1
|
Piergiorge RM, Vasconcelos ATRD, Santos-Rebouças CB. Understanding the (epi)genetic dysregulation in Parkinson's disease through an integrative brain competitive endogenous RNA network. Mech Ageing Dev 2024; 219:111942. [PMID: 38762037 DOI: 10.1016/j.mad.2024.111942] [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: 04/03/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Parkinson's disease (PD) is a rapidly growing neurodegenerative disorder characterized by dopaminergic neuron loss in the substantia nigra pars compacta (SN) and aggregation of α-synuclein. Its aetiology involves a multifaceted interplay among genetic, environmental, and epigenetic factors. We integrated brain gene expression data from PD patients to construct a comprehensive regulatory network encompassing messenger RNAs (mRNAs), microRNAs (miRNAs), circular RNAs (circRNAs) and, for the first time, RNA binding proteins (RBPs). Expression data from the SN of PD patients and controls were systematically selected from public databases to identify combined differentially expressed genes (DEGs). Brain co-expression analysis revealed modules comprising significant DEGs that function cooperatively. The relationships among co-expressed DEGs, miRNAs, circRNAs, and RBPs revealed an intricate competitive endogenous RNA (ceRNA) network responsible for post-transcriptional dysregulation in PD. Many genes in the ceRNA network, including the TOMM20 and HMGCR genes, overlap with the most relevant genes in our previous Alzheimer's disease-associated ceRNA network, suggesting common underlying mechanisms between both conditions. Moreover, in the ceRNA subnetwork, the RBP Aly/REF export factor (ALYREF), which acts as an RNA 5-methylcytosine(m5C)-binding protein, stood out. Our data sheds new light on the potential role of brain ceRNA networks in PD pathogenesis.
Collapse
Affiliation(s)
- Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | | | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil.
| |
Collapse
|
2
|
Redenšek Trampuž S, Vogrinc D, Goričar K, Dolžan V. Shared miRNA landscapes of COVID-19 and neurodegeneration confirm neuroinflammation as an important overlapping feature. Front Mol Neurosci 2023; 16:1123955. [PMID: 37008787 PMCID: PMC10064073 DOI: 10.3389/fnmol.2023.1123955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionDevelopment and worsening of most common neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, and multiple sclerosis, have been associated with COVID-19 However, the mechanisms associated with neurological symptoms in COVID-19 patients and neurodegenerative sequelae are not clear. The interplay between gene expression and metabolite production in CNS is driven by miRNAs. These small non-coding molecules are dysregulated in most common neurodegenerative diseases and COVID-19.MethodsWe have performed a thorough literature screening and database mining to search for shared miRNA landscapes of SARS-CoV-2 infection and neurodegeneration. Differentially expressed miRNAs in COVID-19 patients were searched using PubMed, while differentially expressed miRNAs in patients with five most common neurodegenerative diseases (Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis, and multiple sclerosis) were searched using the Human microRNA Disease Database. Target genes of the overlapping miRNAs, identified with the miRTarBase, were used for the pathway enrichment analysis performed with Kyoto Encyclopedia of Genes and Genomes and Reactome.ResultsIn total, 98 common miRNAs were found. Additionally, two of them (hsa-miR-34a and hsa-miR-132) were highlighted as promising biomarkers of neurodegeneration, as they are dysregulated in all five most common neurodegenerative diseases and COVID-19. Additionally, hsa-miR-155 was upregulated in four COVID-19 studies and found to be dysregulated in neurodegeneration processes as well. Screening for miRNA targets identified 746 unique genes with strong evidence for interaction. Target enrichment analysis highlighted most significant KEGG and Reactome pathways being involved in signaling, cancer, transcription and infection. However, the more specific identified pathways confirmed neuroinflammation as being the most important shared feature.DiscussionOur pathway based approach has identified overlapping miRNAs in COVID-19 and neurodegenerative diseases that may have a valuable potential for neurodegeneration prediction in COVID-19 patients. Additionally, identified miRNAs can be further explored as potential drug targets or agents to modify signaling in shared pathways.Graphical AbstractShared miRNA molecules among the five investigated neurodegenerative diseases and COVID-19 were identified. The two overlapping miRNAs, hsa-miR-34a and has-miR-132, present potential biomarkers of neurodegenerative sequelae after COVID-19. Furthermore, 98 common miRNAs between all five neurodegenerative diseases together and COVID-19 were identified. A KEGG and Reactome pathway enrichment analyses was performed on the list of shared miRNA target genes and finally top 20 pathways were evaluated for their potential for identification of new drug targets. A common feature of identified overlapping miRNAs and pathways is neuroinflammation. AD, Alzheimer’s disease; ALS, amyotrophic lateral sclerosis; COVID-19, coronavirus disease 2019; HD, Huntington’s disease; KEGG, Kyoto Encyclopedia of Genes and Genomes; MS, multiple sclerosis; PD, Parkinson’s disease.
Collapse
|
3
|
Potential Regulation of miRNA-29 and miRNA-9 by Estrogens in Neurodegenerative Disorders: An Insightful Perspective. Brain Sci 2023; 13:brainsci13020243. [PMID: 36831786 PMCID: PMC9954655 DOI: 10.3390/brainsci13020243] [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: 09/30/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 02/04/2023] Open
Abstract
Finding a link between a hormone and microRNAs (miRNAs) is of great importance since it enables the adjustment of genetic composition or cellular functions without needing gene-level interventions. The dicer-mediated cleavage of precursor miRNAs is an interface link between miRNA and its regulators; any disruption in this process can affect neurogenesis. Besides, the hormonal regulation of miRNAs can occur at the molecular and cellular levels, both directly, through binding to the promoter elements of miRNAs, and indirectly, via regulation of the signaling effects of the post-transcriptional processing proteins. Estrogenic hormones have many roles in regulating miRNAs in the brain. This review discusses miRNAs, their detailed biogenesis, activities, and both the general and estrogen-dependent regulations. Additionally, we highlight the relationship between miR-29, miR-9, and estrogens in the nervous system. Such a relationship could be a possible etiological route for developing various neurodegenerative disorders.
