1
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Chang T, Fu M, Valiente-Banuet L, Wadhwa S, Pasaniuc B, Vossel K. Improving genetic risk modeling of dementia from real-world data in underrepresented populations. RESEARCH SQUARE 2024:rs.3.rs-3911508. [PMID: 38410460 PMCID: PMC10896371 DOI: 10.21203/rs.3.rs-3911508/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
BACKGROUND Genetic risk modeling for dementia offers significant benefits, but studies based on real-world data, particularly for underrepresented populations, are limited. METHODS We employed an Elastic Net model for dementia risk prediction using single-nucleotide polymorphisms prioritized by functional genomic data from multiple neurodegenerative disease genome-wide association studies. We compared this model with APOE and polygenic risk score models across genetic ancestry groups, using electronic health records from UCLA Health for discovery and All of Us cohort for validation. RESULTS Our model significantly outperforms other models across multiple ancestries, improving the area-under-precision-recall curve by 21-61% and the area-under-the-receiver-operating characteristic by 10-21% compared to the APOEand the polygenic risk score models. We identified shared and ancestry-specific risk genes and biological pathways, reinforcing and adding to existing knowledge. CONCLUSIONS Our study highlights benefits of integrating functional mapping, multiple neurodegenerative diseases, and machine learning for genetic risk models in diverse populations. Our findings hold potential for refining precision medicine strategies in dementia diagnosis.
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Affiliation(s)
- Timothy Chang
- David Geffen School of Medicine, University of California, Los Angeles
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2
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Fu M, Valiente-Banuet L, Wadhwa SS, Pasaniuc B, Vossel K, Chang TS. Improving genetic risk modeling of dementia from real-world data in underrepresented populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.05.24302355. [PMID: 38370649 PMCID: PMC10871463 DOI: 10.1101/2024.02.05.24302355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
BACKGROUND Genetic risk modeling for dementia offers significant benefits, but studies based on real-world data, particularly for underrepresented populations, are limited. METHODS We employed an Elastic Net model for dementia risk prediction using single-nucleotide polymorphisms prioritized by functional genomic data from multiple neurodegenerative disease genome-wide association studies. We compared this model with APOE and polygenic risk score models across genetic ancestry groups, using electronic health records from UCLA Health for discovery and All of Us cohort for validation. RESULTS Our model significantly outperforms other models across multiple ancestries, improving the area-under-precision-recall curve by 21-61% and the area-under-the-receiver-operating characteristic by 10-21% compared to the APOE and the polygenic risk score models. We identified shared and ancestry-specific risk genes and biological pathways, reinforcing and adding to existing knowledge. CONCLUSIONS Our study highlights benefits of integrating functional mapping, multiple neurodegenerative diseases, and machine learning for genetic risk models in diverse populations. Our findings hold potential for refining precision medicine strategies in dementia diagnosis.
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Affiliation(s)
- Mingzhou Fu
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, United States
- Medical Informatics Home Area, Department of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90024, United States
| | - Leopoldo Valiente-Banuet
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, United States
| | - Satpal S. Wadhwa
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, United States
| | | | | | - Bogdan Pasaniuc
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Keith Vossel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, United States
| | - Timothy S. Chang
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, United States
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3
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Godfrey RK, Alsop E, Bjork RT, Chauhan BS, Ruvalcaba HC, Antone J, Gittings LM, Michael AF, Williams C, Hala'ufia G, Blythe AD, Hall M, Sattler R, Van Keuren-Jensen K, Zarnescu DC. Modelling TDP-43 proteinopathy in Drosophila uncovers shared and neuron-specific targets across ALS and FTD relevant circuits. Acta Neuropathol Commun 2023; 11:168. [PMID: 37864255 PMCID: PMC10588218 DOI: 10.1186/s40478-023-01656-0] [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: 08/03/2023] [Accepted: 09/19/2023] [Indexed: 10/22/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) comprise a spectrum of neurodegenerative diseases linked to TDP-43 proteinopathy, which at the cellular level, is characterized by loss of nuclear TDP-43 and accumulation of cytoplasmic TDP-43 inclusions that ultimately cause RNA processing defects including dysregulation of splicing, mRNA transport and translation. Complementing our previous work in motor neurons, here we report a novel model of TDP-43 proteinopathy based on overexpression of TDP-43 in a subset of Drosophila Kenyon cells of the mushroom body (MB), a circuit with structural characteristics reminiscent of vertebrate cortical networks. This model recapitulates several aspects of dementia-relevant pathological features including age-dependent neuronal loss, nuclear depletion and cytoplasmic accumulation of TDP-43, and behavioral deficits in working memory and sleep that occur prior to axonal degeneration. RNA immunoprecipitations identify several candidate mRNA targets of TDP-43 in MBs, some of which are unique to the MB circuit and others that are shared with motor neurons. Among the latter is the glypican Dally-like-protein (Dlp), which exhibits significant TDP-43 associated reduction in expression during aging. Using genetic interactions we show that overexpression of Dlp in MBs mitigates TDP-43 dependent working memory deficits, conistent with Dlp acting as a mediator of TDP-43 toxicity. Substantiating our findings in the fly model, we find that the expression of GPC6 mRNA, a human ortholog of dlp, is specifically altered in neurons exhibiting the molecular signature of TDP-43 pathology in FTD patient brains. These findings suggest that circuit-specific Drosophila models provide a platform for uncovering shared or disease-specific molecular mechanisms and vulnerabilities across the spectrum of TDP-43 proteinopathies.
