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Ahammad I, Lamisa AB, Bhattacharjee A, Jamal TB, Arefin MS, Chowdhury ZM, Hossain MU, Das KC, Keya CA, Salimullah M. AITeQ: a machine learning framework for Alzheimer's prediction using a distinctive five-gene signature. Brief Bioinform 2024; 25:bbae291. [PMID: 38877887 PMCID: PMC11179120 DOI: 10.1093/bib/bbae291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
Neurodegenerative diseases, such as Alzheimer's disease, pose a significant global health challenge with their complex etiology and elusive biomarkers. In this study, we developed the Alzheimer's Identification Tool (AITeQ) using ribonucleic acid-sequencing (RNA-seq), a machine learning (ML) model based on an optimized ensemble algorithm for the identification of Alzheimer's from RNA-seq data. Analysis of RNA-seq data from several studies identified 87 differentially expressed genes. This was followed by a ML protocol involving feature selection, model training, performance evaluation, and hyperparameter tuning. The feature selection process undertaken in this study, employing a combination of four different methodologies, culminated in the identification of a compact yet impactful set of five genes. Twelve diverse ML models were trained and tested using these five genes (CNKSR1, EPHA2, CLSPN, OLFML3, and TARBP1). Performance metrics, including precision, recall, F1 score, accuracy, Matthew's correlation coefficient, and receiver operating characteristic area under the curve were assessed for the finally selected model. Overall, the ensemble model consisting of logistic regression, naive Bayes classifier, and support vector machine with optimized hyperparameters was identified as the best and was used to develop AITeQ. AITeQ is available at: https://github.com/ishtiaque-ahammad/AITeQ.
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Affiliation(s)
- Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Anika Bushra Lamisa
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Tabassum Binte Jamal
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Md Shamsul Arefin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
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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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Subramanian K, Varghese R, Pochedly M, Muralidaran V, Yazigi N, Kaufman S, Khan K, Vitola B, Kroemer A, Fishbein T, Ressom H, Ekong UD. Non-fatal outcomes of COVID-19 disease in pediatric organ transplantation associates with down-regulation of senescence pathways. Sci Rep 2024; 14:1877. [PMID: 38253675 PMCID: PMC10803774 DOI: 10.1038/s41598-024-52456-y] [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: 09/28/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
This is a cross-sectional study examining kinetics and durability of immune response in children with solid organ transplants (SOTs) who had COVID-19 disease between November 2020 through June 2022, who were followed for 60-days at a single transplant center. Blood was collected between 1-14 (acute infection), and 15-60 days of a positive PCR (convalescence). SOT children with peripheral blood mononuclear cells (PBMC) cryopreserved before 2019 were non-infected controls (ctrls). PBMCs stimulated with 15-mer peptides from spike protein and anti-CD49d/anti-CD28. Testing done included mass cytometry, mi-RNA sequencing with confirmatory qPCR. 38 children formed the study cohort, 10 in the acute phase and 8 in the convalescence phase. 20 subjects were non-infected controls. Two subjects had severe disease. Subjects in the acute and convalescent phases were different subjects. The median age and tacrolimus level at blood draw was not significantly different. There was no death, and no subject was lost to follow-up. During acute infection CD57 expression was low in NKT, Th17 effector memory, memory Treg, CD4-CD8-, and γδT cells (p = 0.01, p = 0.04, p = 0.03, p = 0.03, p = 0.004 respectively). The frequencies of NK and Th2 effector memory cells increased (p = 0.01, p = 0.02) during acute infection. Non-switched memory B and CD8 central memory cell frequencies were decreased during acute infection (p = 0.02; p = 0.02), but the decrease in CD8 central memory cells did not persist. CD4-CD8- and CD14 monocyte frequencies increased during recovery (p = 0.03; p = 0.007). Our observations suggest down regulation of CD57 with absence of NK cell contraction protect against death from COVID-19 disease in children with SOTs.
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Affiliation(s)
- Kumar Subramanian
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Rency Varghese
- Department of Oncology, Genomics, and Epigenomics Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Molly Pochedly
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Vinona Muralidaran
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Nada Yazigi
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Stuart Kaufman
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Khalid Khan
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Bernadette Vitola
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Alexander Kroemer
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Thomas Fishbein
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA
| | - Habtom Ressom
- Department of Oncology, Genomics, and Epigenomics Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Udeme D Ekong
- Medstar Georgetown Transplant Institute, Medstar Georgetown University Hospital, 3800 Reservoir Rd, NW, Washington, DC, USA.
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Zhang T, Kim BM, Lee TH. Death-associated protein kinase 1 as a therapeutic target for Alzheimer's disease. Transl Neurodegener 2024; 13:4. [PMID: 38195518 PMCID: PMC10775678 DOI: 10.1186/s40035-023-00395-5] [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: 10/04/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024] Open
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia in the elderly and represents a major clinical challenge in the ageing society. Neuropathological hallmarks of AD include neurofibrillary tangles composed of hyperphosphorylated tau, senile plaques derived from the deposition of amyloid-β (Aβ) peptides, brain atrophy induced by neuronal loss, and synaptic dysfunctions. Death-associated protein kinase 1 (DAPK1) is ubiquitously expressed in the central nervous system. Dysregulation of DAPK1 has been shown to contribute to various neurological diseases including AD, ischemic stroke and Parkinson's disease (PD). We have established an upstream effect of DAPK1 on Aβ and tau pathologies and neuronal apoptosis through kinase-mediated protein phosphorylation, supporting a causal role of DAPK1 in the pathophysiology of AD. In this review, we summarize current knowledge about how DAPK1 is involved in various AD pathological changes including tau hyperphosphorylation, Aβ deposition, neuronal cell death and synaptic degeneration. The underlying molecular mechanisms of DAPK1 dysregulation in AD are discussed. We also review the recent progress regarding the development of novel DAPK1 modulators and their potential applications in AD intervention. These findings substantiate DAPK1 as a novel therapeutic target for the development of multifunctional disease-modifying treatments for AD and other neurological disorders.
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Affiliation(s)
- Tao Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Byeong Mo Kim
- Research Center for New Drug Development, AgingTarget Inc., 10F Ace Cheonggye Tower, 53, Seonggogae-Ro, Uiwang-Si, 16006, Gyeonggi-Do, Korea.
| | - Tae Ho Lee
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, 1 Xuefu North Road, Fuzhou, 350122, Fujian, China.
