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Mohammed OA, Elballal MS, El-Husseiny AA, Khidr EG, El Tabaa MM, Elazazy O, Abd-Elmawla MA, Elesawy AE, Ibrahim HM, Abulsoud AI, El-Dakroury WA, Abdel Mageed SS, Elrebehy MA, Nomier Y, Abdel-Reheim MA, El-Husseiny HM, Mahmoud AMA, Saber S, Doghish AS. Unraveling the role of miRNAs in the diagnosis, progression, and therapeutic intervention of Parkinson's disease. Pathol Res Pract 2024; 253:155023. [PMID: 38081104 DOI: 10.1016/j.prp.2023.155023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024]
Abstract
Parkinson's disease (PD) is a debilitating neurological disorder characterized by the impairment of the motor system, resulting in symptoms such as resting tremor, cogwheel rigidity, bradykinesia, difficulty with gait, and postural instability. The occurrence of striatal dopamine insufficiency can be attributed to a notable decline in dopaminergic neurons inside the substantia nigra pars compacta. Additionally, the development of Lewy bodies serves as a pathological hallmark of PD. While current therapy approaches for PD aim to preserve dopaminergic neurons or replenish dopamine levels in the brain, it is important to acknowledge that achieving complete remission of the condition remains elusive. MicroRNAs (miRNAs, miR) are a class of small, non-coding ribonucleic acids involved in regulating gene expression at the post-transcriptional level. The miRNAs play a crucial part in the underlying pathogenic mechanisms of several neurodegenerative illnesses, including PD. The aim of this review is to explore the role of miRNAs in regulating genes associated with the onset and progression of PD, investigate the potential of miRNAs as a diagnostic tool, assess the effectiveness of targeting specific miRNAs as an alternative therapeutic strategy to impede disease advancement, and discuss the utilization of newly developed nanoparticles for delivering miRNAs as neurodegenerative therapies.
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Affiliation(s)
- Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, 11829 Cairo, Egypt
| | - Emad Gamil Khidr
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt
| | - Manar Mohammed El Tabaa
- Pharmacology & Environmental Toxicology, Environmental Studies & Research Institute (ESRI), University of Sadat City, Sadat City, 32897 Menoufia, Egypt
| | - Ola Elazazy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mai A Abd-Elmawla
- Biochemistry, Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ahmed E Elesawy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Henwa M Ibrahim
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt.
| | - Walaa A El-Dakroury
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Yousra Nomier
- Department of Pharmacology and Clinical Pharmacy, College of Medicine and Health Sciences, Sultan Qaboos University, Oman
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef 62521, Egypt.
| | - Hussein M El-Husseiny
- Laboratory of Veterinary Surgery, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt
| | - Abdulla M A Mahmoud
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt.
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The Role of Non-Coding RNAs in the Pathogenesis of Parkinson’s Disease: Recent Advancement. Pharmaceuticals (Basel) 2022; 15:ph15070811. [PMID: 35890110 PMCID: PMC9315906 DOI: 10.3390/ph15070811] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 01/27/2023] Open
Abstract
Parkinson’s disease (PD) is a prevalent neurodegenerative aging disorder that manifests as motor and non-motor symptoms, and its etiopathogenesis is influenced by non-coding RNAs (ncRNAs). Signal pathway and gene sequence studies have proposed that alteration of ncRNAs is relevant to the occurrence and development of PD. Furthermore, many studies on brain tissues and body fluids from patients with PD indicate that variations in ncRNAs and their target genes could trigger or exacerbate neurodegenerative pathogenesis and serve as potential non-invasive biomarkers of PD. Numerous ncRNAs have been considered regulators of apoptosis, α-syn misfolding and aggregation, mitochondrial dysfunction, autophagy, and neuroinflammation in PD etiology, and evidence is mounting for the determination of the role of competing endogenous RNA (ceRNA) mechanisms in disease development. In this review, we discuss the current knowledge regarding the regulation and function of ncRNAs as well as ceRNA networks in PD pathogenesis, focusing on microRNAs, long ncRNAs, and circular RNAs to increase the understanding of the disease and propose potential target identification and treatment in the early stages of PD.