Collapse
|
4
|
Kretzschmar GC, Targa ADS, Soares-Lima SC, dos Santos PI, Rodrigues LS, Macedo DA, Ribeiro Pinto LF, Lima MMS, Boldt ABW. Folic Acid and Vitamin B12 Prevent Deleterious Effects of Rotenone on Object Novelty Recognition Memory and Kynu Expression in an Animal Model of Parkinson's Disease. Genes (Basel) 2022; 13:genes13122397. [PMID: 36553663 PMCID: PMC9778036 DOI: 10.3390/genes13122397] [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: 10/24/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Parkinson's disease (PD) is characterized by a range of motor signs, but cognitive dysfunction is also observed. Supplementation with folic acid and vitamin B12 is expected to prevent cognitive impairment. To test this in PD, we promoted a lesion within the substantia nigra pars compacta of rats using the neurotoxin rotenone. In the sequence, the animals were supplemented with folic acid and vitamin B12 for 14 consecutive days and subjected to the object recognition test. We observed an impairment in object recognition memory after rotenone administration, which was prevented by supplementation (p < 0.01). Supplementation may adjust gene expression through efficient DNA methylation. To verify this, we measured the expression and methylation of the kynureninase gene (Kynu), whose product metabolizes neurotoxic metabolites often accumulated in PD as kynurenine. Supplementation prevented the decrease in Kynu expression induced by rotenone in the substantia nigra (p < 0.05), corroborating the behavioral data. No differences were observed concerning the methylation analysis of two CpG sites in the Kynu promoter. Instead, we suggest that folic acid and vitamin B12 increased global DNA methylation, reduced the expression of Kynu inhibitors, maintained Kynu-dependent pathway homeostasis, and prevented the memory impairment induced by rotenone. Our study raises the possibility of adjuvant therapy for PD with folic acid and vitamin B12.
Collapse
Affiliation(s)
- Gabriela Canalli Kretzschmar
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Adriano D. S. Targa
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Sheila Coelho Soares-Lima
- Molecular Carcinogenesis Program, National Cancer Institute, Research Coordination, Rio de Janeiro 20231-050, RJ, Brazil
| | - Priscila Ianzen dos Santos
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Lais S. Rodrigues
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Daniel A. Macedo
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program, National Cancer Institute, Research Coordination, Rio de Janeiro 20231-050, RJ, Brazil
| | - Marcelo M. S. Lima
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Correspondence: ; Tel.: +55-(41)-3361-1553
| |
Collapse
|
5
|
Seyedabadi N, Shoushtari SY, Soofi A, Arabpour J, Shams Z, Akhavan H, Hosseini-Asl S. Molecular profiles of predictive biomarkers for platinum-based chemotherapy in Non-Small Cell Lung Cancer (NSCLC). Meta Gene 2022. [DOI: 10.1016/j.mgene.2021.100993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
6
|
Zhang L, Shao Y, Tang C, Liu Z, Tang D, Hu C, Liang X, Hu Z, Luo G. Identification of Novel Biomarkers in Platelets for Diagnosing Parkinson's Disease. Eur Neurol 2021; 85:122-131. [PMID: 34875658 DOI: 10.1159/000520102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Parkinson's disease (PD) is a common neurodegenerative disease affecting the elderly, but there is no blood test for PD diagnosis in the clinic currently. This study aimed to explore promising biomarkers in platelets (PLTs) for PD diagnosis. METHODS PLTs were isolated from whole blood samples of PD patients and healthy controls (HCs), and RNA was extracted for sequencing. RNA-seq was performed on the Illumina HiSeq platform. RESULTS A total of 2,221 genes with differential transcript levels (GDTLs) were identified between PD patients and HCs, 1,041 of which are upregulated genes and 1,180 of which are downregulated genes. WASH5P was the most upregulated gene and AC114491.1 was the most downregulated gene. Among the top 12 most relevant genes, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), eukaryotic elongation factor 1A (EEF1A1), and cathepsin S (CTSS) were reported to be associated with PD. Furthermore, gene ontology analysis showed that the most significant term in biological processes was neutrophil degranulation; the most enriched term in cellular components was cytoplasmic vesicle lumen; and tumor necrosis factor receptor superfamily binding was the most significant term in molecular functions. In the Kyoto Encyclopedia of Genes and Genomes enrichment analysis, inflammation-related pathway accounts for the majority. CONCLUSION Our findings demonstrated WASH5P, MALAT1, EEF1A1, and CTSS may be promising biomarkers in PD, which may contribute to improving the effectiveness and accuracy of diagnosis for PD in the future.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China,
| | - Yiye Shao
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunlei Tang
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Zhen Liu
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Dingzhong Tang
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Canfang Hu
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Xuelin Liang
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Zhaoyang Hu
- Fun-Med Pharmaceutical Technology (Shanghai) Co., Ltd., Shanghai, China
| | - Guojun Luo
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| |
Collapse
|
7
|
Chen H, Cheng S, Xiong W, Tan X. The lncRNA-miRNA-mRNA ceRNA network in mural granulosa cells of patients with polycystic ovary syndrome: an analysis of Gene Expression Omnibus data. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1156. [PMID: 34430597 PMCID: PMC8350636 DOI: 10.21037/atm-21-2696] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/22/2021] [Indexed: 12/17/2022]
Abstract
