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Yan X, Hu Z, Li X, Liang J, Zheng J, Gong J, Hu K, Sui X, Li R. Systemic analysis of the prognostic significance and interaction network of miR-26b-3p in cholangiocarcinoma. Appl Biochem Biotechnol 2024; 196:4166-4187. [PMID: 37914963 DOI: 10.1007/s12010-023-04753-x] [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] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
MicroRNAs (miRNAs) reportedly play significant roles in the progression of various cancers and hold huge potential as both diagnostic tools and therapeutic targets. Given the ongoing uncertainty surrounding the precise functions of several miRNAs in cholangiocarcinoma (CCA), this research undertakes a comprehensive analysis of CCA data sourced from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. The present study identified a novel miRNA, specifically miR-26b-3p, which exhibited prognostic value for individuals with CCA. Notably, miR-26b-3p was upregulated within CCA samples, with an inverse correlation established with patient prognosis (Hazard Ratio = 8.19, p = 0.018). Through a combination of functional enrichment analysis, analysis of the LncRNA-miR-26b-3p-mRNA interaction network, and validation by qRT PCR and western blotting, this study uncovered the potential of miR-26b-3p in potentiating the malignant progression of CCA via regulation of essential genes (including PSMD14, XAB2, SLC4A4) implicated in processes such as endoplasmic reticulum (ER) stress and responses to misfolded proteins. Our findings introduce novel and valuable insights that position miR-26b-3p-associated genes as promising biomarkers for the diagnosis and treatment of CCA.
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Affiliation(s)
- Xijing Yan
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
- Department of Breast and Thyroid Surgery, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Zhongying Hu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xuejiao Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jinliang Liang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jun Zheng
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jiao Gong
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Kunpeng Hu
- Department of Breast and Thyroid Surgery, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Xin Sui
- Surgical ICU, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Rong Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
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2
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Villa C, Combi R. Epigenetics in Alzheimer's Disease: A Critical Overview. Int J Mol Sci 2024; 25:5970. [PMID: 38892155 PMCID: PMC11173284 DOI: 10.3390/ijms25115970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Epigenetic modifications have been implicated in a number of complex diseases as well as being a hallmark of organismal aging. Several reports have indicated an involvement of these changes in Alzheimer's disease (AD) risk and progression, most likely contributing to the dysregulation of AD-related gene expression measured by DNA methylation studies. Given that DNA methylation is tissue-specific and that AD is a brain disorder, the limitation of these studies is the ability to identify clinically useful biomarkers in a proxy tissue, reflective of the tissue of interest, that would be less invasive, more cost-effective, and easily obtainable. The age-related DNA methylation changes have also been used to develop different generations of epigenetic clocks devoted to measuring the aging in different tissues that sometimes suggests an age acceleration in AD patients. This review critically discusses epigenetic changes and aging measures as potential biomarkers for AD detection, prognosis, and progression. Given that epigenetic alterations are chemically reversible, treatments aiming at reversing these modifications will be also discussed as promising therapeutic strategies for AD.
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Affiliation(s)
| | - Romina Combi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
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3
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Tsamou M, Roggen EL. Sex-associated microRNAs potentially implicated in sporadic Alzheimer's disease (sAD). Brain Res 2024; 1829:148791. [PMID: 38307153 DOI: 10.1016/j.brainres.2024.148791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/08/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND The onset and pathology of sporadic Alzheimer's disease (sAD) seem to be affected by both sex and genetic mechanisms. Evidence supports that the high prevalence of sAD in women, worldwide, may be attributed to an interplay among aging, sex, and lifestyle, influenced by genetics, metabolic changes, and hormones. Interestingly, epigenetic mechanisms such as microRNAs (miRNAs), known as master regulators of gene expression, may contribute to this observed sexual dimorphism in sAD. OBJECTIVES To investigate the potential impact of sex-associated miRNAs on processes manifesting sAD pathology, as described by the Tau-driven Adverse Outcome Pathway (AOP) leading to memory loss. METHODS Using publicly available human miRNA datasets, sex-biased miRNAs, defined as differentially expressed by sex in tissues possibly affected by sAD pathology, were collected. In addition, sex hormone-related miRNAs were also retrieved from the literature. The compiled sex-biased and sex hormone-related miRNAs were further plugged into the dysregulated processes of the Tau-driven AOP for memory loss. RESULTS Several miRNAs, previously identified as sex-associated, were implicated in dysregulated processes associated with the manifestation of sAD pathology. Importantly, the described pathology processes were not confined to a particular sex. A mechanistic-based approach utilizing miRNAs was adopted in order to elucidate the link between sex and biological processes potentially involved in the development of memory loss. CONCLUSIONS The identification of sex-associated miRNAs involved in the early processes manifesting memory loss may shed light to the complex molecular mechanisms underlying sAD pathogenesis in a sex-specific manner.
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Affiliation(s)
- Maria Tsamou
- ToxGenSolutions (TGS), Oxfordlaan 70, 6229EV Maastricht, The Netherlands.
| | - Erwin L Roggen
- ToxGenSolutions (TGS), Oxfordlaan 70, 6229EV Maastricht, The Netherlands
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Mustafin RN, Khusnutdinova EK. Involvement of transposable elements in Alzheimer's disease pathogenesis. Vavilovskii Zhurnal Genet Selektsii 2024; 28:228-238. [PMID: 38680184 PMCID: PMC11043511 DOI: 10.18699/vjgb-24-27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 05/01/2024] Open
Abstract
Alzheimer's disease affects an average of 5 % of the population with a significant increase in prevalence with age, suggesting that the same mechanisms that underlie aging may influence this pathology. Investigation of these mechanisms is promising for effective methods of treatment and prevention of the disease. Possible participants in these mechanisms are transposons, which serve as drivers of epigenetic regulation, since they form species-specific distributions of non-coding RNA genes in genomes in evolution. Study of miRNA involvement in Alzheimer's disease pathogenesis is relevant, since the associations of protein-coding genes (APOE4, ABCA7, BIN1, CLU, CR1, PICALM, TREM2) with the disease revealed as a result of GWAS make it difficult to explain its complex pathogenesis. Specific expression changes of many genes were found in different brain parts of Alzheimer's patients, which may be due to global regulatory changes under the influence of transposons. Experimental and clinical studies have shown pathological activation of retroelements in Alzheimer's disease. Our analysis of scientific literature in accordance with MDTE DB revealed 28 miRNAs derived from transposons (17 from LINE, 5 from SINE, 4 from HERV, 2 from DNA transposons), the expression of which specifically changes in this disease (decreases in 17 and increases in 11 microRNA). Expression of 13 out of 28 miRNAs (miR-151a, -192, -211, -28, -31, -320c, -335, -340, -378a, -511, -576, -708, -885) also changes with aging and cancer development, which indicates the presence of possible common pathogenetic mechanisms. Most of these miRNAs originated from LINE retroelements, the pathological activation of which is associated with aging, carcinogenesis, and Alzheimer's disease, which supports the hypothesis that these three processes are based on the primary dysregulation of transposons that serve as drivers of epigenetic regulation of gene expression in ontogeny.
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Affiliation(s)
| | - E K Khusnutdinova
- Bashkir State Medical University, Ufa, Russia Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
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5
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Zhang WT, Zhang GX, Gao SS. The potential diagnostic accuracy of circulating microRNAs for Alzheimer's disease: A meta-analysis. Neurologia 2024; 39:147-159. [PMID: 38460993 DOI: 10.1016/j.nrleng.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/06/2021] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND & OBJECTIVE Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disease that seriously affects cognitive ability and has become a key public health problem. Many studies have identified the possibility of peripheral blood microRNA as effective non-invasive biomarkers for AD diagnosis, but the results are inconsistent. Therefore, we carried out this meta-analysis to evaluate the diagnostic accuracy of circulating microRNAs in the diagnosis of AD patients. METHODS We performed a systematic literature search of the following databases: PubMed, EMBASE, Web of Science, Cochrane Library, Wanfang database and China National Knowledge Infrastructure, updated to March 15, 2021. A random effects model was used to pool the sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio and area under the curve. Meta-regression and subgroup analysis were performed to explore the sources of heterogeneity, and Deeks' funnel plot was used to assess whether there was publication bias. RESULTS 62 studies from 18 articles were included in this meta-analysis. The pooled sensitivity was 0.82 (95% CI: 0.78-0.85), specificity was 0.80 (95% CI: 0.76-0.83), PLR was 4. 1 (95% CI: 3.4-4.9), NLR was 0.23 (95% CI: 0.19-0.28), DOR was 18 (95% CI: 13-25) and AUC was 0.88 (95% CI: 0.84-0.90). Subgroup analysis shows that the microRNA clusters of plasma type performed a better diagnostic accuracy of AD patients. In addition, publication bias was not found. CONCLUSIONS Circulating microRNAs can be used as a promising non-invasive biomarker in AD diagnosis.
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Affiliation(s)
- W T Zhang
- Xi'an Daxing Hospital, Shaanxi, China; International Doctoral School, University of Seville, Spain
| | - G X Zhang
- International Doctoral School, University of Seville, Spain
| | - S S Gao
- Xi'an Daxing Hospital, Shaanxi, China; International Doctoral School, University of Seville, Spain.
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6
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Rochín-Hernández LJ, Rochín-Hernández LS, Padilla-Cristerna ML, Duarte-García A, Jiménez-Acosta MA, Figueroa-Corona MP, Meraz-Ríos MA. Mesenchymal Stem Cells from Familial Alzheimer's Patients Express MicroRNA Differently. Int J Mol Sci 2024; 25:1580. [PMID: 38338859 PMCID: PMC10855944 DOI: 10.3390/ijms25031580] [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: 12/31/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the predominant form of dementia globally. No reliable diagnostic, predictive techniques, or curative interventions are available. MicroRNAs (miRNAs) are vital to controlling gene expression, making them valuable biomarkers for diagnosis and prognosis. This study examines the transcriptome of olfactory ecto-mesenchymal stem cells (MSCs) derived from individuals with the PSEN1(A431E) mutation (Jalisco mutation). The aim is to determine whether this mutation affects the transcriptome and expression profile of miRNAs and their target genes at different stages of asymptomatic, presymptomatic, and symptomatic conditions. Expression microarrays compare the MSCs from mutation carriers with those from healthy donors. The results indicate a distinct variation in the expression of miRNAs and mRNAs among different symptomatologic groups and between individuals with the mutation. Using bioinformatics tools allows us to identify target genes for miRNAs, which in turn affect various biological processes and pathways. These include the cell cycle, senescence, transcription, and pathways involved in regulating the pluripotency of stem cells. These processes are closely linked to inter- and intracellular communication, vital for cellular functioning. These findings can enhance our comprehension and monitoring of the disease's physiological processes, identify new disorder indicators, and develop innovative treatments and diagnostic tools for preventing or treating AD.
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Affiliation(s)
- Lory J. Rochín-Hernández
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - Lory S. Rochín-Hernández
- Departamento de Biotecnología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico;
| | - Mayte L. Padilla-Cristerna
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - Andrea Duarte-García
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - Miguel A. Jiménez-Acosta
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - María P. Figueroa-Corona
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - Marco A. Meraz-Ríos
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
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7
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Palade J, Alsop E, Courtright-Lim A, Hsieh M, Whitsett TG, Galasko D, Van Keuren-Jensen K. Small RNA Changes in Plasma Have Potential for Early Diagnosis of Alzheimer's Disease before Symptom Onset. Cells 2024; 13:207. [PMID: 38334599 PMCID: PMC10854972 DOI: 10.3390/cells13030207] [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: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Alzheimer's disease (AD), due to its multifactorial nature and complex etiology, poses challenges for research, diagnosis, and treatment, and impacts millions worldwide. To address the need for minimally invasive, repeatable measures that aid in AD diagnosis and progression monitoring, studies leveraging RNAs associated with extracellular vesicles (EVs) in human biofluids have revealed AD-associated changes. However, the validation of AD biomarkers has suffered from the collection of samples from differing points in the disease time course or a lack of confirmed AD diagnoses. Here, we integrate clinical diagnosis and postmortem pathology data to form more accurate experimental groups and use small RNA sequencing to show that EVs from plasma can serve as a potential source of RNAs that reflect disease-related changes. Importantly, we demonstrated that these changes are identifiable in the EVs of preclinical patients, years before symptom manifestation, and that machine learning models based on differentially expressed RNAs can help predict disease conversion or progression. This research offers critical insight into early disease biomarkers and underscores the significance of accounting for disease progression and pathology in human AD studies.