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Affiliation(s)
- R Keating Godfrey
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA.
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL, 32611, USA.
| | - Eric Alsop
- Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | - Reed T Bjork
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Brijesh S Chauhan
- Cellular and Molecular Physiology, Penn State College of Medicine, 500 University Drive Crescent Building C4605, Hershey, PA, 17033, USA
| | - Hillary C Ruvalcaba
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Jerry Antone
- Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | - Lauren M Gittings
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Allison F Michael
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Christi Williams
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Grace Hala'ufia
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Alexander D Blythe
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Megan Hall
- Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | - Rita Sattler
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | | | - Daniela C Zarnescu
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA.
- Cellular and Molecular Physiology, Penn State College of Medicine, 500 University Drive Crescent Building C4605, Hershey, PA, 17033, USA.
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4
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Webber EK, Fivaz M, Stutzmann GE, Griffioen G. Cytosolic calcium: Judge, jury and executioner of neurodegeneration in Alzheimer's disease and beyond. Alzheimers Dement 2023; 19:3701-3717. [PMID: 37132525 PMCID: PMC10490830 DOI: 10.1002/alz.13065] [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: 09/23/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 05/04/2023]
Abstract
This review discusses the driving principles that may underlie neurodegeneration in dementia, represented most dominantly by Alzheimer's disease (AD). While a myriad of different disease risk factors contribute to AD, these ultimately converge to a common disease outcome. Based on decades of research, a picture emerges where upstream risk factors combine in a feedforward pathophysiological cycle, culminating in a rise of cytosolic calcium concentration ([Ca2+ ]c ) that triggers neurodegeneration. In this framework, positive AD risk factors entail conditions, characteristics, or lifestyles that initiate or accelerate self-reinforcing cycles of pathophysiology, whereas negative risk factors or therapeutic interventions, particularly those mitigating elevated [Ca2+ ]c , oppose these effects and therefore have neuroprotective potential.
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Affiliation(s)
- Elise K. Webber
- Center for Neurodegenerative Disease and Therapeutics, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
| | - Marc Fivaz
- reMYND, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Grace E. Stutzmann
- Center for Neurodegenerative Disease and Therapeutics, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
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5
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Vejux A. Cell Death and Neurodegenerative Diseases: Mechanisms and Cytoprotective Molecules. Int J Mol Sci 2023; 24:11465. [PMID: 37511220 PMCID: PMC10380922 DOI: 10.3390/ijms241411465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
A neurodegenerative disease is a pathological condition affecting neurons, condemning them to death [...].
