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Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. Neurobiol Aging 2023; 131:182-195. [PMID: 37677864 PMCID: PMC10538380 DOI: 10.1016/j.neurobiolaging.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 09/09/2023]
Abstract
A missense variant in the tetratricopeptide repeat domain 3 (TTC3) gene (rs377155188, p.S1038C, NM_003316.4:c 0.3113C>G) was found to segregate with disease in a multigenerational family with late-onset Alzheimer's disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing, and the resulting isogenic pair of iPSC lines was differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3-dimensional morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant.
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Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carolina L Duarte
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mayra J Laverde-Paz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shaina A Simon
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek J Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Amanda T Miyares
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; JJ Vance Memorial Summer Internship in Biological and Computational Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina M Carney
- Mental Health & Behavioral Science Service, Bruce W. Carter VA Medical Center, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
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Mantyh WG, Cochran JN, Taylor JW, Broce IJ, Geier EG, Bonham LW, Anderson AG, Sirkis DW, Joie RL, Iaccarino L, Chaudhary K, Edwards L, Strom A, Grant H, Allen IE, Miller ZA, Gorno‐Tempini ML, Kramer JH, Miller BL, Desikan RS, Rabinovici GD, Yokoyama JS. Early-onset Alzheimer's disease explained by polygenic risk of late-onset disease? ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2023; 15:e12482. [PMID: 37780862 PMCID: PMC10535074 DOI: 10.1002/dad2.12482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
Early-onset Alzheimer's disease (AD) is highly heritable, yet only 10% of cases are associated with known pathogenic mutations. For early-onset AD patients without an identified autosomal dominant cause, we hypothesized that their early-onset disease reflects further enrichment of the common risk-conferring single nucleotide polymorphisms associated with late-onset AD. We applied a previously validated polygenic hazard score for late-onset AD to 193 consecutive patients diagnosed at our tertiary dementia referral center with symptomatic early-onset AD. For comparison, we included 179 participants with late-onset AD and 70 healthy controls. Polygenic hazard scores were similar in early- versus late-onset AD. The polygenic hazard score was not associated with age-of-onset or disease biomarkers within early-onset AD. Early-onset AD does not represent an extreme enrichment of the common single nucleotide polymorphisms associated with late-onset AD. Further exploration of novel genetic risk factors of this highly heritable disease is warranted.Highlights: There is a unique genetic architecture of early- versus late-onset Alzheimer's disease (AD).Late-onset AD polygenic risk is not an explanation for early-onset AD.Polygenic risk of late-onset AD does not predict early-onset AD biology.Unique genetic architecture of early- versus late-onset AD parallels AD heterogeneity.
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Affiliation(s)
- William G. Mantyh
- Department of NeurologyUniversity of MinnesotaMinneapolisMinnesotaUSA
| | | | | | - Iris J. Broce
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Ethan G. Geier
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Luke W. Bonham
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | | | - Daniel W. Sirkis
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Renaud La Joie
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Leonardo Iaccarino
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Kiran Chaudhary
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Lauren Edwards
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Amelia Strom
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Harli Grant
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Isabel E. Allen
- Department of Epidemiology and BiostatisticsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Zachary A. Miller
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Marilu L. Gorno‐Tempini
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Joel H. Kramer
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Bruce L. Miller
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Rahul S. Desikan
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Gil D. Rabinovici
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Life Sciences DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Jennifer S. Yokoyama
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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Cukier HN, Duarte CL, Laverde-Paz MJ, Simon SA, Van Booven DJ, Miyares AT, Whitehead PL, Hamilton-Nelson KL, Adams LD, Carney RM, Cuccaro ML, Vance JM, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM. An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542316. [PMID: 37292815 PMCID: PMC10246004 DOI: 10.1101/2023.05.25.542316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A missense variant in the tetratricopeptide repeat domain 3 ( TTC3 ) gene (rs377155188, p.S1038C, NM_003316.4:c.3113C>G) was found to segregate with disease in a multigenerational family with late onset Alzheimer's disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing and the resulting isogenic pair of iPSC lines were differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3D morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant. Highlights The AD risk variant TTC3 p.S1038C reduces the expression levels of TTC3 The variant modifies the expression of AD specific genes BACE1 , INPP5F , and UNC5C Neurons with the variant are enriched for genes in the PI3K-Akt pathwayiPSC-derived neurons with the alteration have increased neurite length and branchingThe variant interferes with actin cytoskeleton and is ameliorated by Cytochalasin D.
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Integrated regulation of dopaminergic and epigenetic effectors of neuroprotection in Parkinson's disease models. Proc Natl Acad Sci U S A 2023; 120:e2210712120. [PMID: 36745808 PMCID: PMC9963946 DOI: 10.1073/pnas.2210712120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Whole-exome sequencing of Parkinson's disease (PD) patient DNA identified single-nucleotide polymorphisms (SNPs) in the tyrosine nonreceptor kinase-2 (TNK2) gene. Although this kinase had a previously demonstrated activity in preventing the endocytosis of the dopamine reuptake transporter (DAT), a causal role for TNK2-associated dysfunction in PD remains unresolved. We postulated the dopaminergic neurodegeneration resulting from patient-associated variants in TNK2 were a consequence of aberrant or prolonged TNK2 overactivity, the latter being a failure in TNK2 degradation by an E3 ubiquitin ligase, neuronal precursor cell-expressed developmentally down-regulated-4 (NEDD4). Interestingly, systemic RNA interference protein-3 (SID-3) is the sole TNK2 ortholog in the nematode Caenorhabditis elegans, where it is an established effector of epigenetic gene silencing mediated through the dsRNA-transporter, SID-1. We hypothesized that TNK2/SID-3 represents a node of integrated dopaminergic and epigenetic signaling essential to neuronal homeostasis. Use of a TNK2 inhibitor (AIM-100) or a NEDD4 activator [N-aryl benzimidazole 2 (NAB2)] in bioassays for either dopamine- or dsRNA-uptake into worm dopaminergic neurons revealed that sid-3 mutants displayed robust neuroprotection from 6-hydroxydopamine (6-OHDA) exposures, as did AIM-100 or NAB2-treated wild-type animals. Furthermore, NEDD4 activation by NAB2 in rat primary neurons correlated to a reduction in TNK2 levels and the attenuation of 6-OHDA neurotoxicity. CRISPR-edited nematodes engineered to endogenously express SID-3 variants analogous to TNK2 PD-associated SNPs exhibited enhanced susceptibility to dopaminergic neurodegeneration and circumvented the RNAi resistance characteristic of SID-3 dysfunction. This research exemplifies a molecular etiology for PD whereby dopaminergic and epigenetic signaling are coordinately regulated to confer susceptibility or resilience to neurodegeneration.
