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Pasqualetti G, Thayanandan T, Edison P. Influence of genetic and cardiometabolic risk factors in Alzheimer's disease. Ageing Res Rev 2022; 81:101723. [PMID: 36038112 DOI: 10.1016/j.arr.2022.101723] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 01/31/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder. Cardiometabolic and genetic risk factors play an important role in the trajectory of AD. Cardiometabolic risk factors including diabetes, mid-life obesity, mid-life hypertension and elevated cholesterol have been linked with cognitive decline in AD subjects. These potential risk factors associated with cerebral metabolic changes which fuel AD pathogenesis have been suggested to be the reason for the disappointing clinical trial results. In appreciation of the risks involved, using search engines such as PubMed, Scopus, MEDLINE and Google Scholar, a relevant literature search on cardiometabolic and genetic risk factors in AD was conducted. We discuss the role of genetic as well as established cardiovascular risk factors in the neuropathology of AD. Moreover, we show new evidence of genetic interaction between several genes potentially involved in different pathways related to both neurodegenerative process and cardiovascular damage.
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Affiliation(s)
| | - Tony Thayanandan
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, UK
| | - Paul Edison
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, UK; School of Medicine, Cardiff University, UK.
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Willis CRG, Deane CS. Nrf2 deficiency induces skeletal muscle mitochondrial dysfunction: a proteomics/bioinformatics approach. J Physiol 2020; 599:729-730. [PMID: 33022745 DOI: 10.1113/jp280758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/05/2020] [Indexed: 11/08/2022] Open
Affiliation(s)
- Craig R G Willis
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX1 2LU, UK
| | - Colleen S Deane
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX1 2LU, UK.,Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
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3
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Chowdhury HA, Bhattacharyya DK, Kalita JK. (Differential) Co-Expression Analysis of Gene Expression: A Survey of Best Practices. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1154-1173. [PMID: 30668502 DOI: 10.1109/tcbb.2019.2893170] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Analysis of gene expression data is widely used in transcriptomic studies to understand functions of molecules inside a cell and interactions among molecules. Differential co-expression analysis studies diseases and phenotypic variations by finding modules of genes whose co-expression patterns vary across conditions. We review the best practices in gene expression data analysis in terms of analysis of (differential) co-expression, co-expression network, differential networking, and differential connectivity considering both microarray and RNA-seq data along with comparisons. We highlight hurdles in RNA-seq data analysis using methods developed for microarrays. We include discussion of necessary tools for gene expression analysis throughout the paper. In addition, we shed light on scRNA-seq data analysis by including preprocessing and scRNA-seq in co-expression analysis along with useful tools specific to scRNA-seq. To get insights, biological interpretation and functional profiling is included. Finally, we provide guidelines for the analyst, along with research issues and challenges which should be addressed.
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Su J, Long W, Ma Q, Xiao K, Li Y, Xiao Q, Peng G, Yuan J, Liu Q. Identification of a Tumor Microenvironment-Related Eight-Gene Signature for Predicting Prognosis in Lower-Grade Gliomas. Front Genet 2019; 10:1143. [PMID: 31803233 PMCID: PMC6872675 DOI: 10.3389/fgene.2019.01143] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022] Open
Abstract
Lower-grade gliomas (LrGG), characterized by invasiveness and heterogeneity, remain incurable with current therapies. Clinicopathological features provide insufficient information to guide optimal individual treatment and cannot predict prognosis completely. Recently, an increasing amount of studies indicate that the tumor microenvironment plays a pivotal role in tumor malignancy and treatment responses. However, studies focusing on the tumor microenvironment (TME) of LrGG are still limited. In this study, taking advantage of the currently popular computational methods for estimating the infiltration of tumor-associated normal cells in tumor samples and using weighted gene co-expression network analysis, we screened the co-expressed gene modules associated with the TME and further identified the prognostic hub genes in these modules. Furthermore, eight prognostic hub genes (ARHGDIB, CLIC1, OAS3, PDIA4, PARP9, STAT1, TAP2, and TAGLN2) were selected to construct a prognostic risk score model using the least absolute shrinkage and selection operator method. Univariate and multivariate Cox regression analysis demonstrated that the risk score was an independent prognostic factor for LrGG. Moreover, time-dependent ROC curves indicated that our model had favorable efficiency in predicting both short- and long-term prognosis in LrGG patients, and the stratified survival analysis demonstrated that our model had prognostic value for different subgroups of LrGG patients. Additionally, our model had potential value for predicting the sensitivity of LrGG patients to radio- and chemotherapy. Besides, differential expression analysis showed that the eight genes were aberrantly expressed in LrGG compared to normal brain tissue. Correlation analysis revealed that the expression of the eight genes was significantly associated with the infiltration levels of six types of immune cells in LrGG. In summary, the TME-related eight-gene signature was significantly associated with the prognosis of LrGG patients. They might act as potential prognostic biomarkers for LrGG patients, offer better stratification for future clinical trials, and be candidate targets for immunotherapy, thus deserving further investigation.