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Ritiu SA, Rogobete AF, Sandesc D, Bedreag OH, Papurica M, Popovici SE, Toma D, Ivascu RI, Velovan R, Garofil DN, Corneci D, Bratu LM, Pahontu EM, Pistol A. The Impact of General Anesthesia on Redox Stability and Epigenetic Inflammation Pathways: Crosstalk on Perioperative Antioxidant Therapy. Cells 2022; 11:cells11121880. [PMID: 35741011 PMCID: PMC9221536 DOI: 10.3390/cells11121880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 02/07/2023] Open
Abstract
Worldwide, the prevalence of surgery under general anesthesia has significantly increased, both because of modern anesthetic and pain-control techniques and because of better diagnosis and the increased complexity of surgical techniques. Apart from developing new concepts in the surgical field, researchers and clinicians are now working on minimizing the impact of surgical trauma and offering minimal invasive procedures due to the recent discoveries in the field of cellular and molecular mechanisms that have revealed a systemic inflammatory and pro-oxidative impact not only in the perioperative period but also in the long term, contributing to more difficult recovery, increased morbidity and mortality, and a negative financial impact. Detailed molecular and cellular analysis has shown an overproduction of inflammatory and pro-oxidative species, responsible for augmenting the systemic inflammatory status and making postoperative recovery more difficult. Moreover, there are a series of changes in certain epigenetic structures, the most important being the microRNAs. This review describes the most important molecular and cellular mechanisms that impact the surgical patient undergoing general anesthesia, and it presents a series of antioxidant therapies that can reduce systemic inflammation.
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Affiliation(s)
- Stelian Adrian Ritiu
- Clinic of Anaesthesia and Intensive Care, Emergency County Hospital “Pius Brînzeu”, 300723 Timișoara, Romania; (S.A.R.); (D.S.); (O.H.B.); (M.P.); (S.E.P.); (D.T.); (R.V.)
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
| | - Alexandru Florin Rogobete
- Clinic of Anaesthesia and Intensive Care, Emergency County Hospital “Pius Brînzeu”, 300723 Timișoara, Romania; (S.A.R.); (D.S.); (O.H.B.); (M.P.); (S.E.P.); (D.T.); (R.V.)
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
- Anaesthesia and Intensive Care Research Center (CCATITM), “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Correspondence: (A.F.R.); (D.N.G.); Tel.: +40-075-985-2479 (A.F.R.)
| | - Dorel Sandesc
- Clinic of Anaesthesia and Intensive Care, Emergency County Hospital “Pius Brînzeu”, 300723 Timișoara, Romania; (S.A.R.); (D.S.); (O.H.B.); (M.P.); (S.E.P.); (D.T.); (R.V.)
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
- Anaesthesia and Intensive Care Research Center (CCATITM), “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Ovidiu Horea Bedreag
- Clinic of Anaesthesia and Intensive Care, Emergency County Hospital “Pius Brînzeu”, 300723 Timișoara, Romania; (S.A.R.); (D.S.); (O.H.B.); (M.P.); (S.E.P.); (D.T.); (R.V.)
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
- Anaesthesia and Intensive Care Research Center (CCATITM), “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Marius Papurica
- Clinic of Anaesthesia and Intensive Care, Emergency County Hospital “Pius Brînzeu”, 300723 Timișoara, Romania; (S.A.R.); (D.S.); (O.H.B.); (M.P.); (S.E.P.); (D.T.); (R.V.)
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
- Anaesthesia and Intensive Care Research Center (CCATITM), “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Sonia Elena Popovici
- Clinic of Anaesthesia and Intensive Care, Emergency County Hospital “Pius Brînzeu”, 300723 Timișoara, Romania; (S.A.R.); (D.S.); (O.H.B.); (M.P.); (S.E.P.); (D.T.); (R.V.)
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
| | - Daiana Toma
- Clinic of Anaesthesia and Intensive Care, Emergency County Hospital “Pius Brînzeu”, 300723 Timișoara, Romania; (S.A.R.); (D.S.); (O.H.B.); (M.P.); (S.E.P.); (D.T.); (R.V.)
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
| | - Robert Iulian Ivascu
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (R.I.I.); (D.C.); (A.P.)
- Clinic of Anaesthesia and Intensive Care, Central Military Emergency Hospital “Dr. Carol Davila”, 010242 Bucharest, Romania
| | - Raluca Velovan
- Clinic of Anaesthesia and Intensive Care, Emergency County Hospital “Pius Brînzeu”, 300723 Timișoara, Romania; (S.A.R.); (D.S.); (O.H.B.); (M.P.); (S.E.P.); (D.T.); (R.V.)
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
| | - Dragos Nicolae Garofil
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (R.I.I.); (D.C.); (A.P.)
- Correspondence: (A.F.R.); (D.N.G.); Tel.: +40-075-985-2479 (A.F.R.)
| | - Dan Corneci
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (R.I.I.); (D.C.); (A.P.)
