diverse ancestry and ethnicity and thus population-wide data are lacking. SUMMARY The value of genetic information to practitioners in the clinic is distinct from information sought by researchers looking to identify novel therapeutic targets. It is possible to envision a future in which genetic stratification joins other biomarkers to facilitate therapeutic choices and inform prognosis. Genetics already has transformed our understanding of AD pathogenesis and will, no doubt, continue to reveal the complexity of brain biology in health and disease.
Collapse
|
37
|
Alvarez-Mora MI, Blanco-Palmero VA, Quesada-Espinosa JF, Arteche-Lopez AR, Llamas-Velasco S, Palma Milla C, Lezana Rosales JM, Gomez-Manjon I, Hernandez-Lain A, Jimenez Almonacid J, Gil-Fournier B, Ramiro-León S, González-Sánchez M, Herrero-San Martín AO, Pérez-Martínez DA, Gómez-Tortosa E, Carro E, Bartolomé F, Gomez-Rodriguez MJ, Sanchez-Calvin MT, Villarejo-Galende A, Moreno-Garcia M. Heterozygous and Homozygous Variants in SORL1 Gene in Alzheimer's Disease Patients: Clinical, Neuroimaging and Neuropathological Findings. Int J Mol Sci 2022; 23:ijms23084230. [PMID: 35457051 PMCID: PMC9024679 DOI: 10.3390/ijms23084230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/05/2022] [Accepted: 04/09/2022] [Indexed: 02/05/2023] Open
Abstract
In the last few years, the SORL1 gene has been strongly implicated in the development of Alzheimer’s disease (AD). We performed whole-exome sequencing on 37 patients with early-onset dementia or family history suggestive of autosomal dominant dementia. Data analysis was based on a custom panel that included 46 genes related to AD and dementia. SORL1 variants were present in a high proportion of patients with candidate variants (15%, 3/20). We expand the clinical manifestations associated with the SORL1 gene by reporting detailed clinical and neuroimaging findings of six unrelated patients with AD and SORL1 mutations. We also present for the first time a patient with the homozygous truncating variant c.364C>T (p.R122*) in SORL1, who also had severe cerebral amyloid angiopathy. Furthermore, we report neuropathological findings and immunochemistry assays from one patient with the splicing variant c.4519+5G>A in the SORL1 gene, in which AD was confirmed by neuropathological examination. Our results highlight the heterogeneity of clinical presentation and familial dementia background of SORL1-associated AD and suggest that SORL1 might be contributing to AD development as a risk factor gene rather than as a major autosomal dominant gene.
Collapse
Affiliation(s)
- Maria Isabel Alvarez-Mora
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- Biochemistry and Molecular Genetic Service, Hospital Clínic de Barcelona, 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-932275400 (ext. 9940)
| | - Victor Antonio Blanco-Palmero
- Neurology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (V.A.B.-P.); (S.L.-V.); (M.G.-S.); (A.O.H.-S.M.); (D.A.P.-M.); (A.V.-G.)
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain; (E.C.); (F.B.)
- Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Juan Francisco Quesada-Espinosa
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- UdisGen—Unidad de Dismorfología y Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Ana Rosa Arteche-Lopez
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- UdisGen—Unidad de Dismorfología y Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Sara Llamas-Velasco
- Neurology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (V.A.B.-P.); (S.L.-V.); (M.G.-S.); (A.O.H.-S.M.); (D.A.P.-M.); (A.V.-G.)
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain; (E.C.); (F.B.)
- Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Carmen Palma Milla
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- UdisGen—Unidad de Dismorfología y Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Jose Miguel Lezana Rosales
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- UdisGen—Unidad de Dismorfología y Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Irene Gomez-Manjon
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- UdisGen—Unidad de Dismorfología y Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Aurelio Hernandez-Lain
- Neuropathology Unit, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (A.H.-L.); (J.J.A.)
| | | | - Belén Gil-Fournier
- Genetic Service, Hospital Universitario de Getafe, 28905 Madrid, Spain; (B.G.-F.); (S.R.-L.)
| | - Soraya Ramiro-León
- Genetic Service, Hospital Universitario de Getafe, 28905 Madrid, Spain; (B.G.-F.); (S.R.-L.)
| | - Marta González-Sánchez
- Neurology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (V.A.B.-P.); (S.L.-V.); (M.G.-S.); (A.O.H.-S.M.); (D.A.P.-M.); (A.V.-G.)
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain; (E.C.); (F.B.)
- Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Alejandro Octavio Herrero-San Martín
- Neurology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (V.A.B.-P.); (S.L.-V.); (M.G.-S.); (A.O.H.-S.M.); (D.A.P.-M.); (A.V.-G.)
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain; (E.C.); (F.B.)
- Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - David Andrés Pérez-Martínez
- Neurology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (V.A.B.-P.); (S.L.-V.); (M.G.-S.); (A.O.H.-S.M.); (D.A.P.-M.); (A.V.-G.)
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain; (E.C.); (F.B.)
- Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | | | - Eva Carro
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain; (E.C.); (F.B.)
- Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Fernando Bartolomé
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain; (E.C.); (F.B.)
- Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Maria Jose Gomez-Rodriguez
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- UdisGen—Unidad de Dismorfología y Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Network Center for Biomedical Research in Cancer (CIBERONC), 28029 Madrid, Spain
| | - María Teresa Sanchez-Calvin
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- UdisGen—Unidad de Dismorfología y Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Alberto Villarejo-Galende
- Neurology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (V.A.B.-P.); (S.L.-V.); (M.G.-S.); (A.O.H.-S.M.); (D.A.P.-M.); (A.V.-G.)
- Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Marta Moreno-Garcia
- Genetic Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (J.F.Q.-E.); (A.R.A.-L.); (C.P.M.); (J.M.L.R.); (I.G.-M.); (M.J.G.-R.); (M.T.S.-C.); (M.M.-G.)
- UdisGen—Unidad de Dismorfología y Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| |
Collapse
|
38
|
Behl T, Kaur D, Sehgal A, Singh S, Makeen HA, Albratty M, Abdellatif AAH, Dachani SR, Bungau S. Exploring the potential role of rab5 protein in endo-lysosomal impairment in Alzheimer's disease. Biomed Pharmacother 2022; 148:112773. [PMID: 35245734 DOI: 10.1016/j.biopha.2022.112773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/27/2022] [Indexed: 11/02/2022] Open
Abstract
Growing evidence suggests that neuronal dysfunction in the endo-lysosomal and autophagic processes contributes to the onset and progression of neurodegenerative diseases such as Alzheimer's disease (AD). Since they are the primary cellular systems involved in the production and clearance of aggregated amyloid plaques, endo-lysosomal or autophagic equilibrium must be maintained throughout life. As a result, variations in the autophagic and endo-lysosomal torrent, as a measure of degenerative function in these sections or pathways, may have a direct impact on disease-related processes, such as Aß clearance from the brain and interneuronal deposition of Aß and tau aggregates, thus disrupting synaptic plasticity. The discovery of several chromosomal factors for Alzheimer's disease that are clinically linked to regulation of the endocytic pathway, including protein aggregation and removal, supports the theory that the endo-lysosomal/autophagic torrent is more susceptible to impairment, especially as people age, thus catalysing the onset of disease. Although the role of endo-lysosomal/autophagic dysfunction in neurodegeneration has progressed in recent years, the field remains underdeveloped. Because of its possible therapeutic implications in Alzheimer's disease, further study is needed to explain the possibilities for effective autophagy regulation.
Collapse
Affiliation(s)
- Tapan Behl
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India.
| | - Dapinder Kaur
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Aayush Sehgal
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Sukhbir Singh
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Hafiz A Makeen
- Pharmacy Practice Research Unit, Clinical Pharmacy, Department, College of Pharmacy, Jazan University, P.O. Box-114, Jazan 45142, Saudi Arabia
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Ahmed A H Abdellatif
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia; Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Sudharshan Reddy Dachani
- Department of Pharmacy Practice & Pharmacology, College of Pharmacy, Shaqra University, Al-Dawadmi Campus, Al-Dawadmi 11961, Saudi Arabia
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania.
| |
Collapse
|
39
|
Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset. Nat Neurosci 2022; 25:446-457. [PMID: 35379994 PMCID: PMC8986535 DOI: 10.1038/s41593-022-01033-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
The age at onset of motor symptoms in Huntington's disease (HD) is driven by HTT CAG repeat length but modified by other genes. In this study, we used exome sequencing of 683 patients with HD with extremes of onset or phenotype relative to CAG length to identify rare variants associated with clinical effect. We discovered damaging coding variants in candidate modifier genes identified in previous genome-wide association studies associated with altered HD onset or severity. Variants in FAN1 clustered in its DNA-binding and nuclease domains and were associated predominantly with earlier-onset HD. Nuclease activities of purified variants in vitro correlated with residual age at motor onset of HD. Mutating endogenous FAN1 to a nuclease-inactive form in an induced pluripotent stem cell model of HD led to rates of CAG expansion similar to those observed with complete FAN1 knockout. Together, these data implicate FAN1 nuclease activity in slowing somatic repeat expansion and hence onset of HD.