Background Polycystic ovary syndrome (PCOS) is one of the most common endocrine abnormalities in women of reproductive age. In this study, we set out to construct a molecular long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network according to the competitive endogenous RNA (ceRNA) theory and obtain insights into the related biological characteristics and pathways. Methods We downloaded two gene expression profile datasets of mural granulosa cells (MGCs) of women with PCOS and healthy women without PCOS (GSE84376 and GSE106724) from Gene Expression Omnibus (GEO) DataSets. Using GEO2R, we identified the mRNAs and non-coding RNAs with differential expression. The DIANA-microT-CDS algorithm was applied to predict the genes targeted by the differentially expressed miRNAs. The lncRNA-miRNA interactions were predicted using DIANA-LncBase v2. Then, we constructed the lncRNA-miRNA-mRNA network. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was employed to identify the functions and enriched pathways of the genes. Subsequently, STRING was used to construct the protein-protein interaction (PPI) network. cytoHubba in Cytoscape was used to rank the hub genes, and finally, PPI modules were screened with Cytoscape MCODE. Results There were 462 mRNAs, 2,464 lncRNAs, and 55 miRNAs which showed differential expression between the MGCs of patients with PCOS and those of healthy controls. Based on the PPI analysis, differentially expressed genes (DEGs) were significantly enriched in retinol metabolism, drug metabolism—cytochrome P450, malaria, the Hippo signaling pathway, and glycine, serine, and threonine metabolism. The ceRNA network contained 71 lncRNA nodes, 14 miRNA nodes, and 69 mRNA nodes, as well as 167 edges. We identified some novel genes and non-coding RNAs that might be involved in PCOS, including CD163, MRC1, VSIG4, CCL2, CCR2, SPP1, hsa-miR-3135b, hsa-miR-4649-3p, hsa-miR-1231, hsa-miR-3609, and hsa-miR-4433b-3p. Conclusions This study identified a novel lncRNA-miRNA-mRNA network based on the ceRNA mechanism in PCOS. Some novel genes and non-coding RNAs that may be involved in the occurrence and development of PCOS were excavated, including CD163, MRC1, VSIG4, CCL2, CCR2, SPP1, hsa-miR-3135b, hsa-miR-4649-3p, hsa-miR-1231, hsa-miR-3609, and hsa-miR-4433b-3p. However, our findings need to be validated by in vivo and in vitro experiments.
Collapse
Affiliation(s)
- Hengxi Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shuting Cheng
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Wei Xiong
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xin Tan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| |
Collapse
|
8
|
Dong LI, Zheng Y, Gao L, Luo X. lncRNA NEAT1 prompts autophagy and apoptosis in MPTP-induced Parkinson's disease by impairing miR-374c-5p. Acta Biochim Biophys Sin (Shanghai) 2021; 53:870-882. [PMID: 33984130 DOI: 10.1093/abbs/gmab055] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play biological roles in brain disorder and neurodegenerative diseases. As the functions of lncRNA NEAT1 in Parkinson's disease (PD) remain unknown, in the present study, we aimed to explore the roles and underlying molecular mechanisms of NEAT1 in PD. A PD mouse model induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and a cell model of SH-SY5Y induced by N-methyl-4-phenylpyridinium (MPP+) were established. The ratio of tyrosine hydroxylase (TH+) cells was determined by immunofluorescence assay, and the behavioral changes in mice were observed using pole tests and rotarod tests. The cellular viability and apoptosis of SH-SY5Y were detected by MTT assay and flow cytometric analysis, respectively, and the number of autophagosomes was subsequently measured by transmission electron microscopy. High-performance liquid chromatography was performed to detect the content of dopamine, and a dual-luciferase reporter assay was used to clarify the target of NEAT1 simultaneously. The results demonstrated that the level of NEAT1 was upregulated in the MPTP-induced PD mice, dopamine neurons, and the SH-SY5Y cells treated with MPP+, whereas the level of miR-374c-5p was downregulated. NEAT1 level was positively correlated with MPP+ in a concentration-dependent manner. NEAT1 inhibition efficiently facilitated cell proliferation but inhibited apoptosis and autophagy in the MPP+-treated SH-SY5Y cells. Additionally, silencing of NEAT1 increased the TH+ rate of neurons and suppressed autophagy greatly in PD mice. As a possible target of NEAT1, miR-374c-5p could impact on the apoptosis and autophagy of the SH-SY5Y cells. NEAT1 inhibition upregulated the expression of miR-374c-5p, enhanced SH-SY5Y cell viability, and repressed autophagy and apoptosis in MPTP-induced PD mice. These findings indicated a potential therapeutic role of NEAT1 in treating PD.
Collapse
Affiliation(s)
- L i Dong
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Yumin Zheng
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Lianbo Gao
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Xiaoguang Luo
- Department of Neurology, The First Affiliated Hospital of South University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen 518000, China
| |
Collapse
|
9
|
Lin Z, Zhou L, Li Y, Liu S, Xie Q, Xu X, Wu J. Identification of potential genomic biomarkers for Parkinson's disease using data pooling of gene expression microarrays. Biomark Med 2021; 15:585-595. [PMID: 33988461 DOI: 10.2217/bmm-2020-0325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: In this study, we aimed to identify potential diagnostic biomarkers Parkinson's disease (PD) by exploring microarray gene expression data of PD patients. Materials & methods: Differentially expressed genes associated with PD were screened from the GSE99039 dataset using weighted gene co-expression network analysis, followed by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses, gene-gene interaction network analysis and receiver operator characteristics analysis. Results: We identified two PD-associated modules, in which genes from the chemokine signaling pathway were primarily enriched. In particular, CS, PRKCD, RHOG and VAMP2 directly interacted with known PD-associated genes and showed higher expression in the PD samples, and may thus be potential biomarkers in PD diagnosis. Conclusion: A DFG-analysis identified a four-gene panel (CS, PRKCD, RHOG, VAMP2) as a potential diagnostic predictor to diagnose PD.