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Affiliation(s)
- Anne Vejux
- Team Bio-PeroxIL, "Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism" (EA7270), Université de Bourgogne Franche-Comté, UFR Sciences Vie Terre et Environnement, 21000 Dijon, France
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6
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Kaur N, LaForce G, Mallela DP, Saha PP, Buffa J, Li XS, Sangwan N, Rothenberg K, Zhu W. Exploratory Transcriptomic Profiling Reveals the Role of Gut Microbiota in Vascular Dementia. Int J Mol Sci 2023; 24:ijms24098091. [PMID: 37175797 PMCID: PMC10178712 DOI: 10.3390/ijms24098091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Stroke is the second most common cause of cognitive impairment and dementia. Vascular dementia (VaD), a cognitive impairment following a stroke, is common and significantly impacts the quality of life. We recently demonstrated via gut microbe transplant studies that the gut microbe-dependent trimethylamine-N-oxide (TMAO) pathway impacts stroke severity, both infarct size and long-term cognitive outcomes. However, the molecular mechanisms that underly the role of the microbiome in VaD have not been explored in depth. To address this issue, we performed a comprehensive RNA-sequencing analysis to identify differentially expressed (DE) genes in the ischemic cerebral cortex of mouse brains at pre-stroke and post-stroke day 1 and day 3. A total of 4016, 3752 and 7861 DE genes were identified at pre-stroke and post-stroke day 1 and day 3, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated pathways of neurodegeneration in multiple diseases, chemokine signaling, calcium signaling, and IL-17 signaling as the key enriched pathways. Inflammatory response genes interleukin-1 beta (Il-1β), chemokines (C-X-C motif chemokine ligand 10 (Cxcl10), chemokine ligand 2 (Ccl2)), and immune system genes (S100 calcium binding protein 8 (S100a8), lipocalin-2 (Lcn2)) were among the most significantly upregulated genes. Hypocretin neuropeptide precursor (Hcrt), a neuropeptide, and transcription factors such as neuronal PAS domain protein 4 (Npas4), GATA binding protein 3 (Gata3), and paired box 7 (Pax7) were among the most significantly downregulated genes. In conclusion, our results indicate that higher plasma TMAO levels induce differential mRNA expression profiles in the ischemic brain tissue in our pre-clinical stroke model, and the predicted pathways provide the molecular basis for regulating the TMAO-enhanced neuroinflammatory response in the brain.
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Affiliation(s)
- Navdeep Kaur
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Geneva LaForce
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Deepthi P Mallela
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Prasenjit Prasad Saha
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jennifer Buffa
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Xinmin S Li
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Naseer Sangwan
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
- Microbial Sequencing & Analytics Resource (MSAAR) Facility, Shared Laboratory Resources (SLR), Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kasia Rothenberg
- Cleveland Clinic Lou Ruvo Center for Brain Health, Cleveland, OH 44195, USA
| | - Weifei Zhu
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
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7
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Xiao Y, He Y, Xu C, Li M, Hu F, Wang W, Wang Z, Cao Y. Exposure to MoS2 nanosheets or bulk activated Kruppel-like factor 4 in 3D Caco-2 spheroids in vitro and mouse intestines in vivo. ENVIRONMENTAL TOXICOLOGY 2023. [PMID: 37186336 DOI: 10.1002/tox.23819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 05/17/2023]
Abstract
MoS2 nanosheets (NSs) are novel 2D nanomaterials (NMs) being used in many important fields. Recently, we proposed the need to evaluate the influences of NMs on Kruppel-like factors (KLFs) even if these materials are relatively biocompatible. In this study, we investigated the influences of MoS2 NSs or bulk on KLF4 signaling pathway in 3D Caco-2 spheroids in vitro and mouse intestines in vivo. Through the analysis of our previous RNA-sequencing data, we found that exposure to MoS2 NSs or bulk activated KLF4 expression in 3D Caco-2 spheroids. Consistently, these materials also activated KLF4-related gene ontology (GO) terms and down-regulated a panel of KLF4-downstream genes. To verify these findings, we repeatedly exposed mice to MoS2 NSs or bulk materials via intragastrical administration (1 mg/kg bodyweight, once a day, for 4 days). It was shown that oral exposure to these materials decreased bodyweight, leading to relatively higher organ coefficients. As expected, exposure to both types of materials increased Mo elements as well as other trace elements, such as Zn, Fe, and Mn in mouse intestines. The exposure also induced morphological changes of intestines, such as shortening of intestinal villi and decreased crypt depth, which may result in decreased intestinal lipid staining. Consistent with RNA-sequencing data, we found that material exposure increased KLF4 protein staining in mouse intestines and decreased two KLF4 downstream proteins, namely extracellular signal-regulated kinase (ERK) and serine/threonine kinase (AKT). We concluded that MoS2 materials were capable to activate KLF4-signaling pathway in intestines both in vivo and in vitro.