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Affiliation(s)
- Joanna Palade
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (J.P.); (E.A.); (M.H.); (T.G.W.)
| | - Eric Alsop
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (J.P.); (E.A.); (M.H.); (T.G.W.)
| | | | - Michael Hsieh
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (J.P.); (E.A.); (M.H.); (T.G.W.)
| | - Timothy G. Whitsett
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (J.P.); (E.A.); (M.H.); (T.G.W.)
| | - Douglas Galasko
- Department of Neurosciences, San Diego and Shiley-Marcos Alzheimer’s Disease Research Center, University of California, La Jolla, CA 92037, USA;
| | - Kendall Van Keuren-Jensen
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (J.P.); (E.A.); (M.H.); (T.G.W.)
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8
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Van der Auwera S, Ameling S, Wittfeld K, Frenzel S, Bülow R, Nauck M, Völzke H, Völker U, Grabe HJ. Circulating microRNA miR-425-5p Associated with Brain White Matter Lesions and Inflammatory Processes. Int J Mol Sci 2024; 25:887. [PMID: 38255959 PMCID: PMC10815886 DOI: 10.3390/ijms25020887] [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: 12/20/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
White matter lesions (WML) emerge as a consequence of vascular injuries in the brain. While they are commonly observed in aging, associations have been established with neurodegenerative and neurological disorders such as dementia or stroke. Despite substantial research efforts, biological mechanisms are incomplete and biomarkers indicating WMLs are lacking. Utilizing data from the population-based Study of Health in Pomerania (SHIP), our objective was to identify plasma-circulating micro-RNAs (miRNAs) associated with WMLs, thus providing a foundation for a comprehensive biological model and further research. In linear regression models, direct association and moderating factors were analyzed. In 648 individuals, we identified hsa-miR-425-5p as directly associated with WMLs. In subsequent analyses, hsa-miR-425-5p was found to regulate various genes associated with WMLs with particular emphasis on the SH3PXD2A gene. Furthermore, miR-425-5p was found to be involved in immunological processes. In addition, noteworthy miRNAs associated with WMLs were identified, primarily moderated by the factors of sex or smoking status. All identified miRNAs exhibited a strong over-representation in neurodegenerative and neurological diseases. We introduced hsa-miR-425-5p as a promising candidate in WML research probably involved in immunological processes. Mir-425-5p holds the potential as a biomarker of WMLs, shedding light on potential mechanisms and pathways in vascular dementia.
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Affiliation(s)
- Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17475 Greifswald, Germany
| | - Sabine Ameling
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; (M.N.)
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Stefan Frenzel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Robin Bülow
- Institute for Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Matthias Nauck
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; (M.N.)
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Henry Völzke
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; (M.N.)
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; (M.N.)
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17475 Greifswald, Germany
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9
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Adiga D, Eswaran S, Sriharikrishnaa S, Khan NG, Prasada Kabekkodu S, Kumar D. Epigenetics of Alzheimer’s Disease: Past, Present and Future. ENZYMATIC TARGETS FOR DRUG DISCOVERY AGAINST ALZHEIMER'S DISEASE 2023:27-72. [DOI: 10.2174/9789815136142123010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Alzheimer’s disease (AD) exemplifies a looming epidemic lacking effective
treatment and manifests with the accumulation of neurofibrillary tangles, amyloid-β
plaques, neuroinflammation, behavioral changes, and acute cognitive impairments. It is
a complex, multifactorial disorder that arises from the intricate interaction between
environment and genetic factors, restrained via epigenetic machinery. Though the
research progress has improved the understanding of clinical manifestations and
disease advancement, the causal mechanism of detrimental consequences remains
undefined. Despite the substantial improvement in recent diagnostic modalities, it is
challenging to distinguish AD from other forms of dementia. Accurate diagnosis is a
major glitch in AD as it banks on the symptoms and clinical criteria. Several studies are
underway in exploring novel and reliable biomarkers for AD. In this direction,
epigenetic alterations have transpired as key modulators in AD pathogenesis with the
impeding inferences for the management of this neurological disorder. The present
chapter aims to discuss the significance of epigenetic modifications reported in the
pathophysiology of AD such as DNA methylation, hydroxy-methylation, methylation
of mtDNA, histone modifications, and noncoding RNAs. Additionally, the chapter also
describes the possible therapeutic avenues that target epigenetic modifications in AD.
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Affiliation(s)
- Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Sangavi Eswaran
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - S. Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Nadeem G. Khan
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Dileep Kumar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth
(Deemed to be University), Erandwane, Pune – 411038, Maharashtra, India
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10
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Cisterna-García A, Beric A, Ali M, Pardo JA, Chen HH, Fernandez MV, Norton J, Gentsch J, Bergmann K, Budde J, Perlmutter JS, Morris JC, Cruchaga C, Botia JA, Ibanez L. Cell-free RNA signatures predict Alzheimer's disease. iScience 2023; 26:108534. [PMID: 38089583 PMCID: PMC10711471 DOI: 10.1016/j.isci.2023.108534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
There is a need for affordable, scalable, and specific blood-based biomarkers for Alzheimer's disease that can be applied to a population level. We have developed and validated disease-specific cell-free transcriptomic blood-based biomarkers composed by a scalable number of transcripts that capture AD pathobiology even in the presymptomatic stages of the disease. Accuracies are in the range of the current CSF and plasma biomarkers, and specificities are high against other neurodegenerative diseases.
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Affiliation(s)
- Alejandro Cisterna-García
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Muhammad Ali
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Jose Adrian Pardo
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Hsiang-Han Chen
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Joel S. Perlmutter
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Radiology, Neuroscience, Physical Therapy, and Occupational Therapy, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - John C. Morris
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Juan A. Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Laura Ibanez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
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11
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Wang L, Shui X, Diao Y, Chen D, Zhou Y, Lee TH. Potential Implications of miRNAs in the Pathogenesis, Diagnosis, and Therapeutics of Alzheimer's Disease. Int J Mol Sci 2023; 24:16259. [PMID: 38003448 PMCID: PMC10671222 DOI: 10.3390/ijms242216259] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Alzheimer's disease (AD) is a complex multifactorial disorder that poses a substantial burden on patients, caregivers, and society. Considering the increased aging population and life expectancy, the incidence of AD will continue to rise in the following decades. However, the molecular pathogenesis of AD remains controversial, superior blood-based biomarker candidates for early diagnosis are still lacking, and effective therapeutics to halt or slow disease progression are urgently needed. As powerful genetic regulators, microRNAs (miRNAs) are receiving increasing attention due to their implications in the initiation, development, and theranostics of various diseases, including AD. In this review, we summarize miRNAs that directly target microtubule-associated protein tau (MAPT), amyloid precursor protein (APP), and β-site APP-cleaving enzyme 1 (BACE1) transcripts and regulate the alternative splicing of tau and APP. We also discuss related kinases, such as glycogen synthase kinase (GSK)-3β, cyclin-dependent kinase 5 (CDK5), and death-associated protein kinase 1 (DAPK1), as well as apolipoprotein E, that are directly targeted by miRNAs to control tau phosphorylation and amyloidogenic APP processing leading to Aβ pathologies. Moreover, there is evidence of miRNA-mediated modulation of inflammation. Furthermore, circulating miRNAs in the serum or plasma of AD patients as noninvasive biomarkers with diagnostic potential are reviewed. In addition, miRNA-based therapeutics optimized with nanocarriers or exosomes as potential options for AD treatment are discussed.
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Affiliation(s)
| | | | | | | | - Ying Zhou
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (L.W.)
| | - Tae Ho Lee
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (L.W.)
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12
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Piergiorge RM, da Silva Francisco Junior R, de Vasconcelos ATR, Santos-Rebouças CB. Multi-layered transcriptomic analysis reveals a pivotal role of FMR1 and other developmental genes in Alzheimer's disease-associated brain ceRNA network. Comput Biol Med 2023; 166:107494. [PMID: 37769462 DOI: 10.1016/j.compbiomed.2023.107494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023]
Abstract
Alzheimer's disease (AD) is an increasingly neurodegenerative disorder that causes progressive cognitive decline and memory impairment. Despite extensive research, the underlying causes of late-onset AD (LOAD) are still in progress. This study aimed to establish a network of competing regulatory interactions involving circular RNAs (circRNAs), microRNAs (miRNAs), RNA-binding proteins (RBPs), and messenger RNAs (mRNAs) connected to LOAD. A systematic analysis of publicly available expression data was conducted to identify integrated differentially expressed genes (DEGs) from the hippocampus of LOAD patients. Subsequently, gene co-expression analysis identified modules comprising highly expressed DEGs that act cooperatively. The competition between co-expressed DEGs and miRNAs/RBPs and the simultaneous interactions between circRNA and miRNA/RBP revealed a complex ceRNA network responsible for post-transcriptional regulation in LOAD. Hippocampal expression data for miRNAs, circRNAs, and RBPs were used to filter relevant relationships for AD. An integrated topological score was used to identify the highly connected hub gene, from which a brain core ceRNA subnetwork was generated. The Fragile X Messenger Ribonucleoprotein 1 (FMR1) coding for the RBP FMRP emerged as the prominent driver gene in this subnetwork. FMRP has been previously related to AD but not in a ceRNA network context. Also, the substantial number of neurodevelopmental genes in the ceRNA subnetwork and their related biological pathways strengthen that AD shares common pathological mechanisms with developmental conditions. Our results enhance the current knowledge about the convergent ceRNA regulatory pathways underlying AD and provide potential targets for identifying early biomarkers and developing novel therapeutic interventions.
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Affiliation(s)
- Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
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13
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Yadav SK, Jauhari A, Singh N, Pandey A, Sarkar S, Pandey S, Garg RK, Parmar D, Yadav S. Transcriptomics and Proteomics Approach for the Identification of Altered Blood microRNAs and Plasma Proteins in Parkinson's Disease. Cell Mol Neurobiol 2023; 43:3527-3553. [PMID: 37219663 DOI: 10.1007/s10571-023-01362-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder caused by the selective destruction of dopaminergic neurons (DA-nergic). Clinically, PD is diagnosed based on developing signs and symptoms. A neurological and physical examination and sometimes medical and family history also help in the diagnosis of PD. However, most of these features are visible when more than 80% of the dopaminergic neurons have degenerated. An understanding of the selective degeneration process at the cellular and molecular level and the development of new biomarkers are required for effective PD management. Several studies have been carried out using a selected set of miRNAs/ mRNAs and proteins to develop biomarkers of PD; however, an unbiased and combined miRNA-protein profiling study was required to identify the markers of progressive and selected degeneration of dopaminergic neurons in PD patients. In the present study, we have carried out global protein profiling through LC-MS/MS and miRNA profiling by using a "brain-specific" miRNA array panel of 112 miRNAs in PD patients and healthy controls to find the unprejudiced group of proteins and miRNAs that are deregulating in PD. In the whole blood samples of PD patients compared to healthy controls, the expression of 23 miRNAs and 289 proteins was significantly increased, whereas the expression of 4 miRNAs and 132 proteins was considerably downregulated. Network analysis, functional enrichment, annotation, and analysis of miRNA-protein interactions were also performed as part of the bioinformatics investigation of the discovered miRNAs and proteins revealing several pathways that lead to PD development and pathogenesis. Based on the analysis of miRNA and protein profiling, we have identified four miRNAs (hsa-miR-186-5p, miR-29b, miR-139 & has-miR-150-5p) and four proteins (YWHAZ, PSMA4, HYOU1, & SERPINA1), which can be targeted for the development of new biomarkers of PD. In vitro studies have identified the role of miR-186-5p in regulating the levels of the YWHAZ/YWHAB & CALM2 gene, which has shown maximum downregulation in PD patients and is known for its role in neuroprotection from apoptotic cell death & calcium regulation. In conclusion, our research has identified a group of miRNA-proteins that can be developed as PD biomarkers; however, future studies on the release of these miRNAs and proteins in extracellular vesicles circulating in the blood of PD patients can further validate these as specific biomarkers of PD.
