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Faraji P, Kühn H, Ahmadian S. Multiple Roles of Apolipoprotein E4 in Oxidative Lipid Metabolism and Ferroptosis During the Pathogenesis of Alzheimer's Disease. J Mol Neurosci 2024; 74:62. [PMID: 38958788 PMCID: PMC11222241 DOI: 10.1007/s12031-024-02224-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/14/2024] [Indexed: 07/04/2024]
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease worldwide and has a great socio-economic impact. Modified oxidative lipid metabolism and dysregulated iron homeostasis have been implicated in the pathogenesis of this disorder, but the detailed pathophysiological mechanisms still remain unclear. Apolipoprotein E (APOE) is a lipid-binding protein that occurs in large quantities in human blood plasma, and a polymorphism of the APOE gene locus has been identified as risk factors for AD. The human genome involves three major APOE alleles (APOE2, APOE3, APOE4), which encode for three subtly distinct apolipoprotein E isoforms (APOE2, APOE3, APOE4). The canonic function of these apolipoproteins is lipid transport in blood and brain, but APOE4 allele carriers have a much higher risk for AD. In fact, about 60% of clinically diagnosed AD patients carry at least one APOE4 allele in their genomes. Although the APOE4 protein has been implicated in pathophysiological key processes of AD, such as extracellular beta-amyloid (Aβ) aggregation, mitochondrial dysfunction, neuroinflammation, formation of neurofibrillary tangles, modified oxidative lipid metabolism, and ferroptotic cell death, the underlying molecular mechanisms are still not well understood. As for all mammalian cells, iron plays a crucial role in neuronal functions and dysregulation of iron homeostasis has also been implicated in the pathogenesis of AD. Imbalances in iron homeostasis and impairment of the hydroperoxy lipid-reducing capacity induce cellular dysfunction leading to neuronal ferroptosis. In this review, we summarize the current knowledge on APOE4-related oxidative lipid metabolism and the potential role of ferroptosis in the pathogenesis of AD. Pharmacological interference with these processes might offer innovative strategies for therapeutic interventions.
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Affiliation(s)
- Parisa Faraji
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Hartmut Kühn
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
| | - Shahin Ahmadian
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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2
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Wen Q, Verheijen M, Wittens MMJ, Czuryło J, Engelborghs S, Hauser D, van Herwijnen MHM, Lundh T, Bergdahl IA, Kyrtopoulos SA, de Kok TM, Smeets HJM, Briedé JJ, Krauskopf J. Lead-exposure associated miRNAs in humans and Alzheimer’s disease as potential biomarkers of the disease and disease processes. Sci Rep 2022; 12:15966. [PMID: 36153426 PMCID: PMC9509380 DOI: 10.1038/s41598-022-20305-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease that eventually affects memory and behavior. The identification of biomarkers based on risk factors for AD provides insight into the disease since the exact cause of AD remains unknown. Several studies have proposed microRNAs (miRNAs) in blood as potential biomarkers for AD. Exposure to heavy metals is a potential risk factor for onset and development of AD. Blood cells of subjects that are exposed to lead detected in the circulatory system, potentially reflect molecular responses to this exposure that are similar to the response of neurons. In this study we analyzed blood cell-derived miRNAs derived from a general population as proxies of potentially AD-related mechanisms triggered by lead exposure. Subsequently, we analyzed these mechanisms in the brain tissue of AD subjects and controls. A total of four miRNAs were identified as lead exposure-associated with hsa-miR-3651, hsa-miR-150-5p and hsa-miR-664b-3p being negatively and hsa-miR-627 positively associated. In human brain derived from AD and AD control subjects all four miRNAs were detected. Moreover, two miRNAs (miR-3651, miR-664b-3p) showed significant differential expression in AD brains versus controls, in accordance with the change direction of lead exposure. The miRNAs’ gene targets were validated for expression in the human brain and were found enriched in AD-relevant pathways such as axon guidance. Moreover, we identified several AD relevant transcription factors such as CREB1 associated with the identified miRNAs. These findings suggest that the identified miRNAs are involved in the development of AD and might be useful in the development of new, less invasive biomarkers for monitoring of novel therapies or of processes involved in AD development.
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3
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Yoon S, Kim SE, Ko Y, Jeong GH, Lee KH, Lee J, Solmi M, Jacob L, Smith L, Stickley A, Carvalho AF, Dragioti E, Kronbichler A, Koyanagi A, Hong SH, Thompson T, Oh H, Salazar de Pablo G, Radua J, Shin JI, Fusar-Poli P. Differential expression of MicroRNAs in Alzheimer's disease: a systematic review and meta-analysis. Mol Psychiatry 2022; 27:2405-2413. [PMID: 35264731 DOI: 10.1038/s41380-022-01476-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/10/2022]
Abstract
Alzheimer's disease (AD) results in progressive cognitive decline owing to the accumulation of amyloid plaques and hyperphosphorylated tau. MicroRNAs (miRNAs) have attracted attention as a putative diagnostic and therapeutic target for neurodegenerative diseases. However, existing meta-analyses on AD and its association with miRNAs have produced inconsistent results. The primary objective of this study is to evaluate the magnitude and consistency of differences in miRNA levels between AD patients, mild cognitive impairment (MCI) patients and healthy controls (HC). Articles investigating miRNA levels in blood, brain tissue, or cerebrospinal fluid (CSF) of AD and MCI patients versus HC were systematically searched in PubMed/Medline from inception to February 16th, 2021. Fixed- and random-effects meta-analyses were complemented with the I2 statistic to measure the heterogeneity, assessment of publication bias, sensitivity subgroup analyses (AD severity, brain region, post-mortem versus ante-mortem specimen for CSF and type of analysis used to quantify miRNA) and functional enrichment pathway analysis. Of the 1512 miRNAs included in 61 articles, 425 meta-analyses were performed on 334 miRNAs. Fifty-six miRNAs were significantly upregulated (n = 40) or downregulated (n = 16) in AD versus HC and all five miRNAs were significantly upregulated in MCI versus HC. Functional enrichment analysis confirmed that pathways related to apoptosis, immune response and inflammation were statistically enriched with upregulated pathways in participants with AD relative to HC. This study confirms that miRNAs' expression is altered in AD and MCI compared to HC. These findings open new diagnostic and therapeutic perspectives for this disorder.
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Affiliation(s)
- Sojung Yoon
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sung Eun Kim
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Kyoungki-do, Republic of Korea
| | - Gwang Hun Jeong
- College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinhee Lee
- Department of Psychiatry, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Marco Solmi
- Department of Psychiatry, University of Ottawa, Ontario, ON, Canada.,Department of Mental Health, The Ottawa Hospital, Ontario, ON, Canada.,Clinical Epidemiology Program, Ottawa Hospital Research Institute (OHRI), Ottawa, ON, Canada.,School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Louis Jacob
- Faculty of Medicine, University of Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France.,Parc Sanitari Sant Joan de Déu/CIBERSAM, Universitat de Barcelona, Fundació Sant Joan de Déu, Sant Boi de Llobregat, Barcelona, Spain
| | - Lee Smith
- Centre for Health, Performance, and Wellbeing, Anglia Ruskin University, Cambridge, UK
| | - Andrew Stickley
- Department of Preventive Intervention for Psychiatric Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan.,Stockholm Center for Health and Social Change (SCOHOST), Södertörn University, Huddinge, Sweden
| | - Andre F Carvalho
- Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Elena Dragioti
- Pain and Rehabilitation Centre and Department of Health, Medicine and Caring Sciences, Linkoping University, Linkoping, Sweden
| | | | - Ai Koyanagi
- Parc Sanitari Sant Joan de Déu/CIBERSAM, Universitat de Barcelona, Fundació Sant Joan de Déu, Sant Boi de Llobregat, Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona, Spain
| | - Sung Hwi Hong
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Trevor Thompson
- Centre of Chronic Illness and Ageing, University of Greenwich, London, UK
| | - Hans Oh
- Suzanne Dworak-Peck School of Social Work, University of Southern California, Los Angeles, CA, 90015, USA
| | - Gonzalo Salazar de Pablo
- Early Psychosis: Interventions and Clinical-detection (EPIC) lab, Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Institute of Psychiatry and Mental Health. Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón School of Medicine, Universidad Complutense, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), CIBERSAM, Madrid, Spain
| | - Joaquim Radua
- Early Psychosis: Interventions and Clinical-detection (EPIC) lab, Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Imaging of Mood- and Anxiety-Related Disorders (IMARD) Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBERSAM, Barcelona, Spain.,Department of Clinical Neuroscience, Centre for Psychiatric Research and Education, Karolinska Institutet, Stockholm, Sweden
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Paolo Fusar-Poli
- Early Psychosis: Interventions and Clinical-detection (EPIC) lab, Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy.,OASIS service, South London and Maudsley NHS Foundation Trust, London, UK.,National Institute of Health Research Maudsley Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London, UK
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Aslani M, Mortazavi-Jahromi SS, Mirshafiey A. Efficient roles of miR-146a in cellular and molecular mechanisms of neuroinflammatory disorders: An effectual review in neuroimmunology. Immunol Lett 2021; 238:1-20. [PMID: 34293378 DOI: 10.1016/j.imlet.2021.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/03/2021] [Accepted: 07/15/2021] [Indexed: 12/16/2022]
Abstract
Known as one of the most sophisticated systems of the human body, the nervous system consists of neural cells and controls all parts of the body. It is closely related to the immune system. The effects of inflammation and immune reactions have been observed in the pathogenesis of some neurological disorders. Defined as the gene expression regulators, miRNAs participate in cellular processes. miR-146a is a mediator in the neuroimmune system, leaving substantial effects on the homeostasis of immune and brain cells, neuronal identities acquisition, and immune responses regulation in the nervous system. Its positive efficiency has been proven in modulating inflammatory reactions, hemorrhagic complications, and pain. Moreover, the miR-146a targets play a key role in the pathogenesis of these illnesses. Based on the performance of its targets, miR-146a can have various effects on the disease progress. The abnormal expression/function of miR-146a has been reported in neuroinflammatory disorders. There is research evidence that this molecule qualifies as a desirable biomarker for some disorders and can even be a therapeutic target. This study aims to provide a meticulous review regarding the roles of miR-146a in the pathogenesis and progression of several neuroinflammatory disorders such as multiple sclerosis, amyotrophic lateral sclerosis, Alzheimer's disease, temporal lobe epilepsy, ischemic stroke, etc. The study also considers its eligibility for use as an ideal biomarker and therapeutic target in these diseases. The awareness of these mechanisms can facilitate the disease management/treatment, lead to patients' amelioration, improve the quality of life, and mitigate the risk of death.
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Affiliation(s)
- Mona Aslani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Abbas Mirshafiey
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Wang T, Shao W, Huang Z, Tang H, Zhang J, Ding Z, Huang K. MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification. Nat Commun 2021; 12:3445. [PMID: 34103512 PMCID: PMC8187432 DOI: 10.1038/s41467-021-23774-w] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
To fully utilize the advances in omics technologies and achieve a more comprehensive understanding of human diseases, novel computational methods are required for integrative analysis of multiple types of omics data. Here, we present a novel multi-omics integrative method named Multi-Omics Graph cOnvolutional NETworks (MOGONET) for biomedical classification. MOGONET jointly explores omics-specific learning and cross-omics correlation learning for effective multi-omics data classification. We demonstrate that MOGONET outperforms other state-of-the-art supervised multi-omics integrative analysis approaches from different biomedical classification applications using mRNA expression data, DNA methylation data, and microRNA expression data. Furthermore, MOGONET can identify important biomarkers from different omics data types related to the investigated biomedical problems.