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Affiliation(s)
- You Xiao
- Fifth Department of Anorectal, The Second Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Yuanyuan He
- Graduate School of Hunan University, Hunan University of Chinese Medicine, Changsha, China
| | - Chongsi Xu
- Fifth Department of Anorectal, The Second Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Mei Li
- Fifth Department of Anorectal, The Second Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Fan Hu
- Fifth Department of Anorectal, The Second Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Wei Wang
- Fifth Department of Anorectal, The Second Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Zhenquan Wang
- Third Department of Anorectal, The Second Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Yi Cao
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang, China
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8
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Ramos-Campoy O, Lladó A, Bosch B, Ferrer M, Pérez-Millan A, Vergara M, Molina-Porcel L, Fort-Aznar L, Gonzalo R, Moreno-Izco F, Fernandez-Villullas G, Balasa M, Sánchez-Valle R, Antonell A. Differential Gene Expression in Sporadic and Genetic Forms of Alzheimer's Disease and Frontotemporal Dementia in Brain Tissue and Lymphoblastoid Cell Lines. Mol Neurobiol 2022; 59:6411-6428. [PMID: 35962298 DOI: 10.1007/s12035-022-02969-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/21/2022] [Indexed: 10/15/2022]
Abstract
Sporadic early-onset Alzheimer's disease (EOAD) and autosomal dominant Alzheimer's disease (ADAD) provide the opportunity to investigate the physiopathological mechanisms in the absence of aging, present in late-onset forms. Frontotemporal dementia (FTD) causes early-onset dementia associated to tau or TDP43 protein deposits. A 15% of FTD cases are caused by mutations in C9orf72, GRN, or MAPT genes. Lymphoblastoid cell lines (LCLs) have been proposed as an alternative to brain tissue for studying earlier phases of neurodegenerative diseases. The aim of this study is to investigate the expression profile in EOAD, ADAD, and sporadic and genetic FTD (sFTD and gFTD, respectively), using brain tissue and LCLs. Sixty subjects of the following groups were included: EOAD, ADAD, sFTD, gFTD, and controls. Gene expression was analyzed with Clariom D microarray (Affymetrix). Brain tissue pairwise comparisons revealed six common differentially expressed genes (DEG) for all the patients' groups compared with controls: RGS20, WIF1, HSPB1, EMP3, S100A11 and GFAP. Common up-regulated biological pathways were identified both in brain and LCLs (including inflammation and glial cell differentiation), while down-regulated pathways were detected mainly in brain tissue (including synaptic signaling, metabolism and mitochondrial dysfunction). CD163, ADAMTS9 and LIN7A gene expression disruption was validated by qPCR in brain tissue and NrCAM in LCLs in their respective group comparisons. In conclusion, our study highlights neuroinflammation, metabolism and synaptic signaling disturbances as common altered pathways in different AD and FTD forms. The use of LCLs might be appropriate for studying early immune system and inflammation, and some neural features in neurodegenerative dementias.
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Affiliation(s)
- Oscar Ramos-Campoy
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Albert Lladó
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Beatriz Bosch
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Mireia Ferrer
- Statistics and Bioinformatics Unit, Vall d'Hebrón Institut de Recerca, Passeig Vall d'Hebrón, Barcelona, Spain
| | - Agnès Pérez-Millan
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.,Institute of Neurosciences, Department of Biomedicine, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Miguel Vergara
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Laura Molina-Porcel
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.,Neurological Tissue Bank, Biobank-Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Laura Fort-Aznar
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Ricardo Gonzalo
- Statistics and Bioinformatics Unit, Vall d'Hebrón Institut de Recerca, Passeig Vall d'Hebrón, Barcelona, Spain
| | - Fermín Moreno-Izco
- Cognitive Disorders Unit, Department of Neurology, Hospital Universitario Donostia, 20014, Donostia-San Sebastián, Spain.,Biodonostia, Neurosciences Area, Group of Neurodegenerative Diseases, 20014, San Sebastián, Spain
| | - Guadalupe Fernandez-Villullas
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Mircea Balasa
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.
| | - Anna Antonell
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.