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5
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Tavares-Júnior JWL, Ciurleo GCV, Feitosa EDAAF, Oriá RB, Braga-Neto P. The Clinical Aspects of COVID and Alzheimer's Disease: A Round-Up of Where Things Stand and Are Headed. J Alzheimers Dis 2024; 99:1159-1171. [PMID: 38848177 DOI: 10.3233/jad-231368] [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] [Indexed: 06/09/2024]
Abstract
The link between long COVID-19 and brain/cognitive impairments is concerning and may foster a worrisome worldwide emergence of novel cases of neurodegenerative diseases with aging. This review aims to update the knowledge, crosstalk, and possible intersections between the Post-COVID Syndrome (PCS) and Alzheimer's disease (AD). References included in this review were obtained from PubMed searches conducted between October 2023 and November 2023. PCS is a very heterogenous and poorly understood disease with recent evidence of a possible association with chronic diseases such as AD. However, more scientific data is required to establish the link between PCS and AD.
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Affiliation(s)
| | - Gabriella Cunha Vieira Ciurleo
- Department of Clinical Medicine, Neurology Section, Faculty of Medicine, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
- Department of Morphology and Institute of Biomedicine, Laboratory of the Biology of Tissue Healing, Ontogeny and Nutrition, School of Medicine, Federal University of Ceara, Fortaleza, CE, Brazil
| | | | - Reinaldo B Oriá
- Department of Clinical Medicine, Neurology Section, Faculty of Medicine, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
- Department of Morphology and Institute of Biomedicine, Laboratory of the Biology of Tissue Healing, Ontogeny and Nutrition, School of Medicine, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Pedro Braga-Neto
- Department of Clinical Medicine, Neurology Section, Faculty of Medicine, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
- Center of Health Sciences, State University of Ceará, Fortaleza, CE, Brazil
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Shvetcov A, Thomson S, Spathos J, Cho AN, Wilkins HM, Andrews SJ, Delerue F, Couttas TA, Issar JK, Isik F, Kaur S, Drummond E, Dobson-Stone C, Duffy SL, Rogers NM, Catchpoole D, Gold WA, Swerdlow RH, Brown DA, Finney CA. Blood-Based Transcriptomic Biomarkers Are Predictive of Neurodegeneration Rather Than Alzheimer's Disease. Int J Mol Sci 2023; 24:15011. [PMID: 37834458 PMCID: PMC10573468 DOI: 10.3390/ijms241915011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
Alzheimer's disease (AD) is a growing global health crisis affecting millions and incurring substantial economic costs. However, clinical diagnosis remains challenging, with misdiagnoses and underdiagnoses being prevalent. There is an increased focus on putative, blood-based biomarkers that may be useful for the diagnosis as well as early detection of AD. In the present study, we used an unbiased combination of machine learning and functional network analyses to identify blood gene biomarker candidates in AD. Using supervised machine learning, we also determined whether these candidates were indeed unique to AD or whether they were indicative of other neurodegenerative diseases, such as Parkinson's disease (PD) and amyotrophic lateral sclerosis (ALS). Our analyses showed that genes involved in spliceosome assembly, RNA binding, transcription, protein synthesis, mitoribosomes, and NADH dehydrogenase were the best-performing genes for identifying AD patients relative to cognitively healthy controls. This transcriptomic signature, however, was not unique to AD, and subsequent machine learning showed that this signature could also predict PD and ALS relative to controls without neurodegenerative disease. Combined, our results suggest that mRNA from whole blood can indeed be used to screen for patients with neurodegeneration but may be less effective in diagnosing the specific neurodegenerative disease.
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Affiliation(s)
- Artur Shvetcov
- Department of Psychological Medicine, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shannon Thomson
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Jessica Spathos
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Ann-Na Cho
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Heather M. Wilkins
- University of Kansas Alzheimer’s Disease Research Centre, Kansas City, KS 66160, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
- Department of Neurology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
| | - Shea J. Andrews
- Department of Psychiatry & Behavioral Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Fabien Delerue
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy A. Couttas
- Brain and Mind Centre, Translational Research Collective, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Jasmeen Kaur Issar
- Molecular Neurobiology Research Laboratory, Kids Research, Children’s Medical Research Institute, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Finula Isik
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Simranpreet Kaur
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Department of Pediatrics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Eleanor Drummond
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Carol Dobson-Stone
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Shantel L. Duffy
- Allied Health, Research and Strategic Partnerships, Nepean Blue Mountains Local Health District, Penrith, NSW 2750, Australia
| | - Natasha M. Rogers
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Renal and Transplant Medicine Unit, Westmead Hospital, Westmead, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Daniel Catchpoole
- The Tumor Bank, Kids Research, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Children’s Cancer Research Institute, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Wendy A. Gold
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
- Molecular Neurobiology Research Laboratory, Kids Research, Children’s Medical Research Institute, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Russell H. Swerdlow
- University of Kansas Alzheimer’s Disease Research Centre, Kansas City, KS 66160, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
- Department of Neurology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Centre, Kansas City, KS 66160, USA
| | - David A. Brown
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Immunopathology, Institute for Clinical Pathology and Medical Research-New South Wales Health Pathology, Sydney, NSW 2145, Australia
| | - Caitlin A. Finney
- Neuroinflammation Research Group, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- School of Medical Sciences, Faculty of Medicine Health, The University of Sydney, Sydney, NSW 2050, Australia
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Lilhore UK, Dalal S, Faujdar N, Margala M, Chakrabarti P, Chakrabarti T, Simaiya S, Kumar P, Thangaraju P, Velmurugan H. Hybrid CNN-LSTM model with efficient hyperparameter tuning for prediction of Parkinson's disease. Sci Rep 2023; 13:14605. [PMID: 37669970 PMCID: PMC10480168 DOI: 10.1038/s41598-023-41314-y] [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: 02/21/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
The patients' vocal Parkinson's disease (PD) changes could be identified early on, allowing for management before physically incapacitating symptoms appear. In this work, static as well as dynamic speech characteristics that are relevant to PD identification are examined. Speech changes or communication issues are among the challenges that Parkinson's individuals may encounter. As a result, avoiding the potential consequences of speech difficulties brought on by the condition depends on getting the appropriate diagnosis early. PD patients' speech signals change significantly from those of healthy individuals. This research presents a hybrid model utilizing improved speech signals with dynamic feature breakdown using CNN and LSTM. The proposed hybrid model employs a new, pre-trained CNN with LSTM to recognize PD in linguistic features utilizing Mel-spectrograms derived from normalized voice signal and dynamic mode decomposition. The proposed Hybrid model works in various phases, which include Noise removal, extraction of Mel-spectrograms, feature extraction using pre-trained CNN model ResNet-50, and the final stage is applied for classification. An experimental analysis was performed using the PC-GITA disease dataset. The proposed hybrid model is compared with traditional NN and well-known machine learning-based CART and SVM & XGBoost models. The accuracy level achieved in Neural Network, CART, SVM, and XGBoost models is 72.69%, 84.21%, 73.51%, and 90.81%. The results show that under these four machine approaches of tenfold cross-validation and dataset splitting without samples overlapping one individual, the proposed hybrid model achieves an accuracy of 93.51%, significantly outperforming traditional ML models utilizing static features in detecting Parkinson's disease.
