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Lin J, Liu C, Hu E. Elucidating sleep disorders: a comprehensive bioinformatics analysis of functional gene sets and hub genes. Front Immunol 2024; 15:1381765. [PMID: 38919616 PMCID: PMC11196417 DOI: 10.3389/fimmu.2024.1381765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Background Sleep disorders (SD) are known to have a profound impact on human health and quality of life although their exact pathogenic mechanisms remain poorly understood. Methods The study first accessed SD datasets from the GEO and identified DEGs. These DEGs were then subjected to gene set enrichment analysis. Several advanced techniques, including the RF, SVM-RFE, PPI networks, and LASSO methodologies, were utilized to identify hub genes closely associated with SD. Additionally, the ssGSEA approach was employed to analyze immune cell infiltration and functional gene set scores in SD. DEGs were also scrutinized in relation to miRNA, and the DGIdb database was used to explore potential pharmacological treatments for SD. Furthermore, in an SD murine model, the expression levels of these hub genes were confirmed through RT-qPCR and Western Blot analyses. Results The findings of the study indicate that DEGs are significantly enriched in functions and pathways related to immune cell activity, stress response, and neural system regulation. The analysis of immunoinfiltration demonstrated a marked elevation in the levels of Activated CD4+ T cells and CD8+ T cells in the SD cohort, accompanied by a notable rise in Central memory CD4 T cells, Central memory CD8 T cells, and Natural killer T cells. Using machine learning algorithms, the study also identified hub genes closely associated with SD, including IPO9, RAP2A, DDX17, MBNL2, PIK3AP1, and ZNF385A. Based on these genes, an SD diagnostic model was constructed and its efficacy validated across multiple datasets. In the SD murine model, the mRNA and protein expressions of these 6 hub genes were found to be consistent with the results of the bioinformatics analysis. Conclusion In conclusion, this study identified 6 genes closely linked to SD, which may play pivotal roles in neural system development, the immune microenvironment, and inflammatory responses. Additionally, the key gene-based SD diagnostic model constructed in this study, validated on multiple datasets showed a high degree of reliability and accuracy, predicting its wide potential for clinical applications. However, limited by the range of data sources and sample size, this may affect the generalizability of the results.
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Affiliation(s)
- Junhan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
| | - Changyuan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
| | - Ende Hu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
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Penalva YCM, Paschkowsky S, Yang J, Recinto SJ, Cinkorpumin J, Xiao B, Nitu A, Wu H, Munter HM, Michalski B, Fahnestock M, Pastor W, Bennett DA, Munter LM. Loss of the APP regulator RHBDL4 preserves memory in an Alzheimer's disease mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.579698. [PMID: 38464180 PMCID: PMC10925189 DOI: 10.1101/2024.02.22.579698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Characteristic cerebral pathological changes of Alzheimer's disease (AD) such as glucose hypometabolism or the accumulation of cleavage products of the amyloid precursor protein (APP), known as Aβ peptides, lead to sustained endoplasmic reticulum (ER) stress and neurodegeneration. To preserve ER homeostasis, cells activate their unfolded protein response (UPR). The rhomboid-like-protease 4 (RHBDL4) is an enzyme that participates in the UPR by targeting proteins for proteasomal degradation. We demonstrated previously that RHBLD4 cleaves APP in HEK293T cells, leading to decreased total APP and Aβ. More recently, we showed that RHBDL4 processes APP in mouse primary mixed cortical cultures as well. Here, we aim to examine the physiological relevance of RHBDL4 in the brain. We first found that brain samples from AD patients and an AD mouse model (APPtg) showed increased RHBDL4 mRNA and protein expression. To determine the effects of RHBDL4's absence on APP physiology in vivo, we crossed APPtg mice to a RHBDL4 knockout (R4 KO) model. RHBDL4 deficiency in APPtg mice led to increased total cerebral APP and Aβ levels when compared to APPtg controls. Contrary to expectations, as assessed by cognitive tests, RHBDL4 absence rescued cognition in 5-month-old female APPtg mice. Informed by unbiased RNAseq data, we demonstrated in vitro and in vivo that RHBDL4 absence leads to greater levels of active β-catenin due to decreased proteasomal clearance. Decreased β-catenin activity is known to underlie cognitive defects in APPtg mice and AD. Our work suggests that RHBDL4's increased expression in AD, in addition to regulating APP levels, leads to aberrant degradation of β-catenin, contributing to cognitive impairment.
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Affiliation(s)
- Ylauna Christine Megane Penalva
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
| | - Sandra Paschkowsky
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Sherilyn Junelle Recinto
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
| | | | - Bin Xiao
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
| | - Albert Nitu
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada H3A 2B4
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
| | - Helen Wu
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
| | - Hans Markus Munter
- Department of Human Genetics, McGill University, Montreal, QC, Canada H3A 0C7
| | - Bernadeta Michalski
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - Margaret Fahnestock
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - William Pastor
- Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 0B1
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Lisa Marie Munter
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H3G 0B1
- Cell Information Systems group, Bellini Life Sciences Complex, McGill University, Montreal, QC, Canada H3G 0B1
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Montréal H3G 0B1, Québec, Canada
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Zammit AR, Bennett DA, Buchman AS. From theory to practice: translating the concept of cognitive resilience to novel therapeutic targets that maintain cognition in aging adults. Front Aging Neurosci 2024; 15:1303912. [PMID: 38283067 PMCID: PMC10811007 DOI: 10.3389/fnagi.2023.1303912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024] Open
Abstract
While the concept of cognitive resilience is well-established it has not been defined in a way that can be measured. This has been an impediment to studying its underlying biology and to developing instruments for its clinical assessment. This perspective highlights recent work that has quantified the expression of cortical proteins associated with cognitive resilience, thus facilitating studies of its complex underlying biology and the full range of its clinical effects in aging adults. These initial studies provide empirical support for the conceptualization of resilience as a continuum. Like other conventional risk factors, some individuals manifest higher-than-average cognitive resilience and other individuals manifest lower-than-average cognitive resilience. These novel approaches for advancing studies of cognitive resilience can be generalized to other aging phenotypes and can set the stage for the development of clinical tools that might have the potential to measure other mechanisms of resilience in aging adults. These advances also have the potential to catalyze a complementary therapeutic approach that focuses on augmenting resilience via lifestyle changes or therapies targeting its underlying molecular mechanisms to maintain cognition and brain health even in the presence of untreatable stressors like brain pathologies that accumulate in aging adults.