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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.
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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
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A Patient with Corticobasal Syndrome and Progressive Non-Fluent Aphasia (CBS-PNFA), with Variants in ATP7B, SETX, SORL1, and FOXP1 Genes. Genes (Basel) 2022; 13:genes13122361. [PMID: 36553628 PMCID: PMC9778325 DOI: 10.3390/genes13122361] [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: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Our aim was to analyze the phenotypic-genetic correlations in a patient diagnosed with early onset corticobasal syndrome with progressive non-fluent aphasia (CBS-PNFA), characterized by predominant apraxia of speech, accompanied by prominent right-sided upper-limb limb-kinetic apraxia, alien limb phenomenon, synkinesis, myoclonus, mild cortical sensory loss, and right-sided hemispatial neglect. Whole-exome sequencing (WES) identified rare single heterozygous variants in ATP7B (c.3207C>A), SORL1 (c.352G>A), SETX (c.2385_2387delAAA), and FOXP1 (c.1762G>A) genes. The functional analysis revealed that the deletion in the SETX gene changed the splicing pattern, which was accompanied by lower SETX mRNA levels in the patient's fibroblasts, suggesting loss-of-function as the underlying mechanism. In addition, the patient's fibroblasts demonstrated altered mitochondrial architecture with decreased connectivity, compared to the control individuals. This is the first association of the CBS-PNFA phenotype with the most common ATP7B pathogenic variant p.H1069Q, previously linked to Wilson's disease, and early onset Parkinson's disease. This study expands the complex clinical spectrum related to variants in well-known disease genes, such as ATP7B, SORL1, SETX, and FOXP1, corroborating the hypothesis of oligogenic inheritance. To date, the FOXP1 gene has been linked exclusively to neurodevelopmental speech disorders, while our study highlights its possible relevance for adult-onset progressive apraxia of speech, which guarantees further study.
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Bartoletti-Stella A, Tarozzi M, Mengozzi G, Asirelli F, Brancaleoni L, Mometto N, Stanzani-Maserati M, Baiardi S, Linarello S, Spallazzi M, Pantieri R, Ferriani E, Caffarra P, Liguori R, Parchi P, Capellari S. Dementia-related genetic variants in an Italian population of early-onset Alzheimer’s disease. Front Aging Neurosci 2022; 14:969817. [PMID: 36133075 PMCID: PMC9484406 DOI: 10.3389/fnagi.2022.969817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Early-onset Alzheimer’s disease (EOAD) is the most common form of early-onset dementia. Although three major genes have been identified as causative, the genetic contribution to the disease remains unsolved in many patients. Recent studies have identified pathogenic variants in genes representing a risk factor for developing Alzheimer’s disease (AD) and in causative genes for other degenerative dementias as responsible for EOAD. To study them further, we investigated a panel of candidate genes in 102 Italian EOAD patients, 45.10% of whom had a positive family history and 21.74% with a strong family history of dementia. We found that 10.78% of patients carried pathogenic or likely pathogenic variants, including a novel variant, in PSEN1, PSEN2, or APP, and 7.84% showed homozygosity for the ε4 APOE allele. Additionally, 7.84% of patients had a moderate risk allele in PSEN1, PSEN2, or TREM2 genes. Besides, we observed that 12.75% of our patients carried only a variant in genes associated with other neurodegenerative diseases. The combination of these variants contributes to explain 46% of cases with a definite familiarity and 32% of sporadic forms. Our results confirm the importance of extensive genetic screening in EOAD for clinical purposes, to select patients for future treatments and to contribute to the definition of overlapping pathogenic mechanisms between AD and other forms of dementia.