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Affiliation(s)
- Sanjeev Kumar Yadav
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
- Department of Neuroscience, UConn Health, Farmington, CT, 06032, USA
| | - Abhishek Jauhari
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Nishant Singh
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- Department of Molecular Medicine, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Anuj Pandey
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Sana Sarkar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Shweta Pandey
- Department of Neurology, King George's Medical University, Lucknow, 226003, UP, India
| | - Ravindra K Garg
- Department of Neurology, King George's Medical University, Lucknow, 226003, UP, India
| | - Devendra Parmar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
| | - Sanjay Yadav
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India.
- Department of Biochemistry, All India Institute of Medical Sciences, Munshiganj, Raebareli, 229405, Uttar Pradesh, India.
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14
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Hashemi KS, Aliabadi MK, Mehrara A, Talebi E, Hemmati AA, Rezaeiye RD, Ghanbary MJ, Motealleh M, Dayeri B, Alashti SK. A meta-analysis of microarray datasets to identify biological regulatory networks in Alzheimer's disease. Front Genet 2023; 14:1225196. [PMID: 37705610 PMCID: PMC10497115 DOI: 10.3389/fgene.2023.1225196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
Background: Alzheimer's Disease (AD) is an age-related progressive neurodegenerative disorder characterized by mental deterioration, memory deficit, and multiple cognitive abnormalities, with an overall prevalence of ∼2% among industrialized countries. Although a proper diagnosis is not yet available, identification of miRNAs and mRNAs could offer valuable insights into the molecular pathways underlying AD's prognosis. Method: This study aims to utilize microarray bioinformatic analysis to identify potential biomarkers of AD, by analyzing six microarray datasets (GSE4757, GSE5281, GSE16759, GSE28146, GSE12685, and GSE1297) of AD patients, and control groups. Furthermore, this study conducted gene ontology, pathways analysis, and protein-protein interaction network to reveal major pathways linked to probable biological events. The datasets were meta-analyzed using bioinformatics tools, to identify significant differentially expressed genes (DEGs) and hub genes and their targeted miRNAs'. Results: According to the findings, CXCR4, TGFB1, ITGB1, MYH11, and SELE genes were identified as hub genes in this study. The analysis of DEGs using GO (gene ontology) revealed that these genes were significantly enriched in actin cytoskeleton regulation, ECM-receptor interaction, and hypertrophic cardiomyopathy. Eventually, hsa-mir-122-5p, hsa-mir-106a-5p, hsa-mir-27a-3p, hsa-mir16-5p, hsa-mir-145-5p, hsa-mir-12-5p, hsa-mir-128-3p, hsa-mir 3200-3p, hsa-mir-103a-3p, and hsa-mir-9-3p exhibited significant interactions with most of the hub genes. Conclusion: Overall, these genes can be considered as pivotal biomarkers for diagnosing the pathogenesis and molecular functions of AD.
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Affiliation(s)
- Kimia Sadat Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohadese Koohi Aliabadi
- Faculty of Interdisciplinary Science and Technology, Tarbiat Modares University, Tehran, Iran
| | - Arian Mehrara
- School of Pharmacy, Ramsar International Campus, Mazandaran University of Medical Sciences, Ramsar, Iran
| | - Elham Talebi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Akbar Hemmati
- Department of Biology and Biotechnology, Molecular Biology, and Genetics, Pavia University, Lombardi, Italy
| | | | | | - Maryam Motealleh
- Department of System Biology Lab, University of Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Behnaz Dayeri
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Biotechnology, University of Milan, Milan, Italy
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15
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Noor Eddin A, Hamsho K, Adi G, Al-Rimawi M, Alfuwais M, Abdul Rab S, Alkattan K, Yaqinuddin A. Cerebrospinal fluid microRNAs as potential biomarkers in Alzheimer's disease. Front Aging Neurosci 2023; 15:1210191. [PMID: 37476007 PMCID: PMC10354256 DOI: 10.3389/fnagi.2023.1210191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023] Open
Abstract
Alzheimer's disease (AD) is the leading form of dementia worldwide, but its early detection and diagnosis remain a challenge. MicroRNAs (miRNAs) are a group of small endogenous RNA molecules that regulate mRNA expression. Recent evidence suggests miRNAs play an important role in the five major hallmarks of AD pathophysiology: amyloidogenesis, tauopathy, neuroinflammation, synaptic dysfunction, and neuronal death. Compared to traditional biomarkers of AD, miRNAs display a greater degree of stability in cerebrospinal fluid. Moreover, aberrant changes in miRNA expression can be measured over time to monitor and guide patient treatment. Specific miRNA profiles and combinations may also be used to distinguish AD subjects from normal controls and other causes of dementia. Because of these properties, miRNAs are now being considered as promising and potential biomarkers of AD. This review comprehensively summarizes the diagnostic potential and regulatory roles miRNAs play in AD.
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16
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Pishbin E, Sadri F, Dehghan A, Kiani MJ, Hashemi N, Zare I, Mousavi P, Rahi A. Recent advances in isolation and detection of exosomal microRNAs related to Alzheimer's disease. ENVIRONMENTAL RESEARCH 2023; 227:115705. [PMID: 36958383 DOI: 10.1016/j.envres.2023.115705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 05/08/2023]
Abstract
Alzheimer's disease, a progressive neurological condition, is associated with various internal and external risk factors in the disease's early stages. Early diagnosis of Alzheimer's disease is essential for treatment management. Circulating exosomal microRNAs could be a new class of valuable biomarkers for early Alzheimer's disease diagnosis. Different kinds of biosensors have been introduced in recent years for the detection of these valuable biomarkers. Isolation of the exosomes is a crucial step in the detection process which is traditionally carried out by multi-step ultrafiltration. Microfluidics has improved the efficiency and costs of exosome isolation by implementing various effects and forces on the nano and microparticles in the microchannels. This paper reviews recent advancements in detecting Alzheimer's disease related exosomal microRNAs based on methods such as electrochemical, fluorescent, and SPR. The presented devices' pros and cons and their efficiencies compared with the gold standard methods are reported. Moreover, the application of microfluidic devices to detect Alzheimer's disease related biomarkers is summarized and presented. Finally, some challenges with the performance of novel technologies for isolating and detecting exosomal microRNAs are addressed.
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Affiliation(s)
- Esmail Pishbin
- Bio-microfluidics Laboratory, Department of Electrical Engineering and Information Technology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Fatemeh Sadri
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Amin Dehghan
- School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Mohammad Javad Kiani
- School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Nader Hashemi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz 7178795844, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Amid Rahi
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.
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17
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Devara D, Choudhary Y, Kumar S. Role of MicroRNA-502-3p in Human Diseases. Pharmaceuticals (Basel) 2023; 16:ph16040532. [PMID: 37111289 PMCID: PMC10144852 DOI: 10.3390/ph16040532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs that play a major role in gene regulation in several diseases. MicroRNA-502-3p (MiR-502-3p) has been previously characterized in a variety of human diseases such as osteoporosis, diabetes, tuberculosis, cancers, and neurological disorders. Our studies recently explored the new role of miR-502-3p in regulating synapse function in Alzheimer’s disease (AD). AD is the most common cause of dementia in elderly individuals. Synapse is the initial target that is hit during AD progression. The most common causes of synapse dysfunction in AD are amyloid beta, hyperphosphorylated tau, and microglia activation. MiR-502-3p was found to be localized and overexpressed in the AD synapses. Overexpression of miR-502-3p was correlated with AD severity in terms of Braak stages. Studies have shown that miR-502-3p modulates the glutaminergic and GABAergic synapse function in AD. The current study’s emphasis is to discuss the in-depth roles of miR-502-3p in human diseases and AD and the future possibilities concerning miR-502-3p as a therapeutic for AD treatment.
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Affiliation(s)
- Davin Devara
- Center of Emphasis in Neuroscience, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
| | - Yashmit Choudhary
- Maxine L. Silva Health Magnet High School, 121 Val Verde St., El Paso, TX 79905, USA
| | - Subodh Kumar
- Center of Emphasis in Neuroscience, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
- L. Frederick Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
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18
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Traumatic MicroRNAs: Deconvolving the Signal After Severe Traumatic Brain Injury. Cell Mol Neurobiol 2023; 43:1061-1075. [PMID: 35852739 DOI: 10.1007/s10571-022-01254-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/02/2022] [Indexed: 11/03/2022]
Abstract
History of traumatic brain injury (TBI) represents a significant risk factor for development of dementia and neurodegenerative disorders in later life. While histopathological sequelae and neurological diagnostics of TBI are well defined, the molecular events linking the post-TBI signaling and neurodegenerative cascades remain unknown. It is not only due to the brain's inaccessibility to direct molecular analysis but also due to the lack of well-defined and highly informative peripheral biomarkers. MicroRNAs (miRNAs) in blood are promising candidates to address this gap. Using integrative bioinformatics pipeline including miRNA:target identification, pathway enrichment, and protein-protein interactions analysis we identified set of genes, interacting proteins, and pathways that are connected to previously reported peripheral miRNAs, deregulated following severe traumatic brain injury (sTBI) in humans. This meta-analysis revealed a spectrum of genes closely related to critical biological processes, such as neuroregeneration including axon guidance and neurite outgrowth, neurotransmission, inflammation, proliferation, apoptosis, cell adhesion, and response to DNA damage. More importantly, we have identified molecular pathways associated with neurodegenerative conditions, including Alzheimer's and Parkinson's diseases, based on purely peripheral markers. The pathway signature after acute sTBI is similar to the one observed in chronic neurodegenerative conditions, which implicates a link between the post-sTBI signaling and neurodegeneration. Identified key hub interacting proteins represent a group of novel candidates for potential therapeutic targets or biomarkers.
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19
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Chen J, Bai X, Wu Q, Chen L, Wang H, Zhang J. Exercise Protects Against Cognitive Injury and Inflammation in Alzheimer's Disease Through Elevating miR-148a-3p. Neuroscience 2023; 513:126-133. [PMID: 36681141 DOI: 10.1016/j.neuroscience.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/08/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Alzheimer's disease (AD) is a chronic neurological disorder with high morbidity. Exercise is one of the effective ways to ameliorate AD. In this study, we assessed the effects of exercise on cognition and inflammation and studied the role of miR-148a-3p in AD. In 88 patients with AD, the expression of miR-148a-3p was studied using qRT-PCR. ROC curve and Pearson analysis were utilized to evaluate the roles of miR-148a-3p in AD. MWM test was conducted to investigate the effects of miR-148a-3p and exercise on cognition and memory. Moreover, inflammatory indicators were identified using an enzyme-linked immunosorbent assay. Relative luciferase levels reflected whether miR-148a-3p targeted SYNJ1. miR-148a-3p levels declined in patients with AD, indicating its potential as a biomarker. Interestingly, miR-148a-3p levels were elevated in patients with AD after exercise. MiR-148a-3p levels correlated with cognitive scores and proinflammatory levels. The cognitive situation and pro-inflammatory state were partly recovered in the mice after exercise. MiR-148a-3p silencing reversed these abovementioned tendencies. Patients with AD exhibited a low level of miR-148a-3p, which was increased after exercise. Therefore, exercise might improve the cognitive function and memory of mice with AD by upregulating miR-148a-3p.
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Affiliation(s)
- Jinli Chen
- Department of Neurology, Tinglin Hospital of Jinshan District, Shanghai 201505, China
| | - Xiaojing Bai
- Department of Neurology, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Quan Wu
- Department of Neurology, Tinglin Hospital of Jinshan District, Shanghai 201505, China
| | - Lilong Chen
- Department of Neurology, Tinglin Hospital of Jinshan District, Shanghai 201505, China
| | - Hui Wang
- Department of Neurology, Tinglin Hospital of Jinshan District, Shanghai 201505, China
| | - Jianfeng Zhang
- Department of Neurology, Jinshan Hospital, Fudan University, Shanghai 201508, China.