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Affiliation(s)
- Andrea R. Zammit
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
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Zhong Y, Tubbs JD, Leung PBM, Zhan N, Hui TCK, Ho KKY, Hung KSY, Cheung EFC, So HC, Lui SSY, Sham PC. Early-onset schizophrenia is associated with immune-related rare variants in a Chinese sample. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.21.23298115. [PMID: 38045317 PMCID: PMC10690336 DOI: 10.1101/2023.11.21.23298115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background Rare variants are likely to contribute to schizophrenia (SCZ), given the large discrepancy between the heritability estimated from twin and GWAS studies. Furthermore, the nature of the rare-variant contribution to SCZ may vary with the "age-at-onset" (AAO), since early-onset has been suggested as being indicative of neurodevelopment deviance. Objective To examine the association of rare deleterious coding variants in early- and adult-onset SCZ in a Chinese sample. Method Exome sequencing was performed on DNA from 197 patients with SCZ spectrum disorder and 82 healthy controls (HC) of Chinese ancestry recruited in Hong Kong. We also gathered AAO information in the majority of SCZ samples. Patients were classified into early-onset (EOS, AAO<18) and adult-onset (AOS, AAO>18). We collapsed the rare variants to improve statistical power and examined the overall association of rare variants in SCZ versus HC, EOS versus HC, and AOS versus HC at the gene and gene-set levels by Sequence Kernel Association Test. The quantitative rare-variant association test of AAO was also conducted. We focused on variants which were predicted to have a medium or high impact on the protein-encoding process as defined by Ensembl. We applied a 100000-time permutation test to obtain empirical p-values, with significance threshold set at p < 1e -3 to control family-wise error rates. Moreover, we compared the burden of targeted rare variants in significant risk genes and gene sets in cases and controls. Results Based on several binary-trait association tests (i.e., SCZ vs HC, EOS vs HC and AOS vs HC), we identified 7 candidate risk genes and 20 gene ontology biological processes (GOBP) terms, which exhibited higher burdens in SCZ than in controls. Based on quantitative rare-variant association tests, we found that alterations in 5 candidate risk genes and 7 GOBP pathways were significantly correlated with AAO. Based on biological and functional profiles of the candidate risk genes and gene sets, our findings suggested that, in addition to the involvement of perturbations in neural systems in SCZ in general, altered immune responses may be specifically implicated in EOS. Conclusion Disrupted immune responses may exacerbate abnormal perturbations during neurodevelopment and trigger the early onset of SCZ. We provided evidence of rare variants increasing SCZ risk in the Chinese population.
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Tandon R, Levey AI, Lah JJ, Seyfried NT, Mitchell CS. Machine Learning Selection of Most Predictive Brain Proteins Suggests Role of Sugar Metabolism in Alzheimer's Disease. J Alzheimers Dis 2023; 92:411-424. [PMID: 36776048 PMCID: PMC10041447 DOI: 10.3233/jad-220683] [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] [Accepted: 01/05/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND The complex and not yet fully understood etiology of Alzheimer's disease (AD) shows important proteopathic signs which are unlikely to be linked to a single protein. However, protein subsets from deep proteomic datasets can be useful in stratifying patient risk, identifying stage dependent disease markers, and suggesting possible disease mechanisms. OBJECTIVE The objective was to identify protein subsets that best classify subjects into control, asymptomatic Alzheimer's disease (AsymAD), and AD. METHODS Data comprised 6 cohorts; 620 subjects; 3,334 proteins. Brain tissue-derived predictive protein subsets for classifying AD, AsymAD, or control were identified and validated with label-free quantification and machine learning. RESULTS A 29-protein subset accurately classified AD (AUC = 0.94). However, an 88-protein subset best predicted AsymAD (AUC = 0.92) or Control (AUC = 0.92) from AD (AUC = 0.98). AD versus Control: APP, DHX15, NRXN1, PBXIP1, RABEP1, STOM, and VGF. AD versus AsymAD: ALDH1A1, BDH2, C4A, FABP7, GABBR2, GNAI3, PBXIP1, and PRKAR1B. AsymAD versus Control: APP, C4A, DMXL1, EXOC2, PITPNB, RABEP1, and VGF. Additional predictors: DNAJA3, PTBP2, SLC30A9, VAT1L, CROCC, PNP, SNCB, ENPP6, HAPLN2, PSMD4, and CMAS. CONCLUSION Biomarkers were dynamically separable across disease stages. Predictive proteins were significantly enriched to sugar metabolism.