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Affiliation(s)
- Anna Bartoletti-Stella
- Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Martina Tarozzi
- Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Giacomo Mengozzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
| | - Francesca Asirelli
- Department of Medical Science and Surgery (DIMEC), University of Bologna, Bologna, Italy
| | - Laura Brancaleoni
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
- Neurologia e Rete Stroke Metropolitana, Ospedale Maggiore, Bologna, Italy
| | - Nicola Mometto
- UOC Neurologia, Ospedale Guglielmo da Saliceto, Piacenza, Italy
| | | | - Simone Baiardi
- Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
| | - Simona Linarello
- Programma Cure Intermedie - Azienda USL di Bologna, Bologna, Italy
| | - Marco Spallazzi
- U.O. di Neurologia, Azienda Ospedaliero-Universitaria, Parma, Italy
| | - Roberta Pantieri
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
| | - Elisa Ferriani
- UOC Psicologia Clinica Ospedaliera, Ospedale Bellaria, Azienda USL di Bologna, Bologna, Italy
| | - Paolo Caffarra
- Unità di Neuroscienze, Università di Parma, Parma, Italy
| | - Rocco Liguori
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Piero Parchi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Sabina Capellari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- *Correspondence: Sabina Capellari,
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Huq AJ, Thompson B, Bennett MF, Bournazos A, Bommireddipalli S, Gorelik A, Schultz J, Sexton A, Purvis R, West K, Cotter M, Valente G, Hughes A, Riaz M, Walsh M, Farrand S, Loi SM, Kilpatrick T, Brodtmann A, Darby D, Eratne D, Walterfang M, Delatycki MB, Storey E, Fahey M, Cooper S, Lacaze P, Masters CL, Velakoulis D, Bahlo M, James PA, Winship I. Clinical impact of whole-genome sequencing in patients with early-onset dementia. J Neurol Neurosurg Psychiatry 2022; 93:jnnp-2021-328146. [PMID: 35906014 DOI: 10.1136/jnnp-2021-328146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/07/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND In the clinical setting, identification of the genetic cause in patients with early-onset dementia (EOD) is challenging due to multiple types of genetic tests required to arrive at a diagnosis. Whole-genome sequencing (WGS) has the potential to serve as a single diagnostic platform, due to its superior ability to detect common, rare and structural genetic variation. METHODS WGS analysis was performed in 50 patients with EOD. Point mutations, small insertions/deletions, as well as structural variants (SVs) and short tandem repeats (STRs), were analysed. An Alzheimer's disease (AD)-related polygenic risk score (PRS) was calculated in patients with AD. RESULTS Clinical genetic diagnosis was achieved in 7 of 50 (14%) of the patients, with a further 8 patients (16%) found to have established risk factors which may have contributed to their EOD. Two pathogenic variants were identified through SV analysis. No expanded STRs were found in this study cohort, but a blinded analysis with a positive control identified a C9orf72 expansion accurately. Approximately 37% (7 of 19) of patients with AD had a PRS equivalent to >90th percentile risk. DISCUSSION WGS acts as a single genetic test to identify different types of clinically relevant genetic variations in patients with EOD. WGS, if used as a first-line clinical diagnostic test, has the potential to increase the diagnostic yield and reduce time to diagnosis for EOD.
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Affiliation(s)
- Aamira J Huq
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Bryony Thompson
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
- Department of Pathology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Adam Bournazos
- Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Shobhana Bommireddipalli
- Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Alexandra Gorelik
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Joshua Schultz
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Rebecca Purvis
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Kirsty West
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Megan Cotter
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Giulia Valente
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Andrew Hughes
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Moeen Riaz
- Public Health and Preventative Medicine, Monash University Faculty of Medicine, Nursing and Health Sciences, Melbourne, Victoria, Australia
| | - Maie Walsh
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Sarah Farrand
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Samantha M Loi
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Trevor Kilpatrick
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Amy Brodtmann
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Heidelberg, Victoria, Australia
- Florey Neurosciences Institutes, University of Melbourne, Carlton South, Victoria, Australia
| | - David Darby
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Heidelberg, Victoria, Australia
- Mental Health Research Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Dhamidhu Eratne
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Mark Walterfang
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - Elsdon Storey
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
- Neuroscience, Alfred Health, Melbourne, Victoria, Australia
| | - Michael Fahey
- Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Sandra Cooper
- Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Paul Lacaze
- Public Health and Preventative Medicine, Monash University Faculty of Medicine, Nursing and Health Sciences, Melbourne, Victoria, Australia
| | - Colin L Masters
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Dennis Velakoulis
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Paul A James
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Ingrid Winship
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
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9
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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.
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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
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10
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Acosta-Uribe J, Aguillón D, Cochran JN, Giraldo M, Madrigal L, Killingsworth BW, Singhal R, Labib S, Alzate D, Velilla L, Moreno S, García GP, Saldarriaga A, Piedrahita F, Hincapié L, López HE, Perumal N, Morelo L, Vallejo D, Solano JM, Reiman EM, Surace EI, Itzcovich T, Allegri R, Sánchez-Valle R, Villegas-Lanau A, White CL, Matallana D, Myers RM, Browning SR, Lopera F, Kosik KS. A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects. Genome Med 2022; 14:27. [PMID: 35260199 PMCID: PMC8902761 DOI: 10.1186/s13073-022-01035-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 02/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Colombian population, as well as those in other Latin American regions, arose from a recent tri-continental admixture among Native Americans, Spanish invaders, and enslaved Africans, all of whom passed through a population bottleneck due to widespread infectious diseases that left small isolated local settlements. As a result, the current population reflects multiple founder effects derived from diverse ancestries. METHODS We characterized the role of admixture and founder effects on the origination of the mutational landscape that led to neurodegenerative disorders under these historical circumstances. Genomes from 900 Colombian individuals with Alzheimer's disease (AD) [n = 376], frontotemporal lobar degeneration-motor neuron disease continuum (FTLD-MND) [n = 197], early-onset dementia not otherwise specified (EOD) [n = 73], and healthy participants [n = 254] were analyzed. We examined their global and local ancestry proportions and screened this cohort for deleterious variants in disease-causing and risk-conferring genes. RESULTS We identified 21 pathogenic variants in AD-FTLD related genes, and PSEN1 harbored the majority (11 pathogenic variants). Variants were identified from all three continental ancestries. TREM2 heterozygous and homozygous variants were the most common among AD risk genes (102 carriers), a point of interest because the disease risk conferred by these variants differed according to ancestry. Several gene variants that have a known association with MND in European populations had FTLD phenotypes on a Native American haplotype. Consistent with founder effects, identity by descent among carriers of the same variant was frequent. CONCLUSIONS Colombian demography with multiple mini-bottlenecks probably enhanced the detection of founder events and left a proportionally higher frequency of rare variants derived from the ancestral populations. These findings demonstrate the role of genomically defined ancestry in phenotypic disease expression, a phenotypic range of different rare mutations in the same gene, and further emphasize the importance of inclusiveness in genetic studies.