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9
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Miedema SSM, Mol MO, Koopmans FTW, Hondius DC, van Nierop P, Menden K, de Veij Mestdagh CF, van Rooij J, Ganz AB, Paliukhovich I, Melhem S, Li KW, Holstege H, Rizzu P, van Kesteren RE, van Swieten JC, Heutink P, Smit AB. Distinct cell type-specific protein signatures in GRN and MAPT genetic subtypes of frontotemporal dementia. Acta Neuropathol Commun 2022; 10:100. [PMID: 35799292 PMCID: PMC9261008 DOI: 10.1186/s40478-022-01387-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/22/2022] [Indexed: 11/16/2022] Open
Abstract
Frontotemporal dementia is characterized by progressive atrophy of frontal and/or temporal cortices at an early age of onset. The disorder shows considerable clinical, pathological, and genetic heterogeneity. Here we investigated the proteomic signatures of frontal and temporal cortex from brains with frontotemporal dementia due to GRN and MAPT mutations to identify the key cell types and molecular pathways in their pathophysiology. We compared patients with mutations in the GRN gene (n = 9) or with mutations in the MAPT gene (n = 13) with non-demented controls (n = 11). Using quantitative proteomic analysis on laser-dissected tissues we identified brain region-specific protein signatures for both genetic subtypes. Using published single cell RNA expression data resources we deduced the involvement of major brain cell types in driving these different protein signatures. Subsequent gene ontology analysis identified distinct genetic subtype- and cell type-specific biological processes. For the GRN subtype, we observed a distinct role for immune processes related to endothelial cells and for mitochondrial dysregulation in neurons. For the MAPT subtype, we observed distinct involvement of dysregulated RNA processing, oligodendrocyte dysfunction, and axonal impairments. Comparison with an in-house protein signature of Alzheimer’s disease brains indicated that the observed alterations in RNA processing and oligodendrocyte function are distinct for the frontotemporal dementia MAPT subtype. Taken together, our results indicate the involvement of different brain cell types and biological mechanisms in genetic subtypes of frontotemporal dementia. Furthermore, we demonstrate that comparison of proteomic profiles of different disease entities can separate general neurodegenerative processes from disease-specific pathways, which may aid the development of disease subtype-specific treatment strategies.
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Affiliation(s)
- Suzanne S M Miedema
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands.
| | - Merel O Mol
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Frank T W Koopmans
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - David C Hondius
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Pim van Nierop
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Kevin Menden
- German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Tübingen, Germany
| | - Christina F de Veij Mestdagh
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands.,Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, Groningen, the Netherlands.,Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Jeroen van Rooij
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andrea B Ganz
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands.,Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Iryna Paliukhovich
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Shamiram Melhem
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Henne Holstege
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands.,Department of Clinical Genetics, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Tübingen, Germany
| | - Ronald E van Kesteren
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - John C van Swieten
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Tübingen, Germany
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, W&N Building, C314. De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
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10
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Chen Y, Sun Y, Luo Z, Chen X, Wang Y, Qi B, Lin J, Lin WW, Sun C, Zhou Y, Huang J, Xu Y, Chen J, Chen S. Exercise Modifies the Transcriptional Regulatory Features of Monocytes in Alzheimer's Patients: A Multi-Omics Integration Analysis Based on Single Cell Technology. Front Aging Neurosci 2022; 14:881488. [PMID: 35592698 PMCID: PMC9110789 DOI: 10.3389/fnagi.2022.881488] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/11/2022] [Indexed: 02/05/2023] Open
Abstract
Monocytes have been reported to be important mediators of the protective effect of exercise against the development of Alzheimer's disease (AD). This study aims explored the mechanism by which monocytes achieve this. Using single cell transcriptome analysis, results showed that CD14 + and CD16 + monocytes interacted with other cells in the circulating blood. TNF, CCR1, APP, and AREG, the key ligand-receptor-related genes, were found to be differentially expressed between exercise-treated and AD patients. The SCENIC analysis was performed to identify individual clusters of the key transcription factors (TFs). Nine clusters (M1-M9) were obtained from the co-expression network. Among the identified TFs, MAFB, HES4, and FOSL1 were found to be differentially expressed in AD. Moreover, the M4 cluster to which MAFB, HES4, and FOSL1 belonged was defined as the signature cluster for AD phenotype. Differential analysis by bulkRNA-seq revealed that the expression of TNF, CCR1, and APP were all upregulated after exercise (p < 0.05). And ATF3, MAFB, HES4, and KLF4 that were identified in M4 clusters may be the TFs that regulate TNF, CCR1, and APP in exercise prescription. After that, APP, CCR1, TNF, ATF3, KLF4, HES4, and MAFB formed a regulatory network in the ERADMT gene set, and all of them were mechanistically linked. The ERADMT gene set has been found to be a potential risk marker for the development of AD and can be used as an indicator of compliance to exercise therapy in AD patients. Using single-cell integration analysis, a network of exercise-regulating TFs in monocytes was constructed for AD disease. The constructed network reveals the mechanism by which exercise regulated monocytes to confer therapeutic benefits against AD and its complications. However, this study, as a bioinformatic research, requires further experimental validation.