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Affiliation(s)
- Tongxin Wang
- Department of Computer Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Wei Shao
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhi Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
| | - Haixu Tang
- Department of Computer Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhengming Ding
- Department of Computer Science, Tulane University, New Orleans, LA, USA.
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
- Regenstrief Institute, Indianapolis, IN, USA.
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6
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MiR-216a-5p ameliorates learning-memory deficits and neuroinflammatory response of Alzheimer's disease mice via regulation of HMGB1/NF-κB signaling. Brain Res 2021; 1766:147511. [PMID: 33957091 DOI: 10.1016/j.brainres.2021.147511] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 01/25/2023]
Abstract
OBJECTIVE The objective of this study was to explore whether miR-216a-5p could affect the learning-memory ability and inflammatory response of Alzheimer's disease (AD) mice via regulation of the HMGB1/NF-κB pathway. METHODS Mice were divided into the normal (wild-type C57BL/6 mice), AD (APP/PS1 double-transgenic mice), AD + miR-216a-5p, and AD + vector groups. The Morris water maze test was used to examine learning and memory ability. Nissl staining and TUNEL staining were performed to observe the survival and apoptosis of hippocampal neurons. In addition, Aβ deposition and the expression of inflammatory cytokines were determined, while miR-216a-5p expression and HMGB1/NF-κB pathway-related proteins were detected by qRT-PCR and Western blotting, respectively. RESULTS AD mice exhibited decreased miR-216a-5p expression but increased HMGB-1 protein expression in the hippocampus, and these mice had a prolonged escape latency, fewer number of times crossing the platform location and shortened time in the target quadrant compared to those in normal mice. AD mice also had an elevated number of TUNEL-positive cells, increased deposition of Aβ, increased expression of inflammatory cytokines and decreased number of Nissl-positive cells. In addition, AD mice presented with downregulated expression of cytoplasmic NF-κB p65 protein but upregulated expression of nuclear NF-κB p65 protein. However, AD mice treated with miR-216a-5p exhibited significant improvements of the abovementioned parameters. The dual-luciferase reporter assay confirmed that HMGB1 is a target gene of miR-216a-5p. CONCLUSION MiR-216a-5p can improve learning-memory ability and attenuate the inflammatory response of AD mice through targeted inhibition of the HMGB1/NF-κB pathway.
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Ma Y, Ye J, Zhao L, Pan D. MicroRNA-146a inhibition promotes total neurite outgrowth and suppresses cell apoptosis, inflammation, and STAT1/MYC pathway in PC12 and cortical neuron cellular Alzheimer's disease models. ACTA ACUST UNITED AC 2021; 54:e9665. [PMID: 33729395 PMCID: PMC7959174 DOI: 10.1590/1414-431x20209665] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/30/2020] [Indexed: 01/20/2023]
Abstract
This study aimed to explore the effect of microRNA (miR)-146a inhibition on regulating cell apoptosis, total neurite outgrowth, inflammation, and STAT1/MYC pathway in Alzheimer's disease (AD). PC12 and cortical neuron cellular AD models were constructed by Aβ1-42 insult. For the former model, nerve growth factor (NGF) stimulation was previously conducted. miR-146a inhibitor and negative-control (NC) inhibitor were transfected into the two cellular AD models, and then cells were named miR-inhibitor group and NC-inhibitor group, respectively. After transfection, cell apoptosis, total neurite outgrowth, supernatant inflammation cytokines, and STAT1/MYC pathway were detected. miR-146a expression was similar between PC12 cellular AD model and control cells (NGF-stimulated PC12 cells), while miR-146a expression was increased in cortical neuron cellular AD model compared with control cells (rat embryo primary cortical neurons). In both PC12 and cortical neuron cellular AD models, miR-146a expression was reduced in miR-inhibitor group compared with NC-inhibitor group after transfection. Furthermore, cell apoptosis was attenuated, while total neurite outgrowth was elevated in miR-inhibitor group compared with NC-inhibitor group. As for supernatant inflammatory cytokines, tumor necrosis factor-α, interleukin (IL)-1β, IL-6, and IL-17 levels were lower in miR-inhibitor group than in NC-inhibitor group. Additionally, STAT1 and c-Myc mRNA and protein expressions were attenuated in miR-inhibitor group compared with NC-inhibitor group. In conclusion, miR-146a potentially represented a viable therapeutic target for AD.
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Affiliation(s)
- Yinghui Ma
- Department of Neurosurgery, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, China
| | - Jiye Ye
- Department of Neurosurgery, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, China
| | | | - Dongmei Pan
- Department of Gerontology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, China
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Loeffler DA. Modifiable, Non-Modifiable, and Clinical Factors Associated with Progression of Alzheimer's Disease. J Alzheimers Dis 2021; 80:1-27. [PMID: 33459643 DOI: 10.3233/jad-201182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is an extensive literature relating to factors associated with the development of Alzheimer's disease (AD), but less is known about factors which may contribute to its progression. This review examined the literature with regard to 15 factors which were suggested by PubMed search to be positively associated with the cognitive and/or neuropathological progression of AD. The factors were grouped as potentially modifiable (vascular risk factors, comorbidities, malnutrition, educational level, inflammation, and oxidative stress), non-modifiable (age at clinical onset, family history of dementia, gender, Apolipoprotein E ɛ4, genetic variants, and altered gene regulation), and clinical (baseline cognitive level, neuropsychiatric symptoms, and extrapyramidal signs). Although conflicting results were found for the majority of factors, a positive association was found in nearly all studies which investigated the relationship of six factors to AD progression: malnutrition, genetic variants, altered gene regulation, baseline cognitive level, neuropsychiatric symptoms, and extrapyramidal signs. Whether these or other factors which have been suggested to be associated with AD progression actually influence the rate of decline of AD patients is unclear. Therapeutic approaches which include addressing of modifiable factors associated with AD progression should be considered.
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Affiliation(s)
- David A Loeffler
- Beaumont Research Institute, Department of Neurology, Beaumont Health, Royal Oak, MI, USA
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Wee JJ, Kumar S. Prediction of hub genes of Alzheimer's disease using a protein interaction network and functional enrichment analysis. Genomics Inform 2020; 18:e39. [PMID: 33412755 PMCID: PMC7808865 DOI: 10.5808/gi.2020.18.4.e39] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023] Open
Abstract
Alzheimer's disease (AD) is a chronic, progressive brain disorder that slowly destroys affected individuals’ memory and reasoning faculties, and consequently, their ability to perform the simplest tasks. This study investigated the hub genes of AD. Proteins interact with other proteins and non-protein molecules, and these interactions play an important role in understanding protein function. Computational methods are useful for understanding biological problems, in particular, network analyses of protein-protein interactions. Through a protein network analysis, we identified the following top 10 hub genes associated with AD: PTGER3, C3AR1, NPY, ADCY2, CXCL12, CCR5, MTNR1A, CNR2, GRM2, and CXCL8. Through gene enrichment, it was identified that most gene functions could be classified as integral to the plasma membrane, G-protein coupled receptor activity, and cell communication under gene ontology, as well as involvement in signal transduction pathways. Based on the convergent functional genomics ranking, the prioritized genes were NPY, CXCL12, CCR5, and CNR2.
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Affiliation(s)
- Jia Jin Wee
- Faculty of Health and Life Sciences, Management and Science University, 40100 Shah Alam, Malaysia
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, 40100 Shah Alam, Malaysia
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10
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Varma-Doyle AV, Lukiw WJ, Zhao Y, Lovera J, Devier D. A hypothesis-generating scoping review of miRs identified in both multiple sclerosis and dementia, their protein targets, and miR signaling pathways. J Neurol Sci 2020; 420:117202. [PMID: 33183778 DOI: 10.1016/j.jns.2020.117202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/26/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
Cognitive impairment (CI) is a frequent complication affecting people with multiple sclerosis (MS). The causes of CI in MS are not fully understood. Besides MRI measures, few other biomarkers exist to help us predict the development of CI and understand its biology. MicroRNAs (miRs) are relatively stable, non-coding RNA molecules about 22 nucleotides in length that can serve as biomarkers and possible therapeutic targets in several autoimmune and neurodegenerative diseases, including the dementias. In this review, we identify dysregulated miRs in MS that overlap with dysregulated miRs in cognitive disorders and dementia and explore how these overlapping miRs play a role in CI in MS. MiR-15, miR-21, miR-128, miR-132, miR-138, miR-142, miR-146a, miR-155, miR-181, miR-572, and let-7 are known to contribute to various forms of dementia and show abnormal expression in MS. These overlapping miRs are involved in pathways related to apoptosis, neuroinflammation, glutamate toxicity, astrocyte activation, microglial burst activity, synaptic dysfunction, and remyelination. The mechanisms of action suggest that these miRs may be related to CI in MS. From our review, we also delineated miRs that could be neuroprotective in MS, namely miR-23a, miR-219, miR-214, and miR-22. Further studies can help clarify if these miRs are responsible for CI in MS, leading to potential therapeutic targets.
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Affiliation(s)
- Aditi Vian Varma-Doyle
- Louisiana State University Health Sciences Center -New Orleans School of Medicine, Department of Neurology, New Orleans, United States of America
| | - Walter J Lukiw
- Louisiana State University Health Sciences Center -New Orleans School of Medicine, Department of Neurology, New Orleans, United States of America; Louisiana State University Health Sciences Center - New Orleans Neuroscience Center, United States of America; Louisiana State University Health Sciences Center - New Orleans Department of Ophthalmology, United States of America
| | - Yuhai Zhao
- Louisiana State University Health Sciences Center - New Orleans Department of Cell Biology and Anatomy, United States of America; Louisiana State University Health Sciences Center - New Orleans Neuroscience Center, United States of America
| | - Jesus Lovera
- Louisiana State University Health Sciences Center -New Orleans School of Medicine, Department of Neurology, New Orleans, United States of America.
| | - Deidre Devier
- Louisiana State University Health Sciences Center -New Orleans School of Medicine, Department of Neurology, New Orleans, United States of America; Louisiana State University Health Sciences Center - New Orleans Department of Cell Biology and Anatomy, United States of America.
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Henriques AD, Machado-Silva W, Leite RE, Suemoto CK, Leite KR, Srougi M, Pereira AC, Jacob-Filho W, Nóbrega OT. Genome-wide profiling and predicted significance of post-mortem brain microRNA in Alzheimer’s disease. Mech Ageing Dev 2020; 191:111352. [DOI: 10.1016/j.mad.2020.111352] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022]
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12
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Tong Z, Cui Q, Wang J, Zhou Y. TransmiR v2.0: an updated transcription factor-microRNA regulation database. Nucleic Acids Res 2020; 47:D253-D258. [PMID: 30371815 PMCID: PMC6323981 DOI: 10.1093/nar/gky1023] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression and play vital roles in various biological processes. It has been reported that aberrant regulation of miRNAs was associated with the development and progression of various diseases, but the underlying mechanisms are not fully deciphered. Here, we described our updated TransmiR v2.0 database for more comprehensive information about transcription factor (TF)-miRNA regulations. 3730 TF–miRNA regulations among 19 species from 1349 reports were manually curated by surveying >8000 publications, and more than 1.7 million tissue-specific TF–miRNA regulations were further incorporated based on ChIP-seq data. Besides, we constructed a ‘Predict’ module to query the predicted TF–miRNA regulations in human based on binding motifs of TFs. To facilitate the community, we provided a ‘Network’ module to visualize TF–miRNA regulations for each TF and miRNA, or for a specific disease. An ‘Enrichment analysis’ module was also included to predict TFs that are likely to regulate a miRNA list of interest. In conclusion, with improved data coverage and webserver functionalities, TransmiR v2.0 would be a useful resource for investigating the regulation of miRNAs. TransmiR v2.0 is freely accessible at http://www.cuilab.cn/transmir.