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Affiliation(s)
- Raghav Tandon
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- Center for Machine Learning, Georgia Institute of Technology, Atlanta, GA, USA
| | - Allan I. Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Cassie S. Mitchell
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- Center for Machine Learning, Georgia Institute of Technology, Atlanta, GA, USA
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Goodenowe DB, Senanayake V. Brain ethanolamine phospholipids, neuropathology and cognition: A comparative post-mortem analysis of structurally specific plasmalogen and phosphatidyl species. Front Cell Dev Biol 2022; 10:866156. [PMID: 36092723 PMCID: PMC9451657 DOI: 10.3389/fcell.2022.866156] [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: 01/30/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022] Open
Abstract
Reduced cognition in the elderly is associated with low levels of plasmalogens and high levels of lipid rafts, amyloid plaques, and neurofibrillary tangles in the temporal cortex. A systematic integrative analysis of key indices of these pathologies to determine their collective and independent contributions to cognition was performed. Levels of four phosphatidylethanolamines (PE) and four ethanolamine plasmalogens (PL) of identical sn-1 carbon length and desaturation (stearic, 18:0) and identical sn-2 fatty acid compositions of varying side chain lengths and degrees of unsaturation (oleic, 18:1; linoleic, 18:2; arachidonic, 20:4; docosahexaenoic, 22:6), flotillin-1 expression and amyloid plaque and neurofibrillary tangle densities were measured in inferior temporal cortex tissue from 100 elderly subjects (Rush University Memory and Aging Project, 88.5 ± 5.8 years old). Subjects were evenly distributed with respect to gender (52/48, F/M) and cognitive status (38/24/38, no cognitive impairment/mild cognitive impairment/Alzheimer’s dementia) proximate to death. Multivariate logistic regression analyses were used to determine the relative and collective associations of the neuropathological indices with cognition. Higher levels of tangles, amyloid, or flotillin and lower levels of PL 18:0/22:6 were significantly associated with lower cognition in the base model (adjusted for age, sex, education). Multivariate analysis revealed that only PL 18:0/22:6 (β = 0.506; p < 0.00001), tangles (−0.307; p < 0.01), and flotillin (−0.2027; p < 0.05) were independently associated with reduced cognition. PL 18:0/22:6 and PE 18:0/22:6 levels were independently associated with cognition in the presence of tangles, amyloid, and flotillin, but only PL 18:0/22:6 retained its association with cognition when both PL and PE 18:0/22:6 were included in the model indicating that PE 18:0/22:6 levels were associated with PL 18:0/22:6, not cognition. Only high brain levels of PL 18:0/22:6 (>mean+1SD) was predictive of normal cognition (coef = 1.67, p < 0.05) and non-demented state (coef = −2.73, p < 0.001), whereas low levels of PL 18:0/22:6 and high levels of tangles or flotillin were predictive of dementia. The association of high brain polyunsaturated (PUFA)-PL levels with better cognition was independent of amyloid plaque, neurofibrillary tangle, PE, and flotillin-1 expression. Maintenance or augmentation of brain docosahexaenoic (DHA)-PL levels warrants further investigation as a target for preventing cognitive decline or improving cognition in the elderly, respectively.
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Baik JY, Kim M, Bao J, Long Q, Shen L. Identifying Alzheimer's genes via brain transcriptome mapping. BMC Med Genomics 2022; 15:116. [PMID: 35590321 PMCID: PMC9118564 DOI: 10.1186/s12920-022-01260-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is one of the most common neurodegenerative disorders characterized by progressive decline in cognitive function. Targeted genetic analyses, genome-wide association studies, and imaging genetic analyses have been performed to detect AD risk and protective genes and have successfully identified dozens of AD susceptibility loci. Recently, brain imaging transcriptomics analyses have also been conducted to investigate the relationship between neuroimaging traits and gene expression measures to identify interesting gene-traits associations. These imaging transcriptomic studies typically do not involve the disease outcome in the analysis, and thus the identified brain or transcriptomic markers may not be related or specific to the disease outcome. RESULTS We propose an innovative two-stage approach to identify genes whose expression profiles are related to diagnosis phenotype via brain transcriptome mapping. Specifically, we first map the effects of a diagnosis phenotype onto imaging traits across the brain using a linear regression model. Then, the gene-diagnosis association is assessed by spatially correlating the brain transcriptome map with the diagnostic effect map on the brain-wide imaging traits. To demonstrate the promise of our approach, we apply it to the integrative analysis of the brain transcriptome data from the Allen Human Brain Atlas (AHBA) and the amyloid imaging data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Our method identifies 12 genes whose brain-wide transcriptome patterns are highly correlated with six different diagnostic effect maps on the amyloid imaging traits. These 12 genes include four confirmatory findings (i.e., AD genes reported in DisGeNET) and eight novel genes that have not be associated with AD in DisGeNET. CONCLUSION We have proposed a novel disease-related brain transcriptomic mapping method to identify genes whose expression profiles spatially correlated with regional diagnostic effects on a studied brain trait. Our empirical study on the AHBA and ADNI data shows the promise of the approach, and the resulting AD gene discoveries provide valuable information for better understanding biological pathways from transcriptomic signatures to intermediate brain traits and to phenotypic disease outcomes.
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Affiliation(s)
- Jae Young Baik
- grid.25879.310000 0004 1936 8972School of Arts and Sciences, University of Pennsylvania, Philadelphia, USA
| | - Mansu Kim
- grid.411947.e0000 0004 0470 4224Department of Artificial intelligence, Catholic University of Korea, Bucheon, Republic of Korea
| | - Jingxuan Bao
- grid.25879.310000 0004 1936 8972Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Qi Long
- grid.25879.310000 0004 1936 8972Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA.