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Affiliation(s)
- Yisheng Chen
- Huashan Hospital, Fudan University, Shanghai, China
| | - Yaying Sun
- Huashan Hospital, Fudan University, Shanghai, China
| | - Zhiwen Luo
- Huashan Hospital, Fudan University, Shanghai, China
| | | | - Yi Wang
- Huashan Hospital, Fudan University, Shanghai, China
| | - Beijie Qi
- Huashan Hospital, Fudan University, Shanghai, China
| | - Jinrong Lin
- Huashan Hospital, Fudan University, Shanghai, China
| | - Wei-Wei Lin
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Chenyu Sun
- AMITA Health Saint Joseph Hospital Chicago, Chicago, IL, United States
| | - Yifan Zhou
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Ophthalmology, Putuo People’ s Hospital, Tongji University, Shanghai, China
| | - Jiebin Huang
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- *Correspondence: Yuzhen Xu,
| | - Jiwu Chen
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Jiwu Chen,
| | - Shiyi Chen
- Huashan Hospital, Fudan University, Shanghai, China
- Shiyi Chen,
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11
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Bottero V, Alrafati F, Santiago JA, Potashkin JA. Transcriptomic and Network Meta-Analysis of Frontotemporal Dementias. Front Mol Neurosci 2021; 14:747798. [PMID: 34720873 PMCID: PMC8554122 DOI: 10.3389/fnmol.2021.747798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD), also known as frontotemporal dementia (FTD), results in a progressive decline in executive function, leading to behavioral changes, speech problems, and movement disorders. FTD is the second most common cause of young-onset dementia affecting approximately 50–60,000 Americans. FTD exists in familial and sporadic forms, with GRN progranulin and C9orf72 mutations being the most common causes. In this study, we compared the sporadic and familial transcriptome within the cerebellum, frontal cortex, hippocampus, and Brodmann’s area 8 of patients with FTD to determine genes and pathways involved in the disease process. Most dysregulated genes expression occurred in the frontal cortex and Brodmann’s area 8 for genetic and sporadic forms of FTD, respectively. A meta-analysis revealed 50 genes and 95 genes are dysregulated in at least three brain regions in patients with familial mutations and sporadic FTD patients, respectively. Familial FTD genes centered on the Wnt signaling pathway, whereas genes associated with the sporadic form of FTD centered on MAPK signaling. The results reveal the similarities and differences between sporadic and familial FTD. In addition, valproic acid and additional therapeutic agents may be beneficial in treating patients with FTD.