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Affiliation(s)
- Umesh Kumar Lilhore
- Department of Computer Science and Engineering, Chandigarh University, Chandigarh, Punjab, India
| | - Surjeet Dalal
- Amity School of Engineering and Technology, Amity University Haryana, Gurugram, India
| | - Neetu Faujdar
- Department of Computer Engineering and Application, GLA University, Mathura, Uttar Pradesh, India
| | - Martin Margala
- School of Computing and Informatics, University of Louisiana at Lafayette, Lafayette, USA
| | - Prasun Chakrabarti
- Department of Computer Science and Engineering, Sir Padampat Singhania University, Udaipur, 313601, Rajasthan, India
| | | | - Sarita Simaiya
- Department of Computer Science and Engineering, Chandigarh University, Chandigarh, Punjab, India
- Apex Institute of Technology, Department of Computer Science and Engineering, Chandigarh University, Mohali, Punjab, India
| | - Pawan Kumar
- Department of Computer Science and Engineering, Chandigarh University, Chandigarh, Punjab, India
- College of Computing Sciences & IT, Teerthanker Mahaveer University, Moradabad, Uttar Pradesh, India
| | - Pugazhenthan Thangaraju
- Department of Pharmacology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India.
| | - Hemasri Velmurugan
- Department of Pharmacology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
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Awuson-David B, Williams AC, Wright B, Hill LJ, Di Pietro V. Common microRNA regulated pathways in Alzheimer's and Parkinson's disease. Front Neurosci 2023; 17:1228927. [PMID: 37719162 PMCID: PMC10502311 DOI: 10.3389/fnins.2023.1228927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in gene regulation. Recently, miRNA dysregulation has been found in neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). The diagnosis of Alzheimer's and Parkinson's is currently challenging, mainly occurring when pathology is already present, and although treatments are available for both diseases, the role of treatment is primarily to prevent or delay the progress of the diseases instead of fully overcoming the diseases. Therefore, the challenge in the near future will be to determine effective drugs to tackle the dysregulated biological pathways in neurodegenerative diseases. In the present study, we describe the dysregulation of miRNAs in blood of Alzheimer's and Parkinson's patients with the aim to identify common mechanisms between the 2 pathologies and potentially to identify common therapeutic targets which can stop or delay the progression of two most frequent neuropathologies. Two independent systematic reviews, bioinformatic analysis, and experiment validation were performed to identify whether AD and PD share common pathways. A total of 15 common miRNAs were found in the literature and 13 common KEGG pathways. Among the common miRNAs, two were selected for validation in a small cohort of AD and PD patients. Let-7f-5p and miR-29b-3p showed to be good predictors in blood of PD patients.
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Affiliation(s)
- Betina Awuson-David
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Adrian C. Williams
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Benjamin Wright
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Lisa J. Hill
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Valentina Di Pietro
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
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Li M, Larsen PA. Single-cell sequencing of entorhinal cortex reveals widespread disruption of neuropeptide networks in Alzheimer's disease. Alzheimers Dement 2023; 19:3575-3592. [PMID: 36825405 DOI: 10.1002/alz.12979] [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: 11/30/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 02/25/2023]
Abstract
INTRODUCTION Abnormalities of neuropeptides (NPs) that play important roles in modulating neuronal activities are commonly observed in Alzheimer's disease (AD). We hypothesize that NP network disruption is widespread in AD brains. METHODS Single-cell transcriptomic data from the entorhinal cortex (EC) were used to investigate the NP network disruption in AD. Bulk RNA-sequencing data generated from the temporal cortex by independent groups and machine learning were employed to identify key NPs involved in AD. The relationship between aging and AD-associated NP (ADNP) expression was studied using GTEx data. RESULTS The proportion of cells expressing NPs but not their receptors decreased significantly in AD. Neurons expressing higher level and greater diversity of NPs were disproportionately absent in AD. Increased age coincides with decreased ADNP expression in the hippocampus. DISCUSSION NP network disruption is widespread in AD EC. Neurons expressing more NPs may be selectively vulnerable to AD. Decreased expression of NPs participates in early AD pathogenesis. We predict that the NP network can be harnessed for treatment and/or early diagnosis of AD.
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Affiliation(s)
- Manci Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA
- Minnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA
- Minnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
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Magen I, Yacovzada NS, Warren JD, Heller C, Swift I, Bobeva Y, Malaspina A, Rohrer JD, Fratta P, Hornstein E. microRNA-based predictor for diagnosis of frontotemporal dementia. Neuropathol Appl Neurobiol 2023; 49:e12916. [PMID: 37317649 DOI: 10.1111/nan.12916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/28/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023]
Abstract
AIMS This study aimed to explore the non-linear relationships between cell-free microRNAs (miRNAs) and their contribution to prediction of Frontotemporal dementia (FTD), an early onset dementia that is clinically heterogeneous, and too often suffers from delayed diagnosis. METHODS We initially studied a training cohort of 219 subjects (135 FTD and 84 non-neurodegenerative controls) and then validated the results in a cohort of 74 subjects (33 FTD and 41 controls). RESULTS On the basis of cell-free plasma miRNA profiling by next generation sequencing and machine learning approaches, we develop a non-linear prediction model that accurately distinguishes FTD from non-neurodegenerative controls in ~90% of cases. CONCLUSIONS The fascinating potential of diagnostic miRNA biomarkers might enable early-stage detection and a cost-effective screening approach for clinical trials that can facilitate drug development.