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Investigation of the magnetic susceptibility properties of fresh and fixed mouse heart, liver, skeletal muscle and brain tissue. Phys Med 2021; 88:37-44. [PMID: 34171574 DOI: 10.1016/j.ejmp.2021.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Several magnetic resonance imaging (MRI) techniques exploit the difference in magnetic susceptibilities between tissues, but systematic measurements of tissue susceptibility are lacking. Furthermore, there is the question as to whether chemical fixation that is used for ex vivo MRI studies, affects the magnetic properties of the tissue. Here, we determined the magnetic susceptibility and water content of fresh and chemically fixed mouse tissue. METHODS Mass susceptibility of brain, heart, liver and skeletal muscle samples were determined on a vibrating sample magnetometer at room temperature. Measurements at 50, 125, 200 and 295 K were performed to assess the temperature dependence of susceptibility. Moreover, we measured water content of fresh and fixed samples. RESULTS All samples show mass susceptibilities between -0.068 and -1.929 × 10-8 m3/kg, compared to -9.338 × 10-9 m3/kg of double distilled water. Heart tissue has a more diamagnetic susceptibility than the other tissues. Compared to fresh tissue, fixed tissue has a less diamagnetic susceptibility. Fixed tissue was not different in water content to fresh tissue and showed no consistent dependence of susceptibility with temperature, whereas fresh tissue shows a decrease to at least 125 K, indicative of a paramagnetic component. CONCLUSIONS Biological tissues are diamagnetic in comparison to water, where the heart is more diamagnetic than the other tissues, with paramagnetic contributions. Fixation rendered tissue less diamagnetic compared to fresh tissue. Our measurements revealed differences in tissue susceptibility between VSM and QSM, inviting more research to compare susceptibility-based MRI methods with physical measurements of tissue susceptibility.
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Kazemi Moghadam V, Dickerson AS, Shahedi F, Bazrafshan E, Seyedhasani SN, Sarmadi M. Association of the global distribution of multiple sclerosis with ultraviolet radiation and air pollution: an ecological study based on GBD data. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:17802-17811. [PMID: 33403633 DOI: 10.1007/s11356-020-11761-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Given the growing global trend of multiple sclerosis (MS), this study was designed to evaluate environmental determinates of the worldwide distribution of MS in the presence of socioeconomic and geographic indices. MS data was obtained from the Institute for Health Metrics and Evaluation website. The air pollution parameters, including particles with aerodynamic diameter less than 2.5 μm (PM2.5), tropospheric ozone, and solid fuel use, were acquired from global burden of disease resources and the World Health Organization. Ultraviolet index (UVI) values were obtained from the Tropospheric Emission Monitoring Internet Service website. Correlation and linear regression analyses were used to investigate the relationship between air pollution and environmental parameters with MS variables. The average prevalence and incidence rates in countries with high UVI were 5.17 and 0.25 per 100,000, respectively, and in countries with low UVI were 101.37 and 0.78, respectively. The results showed negative associations between prevalence, incidence and mortality of MS with ozone concentrations (β = - 1.04, - 0.04, and - 0.01 respectively; P < 0.01). Also, the fully adjusted model showed significant negative correlation of UVI with the MS variables in the presence of other variables (P < 0.01). Our findings demonstrated that UVI had the strongest significant inverse association with MS distribution. Consequently, vitamin D intake may be a major contributor to MS development. However, this study showed a slight influence of air pollution on the prevalence of MS in the presence of other parameters. Given the inconsistent results of previous studies, further studies may be required.
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Affiliation(s)
- Vahid Kazemi Moghadam
- Department of Environmental Health Engineering, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Aisha S Dickerson
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Fateme Shahedi
- Department of Radiology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Neuroscience Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Edris Bazrafshan
- Department of Environmental Health Engineering, School of Health, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Seyedeh Nahid Seyedhasani
- Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Department of Health Information Technology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Mohammad Sarmadi
- Neuroscience Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran.
- Department of Environmental Health Engineering, School of Health, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran.
- Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran.
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Chang K, Yuan C, Liu X. A New RBPs-Related Signature Predicts the Prognosis of Colon Adenocarcinoma Patients. Front Oncol 2021; 11:627504. [PMID: 33767995 PMCID: PMC7985171 DOI: 10.3389/fonc.2021.627504] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/27/2021] [Indexed: 11/13/2022] Open
Abstract
The dysregulation of RNA binding proteins (RBPs) is closely related to tumorigenesis and development. However, the role of RBPs in Colon adenocarcinoma (COAD) is still poorly understood. We downloaded COAD’s RNASeq data from the Cancer Genome Atlas (TCGA) database, screened the differently expressed RBPs in normal tissues and tumor, and constructed a protein interaction network. COAD patients were randomly divided into a training set (N = 315) and a testing set (N = 132). In the training set, univariate Cox analysis identified 12 RBPs significantly related to the prognosis of COAD. By multivariate COX analysis, we constructed a prognostic model composed of five RBPs (CELF4, LRRFIP2, NOP14, PPARGC1A, ZNF385A) based on the lowest Akaike information criterion. Each COAD patient was scored according to the model formula. Further analysis showed that compared with the low-risk group, the overall survival rate (OS) of patients in the high-risk group was significantly lower. The area under the curve of the time-dependent receiver operator characteristic (ROC) curve was 0.722 in the training group and 0.738 in the test group, which confirmed a good prediction feature. In addition, a nomogram was constructed based on clinicopathological characteristics and risk scores. C-index and calibration curve proved the accuracy in predicting the 1-, 3-, and 5-year survival rates of COAD patients. In short, we constructed a superior prognostic and diagnostic signature composed of five RBPs, which indicates new possibilities for individualized treatment of COAD patients.