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Affiliation(s)
- Juliana Acosta-Uribe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - David Aguillón
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Margarita Giraldo
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
- Instituto Neurológico de Colombia (INDEC), Medellín, Colombia
| | - Lucía Madrigal
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Bradley W Killingsworth
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Rijul Singhal
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Sarah Labib
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Diana Alzate
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Lina Velilla
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Sonia Moreno
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Gloria P García
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Amanda Saldarriaga
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Francisco Piedrahita
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Liliana Hincapié
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Hugo E López
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Nithesh Perumal
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Leonilde Morelo
- Department of Internal Medicine, School of Medicine, Universidad del Sinú, Montería, Colombia
| | - Dionis Vallejo
- Department of Neurology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Juan Marcos Solano
- Department of Neurology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Ezequiel I Surace
- Laboratorio de Enfermedades Neurodegenerativas (Fleni-CONICET), Buenos Aires, Argentina
| | - Tatiana Itzcovich
- Laboratorio de Enfermedades Neurodegenerativas (Fleni-CONICET), Buenos Aires, Argentina
| | - Ricardo Allegri
- Centro de Memoria y Envejecimiento (Fleni-CONICET), Buenos Aires, Argentina
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Andrés Villegas-Lanau
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Charles L White
- Neuropathology Section, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diana Matallana
- Instituto de Envejecimiento, Department of Psychiatry, School of Medicine, Pontifical Xaverian University, Bogotá, Colombia
- Department of Mental Health, Hospital Universitario Santa Fe de Bogotá, Bogotá, Colombia
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.
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11
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A human tau seeded neuronal cell model recapitulates molecular responses associated with Alzheimer's disease. Sci Rep 2022; 12:2673. [PMID: 35177665 PMCID: PMC8854741 DOI: 10.1038/s41598-022-06411-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022] Open
Abstract
Cellular models recapitulating features of tauopathies are useful tools to investigate the causes and consequences of tau aggregation and the identification of novel treatments. We seeded rat primary cortical neurons with tau isolated from Alzheimer’s disease brains to induce a time-dependent increase in endogenous tau inclusions. Transcriptomics of seeded and control cells identified 1075 differentially expressed genes (including 26 altered at two time points). These were enriched for lipid/steroid metabolism and neuronal/glial cell development genes. 50 genes were correlated with tau inclusion formation at both transcriptomic and proteomic levels, including several microtubule and cytoskeleton-related proteins such as Tubb2a, Tubb4a, Nefl and Snca. Several genes (such as Fyn kinase and PTBP1, a tau exon 10 repressor) interact directly with or regulate tau. We conclude that this neuronal model may be a suitable platform for high-throughput screens for target or hit compound identification and validation.
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12
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Tarozzi M, Bartoletti-Stella A, Dall'Olio D, Matteuzzi T, Baiardi S, Parchi P, Castellani G, Capellari S. Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases. BMC Med Genomics 2022; 15:26. [PMID: 35144616 PMCID: PMC8830183 DOI: 10.1186/s12920-022-01173-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background Targeted Next Generation Sequencing is a common and powerful approach used in both clinical and research settings. However, at present, a large fraction of the acquired genetic information is not used since pathogenicity cannot be assessed for most variants. Further complicating this scenario is the increasingly frequent description of a poli/oligogenic pattern of inheritance showing the contribution of multiple variants in increasing disease risk. We present an approach in which the entire genetic information provided by target sequencing is transformed into binary data on which we performed statistical, machine learning, and network analyses to extract all valuable information from the entire genetic profile. To test this approach and unbiasedly explore the presence of recurrent genetic patterns, we studied a cohort of 112 patients affected either by genetic Creutzfeldt–Jakob (CJD) disease caused by two mutations in the PRNP gene (p.E200K and p.V210I) with different penetrance or by sporadic Alzheimer disease (sAD). Results Unsupervised methods can identify functionally relevant sources of variation in the data, like haplogroups and polymorphisms that do not follow Hardy–Weinberg equilibrium, such as the NOTCH3 rs11670823 (c.3837 + 21 T > A). Supervised classifiers can recognize clinical phenotypes with high accuracy based on the mutational profile of patients. In addition, we found a similar alteration of allele frequencies compared the European population in sporadic patients and in V210I-CJD, a poorly penetrant PRNP mutation, and sAD, suggesting shared oligogenic patterns in different types of dementia. Pathway enrichment and protein–protein interaction network revealed different altered pathways between the two PRNP mutations. Conclusions We propose this workflow as a possible approach to gain deeper insights into the genetic information derived from target sequencing, to identify recurrent genetic patterns and improve the understanding of complex diseases. This work could also represent a possible starting point of a predictive tool for personalized medicine and advanced diagnostic applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01173-4.