- Clinic of Anaesthesia and Intensive Care, Central Military Emergency Hospital “Dr. Carol Davila”, 010242 Bucharest, Romania
| | - Lavinia Melania Bratu
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
| | - Elena Mihaela Pahontu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Adriana Pistol
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (R.I.I.); (D.C.); (A.P.)
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Chen X, Cao W, Zhuang Y, Chen S, Li X. Integrative analysis of potential biomarkers and immune cell infiltration in Parkinson's disease. Brain Res Bull 2021; 177:53-63. [PMID: 34536521 DOI: 10.1016/j.brainresbull.2021.09.010] [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: 06/12/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Parkinson's disease (PD) is a common neurodegenerative disease in the elderly population. However, there are no reliable diagnostic biomarkers for PD, and the pathogenesis of PD still needs further study. The aim of the current study was to identify potential biomarkers and explore the pathogenesis of PD. METHODS We conducted an integrative analysis of messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) expression profiles of PD using data from the Gene Expression Omnibus (GEO). The GSE110720, GSE110719 and GSE133347 data sets were selected and analysed. Gene ontology (GO) enrichment and gene set variation analysis (GSVA) were performed for annotation, visualization, and integrated discovery. Protein-protein interaction (PPI) and competing endogenous RNA (ceRNA) networks were constructed, and hub genes were identified. Meanwhile, the immune infiltration analysis of hub genes was analysed. Moreover, receiver operating characteristic (ROC) curves were generated to verify the diagnostic value of the differentially expressed genes (DEGs). Finally, the genes with high area under the curve (AUC) values were verified by human samples. RESULTS We identified 464 DEGs closely related to PD, including 154 mRNAs, 134 miRNAs, and 176 lncRNAs. The GO analyses indicated that changes in PD were mainly enriched in receptor ligand activity and cytokine receptor binding. The KEGG enrichment analysis showed that these DEGs were significantly involved in cytokine-cytokine receptor interactions, signalling pathways regulating the pluripotency of stem cells and Th17 cell differentiation. GSVA suggested that growth factor binding, IL2-stat5 signalling, and IL6-jak-stat3 signalling were crucial in the development of PD. A total of five hub genes (NPBWR2, CXCL10, CXCL5, S1PR5, and GALR1) were selected via the PPI network. A ceRNA network of the CXCL5, CXCL10 and S1PR5 genes was constructed, and target genes of the three genes were screened. The immune infiltration analysis showed that there were significant differences in a variety of immune cells between the hub genes. The expression of DEGs was validated in clinical human samples by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The expression levels of hsa-miR6895-5p, hsa-miR6791-5p, hsa-miR518f-5p, hsa-miR455-3p and TEKT4P2 were decreased, while the levels of TPTE2P6 were increased in human samples. These findings are consistent with the bioinformatics analysis results. CONCLUSION We found that the immune inflammatory response and immune cell regulation were involved in the pathogenesis of PD. Five hub genes involved in the immune infiltration biological processes of PD based on bioinformatics. We verified the DEGs with significant differences by qRT-PCR. These findings might provide new insight into the pathogenesis of PD and the development of diagnostic and therapeutic strategies for PD.
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Affiliation(s)
- Xiaopeng Chen
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China
| | - Wei Cao
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China
| | - Yuansu Zhuang
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China
| | - Siyuan Chen
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China
| | - Xuezhong Li
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China.