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Affiliation(s)
- Kaili Chang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chong Yuan
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xueguang Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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Mroczek M, Desouky A, Sirry W. Imaging Transcriptomics in Neurodegenerative Diseases. J Neuroimaging 2020; 31:244-250. [PMID: 33368775 DOI: 10.1111/jon.12827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/30/2022] Open
Abstract
Imaging transcriptomics investigates the relationship between neuroanatomical/neuroimaging features and gene expression. The spatial and temporal distribution of the expressed genes and their pattern of spreading over time can contribute to elucidating cellular and molecular processes involved in neurodegeneration. In this study, we review recent findings regarding the correlation between neuroimaging and expression data in neurodegenerative diseases with a focus on Alzheimer's disease and Parkinson's disease. An association between gene expression data and different neuroimaging neurodegeneration features, such as R2 relaxation time and volumetric cortical atrophy, was established. Several positive and negative expression correlations were identified, and they confirmed the focal nature of neurodegeneration. Positively correlated genes were associated with cell motility, immune system activity, neuroinflammation, and microglia. Data from connectome studies support the hypothesis of selective network vulnerability and a temporal spreading pattern in neurodegenerative pathologies. Genes related to cellular mobility and transport are overexpressed in the neuroimaging-defined delineated areas of degeneration. In addition, expression enrichment of genes involved in immunological processes in vulnerable regions-such as the Toll-like receptor, a receptor involved in innate immunity-plays a major role in neuroinflammation in neurodegenerative diseases. However, substantial limitations must be overcome in future studies: the lack of high-quality resolution expression data, the lack of standardized study protocols, and insufficient sensitive early stage neuroimaging markers of degeneration. Identifying neuroimaging and expression prodromal biomarkers and investigating their causal relation in the preclinical disease stage may enable early targeted therapy before the onset of irreversible brain changes.
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Affiliation(s)
- Magdalena Mroczek
- Centre for Gerontopsychiatric Medicine, Department of Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland
| | - Ahmed Desouky
- School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Wadid Sirry
- Faculty of Medicine, Cairo University, Cairo, Egypt
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12
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Wang C, Plusquin M, Ghantous A, Herceg Z, Alfano R, Cox B, Nawrot TS. DNA methylation of insulin-like growth factor 2 and H19 cluster in cord blood and prenatal air pollution exposure to fine particulate matter. Environ Health 2020; 19:129. [PMID: 33287817 PMCID: PMC7720562 DOI: 10.1186/s12940-020-00677-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/13/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The IGF2 (insulin-like growth factor 2) and H19 gene cluster plays an important role during pregnancy as it promotes both foetal and placental growth. We investigated the association between cord blood DNA methylation status of the IGF2/H19 gene cluster and maternal fine particulate matter exposure during fetal life. To the best of our knowledge, this is the first study investigating the association between prenatal PM2.5 exposure and newborn DNA methylation of the IGF2/H19. METHODS Cord blood DNA methylation status of IGF2/H19 cluster was measured in 189 mother-newborn pairs from the ENVIRONAGE birth cohort (Flanders, Belgium). We assessed the sex-specific association between residential PM2.5 exposure during pregnancy and the methylation level of CpG loci mapping to the IGF2/H19 cluster, and identified prenatal vulnerability by investigating susceptible time windows of exposure. We also addressed the biological functionality of DNA methylation level in the gene cluster. RESULTS Prenatal PM2.5 exposure was found to have genetic region-specific significant association with IGF2 and H19 during specific gestational weeks. The association was found to be sex-specific in both gene regions. Functionality of the DNA methylation was annotated by the association to fetal growth and cellular pathways. CONCLUSIONS The results of our study provided evidence that prenatal PM2.5 exposure is associated with DNA methylation in newborns' IGF2/H19. The consequences within the context of fetal development of future phenotyping should be addressed.
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Affiliation(s)
- Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, 3590 Diepenbeek, Hasselt, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, 3590 Diepenbeek, Hasselt, Belgium
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, 3590 Diepenbeek, Hasselt, Belgium
| | - Bianca Cox
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, 3590 Diepenbeek, Hasselt, Belgium
| | - Tim S. Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, 3590 Diepenbeek, Hasselt, Belgium
- Department of Public Health and Primary Care, Leuven University, Leuven, Belgium
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13
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Systematic analysis to identify transcriptome-wide dysregulation of Alzheimer's disease in genes and isoforms. Hum Genet 2020; 140:609-623. [PMID: 33140241 DOI: 10.1007/s00439-020-02230-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/20/2020] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is one of the most common neurodegeneration diseases caused by multiple factors. The mechanistic insight of AD remains limited. To disclose molecular mechanisms of AD, many studies have been proposed from transcriptome analyses. However, no analysis across multiple levels of transcription has been conducted to discover co-expression networks of AD. We performed gene-level and isoform-level analyses of RNA sequencing (RNA-seq) data from 544 brain tissues of AD patients, mild cognitive impaired (MCI) patients, and healthy controls. Gene and isoform levels of co-expression modules were constructed by RNA-seq data. The associations of modules with AD were evaluated by integrating cognitive scores of patients, Genome-wide association studies (GWAS), alternative splicing analysis, and dementia-related genes expressed in brain tissues. Totally, 29 co-expression modules were found with expressions significantly correlated with the cognitive scores. Among them, two isoform modules were enriched with AD-associated SNPs and genes whose mRNA splicing displayed significant alteration in relation to AD disease. These two modules were further found enriched with dementia-related genes expressed in four brain regions of 125 AD patients. Analyzing expressions of these two modules revealed expressions of 39 isoforms (corresponding to 35 genes) significantly correlated with cognitive scores of AD patients, in which 38 isoforms were significantly up-regulated in AD patients comparing to controls, and 33 isoforms (corresponding to 29 genes) were not reported as AD-related previously. Employing the co-expression modules and the drug-induced gene expression data from Connectivity Map (CMAP), 12 drugs were predicted as significant in restoring the gene expression of AD patients towards health, which include nine drugs reported for relieving AD. In comparison, four of the top 12 significant drugs were known for relieving AD if the drug prediction was performed by the genes expressed significantly different in AD and healthy controls. Analysis of multiple levels of the transcriptomic organization is useful in suggesting AD-related co-expression networks and discovering drugs.