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20
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Dexmedetomidine Attenuates Methotrexate-Induced Neurotoxicity and Memory Deficits in Rats through Improving Hippocampal Neurogenesis: The Role of miR-15a/ROCK-1/ERK1/2/CREB/BDNF Pathway Modulation. Int J Mol Sci 2023; 24:ijms24010766. [PMID: 36614208 PMCID: PMC9821704 DOI: 10.3390/ijms24010766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
Methotrexate (MTX) is a widely used neurotoxic drug with broad antineoplastic and immunosuppressant spectra. However, the exact molecular mechanisms by which MTX inhibits hippocampal neurogenesis are yet unclear. Dexmedetomidine (Dex), an α2-adrenergic receptor agonist, has recently shown neuroprotective effects; however, its full mechanism is unexplored. This study investigated the potential of Dex to mitigate MTX-induced neurotoxicity and memory impairment in rats and the possible role of the miR-15a/ROCK-1/ERK1/2/CREB/BDNF pathway. Notably, no former studies have linked this pathway to MTX-induced neurotoxicity. Male Sprague Dawley rats were placed into four groups. Group 1 received saline i.p. daily and i.v. on days 8 and 15. Group 2 received Dex at 10 μg/kg/day i.p. for 30 days. Group 3 received MTX at 75 mg/kg i.v. on days 8 and 15, followed by four i.p. doses of leucovorin at 6 mg/kg after 18 h and 3 mg/kg after 26, 42, and 50 h. Group 4 received MTX and leucovorin as in group 3 and Dex daily dosages as in group 2. Bioinformatic analysis identified the association of miR-15a with ROCK-1/ERK1/2/CREB/BDNF and neurogenesis. MTX lowered hippocampal doublecortin and Ki-67, two markers of neurogenesis. This was associated with the downregulation of miR-15a, upregulation of its target ROCK-1, and reduction in the downstream ERK1/2/CREB/BDNF pathway, along with disturbed hippocampal redox state. Novel object recognition and Morris water maze tests demonstrated the MTX-induced memory deficiencies. Dex co-treatment reversed the MTX-induced behavioral, biochemical, and histological alterations in the rats. These neuroprotective actions could be partly mediated through modulating the miR-15a/ROCK-1/ERK1/2/CREB/BDNF pathway, which enhances hippocampal neurogenesis.
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21
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GeneSelectML: a comprehensive way of gene selection for RNA-Seq data via machine learning algorithms. Med Biol Eng Comput 2023; 61:229-241. [PMID: 36355333 DOI: 10.1007/s11517-022-02695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 10/02/2022] [Indexed: 11/11/2022]
Abstract
Selection of differentially expressed genes (DEGs) is a vital process to discover the causes of diseases. It has been shown that modelling of genomics data by considering relation among genes increases the predictive performance of methods compared to univariate analysis. However, there exist serious differences among most studies analyzing the same dataset for the reasons arising from the methods. Therefore, there is a strong need for easily accessible, user-friendly, and interactive tool to perform gene selection for RNA-seq data via machine learning algorithms simultaneously not to miss DEGs. We develop an open-source and freely available web-based tool for gene selection via machine learning algorithms that can deal with high performance computation. This tool includes six machine learning algorithms having different aspects. Moreover, the tool involves classical pre-processing steps; filtering, normalization, transformation, and univariate analysis. It also offers well-arranged graphical approaches; network plot, heatmap, venn diagram, and box-and-whisker plot. Gene ontology analysis is provided for both mRNA and miRNA DEGs. The implementation is carried out on Alzheimer RNA-seq data to demonstrate the use of this web-based tool. Eleven genes are suggested by at least two out of six methods. One of these genes, hsa-miR-148a-3p, might be considered as a new biomarker for Alzheimer's disease diagnosis. Kidney Chromophobe dataset is also analyzed to demonstrate the validity of GeneSelectML web tool on a different dataset. GeneSelectML is distinguished in that it simultaneously uses different machine learning algorithms for gene selection and can perform pre-processing, graphical representation, and gene ontology analyses on the same tool. This tool is freely available at www.softmed.hacettepe.edu.tr/GeneSelectML .
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Emerging Role of MicroRNA-30c in Neurological Disorders. Int J Mol Sci 2022; 24:ijms24010037. [PMID: 36613480 PMCID: PMC9819962 DOI: 10.3390/ijms24010037] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are a class of small non-coding RNAs that negatively regulate the expression of target genes by interacting with 3' untranslated regions of target mRNAs to induce mRNA degradation and translational repression. The miR-30 family members are involved in the development of many tissues and organs and participate in the pathogenesis of human diseases. As a key member of the miR-30 family, miR-30c has been implicated in neurological disorders such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, and stroke. Mechanistically, miR-30c may act as a multi-functional regulator of different pathogenic processes such as autophagy, apoptosis, endoplasmic reticulum stress, inflammation, oxidative stress, thrombosis, and neurovascular function, thereby contributing to different disease states. Here, we review and discuss the biogenesis, gene regulation, and the role and mechanisms of action of miR-30c in several neurological disorders and therapeutic potential in clinics.
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Villegas-Mirón P, Gallego A, Bertranpetit J, Laayouni H, Espinosa-Parrilla Y. Signatures of genetic variation in human microRNAs point to processes of positive selection and population-specific disease risks. Hum Genet 2022; 141:1673-1693. [PMID: 35249174 PMCID: PMC9522702 DOI: 10.1007/s00439-021-02423-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 12/19/2021] [Indexed: 12/11/2022]
Abstract
The occurrence of natural variation in human microRNAs has been the focus of numerous studies during the last 20 years. Most of them have been focused on the role of specific mutations in disease, while a minor proportion seek to analyse microRNA diversity in the genomes of human populations. We analyse the latest human microRNA annotations in the light of the most updated catalogue of genetic variation provided by the 1000 Genomes Project. By means of the in silico analysis of microRNA genetic variation we show that the level of evolutionary constraint of these sequences is governed by the interplay of different factors, like their evolutionary age or genomic location. The role of mutations in the shaping of microRNA-driven regulatory interactions is emphasized with the acknowledgement that, while the whole microRNA sequence is highly conserved, the seed region shows a pattern of higher genetic diversity that appears to be caused by the dramatic frequency shifts of a fraction of human microRNAs. We highlight the participation of these microRNAs in population-specific processes by identifying that not only the seed, but also the loop, are particularly differentiated regions among human populations. The quantitative computational comparison of signatures of population differentiation showed that candidate microRNAs with the largest differences are enriched in variants implicated in gene expression levels (eQTLs), selective sweeps and pathological processes. We explore the implication of these evolutionary-driven microRNAs and their SNPs in human diseases, such as different types of cancer, and discuss their role in population-specific disease risk.
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Affiliation(s)
- Pablo Villegas-Mirón
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Alicia Gallego
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain.
| | - Yolanda Espinosa-Parrilla
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas, Chile.
- Laboratorio de Medicina Molecular-LMM, Centro Asistencial, Docente Y de Investigación-CADI, Universidad de Magallanes, Punta Arenas, Chile.
- Interuniversity Center on Healthy Aging, Punta Arenas, Chile.
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Biomarkers of Frailty: miRNAs as Common Signatures of Impairment in Cognitive and Physical Domains. BIOLOGY 2022; 11:biology11081151. [PMID: 36009778 PMCID: PMC9405439 DOI: 10.3390/biology11081151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022]
Abstract
The past years have seen an increasing concern about frailty, owing to the growing number of elderly people and the major impact of this syndrome on health and social care. The identification of frail people passes through the use of different tests and biomarkers, whose concerted analysis helps to stratify the populations of patients according to their risk profile. However, their efficiency in prognosis and their capability to reflect the multisystemic impairment of frailty is discussed. Recent works propose the use of miRNAs as biological hallmarks of physiological impairment in different organismal districts. Changes in miRNAs expression have been described in biological processes associated with phenotypic outcomes of frailty, opening intriguing possibilities for their use as biomarkers of fragility. Here, with the aim of finding reliable biomarkers of frailty, while considering its complex nature, we revised the current literature on the field, for uncovering miRNAs shared across physical and cognitive frailty domains. By applying in silico analyses, we retrieved the top-ranked shared miRNAs and their targets, finally prioritizing the most significant ones. From this analysis, ten miRNAs emerged which converge into two main biological processes: inflammation and energy homeostasis. Such markers, if validated, may offer promising capabilities for early diagnosis of frailty in the elderly population.
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Chen S, Zhang L, Feng B, Wang W, Liu D, Zhao X, Yu C, Wang X, Gao Y. MiR-550a-3p restores damaged vascular smooth muscle cells by inhibiting thrombomodulin in an <em>in vitro</em> atherosclerosis model. Eur J Histochem 2022; 66. [PMID: 35855629 PMCID: PMC9335314 DOI: 10.4081/ejh.2022.3429] [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: 04/23/2022] [Accepted: 07/04/2022] [Indexed: 11/22/2022] Open
Abstract
Thrombomodulin (TM) is involved in the pathological process of atherosclerosis; however, the underlying mechanism remains unclear. Oxidised low-density lipoprotein (Ox-LDL; 100 μg/mL) was used to induce human vascular smooth muscle cells (HVSMCs) into a stable atherosclerotic cell model. The expression levels of miR-550a-3p and TM were detected by real-time reverse transcription-polymerase chain reaction. Cell proliferation was estimated using CCK8 and EDU assays. Wound scratch and transwell assays were used to measure the ability of cells to invade and migrate. Propidium iodide fluorescence-activated cell sorting was used to detect apoptosis and cell cycle changes. A dual-luciferase reporter assay was performed to determine the binding of miR-550a-3p to TM. Our results suggested the successful development of a cellular atherosclerosis model. Our data revealed that TM overexpression significantly promoted the proliferation, invasion, migration, and apoptosis of HVSMCs as well as cell cycle changes. Upregulation of miR-550a-3p inhibited the growth and metastasis of HVSMCs. Furthermore, miR-550a-3p was confirmed to be a direct target of TM. Restoration of miR-550a-3p expression rescued the effects of TM overexpression. Thus, miR-550a-3p might play a role in atherosclerosis and, for the first time, normalised the function of injured vascular endothelial cells by simultaneous transfection of TM and miR-550a-3p. These results suggest that the miR-550a-3p/TM axis is a potential therapeutic target for atherosclerosis.
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Affiliation(s)
- Shiyuan Chen
- The First Clinical College, Jinan University, Guangzhou, Guangdong; Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
| | - Longfei Zhang
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
| | - Benchi Feng
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
| | - Wei Wang
- Department of Oncological Surgery, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
| | - Delang Liu
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
| | - Xinyu Zhao
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
| | - Chaowen Yu
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
| | - Xiaogao Wang
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
| | - Yong Gao
- The First Clinical College, Jinan University, Guangzhou, Guangdong; Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui.
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Vázquez-Villaseñor I, Smith CI, Thang YJR, Heath PR, Wharton SB, Blackburn DJ, Ridger VC, Simpson JE. RNA-Seq Profiling of Neutrophil-Derived Microvesicles in Alzheimer's Disease Patients Identifies a miRNA Signature That May Impact Blood-Brain Barrier Integrity. Int J Mol Sci 2022; 23:ijms23115913. [PMID: 35682592 PMCID: PMC9180128 DOI: 10.3390/ijms23115913] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/21/2022] [Accepted: 05/21/2022] [Indexed: 02/01/2023] Open
Abstract
(1) Background: Systemic infection is associated with increased neuroinflammation and accelerated cognitive decline in AD patients. Activated neutrophils produce neutrophil-derived microvesicles (NMV), which are internalised by human brain microvascular endothelial cells and increase their permeability in vitro, suggesting that NMV play a role in blood–brain barrier (BBB) integrity during infection. The current study investigated whether microRNA content of NMV from AD patients is significantly different compared to healthy controls and could impact cerebrovascular integrity. (2) Methods: Neutrophils isolated from peripheral blood samples of five AD and five healthy control donors without systemic infection were stimulated to produce NMV. MicroRNAs isolated from NMV were analysed by RNA-Seq, and online bioinformatic tools were used to identify significantly differentially expressed microRNAs in the NMV. Target and pathway analyses were performed to predict the impact of the candidate microRNAs on vascular integrity. (3) Results: There was no significant difference in either the number of neutrophils (p = 0.309) or the number of NMV (p = 0.3434) isolated from AD donors compared to control. However, 158 microRNAs were significantly dysregulated in AD NMV compared to controls, some of which were associated with BBB dysfunction, including miR-210, miR-20b-5p and miR-126-5p. Pathway analysis revealed numerous significantly affected pathways involved in regulating vascular integrity, including the TGFβ and PDGFB pathways, as well as Hippo, IL-2 and DNA damage signalling. (4) Conclusions: NMV from AD patients contain miRNAs that may alter the integrity of the BBB and represent a novel neutrophil-mediated mechanism for BBB dysfunction in AD and the accelerated cognitive decline seen as a result of a systemic infection.