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Wang H. MicroRNAs, Parkinson's Disease, and Diabetes Mellitus. Int J Mol Sci 2021; 22:ijms22062953. [PMID: 33799467 PMCID: PMC8001823 DOI: 10.3390/ijms22062953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder that affects 1% of the population over the age of 60. Diabetes Mellitus (DM) is a metabolic disorder that affects approximately 25% of adults over the age of 60. Recent studies showed that DM increases the risk of developing PD. The link between DM and PD has been discussed in the literature in relation to different mechanisms including mitochondrial dysfunction, oxidative stress, and protein aggregation. In this paper, we review the common microRNA (miRNA) biomarkers of both diseases. miRNAs play an important role in cell differentiation, development, the regulation of the cell cycle, and apoptosis. They are also involved in the pathology of many diseases. miRNAs can mediate the insulin pathway and glucose absorption. miRNAs can also regulate PD-related genes. Therefore, exploring the common miRNA biomarkers of both PD and DM can shed a light on how these two diseases are correlated, and targeting miRNAs is a potential therapeutic opportunity for both diseases.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
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Lu W, Lin J, Zheng D, Hong C, Ke L, Wu X, Chen P. Overexpression of MicroRNA-133a Inhibits Apoptosis and Autophagy in a Cell Model of Parkinson's Disease by Downregulating Ras-Related C3 Botulinum Toxin Substrate 1 (RAC1). Med Sci Monit 2020; 26:e922032. [PMID: 32713934 PMCID: PMC7409387 DOI: 10.12659/msm.922032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Parkinson’s disease (PD) is a movement disorder. microRNA (miR)-133 expression is reduced in PD patients and in mice with a dopamine neuron deficiency. We aimed to identify the mechanism of miR-133a in apoptosis and autophagy in PD. Material/Methods The optimal concentration of MPP+ (1-methyl-4-phenylpyridinium ion) was initially determined to construct a PD cell model. Gain-of function experiments were carried out to evaluate the role of miR-133a in PD. The levels of miR-133a, RAC1 (Ras-related C3 botulinum toxin substrate 1), apoptosis-related factors, and autophagy-related factors were detected after detection of cell proliferation, cell cycle, and apoptosis. Transmission electron microscopy was applied to observe autophagosomes, and immunofluorescence staining was performed to detect LC3 and further analyze the effect of miR-133a on autophagy in a PD cell model. Results Low miR-133a expression was detected in a cell model of MPP+-induced PD. After overexpressing miR-133a, cell proliferation increased, and apoptosis (cleaved caspase-3 and Bax levels decreased, while Bcl2 levels increased) and autophagy was inhibited (LC3II/I and Beclin-1 levels decreased, while p62 levels increased). MiR-133a targeted RAC1. RACY upregulation attenuated the inhibitory effects of miR-133a on PC12 cell apoptosis and autophagy. Conclusions Our data highlighted that miR-133a overexpression prevented apoptosis and autophagy in a cell model of MPP+-induced PD by inhibiting RAC1 expression.
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Affiliation(s)
- Wusheng Lu
- Department of Neurology, The 909th Hospital of (People's Liberation Army) PLA, Zhangzhou, Fujian, China (mainland)
| | - Jinhuang Lin
- Department of Neurology, The 909th Hospital of (People's Liberation Army) PLA, Zhangzhou, Fujian, China (mainland)
| | - Dequan Zheng
- Department of Neurology, The 909th Hospital of (People's Liberation Army) PLA, Zhangzhou, Fujian, China (mainland)
| | - Chunyong Hong
- Department of Neurology, The 909th Hospital of (People's Liberation Army) PLA, Zhangzhou, Fujian, China (mainland)
| | - Laishun Ke
- Department of Neurology, The 909th Hospital of (People's Liberation Army) PLA, Zhangzhou, Fujian, China (mainland)
| | - Xinyu Wu
- Department of Neurology, The 909th Hospital of (People's Liberation Army) PLA, Zhangzhou, Fujian, China (mainland)
| | - Peineng Chen
- Department of Neurology, The 909th Hospital of (People's Liberation Army) PLA, Zhangzhou, Fujian, China (mainland)
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Bai Z, Li Y, Li Y, Pan J, Wang J, Fang F. Long noncoding RNA and messenger RNA abnormalities in pediatric sepsis: a preliminary study. BMC Med Genomics 2020; 13:36. [PMID: 32151258 PMCID: PMC7063742 DOI: 10.1186/s12920-020-0698-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/21/2020] [Indexed: 12/13/2022] Open
Abstract
Background Sepsis represents a complex disease with dysregulated inflammatory response and high mortality rate. Long noncoding RNAs (lncRNAs) have been reported to play regulatory roles in a variety of biological processes. However, studies evaluating the function of lncRNAs in pediatric sepsis are scarce, and current knowledge of the role of lncRNAs in pediatric sepsis is still limited. The present study explored the expression patterns of both lncRNAs and mRNAs between pediatric sepsis patients and healthy controls based on a comprehensive microarray analysis. Methods LncRNA and mRNA microarray was used to detect the expression of lncRNAs and mRNAs in the septic and control groups. Aberrantly expressed mRNAs and lncRNAs identified were further interpreted by enrichment analysis, receiver operating characteristic (ROC) curve analysis, co-expression network analysis, and quantitative real-time PCR (qPCR). Results A total of 1488 differetially expressed lncRNAs and 1460 differentially expressed mRNAs were identified. A co-expression network of the identified lncRNAs and mRNAs was constructed. In this network, lncRNA lnc-RP11-1220 K2.2.1–7 is correlated with mRNA CXCR1 and CLEC4D; lncRNA lnc-ANXA3–2 is correlated with mRNA CLEC4D; lncRNA lnc-TRAPPC5–1 is correlated with mRNA DYSF and HLX; lncRNA lnc-ZNF638–1 is correlated with mRNA DYSF and HLX. Significantly different expressions between pediatric sepsis patients and controls were validated by qPCR for the 4 lncRNAs and 4 co-expressed mRNAs, validating the microarray results. Conclusions Our study contributes to a comprehensive understading of the involvment of lncRNAs and mRNAs in pediatric sepsis, which may guide subsequent experimental research. Furthermore, our study may also provide potential candidate lncRNAs and mRNAs for the diagnosis and treatment of pediatric sepsis.