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Affiliation(s)
- Zhan Tong
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Juan Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
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Shao W, Xiang S, Zhang Z, Huang K, Zhang J. Hyper-graph based sparse canonical correlation analysis for the diagnosis of Alzheimer's disease from multi-dimensional genomic data. Methods 2020; 189:86-94. [PMID: 32360353 DOI: 10.1016/j.ymeth.2020.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/30/2020] [Accepted: 04/23/2020] [Indexed: 10/24/2022] Open
Abstract
The effective and accurate diagnosis of Alzheimer's disease (AD), especially in the early stage (i.e., mild cognitive impairment (MCI)) remains a big challenge in AD research. So far, multiple biomarkers have been associated with AD diagnosis and progression. However, most of the existing research only utilized single modality data for diagnostic biomarker identification, which did not take the advantages of multi-modal data that provide comprehensive and complementary information at multiple levels into consideration. In this paper, we integrate multi-modal genomic data from postmortem AD brains (i.e., mRNA, miRNA and epigenomic data) and propose a hyper-graph based sparse canonical correlation analysis (HGSCCA) method to extract the most correlated multi-modal biomarkers associated with AD and MCI. Specifically, our model utilizes the sparse canonical correlation analysis framework (SCCA), which aims at finding the best linear projections for each input modality so that the strongest correlation within the selected features of multi-dimensional genomic data can be captured. In addition, with the consideration of high-order relationships among different subjects, we also introduce a hyper-graph-based regularization term that will lead to the selection of more discriminative biomarkers. To evaluate the effectiveness of the proposed method, we conduct the experiments on the well-known AD cohort study, The Religious Orders Study and Memory and Aging Project (ROSMAP) dataset, and the results show that our method can not only identify meaningful biomarkers for the diagnosis AD disease, but also achieve superior classification performance than the comparing methods.
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Affiliation(s)
- Wei Shao
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Shunian Xiang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen 518060, China; Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Zuoyi Zhang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202 USA; Regenstrief Institute, Indianapolis, IN 46202, USA
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202 USA; Regenstrief Institute, Indianapolis, IN 46202, USA.
| | - Jie Zhang
- Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA.
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14
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Zhang Y, Yu F, Bao S, Sun J. Systematic Characterization of Circular RNA-Associated CeRNA Network Identified Novel circRNA Biomarkers in Alzheimer's Disease. Front Bioeng Biotechnol 2019; 7:222. [PMID: 31572720 PMCID: PMC6749152 DOI: 10.3389/fbioe.2019.00222] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD), a degenerative disease of the central nervous system, is the most common form of dementia in old age. The complexity and behavior of circular RNA (circRNA)-associated competing endogenous RNA (ceRNA) network remained poorly characterized in AD. The aim of this study was to elucidate the regulatory networks of dysregulated circRNAs from ceRNA view and identify potential risk circRNAs involved in AD pathogenesis. Consistent differentially expressed genes (CDEGs) were obtained using meta-analysis for multiple microarrays, and differentially expressed miRNAs (DEmiRs) were identified using empirical Bayes method. The circRNA-associated ceRNA network (cirCeNET) was constructed based on “ceRNA hypothesis” using an integrated system biology method. A total of 1,872 CDEGs and 48 DEmiRs were screened across different datasets. By mapping CDEGs and DEmiRs into the cirCeNET, an AD-related circRNA-associated ceRNA network (ADcirCeNET) was constructed, including 3,907 edges and 1,407 nodes (276 circRNAs, 14 miRNAs and 1,117 mRNAs). By prioritizing AD risk circRNA-associated ceRNAs, we found that the circRNA KIAA1586 occurred most frequently in the AD risk circRNA-associated ceRNAs and function as a ceRNA that operates by competitively binding three known AD-risk miRNAs. In silico functional analysis suggested that circRNA KIAA1586-related ceRNA network was significantly enriched in known AD-associated biological processes. Our study provided a global view and systematic dissection of circRNA-associated ceRNA network. The identified circRNA KIAA1586 may be a key risk factor involved in AD pathogenesis.
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Affiliation(s)
- Yan Zhang
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Fulong Yu
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Siqi Bao
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jie Sun
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
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15
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Li J, Xie Y, Zhang C, Wang J, Wu Y, Yang Y, Xie Y, Lv Z. A network-based analysis for mining the risk pathways in glioblastoma. Oncol Lett 2019; 18:2712-2717. [PMID: 31402957 PMCID: PMC6676740 DOI: 10.3892/ol.2019.10598] [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: 11/01/2018] [Accepted: 06/13/2019] [Indexed: 11/05/2022] Open
Abstract
The most malignant type of brain tumour is glioblastoma multiforme (GBM). Patients with GBM often have a poor prognosis, as a result of incomplete or inaccurate diagnoses. Regulatory pathways have been demonstrated to serve important roles in complex human diseases. Therefore, deciphering these risk pathways may shed light on the molecular mechanisms underlying GBM progression. In the present study, differentially expressed genes and microRNAs (miRNAs) in a publicly available database were identified between normal and tumour samples. To determine the pathophysiology and molecular mechanisms underlying GBM, integrated network analysis was performed to mine GBM-specific risk pathways. Specifically, a GBM-specific regulatory network was constructed that integrated manually curated GBM-associated transcription and post-transcriptional data resources, including transcription factors and miRNAs. A total of 1,827 differentially expressed genes and 30 miRNAs were identified. The differentially expressed genes were significantly enriched in a number of immune response-associated functions. Based on the GBM-specific regulatory network, 15 risk regulatory pathways containing not only known regulators, but also potential novel targets that might be involved in tumourigenesis were identified. Network analysis provides a strategy for leveraging genomic data to identify potential oncogenic pathways and molecular targets for GBM.
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Affiliation(s)
- Jing Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yujie Xie
- Department of Rehabilitation Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Chi Zhang
- Department of Rehabilitation Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jianxiong Wang
- Department of Rehabilitation Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yong Wu
- Department of Neurology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yuan Yang
- Department of Neurology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yang Xie
- Department of Neurology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Zhiyu Lv
- Department of Neurology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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16
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Rahman MR, Islam T, Zaman T, Shahjaman M, Karim MR, Huq F, Quinn JMW, Holsinger RMD, Gov E, Moni MA. Identification of molecular signatures and pathways to identify novel therapeutic targets in Alzheimer's disease: Insights from a systems biomedicine perspective. Genomics 2019; 112:1290-1299. [PMID: 31377428 DOI: 10.1016/j.ygeno.2019.07.018] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/01/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by the accumulation of amyloid plaques and neurofibrillary tangles in the brain. However, there are no peripheral biomarkers available that can detect AD onset. This study aimed to identify the molecular signatures in AD through an integrative analysis of blood gene expression data. We used two microarray datasets (GSE4226 and GSE4229) comparing peripheral blood transcriptomes of AD patients and controls to identify differentially expressed genes (DEGs). Gene set and protein overrepresentation analysis, protein-protein interaction (PPI), DEGs-Transcription Factors (TFs) interactions, DEGs-microRNAs (miRNAs) interactions, protein-drug interactions, and protein subcellular localizations analyses were performed on DEGs common to the datasets. We identified 25 common DEGs between the two datasets. Integration of genome scale transcriptome datasets with biomolecular networks revealed hub genes (NOL6, ATF3, TUBB, UQCRC1, CASP2, SND1, VCAM1, BTF3, VPS37B), common transcription factors (FOXC1, GATA2, NFIC, PPARG, USF2, YY1) and miRNAs (mir-20a-5p, mir-93-5p, mir-16-5p, let-7b-5p, mir-708-5p, mir-24-3p, mir-26b-5p, mir-17-5p, mir-193-3p, mir-186-5p). Evaluation of histone modifications revealed that hub genes possess several histone modification sites associated with AD. Protein-drug interactions revealed 10 compounds that affect the identified AD candidate biomolecules, including anti-neoplastic agents (Vinorelbine, Vincristine, Vinblastine, Epothilone D, Epothilone B, CYT997, and ZEN-012), a dermatological (Podofilox) and an immunosuppressive agent (Colchicine). The subcellular localization of molecular signatures varied, including nuclear, plasma membrane and cytosolic proteins. In the present study, it was identified blood-cell derived molecular signatures that might be useful as candidate peripheral biomarkers in AD. It was also identified potential drugs and epigenetic data associated with these molecules that may be useful in designing therapeutic approaches to ameliorate AD.
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Affiliation(s)
- Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Enayetpur, Sirajgonj, Bangladesh.
| | - Tania Islam
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Toyfiquz Zaman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Enayetpur, Sirajgonj, Bangladesh
| | - Md Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur, Bangladesh
| | - Md Rezaul Karim
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Enayetpur, Sirajgonj, Bangladesh
| | - Fazlul Huq
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, NSW 2006, Australia
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - R M Damian Holsinger
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, NSW 2006, Australia; Laboratory of Molecular Neuroscience and Dementia, Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Esra Gov
- Department of Bioengineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
| | - Mohammad Ali Moni
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, NSW 2006, Australia; Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
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17
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Wang L, Zhang C, Xie Y, Jiang W, Huang J, Guo S, Xu F, Wang J. Detecting the long non‑coding RNA signature related to spinal cord ependymal tumor subtype using a genome‑wide methylome analysis approach. Mol Med Rep 2019; 20:1531-1540. [PMID: 31257484 PMCID: PMC6625447 DOI: 10.3892/mmr.2019.10388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/30/2019] [Indexed: 11/16/2022] Open
Abstract
Ependymoma is a type of intramedullary tumor that tends to occur in the adult spinal cord. Ependymoma affects the nervous system and has significant impacts on the quality of life, and it may lead to mortality. Previous studies have performed molecular classification of spinal cord ependymal tumors at the DNA methylation level. However, the DNA methylation status of non-coding regions in spinal cord ependymal tumors remains unclear. In the present study, a genome-wide methylome method was used to characterize the DNA methylation landscape of long non-coding RNAs (lncRNAs) in spinal cord ependymal tumor samples. The present study identified lncRNA signatures associated with tumor subtypes based on the methylation status of lncRNA promoters. The present results suggested that the identified lncRNA signatures were associated with cancer- or nervous system-related protein-coding genes. The majority of the identified lncRNAs was hypomethylated, and may have a role in spinal cord development. The present findings suggested that detection of tumor subtype-specific lncRNAs may facilitate the identification of novel diagnostic and therapeutic strategies to treat patients with spinal cord ependymal tumor.