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Affiliation(s)
- Iddo Magen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy-Sarah Yacovzada
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Jason D Warren
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Carolin Heller
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Imogen Swift
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Yoana Bobeva
- Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Jonathan D Rohrer
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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11
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Ruan Y, Deng X, Liu J, Xiao X, Yang Z. Identification of miRNAs in extracellular vesicles as potential diagnostic markers for pediatric epilepsy and drug-resistant epilepsy via bioinformatics analysis. Front Pediatr 2023; 11:1199780. [PMID: 37469680 PMCID: PMC10352456 DOI: 10.3389/fped.2023.1199780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023] Open
Abstract
Background Pediatric epilepsy (PE) is a common neurological disease. However, many challenges regarding the clinical diagnosis and treatment of PE and drug-resistant epilepsy (DRE) remain unsettled. Our study aimed to identify potential miRNA biomarkers in children with epilepsy and drug-resistant epilepsy by scrutinizing differential miRNA expression profiles. Methods In this study, miRNA expression profiles in plasma extracellular vesicles (EV) of normal controls, children with drug-effective epilepsy (DEE), and children with DRE were obtained. In addition, differential analysis, transcription factor (TF) enrichment analysis, Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, and target gene prediction were used to identify specifically expressed miRNAs and their potential mechanisms of action. Potential diagnostic markers for DRE were identified using machine learning algorithms, and their diagnostic efficiency was assessed by the receiver operating characteristic curve (ROC). Results The hsa-miR-1307-3p, hsa-miR-196a-5p, hsa-miR-199a-3p, and hsa-miR-21-5p were identified as diagnostic markers for PE, with values of area under curve (AUC) 0.780, 0.840, 0.832, and 0.816, respectively. In addition, the logistic regression model incorporating these four miRNAs had an AUC value of 0.940, and its target gene enrichment analysis highlighted that these miRNAs were primarily enriched in the PI3K-Akt, MAPK signaling pathways, and cell cycle. Furthermore, hsa-miR-99a-5p, hsa-miR-532-5p, hsa-miR-181d-5p, and hsa-miR-181a-5p showed good performance in differentiating children with DRE from those with DEE, with AUC values of 0.737 (0.534-0.940), 0.737 (0.523-0.952), 0.788 (0.592-0.985), and 0.788 (0.603-0.974), respectively. Conclusion This study characterized the expression profile of miRNAs in plasma EVs of children with epilepsy and identified miRNAs that can be used for the diagnosis of DRE.
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Affiliation(s)
- Yucai Ruan
- Department of Pediatrics, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Xuhui Deng
- Department of Neurology, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Jun Liu
- Medical Research Center and Clinical Laboratory Medicine, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Xiaobing Xiao
- Department of Pediatrics, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Zhi Yang
- Department of Pediatrics, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Department of Neurology, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
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12
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Dongiovanni P, Meroni M, Casati S, Goldoni R, Thomaz DV, Kehr NS, Galimberti D, Del Fabbro M, Tartaglia GM. Salivary biomarkers: novel noninvasive tools to diagnose chronic inflammation. Int J Oral Sci 2023; 15:27. [PMID: 37386003 DOI: 10.1038/s41368-023-00231-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 07/01/2023] Open
Abstract
Several chronic disorders including type 2 diabetes (T2D), obesity, heart disease and cancer are preceded by a state of chronic low-grade inflammation. Biomarkers for the early assessment of chronic disorders encompass acute phase proteins (APP), cytokines and chemokines, pro-inflammatory enzymes, lipids and oxidative stress mediators. These substances enter saliva through the blood flow and, in some cases, there is a close relation between their salivary and serum concentration. Saliva can be easily collected and stored with non-invasive and cost-saving procedures, and it is emerging the concept to use it for the detection of inflammatory biomarkers. To this purpose, the present review aims to discuss the advantages and challenges of using standard and cutting-edge techniques to discover salivary biomarkers which may be used in diagnosis/therapy of several chronic diseases with inflammatory consequences with the pursuit to possibly replace conventional paths with detectable soluble mediators in saliva. Specifically, the review describes the procedures used for saliva collection, the standard approaches for the measurement of salivary biomarkers and the novel methodological strategies such as biosensors to improve the quality of care for chronically affected patients.
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Affiliation(s)
- Paola Dongiovanni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marica Meroni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sara Casati
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy.
| | - Riccardo Goldoni
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milan, Italy
- Istituto di Elettronica e di Ingegneria dell'Informazione e delle Telecomunicazioni, CNR, Pisa, Italy
| | - Douglas Vieira Thomaz
- Laboratory of Medicinal Pharmaceutical Chemistry, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil
| | - Nermin Seda Kehr
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Department of Chemistry, İzmir Institute of Technology, Gülbahçe Kampüsü, Urla İzmir, Turkey
| | - Daniela Galimberti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Neurology-Neurodegenerative Diseases, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Massimo Del Fabbro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- UOC Maxillo-Facial Surgery and Dentistry Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Gianluca M Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- UOC Maxillo-Facial Surgery and Dentistry Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
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13
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Vrahatis AG, Skolariki K, Krokidis MG, Lazaros K, Exarchos TP, Vlamos P. Revolutionizing the Early Detection of Alzheimer's Disease through Non-Invasive Biomarkers: The Role of Artificial Intelligence and Deep Learning. SENSORS (BASEL, SWITZERLAND) 2023; 23:4184. [PMID: 37177386 PMCID: PMC10180573 DOI: 10.3390/s23094184] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
Alzheimer's disease (AD) is now classified as a silent pandemic due to concerning current statistics and future predictions. Despite this, no effective treatment or accurate diagnosis currently exists. The negative impacts of invasive techniques and the failure of clinical trials have prompted a shift in research towards non-invasive treatments. In light of this, there is a growing need for early detection of AD through non-invasive approaches. The abundance of data generated by non-invasive techniques such as blood component monitoring, imaging, wearable sensors, and bio-sensors not only offers a platform for more accurate and reliable bio-marker developments but also significantly reduces patient pain, psychological impact, risk of complications, and cost. Nevertheless, there are challenges concerning the computational analysis of the large quantities of data generated, which can provide crucial information for the early diagnosis of AD. Hence, the integration of artificial intelligence and deep learning is critical to addressing these challenges. This work attempts to examine some of the facts and the current situation of these approaches to AD diagnosis by leveraging the potential of these tools and utilizing the vast amount of non-invasive data in order to revolutionize the early detection of AD according to the principles of a new non-invasive medicine era.