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Affiliation(s)
- Zhenjiang Bai
- Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, China
| | - Yiping Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Yanhong Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China.,Department of Nephrology, Children's Hospital of Soochow University, Suzhou, China
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Jian Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China.
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Taguchi YH, Wang H. Exploring MicroRNA Biomarkers for Parkinson's Disease from mRNA Expression Profiles. Cells 2018; 7:E245. [PMID: 30563060 PMCID: PMC6315543 DOI: 10.3390/cells7120245] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease (PD) is a chronic, progressive neurodegenerative disease characterized by both motor and nonmotor features. The diagnose of PD is based on a review of patients' signs and symptoms, and neurological and physical examinations. So far, no tests have been devised that can conclusively diagnose PD. In this study, we explore both microRNA and gene biomarkers for PD. Microarray gene expression profiles for PD patients and healthy control are analyzed using a principal component analysis (PCA)-based unsupervised feature extraction (FE). 244 genes are selected to be potential gene biomarkers for PD. In addition, we implement these genes into Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and find that the 15 microRNAs (miRNAs), hsa-miR-92a-3p, 16-5p, 615-3p, 877-3p, 100-5p, 320a, 877-5p, 23a-3p, 484, 23b-3p, 15a-5p, 324-3p, 19b-3p, 7b-5p and 505-3p, significantly target these 244 genes. These miRNAs are shown to be significantly related to PD. This reveals that both selected genes and miRNAs are potential biomarkers for PD.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, 1-13-27 Kasuga, Bunky-ku, Tokyo 112-8551, Japan.
| | - Hsiuying Wang
- Institute of Statistics, National Chiao Tung University, Hsinchu 30010, Taiwan.
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Tolosa E, Botta-Orfila T, Morató X, Calatayud C, Ferrer-Lorente R, Martí MJ, Fernández M, Gaig C, Raya Á, Consiglio A, Ezquerra M, Fernández-Santiago R. MicroRNA alterations in iPSC-derived dopaminergic neurons from Parkinson disease patients. Neurobiol Aging 2018; 69:283-291. [PMID: 29935433 DOI: 10.1016/j.neurobiolaging.2018.05.032] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 12/21/2022]
Abstract
MicroRNA (miRNA) misregulation in peripheral blood has been linked to Parkinson disease (PD) but its role in the disease progression remains elusive. We performed an explorative genome-wide study of miRNA expression levels in dopaminergic neurons (DAn) from PD patients generated by somatic cell reprogramming and induced pluripotent stem cells differentiation. We quantified expression levels of 377 miRNAs in DAn from 3 sporadic PD patients (sPD), 3 leucine-rich repeat kinase 2-associated PD patients (L2PD) (total 6 PD), and 4 healthy controls. We identified differential expression of 10 miRNA of which 5 were upregulated in PD (miR-9-5p, miR-135a-5p, miR-135b-5p, miR-449a, and miR-449b-5p) and 5 downregulated (miR-141-3p, miR-199a-5p, miR-299-5p, miR-518e-3p, and miR-519a-3p). Changes were similar in sPD and L2PD. Integrative analysis revealed significant correlations between miRNA/mRNA expression. Moreover, upregulation of miR-9-5p and miR-135b-5p was associated with downregulation of transcription factors related to the DNA hypermethylation of enhancer elements in PD DAn (FOXA1 and NR3C1). In summary, miRNA changes are associated with monogenic L2PD and sPD and co-occur with epigenetic changes in DAn from PD patients.