Collapse
|
40
|
Mishra S, Knupp A, Szabo MP, Williams CA, Kinoshita C, Hailey DW, Wang Y, Andersen OM, Young JE. The Alzheimer's gene SORL1 is a regulator of endosomal traffic and recycling in human neurons. Cell Mol Life Sci 2022; 79:162. [PMID: 35226190 PMCID: PMC8885486 DOI: 10.1007/s00018-022-04182-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Loss of the Sortilin-related receptor 1 (SORL1) gene seems to act as a causal event for Alzheimer's disease (AD). Recent studies have established that loss of SORL1, as well as mutations in autosomal dominant AD genes APP and PSEN1/2, pathogenically converge by swelling early endosomes, AD's cytopathological hallmark. Acting together with the retromer trafficking complex, SORL1 has been shown to regulate the recycling of the amyloid precursor protein (APP) out of the endosome, contributing to endosomal swelling and to APP misprocessing. We hypothesized that SORL1 plays a broader role in neuronal endosomal recycling and used human induced pluripotent stem cell-derived neurons (hiPSC-Ns) to test this hypothesis. We examined endosomal recycling of three transmembrane proteins linked to AD pathophysiology: APP, the BDNF receptor Tropomyosin-related kinase B (TRKB), and the glutamate receptor subunit AMPA1 (GLUA1). METHODS We used isogenic hiPSCs engineered to have SORL1 depleted or to have enhanced SORL1 expression. We differentiated neurons from these cell lines and mapped the trafficking of APP, TRKB and GLUA1 within the endosomal network using confocal microscopy. We also performed cell surface recycling and lysosomal degradation assays to assess the functionality of the endosomal network in both SORL1-depleted and -overexpressing neurons. The functional impact of GLUA1 recycling was determined by measuring synaptic activity. Finally, we analyzed alterations in gene expression in SORL1-depleted neurons using RNA sequencing. RESULTS We find that as with APP, endosomal trafficking of GLUA1 and TRKB is impaired by loss of SORL1. We show that trafficking of all three cargoes to late endosomes and lysosomes is affected by manipulating SORL1 expression. We also show that depletion of SORL1 significantly impacts the endosomal recycling pathway for APP and GLUA1 at the level of the recycling endosome and trafficking to the cell surface. This has a functional effect on neuronal activity as shown by multi-electrode array (MEA). Conversely, increased SORL1 expression enhances endosomal recycling for APP and GLUA1. Our unbiased transcriptomic data further support SORL1's role in endosomal recycling. We observe altered expression networks that regulate cell surface trafficking and neurotrophic signaling in SORL1-depleted neurons. CONCLUSION Collectively, and together with other recent observations, these findings suggest that one role for SORL1 is to contribute to endosomal degradation and recycling pathways in neurons, a conclusion that has both pathogenic and therapeutic implications for Alzheimer's disease.
Collapse
Affiliation(s)
- Swati Mishra
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195 USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
| | - Allison Knupp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195 USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
| | - Marcell P. Szabo
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195 USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
| | - Charles A. Williams
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195 USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
| | - Chizuru Kinoshita
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195 USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
| | - Dale W. Hailey
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195 USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195 USA
| | - Olav M. Andersen
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience (DANDRITE), Aarhus University, Aarhus, Denmark
| | - Jessica E. Young
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195 USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
| |
Collapse
|
41
|
Deng W, Murugan S, Lindberg J, Chellappa V, Shen X, Pawitan Y, Vu TN. Fusion Gene Detection Using Whole-Exome Sequencing Data in Cancer Patients. Front Genet 2022; 13:820493. [PMID: 35251131 PMCID: PMC8888970 DOI: 10.3389/fgene.2022.820493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/31/2022] [Indexed: 12/13/2022] Open
Abstract
Several fusion genes are directly involved in the initiation and progression of cancers. Numerous bioinformatics tools have been developed to detect fusion events, but they are mainly based on RNA-seq data. The whole-exome sequencing (WES) represents a powerful technology that is widely used for disease-related DNA variant detection. In this study, we build a novel analysis pipeline called Fuseq-WES to detect fusion genes at DNA level based on the WES data. The same method applies also for targeted panel sequencing data. We assess the method to real datasets of acute myeloid leukemia (AML) and prostate cancer patients. The result shows that two of the main AML fusion genes discovered in RNA-seq data, PML-RARA and CBFB-MYH11, are detected in the WES data in 36 and 63% of the available samples, respectively. For the targeted deep-sequencing of prostate cancer patients, detection of the TMPRSS2-ERG fusion, which is the most frequent chimeric alteration in prostate cancer, is 91% concordant with a manually curated procedure based on four other methods. In summary, the overall results indicate that it is challenging to detect fusion genes in WES data with a standard coverage of ∼ 15–30x, where fusion candidates discovered in the RNA-seq data are often not detected in the WES data and vice versa. A subsampling study of the prostate data suggests that a coverage of at least 75x is necessary to achieve high accuracy.