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Affiliation(s)
| | | | - Marios G. Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece
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14
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Alamro H, Thafar MA, Albaradei S, Gojobori T, Essack M, Gao X. Exploiting machine learning models to identify novel Alzheimer’s disease biomarkers and potential targets. Sci Rep 2023; 13:4979. [PMID: 36973386 PMCID: PMC10043000 DOI: 10.1038/s41598-023-30904-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
AbstractWe still do not have an effective treatment for Alzheimer's disease (AD) despite it being the most common cause of dementia and impaired cognitive function. Thus, research endeavors are directed toward identifying AD biomarkers and targets. In this regard, we designed a computational method that exploits multiple hub gene ranking methods and feature selection methods with machine learning and deep learning to identify biomarkers and targets. First, we used three AD gene expression datasets to identify 1/ hub genes based on six ranking algorithms (Degree, Maximum Neighborhood Component (MNC), Maximal Clique Centrality (MCC), Betweenness Centrality (BC), Closeness Centrality, and Stress Centrality), 2/ gene subsets based on two feature selection methods (LASSO and Ridge). Then, we developed machine learning and deep learning models to determine the gene subset that best distinguishes AD samples from the healthy controls. This work shows that feature selection methods achieve better prediction performances than the hub gene sets. Beyond this, the five genes identified by both feature selection methods (LASSO and Ridge algorithms) achieved an AUC = 0.979. We further show that 70% of the upregulated hub genes (among the 28 overlapping hub genes) are AD targets based on a literature review and six miRNA (hsa-mir-16-5p, hsa-mir-34a-5p, hsa-mir-1-3p, hsa-mir-26a-5p, hsa-mir-93-5p, hsa-mir-155-5p) and one transcription factor, JUN, are associated with the upregulated hub genes. Furthermore, since 2020, four of the six microRNA were also shown to be potential AD targets. To our knowledge, this is the first work showing that such a small number of genes can distinguish AD samples from healthy controls with high accuracy and that overlapping upregulated hub genes can narrow the search space for potential novel targets.
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15
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Liang X, Fa W, Wang N, Peng Y, Liu C, Zhu M, Tian N, Wang Y, Han X, Qiu C, Hou T, Du Y. Exosomal miR-532-5p induced by long-term exercise rescues blood-brain barrier function in 5XFAD mice via downregulation of EPHA4. Aging Cell 2022; 22:e13748. [PMID: 36494892 PMCID: PMC9835579 DOI: 10.1111/acel.13748] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
The breakdown of the blood-brain barrier, which develops early in Alzheimer's disease (AD), contributes to cognitive impairment. Exercise not only reduces the risk factors for AD but also confers direct protection against cognitive decline. However, the exact molecular mechanisms remain elusive, particularly whether exercise can liberate the function of the blood-brain barrier. Here, we demonstrate that long-term exercise promotes the clearance of brain amyloid-β by improving the function of the blood-brain barrier in 5XFAD mice. Significantly, treating primary brain pericytes or endothelial cells with exosomes isolated from the brain of exercised 5XFAD mice improves cell proliferation and upregulates PDGFRβ, ZO-1, and claudin-5. Moreover, exosomes isolated from exercised mice exhibit significant changes in miR-532-5p. Administration or transfection of miR-532-5p to sedentary mice or primary brain pericytes and endothelial cells reproduces the improvement of blood-brain barrier function. Exosomal miR-532-5p targets EPHA4, and accordingly, expression of EphA4 is decreased in exercised mice and miR-532-5p overexpressed mice. A specific siRNA targeting EPHA4 recapitulates the effects on blood-brain barrier-associated cells observed in exercised 5XFAD mice. Overall, our findings suggest that exosomes released by the brain contain a specific miRNA that is altered by exercise and has an impact on blood-brain barrier function in AD.
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Affiliation(s)
- Xiaoyan Liang
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina
| | - Wenxin Fa
- Department of NeurologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
| | - Nan Wang
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina
| | - Yuanming Peng
- Department of Clinical LaboratoryThird Hospital of JinanShandongChina
| | - Cuicui Liu
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina,Department of NeurologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina,Shandong Provincial Clinical Research Center for Neurological DiseasesJinanShandongChina
| | - Min Zhu
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina,Department of NeurologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina,Shandong Provincial Clinical Research Center for Neurological DiseasesJinanShandongChina
| | - Na Tian
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina,Department of NeurologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina,Shandong Provincial Clinical Research Center for Neurological DiseasesJinanShandongChina
| | - Yongxiang Wang
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina,Department of NeurologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina,Shandong Provincial Clinical Research Center for Neurological DiseasesJinanShandongChina
| | - Xiaolei Han
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina
| | - Chengxuan Qiu
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina,Aging Research Center and Center for Alzheimer Research, Department of Neurobiology, Care Sciences and SocietyKarolinska Institutet‐Stockholm UniversitySolnaSweden
| | - Tingting Hou
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina,Department of NeurologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina,Shandong Provincial Clinical Research Center for Neurological DiseasesJinanShandongChina
| | - Yifeng Du
- Department of NeurologyShandong Provincial Hospital, Shandong UniversityJinanShandongChina,Department of NeurologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina,Shandong Provincial Clinical Research Center for Neurological DiseasesJinanShandongChina
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16
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Feng H, Tang Q, Yu Z, Tang H, Yin M, Wei A. A Machine Learning Applied Diagnosis Method for Subcutaneous Cyst by Ultrasonography. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1526540. [PMID: 36299601 PMCID: PMC9592196 DOI: 10.1155/2022/1526540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 11/18/2022]
Abstract
For decades, ultrasound images have been widely used in the detection of various diseases due to their high security and efficiency. However, reading ultrasound images requires years of experience and training. In order to support the diagnosis of clinicians and reduce the workload of doctors, many ultrasonic computer aided diagnostic systems have been proposed. In recent years, the success of deep learning in image classification and segmentation has made more and more scholars realize the potential performance improvement brought by the application of deep learning in ultrasonic computer-aided diagnosis systems. This study is aimed at applying several machine learning algorithms and develop a machine learning method to diagnose subcutaneous cyst. Clinical features are extracted from datasets and images of ultrasonography of 132 patients from Hunan Provincial People's Hospital in China. All datasets are separated into 70% training and 30% testing. Four kinds of machine learning algorithms including decision tree (DT), support vector machine (SVM), K-nearest neighbors (KNN), and neural networks (NN) had been approached to determine the best performance. Compared with all the results from each feature, SVM achieved the best performance from 91.7% to 100%. Results show that SVM performed the highest accuracy in the diagnosis of subcutaneous cyst by ultrasonography, which provide a good reference in further application to clinical practice of ultrasonography of subcutaneous cyst.