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Affiliation(s)
- Eduard Tolosa
- Department of Neurology, Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Teresa Botta-Orfila
- Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Xavier Morató
- Departament Patologia i Terapèutica Experimental, Unitat de Farmacologia, Facultat de Medicina, IDIBELL-Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain; Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Carles Calatayud
- Department of Pathology and Experimental Therapeutics, Institute of Biomedicine of the University of Barcelona (IBUB), Bellvitge University Hospital-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Raquel Ferrer-Lorente
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Hospitalet de Llobregat, Barcelona, Spain; Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - María-José Martí
- Department of Neurology, Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Manel Fernández
- Department of Neurology, Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Carles Gaig
- Department of Neurology, Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain; Department of Neurology, Multidisciplinary Sleep Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Ángel Raya
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Hospitalet de Llobregat, Barcelona, Spain; Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonella Consiglio
- Department of Pathology and Experimental Therapeutics, Institute of Biomedicine of the University of Barcelona (IBUB), Bellvitge University Hospital-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Department of Pathology and Experimental Therapeutics, Faculty of Medicine, IDIBELL- University of Barcelona, Barcelona, Spain; Department of Molecular and Translational Medicine, University of Brescia and National Institute of Neuroscience, Brescia, Italy.
| | - Mario Ezquerra
- Department of Neurology, Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
| | - Rubén Fernández-Santiago
- Department of Neurology, Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
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10
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Mo M, Xiao Y, Huang S, Cen L, Chen X, Zhang L, Luo Q, Li S, Yang X, Lin X, Xu P. MicroRNA expressing profiles in A53T mutant alpha-synuclein transgenic mice and Parkinsonian. Oncotarget 2018; 8:15-28. [PMID: 27965467 PMCID: PMC5352072 DOI: 10.18632/oncotarget.13905] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/01/2016] [Indexed: 12/23/2022] Open
Abstract
α-synuclein gene mutations can cause α-synuclein protein aggregation in the midbrain of Parkinson's disease (PD) patients. MicroRNAs (miRNAs) play a key role in the metabolism of α-synuclein but the mechanism involved in synucleinopathy remains unclear. In this study, we investigated the miRNA profiles in A53T-α-synuclein transgenic mice and analyzed the candidate miRNAs in the cerebrospinal fluid (CSF) of PD patients. The 12-month A53T-transgenic mouse displayed hyperactive movement and anxiolytic-like behaviors with α-synuclein aggregation in midbrain. A total of 317,759 total and 289,207 unique small RNA sequences in the midbrain of mice were identified by high-throughput deep sequencing. We found 644 miRNAs were significantly changed in the transgenic mice. Based on the conserved characteristic of miRNAs, we selected 11 candidates from the 40 remarkably expressed miRNAs and explored their expression in 44 CSF samples collected from PD patients. The results revealed that 11 microRNAs were differently expressed in CSF, emphatically as miR-144-5p, miR-200a-3p and miR-542-3p, which were dramatically up-regulated in both A53T-transgenic mice and PD patients, and had a helpful accuracy for the PD prediction. The ordered logistic regression analysis showed that the severity of PD has strong correlation with an up-expression of miR-144-5p, miR-200a-3p and miR-542-3p in CSF. Taken together, our data suggested that miRNAs in CSF, such as miR-144-5p, miR-200a-3p and miR-542-3p, may be useful to the PD diagnosis as potential biomarkers.
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Affiliation(s)
- Mingshu Mo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Yousheng Xiao
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Shuxuan Huang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Luan Cen
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Xiang Chen
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Limin Zhang
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Qin Luo
- Department of Neurology, The Third Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shaomin Li
- Ann Romney Center for Neurologic Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinling Yang
- Department of Neurology, The Third Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xian Lin
- Department of Anatomy & Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong, China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
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11
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Borrageiro G, Haylett W, Seedat S, Kuivaniemi H, Bardien S. A review of genome-wide transcriptomics studies in Parkinson's disease. Eur J Neurosci 2017; 47:1-16. [DOI: 10.1111/ejn.13760] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/26/2017] [Accepted: 10/19/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Genevie Borrageiro
- Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences; Faculty of Medicine and Health Sciences; Stellenbosch University; PO Box 241 Cape Town South Africa
| | - William Haylett
- Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences; Faculty of Medicine and Health Sciences; Stellenbosch University; PO Box 241 Cape Town South Africa
| | - Soraya Seedat
- Department of Psychiatry; Faculty of Medicine and Health Sciences; Stellenbosch University; Cape Town South Africa
| | - Helena Kuivaniemi
- Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences; Faculty of Medicine and Health Sciences; Stellenbosch University; PO Box 241 Cape Town South Africa
- Department of Psychiatry; Faculty of Medicine and Health Sciences; Stellenbosch University; Cape Town South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences; Faculty of Medicine and Health Sciences; Stellenbosch University; PO Box 241 Cape Town South Africa
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12
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Comparative analysis of RNA-Seq data from brain and blood samples of Parkinson's disease. Biochem Biophys Res Commun 2017; 484:557-564. [DOI: 10.1016/j.bbrc.2017.01.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 01/17/2023]
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13
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Bhattacharyya M, Nath J, Bandyopadhyay S. Identifying significant microRNA–mRNA pairs associated with breast cancer subtypes. Mol Biol Rep 2016; 43:591-9. [DOI: 10.1007/s11033-016-4021-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 05/23/2016] [Indexed: 01/03/2023]
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14
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Abstract
The difficulty to understand, diagnose, and treat neurological disorders stems from the great complexity of the central nervous system on different levels of physiological granularity. The individual components, their interactions, and dynamics involved in brain development and function can be represented as molecular, cellular, or functional networks, where diseases are perturbations of networks. These networks can become a useful research tool in investigating neurological disorders if they are properly tailored to reflect corresponding mechanisms. Here, we review approaches to construct networks specific for neurological disorders describing disease-related pathology on different scales: the molecular, cellular, and brain level. We also briefly discuss cross-scale network analysis as a necessary integrator of these scales.