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Affiliation(s)
- M Tarozzi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - A Bartoletti-Stella
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - D Dall'Olio
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - T Matteuzzi
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - S Baiardi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - P Parchi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - G Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.
| | - S Capellari
- IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
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13
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Hu B, Duan S, Wang Z, Li X, Zhou Y, Zhang X, Zhang YW, Xu H, Zheng H. Insights Into the Role of CSF1R in the Central Nervous System and Neurological Disorders. Front Aging Neurosci 2021; 13:789834. [PMID: 34867307 PMCID: PMC8634759 DOI: 10.3389/fnagi.2021.789834] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/26/2021] [Indexed: 01/15/2023] Open
Abstract
The colony-stimulating factor 1 receptor (CSF1R) is a key tyrosine kinase transmembrane receptor modulating microglial homeostasis, neurogenesis, and neuronal survival in the central nervous system (CNS). CSF1R, which can be proteolytically cleaved into a soluble ectodomain and an intracellular protein fragment, supports the survival of myeloid cells upon activation by two ligands, colony stimulating factor 1 and interleukin 34. CSF1R loss-of-function mutations are the major cause of adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) and its dysfunction has also been implicated in other neurodegenerative disorders including Alzheimer’s disease (AD). Here, we review the physiological functions of CSF1R in the CNS and its pathological effects in neurological disorders including ALSP, AD, frontotemporal dementia and multiple sclerosis. Understanding the pathophysiology of CSF1R is critical for developing targeted therapies for related neurological diseases.
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Affiliation(s)
- Banglian Hu
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China
| | - Shengshun Duan
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China
| | - Ziwei Wang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China
| | - Xin Li
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China
| | - Yuhang Zhou
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China
| | - Xian Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China
| | - Yun-Wu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China
| | - Huaxi Xu
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China
| | - Honghua Zheng
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Institute of Neuroscience, Xiamen University, Xiamen, China.,Basic Medical Sciences, School of Medicine, Xiamen University, Xiamen, China
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14
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Salazar JL, Yang SA, Lin YQ, Li-Kroeger D, Marcogliese PC, Deal SL, Neely GG, Yamamoto S. TM2D genes regulate Notch signaling and neuronal function in Drosophila. PLoS Genet 2021; 17:e1009962. [PMID: 34905536 PMCID: PMC8714088 DOI: 10.1371/journal.pgen.1009962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/28/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
TM2 domain containing (TM2D) proteins are conserved in metazoans and encoded by three separate genes in each model organism species that has been sequenced. Rare variants in TM2D3 are associated with Alzheimer's disease (AD) and its fly ortholog almondex is required for embryonic Notch signaling. However, the functions of this gene family remain elusive. We knocked-out all three TM2D genes (almondex, CG11103/amaretto, CG10795/biscotti) in Drosophila and found that they share the same maternal-effect neurogenic defect. Triple null animals are not phenotypically worse than single nulls, suggesting these genes function together. Overexpression of the most conserved region of the TM2D proteins acts as a potent inhibitor of Notch signaling at the γ-secretase cleavage step. Lastly, Almondex is detected in the brain and its loss causes shortened lifespan accompanied by progressive motor and electrophysiological defects. The functional links between all three TM2D genes are likely to be evolutionarily conserved, suggesting that this entire gene family may be involved in AD.
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Affiliation(s)
- Jose L. Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Sheng-An Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Yong Qi Lin
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - David Li-Kroeger
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Neurology, BCM, Houston, Texas, United States of America
- Center for Alzheimer’s and Neurodegenerative Diseases, BCM, Houston, Texas, United States of America
| | - Paul C. Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Samantha L. Deal
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Program in Developmental Biology, BCM, Houston, Texas, United States of America
| | - G. Gregory Neely
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Center for Alzheimer’s and Neurodegenerative Diseases, BCM, Houston, Texas, United States of America
- Program in Developmental Biology, BCM, Houston, Texas, United States of America
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, Texas, United States of America
- Department of Neuroscience, BCM, Houston, Texas, United States of America
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15
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Gaweda-Walerych K, Sitek EJ, Borczyk M, Berdyński M, Narożańska E, Brockhuis B, Korostyński M, Sławek J, Zekanowski C. Two Rare Variants in PLAU and BACE1 Genes-Do They Contribute to Semantic Dementia Clinical Phenotype? Genes (Basel) 2021; 12:genes12111806. [PMID: 34828412 PMCID: PMC8624613 DOI: 10.3390/genes12111806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
We have performed whole-genome sequencing to identify the genetic variants potentially contributing to the early-onset semantic dementia phenotype in a patient with family history of dementia and episodic memory deficit accompanied with profound semantic loss. Only very rare variants of unknown significance (VUS) have been identified: a nonsense variant c.366C>A/p.Cys122* in plasminogen activator, urokinase (PLAU) and a missense variant c.944C>T/p.Thr315Met in β-site APP-cleaving enzyme 1 (BACE1)-along with known disease-modifying variants of moderate penetrance. Patient-derived fibroblasts showed reduced PLAU and elevated BACE1 mRNA and protein levels compared to control fibroblasts. Successful rescue of PLAU mRNA levels by nonsense-mediated mRNA decay (NMD) inhibitor (puromycin) confirmed NMD as the underlying mechanism. This is the first report of the PLAU variant with the confirmed haploinsufficiency, associated with semantic dementia phenotype. Our results suggest that rare variants in the PLAU and BACE1 genes should be considered in future studies on early-onset dementias.
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Affiliation(s)
- Katarzyna Gaweda-Walerych
- Laboratory of Neurogenetics, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland; (M.B.); (C.Z.)
- Correspondence: (K.G.-W.); (E.J.S.)
| | - Emilia J. Sitek
- Neurology Department, St. Adalbert Hospital, Copernicus PL, 80-462 Gdansk, Poland; (E.N.); (J.S.)