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Affiliation(s)
- Li Wang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Chi Zhang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yujie Xie
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Wei Jiang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Juan Huang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Shengmin Guo
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Fangyuan Xu
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jianxiong Wang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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18
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Systems biology approach identifies key regulators and the interplay between miRNAs and transcription factors for pathological cardiac hypertrophy. Gene 2019; 698:157-169. [DOI: 10.1016/j.gene.2019.02.056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/31/2019] [Accepted: 02/20/2019] [Indexed: 12/16/2022]
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19
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Wang S, Wang W, Meng Q, Zhou S, Liu H, Ma X, Zhou X, Liu H, Chen X, Jiang W. Inferring Novel Autophagy Regulators Based on Transcription Factors and Non-Coding RNAs Coordinated Regulatory Network. Cells 2018; 7:cells7110194. [PMID: 30400235 PMCID: PMC6262548 DOI: 10.3390/cells7110194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 01/06/2023] Open
Abstract
Autophagy is a complex cellular digestion process involving multiple regulators. Compared to post-translational autophagy regulators, limited information is now available about transcriptional and post-transcriptional regulators such as transcription factors (TFs) and non-coding RNAs (ncRNAs). In this study, we proposed a computational method to infer novel autophagy-associated TFs, micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs) based on TFs and ncRNAs coordinated regulatory (TNCR) network. First, we constructed a comprehensive TNCR network, including 155 TFs, 681 miRNAs and 1332 lncRNAs. Next, we gathered the known autophagy-associated factors, including TFs, miRNAs and lncRNAs, from public data resources. Then, the random walk with restart (RWR) algorithm was conducted on the TNCR network by using the known autophagy-associated factors as seeds and novel autophagy regulators were finally prioritized. Leave-one-out cross-validation (LOOCV) produced an area under the curve (AUC) of 0.889. In addition, functional analysis of the top 100 ranked regulators, including 55 TFs, 26 miRNAs and 19 lncRNAs, demonstrated that these regulators were significantly enriched in cell death related functions and had significant semantic similarity with autophagy-related Gene Ontology (GO) terms. Finally, extensive literature surveys demonstrated the credibility of the predicted autophagy regulators. In total, we presented a computational method to infer credible autophagy regulators of transcriptional factors and non-coding RNAs, which would improve the understanding of processes of autophagy and cell death and provide potential pharmacological targets to autophagy-related diseases.
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Affiliation(s)
- Shuyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Wencan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Qianqian Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Shunheng Zhou
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
| | - Haizhou Liu
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
| | - Xueyan Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Xu Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Hui Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Xiaowen Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Wei Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
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20
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Kawalia SB, Raschka T, Naz M, de Matos Simoes R, Senger P, Hofmann-Apitius M. Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data. J Alzheimers Dis 2018; 59:1237-1254. [PMID: 28800327 PMCID: PMC5611835 DOI: 10.3233/jad-170011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alzheimer’s disease (AD) progressively destroys cognitive abilities in the aging population with tremendous effects on memory. Despite recent progress in understanding the underlying mechanisms, high drug attrition rates have put a question mark behind our knowledge about its etiology. Re-evaluation of past studies could help us to elucidate molecular-level details of this disease. Several methods to infer such networks exist, but most of them do not elaborate on context specificity and completeness of the generated networks, missing out on lesser-known candidates. In this study, we present a novel strategy that corroborates common mechanistic patterns across large scale AD gene expression studies and further prioritizes potential biomarker candidates. To infer gene regulatory networks (GRNs), we applied an optimized version of the BC3Net algorithm, named BC3Net10, capable of deriving robust and coherent patterns. In principle, this approach initially leverages the power of literature knowledge to extract AD specific genes for generating viable networks. Our findings suggest that AD GRNs show significant enrichment for key signaling mechanisms involved in neurotransmission. Among the prioritized genes, well-known AD genes were prominent in synaptic transmission, implicated in cognitive deficits. Moreover, less intensive studied AD candidates (STX2, HLA-F, HLA-C, RAB11FIP4, ARAP3, AP2A2, ATP2B4, ITPR2, and ATP2A3) are also involved in neurotransmission, providing new insights into the underlying mechanism. To our knowledge, this is the first study to generate knowledge-instructed GRNs that demonstrates an effective way of combining literature-based knowledge and data-driven analysis to identify lesser known candidates embedded in stable and robust functional patterns across disparate datasets.
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Affiliation(s)
- Shweta Bagewadi Kawalia
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for Information Technology, Bonn, Germany
| | - Tamara Raschka
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.,University of Applied Sciences Koblenz, RheinAhrCampus, Remagen, Germany
| | - Mufassra Naz
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for Information Technology, Bonn, Germany
| | | | - Philipp Senger
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany
| | - Martin Hofmann-Apitius
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for Information Technology, Bonn, Germany
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21
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Cheng L, Liu P, Leung K. SMILE: a novel procedure for subcellular module identification with localisation expansion. IET Syst Biol 2018. [PMID: 29533218 PMCID: PMC8687326 DOI: 10.1049/iet-syb.2017.0085] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Computational clustering methods help identify functional modules in protein–protein interaction (PPI) network, in which proteins participate in the same biological pathways or specific functions. Subcellular localisation is crucial for proteins to implement biological functions and each compartment accommodates specific portions of the protein interaction structure. However, the importance of protein subcellular localisation is often neglected in the studies of module identification. In this study, the authors propose a novel procedure, subcellular module identification with localisation expansion (SMILE), to identify super modules that consist of several subcellular modules performing specific biological functions among cell compartments. These super modules identified by SMILE are more functionally diverse and have been verified to be more associated with known protein complexes and biological pathways compared with the modules identified from the global PPI networks in both the compartmentalised PPI and InWeb_InBioMap datasets. The authors’ results reveal that subcellular localisation is a principal feature of functional modules and offers important guidance in detecting biologically meaningful results.
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Affiliation(s)
- Lixin Cheng
- Department of Computer Science & EngineeringChinese University of Hong KongMa Liu ShuiHong Kong
| | - Pengfei Liu
- Department of Computer Science & EngineeringChinese University of Hong KongMa Liu ShuiHong Kong
| | - Kwong‐Sak Leung
- Department of Computer Science & EngineeringChinese University of Hong KongMa Liu ShuiHong Kong
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22
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Moradifard S, Hoseinbeyki M, Ganji SM, Minuchehr Z. Analysis of microRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach. Sci Rep 2018; 8:4767. [PMID: 29555910 PMCID: PMC5859169 DOI: 10.1038/s41598-018-20959-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
Understanding the molecular mechanisms underlying Alzheimer’s disease (AD) is necessary for the diagnosis and treatment of this neurodegenerative disorder. It is therefore important to detect the most important genes and miRNAs, which are associated with molecular events, and studying their interactions for recognition of AD mechanisms. Here we focus on the genes and miRNAs expression profile, which we have detected the miRNA target genes involved in AD. These are the most quintessential to find the most important miRNA, to target genes and their important pathways. A total of 179 differentially expressed miRNAs (DEmiRs) and 1404 differentially expressed genes (DEGs) were obtained from a comprehensive meta-analysis. Also, regions specific genes with their molecular function in AD have been demonstrated. We then focused on miRNAs which regulated most genes in AD, alongside we analyzed their pathways. The miRNA-30a-5p and miRNA-335 elicited a major function in AD after analyzing the regulatory network, we showed they were the most regulatory miRNAs in the AD. In conclusion, we demonstrated the most important genes, miRNAs, miRNA-mRNA interactions and their related pathways in AD using Bioinformatics methods. Accordingly, our defined genes and miRNAs could be used for future molecular studies in the context of AD.
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Affiliation(s)
- Shirin Moradifard
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Moslem Hoseinbeyki
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | | | - Zarrin Minuchehr
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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23
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Barh D, García-Solano ME, Tiwari S, Bhattacharya A, Jain N, Torres-Moreno D, Ferri B, Silva A, Azevedo V, Ghosh P, Blum K, Conesa-Zamora P, Perry G. BARHL1 Is Downregulated in Alzheimer's Disease and May Regulate Cognitive Functions through ESR1 and Multiple Pathways. Genes (Basel) 2017; 8:genes8100245. [PMID: 28956815 PMCID: PMC5664095 DOI: 10.3390/genes8100245] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/13/2017] [Accepted: 09/20/2017] [Indexed: 12/22/2022] Open
Abstract
The Transcription factor BarH like homeobox 1 (BARHL1) is overexpressed in medulloblastoma and plays a role in neurogenesis. However, much about the BARHL1 regulatory networks and their functions in neurodegenerative and neoplastic disorders is not yet known. In this study, using a tissue microarray (TMA), we report for the first time that BARHL1 is downregulated in hormone-negative breast cancers and Alzheimer’s disease (AD). Furthermore, using an integrative bioinformatics approach and mining knockout mouse data, we show that: (i) BARHL1 and Estrogen Receptor 1 (ESR1) may constitute a network that regulates Neurotrophin 3 (NTF3)- and Brain Derived Neurotrophic Factor (BDNF)-mediated neurogenesis and neural survival; (ii) this is probably linked to AD pathways affecting aberrant post-translational modifications including SUMOylation and ubiquitination; (iii) the BARHL1-ESR1 network possibly regulates β-amyloid metabolism and memory; and (iv) hsa-mir-18a, having common key targets in the BARHL1-ESR1 network and AD pathway, may modulate neuron death, reduce β-amyloid processing and might also be involved in hearing and cognitive decline associated with AD. We have also hypothesized why estrogen replacement therapy improves AD condition. In addition, we have provided a feasible new mechanism to explain the abnormal function of mossy fibers and cerebellar granule cells related to memory and cognitive decline in AD apart from the Tau and amyloid pathogenesis through our BARHL1-ESR1 axis.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal 721172, India.
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
| | - María E García-Solano
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain.
- Catholic University of Murcia (UCAM), 30107 Murcia, Spain.
| | - Sandeep Tiwari
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal 721172, India.
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
| | - Antaripa Bhattacharya
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal 721172, India.
| | - Neha Jain
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal 721172, India.
| | - Daniel Torres-Moreno
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain.
- Catholic University of Murcia (UCAM), 30107 Murcia, Spain.
| | - Belén Ferri
- Department of Pathology, Virgen Arrixaca University Hospital (HUVA), Ctra. Madrid Cartagena sn, 30120 El Palmar, Spain.
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01-Guamá, Belém, PA 66075-110, Brazil.
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
| | - Preetam Ghosh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal 721172, India.
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Kenneth Blum
- Department of Psychiatry & McKnight Brain Institute, University of Florida College of Medicine, Gainesville, FL 32610, USA.
| | - Pablo Conesa-Zamora
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain.
- Catholic University of Murcia (UCAM), 30107 Murcia, Spain.
| | - George Perry
- UTSA Neurosciences Institute and Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA.
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
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24
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Soares CT, Trombone APF, Fachin LRV, Rosa PS, Ghidella CC, Ramalho RF, Pinilla MG, Carvalho AF, Carrara DN, Soares FA, Belone AFF. Differential Expression of MicroRNAs in Leprosy Skin Lesions. Front Immunol 2017; 8:1035. [PMID: 28970833 PMCID: PMC5609578 DOI: 10.3389/fimmu.2017.01035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 08/10/2017] [Indexed: 12/19/2022] Open
Abstract
Leprosy, a chronic infectious disease caused by Mycobacterium leprae, is a major public health problem in poor and developing countries of the Americas, Africa, and Asia. MicroRNAs (miRNAs), which are small non-coding RNAs (18–24 nucleotides), play an important role in regulating cell and tissue homeostasis through translational downregulation of messenger RNAs (mRNAs). Deregulation of miRNA expression is important for the pathogenesis of various neoplastic and non-neoplastic diseases and has been the focus of many publications; however, studies on the expression of miRNAs in leprosy are rare. Herein, an extensive evaluation of differentially expressed miRNAs was performed on leprosy skin lesions using microarrays. Leprosy patients, classified according to Ridley and Jopling’s classification or reactional states (R1 and R2), and healthy controls (HCs) were included. Punch biopsies were collected from the borders of leprosy lesions (10 tuberculoid, 10 borderline tuberculoid, 10 borderline borderline, 10 borderline lepromatous, 4 lepromatous, 14 R1, and 9 R2) and from 9 HCs. miRNA expression profiles were obtained using the Agilent Microarray platform with miRBase, which consists of 1,368 Homo sapiens (hsa)-miRNA candidates. TaqMan quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) was used to validate differentially expressed miRNAs. Sixty-four differentially expressed miRNAs, including 50 upregulated and 14 downregulated (fold change ≥2.0, p-value ≤ 0.05) were identified after comparing samples from patients to those of controls. Twenty differentially expressed miRNAs were identified exclusively in the reactional samples (14 type 1 and 6 type 2). Eight miRNAs were validated by RT-PCR, including seven upregulated (hsa-miR-142-3p, hsa-miR-142-5p, hsa-miR-146b-5p, hsa-miR-342-3p, hsa-miR-361-3p, hsa-miR-3653, and hsa-miR-484) and one downregulated (hsa-miR-1290). These miRNAs were differentially expressed in leprosy and several other diseases, especially those related to the immune response. Moreover, the integration of analysis of validated mi/mRNAs obtained from the same samples allowed target pairs opposite expression pattern of hsa-miRNA-142-3p and AKR1B10, hsa-miRNA-342-3p and FAM180b, and hsa-miRNA-484 and FASN. This study identified several miRNAs that might play an important role in the molecular pathogenesis of the disease. Moreover, these deregulated miRNAs and their respective signaling pathways might be useful as therapeutic markers, therapeutic targets, which could help in the development of drugs to treat leprosy.