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15
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Saghazadeh A, Rezaei N. MicroRNA machinery in Parkinson's disease: a platform for neurodegenerative diseases. Expert Rev Neurother 2015; 22:427-453. [PMID: 26574782 DOI: 10.1586/14737175.2015.1114886] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
MicroRNAs (miRNAs) are noncoding RNAs that recognize their protein-coding target genes and whereby subjugate them after transcription. Despite the infancy of this field of science, the role of miRNAs in neurodegeneration is well-acknowledged. This review was conducted to indicate that Parkinson's disease (PD) is not excluded from this rule. To this end, we evaluated the existing literature and arranged PD-associated miRNAs according to their mechanism of action, particularly apoptosis, autophagy, inflammation, mitochondrial dysfunction and oxidative stress. According to this arrangement, a majority of PD-associated miRNAs were indicated to influence autophagic/apoptotic pathways. We also categorized PD-associated miRNAs according to that they could exert detrimental or beneficial or both into three sets, activator, inhibitor, and double-edged, correspondingly. Considering this criterion, a majority of PD-associated miRNAs were included in the activator category. In addition, evidences from genetic association studies investigating genetic variants of or related to miRNAs in PD patients are presented. Finally, possible applications of the miRNA machinery in PD, including mechanistic networks, diagnostic, prognostic and therapeutic potentials, are discussed. But there may be additional miRNAs involved in the pathogenesis of PD which have hitherto remained unknown and thus further studies are needed to explore the issue and to extend this platform.
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Affiliation(s)
- Amene Saghazadeh
- a Molecular Immunology Research Center and Department of Immunology, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Nima Rezaei
- a Molecular Immunology Research Center and Department of Immunology, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran.,b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran.,c Universal Scientific Education and Research Network (USERN) , Tehran , Iran
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16
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Wang HY, Lin ZL, Yu XF, Bao Y, Cui XS, Kim NH. Computational Prediction of Alzheimer's and Parkinson's Disease MicroRNAs in Domestic Animals. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 29:782-92. [PMID: 26954182 PMCID: PMC4852244 DOI: 10.5713/ajas.15.0413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/23/2015] [Accepted: 08/14/2015] [Indexed: 12/27/2022]
Abstract
As the most common neurodegenerative diseases, Alzheimer’s disease (AD) and Parkinson’s disease (PD) are two of the main health concerns for the elderly population. Recently, microRNAs (miRNAs) have been used as biomarkers of infectious, genetic, and metabolic diseases in humans but they have not been well studied in domestic animals. Here we describe a computational biology study in which human AD- and PD-associated miRNAs (ADM and PDM) were utilized to predict orthologous miRNAs in the following domestic animal species: dog, cow, pig, horse, and chicken. In this study, a total of 121 and 70 published human ADM and PDM were identified, respectively. Thirty-seven miRNAs were co-regulated in AD and PD. We identified a total of 105 unrepeated human ADM and PDM that had at least one 100% identical animal homolog, among which 81 and 54 showed 100% sequence identity with 241 and 161 domestic animal miRNAs, respectively. Over 20% of the total mature horse miRNAs (92) showed perfect matches to AD/PD-associated miRNAs. Pigs, dogs, and cows have similar numbers of AD/PD-associated miRNAs (63, 62, and 59). Chickens had the least number of perfect matches (34). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses suggested that humans and dogs are relatively similar in the functional pathways of the five selected highly conserved miRNAs. Taken together, our study provides the first evidence for better understanding the miRNA-AD/PD associations in domestic animals, and provides guidance to generate domestic animal models of AD/PD to replace the current rodent models.