Collapse
Affiliation(s)
- Wenjiang Deng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sarath Murugan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Venkatesh Chellappa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xia Shen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine, Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Yudi Pawitan, ; Trung Nghia Vu,
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Yudi Pawitan, ; Trung Nghia Vu,
| |
Collapse
|
42
|
Whole exome sequencing in Alopecia Areata identifies rare variants in KRT82. Nat Commun 2022; 13:800. [PMID: 35145093 PMCID: PMC8831607 DOI: 10.1038/s41467-022-28343-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 11/22/2021] [Indexed: 01/31/2023] Open
Abstract
Alopecia areata is a complex genetic disease that results in hair loss due to the autoimmune-mediated attack of the hair follicle. We previously defined a role for both rare and common variants in our earlier GWAS and linkage studies. Here, we identify rare variants contributing to Alopecia Areata using a whole exome sequencing and gene-level burden analyses approach on 849 Alopecia Areata patients compared to 15,640 controls. KRT82 is identified as an Alopecia Areata risk gene with rare damaging variants in 51 heterozygous Alopecia Areata individuals (6.01%), achieving genome-wide significance (p = 2.18E−07). KRT82 encodes a hair-specific type II keratin that is exclusively expressed in the hair shaft cuticle during anagen phase, and its expression is decreased in Alopecia Areata patient skin and hair follicles. Finally, we find that cases with an identified damaging KRT82 variant and reduced KRT82 expression have elevated perifollicular CD8 infiltrates. In this work, we utilize whole exome sequencing to successfully identify a significant Alopecia Areata disease-relevant gene, KRT82, and reveal a proposed mechanism for rare variant predisposition leading to disrupted hair shaft integrity. Common variants have been discovered to be associated with Alopecia Areata; however, rare variants have been less well studied. Here, the authors use whole-exome sequencing to identify associated rare variants in the hair keratin gene KRT82. Further, they find that individuals with Alopecia Areata have reduced expression of KRT82 in the skin and hair follicle.
Collapse
|
43
|
Prokopenko D, Lee S, Hecker J, Mullin K, Morgan S, Katsumata Y, Weiner MW, Fardo DW, Laird N, Bertram L, Hide W, Lange C, Tanzi RE. Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer's disease-associated genes: DTNB and DLG2. Mol Psychiatry 2022; 27:1963-1969. [PMID: 35246634 PMCID: PMC9126808 DOI: 10.1038/s41380-022-01475-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/25/2022] [Accepted: 02/04/2022] [Indexed: 01/01/2023]
Abstract
Alzheimer's disease (AD) is a genetically complex disease for which nearly 40 loci have now been identified via genome-wide association studies (GWAS). We attempted to identify groups of rare variants (alternate allele frequency <0.01) associated with AD in a region-based, whole-genome sequencing (WGS) association study (rvGWAS) of two independent AD family datasets (NIMH/NIA; 2247 individuals; 605 families). Employing a sliding window approach across the genome, we identified several regions that achieved association p values <10-6, using the burden test or the SKAT statistic. The genomic region around the dystobrevin beta (DTNB) gene was identified with the burden and SKAT test and replicated in case/control samples from the ADSP study reaching genome-wide significance after meta-analysis (pmeta = 4.74 × 10-8). SKAT analysis also revealed region-based association around the Discs large homolog 2 (DLG2) gene and replicated in case/control samples from the ADSP study (pmeta = 1 × 10-6). In conclusion, in a region-based rvGWAS of AD we identified two novel AD genes, DLG2 and DTNB, based on association with rare variants.
Collapse
Affiliation(s)
- Dmitry Prokopenko
- grid.32224.350000 0004 0386 9924Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Sanghun Lee
- grid.411982.70000 0001 0705 4288Department of Medical Consilience, Graduate School, Dankook University, Yongin, South Korea ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Julian Hecker
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Kristina Mullin
- grid.32224.350000 0004 0386 9924Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA USA
| | - Sarah Morgan
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA USA
| | - Yuriko Katsumata
- grid.266539.d0000 0004 1936 8438Department of Biostatistics, University of Kentucky, Lexington, KY USA ,grid.266539.d0000 0004 1936 8438Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY USA
| | | | - Michael W. Weiner
- grid.266102.10000 0001 2297 6811Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA USA
| | - David W. Fardo
- grid.266539.d0000 0004 1936 8438Department of Biostatistics, University of Kentucky, Lexington, KY USA ,grid.266539.d0000 0004 1936 8438Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY USA
| | - Nan Laird
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Lars Bertram
- grid.4562.50000 0001 0057 2672Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany ,grid.5510.10000 0004 1936 8921Department of Psychology, University of Oslo, Oslo, Norway
| | - Winston Hide
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA USA
| | - Christoph Lange
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Rudolph E. Tanzi
- grid.32224.350000 0004 0386 9924Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| |
Collapse
|
44
|
Szabo MP, Mishra S, Knupp A, Young JE. The role of Alzheimer's disease risk genes in endolysosomal pathways. Neurobiol Dis 2021; 162:105576. [PMID: 34871734 PMCID: PMC9071255 DOI: 10.1016/j.nbd.2021.105576] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 11/23/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022] Open
Abstract