- Division of Neurological and Psychiatric Nursing, Faculty of Health Sciences, Medical University of Gdansk, 80-462 Gdansk, Poland
- Correspondence: (K.G.-W.); (E.J.S.)
| | - Małgorzata Borczyk
- Laboratory of Pharmacogenomics, Department of Molecular Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland; (M.B.); (M.K.)
| | - Mariusz Berdyński
- Laboratory of Neurogenetics, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland; (M.B.); (C.Z.)
| | - Ewa Narożańska
- Neurology Department, St. Adalbert Hospital, Copernicus PL, 80-462 Gdansk, Poland; (E.N.); (J.S.)
| | - Bogna Brockhuis
- Division of Nuclear Medicine, Faculty of Health Sciences, Medical University of Gdansk, 80-214 Gdansk, Poland;
| | - Michał Korostyński
- Laboratory of Pharmacogenomics, Department of Molecular Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland; (M.B.); (M.K.)
| | - Jarosław Sławek
- Neurology Department, St. Adalbert Hospital, Copernicus PL, 80-462 Gdansk, Poland; (E.N.); (J.S.)
- Division of Neurological and Psychiatric Nursing, Faculty of Health Sciences, Medical University of Gdansk, 80-462 Gdansk, Poland
| | - Cezary Zekanowski
- Laboratory of Neurogenetics, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland; (M.B.); (C.Z.)
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16
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Rostalski H, Korhonen V, Kuulasmaa T, Solje E, Krüger J, Gen F, Kaivola K, Eide PK, Lambert JC, Julkunen V, Tienari PJ, Remes AM, Leinonen V, Hiltunen M, Haapasalo A. A Novel Genetic Marker for the C9orf72 Repeat Expansion in the Finnish Population. J Alzheimers Dis 2021; 83:1325-1332. [PMID: 34397416 DOI: 10.3233/jad-210599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND C9orf72 repeat expansion (C9exp) is the most common genetic cause underlying frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). However, detection of the C9exp requires elaborative methods. OBJECTIVE Identification of C9exp carriers from genotyped cohorts could be facilitated by using single nucleotide polymorphisms (SNPs) as markers for the C9exp. METHODS We elucidated the potential of the previously described Finnish risk haplotype, defined by the SNP rs3849942, to identify potential C9exp carriers among 218,792 Finns using the FinnGen database. The haplotype approach was first tested in an idiopathic normal pressure hydrocephalus (iNPH) patient cohort (European Alzheimer's Disease DNA BioBank) containing C9exp carriers by comparing intermediate (15-30) and full-length (> 60 repeats) C9exp carriers (n = 41) to C9exp negative patients (< 15 repeats, n = 801). RESULTS In this analysis, rs3849942 was associated with carriership of C9exp (OR 8.44, p < 2×10-15), while the strongest association was found with rs139185008 (OR 39.4, p < 5×10-18). Unbiased analysis of rs139185008 in FinnGen showed the strongest association with FTLD (OR 4.38, 3×10-15) and motor neuron disease ALS (OR 5.19, 3×10-21). rs139185008 was the top SNP in all diseases (iNPH, FTLD, ALS), and further showed a strong association with ALS in the UK Biobank (p = 9.0×10-8). CONCLUSION Our findings suggest that rs139185008 is a useful marker to identify potential C9exp carriers in the genotyped cohorts and biobanks originating from Finland.
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Affiliation(s)
- Hannah Rostalski
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ville Korhonen
- Neurocenter, Neurosurgery, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Teemu Kuulasmaa
- Institute of Biomedicine, Yliopistonranta 1E, University of Eastern Finland, Kuopio, Finland
| | - Eino Solje
- Institute of Clinical Medicine - Neurology, University of Eastern Finland.,Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Johanna Krüger
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland.,Medical Research Center (MRC), Oulu University Hospital, Oulu, Finland
| | - Finn Gen
- Department of Neurology, Helsinki University Hospital and Translational Immunology Program, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Karri Kaivola
- Department of Neurology, Helsinki University Hospital and Translational Immunology Program, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Per Kristian Eide
- Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liés au vieillissement, Lille, France
| | - Valtteri Julkunen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland.,Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Pentti J Tienari
- Department of Neurology, Helsinki University Hospital and Translational Immunology Program, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Anne M Remes
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland.,Medical Research Center (MRC), Oulu University Hospital, Oulu, Finland
| | - Ville Leinonen
- Neurocenter, Neurosurgery, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, Yliopistonranta 1E, University of Eastern Finland, Kuopio, Finland
| | - Annakaisa Haapasalo
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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17
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Huq AJ, Sexton A, Lacaze P, Masters CL, Storey E, Velakoulis D, James PA, Winship IM. Genetic testing in dementia-A medical genetics perspective. Int J Geriatr Psychiatry 2021; 36:1158-1170. [PMID: 33779003 DOI: 10.1002/gps.5535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/26/2021] [Indexed: 01/11/2023]
Abstract
OBJECTIVE When a genetic cause is suspected in a person with dementia, it creates unique diagnostic and management challenges to the treating clinician. Many clinicians may be unaware of the practicalities surrounding genetic testing for their patients, such as when to test and what tests to use and how to counsel patients and their families. This review was conducted to provide guidance to clinicians caring for patients with dementia regarding clinically relevant genetics. METHODS We searched PubMed for studies that involved genetics of dementia up to March 2020. Patient file reviews were also conducted to create composite cases. RESULTS In addition to families where a strong Mendelian pattern of family history is seen, people with younger age of onset, especially before the age of 65 years were found to be at an increased risk of harbouring a genetic cause for their dementia. This review discusses some of the most common genetic syndromes, including Alzheimer disease, frontotemporal dementia, vascular dementia, Parkinson disease dementia/dementia with Lewy bodies and some rarer types of genetic dementias, along with illustrative clinical case studies. This is followed by a brief review of the current genetic technologies and a discussion on the unique genetic counselling issues in dementia. CONCLUSIONS Inclusion of genetic testing in the diagnostic pathway in some patients with dementia could potentially reduce the time taken to diagnose the cause of their dementia. Although a definite advantage as an addition to the diagnostic repository, genetic testing has many pros and cons which need to be carefully considered first.