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Affiliation(s)
- Jun Su
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Wenyong Long
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Qianquan Ma
- Department of Neurosurgery in Peking University Third Hospital, Peking University, Beijing, China
| | - Kai Xiao
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Yang Li
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Qun Xiao
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Gang Peng
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Jian Yuan
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Qing Liu
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China.,Institute of Skull Base Surgery & Neuro-oncology at Hunan, Changsha, China
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Chew G, Petretto E. Transcriptional Networks of Microglia in Alzheimer's Disease and Insights into Pathogenesis. Genes (Basel) 2019; 10:E798. [PMID: 31614849 PMCID: PMC6826883 DOI: 10.3390/genes10100798] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Microglia, the main immune cells of the central nervous system, are increasingly implicated in Alzheimer's disease (AD). Manifold transcriptomic studies in the brain have not only highlighted microglia's role in AD pathogenesis, but also mapped crucial pathological processes and identified new therapeutic targets. An important component of many of these transcriptomic studies is the investigation of gene expression networks in AD brain, which has provided important new insights into how coordinated gene regulatory programs in microglia (and other cell types) underlie AD pathogenesis. Given the rapid technological advancements in transcriptional profiling, spanning from microarrays to single-cell RNA sequencing (scRNA-seq), tools used for mapping gene expression networks have evolved to keep pace with the unique features of each transcriptomic platform. In this article, we review the trajectory of transcriptomic network analyses in AD from brain to microglia, highlighting the corresponding methodological developments. Lastly, we discuss examples of how transcriptional network analysis provides new insights into AD mechanisms and pathogenesis.
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Affiliation(s)
- Gabriel Chew
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 69857 Singapore, Singapore.
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 69857 Singapore, Singapore.
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Lin L, Murphy JG, Karlsson RM, Petralia RS, Gutzmann JJ, Abebe D, Wang YX, Cameron HA, Hoffman DA. DPP6 Loss Impacts Hippocampal Synaptic Development and Induces Behavioral Impairments in Recognition, Learning and Memory. Front Cell Neurosci 2018; 12:84. [PMID: 29651237 PMCID: PMC5884885 DOI: 10.3389/fncel.2018.00084] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
DPP6 is well known as an auxiliary subunit of Kv4-containing, A-type K+ channels which regulate dendritic excitability in hippocampal CA1 pyramidal neurons. We have recently reported, however, a novel role for DPP6 in regulating dendritic filopodia formation and stability, affecting synaptic development and function. These results are notable considering recent clinical findings associating DPP6 with neurodevelopmental and intellectual disorders. Here we assessed the behavioral consequences of DPP6 loss. We found that DPP6 knockout (DPP6-KO) mice are impaired in hippocampus-dependent learning and memory. Results from the Morris water maze and T-maze tasks showed that DPP6-KO mice exhibit slower learning and reduced memory performance. DPP6 mouse brain weight is reduced throughout development compared with WT, and in vitro imaging results indicated that DPP6 loss affects synaptic structure and motility. Taken together, these results show impaired synaptic development along with spatial learning and memory deficiencies in DPP6-KO mice.
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Affiliation(s)
- Lin Lin
- Molecular Neurophysiology and Biophysics Section, Program in Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Jonathan G Murphy
- Molecular Neurophysiology and Biophysics Section, Program in Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Rose-Marie Karlsson
- Section on Neuroplasticity, National Institute of Mental Health, Bethesda, MD, United States
| | - Ronald S Petralia
- Advanced Imaging Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States
| | - Jakob J Gutzmann
- Molecular Neurophysiology and Biophysics Section, Program in Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Daniel Abebe
- Molecular Neurophysiology and Biophysics Section, Program in Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Ya-Xian Wang
- Advanced Imaging Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States
| | - Heather A Cameron
- Section on Neuroplasticity, National Institute of Mental Health, Bethesda, MD, United States
| | - Dax A Hoffman
- Molecular Neurophysiology and Biophysics Section, Program in Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
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