There is ample pathological and biological evidence for endo-lysosomal dysfunction in Alzheimer's disease (AD) and emerging genetic studies repeatedly implicate endo-lysosomal genes as associated with increased AD risk. The endo-lysosomal network (ELN) is essential for all cell types of the central nervous system (CNS), yet each unique cell type utilizes cellular trafficking differently (see Fig. 1). Challenges ahead involve defining the role of AD associated genes in the functionality of the endo-lysosomal network (ELN) and understanding how this impacts the cellular dysfunction that occurs in AD. This is critical to the development of new therapeutics that will impact, and potentially reverse, early disease phenotypes. Here we review some early evidence of ELN dysfunction in AD pathogenesis and discuss the role of selected AD-associated risk genes in this pathway. In particular, we review genes that have been replicated in multiple genome-wide association studies(Andrews et al., 2020; Jansen et al., 2019; Kunkle et al., 2019; Lambert et al., 2013; Marioni et al., 2018) and reviewed in(Andrews et al., 2020) that have defined roles in the endo-lysosomal network. These genes include SORL1, an AD risk gene harboring both rare and common variants associated with AD risk and a role in trafficking cargo, including APP, through the ELN; BIN1, a regulator of clathrin-mediated endocytosis whose expression correlates with Tau pathology; CD2AP, an AD risk gene with roles in endosome morphology and recycling; PICALM, a clathrin-binding protein that mediates trafficking between the trans-Golgi network and endosomes; and Ephrin Receptors, a family of receptor tyrosine kinases with AD associations and interactions with other AD risk genes. Finally, we will discuss how human cellular models can elucidate cell-type specific differences in ELN dysfunction in AD and aid in therapeutic development.
Collapse
Affiliation(s)
- Marcell P Szabo
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, United States of America; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, United States of America
| | - Swati Mishra
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, United States of America; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, United States of America
| | - Allison Knupp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, United States of America; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, United States of America
| | - Jessica E Young
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, United States of America; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, United States of America.
| |
Collapse
|
45
|
Association of low-frequency and rare coding variants with information processing speed. Transl Psychiatry 2021; 11:613. [PMID: 34864818 PMCID: PMC8643353 DOI: 10.1038/s41398-021-01736-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/20/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
Measures of information processing speed vary between individuals and decline with age. Studies of aging twins suggest heritability may be as high as 67%. The Illumina HumanExome Bead Chip genotyping array was used to examine the association of rare coding variants with performance on the Digit-Symbol Substitution Test (DSST) in community-dwelling adults participating in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. DSST scores were available for 30,576 individuals of European ancestry from nine cohorts and for 5758 individuals of African ancestry from four cohorts who were older than 45 years and free of dementia and clinical stroke. Linear regression models adjusted for age and gender were used for analysis of single genetic variants, and the T5, T1, and T01 burden tests that aggregate the number of rare alleles by gene were also applied. Secondary analyses included further adjustment for education. Meta-analyses to combine cohort-specific results were carried out separately for each ancestry group. Variants in RNF19A reached the threshold for statistical significance (p = 2.01 × 10-6) using the T01 test in individuals of European descent. RNF19A belongs to the class of E3 ubiquitin ligases that confer substrate specificity when proteins are ubiquitinated and targeted for degradation through the 26S proteasome. Variants in SLC22A7 and OR51A7 were suggestively associated with DSST scores after adjustment for education for African-American participants and in the European cohorts, respectively. Further functional characterization of its substrates will be required to confirm the role of RNF19A in cognitive function.
Collapse
|
46
|
Li Y, Laws SM, Miles LA, Wiley JS, Huang X, Masters CL, Gu BJ. Genomics of Alzheimer's disease implicates the innate and adaptive immune systems. Cell Mol Life Sci 2021; 78:7397-7426. [PMID: 34708251 PMCID: PMC11073066 DOI: 10.1007/s00018-021-03986-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/14/2021] [Accepted: 10/16/2021] [Indexed: 02/08/2023]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterised by cognitive impairment, behavioural alteration, and functional decline. Over 130 AD-associated susceptibility loci have been identified by genome-wide association studies (GWAS), while whole genome sequencing (WGS) and whole exome sequencing (WES) studies have identified AD-associated rare variants. These variants are enriched in APOE, TREM2, CR1, CD33, CLU, BIN1, CD2AP, PILRA, SCIMP, PICALM, SORL1, SPI1, RIN3, and more genes. Given that aging is the single largest risk factor for late-onset AD (LOAD), the accumulation of somatic mutations in the brain and blood of AD patients have also been explored. Collectively, these genetic findings implicate the role of innate and adaptive immunity in LOAD pathogenesis and suggest that a systemic failure of cell-mediated amyloid-β (Aβ) clearance contributes to AD onset and progression. AD-associated variants are particularly enriched in myeloid-specific regulatory regions, implying that AD risk variants are likely to perturbate the expression of myeloid-specific AD-associated genes to interfere Aβ clearance. Defective phagocytosis, endocytosis, and autophagy may drive Aβ accumulation, which may be related to naturally-occurring antibodies to Aβ (Nabs-Aβ) produced by adaptive responses. Passive immunisation is providing efficiency in clearing Aβ and slowing cognitive decline, such as aducanumab, donanemab, and lecanemab (ban2401). Causation of AD by impairment of the innate immunity and treatment using the tools of adaptive immunity is emerging as a new paradigm for AD, but immunotherapy that boosts the innate immune functions of myeloid cells is highly expected to modulate disease progression at asymptomatic stage.
