1
|
Lin Q, Zheng Z, Ni H, Xu Y, Nie H. Cellular senescence-Related genes define the immune microenvironment and molecular characteristics in severe asthma patients. Gene 2024; 919:148502. [PMID: 38670389 DOI: 10.1016/j.gene.2024.148502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Recent studies have shown that cellular senescence is involved in the pathogenesis of severe asthma (SA). The objective of this study was to investigate the role of cellular senescence-related genes (CSGs) in the pathogenesis of SA. Here, 54 differentially expressed CSGs were identified in SA patients compared to healthy control individuals. Among the 54 differentially expressed CSGs, 3 CSGs (ETS2, ETS1 and AURKA) were screened using the LASSO regression analysis and logistic regression analysis to establish the CSG-based prediction model to predict severe asthma. Moreover, we found that the protein expression levels of ETS2, ETS1 and AURKA were increased in the severe asthma mouse model. Then, two distinct senescence subtypes of SA with distinct immune microenvironments and molecular biological characteristics were identified. Cluster 1 was characterized by increased infiltration of immature dendritic cells, regulatory T cells, and other cells. Cluster 2 was characterized by increased infiltration levels of eosinophils, neutrophils, and other cells. The molecular biological characteristics of Cluster 1 included aerobic respiration and oxidative phosphorylation, whereas the molecular biological characteristics of Cluster 2 included activation of the immune response and immune receptor activity. Then, we established an Random Forest model to predict the senescence subtypes of SA to guide treatment. Finally, potential drugs were searched for each senescence subgroup of SA patients via the Connectivity Map database. A peroxisome proliferator-activated receptor agonist may be a potential therapeutic drug for patients in Cluster 1, whereas a tachykinin antagonist may be a potential therapeutic drug for patients in Cluster 2. In summary, CSGs are likely involved in the pathogenesis of SA, which may lead to new therapeutic options for SA patients.
Collapse
Affiliation(s)
- Qibin Lin
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Zhishui Zheng
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Haiyang Ni
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Yaqing Xu
- Department of Geriatric Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China.
| | - Hanxiang Nie
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China.
| |
Collapse
|
2
|
Liao W, Wang P, He Y, Liu Z, Wang L. Investigation of the underlying mechanism of Buyang Huanwu decoction in ischemic stroke by integrating systems pharmacology-proteomics and in vivo experiments. Fitoterapia 2024; 175:105935. [PMID: 38580032 DOI: 10.1016/j.fitote.2024.105935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
Buyang Huanwu Decoction (BHD) has been effective in treating ischemic stroke (IS). However, its mechanism of action remains unclear. The study intended to explore the potential mechanism of BHD against IS using systems pharmacology, proteomics, and animal experiments. The active components of BHD were identified from UPLC-Q-TOF-MS and literature mining. Systems pharmacology and proteomics were employed to investigate the underlying mechanism of BHD against IS. The AutoDock tool was used for molecular docking. A middle cerebral artery occlusion (MCAO) model rat was utilized to explore the therapeutic benefits of BHD. The rats were divided into sham, model, BHD (5, 10, 20 g/kg, ig) groups. The neurological scores, pathological section characteristics, brain infarct volumes, inflammatory cytokines, and signaling pathways were investigated in vivo experiments. The results of systems pharmacology showed that 13 active compounds and 112 common targets were screened in BHD. The docking results suggested that the active compounds in BHD had a high affinity for the key targets. In vivo experiments demonstrated that BHD exhibited neuroprotective benefits by lowering the neurological score, the volume of the cerebral infarct, the release of inflammatory cytokines, and reducing neuroinflammatory damage in MCAO rats. Furthermore, BHD decreased TNF-α and CD38 levels while increasing ATP2B2, PDE1A, CaMK4, p-PI3K, and p-AKT. Combined with systems pharmacology and proteomic studies, we confirmed that PI3K-Akt and calcium signaling pathways are the key mechanisms for BHD against IS. Furthermore, this study demonstrated the feasibility of combining proteomics with systems pharmacology to study the mechanism of herbal medicine.