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Affiliation(s)
- Hao Feng
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, China
| | - Qian Tang
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, China
| | - Zhengyu Yu
- Faculty of Engineering and IT, University of Technology, Sydney, Sydney, NSW 2007, Australia
| | - Hua Tang
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, China
| | - Ming Yin
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, China
| | - An Wei
- Department of Ultrasound, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, China
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17
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Ramírez AE, Gil-Jaramillo N, Tapias MA, González-Giraldo Y, Pinzón A, Puentes-Rozo PJ, Aristizábal-Pachón AF, González J. MicroRNA: A Linking between Astrocyte Dysfunction, Mild Cognitive Impairment, and Neurodegenerative Diseases. Life (Basel) 2022; 12:life12091439. [PMID: 36143475 PMCID: PMC9505027 DOI: 10.3390/life12091439] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 12/06/2022] Open
Abstract
Simple Summary Neurodegenerative diseases are complex neurological disorders with a high incidence worldwide in older people, increasing hospital visits and requiring expensive treatments. As a precursor phase of neurodegenerative diseases, cognitive impairment needs to be studied to understand the factors that influence its development and improve patients’ quality of life. The present review compiles possible factors and biomarkers for diagnosing mild cognitive impairment based on the most recent studies involving miRNAs. These molecules can direct the gene expression in multiple cells, affecting their behavior under certain conditions, such as stressing factors. This review encourages further research into biomarkers that identify cognitive impairment in cellular models such as astrocytes, which are brain cells capable of maintaining the optimal conditions for the central nervous system functioning. Abstract The importance of miRNAs in cellular processes and their dysregulation has taken significant importance in understanding different pathologies. Due to the constant increase in the prevalence of neurodegenerative diseases (ND) worldwide and their economic impact, mild cognitive impairment (MCI), considered a prodromal phase, is a logical starting point to study this public health problem. Multiple studies have established the importance of miRNAs in MCI, including astrocyte regulation during stressful conditions. Additionally, the protection mechanisms exerted by astrocytes against some damage in the central nervous system (CNS) lead to astrocytic reactivation, in which a differential expression of miRNAs has been shown. Nevertheless, excessive reactivation can cause neurodegeneration, and a clear pattern defining the equilibrium point between a neuroprotective or detrimental astrocytic phenotype is unknown. Therefore, the miRNA expression has gained significant attention to understand the maintenance of brain balance and improve the diagnosis and treatment at earlier stages in the ND. Here, we provide a comprehensive review of the emerging role of miRNAs in cellular processes that contribute to the loss of cognitive function, including lipotoxicity, which can induce chronic inflammation, also considering the fundamental role of astrocytes in brain homeostasis.
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Affiliation(s)
- Angelica E. Ramírez
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Natalia Gil-Jaramillo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - María Alejandra Tapias
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Pedro J. Puentes-Rozo
- Grupo de Neurociencias del Caribe, Unidad de Neurociencias Cognitivas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Grupo de Neurociencias del Caribe, Universidad del Atlántico, Barranquilla 080007, Colombia
| | | | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
- Correspondence:
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18
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Mégret L, Mendoza C, Arrieta Lobo M, Brouillet E, Nguyen TTY, Bouaziz O, Chambaz A, Néri C. Precision machine learning to understand micro-RNA regulation in neurodegenerative diseases. Front Mol Neurosci 2022; 15:914830. [PMID: 36157078 PMCID: PMC9500540 DOI: 10.3389/fnmol.2022.914830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Micro-RNAs (miRNAs) are short (∼21 nt) non-coding RNAs that regulate gene expression through the degradation or translational repression of mRNAs. Accumulating evidence points to a role of miRNA regulation in the pathogenesis of a wide range of neurodegenerative (ND) diseases such as, for example, Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis and Huntington disease (HD). Several systems level studies aimed to explore the role of miRNA regulation in NDs, but these studies remain challenging. Part of the problem may be related to the lack of sufficiently rich or homogeneous data, such as time series or cell-type-specific data obtained in model systems or human biosamples, to account for context dependency. Part of the problem may also be related to the methodological challenges associated with the accurate system-level modeling of miRNA and mRNA data. Here, we critically review the main families of machine learning methods used to analyze expression data, highlighting the added value of using shape-analysis concepts as a solution for precisely modeling highly dimensional miRNA and mRNA data such as the ones obtained in the study of the HD process, and elaborating on the potential of these concepts and methods for modeling complex omics data.
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Affiliation(s)
- Lucile Mégret
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
- *Correspondence: Lucile Mégret,
| | - Cloé Mendoza
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
| | - Maialen Arrieta Lobo
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
| | - Emmanuel Brouillet
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
| | - Thi-Thanh-Yen Nguyen
- Université Paris Cité, MAP5 (Centre National de la Recherche Scientifique UMR 8145), Paris, France
| | - Olivier Bouaziz
- Université Paris Cité, MAP5 (Centre National de la Recherche Scientifique UMR 8145), Paris, France
| | - Antoine Chambaz
- Université Paris Cité, MAP5 (Centre National de la Recherche Scientifique UMR 8145), Paris, France
| | - Christian Néri
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
- Christian Néri,
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19
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Dobricic V, Schilling M, Schulz J, Zhu LS, Zhou CW, Fuß J, Franzenburg S, Zhu LQ, Parkkinen L, Lill CM, Bertram L. Differential microRNA expression analyses across two brain regions in Alzheimer's disease. Transl Psychiatry 2022; 12:352. [PMID: 36038535 PMCID: PMC9424308 DOI: 10.1038/s41398-022-02108-4] [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: 02/10/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
Dysregulation of microRNAs (miRNAs) is involved in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease (AD). Hitherto, sample sizes from differential miRNA expression studies in AD are exceedingly small aggravating any biological inference. To overcome this limitation, we investigated six candidate miRNAs in a large collection of brain samples. Brain tissue was derived from superior temporal gyrus (STG) and entorhinal cortex (EC) from 99 AD patients and 91 controls. MiRNA expression was examined by qPCR (STG) or small RNA sequencing (EC). Brain region-dependent differential miRNA expression was investigated in a transgenic AD mouse model using qPCR and FISH. Total RNA sequencing was used to assess differential expression of miRNA target genes. MiR-129-5p, miR-132-5p, and miR-138-5p were significantly downregulated in AD vs. controls both in STG and EC, while miR-125b-5p and miR-501-3p showed no evidence for differential expression in this dataset. In addition, miR-195-5p was significantly upregulated in EC but not STG in AD patients. The brain region-specific pattern of miR-195-5p expression was corroborated in vivo in transgenic AD mice. Total RNA sequencing identified several novel and functionally interesting target genes of these miRNAs involved in synaptic transmission (GABRB1), the immune-system response (HCFC2) or AD-associated differential methylation (SLC16A3). Using two different methods (qPCR and small RNA-seq) in two separate brain regions in 190 individuals we more than doubled the available sample size for most miRNAs tested. Differential gene expression analyses confirm the likely involvement of miR-129-5p, miR-132-5p, miR-138-5p, and miR-195-5p in AD pathogenesis and highlight several novel potentially relevant target mRNAs.