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14
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Sherva R, Gross A, Mukherjee S, Koesterer R, Amouyel P, Bellenguez C, Dufouil C, Bennett DA, Chibnik L, Cruchaga C, del-Aguila J, Farrer LA, Mayeux R, Munsie L, Winslow A, Newhouse S, Saykin AJ, Kauwe JS, Crane PK, Green RC. Genome-wide association study of rate of cognitive decline in Alzheimer's disease patients identifies novel genes and pathways. Alzheimers Dement 2020; 16:1134-1145. [PMID: 32573913 PMCID: PMC7924136 DOI: 10.1002/alz.12106] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/18/2019] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Variability exists in the disease trajectories of Alzheimer's disease (AD) patients. We performed a genome-wide association study to examine rate of cognitive decline (ROD) in patients with AD. METHODS We tested for interactions between genetic variants and time since diagnosis to predict the ROD of a composite cognitive score in 3946 AD cases and performed pathway analysis on the top genes. RESULTS Suggestive associations (P < 1.0 × 10-6 ) were observed on chromosome 15 in DNA polymerase-γ (rs3176205, P = 1.11 × 10-7 ), chromosome 7 (rs60465337,P = 4.06 × 10-7 ) in contactin-associated protein-2, in RP11-384F7.1 on chromosome 3 (rs28853947, P = 5.93 × 10-7 ), family with sequence similarity 214 member-A on chromosome 15 (rs2899492, P = 5.94 × 10-7 ), and intergenic regions on chromosomes 16 (rs4949142, P = 4.02 × 10-7 ) and 4 (rs1304013, P = 7.73 × 10-7 ). Significant pathways involving neuronal development and function, apoptosis, memory, and inflammation were identified. DISCUSSION Pathways related to AD, intelligence, and neurological function determine AD progression, while previously identified AD risk variants, including the apolipoprotein (APOE) ε4 and ε2 variants, do not have a major impact.
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Affiliation(s)
- Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, 72 East Concord St., E-200, Boston, MA 02118, USA
| | - Alden Gross
- Johns Hopkins Bloomberg School of Public Health, 2024 E. Monument St, Johns Hopkins Center on Aging and Health, Suite 2-700, Baltimore, MD 21205, USA
| | - Shubhabrata Mukherjee
- Department of Medicine, University of Washington, Box 359780, 325 Ninth Avenue, Seattle, WA 98104, USA
| | - Ryan Koesterer
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000 Inserm UMR-1167, Institut Pasteur de Lille, 1 rue du Professeur Calmette, BP 245 - 59019 LILLE cedex, FRANCE
- Institut Pasteur de Lille, Lille, France
- University of Lille, DISTALZ Laboratory of Excellence (LabEx), Lille, France
| | - Celine Bellenguez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000 Inserm UMR-1167, Institut Pasteur de Lille, 1 rue du Professeur Calmette, BP 245 - 59019 LILLE cedex, FRANCE
- Institut Pasteur de Lille, Lille, France
- University of Lille, DISTALZ Laboratory of Excellence (LabEx), Lille, France
| | - Carole Dufouil
- Inserm Unit 1219 Bordeaux Population Health, CIC 1401-EC (Clinical Epidemiology), University of Bordeaux, ISPED (Bordeaux School of Public Health), Bordeaux University Hospital, Bordeaux, France
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Lori Chibnik
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Carlos Cruchaga
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, Office 9607, St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics. Washington University School of Medicine, Saint Louis, USA
| | - Jorge del-Aguila
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, Office 9607, St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics. Washington University School of Medicine, Saint Louis, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, 72 East Concord St., E-200, Boston, MA 02118, USA
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, USA
| | - Leanne Munsie
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Ashley Winslow
- Orphan Disease Center, Perelman School of Medicine, University of Pennsylvania, 125 South 31st Street, Pennsylvania, PA 19104, USA
| | - Stephen Newhouse
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London, UK
- Health Data Research UK London, University College London, London, UK
- dd Institute of Health Informatics, University College London, London, UK
- The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, London, UK
| | - Andrew J. Saykin
- Indiana Alzheimer Disease Center and Department of Radiology and Imaging Sciences, Indiana University School of Medicine, IU Health Neuroscience Center, Suite 4100, 355 West 16th Street, Indianapolis, IN 46202, USA
| | - John S.K. Kauwe
- Department of Biology, Brigham Young University, 105 FPH, Provo, UT 84602, USA
| | | | - Paul K. Crane
- Department of Medicine, University of Washington, Box 359780, 325 Ninth Avenue, Seattle, WA 98104, USA
| | - Robert C. Green
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, EC Alumnae Building, Suite 301, 41 Avenue Louis Pasteur, Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Partners HealthCare Personalized Medicine, Boston, MA, USA
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15
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Gaiteri C, Dawe R, Mostafavi S, Blizinsky KD, Tasaki S, Komashko V, Yu L, Wang Y, Schneider JA, Arfanakis K, De Jager PL, Bennett DA. Gene expression and DNA methylation are extensively coordinated with MRI-based brain microstructural characteristics. Brain Imaging Behav 2020; 13:963-972. [PMID: 29934819 PMCID: PMC6309607 DOI: 10.1007/s11682-018-9910-4] [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] [Indexed: 01/07/2023]
Abstract
Cognitive function relies on both molecular levels and cellular structures. However, systematic relationships between these two components of cognitive function, and their joint contribution to disease, are largely unknown. We utilize postmortem neuroimaging in tandem with gene expression and DNA methylation, from 222 deeply-phenotyped persons in a longitudinal aging cohort. Expression of hundreds of genes and methylation at thousands of loci are related to the microstructure of extensive regions of this same set of brains, as assessed by MRI. The genes linked to brain microstructure perform functions related to cell motility, transcriptional regulation and nuclear processes, and are selectively associated with Alzheimer’s phenotypes. Similar methodology can be applied to other diseases to identify their joint molecular and structural basis, or to infer molecular levels in the brain on the basis of neuroimaging for precision medicine applications.