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Affiliation(s)
- Cleverson T Soares
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima, São Paulo, Brazil
| | - Ana P F Trombone
- Department of Health Science, Universidade do Sagrado Coração, São Paulo, Brazil
| | - Luciana R V Fachin
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima, São Paulo, Brazil
| | - Patricia S Rosa
- Division of Research and Education, Instituto Lauro de Souza Lima, São Paulo, Brazil
| | - Cássio C Ghidella
- Ambulatory of Leprosy, Jardim Guanabara Health Center, Rondonópolis, Brazil
| | - Rodrigo F Ramalho
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Mabel G Pinilla
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, São Paulo, Brazil.,Department of Medical Technology, School of Medicine, University of Concepción, Concepción, Chile
| | - Alex F Carvalho
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, São Paulo, Brazil.,Department of Preventive Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Dirce N Carrara
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Fernando A Soares
- Department of Anatomic Pathology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Andrea F F Belone
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima, São Paulo, Brazil
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25
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Abstract
Medulloblastoma is the most common malignant brain tumor in children. SPARC (secreted protein acidic and rich in cysteine), a multicellular non-structural glycoprotein is known to be involved in multiple processes in various cancers. Previously, we reported that SPARC expression significantly impairs medulloblastoma tumor growth in vitro and in vivo and also alters chemo sensitivity. MicroRNAs are a class of post-transcriptional gene regulators with critical functions in tumor progression. In addition, microRNA (miRNA) expression changes are also involved in chemo-resistance. Herein, we assessed microRNA (miRNA) profiling to identify the functional network and biological pathways altered in SPARC-overexpressed medulloblastoma cells. A total of 27 differentially expressed miRNAs were identified between the control and SPARC-overexpressed samples. Potential messenger RNA (mRNA) targets of the differentially expressed miRNA were identified using Ingenuity Pathway Analysis (IPA). Network-based functional analyses were performed on the available human protein interaction and miRNA-gene association data to highlight versatile miRNAs among the significantly deregulated miRNAs using the IPA, and the biological pathway analysis using the PANTHER web-based tool. We have identified six miRNAs (miR-125b1*, miR-146a-5p, miR-181a-5p, miR-204-5p, miR-219-5p and miR-509-3p) that are associated with SPARC sensitivity by comparison of miRNA expression patterns from the SPARC treated cells with the control cells. Furthermore, pathway enrichment analysis outline that these six microRNAs mainly belong to biological processes related to cancer related signaling pathways. Collectively, these studies have the potential to indicate novel biomarkers for treatment response and can also be applied to develop novel therapeutic treatment for medulloblastoma.
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26
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Wang P, Guo Q, Gao Y, Zhi H, Zhang Y, Liu Y, Zhang J, Yue M, Guo M, Ning S, Zhang G, Li X. Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data. Oncotarget 2017; 8:4642-4655. [PMID: 27992375 PMCID: PMC5354861 DOI: 10.18632/oncotarget.13964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 12/07/2016] [Indexed: 02/01/2023] Open
Abstract
Although several computational models that predict disease-associated lncRNAs (long non-coding RNAs) exist, only a limited number of disease-associated lncRNAs are known. In this study, we mapped lncRNAs to their functional genomics context using competing endogenous RNAs (ceRNAs) theory. Based on the criteria that similar lncRNAs are likely involved in similar diseases, we proposed a disease lncRNA prioritization method, DisLncPri, to identify novel disease-lncRNA associations. Using a leave-one-out cross validation (LOOCV) strategy, DisLncPri achieved reliable area under curve (AUC) values of 0.89 and 0.87 for the LncRNADisease and Lnc2Cancer datasets that further improved to 0.90 and 0.89 by integrating a multiple rank fusion strategy. We found that DisLncPri had the highest rank enrichment score and AUC value in comparison to several other methods for case studies of alzheimer's disease, ovarian cancer, pancreatic cancer and gastric cancer. Several novel lncRNAs in the top ranks of these diseases were found to be newly verified by relevant databases or reported in recent studies. Prioritization of lncRNAs from a microarray (GSE53622) of oesophageal cancer patients highlighted ENSG00000226029 (top 2), a previously unidentified lncRNA as a potential prognostic biomarker. Our analysis thus indicates that DisLncPri is an excellent tool for identifying lncRNAs that could be novel biomarkers and therapeutic targets in a variety of human diseases.
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Affiliation(s)
- Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qiuyan Guo
- The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yue Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jizhou Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ming Yue
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Maoni Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, China
| | - Guangmei Zhang
- The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, China
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27
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Liang G, Li Y, Feng W, Wang X, Jing A, Li J, Ma K. Polyethyleneimine-coated quantum dots for miRNA delivery and its enhanced suppression in HepG2 cells. Int J Nanomedicine 2016; 11:6079-6088. [PMID: 27895481 PMCID: PMC5117883 DOI: 10.2147/ijn.s120828] [Citation(s) in RCA: 16] [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: 12/15/2022] Open
Abstract
Quantum dots (QDs) have been intensively investigated for bioimaging, drug delivery, and labeling probes because of their unique optical properties. In this study, CdSe/ZnS QDs-based nonviral vectors with the dual functions of delivering miR-26a plasmid and bioimaging were formulated by capping the surface of CdSe/ZnS QDs with polyethyleneimine (PEI). The PEI-coated QDs were capable of condensing miR-26a expression vector into nanocomplexes that can emit strong red luminescence when loaded with CdSe/ZnS QDs. Further results showed that PEI-modified nanoparticles (NPs) could transfect miR-26a plasmid into HepG2 cells in vitro. Meanwhile, imaging of living cells could be achieved based on the CdSe/ZnS QDs. Further study suggested that miR-26a transfection up-regulated miR-26a expression, induced cycle arrest, and triggered proliferation inhibition in HepG2 cells. The results indicated that PEI-coated QD NPs possess the capability of bioimaging and gene delivery and could be a promising vehicle with the engineering of QD NPs for gene therapy in the future.
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Affiliation(s)
- Gaofeng Liang
- Department of Biomedical Engineering, School of Medical Technology & Engineering
| | - Yang Li
- Department of Biomedical Engineering, School of Medical Technology & Engineering
| | - Wenpo Feng
- Department of Biomedical Engineering, School of Medical Technology & Engineering
| | - Xinshuai Wang
- Department of Oncology, The First Affiliated Hospital, Henan University of Science & Technology, Luoyang, People’s Republic of China
| | - Aihua Jing
- Department of Biomedical Engineering, School of Medical Technology & Engineering
| | - Jinghua Li
- Department of Biomedical Engineering, School of Medical Technology & Engineering
| | - Kaiwang Ma
- Department of Biomedical Engineering, School of Medical Technology & Engineering
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28
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Hu YB, Zou Y, Huang Y, Zhang YF, Lourenco GF, Chen SD, Halliday GM, Wang G, Ren RJ. ROCK1 Is Associated with Alzheimer's Disease-Specific Plaques, as well as Enhances Autophagosome Formation But not Autophagic Aβ Clearance. Front Cell Neurosci 2016; 10:253. [PMID: 27853422 PMCID: PMC5089992 DOI: 10.3389/fncel.2016.00253] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/14/2016] [Indexed: 01/01/2023] Open
Abstract
Alzheimer's disease (AD) is the most prevalent form of late-life dementia in the population, characterized by amyloid plaque formation and increased tau deposition, which is modulated by Rho-associated coiled-coil kinase 1 (ROCK1). In this study, we further analyze whether ROCK1 regulates the metabolism of amyloid precursor protein (APP). We show that ROCK1 is colocalized with mature amyloid-β (Aβ) plaques in patients with AD, in that ROCK1 enhances the amyloidogenic pathway, and that ROCK1 mediated autophagy enhances the intracellular buildup of Aβ in a cell model of AD (confirmed by increased ROCK1 and decreased Beclin 1 protein levels, with neuronal autophagosome accumulation in prefrontal cortex of AD APP/PS1 mouse model). In vitro over-expression of ROCK1 leads to a decrease in Aβ secretion and an increase in the expression of autophagy-related molecules. ROCK1 interacts with Beclin1, an autophagy initiator, and enhances the intracellular accumulation of Aβ. Reciprocally, overexpression of APP/Aβ promotes ROCK1 expression. Our data suggest ROCK1 participates in regulating Aβ secretion, APP shedding and autophagosome accumulation, and that ROCK1, rather than other kinases, is more likely to be a targetable enzyme for AD therapy.
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Affiliation(s)
- Yong-Bo Hu
- Department of Neurology and Neuroscience Institute, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Yang Zou
- Department of Neurology and Neuroscience Institute, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Yue Huang
- Neuroscience Research Australia and Faculty of Medicine, University of New South Wales (UNSW) Sydney, NSW, Australia
| | - Yong-Fang Zhang
- Research Laboratory of Cell Regulation, School of Medicine, Shanghai Jiao Tong University Shanghai, China
| | - Guinevere F Lourenco
- Neuroscience Research Australia and Faculty of Medicine, University of New South Wales (UNSW) Sydney, NSW, Australia
| | - Sheng-Di Chen
- Department of Neurology and Neuroscience Institute, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Glenda M Halliday
- Neuroscience Research Australia and Faculty of Medicine, University of New South Wales (UNSW) Sydney, NSW, Australia
| | - Gang Wang
- Department of Neurology and Neuroscience Institute, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Ru-Jing Ren
- Department of Neurology and Neuroscience Institute, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai, China
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29
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Ma Z, Liu T, Huang W, Liu H, Zhang HM, Li Q, Chen Z, Guo AY. MicroRNA regulatory pathway analysis identifies miR-142-5p as a negative regulator of TGF-β pathway via targeting SMAD3. Oncotarget 2016; 7:71504-71513. [PMID: 27683030 PMCID: PMC5342096 DOI: 10.18632/oncotarget.12229] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs with functions of posttranscriptional regulation. The abnormally expressed miRNAs have been shown to be crucial contributors and may serve as biomarkers in many diseases. However, determining the biological function of miRNAs is an ongoing challenge. By combining miRNA targets prediction, miRNA and mRNA expression profiles in TCGA cancers, and pathway data, we performed a miRNA-pathway regulation inference by Fisher's exact test for enrichment analysis. Then we constructed a database to show the cancer related miRNA-pathway regulatory network (http://bioinfo.life.hust.edu.cn/miR_path). As one of the miRNAs targeting many cancer related pathways, miR-142-5p potentially regulates the maximum number of genes in TGF-β signaling pathway. We experimentally confirmed that miR-142-5p directly targeted and suppressed SMAD3, a key component in TGF-β signaling. Ectopic overexpression of miR-142-5p significantly promoted tumor cell proliferation and inhibited apoptosis, while silencing of miR-142-5p inhibited the tumor cell proliferation and promoted apoptosis in vitro. These findings indicate that miR-142-5p plays as a negative regulator in TGF-β pathway by targeting SMAD3 and suppresses TGF-β-induced growth inhibition in cancer cells. Our study proved the feasibility of miRNA regulatory pathway analysis and shed light on combining bioinformatics with experiments in the research of complex diseases.