Collapse
Affiliation(s)
- Zhijian Lin
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518036, PR China
| | - Lishu Zhou
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518036, PR China.,The Clinical College of Peking University, Shenzhen Hospital of Anhui Medical University, Shenzhen, 518036, PR China
| | - Yaosha Li
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518036, PR China
| | - Suni Liu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518036, PR China
| | - Qizhi Xie
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518036, PR China
| | - Xu Xu
- College of Life Sciences & Oceanography, Shenzhen University, Shenzhen, 518060, PR China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518036, PR China
| |
Collapse
|
10
|
Shen J, Chen XC, Li WJ, Han Q, Chen C, Lu JM, Zheng JY, Xue SR. Identification of Parkinson's disease-related pathways and potential risk factors. J Int Med Res 2021; 48:300060520957197. [PMID: 33021140 PMCID: PMC7543192 DOI: 10.1177/0300060520957197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Objective To identify Parkinson’s disease (PD)-associated deregulated pathways and
genes, to further elucidate the pathogenesis of PD. Methods Dataset GSE100054 was downloaded from the Gene Expression Omnibus, and
differentially expressed genes (DEGs) in PD samples were identified.
Functional enrichment analyses were conducted for the DEGs. The top 10 hub
genes in the protein–protein interaction (PPI) network were screened out and
used to construct a support vector machine (SVM) model. The expression of
the top 10 genes was then validated in another dataset, GSE46129, and a
clinical patient cohort. Results A total of 333 DEGs were identified. The DEGs were clustered into two gene
sets that were significantly enriched in 12 pathways, of which 8 were
significantly deregulated in PD, including cytokine–cytokine receptor
interaction, gap junction, and actin cytoskeleton regulation. The signature
of the top 10 hub genes in the PPI network was used to construct the SVM
model, which had high performance for predicting PD. Of the 10 genes,
GP1BA, GP6, ITGB5,
and P2RY12 were independent risk factors of PD. Conclusion Genes such as GP1BA, GP6,
P2RY12, and ITGB5 play critical roles
in PD pathology through pathways including cytokine−cytokine receptor
interaction, gap junctions, and actin cytoskeleton regulation.
Collapse
Affiliation(s)
- Jun Shen
- Department of Neurology, The First Affiliated Hospital of
Soochow University, Suzhou, Jiangsu Province, China
- Department of Neurology, The Affiliated Huai’an Hospital of
Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huai’an,
Jiangsu Province, China
| | - Xiao-Chang Chen
- Department of Neurology, Hongze Huai’an District People’s
Hospital, Huai’an, Jiangsu Province, China
| | - Wang-Jun Li
- Department of Neurology, Changshu No. 2 People’s Hospital (The
5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu
Province, China
| | - Qiu Han
- Department of Neurology, Huai’an First People’s Hospital, The
Affiliated Huai’an No. 1 People’s Hospital of Nanjing Medical University,
Huai’an, Jiangsu Province, China
| | - Chun Chen
- Department of Neurology, Hongze Huai’an District People’s
Hospital, Huai’an, Jiangsu Province, China
| | - Jing-Min Lu
- Department of Neurology, The Affiliated Huai’an Hospital of
Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huai’an,
Jiangsu Province, China
| | - Jin-Yu Zheng
- Department of Neurology, The Affiliated Huai’an Hospital of
Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huai’an,
Jiangsu Province, China
| | - Shou-Ru Xue
- Department of Neurology, The First Affiliated Hospital of
Soochow University, Suzhou, Jiangsu Province, China
- Shou-Ru Xue, Department of Neurology, The
First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu
Province 215006, China.
| |
Collapse
|
11
|
Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson’s disease progression. ACTA ACUST UNITED AC 2021; 1:309-322. [PMID: 37118411 DOI: 10.1038/s43587-021-00042-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Noncoding RNAs have diagnostic and prognostic importance in Parkinson's disease (PD). We studied circulating small noncoding RNAs (sncRNAs) in two large-scale longitudinal PD cohorts (Parkinson's Progression Markers Initiative (PPMI) and Luxembourg Parkinson's Study (NCER-PD)) and modeled their impact on the transcriptome. Sequencing of sncRNAs in 5,450 blood samples of 1,614 individuals in PPMI yielded 323 billion reads, most of which mapped to microRNAs but covered also other RNA classes such as piwi-interacting RNAs, ribosomal RNAs and small nucleolar RNAs. Dysregulated microRNAs associated with disease and disease progression occur in two distinct waves in the third and seventh decade of life. Originating predominantly from immune cells, they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. Profiling 1,553 samples from 1,024 individuals in the NCER-PD cohort validated biomarkers and main findings by an independent technology. Finally, network analysis of sncRNA and transcriptome sequencing from PPMI identified regulatory modules emerging in patients with progressing PD.