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Affiliation(s)
- Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
| | - Robert Dawe
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.,Department of Diagnostic Radiology and Nuclear Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sara Mostafavi
- Department of Statistics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Katherine D Blizinsky
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.,National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vitalina Komashko
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Konstantinos Arfanakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.,Department of Diagnostic Radiology and Nuclear Medicine, Rush University Medical Center, Chicago, IL, USA.,Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Philip L De Jager
- Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
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16
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Ye Z, Sun B, Mi X, Xiao Z. Gene co-expression network for analysis of plasma exosomal miRNAs in the elderly as markers of aging and cognitive decline. PeerJ 2020; 8:e8318. [PMID: 31934508 PMCID: PMC6951281 DOI: 10.7717/peerj.8318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/29/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evidence has shown that microRNA (miRNAs) are involved in molecular pathways responsible for aging and age-related cognitive decline. However, there is a lack of research linked plasma exosome-derived miRNAs changes with cognitive function in older people and aging, which might prove a new insight on the transformation of miRNAs on clinical applications for cognitive decline for older people. METHODS We applied weighted gene co-expression network analysis to investigated miRNAs within plasma exosomes of older people for a better understanding of the relationship of exosome-derived miRNAs with cognitive decline in elderly adults. We identified network modules of co-expressed miRNAs in the elderly exosomal miRNAs dataset. In each module, we selected vital miRNAs and carried out functional enrichment analyses of their experimentally known target genes and their function. RESULTS We found that plasma exosomal miRNAs hsa-mir-376a-3p, miR-10a-5p, miR-125-5p, miR-15a-5p have critical regulatory roles in the development of aging and cognitive dysfunction in the elderly and may serve as biomarkers and putative novel therapeutic targets for aging and cognitive decline.
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Affiliation(s)
- Zheng Ye
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Bo Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Xue Mi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Zhongdang Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
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17
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Kim N, Yu L, Dawe R, Petyuk VA, Gaiteri C, De Jager PL, Schneider JA, Arfanakis K, Bennett DA. Microstructural changes in the brain mediate the association of AK4, IGFBP5, HSPB2, and ITPK1 with cognitive decline. Neurobiol Aging 2019; 84:17-25. [PMID: 31479860 DOI: 10.1016/j.neurobiolaging.2019.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/13/2022]
Abstract
The associations of 4 proteins-AK4, ITPK1, HSPB2, and IGFBP5-with cognitive function in older adults were largely unexplained by known brain pathologies. We examined the extent to which individual protein associations with cognitive decline were attributable to microstructural changes in the brain. This study included 521 participants (mean age 90.3, 65.9-108.3) with the postmortem reciprocal of transverse relaxation time (R2) magnetic resonance image. All participants came from one of the 2 ongoing longitudinal cohorts of aging and dementia, the Religious Orders Study and Rush Memory and Aging Project. Higher abundance of AK4, HSPB2, and IGFBP5 was associated with faster cognitive decline and mediated through lower postmortem R2 in the frontal and temporal white matter regions. In contrast, higher abundance of ITPK1 was associated with slower cognitive decline and mediated through higher postmortem R2 in the frontal and temporal white matter regions. The associations of 4 proteins-AK4, ITPK1, IGFBP5, and HSPB2-with cognition in late life were explained via microstructural changes in the brain.
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Affiliation(s)
- Namhee Kim
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Robert Dawe
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Diagnostic Radiology and Nuclear Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Vladislav A Petyuk
- Biological Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA; Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA; Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Konstantinos Arfanakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Diagnostic Radiology and Nuclear Medicine, Rush University Medical Center, Chicago, IL, USA; Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
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18
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Tian XL, Jiang SY, Zhang XL, Yang J, Cui JH, Liu XL, Gong KR, Yan SC, Zhang CY, Shao G. Potassium bisperoxo (1,10-phenanthroline) oxovanadate suppresses proliferation of hippocampal neuronal cell lines by increasing DNA methyltransferases. Neural Regen Res 2019; 14:826-833. [PMID: 30688268 PMCID: PMC6375031 DOI: 10.4103/1673-5374.249230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bisperoxo (1,10-phenanthroline) oxovanadate (BpV) can reportedly block the cell cycle. The present study examined whether BpV alters gene expression by affecting DNA methyltransferases (DNMTs), which would impact the cell cycle. Immortalized mouse hippocampal neuronal precursor cells (HT22) were treated with 0.3 or 3 μM BpV. Proliferation, morphology, and viability of HT22 cells were detected with an IncuCyte real-time video imaging system or inverted microscope and 3-(4,5-dimethylthiazol-2-yl)-5(3-carboxymethonyphenol)-2-(4-sulfophenyl)-2H-tetrazolium, respectively. mRNA and protein expression of DNMTs and p21 in HT22 cells was detected by real-time polymerase chain reaction and immunoblotting, respectively. In addition, DNMT activity was measured with an enzyme-linked immunosorbent assay. Effects of BpV on the cell cycle were analyzed using flow cytometry. Results demonstrated that treatment with 0.3 μM BpV did not affect cell proliferation, morphology, or viability; however, treatment with 3 μM BpV decreased cell viability, increased expression of both DNMT3B mRNA and protein, and inhibited the proliferation of HT22 cells; and 3 μM BpV also blocked the cell cycle and increased expression of the regulatory factor p21 by increasing DNMT expression in mouse hippocampal neurons.