Collapse
Affiliation(s)
- Weiguo Liao
- College of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 51006, People's Republic of China
| | - Pengcheng Wang
- College of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 51006, People's Republic of China; Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 51006, People's Republic of China
| | - Yingying He
- College of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 51006, People's Republic of China; Guangzhou HanFang Pharmaceutical Company Limited, National Engineering Research Center of Pharmaceutical Processing Technology of Traditional Chinese Medicine and Drug Innovation, Guangdong Provincial Key Laboratory of Medicinal Lipid, Guangzhou 510240, China
| | - Zai Liu
- Pharmacy Department, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, Guangdong 523000, People's Republic of China.
| | - Lisheng Wang
- College of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 51006, People's Republic of China.
| |
Collapse
|
3
|
Shi J, Liu D, Jin Q, Chen X, Zhang R, Shi T, Zhu S, Zhang Y, Zong X, Wang C, Li L. Whole-Transcriptome Analysis of Repeated Low-Level Sarin-Exposed Rat Hippocampus and Identification of Cerna Networks to Investigate the Mechanism of Sarin-Induced Cognitive Impairment. BIOLOGY 2023; 12:biology12040627. [PMID: 37106826 PMCID: PMC10136365 DOI: 10.3390/biology12040627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
Sarin is a potent organophosphorus nerve agent that causes cognitive dysfunction, but its underlying molecular mechanisms are poorly understood. In this study, a rat model of repeated low-level sarin exposure was established using the subcutaneous injection of 0.4 × LD50 for 21 consecutive days. Sarin-exposed rats showed persistent learning and memory impairment and reduced hippocampal dendritic spine density. A whole-transcriptome analysis was applied to study the mechanism of sarin-induced cognitive impairment, and a total of 1035 differentially expressed mRNA (DEmRNA), including 44 DEmiRNA, 305 DElncRNA, and 412 DEcircRNA, were found in the hippocampus of sarin-treated rats. According to Gene Ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and Protein-Protein Interaction (PPI) analysis, these DERNAs were mainly involved in neuronal synaptic plasticity and were related to the pathogenesis of neurodegenerative diseases. The circRNA/lncRNA-miRNA-mRNA ceRNA network was constructed, in which Circ_Fmn1, miR-741-3p, miR-764-3p, miR-871-3p, KIF1A, PTPN11, SYN1, and MT-CO3 formed one circuit, and Circ_Cacna1c, miR-10b-5p, miR-18a-5p, CACNA1C, PRKCD, and RASGRP1 constituted another circuit. The balance between the two circuits was crucial for maintaining synaptic plasticity and may be the regulatory mechanism by which sarin causes cognitive impairment. Our study reveals the ceRNA regulation mechanism of sarin exposure for the first time and provides new insights into the molecular mechanisms of other organophosphorus toxicants.
Collapse
Affiliation(s)
- Jingjing Shi
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Dongxin Liu
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Qian Jin
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Xuejun Chen
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Ruihua Zhang
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Tong Shi
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Siqing Zhu
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Yi Zhang
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Xingxing Zong
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Chen Wang
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| | - Liqin Li
- State Key Laboratory of NBC Protection for Civilians, Beijing 102205, China
| |
Collapse
|
4
|
RNAseq Analysis of FABP4 Knockout Mouse Hippocampal Transcriptome Suggests a Role for WNT/β-Catenin in Preventing Obesity-Induced Cognitive Impairment. Int J Mol Sci 2023; 24:ijms24043381. [PMID: 36834799 PMCID: PMC9961923 DOI: 10.3390/ijms24043381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Microglial fatty-acid binding protein 4 (FABP4) is a regulator of neuroinflammation. We hypothesized that the link between lipid metabolism and inflammation indicates a role for FABP4 in regulating high fat diet (HFD)-induced cognitive decline. We have previously shown that obese FABP4 knockout mice exhibit decreased neuroinflammation and cognitive decline. FABP4 knockout and wild type mice were fed 60% HFD for 12 weeks starting at 15 weeks old. Hippocampal tissue was dissected and RNA-seq was performed to measure differentially expressed transcripts. Reactome molecular pathway analysis was utilized to examine differentially expressed pathways. Results showed that HFD-fed FABP4 knockout mice have a hippocampal transcriptome consistent with neuroprotection, including associations with decreased proinflammatory signaling, ER stress, apoptosis, and cognitive decline. This is accompanied by an increase in transcripts upregulating neurogenesis, synaptic plasticity, long-term potentiation, and spatial working memory. Pathway analysis revealed that mice lacking FABP4 had changes in metabolic function that support reduction in oxidative stress and inflammation, and improved energy homeostasis and cognitive function. Analysis suggested a role for WNT/β-Catenin signaling in the protection against insulin resistance, alleviating neuroinflammation and cognitive decline. Collectively, our work shows that FABP4 represents a potential target in alleviating HFD-induced neuroinflammation and cognitive decline and suggests a role for WNT/β-Catenin in this protection.