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Affiliation(s)
- Irina Vázquez-Villaseñor
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK; (C.I.S.); (Y.J.R.T.); (P.R.H.); (S.B.W.); (D.J.B.)
- Correspondence: (I.V.-V.); (J.E.S.)
| | - Cynthia I. Smith
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK; (C.I.S.); (Y.J.R.T.); (P.R.H.); (S.B.W.); (D.J.B.)
| | - Yung J. R. Thang
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK; (C.I.S.); (Y.J.R.T.); (P.R.H.); (S.B.W.); (D.J.B.)
| | - Paul R. Heath
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK; (C.I.S.); (Y.J.R.T.); (P.R.H.); (S.B.W.); (D.J.B.)
| | - Stephen B. Wharton
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK; (C.I.S.); (Y.J.R.T.); (P.R.H.); (S.B.W.); (D.J.B.)
| | - Daniel J. Blackburn
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK; (C.I.S.); (Y.J.R.T.); (P.R.H.); (S.B.W.); (D.J.B.)
| | - Victoria C. Ridger
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK;
| | - Julie E. Simpson
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK; (C.I.S.); (Y.J.R.T.); (P.R.H.); (S.B.W.); (D.J.B.)
- Correspondence: (I.V.-V.); (J.E.S.)
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Nguyen HD, Kim MS. Exposure to a mixture of heavy metals induces cognitive impairment: Genes and microRNAs involved. Toxicology 2022; 471:153164. [PMID: 35346790 DOI: 10.1016/j.tox.2022.153164] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/10/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022]
Abstract
Converging evidence demonstrates that microRNAs (miRNAs) play an important role in the etiology of cognitive impairment. Thus, we aim to: (i) identify the molecular mechanisms of heavy metals, particularly miRNAs involved in the development of cognitive impairment; and (ii) generate miRNA sponges to prevent them from binding with their target messenger RNAs. The Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org), MicroRNA ENrichment TURned NETwork (MIENTURNET, http://userver.bio.uniroma1.it/apps/mienturnet/) and the microRNA sponge generator and tester (miRNAsong, http://www.med.muni.cz/histology/miRNAsong) were used as the core data-mining approaches in the current study. We observed that lead acetate, arsenic, gold, copper, iron, and aluminum, as well as their mixtures, had significant effects on the development of cognitive impairment. Although prevalent genes obtained from investigated heavy metals of cognitive impairment were different, the "PI3K-Akt signaling pathway", "pathways of neurodegeneration-multiple diseases", "apoptosis", "apoptosis-multiple species", "p53 signaling pathway", "NF-kappa B signaling pathway", and "Alzheimer's disease pathway" were highlighted. The mixed heavy metals altered the genes BAX, CASP3, BCL2, TNF, and IL-1B, indicating the significance of apoptosis and pro-inflammatory cytokines in the pathogenesis of cognitive impairment and the possibility of targeting these genes in future neuroprotective therapy. In addition, we used a network-based approach to identify key genes, miRNAs, pathways, and diseases related to the development of cognitive impairment. We also found 16 significant miRNAs related to cognitive impairment (hsa-miR-1-3p, hsa-let-7a-5p, hsa-miR-9-5p, hsa-miR-16-5p, hsa-miR-17-5p, hsa-miR-20a-5p, hsa-miR-26a-5p, hsa-miR-26b-5p, hsa-miR-34a-5p, hsa-miR-101-3p, hsa-miR-106a-5p, hsa-miR-128-3p, hsa-miR-144-3p, hsa-miR-199a-3p, hsa-miR-204-5p, and hsa-miR-335-5p). Finally, we created and evaluated miRNA sponge sequences for these miRNAs in silico. Further studies, including in vivo and in vitro, are needed to assess the link between these genes, miRNAs, pathways, and cognitive impairment.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Min-Sun Kim
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea.
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Duc Nguyen H, Hee Jo W, Hong Minh Hoang N, Kim MS. Anti-inflammatory effects of B vitamins protect against tau hyperphosphorylation and cognitive impairment induced by 1,2 diacetyl benzene: An in vitro and in silico study. Int Immunopharmacol 2022; 108:108736. [PMID: 35364429 DOI: 10.1016/j.intimp.2022.108736] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 12/13/2022]
Abstract
1,2 diacetyl benzene (DAB) penetrates the blood-brain barrier, causing neuroinflammation, tau hyperphosphorylation, and cognitive impairment. Converging evidence supports the anti-inflammatory effects of B vitamins on cognitive impairment, but the effects of B vitamins on cognitive impairment induced by DAB remain unclear. Here, we investigated the anti-inflammatory properties of B vitamins in DAB-stimulated human neuroblastoma SH-SY5Y cells. In this in-silico analysis, we investigated the genes, transcription factors, miRNAs, and sponges linked with DAB, B vitamins and the pathogenesis of cognitive impairment. We found vitamins B1, B2, and B3 had anti-inflammatory properties in DAB-stimulated SH-SY5Y cells, possibly via inhibiting NF-κB activation. Furthermore, vitamins B1, B2, and B3 inhibited GSK-3β, β-amyloid, and tau hyperphosphorylation in SH-SY5Y cells. These vitamins can also modulate genes induced by DAB (IL1B, IL6, IL10, iNOS, COX2, NFκB, GSK3B, TNF, and APP) in SH-SY5Y cells. In silico analyses, inflammatory response related pathways, "Alzheimer's disease", "pathways of neurodegeneration-multiple disease", and "prolactin signaling pathway", were highlighted. Additionally, we explored a network-based approach to identify key genes, transcription factors, miRNAs, and pathways in cognitive impairment. The transcription factors NFKB2 and BATF3 were shown to be the most important in regulating genes. We also found eight significant miRNAs related to cognitive impairment, and these miRNAs were also validated by qPCR. Finally, we developed and tested in silico miRNA sponge sequences for these miRNAs.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Won Hee Jo
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Ngoc Hong Minh Hoang
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Min-Sun Kim
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea.
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Dysregulation of miR-144-5p/RNF187 axis contributes to the progression of colorectal cancer. J Transl Int Med 2022; 10:65-75. [PMID: 35702180 PMCID: PMC8997807 DOI: 10.2478/jtim-2021-0043] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background and Objectives RING finger protein 187 (RNF187) belongs to RING domain-containing E3 ligases family, which was recently reported to be involved in oncogenesis and development of several cancers. This research aims to clarify the role of RNF187 in colorectal cancer (CRC) development. Methods The expression of RNF187 and miR-144-4p were determined by quantitative real-time polymerase chain reaction (qRT-PCR). The levels of RNF187 protein were assessed by western blot analysis. Cell Counting Kit-8 (CCK8) assay, clonogenic assay, cell scratch test and transwell assay were used to determine the proliferation, migration and invasion of CRC cells in vitro. The binding of miR-144-5p and RNF197 mRNA was validated by luciferase reporter assays. Tumor-bearing nude mice were used to determine CRC cells growth in vivo. Results RNF187 expression significantly increased in CRC specimens and cell lines compared to normal colon tissues and normal colonic mucosa cell line, respectively. Upregulation of RNF187 expression was inversely correlated to poor prognosis in CRC patients. In addition, knockdown of RNF187 expression inhibited the proliferation, migration, and invasion but promoted the apoptosis of CRC lines Caco-2 and SW480 cells. Further studies validated that RNF187 was the direct target of miR-144-5p. The expression of miR-144-5p was downregulated in CRC tissues, which was negatively correlated to the expression of RNF187. Restoration of miR-144-5p significantly inhibited the progression of CRC cells and its anti-tumor effects could be abrogated by overexpression of RNF187. Conclusion Our findings demonstrate the deregulation of miR-144-5p/ RNF187 axis in CRC, as well as its role in regulation of the tumor progression, thus providing a novel therapeutic strategy for CRC treatment.
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Identification of Potential Biomarkers in the Peripheral Blood Mononuclear Cells of Relapsing–Remitting Multiple Sclerosis Patients. Inflammation 2022; 45:1815-1828. [DOI: 10.1007/s10753-022-01662-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/07/2022] [Accepted: 03/10/2022] [Indexed: 11/26/2022]
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Wang H, Zeng Z, Yi R, Luo J, Chen J, Lou J. MicroRNA-3200-3p targeting CAMK2A modulates the proliferation and metastasis of glioma in vitro. Bioengineered 2022; 13:7785-7797. [PMID: 35287547 PMCID: PMC9208524 DOI: 10.1080/21655979.2022.2048995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
MicroRNA (miRNA) is strongly interrelated with the pathogenesis of glioma. However, its potential biological effect and underlying mechanism of miR-3200-3p in human glioma remain elusive. In the current study, we checked the level of miR-3200-3p in different glioma cells. Then, its biological functions on glioma cell proliferation metastasis was investigated using the miR-3200-3p mimic and inhibitor. The direct target of miR-3200-3p was tested in these cells. Results demonstrated that miR-3200-3p is remarkably downregulated in human glioma cells. The relative level of miR-3200-3p is strongly associated with biological features, including proliferation, colony formation, and metastasis. Additionally, Ca2+/calmodulin dependent kinase 2a (CAMK2A) might be the direct target gene of miR-3200-3p, and CAMK2A overexpression reversed the anticancer roles of miR-3200-3p on glioma cellular function. Importantly, these results further showed that miR-3200-3p downregulated the proliferation and metastasis by suppressing the expression of CAMK2A, thus regulating the Ras/Raf/MEK/ERK pathway. This study provided provided insights into the biological role of miR-3200-3p, which might function as a potential biomarker in glioma therapy.
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Affiliation(s)
- Haibin Wang
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical College, Ganzhou, Jiangxi, China
| | - Zhaobin Zeng
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical College, Ganzhou, Jiangxi, China
| | - Renhui Yi
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical College, Ganzhou, Jiangxi, China
| | - Jun Luo
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical College, Ganzhou, Jiangxi, China
| | - Jinming Chen
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical College, Ganzhou, Jiangxi, China
| | - Jianyun Lou
- Department of Neurosurgery, The First Affiliated Hospital of Gannan Medical College, Ganzhou, Jiangxi, China
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Differential Transcriptome Profiling Unveils Novel Deregulated Gene Signatures Involved in Pathogenesis of Alzheimer's Disease. Biomedicines 2022; 10:biomedicines10030611. [PMID: 35327413 PMCID: PMC8945049 DOI: 10.3390/biomedicines10030611] [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: 01/19/2022] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 02/01/2023] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder that is characterized by a progressive loss of cognitive functions at a higher level than normal aging. Although the apolipoprotein (APOE) gene is a major risk factor in developing AD, other genes have also been reported to be linked with complex phenotypes. Therefore, this genome-wide expression study explored differentially expressed genes as possible novel biomarkers involved in AD. The mRNA expression dataset, GSE28146, containing 15 sample data composed of 7 AD cases from the hippocampus region with age-matched control (n = 8, >80 years), was analyzed. Using “affy” R-package, mRNA expression was calculated, while pathway enrichment analysis was performed to determine related biological processes. Of 58 differentially expressed genes, 44 downregulated and 14 upregulated genes were found to be significantly (p < 0.001) altered. The pathway enrichment analysis revealed two altered genes, i.e., dynein light chain 1 (DYNLL1) and kalirin (KLRN), associated with AD in the elderly population. The majority of genes were associated with retrograde endocannabinoid as well as vascular endothelial growth factors affecting the complex phenotypes. The DYNLL1 and KLRN genes may be involved with AD and Huntington’s disease (HD) phenotypes and represent a common genetic basis of these diseases. However, the hallmark of AD is dementia, while the classic motor sign of HD includes chorea. Our data warrant further investigation to identify the role of these genes in disease pathogenesis.