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Affiliation(s)
- Aamira J Huq
- Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Medicine, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Paul Lacaze
- Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, The Alfred Centre, Melbourne, Victoria, Australia
| | - Colin L Masters
- Neurosciences, The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Elsdon Storey
- Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Dennis Velakoulis
- Department of Neuropsychiatry, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Paul A James
- Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Medicine, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
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18
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Zhou X, Chen X, Hong T, Zhang M, Cai Y, Cui L. TTC3-Mediated Protein Quality Control, A Potential Mechanism for Cognitive Impairment. Cell Mol Neurobiol 2021; 42:1659-1669. [PMID: 33638766 PMCID: PMC9239942 DOI: 10.1007/s10571-021-01060-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/11/2021] [Indexed: 01/14/2023]
Abstract
The tetrapeptide repeat domain 3 (TTC3) gene falls within Down's syndrome (DS) critical region. Cognitive impairment is a common phenotype of DS and Alzheimer’s disease (AD), and overexpression of TTC3 can accelerate cognitive decline, but the specific mechanism is unknown. The TTC3-mediated protein quality control (PQC) mechanism, similar to the PQC system, is divided into three parts: it acts as a cochaperone to assist proteins in folding correctly; it acts as an E3 ubiquitin ligase (E3s) involved in protein degradation processes through the ubiquitin–proteasome system (UPS); and it may also eventually cause autophagy by affecting mitochondrial function. Thus, this article reviews the research progress on the structure, function, and metabolism of TTC3, including the recent research progress on TTC3 in DS and AD; the role of TTC3 in cognitive impairment through PQC in combination with the abovementioned attributes of TTC3; and the potential targets of TTC3 in the treatment of such diseases.
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Affiliation(s)
- Xu Zhou
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Xiongjin Chen
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Tingting Hong
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Miaoping Zhang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Yujie Cai
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China
| | - Lili Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, No.57, Renmindadaonan Road, Xiashan District, Zhanjiang, China.
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19
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Zhou M, Lin Y, Lu L, Zhang Z, Guo W, Peng G, Zhang W, Zhu Z, Wu Z, Mo M, Yang X, Zhu X, Chen C, Chen X, Xu P. Association of ADAM10 gene variants with sporadic Parkinson's disease in Chinese Han population. J Gene Med 2021; 23:e3319. [PMID: 33527480 DOI: 10.1002/jgm.3319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/07/2021] [Accepted: 01/24/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide. Genetic factors play important roles in PD risk. rs653765 and rs514049 of ADAM10 were reported to be associated with Alzheimer's disease (AD) in Caucasian population; however, the association of the two variants with PD in Chinese Han population remains unknown. The present investigation aimed to explore the possible association of ADAM10 variants with PD in Chinese Han population. METHODS We enrolled 565 PD patients and 518 healthy controls to conduct a case-control study. DNA samples were extracted from peripheral blood leukocytes, and the genotypes were determined by utilization of MassARRAY platform. Plasma levels were measured by enzyme-linked immunosorbent assay (ELISA). RESULTS We found CC genotype of rs514049 was associated with an increased risk of PD (OR (95% CI) = 3.776 (1.127-11.217), p = 0.018). The C allele frequency of rs514049 was significantly higher in PD group (OR (95% CI) = 1.328 (1.031-1.709), p = 0.028), especially in male subgroup (OR (95% CI) = 1.484 (1.053-2.092), p = 0.024). However, there was no significant difference in the genotype or allele frequencies for rs653765 within the groups. Plasma levels were significantly decreased in PD patients compared with controls (p < 0.001). CONCLUSIONS Our data suggested that C allele of rs514049 in ADAM10 may increase the risk of PD in Chinese Han population, especially in males. The decreased plasma levels are probably involved in PD development.
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Affiliation(s)
- Miaomiao Zhou
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuwan Lin
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lin Lu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiling Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenyuan Guo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guoyou Peng
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenlong Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ziting Zhu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhuohua Wu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mingshu Mo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinling Yang
- Department of Neurology, The Second Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiaoqin Zhu
- Department of Physiology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Chaojun Chen
- Department of Neurology, Guangzhou Chinese Medical Integrated Hospital (Huadu), Guangzhou, China
| | - Xiang Chen
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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20
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A Novel Putative Role of TNK1 in Atherosclerotic Inflammation Implicating the Tyk2/STAT1 Pathway. Mediators Inflamm 2020; 2020:6268514. [PMID: 32694928 PMCID: PMC7368939 DOI: 10.1155/2020/6268514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/02/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022] Open
Abstract
Objective Atherosclerosis is a chronic inflammatory disease which is responsible for many clinical manifestations. The present study was to investigate the anti-inflammatory functions and mechanisms of TNK1 in atherosclerosis. Methods The ApoE(-/-) mice and human carotid endarterectomy (CEA) atherosclerotic plaques were used to investigate the differential expression of TNK1. The ApoE(-/-) mice were fed with high-fat diet (HFD) or normal-fat diet (NFD) for 8 weeks; the aorta was separated and stained with oil red O to evaluate the formation of atherosclerosis. TNK1 in mice aorta was measured by qPCR. The human CEA were obtained and identified as ruptured and stable plaques. The level of TNK1 was measured by qPCR and Western-blot staining. Further studies were conducted in THP-1 cells to explore the anti-inflammatory effects of TNK1. We induced the formation of macrophages by incubating THP-1 cells with PMA (phorbol 12-myristate 13-acetate). Afterwards, oxidized low-density lipoprotein (oxLDL) was used to stimulate the inflammation, and the secretion of inflammatory factors was measured by ELISA and qPCR. The levels of TNK1, total STAT1 and Tyk2, and the phosphorylation of STAT1 and Tyk2 were measured by western blot to uncover the mechanisms of TNK1. Results The oil red O staining indicated obvious deposition of lipid on the aorta of ApoE(-/-) mice after 8-week HFD treatment. The TNK1 level was much higher in both the HFD-fed ApoE(-/-) mice aorta arch and the ruptured human CEA plaques. We found that TNK1 was highly expressed in THP-1 cells, compared to other atherosclerotic related cells (HUVEC, HBMEC, and HA-VSMC), indicating TNK1 might be involved in the inflammation. Suppressing the expression of TNK1 by shTNK1 inhibited the oxLDL-induced secretion of inflammatory factors, such as IL-12, IL-6, and TNF-α. ShTNK1 also inhibited the uptake of lipid and decreased the cellular cholesterol content in THP-1 cells. Furthermore, the shTNK1 suppressed the oxLDL-induced phosphorylation of Tyk2 and STAT1. Conclusion TNK1 participated in the inflammation in atherosclerosis. shTNK1 suppressed the oxLDL-induced inflammation and lipid deposition in THP-1 cells. The mechanism might be related to the Tyk2/STAT signal pathway.