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Affiliation(s)
- Virginie Bottero
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Fahed Alrafati
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | | | - Judith A Potashkin
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
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12
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Shi F, He Y, Chen Y, Yin X, Sha X, Wang Y. Comparative Analysis of Multiple Neurodegenerative Diseases Based on Advanced Epigenetic Aging Brain. Front Genet 2021; 12:657636. [PMID: 34093653 PMCID: PMC8173158 DOI: 10.3389/fgene.2021.657636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Neurodegenerative Diseases (NDs) are age-dependent and include Alzheimer’s disease (AD), Parkinson’s disease (PD), progressive supranuclear palsy (PSP), frontotemporal dementia (FTD), and so on. There have been numerous studies showing that accelerated aging is closely related (even the driver of) ND, thus promoting imbalances in cellular homeostasis. However, the mechanisms of how different ND types are related/triggered by advanced aging are still unclear. Therefore, there is an urgent need to explore the potential markers/mechanisms of different ND types based on aging acceleration at a system level. Methods: AD, PD, PSP, FTD, and aging markers were identified by supervised machine learning methods. The aging acceleration differential networks were constructed based on the aging score. Both the enrichment analysis and sensitivity analysis were carried out to investigate both common and specific mechanisms among different ND types in the context of aging acceleration. Results: The extracellular fluid, cellular metabolisms, and inflammatory response were identified as the common driving factors of cellular homeostasis imbalances during the accelerated aging process. In addition, Ca ion imbalance, abnormal protein depositions, DNA damage, and cytoplasmic DNA in macrophages were also revealed to be special mechanisms that further promote AD, PD, PSP, and FTD, respectively. Conclusion: The accelerated epigenetic aging mechanisms of different ND types were integrated and compared through our computational pipeline.
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Affiliation(s)
- Feitong Shi
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Yudan He
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Yao Chen
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Xinman Yin
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Xianzheng Sha
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Yin Wang
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China.,Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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13
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Badr MT, Omar M, Häcker G. Comprehensive Integration of Genome-Wide Association and Gene Expression Studies Reveals Novel Gene Signatures and Potential Therapeutic Targets for Helicobacter pylori-Induced Gastric Disease. Front Immunol 2021; 12:624117. [PMID: 33717131 PMCID: PMC7945594 DOI: 10.3389/fimmu.2021.624117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori is a gram-negative bacterium that colonizes the human gastric mucosa and can lead to gastric inflammation, ulcers, and stomach cancer. Due to the increase in H. pylori antimicrobial resistance new methods to identify the molecular mechanisms of H. pylori-induced pathology are urgently needed. Here we utilized a computational biology approach, harnessing genome-wide association and gene expression studies to identify genes and pathways determining disease development. We mined gene expression data related to H. pylori-infection and its complications from publicly available databases to identify four human datasets as discovery datasets and used two different multi-cohort analysis pipelines to define a H. pylori-induced gene signature. An initial Helicobacter-signature was curated using the MetaIntegrator pipeline and validated in cell line model datasets. With this approach we identified cell line models that best match gene regulation in human pathology. A second analysis pipeline through NetworkAnalyst was used to refine our initial signature. This approach defined a 55-gene signature that is stably deregulated in disease conditions. The 55-gene signature was validated in datasets from human gastric adenocarcinomas and could separate tumor from normal tissue. As only a small number of H. pylori patients develop cancer, this gene-signature must interact with other host and environmental factors to initiate tumorigenesis. We tested for possible interactions between our curated gene signature and host genomic background mutations and polymorphisms by integrating genome-wide association studies (GWAS) and known oncogenes. We analyzed public databases to identify genes harboring single nucleotide polymorphisms (SNPs) associated with gastric pathologies and driver genes in gastric cancers. Using this approach, we identified 37 genes from GWA studies and 61 oncogenes, which were used with our 55-gene signature to map gene-gene interaction networks. In conclusion, our analysis defines a unique gene signature driven by H. pylori-infection at early phases and that remains relevant through different stages of pathology up to gastric cancer, a stage where H. pylori itself is rarely detectable. Furthermore, this signature elucidates many factors of host gene and pathway regulation in infection and can be used as a target for drug repurposing and testing of infection models suitability to investigate human infection.
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Affiliation(s)
- Mohamed Tarek Badr
- Faculty of Medicine, Institute of Medical Microbiology and Hygiene, Medical Center—University of Freiburg, Freiburg, Germany
- IMM-PACT-Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mohamed Omar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Georg Häcker
- Faculty of Medicine, Institute of Medical Microbiology and Hygiene, Medical Center—University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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14
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Blue EE, Thornton TA, Kooperberg C, Liu S, Wactawski-Wende J, Manson J, Kuller L, Hayden K, Reiner AP. Non-coding variants in MYH11, FZD3, and SORCS3 are associated with dementia in women. Alzheimers Dement 2021; 17:215-225. [PMID: 32966694 PMCID: PMC7920533 DOI: 10.1002/alz.12181] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/17/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Recent studies suggest that both sex-specific genetic risk factors and those shared between dementia and stroke are involved in dementia pathogenesis. METHODS We performed both single-variant and gene-based genome-wide association studies of >11,000 whole genome sequences from the Women's Health Initiative cohort to discover loci associated with dementia, with adjustment for age, ethnicity, stroke, and venous thromboembolism status. Evidence for prior evidence of association and differential gene expression in dementia-related tissues and samples was gathered for each locus. RESULTS Our multiethnic studies identified significant associations between variants within APOE, MYH11, FZD3, SORCS3, and GOLGA8B and risk of dementia. Ten genes implicated by these loci, including MYH11, FZD3, SORCS3, and GOLGA8B, were differentially expressed in the context of Alzheimer's disease. DISCUSSION Our association of MYH11, FZD3, SORCS3, and GOLGA8B with dementia is supported by independent functional studies in human subjects, model systems, and associations with shared risk factors for stroke and dementia.