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De Sousa RAL, Improta-Caria AC. Regulation of microRNAs in Alzheimer´s disease, type 2 diabetes, and aerobic exercise training. Metab Brain Dis 2022; 37:559-580. [PMID: 35075500 DOI: 10.1007/s11011-022-00903-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is the most common type of dementia. The evolution and aggregation of amyloid beta (β) oligomers is linked to insulin resistance in AD, which is also the major characteristic of type 2 diabetes (T2D). Being physically inactive can contribute to the development of AD and/or T2D. Aerobic exercise training (AET), a type of physical exercise, can be useful in preventing or treating the negative outcomes of AD and T2D. AD, T2D and AET can regulate the expression of microRNAs (miRNAs). Here, we review some of the changes in miRNAs expression regulated by AET, AD and T2D. MiRNAs play an important role in the gene regulation of key signaling pathways in both pathologies, AD and T2D. MiRNA dysregulation is evident in AD and has been associated with several neuropathological alterations, such as the development of a reactive gliosis. Expression of miRNAs are associated with many pathophysiological mechanisms involved in T2D like insulin synthesis, insulin resistance, glucose intolerance, hyperglycemia, intracellular signaling, and lipid profile. AET regulates miRNAs levels. We identified 5 miRNAs (miR-21, miR-29a/b, miR-103, miR-107, and miR-195) that regulate gene expression and are modulated by AET on AD and T2D. The identified miRNAs are potential targets to treat the symptoms of AD and T2D. Thus, AET is a non-pharmacological tool that can be used to prevent and fight the negative outcomes in AD and T2D.
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Affiliation(s)
- Ricardo Augusto Leoni De Sousa
- Programa Multicêntrico de Pós-Graduação Em Ciências Fisiológicas- Sociedade Brasileira de Fisiologia (SBFis), Universidade Federal Dos Vales Do Jequitinhonha E Mucuri (UFVJM), Campus JK, Rodovia MGT 367, Km 583, Alto da Jacuba, nº 5000, Diamantina, Minas Gerais, CEP 39100-000, Brazil.
| | - Alex Cleber Improta-Caria
- Post-Graduate Program in Medicine and Health, Faculty of Medicine, Federal University of Bahia, Bahia, Brazil
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Tsamou M, Carpi D, Pistollato F, Roggen EL. Sporadic Alzheimer's Disease- and Neurotoxicity-Related microRNAs Affecting Key Events of Tau-Driven Adverse Outcome Pathway Toward Memory Loss. J Alzheimers Dis 2022; 86:1427-1457. [PMID: 35213375 DOI: 10.3233/jad-215434] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND A complex network of aging-related homeostatic pathways that are sensitive to further deterioration in the presence of genetic, systemic, and environmental risk factors, and lifestyle, is implicated in the pathogenesis of progressive neurodegenerative diseases, such as sporadic (late-onset) Alzheimer's disease (sAD). OBJECTIVE Since sAD pathology and neurotoxicity share microRNAs (miRs) regulating common as well as overlapping pathological processes, environmental neurotoxic compounds are hypothesized to exert a risk for sAD initiation and progression. METHODS Literature search for miRs associated with human sAD and environmental neurotoxic compounds was conducted. Functional miR analysis using PathDip was performed to create miR-target interaction networks. RESULTS The identified miRs were successfully linked to the hypothetical starting point and key events of the earlier proposed tau-driven adverse outcome pathway toward memory loss. Functional miR analysis confirmed most of the findings retrieved from literature and revealed some interesting findings. The analysis identified 40 miRs involved in both sAD and neurotoxicity that dysregulated processes governing the plausible adverse outcome pathway for memory loss. CONCLUSION Creating miR-target interaction networks related to pathological processes involved in sAD initiation and progression, and environmental chemical-induced neurotoxicity, respectively, provided overlapping miR-target interaction networks. This overlap offered an opportunity to create an alternative picture of the mechanisms underlying sAD initiation and early progression. Looking at initiation and progression of sAD from this new angle may open for new biomarkers and novel drug targets for sAD before the appearance of the first clinical symptoms.
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Affiliation(s)
- Maria Tsamou
- ToxGenSolutions (TGS), Maastricht, The Netherlands
| | - Donatella Carpi
- European Commission, Joint Research Centre (JRC), Ispra VA, Italy
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Su L, Li R, Zhang Z, Liu J, Du J, Wei H. Identification of altered exosomal microRNAs and mRNAs in Alzheimer's disease. Ageing Res Rev 2022; 73:101497. [PMID: 34710587 DOI: 10.1016/j.arr.2021.101497] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by decreased memory and cognitive functions. Exosomes carry a variety of important information such as proteins, lipids, DNA and RNA of mother cells. It is reported that exosomes play critical roles in nervous system physiology and neurodegenerative diseases. However, the functions of exosomes in AD progression are not fully elucidated. In this study, we detected the expression pattern of mRNAs and miRNAs in exosomes derived from the AD and health mice. A total of 1320 mRNAs and 29 miRNAs were differentially expressed in exosomes between the two groups. Subsequently, the downregulation of Chi3l1 and upregulation of Rhog in AD mice were verified by qRT-PCR. Meanwhile, the downregulation of miR-148a-5p and upregulation of miR-27a-5p in AD group were also tested by qRT-PCR. The functions of differentially expressed mRNAs and potential target genes of miRNAs were determined by GO and KEGG analysis. According to the ceRNA hypothesis, we established an integrated ceRNA network of circRNA-lncRNA-miRNA-mRNA. In conclusion, exosomal lncRNAs, mRNAs, circRNAs and miRNAs were identified to participate in the progression of AD which might be possible biomarkers and therapeutic targets for AD.
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Affiliation(s)
- Lining Su
- Department of Basic Medicine, Hebei North University, Zhangjiakou, China.
| | - Renqing Li
- Department of Basic Medicine, Hebei North University, Zhangjiakou, China.
| | - Zhiqing Zhang
- Department of Basic Medicine, Hebei North University, Zhangjiakou, China.
| | - Jijia Liu
- Department of Basic Medicine, Hebei North University, Zhangjiakou, China.
| | - Jingkao Du
- Department of Basic Medicine, Hebei North University, Zhangjiakou, China.
| | - Huiping Wei
- Department of Basic Medicine, Hebei North University, Zhangjiakou, China.
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36
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Gowda P, Reddy PH, Kumar S. Deregulated mitochondrial microRNAs in Alzheimer's disease: Focus on synapse and mitochondria. Ageing Res Rev 2022; 73:101529. [PMID: 34813976 PMCID: PMC8692431 DOI: 10.1016/j.arr.2021.101529] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/17/2021] [Accepted: 11/16/2021] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia and is currently one of the biggest public health concerns in the world. Mitochondrial dysfunction in neurons is one of the major hallmarks of AD. Emerging evidence suggests that mitochondrial miRNAs potentially play important roles in the mitochondrial dysfunctions, focusing on synapse in AD progression. In this meta-analysis paper, a comprehensive literature review was conducted to identify and discuss the (1) role of mitochondrial miRNAs that regulate mitochondrial and synaptic functions; (2) the role of various factors such as mitochondrial dynamics, biogenesis, calcium signaling, biological sex, and aging on synapse and mitochondrial function; (3) how synapse damage and mitochondrial dysfunctions contribute to AD; (4) the structure and function of synapse and mitochondria in the disease process; (5) latest research developments in synapse and mitochondria in healthy and disease states; and (6) therapeutic strategies that improve synaptic and mitochondrial functions in AD. Specifically, we discussed how differences in the expression of mitochondrial miRNAs affect ATP production, oxidative stress, mitophagy, bioenergetics, mitochondrial dynamics, synaptic activity, synaptic plasticity, neurotransmission, and synaptotoxicity in neurons observed during AD. However, more research is needed to confirm the locations and roles of individual mitochondrial miRNAs in the development of AD.
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Affiliation(s)
- Prashanth Gowda
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Subodh Kumar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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Sun C, Liu J, Duan F, Cong L, Qi X. The role of the microRNA regulatory network in Alzheimer's disease: a bioinformatics analysis. Arch Med Sci 2022; 18:206-222. [PMID: 35154541 PMCID: PMC8826944 DOI: 10.5114/aoms/80619] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disease which presents with an earlier age of onset and increased symptom severity. The objective of this study was to evaluate the relationship between regulation of miRNAs and AD. MATERIAL AND METHODS We completed a bioinformatic analysis of miRNA-AD studies through multiple databases such as TargetScan, Database for Annotation, Visualization and Integrated Discovery (DAVID), FunRich and String and assessed which miRNAs are commonly elevated or decreased in brain tissues, cerebrospinal fluid (CSF) and blood of AD patients. All identified articles were assessed using specific inclusion and exclusion criteria. RESULTS MiRNAs related to AD of twenty-eight studies were assessed in this study. A wide range of miRNAs were up-regulated or down-regulated in tissues of AD patients' brain, blood and CSF. Twenty-seven differentially dysregulated miRNAs involved in amyloidogenesis, inflammation, tau phosphorylation, apoptosis, synaptogenesis, neurotrophism, neuron degradation, and activation of cell cycle entry were identified. Additionally, our bioinformatics analysis identified the top ten functions of common miRNAs in candidate studies. The functions of common up-regulated miRNAs primarily target the nucleus and common down-regulated miRNAs primarily target transcription, DNA-templated. CONCLUSIONS Comprehensive analysis of all miRNA studies reveals cooperation in miRNA signatures whether in brain tissues or in CSF and peripheral blood. More and more studies suggest that miRNAs may play crucial roles as diagnostic biomarkers and/or as new therapeutic targets in AD. According to biomarkers, we can identify the preclinical phase early, which provides an important time window for therapeutic intervention.
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Affiliation(s)
- Chenjing Sun
- Department of Neurology, PLA Navy General Hospital, Haidian District, Beijing, China
| | - Jianguo Liu
- Department of Neurology, PLA Navy General Hospital, Haidian District, Beijing, China
| | - Feng Duan
- Department of Neurology, PLA Navy General Hospital, Haidian District, Beijing, China
| | - Lin Cong
- Department of Orthopedic Surgery, The First Hospital of China Medical University, Heping District, Shenyang City, Liaoning Province, China
| | - Xiaokun Qi
- Department of Neurology, PLA Navy General Hospital, Haidian District, Beijing, China
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38
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Belkozhayev AM, Al-Yozbaki M, George A, Niyazova RY, Sharipov KO, Byrne LJ, Wilson CM. Extracellular Vesicles, Stem Cells and the Role of miRNAs in Neurodegeneration. Curr Neuropharmacol 2022; 20:1450-1478. [PMID: 34414870 PMCID: PMC9881087 DOI: 10.2174/1570159x19666210817150141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/16/2021] [Accepted: 06/14/2021] [Indexed: 11/22/2022] Open
Abstract
There are different modalities of intercellular communication governed by cellular homeostasis. In this review, we will explore one of these forms of communication called extracellular vesicles (EVs). These vesicles are released by all cells in the body and are heterogeneous in nature. The primary function of EVs is to share information through their cargo consisting of proteins, lipids and nucleic acids (mRNA, miRNA, dsDNA etc.) with other cells, which have a direct consequence on their microenvironment. We will focus on the role of EVs of mesenchymal stem cells (MSCs) in the nervous system and how these participate in intercellular communication to maintain physiological function and provide neuroprotection. However, deregulation of this same communication system could play a role in several neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, multiple sclerosis, prion disease and Huntington's disease. The release of EVs from a cell provides crucial information to what is happening inside the cell and thus could be used in diagnostics and therapy. We will discuss and explore new avenues for the clinical applications of using engineered MSC-EVs and their potential therapeutic benefit in treating neurodegenerative diseases.
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Affiliation(s)
- Ayaz M. Belkozhayev
- Al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, Almaty, Republic of Kazakhstan
- Structural and Functional Genomics Laboratory of M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Minnatallah Al-Yozbaki
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Alex George
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
- Jubilee Centre for Medical Research, Jubilee Mission Medical College & Research Institute, Thrissur, Kerala, India
| | - Raigul Ye Niyazova
- Al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, Almaty, Republic of Kazakhstan
| | - Kamalidin O. Sharipov
- Structural and Functional Genomics Laboratory of M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Lee J. Byrne
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Cornelia M. Wilson
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
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Ye Y, Ke Y, Liu L, Xiao T, Yu J. CircRNA FAT1 Regulates Osteoblastic Differentiation of Periodontal Ligament Stem Cells via miR-4781-3p/SMAD5 Pathway. Stem Cells Int 2021; 2021:5177488. [PMID: 35003269 PMCID: PMC8731273 DOI: 10.1155/2021/5177488] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 12/13/2022] Open
Abstract
The ability of human periodontal ligament stem cells (PDLSCs) to differentiate into osteoblasts is significant in periodontal regeneration tissue engineering. In this study, we explored the role and mechanism of circRNA FAT1 (circFAT1) in the osteogenic differentiation of human PDLSCs. The proliferation capacity of PDLSCs was evaluated by EdU and CCK-8 assay. The abilities of circFAT1 and miR-4781-3p in regulating PDLSC differentiation were analyzed by western blot, reverse transcription-polymerase chain reaction (RT-PCR), alkaline phosphatase (ALP), and Alizarin red staining (ARS). A nucleocytoplasmic separation experiment was utilized for circFAT1 localization. A dual-luciferase reporter assay confirmed the binding relationship between miR-4781-3p and circFAT1. It was showed that circFAT1 does not affect the proliferation of PDLSCs. The osteogenic differentiation of PDLSCs was benefited from circFAT1, which serves as a miRNA sponge for miR-4781-3p targeting SMAD5. Both knockdown of circFAT1 and overexpression of miR-4781-3p suppressed the osteogenic differentiation of PDLSCs. Thus, circFAT1 might be considered as a potential target of PDLSCs mediated periodontal bone regeneration.