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Affiliation(s)
- Valerija Dobricic
- grid.4562.50000 0001 0057 2672Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Marcel Schilling
- grid.4562.50000 0001 0057 2672Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Jessica Schulz
- grid.4562.50000 0001 0057 2672Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Ling-Shuang Zhu
- grid.33199.310000 0004 0368 7223Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chao-Wen Zhou
- grid.33199.310000 0004 0368 7223Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Janina Fuß
- grid.412468.d0000 0004 0646 2097Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Sören Franzenburg
- grid.412468.d0000 0004 0646 2097Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ling-Qiang Zhu
- grid.33199.310000 0004 0368 7223Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Laura Parkkinen
- grid.4991.50000 0004 1936 8948Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, UK
| | - Christina M. Lill
- grid.4562.50000 0001 0057 2672Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany ,grid.7445.20000 0001 2113 8111Aging and Epidemiology Unit (AGE), School of Public Health, Imperial College London, London, UK ,grid.5949.10000 0001 2172 9288Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany. .,Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, Oslo, Norway.
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20
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Klyucherev TO, Olszewski P, Shalimova AA, Chubarev VN, Tarasov VV, Attwood MM, Syvänen S, Schiöth HB. Advances in the development of new biomarkers for Alzheimer's disease. Transl Neurodegener 2022; 11:25. [PMID: 35449079 PMCID: PMC9027827 DOI: 10.1186/s40035-022-00296-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 03/28/2022] [Indexed: 12/16/2022] Open
Abstract
Alzheimer's disease (AD) is a complex, heterogeneous, progressive disease and is the most common type of neurodegenerative dementia. The prevalence of AD is expected to increase as the population ages, placing an additional burden on national healthcare systems. There is a large need for new diagnostic tests that can detect AD at an early stage with high specificity at relatively low cost. The development of modern analytical diagnostic tools has made it possible to determine several biomarkers of AD with high specificity, including pathogenic proteins, markers of synaptic dysfunction, and markers of inflammation in the blood. There is a considerable potential in using microRNA (miRNA) as markers of AD, and diagnostic studies based on miRNA panels suggest that AD could potentially be determined with high accuracy for individual patients. Studies of the retina with improved methods of visualization of the fundus are also showing promising results for the potential diagnosis of the disease. This review focuses on the recent developments of blood, plasma, and ocular biomarkers for the diagnosis of AD.
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Affiliation(s)
- Timofey O Klyucherev
- Department of Neuroscience, Functional Pharmacology, University of Uppsala, Uppsala, Sweden.,Department of Pharmacology, Institute of Pharmacy, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Pawel Olszewski
- Department of Neuroscience, Functional Pharmacology, University of Uppsala, Uppsala, Sweden
| | - Alena A Shalimova
- Department of Neuroscience, Functional Pharmacology, University of Uppsala, Uppsala, Sweden.,Department of Pharmacology, Institute of Pharmacy, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Vladimir N Chubarev
- Institute of Translational Medicine and Biotechnology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Vadim V Tarasov
- Department of Pharmacology, Institute of Pharmacy, I. M. Sechenov First Moscow State Medical University, Moscow, Russia.,Institute of Translational Medicine and Biotechnology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Misty M Attwood
- Department of Neuroscience, Functional Pharmacology, University of Uppsala, Uppsala, Sweden
| | - Stina Syvänen
- Department of Public Health and Caring Sciences, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, University of Uppsala, Uppsala, Sweden.
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21
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Noncoding RNA as Diagnostic and Prognostic Biomarkers in Cerebrovascular Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8149701. [PMID: 35498129 PMCID: PMC9042605 DOI: 10.1155/2022/8149701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/22/2022] [Indexed: 02/06/2023]
Abstract
Noncoding RNAs (ncRNAs), such as microRNAs, long noncoding RNAs, and circular RNAs, play an important role in the pathophysiology of cerebrovascular diseases (CVDs). They are effectively detectable in body fluids, potentially suggesting new biomarkers for the early detection and prognosis of CVDs. In this review, the physiological functions of circulating ncRNAs and their potential role as diagnostic and prognostic markers in patients with cerebrovascular diseases are discussed, especially in acute ischemic stroke, subarachnoid hemorrhage, and moyamoya disease.
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22
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Varesi A, Carrara A, Pires VG, Floris V, Pierella E, Savioli G, Prasad S, Esposito C, Ricevuti G, Chirumbolo S, Pascale A. Blood-Based Biomarkers for Alzheimer's Disease Diagnosis and Progression: An Overview. Cells 2022; 11:1367. [PMID: 35456047 PMCID: PMC9044750 DOI: 10.3390/cells11081367] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 01/10/2023] Open
Abstract
Alzheimer's Disease (AD) is a progressive neurodegenerative disease characterized by amyloid-β (Aβ) plaque deposition and neurofibrillary tangle accumulation in the brain. Although several studies have been conducted to unravel the complex and interconnected pathophysiology of AD, clinical trial failure rates have been high, and no disease-modifying therapies are presently available. Fluid biomarker discovery for AD is a rapidly expanding field of research aimed at anticipating disease diagnosis and following disease progression over time. Currently, Aβ1-42, phosphorylated tau, and total tau levels in the cerebrospinal fluid are the best-studied fluid biomarkers for AD, but the need for novel, cheap, less-invasive, easily detectable, and more-accessible markers has recently led to the search for new blood-based molecules. However, despite considerable research activity, a comprehensive and up-to-date overview of the main blood-based biomarker candidates is still lacking. In this narrative review, we discuss the role of proteins, lipids, metabolites, oxidative-stress-related molecules, and cytokines as possible disease biomarkers. Furthermore, we highlight the potential of the emerging miRNAs and long non-coding RNAs (lncRNAs) as diagnostic tools, and we briefly present the role of vitamins and gut-microbiome-related molecules as novel candidates for AD detection and monitoring, thus offering new insights into the diagnosis and progression of this devastating disease.