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Affiliation(s)
- Hai Yang Wang
- Department of Animal Sciences, Chungbuk National University, Cheongju 362-763, Korea
| | - Zi Li Lin
- Department of Animal Sciences, Chungbuk National University, Cheongju 362-763, Korea
| | - Xian Feng Yu
- College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
| | - Yuan Bao
- College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
| | - Xiang-Shun Cui
- Department of Animal Sciences, Chungbuk National University, Cheongju 362-763, Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju 362-763, Korea.,College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
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Cardo LF, Coto E, Ribacoba R, Menéndez M, Moris G, Suárez E, Alvarez V. MiRNA profile in the substantia nigra of Parkinson's disease and healthy subjects. J Mol Neurosci 2014; 54:830-6. [PMID: 25284245 DOI: 10.1007/s12031-014-0428-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 09/18/2014] [Indexed: 02/07/2023]
Abstract
The deregulation of several microRNAs (miRNAs) has been associated with neurodegenerative processes, including Parkinson's disease (PD). Our aim was to characterize the level of miRNAs in the substantia nigra (SN) of PD patients and healthy donors. This is an important issue to characterize new putative markers and therapeutic targets for PD. RNA was extracted from the SN of postmortem PD (n=8) and healthy (n=4) subjects, and the level of 733 human miRNAs was assayed with TaqMan low-density arrays (TLDAs). Overall, there was a miRNA downregulation in the SN of patients. The mean level of 11 miRNAs was significantly different (p<0.05) between patients and controls, with 10 downregulated among the patients. MiR-198, -135b, -485-5p, and -548d were the best candidates and were quantified with individual TaqMan assays in the 12 samples. MiR-135b showed the most significant difference between patients and healthy donors. The bioinformatic analysis suggested that this miRNA could bind to genes implicated in several neurodegenerative pathways.
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Affiliation(s)
- Lucía F Cardo
- Genética Molecular-Laboratorio de Medicina, Hospital Universitario Central de Asturias, 33006, Oviedo, Spain
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18
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Rakshit H, Rathi N, Roy D. Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PLoS One 2014; 9:e103047. [PMID: 25170921 PMCID: PMC4149362 DOI: 10.1371/journal.pone.0103047] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 06/26/2014] [Indexed: 11/29/2022] Open
Abstract
Background Parkinson's Disease (PD) is one of the most prevailing neurodegenerative diseases. Improving diagnoses and treatments of this disease is essential, as currently there exists no cure for this disease. Microarray and proteomics data have revealed abnormal expression of several genes and proteins responsible for PD. Nevertheless, few studies have been reported involving PD-specific protein-protein interactions. Results Microarray based gene expression data and protein-protein interaction (PPI) databases were combined to construct the PPI networks of differentially expressed (DE) genes in post mortem brain tissue samples of patients with Parkinson's disease. Samples were collected from the substantia nigra and the frontal cerebral cortex. From the microarray data, two sets of DE genes were selected by 2-tailed t-tests and Significance Analysis of Microarrays (SAM), run separately to construct two Query-Query PPI (QQPPI) networks. Several topological properties of these networks were studied. Nodes with High Connectivity (hubs) and High Betweenness Low Connectivity (bottlenecks) were identified to be the most significant nodes of the networks. Three and four-cliques were identified in the QQPPI networks. These cliques contain most of the topologically significant nodes of the networks which form core functional modules consisting of tightly knitted sub-networks. Hitherto unreported 37 PD disease markers were identified based on their topological significance in the networks. Of these 37 markers, eight were significantly involved in the core functional modules and showed significant change in co-expression levels. Four (ARRB2, STX1A, TFRC and MARCKS) out of the 37 markers were found to be associated with several neurotransmitters including dopamine. Conclusion This study represents a novel investigation of the PPI networks for PD, a complex disease. 37 proteins identified in our study can be considered as PD network biomarkers. These network biomarkers may provide as potential therapeutic targets for PD applications development.
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Affiliation(s)
- Hindol Rakshit
- Integrated Science Education & Research Centre (ISERC), Visva-Bharati University, Shantiniketan, Birbhum, West Bengal, India
| | - Nitin Rathi
- Cognizant Technology Solutions India Pvt. Ltd., Rajiv Gandhi Infotech Park, MIDC, Hinjewadi, Pune, Maharashtra, India
| | - Debjani Roy
- Department of Biophysics, Bose Institute, Acharya J.C. Bose Centenary Building, Kolkata, West Bengal, India
- * E-mail:
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