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Affiliation(s)
- Yu Ye
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University & Department of Endodontic, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Institute of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yue Ke
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University & Department of Endodontic, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Institute of Stomatology, Nanjing Medical University, Nanjing, China
| | - Liu Liu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University & Department of Endodontic, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Institute of Stomatology, Nanjing Medical University, Nanjing, China
| | - Tong Xiao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University & Department of Endodontic, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Institute of Stomatology, Nanjing Medical University, Nanjing, China
| | - Jinhua Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University & Department of Endodontic, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Institute of Stomatology, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
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40
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Li SR, Man QW, Gao X, Lin H, Wang J, Su FC, Wang HQ, Bu LL, Liu B, Chen G. Tissue-derived extracellular vesicles in cancers and non-cancer diseases: Present and future. J Extracell Vesicles 2021; 10:e12175. [PMID: 34918479 PMCID: PMC8678102 DOI: 10.1002/jev2.12175] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/02/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid‐bilayer membrane structures secreted by most cell types. EVs act as messengers via the horizontal transfer of lipids, proteins, and nucleic acids, and influence various pathophysiological processes in both parent and recipient cells. Compared to EVs obtained from body fluids or cell culture supernatants, EVs isolated directly from tissues possess a number of advantages, including tissue specificity, accurate reflection of tissue microenvironment, etc., thus, attention should be paid to tissue‐derived EVs (Ti‐EVs). Ti‐EVs are present in the interstitium of tissues and play pivotal roles in intercellular communication. Moreover, Ti‐EVs provide an excellent snapshot of interactions among various cell types with a common histological background. Thus, Ti‐EVs may be used to gain insights into the development and progression of diseases. To date, extensive investigations have focused on the role of body fluid‐derived EVs or cell culture‐derived EVs; however, the number of studies on Ti‐EVs remains insufficient. Herein, we summarize the latest advances in Ti‐EVs for cancers and non‐cancer diseases. We propose the future application of Ti‐EVs in basic research and clinical practice. Workflows for Ti‐EV isolation and characterization between cancers and non‐cancer diseases are reviewed and compared. Moreover, we discuss current issues associated with Ti‐EVs and provide potential directions.
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Affiliation(s)
- Su-Ran Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Qi-Wen Man
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Oral Maxillofacial Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Xin Gao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hao Lin
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jing Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Fu-Chuan Su
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Han-Qi Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Lin-Lin Bu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Oral Maxillofacial Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Bing Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Oral Maxillofacial Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Gang Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Oral Maxillofacial Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
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Posttranscriptional regulation of Nrf2 through miRNAs and their role in Alzheimer's disease. Pharmacol Res 2021; 175:106018. [PMID: 34863823 DOI: 10.1016/j.phrs.2021.106018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022]
Abstract
The nuclear factor erythroid-derived 2-related factor 2 (NFE2L2/Nrf2) is a pivotal facilitator of cytoprotective responses against the oxidative/electrophilic insults. Upon activation, Nrf2 induces transcription of a wide range of cytoprotective genes having antioxidant response element (ARE) in their promoter region. Dysfunction in Nrf2 signaling has been linked to the pathogenesis of AD and several studies have suggested that boosting Nrf2 expression/activity by genetic or pharmacological approaches is beneficial in AD. Among the diverse mechanisms that regulate the Nrf2 signaling, miRNAs-mediated regulation of Nrf2 has gained much attention in recent years. Several miRNAs have been reported to directly repress the post-transcriptional expression of Nrf2 and thereby negatively regulate the Nrf2-dependent cellular cytoprotective response in AD. Moreover, several Nrf2 targeting miRNAs are misregulated in AD brains. This review is focused on the role of misregulated miRNAs that directly target Nrf2, in AD pathophysiology. Here, alongside a general description of functional interactions between miRNAs and Nrf2, we have reviewed the evidence indicating the possible role of these miRNAs in AD pathogenesis.
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42
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Walgrave H, Zhou L, De Strooper B, Salta E. The promise of microRNA-based therapies in Alzheimer's disease: challenges and perspectives. Mol Neurodegener 2021; 16:76. [PMID: 34742333 PMCID: PMC8572071 DOI: 10.1186/s13024-021-00496-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/17/2021] [Indexed: 02/06/2023] Open
Abstract
Multi-pathway approaches for the treatment of complex polygenic disorders are emerging as alternatives to classical monotarget therapies and microRNAs are of particular interest in that regard. MicroRNA research has come a long way from their initial discovery to the cumulative appreciation of their regulatory potential in healthy and diseased brain. However, systematic interrogation of putative therapeutic or toxic effects of microRNAs in (models of) Alzheimer's disease is currently missing and fundamental research findings are yet to be translated into clinical applications. Here, we review the literature to summarize the knowledge on microRNA regulation in Alzheimer's pathophysiology and to critically discuss whether and to what extent these increasing insights can be exploited for the development of microRNA-based therapeutics in the clinic.
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Affiliation(s)
- Hannah Walgrave
- VIB Center for Brain & Disease Research, Leuven, KU, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Lujia Zhou
- Division of Janssen Pharmaceutica NV, Discovery Neuroscience, Janssen Research and Development, Beerse, Belgium
| | - Bart De Strooper
- VIB Center for Brain & Disease Research, Leuven, KU, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
- UK Dementia Research Institute at University College London, London, UK
| | - Evgenia Salta
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
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Abuelezz NZ, Nasr FE, AbdulKader MA, Bassiouny AR, Zaky A. MicroRNAs as Potential Orchestrators of Alzheimer's Disease-Related Pathologies: Insights on Current Status and Future Possibilities. Front Aging Neurosci 2021; 13:743573. [PMID: 34712129 PMCID: PMC8546247 DOI: 10.3389/fnagi.2021.743573] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/13/2021] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive and deleterious neurodegenerative disease, strongly affecting the cognitive functions and memory of seniors worldwide. Around 58% of the affected patients live in low and middle-income countries, with estimates of increasing deaths caused by AD in the coming decade. AD is a multifactor pathology. Mitochondrial function declines in AD brain and is currently emerging as a hallmark of this disease. It has been considered as one of the intracellular processes severely compromised in AD. Many mitochondrial parameters decline already during aging; mitochondrial efficiency for energy production, reactive oxygen species (ROS) metabolism and the de novo synthesis of pyrimidines, to reach an extensive functional failure, concomitant with the onset of neurodegenerative conditions. Besides its impact on cognitive functions, AD is characterized by loss of synapses, extracellular amyloid plaques composed of the amyloid-β peptide (Aβ), and intracellular aggregates of hyperphosphorylated Tau protein, accompanied by drastic sleep disorders, sensory function alterations and pain sensitization. Unfortunately, till date, effective management of AD-related disorders and early, non-invasive AD diagnostic markers are yet to be found. MicroRNAs (miRNAs) are small non-coding nucleic acids that regulate key signaling pathway(s) in various disease conditions. About 70% of experimentally detectable miRNAs are expressed in the brain where they regulate neurite outgrowth, dendritic spine morphology, and synaptic plasticity. Increasing studies suggest that miRNAs are intimately involved in synaptic function and specific signals during memory formation. This has been the pivotal key for considering miRNAs crucial molecules to be studied in AD. MicroRNAs dysfunctions are increasingly acknowledged as a pivotal contributor in AD via deregulating genes involved in AD pathogenesis. Moreover, miRNAs have been proved to control pain sensitization processes and regulate circadian clock system that affects the sleep process. Interestingly, the differential expression of miRNA panels implies their emerging potential as diagnostic AD biomarkers. In this review, we will present an updated analysis of miRNAs role in regulating signaling processes that are involved in AD-related pathologies. We will discuss the current challenges against wider use of miRNAs and the future promising capabilities of miRNAs as diagnostic and therapeutic means for better management of AD.
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Affiliation(s)
- Nermeen Z Abuelezz
- Biochemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Giza, Egypt
| | - Fayza Eid Nasr
- Department of Biochemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
| | | | - Ahmad R Bassiouny
- Department of Biochemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Amira Zaky
- Department of Biochemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
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García-Fonseca Á, Martin-Jimenez C, Barreto GE, Pachón AFA, González J. The Emerging Role of Long Non-Coding RNAs and MicroRNAs in Neurodegenerative Diseases: A Perspective of Machine Learning. Biomolecules 2021; 11:1132. [PMID: 34439798 PMCID: PMC8391852 DOI: 10.3390/biom11081132] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022] Open
Abstract
Neurodegenerative diseases (NDs) are characterized by progressive neuronal dysfunction and death of brain cells population. As the early manifestations of NDs are similar, their symptoms are difficult to distinguish, making the timely detection and discrimination of each neurodegenerative disorder a priority. Several investigations have revealed the importance of microRNAs and long non-coding RNAs in neurodevelopment, brain function, maturation, and neuronal activity, as well as its dysregulation involved in many types of neurological diseases. Therefore, the expression pattern of these molecules in the different NDs have gained significant attention to improve the diagnostic and treatment at earlier stages. In this sense, we gather the different microRNAs and long non-coding RNAs that have been reported as dysregulated in each disorder. Since there are a vast number of non-coding RNAs altered in NDs, some sort of synthesis, filtering and organization method should be applied to extract the most relevant information. Hence, machine learning is considered as an important tool for this purpose since it can classify expression profiles of non-coding RNAs between healthy and sick people. Therefore, we deepen in this branch of computer science, its different methods, and its meaningful application in the diagnosis of NDs from the dysregulated non-coding RNAs. In addition, we demonstrate the relevance of machine learning in NDs from the description of different investigations that showed an accuracy between 85% to 95% in the detection of the disease with this tool. All of these denote that artificial intelligence could be an excellent alternative to help the clinical diagnosis and facilitate the identification diseases in early stages based on non-coding RNAs.
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Affiliation(s)
- Ángela García-Fonseca
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Á.G.-F.); (C.M.-J.); (A.F.A.P.)
| | - Cynthia Martin-Jimenez
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Á.G.-F.); (C.M.-J.); (A.F.A.P.)
| | - George E. Barreto
- Department of Biological Sciences, University of Limerick, V94 T9PX Limerick, Ireland;
| | - Andres Felipe Aristizábal Pachón
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Á.G.-F.); (C.M.-J.); (A.F.A.P.)
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Á.G.-F.); (C.M.-J.); (A.F.A.P.)
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Zhang WT, Zhang GX, Gao SS. The potential diagnostic accuracy of circulating microRNAs for Alzheimer's disease: A meta-analysis. Neurologia 2021:S0213-4853(21)00103-1. [PMID: 34301434 DOI: 10.1016/j.nrl.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND & OBJECTIVE Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disease that seriously affects cognitive ability and has become a key public health problem. Many studies have identified the possibility of peripheral blood microRNA as effective non-invasive biomarkers for AD diagnosis, but the results are inconsistent. Therefore, we carried out this meta-analysis to evaluate the diagnostic accuracy of circulating microRNAs in the diagnosis of AD patients. METHODS We performed a systematic literature search of the following databases: PubMed, EMBASE, Web of Science, Cochrane Library, Wanfang database and China National Knowledge Infrastructure, updated to March 15, 2021. A random effects model was used to pool the sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio and area under the curve. Meta-regression and subgroup analysis were performed to explore the sources of heterogeneity, and Deeks' funnel plot was used to assess whether there was publication bias. RESULTS 62 studies from 18 articles were included in this meta-analysis. The pooled sensitivity was 0.82 (95% CI: 0.78-0.85), specificity was 0.80 (95% CI: 0.76-0.83), PLR was 4. 1 (95% CI: 3.4-4.9), NLR was 0.23 (95% CI: 0.19-0.28), DOR was 18 (95% CI: 13-25) and AUC was 0.88 (95% CI: 0.84-0.90). Subgroup analysis shows that the microRNA clusters of plasma type performed a better diagnostic accuracy of AD patients. In addition, publication bias was not found. CONCLUSIONS Circulating microRNAs can be used as a promising non-invasive biomarker in AD diagnosis.