Collapse
|
5
|
Mredul MBR, Khan U, Rana HK, Meem TM, Awal MA, Rahman MH, Khan MS. Bioinformatics and System Biology Techniques to Determine Biomolecular Signatures and Pathways of Prion Disorder. Bioinform Biol Insights 2022; 16:11779322221145373. [PMID: 36582393 PMCID: PMC9793038 DOI: 10.1177/11779322221145373] [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: 06/26/2022] [Accepted: 11/21/2022] [Indexed: 12/25/2022] Open
Abstract
Prion disorder (PD) is caused by misfolding and the formation of clumps of proteins in the brain, notably Prion proteins resulting in a steady decrease in brain function. Early detection of PD is difficult due to its unpredictable nature, and diagnosis is limited regarding specificity and sensitivity. Considering the uncertainties, the current study used network-based integrative system biology approaches to reveal promising molecular biomarkers and therapeutic targets for PD. In this study, brain transcriptomics gene expression microarray datasets (GSE160208 and GSE124571) of human PD were evaluated and 35 differentially expressed genes (DEGs) were identified. By employing network-based protein-protein interaction (PPI) analysis on these DEGs, 10 central hub proteins, including SPP1, FKBP5, HPRT1, CDKN1A, BAG3, HSPB1, SYK, TNFRSF1A, PTPN6, and CD44, were identified. Employing bioinformatics approaches, a variety of transcription factors (EGR1, SSRP1, POLR2A, TARDP, and NR2F1) and miRNAs (hsa-mir-8485, hsa-mir-148b-3p, hsa-mir-4295, hsa-mir-26b-5p, and hsa-mir-16-5p) were predicted. EGR1 was found as the most imperative transcription factor (TF), and hsa-mir-16-5p and hsa-mir-148b-3p were found as the most crucial miRNAs targeted in PD. Finally, resveratrol and hypochlorous acid were predicted as possible therapeutic drugs for PD. This study could be helpful in better understanding of molecular systems and prospective pharmacological targets for developing effective PD treatments.
Collapse
Affiliation(s)
- Md Bazlur Rahman Mredul
- Statistics Discipline, Science,
Engineering and Technology School, Khulna University, Khulna, Bangladesh
| | - Umama Khan
- Biotechnology and Genetic Engineering
Discipline, Khulna University, Khulna, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and
Engineering, Green University of Bangladesh, Dhaka, Bangladesh
| | - Tahera Mahnaz Meem
- Statistics Discipline, Science,
Engineering and Technology School, Khulna University, Khulna, Bangladesh
| | - Md Abdul Awal
- Electronics and Communication
Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and
Engineering, Islamic University, Kushtia, Bangladesh
| | - Md Salauddin Khan
- Statistics Discipline, Science,
Engineering and Technology School, Khulna University, Khulna, Bangladesh,Md Salauddin Khan, Statistics Discipline,
Science, Engineering and Technology School, Khulna University, Khulna 9208,
Bangladesh.
| |
Collapse
|
6
|
Disruption of Alternative Splicing in the Amygdala of Pigs Exposed to Maternal Immune Activation. IMMUNO 2021. [DOI: 10.3390/immuno1040035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The inflammatory response of gestating females to infection or stress can disrupt gene expression in the offspring’s amygdala, resulting in lasting neurodevelopmental, physiological, and behavioral disorders. The effects of maternal immune activation (MIA) can be impacted by the offspring’s sex and exposure to additional stressors later in life. The objectives of this study were to investigate the disruption of alternative splicing patterns associated with MIA in the offspring’s amygdala and characterize this disruption in the context of the second stress of weaning and sex. Differential alternative splicing was tested on the RNA-seq profiles of a pig model of viral-induced MIA. Compared to controls, MIA was associated with the differential alternative splicing (FDR-adjusted p-value < 0.1) of 292 and 240 genes in weaned females and males, respectively, whereas 132 and 176 genes were differentially spliced in control nursed female and male, respectively. The majority of the differentially spliced (FDR-adjusted p-value < 0.001) genes (e.g., SHANK1, ZNF672, KCNA6) and many associated enriched pathways (e.g., Fc gamma R-mediated phagocytosis, non-alcoholic fatty liver disease, and cGMP-PKG signaling) have been reported in MIA-related disorders including autism and schizophrenia in humans. Differential alternative splicing associated with MIA was detected in the gene MAG across all sex-stress groups except for unstressed males and SLC2A11 across all groups except unstressed females. Precise understanding of the effect of MIA across second stressors and sexes necessitates the consideration of splicing isoform profiles.