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21
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Cochran JN, Geier EG, Bonham LW, Newberry JS, Amaral MD, Thompson ML, Lasseigne BN, Karydas AM, Roberson ED, Cooper GM, Rabinovici GD, Miller BL, Myers RM, Yokoyama JS. Non-coding and Loss-of-Function Coding Variants in TET2 are Associated with Multiple Neurodegenerative Diseases. Am J Hum Genet 2020; 106:632-645. [PMID: 32330418 PMCID: PMC7212268 DOI: 10.1016/j.ajhg.2020.03.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/20/2020] [Indexed: 12/13/2022] Open
Abstract
We conducted genome sequencing to search for rare variation contributing to early-onset Alzheimer's disease (EOAD) and frontotemporal dementia (FTD). Discovery analysis was conducted on 435 cases and 671 controls of European ancestry. Burden testing for rare variation associated with disease was conducted using filters based on variant rarity (less than one in 10,000 or private), computational prediction of deleteriousness (CADD) (10 or 15 thresholds), and molecular function (protein loss-of-function [LoF] only, coding alteration only, or coding plus non-coding variants in experimentally predicted regulatory regions). Replication analysis was conducted on 16,434 independent cases and 15,587 independent controls. Rare variants in TET2 were enriched in the discovery combined EOAD and FTD cohort (p = 4.6 × 10-8, genome-wide corrected p = 0.0026). Most of these variants were canonical LoF or non-coding in predicted regulatory regions. This enrichment replicated across several cohorts of Alzheimer's disease (AD) and FTD (replication only p = 0.0029). The combined analysis odds ratio was 2.3 (95% confidence interval [CI] 1.6-3.4) for AD and FTD. The odds ratio for qualifying non-coding variants considered independently from coding variants was 3.7 (95% CI 1.7-9.4). For LoF variants, the combined odds ratio (for AD, FTD, and amyotrophic lateral sclerosis, which shares clinicopathological overlap with FTD) was 3.1 (95% CI 1.9-5.2). TET2 catalyzes DNA demethylation. Given well-defined changes in DNA methylation that occur during aging, rare variation in TET2 may confer risk for neurodegeneration by altering the homeostasis of key aging-related processes. Additionally, our study emphasizes the relevance of non-coding variation in genetic studies of complex disease.
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Affiliation(s)
- J Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Ethan G Geier
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Luke W Bonham
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, United States
| | - J Scott Newberry
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Michelle D Amaral
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Michelle L Thompson
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Brittany N Lasseigne
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States; Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Anna M Karydas
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Erik D Roberson
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Departments of Neurology and Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Gil D Rabinovici
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, United States; Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, United States; Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94158, United States.
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22
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D’Argenio V, Sarnataro D. New Insights into the Molecular Bases of Familial Alzheimer's Disease. J Pers Med 2020; 10:jpm10020026. [PMID: 32325882 PMCID: PMC7354425 DOI: 10.3390/jpm10020026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Like several neurodegenerative disorders, such as Prion and Parkinson diseases, Alzheimer's disease (AD) is characterized by spreading mechanism of aggregated proteins in the brain in a typical "prion-like" manner. Recent genetic studies have identified in four genes associated with inherited AD (amyloid precursor protein-APP, Presenilin-1, Presenilin-2 and Apolipoprotein E), rare mutations which cause dysregulation of APP processing and alterations of folding of the derived amyloid beta peptide (A). Accumulation and aggregation of A in the brain can trigger a series of intracellular events, including hyperphosphorylation of tau protein, leading to the pathological features of AD. However, mutations in these four genes account for a small of the total genetic risk for familial AD (FAD). Genome-wide association studies have recently led to the identification of additional AD candidate genes. Here, we review an update of well-established, highly penetrant FAD-causing genes with correlation to the protein misfolding pathway, and novel emerging candidate FAD genes, as well as inherited risk factors. Knowledge of these genes and of their correlated biochemical cascade will provide several potential targets for treatment of AD and aging-related disorders.
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Affiliation(s)
- Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate scarl, via G. Salvatore 486, 80145 Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, via di val Cannuta 247, 00166 Rome, Italy
- Correspondence: (V.D.); (D.S.); Tel.: +39-081-3737909 (V.D.); +39-081-7464575 (D.S.)
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, via S. Pansini 5, 80131 Naples, Italy
- Correspondence: (V.D.); (D.S.); Tel.: +39-081-3737909 (V.D.); +39-081-7464575 (D.S.)
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