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Affiliation(s)
- Xiao-Li Tian
- Biomedicine Research Center, Basic Medical College and Baotou Medical College of Neuroscience Institute; Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, Inner Mongolia Autonomous Region; Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Shu-Yuan Jiang
- Biomedicine Research Center, Basic Medical College and Baotou Medical College of Neuroscience Institute; Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, Inner Mongolia Autonomous Region, China
| | - Xiao-Lu Zhang
- Biomedicine Research Center, Basic Medical College and Baotou Medical College of Neuroscience Institute; Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, Inner Mongolia Autonomous Region; Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jie Yang
- Biomedicine Research Center, Basic Medical College and Baotou Medical College of Neuroscience Institute; Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, Inner Mongolia Autonomous Region, China
| | - Jun-He Cui
- Biomedicine Research Center, Basic Medical College and Baotou Medical College of Neuroscience Institute; Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, Inner Mongolia Autonomous Region, China
| | - Xiao-Lei Liu
- Biomedicine Research Center, Basic Medical College and Baotou Medical College of Neuroscience Institute; Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, Inner Mongolia Autonomous Region, China
| | - Ke-Rui Gong
- Department of Oral and Maxillofacial Surgery, University of California San Francsico, San Francisco, CA, USA
| | - Shao-Chun Yan
- Biomedicine Research Center, Basic Medical College and Baotou Medical College of Neuroscience Institute; Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, Inner Mongolia Autonomous Region, China
| | - Chun-Yang Zhang
- Department of Neurosurgery, the First Affiliated Hospital of Baotou Medical College, Baotou, Inner Mongolia Autonomous Region, China
| | - Guo Shao
- Biomedicine Research Center, Basic Medical College and Baotou Medical College of Neuroscience Institute; Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, Inner Mongolia Autonomous Region; Beijing Key Laboratory of Hypoxic Conditioning Translational Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
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19
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Zhou Y, Lutz P, Ibrahim EC, Courtet P, Tzavara E, Turecki G, Belzeaux R. Suicide and suicide behaviors: A review of transcriptomics and multiomics studies in psychiatric disorders. J Neurosci Res 2018; 98:601-615. [DOI: 10.1002/jnr.24367] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Yi Zhou
- McGill Group for Suicide Studies Douglas Mental Health University Institute, McGill University Montréal Canada
| | - Pierre‐Eric Lutz
- Centre National de la Recherche Scientifique Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212 Strasbourg France
| | - El Chérif Ibrahim
- Institut de Neurosciences de la Timone ‐ UMR7289,CNRS Aix‐Marseille Université Marseille France
- Fondamental, Fondation de Recherche et de Soins en Santé Mentale Créteil France
| | - Philippe Courtet
- Fondamental, Fondation de Recherche et de Soins en Santé Mentale Créteil France
- CHRU Montpellier, University of Montpellier, INSERM unit 1061 Montpellier France
| | - Eleni Tzavara
- Fondamental, Fondation de Recherche et de Soins en Santé Mentale Créteil France
- INSERM, UMRS 1130, CNRS, UMR 8246, Sorbonne University UPMC, Neuroscience Paris‐Seine Paris France
| | - Gustavo Turecki
- McGill Group for Suicide Studies Douglas Mental Health University Institute, McGill University Montréal Canada
| | - Raoul Belzeaux
- Institut de Neurosciences de la Timone ‐ UMR7289,CNRS Aix‐Marseille Université Marseille France
- Fondamental, Fondation de Recherche et de Soins en Santé Mentale Créteil France
- AP‐HM, Pôle de Psychiatrie Marseille France
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Bennett DA, Buchman AS, Boyle PA, Barnes LL, Wilson RS, Schneider JA. Religious Orders Study and Rush Memory and Aging Project. J Alzheimers Dis 2018; 64:S161-S189. [PMID: 29865057 PMCID: PMC6380522 DOI: 10.3233/jad-179939] [Citation(s) in RCA: 630] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The Religious Orders Study and Rush Memory and Aging Project are both ongoing longitudinal clinical-pathologic cohort studies of aging and Alzheimer's disease (AD). OBJECTIVES To summarize progress over the past five years and its implications for understanding neurodegenerative diseases. METHODS Participants in both studies are older adults who enroll without dementia and agree to detailed longitudinal clinical evaluations and organ donation. The last review summarized findings through the end of 2011. Here we summarize progress and study findings over the past five years and discuss new directions for how these studies can inform on aging and AD in the future. RESULTS We summarize 1) findings on the relation of neurobiology to clinical AD; 2) neurobiologic pathways linking risk factors to clinical AD; 3) non-cognitive AD phenotypes including motor function and decision making; 4) the development of a novel drug discovery platform. CONCLUSION Complexity at multiple levels needs to be understood and overcome to develop effective treatments and preventions for cognitive decline and AD dementia.
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Affiliation(s)
- David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Patricia A. Boyle
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA,Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Lisa L. Barnes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA,Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Robert S. Wilson
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA,Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Julie A Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA,Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, IL., USA
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