Collapse
Affiliation(s)
- Yihan Li
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
| | - Luke A Miles
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - James S Wiley
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - Xin Huang
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ben J Gu
- The Florey Institute, The University of Melbourne, 30 Royal Parade, Parkville, VIC, 3052, Australia.
| |
Collapse
|
47
|
Bell KC, Ozaki M, Mori K, Mizoguchi T, Nakano S, Porporato N, Ikeda Y, Chihara E, Inoue K, Manabe S, Hayashi K, Higashide T, Ideta R, Tokumo K, Kiuchi Y, Nakano M, Ueno M, Kinoshita S, Tashiro K, Sotozono C, Inatani M, Sugiyama K, Kubota T, Li Z, Wang Z, Khor CC, Aung T. Association of the CYP39A1 G204E genetic variant with increased risk of glaucoma and blindness in patients with exfoliation syndrome. Ophthalmology 2021; 129:406-413. [PMID: 34763023 DOI: 10.1016/j.ophtha.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 12/01/2022] Open
Abstract
PURPOSE Carriers of functionally deficient mutations in the CYP39A1 gene have been recently reported to have a 2-fold increased risk of exfoliation syndrome (XFS). The aim of this study was to evaluate the risk of blindness and related clinical phenotypes of XFS patients carrying the loss-of-function CYP39A1 G204E mutation in comparison to XFS patients without any CYP39A1 mutation. DESIGN Retrospective case study PARTICIPANTS: 35 patients diagnosed with XFS carrying the CYP39A1 G204E mutation and 150 XFS patients without any CYP39A1 mutation, who were randomly selected from the Japanese XFS cohort. METHODS Two-sided Fisher's Exact Test with an α-level <0.05 was used to estimate the significance of the calculated Odds Ratio (OR) for all categorical measures. Comparisons between groups of subjects were performed using linear mixed effect models with group as random effect and taking possible dependence between eyes within a subject into account. MAIN OUTCOME MEASURES Primary analysis compared the incidence of blindness (defined as visual acuity [VA]<0.05 decimal), prevalence of exfoliation glaucoma (XFG), history of glaucoma surgery, and indices of glaucoma severity such as visual field mean deviation (MD), intraocular pressure (IOP) and vertical cup-disc ratio (CDR), between CYP39A1 G204E carriers and those without any CYP39A1 mutation. RESULTS The overall risk for blindness was significantly higher in XFS patients carrying the CYP39A1 G204E variant (10/35 [28.6%]) compared to XFS patients without any CYP39A1 mutations (8/150 [5.3%]; OR7.1 [95%CI:2.7-20.2]; p<0.001). A higher proportion of XFS patients with the CYP39A1 G204E mutation (23/35 [65.7%]) had evidence of XFG in at least one eye compared to the comparison group (41/150 [27.3%]; OR5.1 [95%CI:2.4-11.4]; p<0.0001). Significantly higher peak IOP, larger vertical CDR and worse visual field MD were also found in CYP39A1 G204E variant carriers (p<0.001). Additionally, patients with the CYP39A1 G204E mutation (18/35 [51.4%]) required more laser or glaucoma surgical interventions compared to those without any CYP39A1 mutation (32/150 [21.3%], p<0.001). CONCLUSIONS Patients with XFS carrying the CYP39A1 G204E mutation had significantly increased risk of blindness, higher occurrence of XFG and more severe glaucoma compared to patients with XFS without any CYP39A1 mutation.