Collapse
|
12
|
Comprehensive metabolic profiling of Parkinson's disease by liquid chromatography-mass spectrometry. Mol Neurodegener 2021; 16:4. [PMID: 33485385 PMCID: PMC7825156 DOI: 10.1186/s13024-021-00425-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Background Parkinson’s disease (PD) is a prevalent neurological disease in the elderly with increasing morbidity and mortality. Despite enormous efforts, rapid and accurate diagnosis of PD is still compromised. Metabolomics defines the final readout of genome-environment interactions through the analysis of the entire metabolic profile in biological matrices. Recently, unbiased metabolic profiling of human sample has been initiated to identify novel PD metabolic biomarkers and dysfunctional metabolic pathways, however, it remains a challenge to define reliable biomarker(s) for clinical use. Methods We presented a comprehensive metabolic evaluation for identifying crucial metabolic disturbances in PD using liquid chromatography-high resolution mass spectrometry-based metabolomics approach. Plasma samples from 3 independent cohorts (n = 460, 223 PD, 169 healthy controls (HCs) and 68 PD-unrelated neurological disease controls) were collected for the characterization of metabolic changes resulted from PD, antiparkinsonian treatment and potential interferences of other diseases. Unbiased multivariate and univariate analyses were performed to determine the most promising metabolic signatures from all metabolomic datasets. Multiple linear regressions were applied to investigate the associations of metabolites with age, duration time and stage of PD. The combinational biomarker model established by binary logistic regression analysis was validated by 3 cohorts. Results A list of metabolites including amino acids, acylcarnitines, organic acids, steroids, amides, and lipids from human plasma of 3 cohorts were identified. Compared with HC, we observed significant reductions of fatty acids (FFAs) and caffeine metabolites, elevations of bile acids and microbiota-derived deleterious metabolites, and alterations in steroid hormones in drug-naïve PD. Additionally, we found that L-dopa treatment could affect plasma metabolome involved in phenylalanine and tyrosine metabolism and alleviate the elevations of bile acids in PD. Finally, a metabolite panel of 4 biomarker candidates, including FFA 10:0, FFA 12:0, indolelactic acid and phenylacetyl-glutamine was identified based on comprehensive discovery and validation workflow. This panel showed favorable discriminating power for PD. Conclusions This study may help improve our understanding of PD etiopathogenesis and facilitate target screening for therapeutic intervention. The metabolite panel identified in this study may provide novel approach for the clinical diagnosis of PD in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s13024-021-00425-8.
Collapse
|
13
|
Eisenhaber B, Sinha S, Jadalanki CK, Shitov VA, Tan QW, Sirota FL, Eisenhaber F. Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites. Biol Direct 2021; 16:4. [PMID: 33436046 PMCID: PMC7801869 DOI: 10.1186/s13062-021-00291-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/04/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The human proteins TMTC1, TMTC2, TMTC3 and TMTC4 have been experimentally shown to be components of a new O-mannosylation pathway. Their own mannosyl-transferase activity has been suspected but their actual enzymatic potential has not been demonstrated yet. So far, sequence analysis of TMTCs has been compromised by evolutionary sequence divergence within their membrane-embedded N-terminal region, sequence inaccuracies in the protein databases and the difficulty to interpret the large functional variety of known homologous proteins (mostly sugar transferases and some with known 3D structure). RESULTS Evolutionary conserved molecular function among TMTCs is only possible with conserved membrane topology within their membrane-embedded N-terminal regions leading to the placement of homologous long intermittent loops at the same membrane side. Using this criterion, we demonstrate that all TMTCs have 11 transmembrane regions. The sequence segment homologous to Pfam model DUF1736 is actually just a loop between TM7 and TM8 that is located in the ER lumen and that contains a small hydrophobic, but not membrane-embedded helix. Not only do the membrane-embedded N-terminal regions of TMTCs share a common fold and 3D structural similarity with subgroups of GT-C sugar transferases. The conservation of residues critical for catalysis, for binding of a divalent metal ion and of the phosphate group of a lipid-linked sugar moiety throughout enzymatically and structurally well-studied GT-Cs and sequences of TMTCs indicates that TMTCs are actually sugar-transferring enzymes. We present credible 3D structural models of all four TMTCs (derived from their closest known homologues 5ezm/5f15) and find observed conserved sequence motifs rationalized as binding sites for a metal ion and for a dolichyl-phosphate-mannose moiety. CONCLUSIONS With the results from both careful sequence analysis and structural modelling, we can conclusively say that the TMTCs are enzymatically active sugar transferases belonging to the GT-C/PMT superfamily. The DUF1736 segment, the loop between TM7 and TM8, is critical for catalysis and lipid-linked sugar moiety binding. Together with the available indirect experimental data, we conclude that the TMTCs are not only part of an O-mannosylation pathway in the endoplasmic reticulum of upper eukaryotes but, actually, they are the sought mannosyl-transferases.