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Affiliation(s)
- Zhaowu Ma
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.,Laboratory of Neuronal Network and Brain Diseases Modulation, School of Medicine, Yangtze University, Jingzhou, Hubei, 434023, China
| | - Teng Liu
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wei Huang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hui Liu
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hong-Mei Zhang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qiubai Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhichao Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - An-Yuan Guo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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30
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Derghal A, Djelloul M, Trouslard J, Mounien L. An Emerging Role of micro-RNA in the Effect of the Endocrine Disruptors. Front Neurosci 2016; 10:318. [PMID: 27445682 PMCID: PMC4928026 DOI: 10.3389/fnins.2016.00318] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/23/2016] [Indexed: 12/15/2022] Open
Abstract
Endocrine-disrupting chemicals (EDCs) are diverse natural and synthetic chemicals that may alter various mechanisms of the endocrine system and produce adverse developmental, reproductive, metabolic, and neurological effects in both humans and wildlife. Research on EDCs has revealed that they use a variety of both nuclear receptor-mediated and non-receptor-mediated mechanisms to modulate different components of the endocrine system. The molecular mechanisms underlying the effects of EDCs are still under investigation. Interestingly, some of the effects of EDCs have been observed to pass on to subsequent unexposed generations, which can be explained by the gametic transmission of deregulated epigenetic marks. Epigenetics is the study of heritable changes in gene expression that occur without a change in the DNA sequence. Epigenetic mechanisms, including histone modifications, DNA methylation, and specific micro-RNAs (miRNAs) expression, have been proposed to mediate transgenerational transmission and can be triggered by environmental factors. MiRNAs are short non-coding RNA molecules that post-transcriptionally repress the expression of genes by binding to 3′-untranslated regions of the target mRNAs. Given that there is mounting evidence that miRNAs are regulated by hormones, then clearly it is important to investigate the potential for environmental EDCs to deregulate miRNA expression and action.
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Affiliation(s)
- Adel Derghal
- Aix Marseille University, PPSN Marseille, France
| | - Mehdi Djelloul
- Aix Marseille University, PPSNMarseille, France; Department of Cell and Molecular Biology, Karolinska InstituteStockholm, Sweden
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31
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MicroRNA-146a suppresses ROCK1 allowing hyperphosphorylation of tau in Alzheimer's disease. Sci Rep 2016; 6:26697. [PMID: 27221467 PMCID: PMC4879631 DOI: 10.1038/srep26697] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/06/2016] [Indexed: 01/01/2023] Open
Abstract
MicroRNA-146a is upregulated in the brains of patients with Alzheimer’s disease (AD). Here, we show that the rho-associated, coiled-coil containing protein kinase 1 (ROCK1) is a target of microRNA-146a in neural cells. Knockdown of ROCK1 mimicked the effects of microRNA-146a overexpression and induced abnormal tau phosphorylation, which was associated with inhibition of phosphorylation of the phosphatase and tensin homolog (PTEN). The ROCK1/PTEN pathway has been implicated in the neuronal hyperphosphorylation of tau that occurs in AD. To determine the function of ROCK1 in AD, brain tissue from 17 donors with low, intermediate or high probability of AD pathology were obtained and analyzed. Data showed that ROCK1 protein levels were reduced and ROCK1 colocalised with hyperphosphorylated tau in early neurofibrillary tangles. Intra-hippocampal delivery of a microRNA-146a specific inhibitor (antagomir) into 5xFAD mice showed enhanced hippocampal levels of ROCK1 protein and repressed tau hyperphosphorylation, partly restoring memory function in the 5xFAD mice. Our in vitro and in vivo results confirm that dysregulation of microRNA-146a biogenesis contributes to tau hyperphosphorylation and AD pathogenesis, and inhibition of this microRNA could be a viable novel in vivo therapy for AD.
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32
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Hu YB, Li CB, Song N, Zou Y, Chen SD, Ren RJ, Wang G. Diagnostic Value of microRNA for Alzheimer's Disease: A Systematic Review and Meta-Analysis. Front Aging Neurosci 2016; 8:13. [PMID: 26903857 PMCID: PMC4746262 DOI: 10.3389/fnagi.2016.00013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/15/2016] [Indexed: 01/12/2023] Open
Abstract
Sound evidence indicates that microRNAs (miRNAs) are aberrantly expressed in Alzheimer's disease (AD) patients. We performed a systematic review and meta-analysis to investigate the role of miRNA in AD pathogenesis and their clinical diagnostic value; a systematic review of literature and meta-analysis of clinical trials were performed. In the systematic review, 236 papers were included, and we reviewed the dysregulated miRNA expression in different parts of AD patients in order to identify the relationship between aberrantly expressed miRNAs and AD pathology. In the subsequent meta-analysis, seven studies were statistically analyzed with the following results: pooled sensitivity 0.86 (95%CI 0.79-0.90), pooled specificity 0.87 (95%CI 0.72-0.95), diagnostic odds ratio (28.29), and the area under the curve (0.87). In conclusion, our review indicated that aberrant expression of various miRNAs plays an important role in the pathological process of AD, and statistical analysis of quantitative studies reveal the potential value of specific miRNAs in the diagnosis of AD.
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Affiliation(s)
- Yong-Bo Hu
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Chun-Bo Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Ning Song
- St George Hospital , Sydney, NSW , Australia
| | - Yang Zou
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Sheng-Di Chen
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Ru-Jing Ren
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Gang Wang
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
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33
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Bai W, Yang W, Wang W, Wang Y, Liu C, Jiang Q, Hua J, Liao M. GED: a manually curated comprehensive resource for epigenetic modification of gametogenesis. Brief Bioinform 2016; 18:98-104. [DOI: 10.1093/bib/bbw007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/29/2015] [Indexed: 12/13/2022] Open
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34
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Jiang W, Jia P, Hutchinson KE, Johnson DB, Sosman JA, Zhao Z. Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach. Oncotarget 2016; 6:2496-508. [PMID: 25537510 PMCID: PMC4385866 DOI: 10.18632/oncotarget.2954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 12/09/2015] [Indexed: 12/25/2022] Open
Abstract
Therapies such as BRAF inhibitors have become standard treatment for melanoma patients whose tumors harbor activating BRAFV600 mutations. However, analogous therapies for inhibiting NRAS mutant signaling have not yet been well established. In this study, we performed an integrative analysis of DNA methylation, gene expression, and microRNA expression data to identify potential regulatory pathways associated with the most common driver mutations in NRAS (Q61K/L/R) through comparison of NRASQ61-mutated melanomas with pan-negative melanomas. Surprisingly, we found dominant hypomethylation (98.03%) in NRASQ61-mutated melanomas. We identified 1,150 and 49 differentially expressed genes and microRNAs, respectively. Integrated functional analyses of alterations in all three data types revealed important signaling pathways associated with NRASQ61 mutations, such as the MAPK pathway, as well as other novel cellular processes, such as axon guidance. Further analysis of the relationship between DNA methylation and gene expression changes revealed 9 hypermethylated and down-regulated genes and 112 hypomethylated and up-regulated genes in NRASQ61 melanomas. Finally, we identified 52 downstream regulatory cascades of three hypomethylated and up-regulated genes (PDGFD, ZEB1, and THRB). Collectively, our observation of predominant gene hypomethylation in NRASQ61 melanomas and the identification of NRASQ61-linked pathways will be useful for the development of targeted therapies against melanomas harboring NRASQ61 mutations.
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Affiliation(s)
- Wei Jiang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Peilin Jia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Katherine E Hutchinson
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Douglas B Johnson
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jeffrey A Sosman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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35
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MicroRNA (miRNA) Signaling in the Human CNS in Sporadic Alzheimer's Disease (AD)-Novel and Unique Pathological Features. Int J Mol Sci 2015; 16:30105-16. [PMID: 26694372 PMCID: PMC4691165 DOI: 10.3390/ijms161226223] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/12/2015] [Accepted: 12/15/2015] [Indexed: 02/07/2023] Open
Abstract
Of the approximately ~2.65 × 103 mature microRNAs (miRNAs) so far identified in Homo sapiens, only a surprisingly small but select subset—about 35–40—are highly abundant in the human central nervous system (CNS). This fact alone underscores the extremely high selection pressure for the human CNS to utilize only specific ribonucleotide sequences contained within these single-stranded non-coding RNAs (ncRNAs) for productive miRNA–mRNA interactions and the down-regulation of gene expression. In this article we will: (i) consolidate some of our still evolving ideas concerning the role of miRNAs in the CNS in normal aging and in health, and in sporadic Alzheimer’s disease (AD) and related forms of chronic neurodegeneration; and (ii) highlight certain aspects of the most current work in this research field, with particular emphasis on the findings from our lab of a small pathogenic family of six inducible, pro-inflammatory, NF-κB-regulated miRNAs including miRNA-7, miRNA-9, miRNA-34a, miRNA-125b, miRNA-146a and miRNA-155. This group of six CNS-abundant miRNAs significantly up-regulated in sporadic AD are emerging as what appear to be key mechanistic contributors to the sporadic AD process and can explain much of the neuropathology of this common, age-related inflammatory neurodegeneration of the human CNS.
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Hill JM, Pogue AI, Lukiw WJ. Pathogenic microRNAs Common to Brain and Retinal Degeneration; Recent Observations in Alzheimer's Disease and Age-Related Macular Degeneration. Front Neurol 2015; 6:232. [PMID: 26579072 PMCID: PMC4630578 DOI: 10.3389/fneur.2015.00232] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 10/20/2015] [Indexed: 12/30/2022] Open
Affiliation(s)
- James M Hill
- Department of Ophthalmology, LSU Neuroscience Center, School of Medicine, Louisiana State University Health Sciences Center , New Orleans, LA , USA
| | | | - Walter J Lukiw
- Department of Ophthalmology, LSU Neuroscience Center, School of Medicine, Louisiana State University Health Sciences Center , New Orleans, LA , USA ; Alchem Biotek , Toronto, ON , Canada ; Neuroscience Center and Department of Neurology, LSU Neuroscience Center, School of Medicine, Louisiana State University Health Sciences Center , New Orleans, LA , USA
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Yang Y, Zhang P, Zhao Y, Yang J, Jiang G, Fan J. Decreased MicroRNA-26a expression causes cisplatin resistance in human non-small cell lung cancer. Cancer Biol Ther 2015; 17:515-25. [PMID: 26492332 DOI: 10.1080/15384047.2015.1095405] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Lung cancer is the most common cancer that is caused by perturbation of regulatory pathways rather than dysfunction of a single gene. Cisplatin (CDDP; cis-diamminedichloroplatinum II) is the first member of a class of platinum-containing anti-cancer medication, which binds to DNA and triggers apoptosis. CDDP-based chemotherapy is used to treat various types of cancers. However, the efficacy of CDDP in the treatment of non-small-cell lung cancer (NSCLC) is limited by acquired drug resistance. MicroRNAs have recently emerged as key regulators of cancers, and miR-26a is one of down-regulated miRNAs in A549/CDDPres cell line. This study aimed to investigate the role of miR-26a in CDDP resistance in NSCLC as well as the underlying mechanisms. METHODS In this study, we analyzed expressional profiles of CDDP resistance-related mRNA, miRNA, and transcription factors (TF) that regulate miRNA expression in NSCLC. A549 cells were treated with CDDP, miR-26a mimic, or miR-26a inhibitor, and followed by biological analysis including drug sensitivity assay, colony formation assay, terminal-deoxynucleoitidyl Transferase Mediated Nick End Labeling (TUNEL) assay, and cell cycle analysis. Luciferase assay was used to determine the target of miR-26a. The regulation of miR-26a in Akt pathway was measured by western blot. RESULTS High mobility group A (HMGA) 2 was identified as the target of miR-26a. Overexpression of miR-26a in A549 cells inhibited G1-S transition, increased cell death in response to CDDP treatment, and decreased the colony formation of A549 cells. MiR-26a significantly decreased the expression of E2F1, diminished Akt phosphorylation, and downregulated Bcl2 expression. Cell growth was suppressed by inhibiting HMGA2-mediated E2F1-Akt pathway. CONCLUSION MiR-26a is responsible for A549 cell sensitivity in the treatment of CDDP through regulating HMGA2-mediated E2F1-Akt pathway.