Collapse
Affiliation(s)
- Katharina C Bell
- Singapore Eye Research Institute and Singapore National Eye Center, Singapore; Duke-NUS Medical School, Singapore
| | - Mineo Ozaki
- Ozaki Eye Hospital, Hyuga, Miyazaki, Japan; Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kazuhiko Mori
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | - Satoko Nakano
- Department of Ophthalmology, Oita University Faculty of Medicine, Yufu-City, Oita, Japan
| | - Natalia Porporato
- Singapore Eye Research Institute and Singapore National Eye Center, Singapore; Duke-NUS Medical School, Singapore
| | - Yoko Ikeda
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | | | | | | | - Tomomi Higashide
- Department of Ophthalmology Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | | | - Kana Tokumo
- Hiroshima University Department of Ophthalmology and Visual Sciences, Hiroshima, Japan
| | - Yoshiaki Kiuchi
- Hiroshima University Department of Ophthalmology and Visual Sciences, Hiroshima, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Morio Ueno
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shigeru Kinoshita
- Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masaru Inatani
- Department of Ophthalmology, Faculty of Medical Science, University of Fukui, Fukui, Japan
| | | | - Toshiaki Kubota
- Department of Ophthalmology, Oita University Faculty of Medicine, Yufu-City, Oita, Japan
| | - Zheng Li
- Genome Institute of Singapore, Singapore
| | - Zhenxun Wang
- Singapore Eye Research Institute and Singapore National Eye Center, Singapore; Genome Institute of Singapore, Singapore
| | - Chiea Chuen Khor
- Singapore Eye Research Institute and Singapore National Eye Center, Singapore; Genome Institute of Singapore, Singapore
| | - Tin Aung
- Singapore Eye Research Institute and Singapore National Eye Center, Singapore; Duke-NUS Medical School, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| |
Collapse
|
48
|
Qiao L, Xu L, Yu L, Wynn J, Hernan R, Zhou X, Farkouh-Karoleski C, Krishnan US, Khlevner J, De A, Zygmunt A, Crombleholme T, Lim FY, Needelman H, Cusick RA, Mychaliska GB, Warner BW, Wagner AJ, Danko ME, Chung D, Potoka D, Kosiński P, McCulley DJ, Elfiky M, Azarow K, Fialkowski E, Schindel D, Soffer SZ, Lyon JB, Zalieckas JM, Vardarajan BN, Aspelund G, Duron VP, High FA, Sun X, Donahoe PK, Shen Y, Chung WK. Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene. Am J Hum Genet 2021; 108:1964-1980. [PMID: 34547244 PMCID: PMC8546037 DOI: 10.1016/j.ajhg.2021.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.
Collapse
Affiliation(s)
- Lu Qiao
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Le Xu
- Department of Pediatrics, University of California, San Diego Medical School, San Diego, CA 92093, USA
| | - Lan Yu
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xueya Zhou
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Usha S Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julie Khlevner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aliva De
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annette Zygmunt
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Foong-Yen Lim
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Howard Needelman
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | - Robert A Cusick
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | | | - Brad W Warner
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amy J Wagner
- Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | | | | | - David J McCulley
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 52726, USA
| | | | - Kenneth Azarow
- Oregon Health & Science University, Portland, OR 97239, USA
| | | | | | | | - Jane B Lyon
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Jill M Zalieckas
- Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Badri N Vardarajan
- Department of Neurology, Taub Institute for Research on Alzheimer Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, NY 10032, USA
| | - Gudrun Aspelund
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vincent P Duron
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xin Sun
- Department of Pediatrics, University of California, San Diego Medical School, San Diego, CA 92093, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
49
|
Qiu S, Palavicini JP, Wang J, Gonzalez NS, He S, Dustin E, Zou C, Ding L, Bhattacharjee A, Van Skike CE, Galvan V, Dupree JL, Han X. Adult-onset CNS myelin sulfatide deficiency is sufficient to cause Alzheimer's disease-like neuroinflammation and cognitive impairment. Mol Neurodegener 2021; 16:64. [PMID: 34526055 PMCID: PMC8442347 DOI: 10.1186/s13024-021-00488-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Human genetic association studies point to immune response and lipid metabolism, in addition to amyloid-beta (Aβ) and tau, as major pathways in Alzheimer's disease (AD) etiology. Accumulating evidence suggests that chronic neuroinflammation, mainly mediated by microglia and astrocytes, plays a causative role in neurodegeneration in AD. Our group and others have reported early and dramatic losses of brain sulfatide in AD cases and animal models that are mediated by ApoE in an isoform-dependent manner and accelerated by Aβ accumulation. To date, it remains unclear if changes in specific brain lipids are sufficient to drive AD-related pathology. METHODS To study the consequences of CNS sulfatide deficiency and gain insights into the underlying mechanisms, we developed a novel mouse model of adult-onset myelin sulfatide deficiency, i.e., tamoxifen-inducible myelinating glia-specific cerebroside sulfotransferase (CST) conditional knockout mice (CSTfl/fl/Plp1-CreERT), took advantage of constitutive CST knockout mice (CST-/-), and generated CST/ApoE double knockout mice (CST-/-/ApoE-/-), and assessed these mice using a broad range of methodologies including lipidomics, RNA profiling, behavioral testing, PLX3397-mediated microglia