Collapse
Affiliation(s)
- Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
- Genome Institute of Singapore (BII), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
| | - Swati Sinha
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Chaitanya K Jadalanki
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Vladimir A Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- Siberian State Medical University, Moskovskiy Trakt, 2, Tomsk, Tomsk Oblast, 634050, Russia
| | - Qiao Wen Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
- Genome Institute of Singapore (BII), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| |
Collapse
|
14
|
Shu Y, Qian J, Wang C. Aberrant expression of microRNA-132-3p and microRNA-146a-5p in Parkinson's disease patients. Open Life Sci 2020; 15:647-653. [PMID: 33817253 PMCID: PMC7747498 DOI: 10.1515/biol-2020-0060] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
Parkinson’s disease (PD) is an age-related neurodegenerative disorder which is assessed based on the motor symptoms. A number of microRNAs (miRNAs) are dysregulated and involved in the pathogenesis or development of PD. However, no confirmed markers are used for the early detection of PD. The present study aimed to elucidate the potential two miRNAs (miR-132-3p and miR-146-5p) as novel markers for early PD diagnosis. In the present study, the expression levels of miR-132-3p and miR-146-5p in serum samples from 82 patients with PD and 44 healthy volunteers were measured by reverse transcription-quantitative polymerase chain reaction. Furthermore, the correlation analysis was performed between aberrant miRNAs and Braak staging, Part V of the Unified Parkinson’s Disease Rating Scale (UPDRS-V; the modified Hoehn and Yahr staging of PD) and Part III of the UPDRS-III. Subsequently, the receiver–operating characteristic (ROC) curve results of miR-132-3p and miR-146-5p from healthy volunteers for PD prediction and from severe PD patients were assessed. From the results it was observed that miR-132-3p and miR-146a-5p expressions were significantly decreased in the serum samples of patients with PD compared to those in the healthy volunteers. Moreover, the expressions of miR-132-3p and miR-146a-5p showed a dramatic decrease in severe PD patients as compared to the normal PD patients. Meanwhile, miR-132-3p and miR-146-5p expressions were negatively correlated with Braak staging (r = −0.45, P < 0.0001; r = −0.51, P < 0.0001), UPDRS-III (r = −0.55, P < 0.0001; r = −0.51, P < 0.0001) and UPDRS-V scores (r = − 0.46, P < 0.0001; r = −0.45, P < 0.0001) in PD patients. The area under the curve (AUC) results of miR-132-3p and miR-146a-5p in discriminating PD patients from the healthy controls were 0.7325 (95% CI = 0.6400–0.8251) and 0.7295 (95% CI = 0.3658–0.8232). Moreover, the AUC results of miR-132-3p and miR-146-5p concerning discriminating severe PD patients from normal PD patients were 0.8175 (95% CI = 0.7229–0.9121) and 0.7921 (95% CI = 0.6937–0.8905). In other words, both miR-132-3p and miR-146a-5p may function as promising biomarkers for early diagnosis of PD.
Collapse
Affiliation(s)
- Yu Shu
- Neurology Department, The Fourth Affiliated People's Hospital of Jiangsu University, Zhenjiang 212000, Jiangsu, China
| | - Jinjun Qian
- Neurology Department, The Fourth Affiliated People's Hospital of Jiangsu University, Zhenjiang 212000, Jiangsu, China
| | - Chunyan Wang
- Clinical Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| |
Collapse
|
15
|
Abstract
Glycosylation is a sophisticated informational system that controls specific biological functions at the cellular and organismal level. Dysregulation of glycosylation may underlie some of the most complex and common diseases of the modern era. In the past 5 years, microRNAs have come to the forefront as a critical regulator of the glycome. Herein, we review the current literature on miRNA regulation of glycosylation and how this work may point to a new way to identify the biological importance of glycosylation enzymes.
Collapse
Affiliation(s)
- Chu T Thu
- Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Lara K Mahal
- Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| |
Collapse
|
16
|
Deng X, Shang L, Du M, Yuan L, Xiong L, Xie X. Mechanism underlying the significant role of the miR-4262/SIRT1 axis in children with inflammatory bowel disease. Exp Ther Med 2020; 20:2227-2235. [PMID: 32765699 PMCID: PMC7401569 DOI: 10.3892/etm.2020.8918] [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: 12/27/2019] [Accepted: 05/15/2020] [Indexed: 11/06/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a term used to describe chronic and recurrent gastrointestinal disease. In total, >2 million individuals worldwide have been diagnosed with IBD, including ulcerative colitis (UC), Crohn's disease (CD) and indeterminate colitis. There is accumulating evidence to indicate that microRNAs (miRNAs or miRs) are involved in the development and progression of IBD. miR-4262, an underlying promoter in tumor diseases, has been reported to regulate inflammatory responses. However, the potential mechanisms underlying the role of miR-4262 in IBD remain unknown. The present study attempted to explore the role and mechanisms of miR-4262 in IBD. Firstly, reverse transcription-quantitative PCR (RT-qPCR) was used to detect the expression of miR-4262 in 30 IBD colonic mucosa tissues, 30 normal tissues, 2% dextran sulfate sodium (DSS)-treated Caco-2 cells and normal cells. It was demonstrated that the expression levels of miR-4262 in IBD colonic mucosa tissues and 2% DSS-stimulated Caco-2 cells were markedly higher compared with those in the control groups. Target gene prediction databases and dual-luciferase reporter assays were then used, and sirtuin 1 (SIRT1) was identified as a target gene of miR-4262. Furthermore, the levels of SIRT1 in 2% DSS-stimulated Caco-2 cells and IBD colonic mucosa tissues were suppressed compared with the corresponding control groups. In addition, it was observed that miR-4262 negatively regulated SIRT1 expression in Caco-2 cells. Thereafter, Caco-2 cells were treated with inhibitor control, miR-4262 inhibitor, control-siRNA or SIRT1-siRNA for 48 h, followed by 2% DSS treatment for 4 days. The secretion of inflammatory factors was analyzed via ELISA and RT-qPCR. MTT assay, flow cytometry and western blot analysis were performed to assess cell viability, apoptosis and NF-κB signaling pathway-related protein levels, respectively. The results indicated that DSS enhanced the inflammatory response, suppressed cell viability and promoted cell apoptosis, and this was decreased following transfection with an miR-4262 inhibitor. In addition, 2% DSS upregulated p-p65 expression and enhanced the ratio of p-p65/p65, while the miR-4246 inhibitor exerted an opposite effect. All the effects of miR-4262 inhibitor on Caco-2 cells were eliminated following transfection with SIRT1-siRNA. It was thus concluded that miR-4262 may serve a role in the progression of IBD via targeting SIRT1, and miR-4262/SIRT1 may represent a potential target for the diagnosis and treatment of IBD.