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Affiliation(s)
- Elizabeth E. Blue
- Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Simin Liu
- Department of Epidemiology, Brown University, Providence, Rhode Island, USA
- Department of Surgery, Brown University, Providence, Rhode Island, USA
- Department of Medicine, Brown University, Providence, Rhode Island, USA
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, New York, USA
| | - JoAnn Manson
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Lew Kuller
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kathleen Hayden
- Department of Social Science and Health Policy, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Alexander P. Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
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15
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A Comparison of Gene Expression Changes in the Blood of Individuals Consuming Diets Supplemented with Olives, Nuts or Long-Chain Omega-3 Fatty Acids. Nutrients 2020; 12:nu12123765. [PMID: 33302351 PMCID: PMC7762614 DOI: 10.3390/nu12123765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/13/2022] Open
Abstract
Background: The Mediterranean diet, which is rich in olive oil, nuts, and fish, is considered healthy and may reduce the risk of chronic diseases. Methods: Here, we compared the transcriptome from the blood of subjects with diets supplemented with olives, nuts, or long-chain omega-3 fatty acids and identified the genes differentially expressed. The dietary genes obtained were subjected to network analysis to determine the main pathways, as well as the transcription factors and microRNA interaction networks to elucidate their regulation. Finally, a gene-associated disease interaction network was performed. Results: We identified several genes whose expression is altered after the intake of components of the Mediterranean diets compared to controls. These genes were associated with infection and inflammation. Transcription factors and miRNAs were identified as potential regulators of the dietary genes. Interestingly, caspase 1 and sialophorin are differentially expressed in the opposite direction after the intake of supplements compared to Alzheimer’s disease patients. In addition, ten transcription factors were identified that regulated gene expression in supplemented diets, mild cognitive impairment, and Alzheimer’s disease. Conclusions: We identified genes whose expression is altered after the intake of the supplements as well as the transcription factors and miRNAs involved in their regulation. These genes are associated with schizophrenia, neoplasms, and rheumatic arthritis, suggesting that the Mediterranean diet may be beneficial in reducing these diseases. In addition, the results suggest that the Mediterranean diet may also be beneficial in reducing the risk of dementia.
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16
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Bioinformatic Analysis Reveals Phosphodiesterase 4D-Interacting Protein as a Key Frontal Cortex Dementia Switch Gene. Int J Mol Sci 2020; 21:ijms21113787. [PMID: 32471155 PMCID: PMC7313474 DOI: 10.3390/ijms21113787] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 12/11/2022] Open
Abstract
The mechanisms that initiate dementia are poorly understood and there are currently no treatments that can slow their progression. The identification of key genes and molecular pathways that may trigger dementia should help reveal potential therapeutic reagents. In this study, SWItch Miner software was used to identify phosphodiesterase 4D-interacting protein as a key factor that may lead to the development of Alzheimer’s disease, vascular dementia, and frontotemporal dementia. Inflammation, PI3K-AKT, and ubiquitin-mediated proteolysis were identified as the main pathways that are dysregulated in these dementias. All of these dementias are regulated by 12 shared transcription factors. Protein–chemical interaction network analysis of dementia switch genes revealed that valproic acid may be neuroprotective for these dementias. Collectively, we identified shared and unique dysregulated gene expression, pathways and regulatory factors among dementias. New key mechanisms that lead to the development of dementia were revealed and it is expected that these data will advance personalized medicine for patients.
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