depletion, mass spectrometry (MS) imaging, immunofluorescence, electron microscopy, and Western blot. RESULTS We found that mild central nervous system (CNS) sulfatide losses within myelinating cells are sufficient to activate disease-associated microglia and astrocytes, and to increase the expression of AD risk genes (e.g., Apoe, Trem2, Cd33, and Mmp12), as well as previously established causal regulators of the immune/microglia network in late-onset AD (e.g., Tyrobp, Dock, and Fcerg1), leading to chronic AD-like neuroinflammation and mild cognitive impairment. Notably, neuroinflammation and mild cognitive impairment showed gender differences, being more pronounced in females than males. Subsequent mechanistic studies demonstrated that although CNS sulfatide losses led to ApoE upregulation, genetically-induced myelin sulfatide deficiency led to neuroinflammation independently of ApoE. These results, together with our previous studies (sulfatide deficiency in the context of AD is mediated by ApoE and accelerated by Aβ accumulation) placed both Aβ and ApoE upstream of sulfatide deficiency-induced neuroinflammation, and suggested a positive feedback loop where sulfatide losses may be amplified by increased ApoE expression. We also demonstrated that CNS sulfatide deficiency-induced astrogliosis and ApoE upregulation are not secondary to microgliosis, and that astrogliosis and microgliosis seem to be driven by activation of STAT3 and PU.1/Spi1 transcription factors, respectively. CONCLUSION Our results strongly suggest that sulfatide deficiency is an important contributor and driver of neuroinflammation and mild cognitive impairment in AD pathology.
Collapse
Affiliation(s)
- Shulan Qiu
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
| | - Juan Pablo Palavicini
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jianing Wang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
- Present Address: State Key Lab. of Environmental & Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hongkong, China
| | - Nancy S Gonzalez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
| | - Sijia He
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
| | - Elizabeth Dustin
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia, 23284, USA
| | - Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Lin Ding
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Anindita Bhattacharjee
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
| | - Candice E Van Skike
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Veronica Galvan
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jeffrey L Dupree
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia, 23284, USA
- Research Division, McGuire Veterans Affairs Medical Center, Richmond, Virginia, 23249, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, 4939 Charles Katz Drive, San Antonio, TX, 78229, USA.
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| |
Collapse
|
50
|
Halvorsen M, Samuels J, Wang Y, Greenberg BD, Fyer AJ, McCracken JT, Geller DA, Knowles JA, Zoghbi AW, Pottinger TD, Grados MA, Riddle MA, Bienvenu OJ, Nestadt PS, Krasnow J, Goes FS, Maher B, Nestadt G, Goldstein DB. Exome sequencing in obsessive-compulsive disorder reveals a burden of rare damaging coding variants. Nat Neurosci 2021; 24:1071-1076. [PMID: 34183866 DOI: 10.1038/s41593-021-00876-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/18/2021] [Indexed: 02/05/2023]
Abstract
Obsessive-compulsive disorder (OCD) affects 1-2% of the population, and, as with other complex neuropsychiatric disorders, it is thought that rare variation contributes to its genetic risk. In this study, we performed exome sequencing in the largest OCD cohort to date (1,313 total cases, consisting of 587 trios, 41 quartets and 644 singletons of affected individuals) and describe contributions to disease risk from rare damaging coding variants. In case-control analyses (n = 1,263/11,580), the most significant single-gene result was observed in SLITRK5 (odds ratio (OR) = 8.8, 95% confidence interval 3.4-22.5, P = 2.3 × 10-6). Across the exome, there was an excess of loss of function (LoF) variation specifically within genes that are LoF-intolerant (OR = 1.33, P = 0.01). In an analysis of trios, we observed an excess of de novo missense predicted damaging variants relative to controls (OR = 1.22, P = 0.02), alongside an excess of de novo LoF mutations in LoF-intolerant genes (OR = 2.55, P = 7.33 × 10-3). These data support a contribution of rare coding variants to OCD genetic risk.
Collapse
Affiliation(s)
- Mathew Halvorsen
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jack Samuels
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ying Wang
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin D Greenberg
- Department of Psychiatry and Human Behavior, Brown Medical School, Providence, RI, USA
| | - Abby J Fyer
- New York State Psychiatric Institute, College of Physicians and Surgeons at Columbia University, New York, NY, USA
| | - James T McCracken
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at Los Angeles, Los Angeles, CA, USA
| | - Daniel A Geller
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - James A Knowles
- SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | - Anthony W Zoghbi
- New York State Psychiatric Institute, College of Physicians and Surgeons at Columbia University, New York, NY, USA
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Tess D Pottinger
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Marco A Grados
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark A Riddle
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - O Joseph Bienvenu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Paul S Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janice Krasnow
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brion Maher
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA.
| |
Collapse
|