Collapse
Affiliation(s)
- Xiaozhi Deng
- Department of Children's Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Lihong Shang
- Department of Children's Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Min Du
- Department of Children's Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Lan Yuan
- Department of Children's Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Lijing Xiong
- Department of Children's Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Xiaoli Xie
- Department of Children's Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| |
Collapse
|
17
|
A Study of Gene Expression Changes in Human Spinal and Oculomotor Neurons; Identifying Potential Links to Sporadic ALS. Genes (Basel) 2020; 11:genes11040448. [PMID: 32325953 PMCID: PMC7230244 DOI: 10.3390/genes11040448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that causes compromised function of motor neurons and neuronal death. However, oculomotor neurons are largely spared from disease symptoms. The underlying causes for sporadic ALS as well as for the resistance of oculomotor neurons to disease symptoms remain poorly understood. In this bioinformatic-analysis, we compared the gene expression profiles of spinal and oculomotor tissue samples from control individuals and sporadic ALS patients. We show that the genes GAD2 and GABRE (involved in GABA signaling), and CALB1 (involved in intracellular Ca2+ ion buffering) are downregulated in the spinal tissues of ALS patients, but their endogenous levels are higher in oculomotor tissues relative to the spinal tissues. Our results suggest that the downregulation of these genes and processes in spinal tissues are related to sporadic ALS disease progression and their upregulation in oculomotor neurons confer upon them resistance to ALS symptoms. These results build upon prevailing models of excitotoxicity that are relevant to sporadic ALS disease progression and point out unique opportunities for better understanding the progression of neurodegenerative properties associated with sporadic ALS.
Collapse
|
18
|
Sancandi M, Uysal-Onganer P, Kraev I, Mercer A, Lange S. Protein Deimination Signatures in Plasma and Plasma-EVs and Protein Deimination in the Brain Vasculature in a Rat Model of Pre-Motor Parkinson's Disease. Int J Mol Sci 2020; 21:ijms21082743. [PMID: 32326590 PMCID: PMC7215947 DOI: 10.3390/ijms21082743] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/01/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
The identification of biomarkers for early diagnosis of Parkinson’s disease (PD) is of pivotal importance for improving approaches for clinical intervention. The use of translatable animal models of pre-motor PD therefore offers optimal opportunities for novel biomarker discovery in vivo. Peptidylarginine deiminases (PADs) are a family of calcium-activated enzymes that contribute to protein misfolding through post-translational deimination of arginine to citrulline. Furthermore, PADs are an active regulator of extracellular vesicle (EV) release. Both protein deimination and extracellular vesicles (EVs) are gaining increased attention in relation to neurodegenerative diseases, including in PD, while roles in pre-motor PD have yet to be investigated. The current study aimed at identifying protein candidates of deimination in plasma and plasma-EVs in a rat model of pre-motor PD, to assess putative contributions of such post-translational changes in the early stages of disease. EV-cargo was further assessed for deiminated proteins as well as three key micro-RNAs known to contribute to inflammation and hypoxia (miR21, miR155, and miR210) and also associated with PD. Overall, there was a significant increase in circulating plasma EVs in the PD model compared with sham animals and inflammatory and hypoxia related microRNAs were significantly increased in plasma-EVs of the pre-motor PD model. A significantly higher number of protein candidates were deiminated in the pre-motor PD model plasma and plasma-EVs, compared with those in the sham animals. KEGG (Kyoto encyclopedia of genes and genomes) pathways identified for deiminated proteins in the pre-motor PD model were linked to “Alzheimer’s disease”, “PD”, “Huntington’s disease”, “prion diseases”, as well as for “oxidative phosphorylation”, “thermogenesis”, “metabolic pathways”, “Staphylococcus aureus infection”, gap junction, “platelet activation”, “apelin signalling”, “retrograde endocannabinoid signalling”, “systemic lupus erythematosus”, and “non-alcoholic fatty liver disease”. Furthermore, PD brains showed significantly increased staining for total deiminated proteins in the brain vasculature in cortex and hippocampus, as well as increased immunodetection of deiminated histone H3 in dentate gyrus and cortex. Our findings identify EVs and post-translational protein deimination as novel biomarkers in early pre-motor stages of PD.
Collapse
Affiliation(s)
- Marco Sancandi
- Department of Pharmacology, UCL School of Pharmacy, London WC1N 1AX, UK; (M.S.); (A.M.)
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6XH, UK;
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Audrey Mercer
- Department of Pharmacology, UCL School of Pharmacy, London WC1N 1AX, UK; (M.S.); (A.M.)
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6XH, UK
- Correspondence: ; Tel.: +44-(0)207-911-5000 (ext. 64832)
| |
Collapse
|
19
|
Gnaq Protects PC12 Cells from Oxidative Damage by Activation of Nrf2 and Inhibition of NF-kB. Neuromolecular Med 2020; 22:401-410. [DOI: 10.1007/s12017-020-08598-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/26/2020] [Indexed: 12/11/2022]
|
20
|
Kelly J, Moyeed R, Carroll C, Luo S, Li X. Genetic networks in Parkinson's and Alzheimer's disease. Aging (Albany NY) 2020; 12:5221-5243. [PMID: 32205467 PMCID: PMC7138567 DOI: 10.18632/aging.102943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
Parkinson’s disease (PD) and Alzheimer’s disease (AD) are the most common neurodegenerative diseases and there is increasing evidence that they share common physiological and pathological links. Here we have conducted the largest network analysis of PD and AD based on their gene expressions in blood to date. We identified modules that were not preserved between disease and healthy control (HC) networks, and important hub genes and transcription factors (TFs) in these modules. We highlighted that the PD module not preserved in HCs was associated with insulin resistance, and HDAC6 was identified as a hub gene in this module which may have the role of influencing tau phosphorylation and autophagic flux in neurodegenerative disease. The AD module associated with regulation of lipolysis in adipocytes and neuroactive ligand-receptor interaction was not preserved in healthy and mild cognitive impairment networks and the key hubs TRPC5 and BRAP identified as potential targets for therapeutic treatments of AD. Our study demonstrated that PD and AD share common disrupted genetics and identified novel pathways, hub genes and TFs that may be new areas for mechanistic study and important targets in both diseases.