Collapse
|
7
|
Hu Y, Tan H, Li C, Zhang H. Identifying genetic risk variants associated with brain volumetric phenotypes via K-sample Ball Divergence method. Genet Epidemiol 2021; 45:710-720. [PMID: 34184773 PMCID: PMC8434958 DOI: 10.1002/gepi.22423] [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: 09/30/2020] [Revised: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 02/05/2023]
Abstract
Regional human brain volumes including total area, average thickness, and total volume are heritable and associated with neurological disorders. However, the genetic architecture of brain structure and function is still largely unknown and worthy of exploring. The Pediatric Imaging, Neurocognition, and Genetics (PING) data set provides an excellent resource with genome-wide genetic data and related neuroimaging data. In this study, we perform genome-wide association studies (GWAS) of 315 brain volumetric phenotypes from the PING data set including 1036 samples with 539,865 single-nucleotide polymorphisms (SNPs). We introduce a nonparametric test based on K-sample Ball Divergence (KBD) to identify genetic risk variants that influence regional brain volumes. We carry out simulations to demonstrate that KBD is a powerful test for identifying significant SNPs associated with multivariate phenotypes although controlling the type I error rate. We successfully identify nine SNPs below a significance level of 5 × 10-5 for the PING data. Among the nine identified genetic variants, two SNPs rs486179 and rs562110 are located in the ADRA1A gene that is a well-known risk factor of mental illness, such as schizophrenia and attention deficit hyperactivity disorder. Our study suggests that the nonparametric test KBD is an effective method for identifying genetic variants associated with complex diseases in large-scale GWAS of multiple phenotypes.
Collapse
Affiliation(s)
- Yue Hu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, 06511
| | - Haizhu Tan
- Department of Preventive Medicine, Shantou University Medical College, Xinling Road 22, Shantou, Guangdong, P. R. China
| | - Cai Li
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, 06511
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, 06511
- Correspondence Author: Heping Zhang, 300 George Street, Ste 523, New Haven, CT, 06511. . Phone: 203-785-5185
| |
Collapse
|
8
|
Integrated Bioinformatics Analysis to Identify Alternative Therapeutic Targets for Alzheimer's Disease: Insights from a Synaptic Machinery Perspective. J Mol Neurosci 2021; 72:273-286. [PMID: 34414562 DOI: 10.1007/s12031-021-01893-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD), the most common type of dementia, is a serious neurodegenerative disease that has no cure yet, but whose symptoms can be alleviated with available medications. Therefore, early and accurate diagnosis of the disease and elucidation of the molecular mechanisms involved in the progression of pathogenesis are critically important. This study aimed to identify dysregulated miRNAs and their target mRNAs through the integrated analysis of miRNA and mRNA expression profiling in AD patients versus unaffected controls. Expression profiles in postmortem brain samples from AD patients and healthy individuals were extracted from the Gene Expression Omnibus database and were analyzed using bioinformatics approaches to identify gene ontologies, pathways, and networks. Finally, the module analysis of the PPI network and hub gene selection was carried out. A total of five differentially expressed miRNAs were extracted from the miRNA dataset, and 4312 differentially expressed mRNAs were obtained from the mRNA dataset. By comparing the DEGs and the putative targets of the altered miRNAs, 116 (3 upregulated and 113 downregulated) coordinated genes were determined. Also, six hub genes (SNAP25, GRIN2A, GRIN2B, DLG2, ATP2B2, and SCN2A) were identified by constructing a PPI network. The results of the present study provide insight into mechanisms such as synaptic machinery and neuronal communication underlying AD pathogenesis, specifically concerning miRNAs.