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Affiliation(s)
- W T Zhang
- Xi'an Daxing Hospital, Shaanxi, China; International Doctoral School, University of Seville, Spain
| | - G X Zhang
- International Doctoral School, University of Seville, Spain
| | - S S Gao
- Xi'an Daxing Hospital, Shaanxi, China; International Doctoral School, University of Seville, Spain.
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Lin F, Zhang H, Bao J, Li L. Identification of Potential Diagnostic miRNAs Biomarkers for Alzheimer Disease Based on Weighted Gene Coexpression Network Analysis. World Neurosurg 2021; 153:e315-e328. [PMID: 34224891 DOI: 10.1016/j.wneu.2021.06.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Alzheimer disease (AD) is an age-related neurodegenerative disease that accounts for nearly three fourths of dementia cases. Searching for potential biomarkers will help clinicians in the early diagnosis and treatment of AD. METHODS Firstly, we downloaded detailed AD data from the Gene Expression Omnibus (GEO) database for identification of differentially expressed microribonucleic acids (DEmiRNAs) and differentially expressed messenger ribonucleic acids (DEmRNAs). Secondly, functional enrichment analysis was used to identify the biological functions of DEmRNAs. Thirdly, weighted gene coexpression network analysis was used to identify important modules and hub miRNAs. In addition, the miRNA-mRNA regulatory network was constructed. Fourthly, the GSE120584 dataset was used for electronic expression verification and diagnostic analysis. Finally, real-time polymerase chain reaction in vitro verification was performed. RESULTS We obtained 1005 DEmiRNAs and 97 DEmRNAs, respectively. Functional enrichment found that DEmRNAs was enriched in the N-glycan biosynthesis pathway, which was associated with AD. In the weighted gene coexpression network analysis, we found that the brown module was the optimal module. Moreover, 11 hub miRNAs were identified. A total of 216 negatively regulated miRNA-mRNA regulation effects are involved. Hub miRNAs were found to have potential diagnostic value in the receiver operating characteristic analysis. CONCLUSION Eleven hub miRNAs were identified, and DEmRNAs was found to be significantly enriched in the N-glycan biosynthesis pathway, which contributes to the early diagnosis and treatment of AD.
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Affiliation(s)
- Feng Lin
- Department of Neurology, The Second People's Hospital of Liaocheng City, The Second Hospital of Liaocheng Affiliated to Shandong First Medical University, Linqing City, China
| | - Haiqi Zhang
- Department of Neurology, The Second People's Hospital of Liaocheng City, The Second Hospital of Liaocheng Affiliated to Shandong First Medical University, Linqing City, China
| | - Jinglei Bao
- Department of Neurology, The Second People's Hospital of Liaocheng City, The Second Hospital of Liaocheng Affiliated to Shandong First Medical University, Linqing City, China.
| | - Long Li
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
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Van der Auwera S, Ameling S, Nauck M, Völzke H, Völker U, Grabe HJ. Association between different dimensions of childhood traumatization and plasma micro-RNA levels in a clinical psychiatric sample. J Psychiatr Res 2021; 139:113-119. [PMID: 34058649 DOI: 10.1016/j.jpsychires.2021.05.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/26/2021] [Accepted: 05/20/2021] [Indexed: 09/30/2022]
Abstract
As an epigenetic regulator micro-RNAs (miRNAs) have gained increasing attention in biomarker research for diseases. Many studies point towards an involvement of miRNAs in neuropsychiatric disorders such as Alzheimer's Disease, schizophrenia or depression. In a recent study we identified a possible relationship between childhood traumatization and miRNAs associated with Alzheimer's Disease in the general population as well as in a small psychiatric clinical sample. In this study we aimed to confirm this biological link in an independent psychiatric clinical sample (N = 104) and to also explore the impact of different childhood trauma dimensions (sum score, abuse dimension and neglect dimension). Analyses revealed their different impact on disease in the combined sample (N = 154; N = 50 from the recent study). We could confirm associations for all of the four recently identified miRNAs in the replication sample (N = 104) on a suggested significance level of p < 0.08 (two with p < 0.05). In the combined sample (N = 154) fifteen miRNAs were significantly associated with the childhood trauma sum score after correction for multiple testing. Most of them showed recently significant associations for Alzheimer's Disease. For the subscores of abuse and neglect only one miRNA was identified in addition, associated with childhood neglect. Bioinformatics analysis identified significant brain-related pathways regulated by the respective miRNAs. At the time of publication our study is the largest study of the association between childhood trauma and miRNAs in a clinical psychiatric sample. The confirmation of our previous results supports the relevance of the association between childhood traumatization and Alzheimer's Disease through miRNA regulation of brain-related pathways.
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Affiliation(s)
- Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; German Centre for Neurodegenerative Diseases (DZNE), Site Rostock, Greifswald, Germany.
| | - Sabine Ameling
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Matthias Nauck
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany; Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; German Centre for Neurodegenerative Diseases (DZNE), Site Rostock, Greifswald, Germany
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48
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Luo Y, Ji H, Cao Y, Ding X, Li M, Song H, Li S, WaTableng C, Wu H, Meng J, Du H. miR-26b-5p/TCF-4 Controls the Adipogenic Differentiation of Human Adipose-derived Mesenchymal Stem Cells. Cell Transplant 2021; 29:963689720934418. [PMID: 32579400 PMCID: PMC7563810 DOI: 10.1177/0963689720934418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In this study, we assessed the ability of miR-26b-5p to regulate T cell factor 4 (TCF-4) expression and thereby control human adipose-derived mesenchymal stem cell (hADMSC) adipogenic differentiation. Adipogenic medium was used to induce hADMSC differentiation over a 6-d period. The ability of miR-26b-5p to interact with the TCF-4 mRNA was confirmed through both predictive bioinformatics analyses and luciferase reporter assays. Immunofluorescent staining was used to visualize the impact of miR-26b-5p inhibition or overexpression on TCF-4 and β-catenin levels in hADMSCs. Further functional analyses were conducted by transfecting these cells with siRNAs specific for TCF-4 and β-catenin. Adipogenic marker and Wnt/β-catenin pathway gene expression levels were assessed via real-time polymerase chain reaction and western blotting. β-catenin localization was assessed via immunofluorescent staining. As expected, our adipogenic media induced the adipocytic differentiation of hADMSCs. In addition, we confirmed that TCF-4 is an miR-26b-5p target gene in these cells, and that protein levels of both TCF-4 and β-catenin were reduced when these cells were transfected with miR-26b-5p mimics. Overexpression of this microRNA also enhanced hADMSC adipogenesis, whereas TCF-4 and β-catenin overexpression inhibited this process. The enhanced hADMSC adipogenic differentiation that was observed following TCF-4 or β-catenin knockdown was partially reversed when miR-26b-5p expression was inhibited. We found that miR-26b-5p serves as a direct negative regulator of TCF-4 expression within hADMSCs, leading to inactivation of the Wnt/β-catenin pathway and thereby promoting the adipogenic differentiation of these cells in vitro.
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Affiliation(s)
- Yadong Luo
- Department of Stomatology, Central Hospital of Xuzhou, the Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, Jiangsu Province, PR China.,These authors contributed equally to this article
| | - Huan Ji
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,These authors contributed equally to this article
| | - Yan Cao
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,These authors contributed equally to this article
| | - Xu Ding
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Meng Li
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Haiyang Song
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Sheng Li
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Chenxing WaTableng
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Heming Wu
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Jian Meng
- Department of Stomatology, Central Hospital of Xuzhou, the Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, Jiangsu Province, PR China.,Both authors are co-corresponding authors
| | - Hongming Du
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province, PR China.,Both authors are co-corresponding authors
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Zhang H, Liu W, Ge H, Li K. Aberrant expression of miR-148a-3p in Alzheimer's disease and its protective role against amyloid-β induced neurotoxicity. Neurosci Lett 2021; 756:135953. [PMID: 33979697 DOI: 10.1016/j.neulet.2021.135953] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/15/2021] [Accepted: 05/07/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The current study investigated the expression change and clinical value of miR-148a-3p in AD patients, and further examined the role of miR-148a-3p in Aβ-induced neurotoxicity in SH-SY5Y cells. MATERIAL AND METHODS qRT-PCR was used for the measurement of miR-148a-3p expression levels. ROC curve was established to calculate the diagnostic value of serum miR-148a-3p for AD. CCK-8 and flow cytometry assay was applied for the detection of cell viability and apoptosis. Additionally, the luciferase reporter assay was performed to confirm the target relationship between ROCK1 and miR-148a-3p. RESULTS Serum miR-148a-3p was downregulated in AD patients compared with that in healthy controls, and was positively associated with the MMSE score in AD patients. Serum miR-148a-3p had the potential to distinguish AD patients from healthy controls, and the diagnostic sensitivity and specificity were respectively 85.5 % and 87.0 % at a cutoff value of 0.827. MiR-148a-3p attenuated Aβ25-35 induced neurotoxicity in SH-SY5Y cells, and ROCK1 was the target gene. CONCLUSION Serum miR-148a-3p is correlated with MMSE score in AD patients, and it might be helpful for the AD diagnosis. Overexpression of miR-148a-3p attenuated Aβ induced neurotoxicity in AD by targeting ROCK1.
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Affiliation(s)
- Hao Zhang
- The First Department of Neurology, Rizhao People's Hospital, Rizhao, 276800, Shandong, China
| | - Wei Liu
- Department of Neurology, Zhucheng People's Hospital, Zhucheng, 262200, Shandong, China
| | - Hongliang Ge
- Department of Neurology, Shanxian Central Hospital, Heze, 274300, Shandong, China
| | - Kun Li
- Department of Neurology, Shanxian Central Hospital, Heze, 274300, Shandong, China.
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50
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Pan Y, Zhan L, Chen L, Chen L, Sun C. miR-660 promotes liver cancer cell proliferation by targeting PPP2R2A. Exp Ther Med 2021; 22:683. [PMID: 33986848 DOI: 10.3892/etm.2021.10115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 11/25/2019] [Indexed: 12/31/2022] Open
Abstract
Liver cancer (LC) is the leading cause for tumor-related death worldwide, and microRNAs (miRs) have been demonstrated to regulate the progression of LC. In the current study, the function of miR-660 in LC cells was investigated, and the results indicated that miR-660 was highly expressed in LC tissues and cells. This increased expression promoted LC cell proliferation and increased the percentage of S phase cells, while miR-660 knockdown inhibited cell proliferation and increased the percentage of G0/G1 phase cells. A Ser/Thr phosphatase protein phosphatase 2 regulatory subunit βα (PPP2R2A) was indicated as the target of miR-660, and miR-660 could inhibit PPP2R2A levels. The luciferase reporter assay suggested that miR-660 directly bound to the 3'-untranslated region of PPP2R2A. Additionally, it was revealed that miR-660 inhibited p21 expression and promoted cyclin D1 expression, confirming that miR-660 regulated LC cell proliferation by regulating cell cycle progression. The double knockdown of miR-660 and PPP2R2A promoted LC cell proliferation, suggesting that miR-660 promoted LC proliferation by targeting PPP2R2A.
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Affiliation(s)
- Yaozhen Pan
- Department of Biliary-Hepatic Surgery, The Affiliated Tumor Hospital of Guizhou Medical University, Guiyang, Guizhou 550000, P.R China.,Department of Biliary-Hepatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550025, P.R China
| | - Lei Zhan
- Department of Biliary-Hepatic Surgery, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550000, P.R China
| | - Ling Chen
- Department of Biliary-Hepatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550025, P.R China
| | - Liwen Chen
- Department of Biliary-Hepatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550025, P.R China
| | - Chengyi Sun
- Department of Biliary-Hepatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550025, P.R China
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