Collapse
Affiliation(s)
- Jack Kelly
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Rana Moyeed
- Faculty of Science and Engineering, Plymouth University, Plymouth PL6 8BU, UK
| | - Camille Carroll
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Shouqing Luo
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Xinzhong Li
- School of Science, Engineering and Design, Teesside University, Middlesbrough TS1 3BX, UK
| |
Collapse
|
21
|
Chen J, Jiang C, Du J, Xie CL. MiR-142-5p Protects Against 6-OHDA-Induced SH-SY5Y Cell Injury by Downregulating BECN1 and Autophagy. Dose Response 2020; 18:1559325820907016. [PMID: 32127787 PMCID: PMC7036514 DOI: 10.1177/1559325820907016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 12/31/2022] Open
Abstract
Background MiR-142-5p has been demonstrated to hold significant implications in neurological diseases. However, the impact and underlying regulatory mechanism of miR-142-5p in Parkinson's disease (PD) are still ominous. Methods To simulate the PD, 6-hydroxydopamine (6-OHDA)-treated SH-SY5Y cell model was used in this study. Levels of messenger RNA and protein were tested by quantitative real-time polymerase chain reaction and Western blot analyses, respectively. The direct interaction between miR-142-5p and Beclin 1 (BECN1) was assessed by luciferase reporter assay. Furthermore, Cell Counting Kit-8 assay was performed to assess cytotoxicity of SH-SY5Y cell. Results In consequence, a significant decrease of miR-142-5p was observed in 6-OHDA-induced SH-SY5Y cells. Over-/Low-expressed miR-142-5p resulted in a significant enhancement/inhibition on cell vitalities of 6-OHDA-treated SH-SY5Y cells, which might be modulated by repressing cellular autophagy through inhibiting level of BECN1 and LC3 II/LC3 I and elevating P62 level. Luciferase reporter assay showed that the BECN1 was the target gene of miR-142-5p. Additionally, the loss/gain of BECN1 rescued/blocked the effects of miR-142-5p on the viability of 6-OHDA-induced SH-SY5Y cells. Conclusions These results highlight that miR-142-5p functions as a neuroprotective regulator in 6-OHDA-induced neuronal SH-SY5Y cells simulating PD model in vitro via regulating autophagy-related protein BECN1 and autophagy to influence cell viability.
Collapse
Affiliation(s)
- Jian Chen
- Department of Senile Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
| | - Chuan Jiang
- Department of Neurology, Shandong Provincial ENT Hospital, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, People's Republic of China
| | - Juan Du
- Department of Center Sterile Supply, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Chun-Li Xie
- Department of Neurology, Fourth People's Hospital of Jinan, Jinan, People's Republic of China
| |
Collapse
|
22
|
Nuzziello N, Ciaccia L, Liguori M. Precision Medicine in Neurodegenerative Diseases: Some Promising Tips Coming from the microRNAs' World. Cells 2019; 9:E75. [PMID: 31892254 PMCID: PMC7017296 DOI: 10.3390/cells9010075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
: Novel insights in the development of a precision medicine approach for treating the neurodegenerative diseases (NDDs) are provided by emerging advances in the field of pharmacoepigenomics. In this context, microRNAs (miRNAs) have been extensively studied because of their implication in several disorders related to the central nervous system, as well as for their potential role as biomarkers of diagnosis, prognosis, and response to treatment. Recent studies in the field of neurodegeneration reported evidence that drug response and efficacy can be modulated by miRNA-mediated mechanisms. In fact, miRNAs seem to regulate the expression of pharmacology target genes, while approved (conventional and non-conventional) therapies can restore altered miRNAs observed in NDDs. The knowledge of miRNA pharmacoepigenomics may offers new clues to develop more effective treatments by providing novel insights into interindividual variability in drug disposition and response. Recently, the therapeutic potential of miRNAs is gaining increasing attention, and miRNA-based drugs (for cancer) have been under observation in clinical trials. However, the effective use of miRNAs as therapeutic target still needs to be investigated. Here, we report a brief review of representative studies in which miRNAs related to therapeutic effects have been investigated in NDDs, providing exciting potential prospects of miRNAs in pharmacoepigenomics and translational medicine.
Collapse
Affiliation(s)
- Nicoletta Nuzziello
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy
| | - Loredana Ciaccia
- Department of Biomedical Science and Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Maria Liguori
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy
| |
Collapse
|
23
|
Evaluation of miR-302b-5p expression and molecular mechanism in hepatocellular carcinoma: Findings based on RT-qPCR and in silico analysis. Pathol Res Pract 2019; 215:152424. [DOI: 10.1016/j.prp.2019.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/07/2019] [Accepted: 04/26/2019] [Indexed: 12/17/2022]
|
24
|
Liu X, Chen J, Guan T, Yao H, Zhang W, Guan Z, Wang Y. Correction to: miRNAs and target genes in the blood as biomarkers for the early diagnosis of Parkinson's disease. BMC SYSTEMS BIOLOGY 2019; 13:20. [PMID: 30755197 PMCID: PMC6372997 DOI: 10.1186/s12918-019-0701-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 11/18/2022]
Affiliation(s)
- Xiaoting Liu
- Department of Physiology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jinhu Chen
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, China
| | - Tianyuan Guan
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Hui Yao
- Department of Physiology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Wenpei Zhang
- Department of Physiology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Zhenlong Guan
- Department of Physiology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Yanqin Wang
- Department of Physiology, College of Life Science, Hebei Normal University, Shijiazhuang, China.
| |
Collapse
|