Collapse
|
9
|
Cheng J, Liu HP, Lin WY, Tsai FJ. Machine learning compensates fold-change method and highlights oxidative phosphorylation in the brain transcriptome of Alzheimer's disease. Sci Rep 2021; 11:13704. [PMID: 34211065 PMCID: PMC8249453 DOI: 10.1038/s41598-021-93085-z] [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: 10/19/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder causing 70% of dementia cases. However, the mechanism of disease development is still elusive. Despite the availability of a wide range of biological data, a comprehensive understanding of AD's mechanism from machine learning (ML) is so far unrealized, majorly due to the lack of needed data density. To harness the AD mechanism's knowledge from the expression profiles of postmortem prefrontal cortex samples of 310 AD and 157 controls, we used seven predictive operators or combinations of RapidMiner Studio operators to establish predictive models from the input matrix and to assign a weight to each attribute. Besides, conventional fold-change methods were also applied as controls. The identified genes were further submitted to enrichment analysis for KEGG pathways. The average accuracy of ML models ranges from 86.30% to 91.22%. The overlap ratio of the identified genes between ML and conventional methods ranges from 19.7% to 21.3%. ML exclusively identified oxidative phosphorylation genes in the AD pathway. Our results highlighted the deficiency of oxidative phosphorylation in AD and suggest that ML should be considered as complementary to the conventional fold-change methods in transcriptome studies.
Collapse
Affiliation(s)
- Jack Cheng
- grid.254145.30000 0001 0083 6092Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402 Taiwan ,grid.411508.90000 0004 0572 9415Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan
| | - Hsin-Ping Liu
- grid.254145.30000 0001 0083 6092Graduate Institute of Acupuncture Science, College of Chinese Medicine, China Medical University, Taichung, 40402 Taiwan
| | - Wei-Yong Lin
- grid.254145.30000 0001 0083 6092Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402 Taiwan ,grid.411508.90000 0004 0572 9415Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan ,grid.254145.30000 0001 0083 6092Brain Diseases Research Center, China Medical University, Taichung, 40402 Taiwan
| | - Fuu-Jen Tsai
- grid.411508.90000 0004 0572 9415Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan ,grid.254145.30000 0001 0083 6092School of Chinese Medicine, China Medical University, Taichung, 40402 Taiwan ,grid.252470.60000 0000 9263 9645Department of Medical Laboratory and Biotechnology, Asia University, Taichung, 41354 Taiwan ,grid.254145.30000 0001 0083 6092Division of Pediatric Genetics, Children’s Hospital of China Medical University, Taichung, 40447 Taiwan
| |
Collapse
|
10
|
Ryan M, Tan VTY, Thompson N, Guévremont D, Mockett BG, Tate WP, Abraham WC, Hughes SM, Williams J. Lentivirus-Mediated Expression of Human Secreted Amyloid Precursor Protein-Alpha Promotes Long-Term Induction of Neuroprotective Genes and Pathways in a Mouse Model of Alzheimer's Disease. J Alzheimers Dis 2021; 79:1075-1090. [PMID: 33386801 DOI: 10.3233/jad-200757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Secreted amyloid precursor protein-alpha (sAPPα) can enhance memory and is neurotrophic and neuroprotective across a range of disease-associated insults, including amyloid-β toxicity. In a significant step toward validating sAPPα as a therapeutic for Alzheimer's disease (AD), we demonstrated that long-term overexpression of human sAPPα (for 8 months) in a mouse model of amyloidosis (APP/PS1) could prevent the behavioral and electrophysiological deficits that develop in these mice. OBJECTIVE To explore the underlying molecular mechanisms responsible for the significant physiological and behavioral improvements observed in sAPPα-treated APP/PS1 mice. METHODS We assessed the long-term effects on the hippocampal transcriptome following continuous lentiviral delivery of sAPPα or empty-vector to male APP/PS1 mice and wild-type controls using Affymetrix Mouse Transcriptome Assays. Data analysis was carried out within the Affymetrix Transcriptome Analysis Console and an integrated analysis of the resulting transcriptomic data was performed with Ingenuity Pathway analysis (IPA). RESULTS Mouse transcriptome assays revealed expected AD-associated gene expression changes in empty-vector APP/PS1 mice, providing validation of the assays used for the analysis. By contrast, there were specific sAPPα-associated gene expression profiles which included increases in key neuroprotective genes such as Decorin, betaine-GABA transporter and protocadherin beta-5, subsequently validated by qRT-PCR. An integrated biological pathways analysis highlighted regulation of GABA receptor signaling, cell survival and inflammatory responses. Furthermore, upstream gene regulatory analysis implicated sAPPα activation of Interleukin-4, which can counteract inflammatory changes in AD. CONCLUSION This study identified key molecular processes that likely underpin the long-term neuroprotective and therapeutic effects of increasing sAPPα levels in vivo.