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Affiliation(s)
- Yong Yang
- a Department of Thoracic Surgery , Shanghai Pulmonary Hospital, Tongji University School of Medicine , Shanghai , China
| | - Peng Zhang
- a Department of Thoracic Surgery , Shanghai Pulmonary Hospital, Tongji University School of Medicine , Shanghai , China
| | - Yanfeng Zhao
- a Department of Thoracic Surgery , Shanghai Pulmonary Hospital, Tongji University School of Medicine , Shanghai , China
| | - Jie Yang
- a Department of Thoracic Surgery , Shanghai Pulmonary Hospital, Tongji University School of Medicine , Shanghai , China
| | - Gening Jiang
- a Department of Thoracic Surgery , Shanghai Pulmonary Hospital, Tongji University School of Medicine , Shanghai , China
| | - Jie Fan
- a Department of Thoracic Surgery , Shanghai Pulmonary Hospital, Tongji University School of Medicine , Shanghai , China.,b Department of Surgery , University of Pittsburgh School of Medicine , Pittsburgh , PA , USA
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Cardoso AL, Guedes JR, de Lima MCP. Role of microRNAs in the regulation of innate immune cells under neuroinflammatory conditions. Curr Opin Pharmacol 2015; 26:1-9. [PMID: 26410391 DOI: 10.1016/j.coph.2015.09.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 01/18/2023]
Abstract
MiRNAs are short, evolutionary conserved noncoding RNA molecules with the ability to control the magnitude of inflammation. The immunosuppressive nature of the brain is sustained by miRNA-dependent regulation of microglial cells, which become activated under neuroinflammatory conditions, such as brain injury and neurodegeneration. The pro-inflammatory and suppressive role of the most studied neuroimmune miRNAs, miR-155 and miR-146a, has been recently challenged. Although the molecular targets of these miRNAs remain unchanged across brain diseases, different kinetics of miRNA expression and degradation can produce different immune outcomes and change microglia phenotypes. Here, we discuss current knowledge regarding the implications of disruption of miRNA networks in neuroinflammation and in the pathophysiology of acute and chronic CNS diseases.
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Affiliation(s)
- Ana L Cardoso
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Joana R Guedes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Doctoral Programme in Experimental Biology and Biomedicine, CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Maria C Pedroso de Lima
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Coimbra, Portugal.
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Zhang Y, Liu D, Wang L, Wang S, Yu X, Dai E, Liu X, Luo S, Jiang W. Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease. J Mol Med (Berl) 2015. [PMID: 26208504 DOI: 10.1007/s00109-015-1315-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
UNLABELLED Coronary artery disease (CAD) is the most common type of heart disease. However, the molecular mechanisms of CAD remain elusive. Regulatory pathways are known to play crucial roles in many pathogenic processes. Thus, inferring risk regulatory pathways is an important step toward elucidating the mechanisms underlying CAD. With advances in high-throughput data, we developed an integrated systems approach to identify CAD risk regulatory pathways and key regulators. Firstly, a CAD-related core subnetwork was identified from a curated transcription factor (TF) and microRNA (miRNA) regulatory network based on a random walk algorithm. Secondly, candidate risk regulatory pathways were extracted from the subnetwork by applying a breadth-first search (BFS) algorithm. Then, risk regulatory pathways were prioritized based on multiple CAD-associated data sources. Finally, we also proposed a new measure to prioritize upstream regulators. We inferred that phosphatase and tensin homolog (PTEN) may be a key regulator in the dysregulation of risk regulatory pathways. This study takes a closer step than the identification of disease subnetworks or modules. From the risk regulatory pathways, we could understand the flow of regulatory information in the initiation and progression of the disease. Our approach helps to uncover its potential etiology. KEY MESSAGES We developed an integrated systems approach to identify risk regulatory pathways. We proposed a new measure to prioritize the key regulators in CAD. PTEN may be a key regulator in dysregulation of the risk regulatory pathways.
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Affiliation(s)
- Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Dianming Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lihong Wang
- Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, China
| | - Shuyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Enyu Dai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xinyi Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shanshun Luo
- Department of Gerontology, The First Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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Li X, Long J, He T, Belshaw R, Scott J. Integrated genomic approaches identify major pathways and upstream regulators in late onset Alzheimer's disease. Sci Rep 2015. [PMID: 26202100 PMCID: PMC4511863 DOI: 10.1038/srep12393] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Previous studies have evaluated gene expression in Alzheimer’s disease (AD) brains to identify mechanistic processes, but have been limited by the size of the datasets studied. Here we have implemented a novel meta-analysis approach to identify differentially expressed genes (DEGs) in published datasets comprising 450 late onset AD (LOAD) brains and 212 controls. We found 3124 DEGs, many of which were highly correlated with Braak stage and cerebral atrophy. Pathway Analysis revealed the most perturbed pathways to be (a) nitric oxide and reactive oxygen species in macrophages (NOROS), (b) NFkB and (c) mitochondrial dysfunction. NOROS was also up-regulated, and mitochondrial dysfunction down-regulated, in healthy ageing subjects. Upstream regulator analysis predicted the TLR4 ligands, STAT3 and NFKBIA, for activated pathways and RICTOR for mitochondrial genes. Protein-protein interaction network analysis emphasised the role of NFKB; identified a key interaction of CLU with complement; and linked TYROBP, TREM2 and DOK3 to modulation of LPS signalling through TLR4 and to phosphatidylinositol metabolism. We suggest that NEUROD6, ZCCHC17, PPEF1 and MANBAL are potentially implicated in LOAD, with predicted links to calcium signalling and protein mannosylation. Our study demonstrates a highly injurious combination of TLR4-mediated NFKB signalling, NOROS inflammatory pathway activation, and mitochondrial dysfunction in LOAD.
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Affiliation(s)
- Xinzhong Li
- Centre for Biostatistics, Bioinformatics and Biomarkers, Plymouth University, Plymouth UK
| | - Jintao Long
- Centre for Biostatistics, Bioinformatics and Biomarkers, Plymouth University, Plymouth UK
| | - Taigang He
- Institute of Cardiovascular and Cell Sciences, St. George University, London UK
| | - Robert Belshaw
- School of Biomedicine and Healthcare Sciences, Plymouth University, Plymouth UK
| | - James Scott
- National Heart and Lung Institute, Imperial College, London UK
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Unraveling novel TF-miRNA regulatory crosstalk in metastasis of Soft Tissue Sarcoma. Sci Rep 2015; 5:9742. [PMID: 25984907 PMCID: PMC4434893 DOI: 10.1038/srep09742] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/13/2015] [Indexed: 12/14/2022] Open
Abstract
Cancer metastasis is a disease of extreme clinical relevance, as it is responsible for more than 90% of cancer-associated mortality. The molecular mechanism and critical regulators involved in this complex multi-stage process of metastasis is poorly deciphered in soft tissue sarcomas (STS), a heterogeneous group of rare tumors with high metastatic potential. Therefore, we aimed at identifying miRNA and transcription factor (TF) regulatory networks and paths in STS metastasis. We integrated mRNA and miRNA expression profiles with curated regulations (TF→gene, TF→miRNA, miRNA→gene) from different databases and constructed a potentially active regulatory sub-network in STS metastasis. From functional and topological analysis, we found nine novel regulators of Notch signaling sub-network which are conjectured to play critical role in metastasis of STS. This illustrated that the sub-network is promising for identification of critical regulators. Further analysis deploying our developed tool ‘RiNAcyc’ and computing coverage ratio of known STS associated genes and miRNAs identified a 15 node active path. This potential path highlights the crucial role of BMP2, hsa-miR-24, AP2 and MYC as the up-stream regulators of the path and hsa-miR-215 and TYMS as potential indicator of chemotherapeutic benefit in STS metastasis.
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Wang S, Li W, Lian B, Liu X, Zhang Y, Dai E, Yu X, Meng F, Jiang W, Li X. TMREC: A Database of Transcription Factor and MiRNA Regulatory Cascades in Human Diseases. PLoS One 2015; 10:e0125222. [PMID: 25932650 PMCID: PMC4416930 DOI: 10.1371/journal.pone.0125222] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 03/22/2015] [Indexed: 11/18/2022] Open
Abstract
Over the past decades, studies have reported that the combinatorial regulation of transcription factors (TFs) and microRNAs (miRNAs) is essential for the appropriate execution of biological events and developmental processes. Dysregulations of these regulators often cause diseases. However, there are no available resources on the regulatory cascades of TFs and miRNAs in the context of human diseases. To fulfill this vacancy, we established the TMREC database in this study. First, we integrated curated transcriptional and post-transcriptional regulations to construct the TF and miRNA regulatory network. Next, we identified all linear paths using the Breadth First Search traversal method. Finally, we used known disease-related genes and miRNAs to measure the strength of association between cascades and diseases. Currently, TMREC consists of 74,248 cascades and 25,194 cascade clusters, involving in 412 TFs, 266 miRNAs and 545 diseases. With the expanding of experimental support regulation data, we will regularly update the database. TMREC aims to help experimental biologists to comprehensively analyse gene expression regulation, to understand the aetiology and to predict novel therapeutic targets.TMREC is freely available at http://bioinfo.hrbmu.edu.cn/TMREC/.
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Affiliation(s)
- Shuyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Wei Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
- EpiRNA Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Baofeng Lian
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
- Shanghai Center for Bioinformation Technology, Shanghai, 201203, P. R. China
| | - Xinyi Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Enyu Dai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Fanlin Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
- * E-mail: (XL); (WJ)
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
- * E-mail: (XL); (WJ)
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Vrijens K, Bollati V, Nawrot TS. MicroRNAs as potential signatures of environmental exposure or effect: a systematic review. ENVIRONMENTAL HEALTH PERSPECTIVES 2015; 123:399-411. [PMID: 25616258 PMCID: PMC4421768 DOI: 10.1289/ehp.1408459] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 01/14/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND The exposome encompasses all life-course environmental exposures from the prenatal period onward that influence health. MicroRNAs (miRNAs) are interesting entities within this concept as markers and causation of disease. MicroRNAs are short oligonucleotide sequences that can interact with several mRNA targets. OBJECTIVES We reviewed the current state of the field on the potential of using miRNAs as biomarkers for environmental exposure. We investigated miRNA signatures in response to all types of environmental exposure to which a human can be exposed, including cigarette smoke, air pollution, nanoparticles, and diverse chemicals; and we examined the health conditions for which the identified miRNAs have been reported (i.e., cardiovascular disease, cancer, and diabetes). METHODS We searched the PubMed and ScienceDirect databases to identify relevant studies. RESULTS For all exposures incorporated in this review, 27 miRNAs were differentially expressed in at least two independent studies. miRNAs that had expression alterations associated with smoking observed in multiple studies are miR-21, miR-34b, miR-125b, miR-146a, miR-223, and miR-340; and those miRNAs that were observed in multiple air pollution studies are miR-9, miR-10b, miR-21, miR-128, miR-143, miR-155, miR-222, miR-223, and miR-338. We found little overlap among in vitro, in vivo, and human studies between miRNAs and exposure. Here, we report on disease associations for those miRNAs identified in multiple studies on exposure. CONCLUSIONS miRNA changes may be sensitive indicators of the effects of acute and chronic environmental exposure. Therefore, miRNAs are valuable novel biomarkers for exposure. Further studies should elucidate the role of the mediation effect of miRNA between exposures and effect through all stages of life to provide a more accurate assessment of the consequences of miRNA changes.