Collapse
Affiliation(s)
- Margaret Ryan
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Valerie T Y Tan
- Department of Psychology, University of Otago, Dunedin, New Zealand.,Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Nasya Thompson
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Diane Guévremont
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Bruce G Mockett
- Department of Psychology, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Warren P Tate
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Wickliffe C Abraham
- Department of Psychology, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Stephanie M Hughes
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Joanna Williams
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, New Zealand.,Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| |
Collapse
|
11
|
Chen X, Lin B, Luo M, Chu W, Li P, Liu H, Xi Z, Fan R. Identifying circRNA- and lncRNA-associated-ceRNA networks in the hippocampi of rats exposed to PM 2.5 using RNA-seq analysis. Genomics 2020; 113:193-204. [PMID: 33338629 DOI: 10.1016/j.ygeno.2020.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/04/2020] [Accepted: 12/13/2020] [Indexed: 11/16/2022]
Abstract
Non-coding RNAs appear to be involved in the regulation of the nervous system. However, no competing endogenous RNA (ceRNA) network related to PM2.5 damage in the hippocampal function has yet been constructed. Herein, we used whole-transcriptome sequencing technology to systematically study the ceRNA network in rat hippocampi after PM2.5 exposure. We identified 100 circRNAs, 67 lncRNAs, 28 miRNAs, and 539 mRNAs and constructed the most comprehensive ceRNA network to date, to our knowledge. Gene Ontology and KEGG analyses showed that the network molecules are involved in synapses, neural projections, and neural development and involve signal pathways such as the synaptic vesicle cycle. Finally, the expression of the differentially expressed RNAs confirmed by quantitative real-time PCR was consistent with the sequencing data. This study systematically dissected the ceRNA atlas related to cognitive memory function in the hippocampal tissue of PM2.5-exposed rats for the first time, to our knowledge, and promotes the development of potential new treatments for cognitive impairment.
Collapse
Affiliation(s)
- Xuewei Chen
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Bencheng Lin
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Mingzhu Luo
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Wenbin Chu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Ping Li
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Huanliang Liu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Zhuge Xi
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Rong Fan
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Central laboratory, Tianjin Xiqing Hospital, Tianjin 300380, China.
| |
Collapse
|
12
|
Yagensky O, Kohansal-Nodehi M, Gunaseelan S, Rabe T, Zafar S, Zerr I, Härtig W, Urlaub H, Chua JJ. Increased expression of heme-binding protein 1 early in Alzheimer's disease is linked to neurotoxicity. eLife 2019; 8:47498. [PMID: 31453805 PMCID: PMC6739868 DOI: 10.7554/elife.47498] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/25/2019] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease is the most prevalent neurodegenerative disorder leading to progressive cognitive decline. Despite decades of research, understanding AD progression at the molecular level, especially at its early stages, remains elusive. Here, we identified several presymptomatic AD markers by investigating brain proteome changes over the course of neurodegeneration in a transgenic mouse model of AD (3×Tg-AD). We show that one of these markers, heme-binding protein 1 (Hebp1), is elevated in the brains of both 3×Tg-AD mice and patients affected by rapidly-progressing forms of AD. Hebp1, predominantly expressed in neurons, interacts with the mitochondrial contact site complex (MICOS) and exhibits a perimitochondrial localization. Strikingly, wildtype, but not Hebp1-deficient, neurons showed elevated cytotoxicity in response to heme-induced apoptosis. Increased survivability in Hebp1-deficient neurons is conferred by blocking the activation of the mitochondrial-associated caspase signaling pathway. Taken together, our data highlight a role of Hebp1 in progressive neuronal loss during AD progression.
Collapse
Affiliation(s)
- Oleksandr Yagensky
- Research Group Protein Trafficking in Synaptic Development and Function, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Saravanan Gunaseelan
- Interactomics and Intracellular Trafficking Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tamara Rabe
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Saima Zafar
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan.,Clinical Dementia Center, Department of Neurology, German Center for Neurodegenerative Diseases, University Medical Center Göttingen, Göttingen, Germany
| | - Inga Zerr
- Clinical Dementia Center, Department of Neurology, German Center for Neurodegenerative Diseases, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang Härtig
- Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Henning Urlaub
- Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - John Je Chua
- Research Group Protein Trafficking in Synaptic Development and Function, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Interactomics and Intracellular Trafficking Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,LSI Neurobiology Programme, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| |
Collapse
|
13
|
Hippocampal transcriptome profiling combined with protein-protein interaction analysis elucidates Alzheimer's disease pathways and genes. Neurobiol Aging 2019; 74:225-233. [DOI: 10.1016/j.neurobiolaging.2018.10.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 10/12/2018] [Accepted: 10/24/2018] [Indexed: 01/28/2023]
|
14
|
Liu Q, Chen C, Gao A, Tong HH, Xie L. VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in Genome-Wide Association Studies: applied to Alzheimer's Disease. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2017; 2017:2177-2182. [PMID: 29692948 DOI: 10.1109/bibm.2017.8217995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is a grand challenge to reveal the causal effects of DNA variants in complex phenotypes. Although statistical techniques can establish correlations between genotypes and phenotypes in Genome-Wide Association Studies (GWAS), they often fail when the variant is rare. The emerging Network-based Association Studies aim to address this shortcoming in statistical analysis, but are mainly applied to coding variations. Increasing evidences suggest that non-coding variants play critical roles in the etiology of complex diseases. However, few computational tools are available to study the effect of rare non-coding variants on phenotypes. Here we have developed a multiscale modeling variant-to-function-to-network framework VariFunNet to address these challenges. VariFunNet first predict the functional variations of molecular interactions, which result from the non-coding variants. Then we incorporate the genes associated with the functional variation into a tissue-specific gene network, and identify subnetworks that transmit the functional variation to molecular phenotypes. Finally, we quantify the functional implication of the subnetwork, and prioritize the association of the non-coding variants with the phenotype. We have applied VariFunNet to investigating the causal effect of rare non-coding variants on Alzheimer's disease (AD). Among top 21 ranked causal non-coding variants, 16 of them are directly supported by existing evidences. The remaining 5 novel variants dysregulate multiple downstream biological processes, all of which are associated with the pathology of AD. Furthermore, we propose potential new drug targets that may modulate diverse pathways responsible for AD. These findings may shed new light on discovering new biomarkers and therapies for the prevention, diagnosis, and treatment of AD. Our results suggest that multiscale modeling is a potentially powerful approach to studying causal genotype-phenotype associations.
Collapse
Affiliation(s)
- Qiao Liu
- Biochemistry, The Graduate Center, The City University of New York, New York, United States
| | - Chen Chen
- School of Computing, Informatics and Decision Systems Engineering, Arizona State University, Tempe, United States
| | - Annie Gao
- Princeton High School, Princeton, United States
| | - Hang Hang Tong
- School of Computing, Informatics and Decision Systems Engineering, Arizona State University, Tempe, United States
| | - Lei Xie
- Department of Computer Science Hunter College, The City University of New York, New York, United States
| |
Collapse
|
15
|
Chen BJ, Yang B, Janitz M. Region-specific expression of circular RNAs in the mouse brain. Neurosci Lett 2017; 666:44-47. [PMID: 29253603 DOI: 10.1016/j.neulet.2017.12.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/04/2017] [Accepted: 12/10/2017] [Indexed: 10/24/2022]
Abstract
Circular RNAs (circRNAs) are abundant in mammalian brain and their expression is regulated in a tissue- and developmental stage-specific manner. Mammalian brain is the most transcriptionally complex organ. While many studies have extensively studied linear transcriptome and its biological functions in the brain, the circular transcriptome remains largely unexplored. This study focused on investigation of circRNA expression patterns in the mammalian brain regions critical for cognitive and memory functions and performed comparative analysis with the linear transcriptome. Altogether our study showed that circular and linear RNAs have independent expression patterns despite being derived from the same genomic locus, and that circular transcriptomes from different brain region have distinct characteristics in terms of transcript abundance and composition.
Collapse
Affiliation(s)
- Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Belinda Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany.
| |
Collapse
|