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Affiliation(s)
- Karen Vrijens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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44
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Liang C, Li Y, Luo J, Zhang Z. A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human. Bioinformatics 2015; 31:2348-55. [DOI: 10.1093/bioinformatics/btv159] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/13/2015] [Indexed: 01/23/2023] Open
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Zhang XM, Guo L, Chi MH, Sun HM, Chen XW. Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation. BMC Bioinformatics 2015; 16:76. [PMID: 25887648 PMCID: PMC4355475 DOI: 10.1186/s12859-015-0512-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/24/2015] [Indexed: 12/21/2022] Open
Abstract
Background Obesity-induced chronic inflammation plays a fundamental role in the pathogenesis of metabolic syndrome (MS). Recently, a growing body of evidence supports that miRNAs are largely dysregulated in obesity and that specific miRNAs regulate obesity-associated inflammation. We applied an approach aiming to identify active miRNA-TF-gene regulatory pathways in obesity. Firstly, we detected differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) from mRNA and miRNA expression profiles, respectively. Secondly, by mapping the DEGs and DEmiRs to the curated miRNA-TF-gene regulatory network as active seed nodes and connect them with their immediate neighbors, we obtained the potential active miRNA-TF-gene regulatory subnetwork in obesity. Thirdly, using a Breadth-First-Search (BFS) algorithm, we identified potential active miRNA-TF-gene regulatory pathways in obesity. Finally, through the hypergeometric test, we identified the active miRNA-TF-gene regulatory pathways that were significantly related to obesity. Results The potential active pathways with FDR < 0.0005 were considered to be the active miRNA-TF regulatory pathways in obesity. The union of the active pathways is visualized and identical nodes of the active pathways were merged. Conclusions We identified 23 active miRNA-TF-gene regulatory pathways that were significantly related to obesity-related inflammation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0512-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xi-Mei Zhang
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, PR China.
| | - Lin Guo
- Department of Endocrinology and Metabolism, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, PR China.
| | - Mei-Hua Chi
- Teaching Experiment Center of Morphology, Harbin Medical University, Harbin, 150081, PR China.
| | - Hong-Mei Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China.
| | - Xiao-Wen Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China.
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Alaimo S, Giugno R, Pulvirenti A. ncPred: ncRNA-Disease Association Prediction through Tripartite Network-Based Inference. Front Bioeng Biotechnol 2014; 2:71. [PMID: 25566534 PMCID: PMC4264506 DOI: 10.3389/fbioe.2014.00071] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/25/2014] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Over the past few years, experimental evidence has highlighted the role of microRNAs to human diseases. miRNAs are critical for the regulation of cellular processes, and, therefore, their aberration can be among the triggering causes of pathological phenomena. They are just one member of the large class of non-coding RNAs, which include transcribed ultra-conserved regions (T-UCRs), small nucleolar RNAs (snoRNAs), PIWI-interacting RNAs (piRNAs), large intergenic non-coding RNAs (lincRNAs) and, the heterogeneous group of long non-coding RNAs (lncRNAs). Their associations with diseases are few in number, and their reliability is questionable. In literature, there is only one recent method proposed by Yang et al. (2014) to predict lncRNA-disease associations. This technique, however, lacks in prediction quality. All these elements entail the need to investigate new bioinformatics tools for the prediction of high quality ncRNA-disease associations. Here, we propose a method called ncPred for the inference of novel ncRNA-disease association based on recommendation technique. We represent our knowledge through a tripartite network, whose nodes are ncRNAs, targets, or diseases. Interactions in such a network associate each ncRNA with a disease through its targets. Our algorithm, starting from such a network, computes weights between each ncRNA-disease pair using a multi-level resource transfer technique that at each step takes into account the resource transferred in the previous one. RESULTS The results of our experimental analysis show that our approach is able to predict more biologically significant associations with respect to those obtained by Yang et al. (2014), yielding an improvement in terms of the average area under the ROC curve (AUC). These results prove the ability of our approach to predict biologically significant associations, which could lead to a better understanding of the molecular processes involved in complex diseases. AVAILABILITY All the ncPred predictions together with the datasets used for the analysis are available at the following url: http://alpha.dmi.unict.it/ncPred/
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Affiliation(s)
- Salvatore Alaimo
- Department of Mathematics and Computer Science, University of Catania , Catania , Italy
| | - Rosalba Giugno
- Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy
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Alexandrov PN, Dua P, Lukiw WJ. Up-Regulation of miRNA-146a in Progressive, Age-Related Inflammatory Neurodegenerative Disorders of the Human CNS. Front Neurol 2014; 5:181. [PMID: 25324823 PMCID: PMC4179622 DOI: 10.3389/fneur.2014.00181] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/05/2014] [Indexed: 12/22/2022] Open
Affiliation(s)
| | - Prerna Dua
- Department of Health Information Management, Louisiana State University , Ruston, LA , USA
| | - Walter J Lukiw
- Department of Neurology, Louisiana State University Health Science Center , New Orleans, LA , USA ; LSU Neuroscience Center and Department of Ophthalmology, Louisiana State University Health Science Center , New Orleans, LA , USA
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48
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Le TD, Liu L, Zhang J, Liu B, Li J. From miRNA regulation to miRNA-TF co-regulation: computational approaches and challenges. Brief Bioinform 2014; 16:475-96. [DOI: 10.1093/bib/bbu023] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/10/2014] [Indexed: 12/14/2022] Open
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Caldeira C, Oliveira AF, Cunha C, Vaz AR, Falcão AS, Fernandes A, Brites D. Microglia change from a reactive to an age-like phenotype with the time in culture. Front Cell Neurosci 2014; 8:152. [PMID: 24917789 PMCID: PMC4040822 DOI: 10.3389/fncel.2014.00152] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/13/2014] [Indexed: 01/25/2023] Open
Abstract
Age-related neurodegenerative diseases have been associated with chronic neuroinflammation and microglia activation. However, cumulative evidence supports that inflammation only occurs at an early stage once microglia change the endogenous characteristics with aging and switch to irresponsive/senescent and dystrophic phenotypes with disease progression. Thus, it will be important to have the means to assess the role of reactive and aged microglia when studying advanced brain neurodegeneration processes and age-associated related disorders. Yet, most studies are done with microglia from neonates since there are no adequate means to isolate degenerating microglia for experimentation. Indeed, only a few studies report microglia isolation from aged animals, using either short-term cultures or high concentrations of mitogens in the medium, which trigger microglia reactivity. The purpose of this study was to develop an experimental process to naturally age microglia after isolation from neonatal mice and to characterize the cultured cells at 2 days in vitro (DIV), 10 DIV, and 16 DIV. We found that 2 DIV (young) microglia had predominant amoeboid morphology and markers of stressed/reactive phenotype. In contrast, 16 DIV (aged) microglia evidenced ramified morphology and increased matrix metalloproteinase (MMP)-2 activation, as well as reduced MMP-9, glutamate release and nuclear factor kappa-B activation, in parallel with decreased expression of Toll-like receptor (TLR)-2 and TLR-4, capacity to migrate and phagocytose. These findings together with the reduced expression of microRNA (miR)-124, and miR-155, decreased autophagy, enhanced senescence associated beta-galactosidase activity and elevated miR-146a expression, are suggestive that 16 DIV cells mainly correspond to irresponsive/senescent microglia. Data indicate that the model represent an opportunity to understand and control microglial aging, as well as to explore strategies to recover microglia surveillance function.
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Affiliation(s)
- Cláudia Caldeira
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal ; Centro de Investigação Interdisciplinar Egas Moniz, Egas Moniz - Cooperativa de Ensino Superior, CRL, Campus Universitário Monte de Caparica, Portugal
| | - Ana F Oliveira
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal
| | - Carolina Cunha
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal
| | - Ana R Vaz
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal ; Department of Biochemistry and Human Biology, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal
| | - Ana S Falcão
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal ; Department of Biochemistry and Human Biology, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal
| | - Adelaide Fernandes
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal ; Department of Biochemistry and Human Biology, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal
| | - Dora Brites
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal ; Department of Biochemistry and Human Biology, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal
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Cui L, Li Y, Ma G, Wang Y, Cai Y, Liu S, Chen Y, Li J, Xie Y, Liu G, Zhao B, Li K. A functional polymorphism in the promoter region of microRNA-146a is associated with the risk of Alzheimer disease and the rate of cognitive decline in patients. PLoS One 2014; 9:e89019. [PMID: 24586483 PMCID: PMC3934871 DOI: 10.1371/journal.pone.0089019] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/14/2014] [Indexed: 12/16/2022] Open
Abstract
miR146a is well known for its regulatory role in the immune response and inflammation. Recent studies have demonstrated the links between miR146a and Alzheimer disease (AD) and suggested that miR146a may be involved in neuroinflammation and the metabolism of amyloid-β (Aβ), which are critical events in AD pathology. Although genetic studies have focused on the association between the miR146a gene and susceptibility to several diseases, no association study of miR146a variability with AD has been conducted. In this report, we performed a case-control association study to analyze the genotype and allele distributions of the miR146a, rs2910464 and rs57095329 polymorphisms in a Chinese population consisting of 292 AD cases and 300 healthy controls. We found a significant difference in the genotypes and allele frequencies of rs57095329 between the AD cases and the controls (p = 0.0147 and p = 0.0184, respectively), where the AA genotype of rs57095329 was associated with an increased risk of AD as well the cognitive decline in AD patients. Additionally, the AA genotype of rs57095329 exhibited significantly higher miR146a expression than the GG+GA genotypes of rs2910164 in the peripheral blood cells (PBMCs) of healthy individuals and had a stronger effect on the production of IL-6 and IL-1β when the cells were stimulated with LPS. Our data provide preliminary evidence that the rs57095329 polymorphism in the miR146a promoter is involved in the genetic susceptibility to AD, and this risk AA genotype may increase the expression of miR146a and influence certain proinflammatory cytokines, thus playing a role in the pathogenesis of AD.
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Affiliation(s)
- Lili Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - You Li
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - Guoda Ma
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - Yan Wang
- Clinical Research Center of Guangdong Medical College, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - Yujie Cai
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - Shengyuan Liu
- Department of Chronic Disease, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, PR China
| | - Yanyan Chen
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - Jia Li
- Intensive Care Unit, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - Yuliu Xie
- Intensive Care Unit, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - Gen Liu
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
- Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
| | - Bin Zhao
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
- Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
- * E-mail: (BZ); (KSL)
| | - Keshen Li
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, PR China
- * E-mail: (BZ); (KSL)
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