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Affiliation(s)
- Angelica Varesi
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
- Almo Collegio Borromeo, 27100 Pavia, Italy
| | - Adelaide Carrara
- Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy; (A.C.); (V.F.)
| | - Vitor Gomes Pires
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA;
| | - Valentina Floris
- Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy; (A.C.); (V.F.)
| | - Elisa Pierella
- School of Medicine, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK;
| | - Gabriele Savioli
- Emergency Department, IRCCS Policlinico San Matteo, 27100 Pavia, Italy;
| | - Sakshi Prasad
- Faculty of Medicine, National Pirogov Memorial Medical University, 21018 Vinnytsya, Ukraine;
| | - Ciro Esposito
- Unit of Nephrology and Dialysis, ICS Maugeri, University of Pavia, 27100 Pavia, Italy;
| | - Giovanni Ricevuti
- Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy
| | - Salvatore Chirumbolo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37129 Verona, Italy;
| | - Alessia Pascale
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, 27100 Pavia, Italy;
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23
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Wang B, Zhong JL, Jiang N, Shang J, Wu B, Chen YF, Lu HD. Exploring the Mystery of Osteoarthritis using Bioinformatics Analysis of Cartilage Tissue. Comb Chem High Throughput Screen 2022; 25:53-63. [PMID: 33292128 DOI: 10.2174/1386207323666201207100905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Osteoarthritis (OA) is a kind of chronic disease relating to joints, which seriously affectsthe daily life activities of the elderly and can also lead to disability. However, the pathogenesis of OA is still unclear, which leads to limited treatment and the therapeutic effect far from people's expectations. This study aims to filter out key genes in the pathogenesis of OA and explore their potential role in the occurrence and development of OA. METHODS The dataset of GSE117999 was obtained and analyzed in order to identify the differentially expressed genes (DEGs), hub genes and key genes. We also identified potential miRNAs which may play a major role in the pathogenesis of OA, and verified their difference in OA by real-time quantitative PCR (RT-qPCR). DGldb was found to serve as an indicator to identify drugs with potential therapeutic effects on key genes and Receiver Operating Characteristic (ROC) analysis was used for identifying underlying biomarkers of OA. RESULTS We identified ten key genes, including MDM2, RB1, EGFR, ESR1, UBE2E3, WWP1, BCL2, OAS2, TYMS and MSH2. Then, we identified hsa-mir-3613-3p, hsa-mir-548e-5p and hsamir- 5692a to be potentially related to key genes. In addition, RT-qPCR confirmed the differential expression of identified genes in mouse cartilage with or without OA. We then identified Etoposide and Everolimus, which were potentially specific to the most key genes. Finally, we speculated that ESR1 might be a potential biomarker of OA. CONCLUSION In this study, potential key genes related to OA and their biological functions were identified, and their potential application value in the diagnosis and treatment of OA has been demonstrated, which will help us to improve the therapeutic effect of OA.
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Affiliation(s)
- Bin Wang
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai 519000, Guangdong,China
| | - Jun-Long Zhong
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai 519000, Guangdong,China
| | - Ning Jiang
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai 519000, Guangdong,China
| | - Jie Shang
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai 519000, Guangdong,China
| | - Biao Wu
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai 519000, Guangdong,China
| | - Yu-Feng Chen
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai 519000, Guangdong,China
| | - Hua-Ding Lu
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai 519000, Guangdong,China
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24
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Jin S, Qin D, Liang BS, Zhang LC, Wei XX, Wang YJ, Zhuang B, Zhang T, Yang ZP, Cao YW, Jin SL, Yang P, Jiang B, Rao BQ, Shi HP, Lu Q. Machine learning predicts cancer-associated deep vein thrombosis using clinically available variables. Int J Med Inform 2022; 161:104733. [DOI: 10.1016/j.ijmedinf.2022.104733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/23/2022] [Accepted: 03/02/2022] [Indexed: 12/17/2022]
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25
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Sh Y, Liu B, Zhang J, Zhou Y, Hu Z, Zhang X. Application of Artificial Intelligence Modeling Technology Based on Fluid Biopsy to Diagnose Alzheimer's Disease. Front Aging Neurosci 2021; 13:768229. [PMID: 34924996 PMCID: PMC8679840 DOI: 10.3389/fnagi.2021.768229] [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] [Received: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Background: There are no obvious clinical signs and symptoms in the early stages of Alzheimer's disease (AD), and most patients usually have mild cognitive impairment (MCI) before diagnosis. Therefore, early diagnosis of AD is very critical. This paper mainly discusses the blood biomarkers of AD patients and uses machine learning methods to study the changes of blood transcriptome during the development of AD and to search for potential blood biomarkers for AD. Methods: Individualized blood mRNA expression data of 711 patients were downloaded from the GEO database, including the control group (CON) (238 patients), MCI (189 patients), and AD (284 patients). Firstly, we analyzed the subcellular localization, protein types and enrichment pathways of the differentially expressed mRNAs in each group, and established an artificial intelligence individualized diagnostic model. Furthermore, the XCell tool was used to analyze the blood mRNA expression data and obtain blood cell composition and quantitative data. Ratio characteristics were established for mRNA and XCell data. Feature engineering operations such as collinearity and importance analysis were performed on all features to obtain the best feature solicitation. Finally, four machine learning algorithms, including linear support vector machine (SVM), Adaboost, random forest and artificial neural network, were used to model the optimal feature combinations and evaluate their classification performance in the test set. Results: Through feature engineering screening, the best feature collection was obtained. Moreover, the artificial intelligence individualized diagnosis model established based on this method achieved a classification accuracy of 91.59% in the test set. The area under curve (AUC) of CON, MCI, and AD were 0.9746, 0.9536, and 0.9807, respectively. Conclusion: The results of cell homeostasis analysis suggested that the homeostasis of Natural killer T cell (NKT) might be related to AD, and the homeostasis of Granulocyte macrophage progenitor (GMP) might be one of the reasons for AD.
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Affiliation(s)
- Yuan Sh
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Benliang Liu
- China National Center for Bioinformation, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jianhu Zhang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Ying Zhou
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Zhiyuan Hu
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Chinese Academy of Sciences Key Laboratory of Standardization and Measurement for Nanotechnology, Chinese Academy of Sciences Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Chinese Academy of Sciences Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China.,School of Nanoscience and Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Xiuli Zhang
- Chinese Academy of Sciences Key Laboratory of Standardization and Measurement for Nanotechnology, Chinese Academy of Sciences Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Chinese Academy of Sciences Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
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26
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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: 59] [Impact Index Per Article: 19.7] [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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27
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Sonnenschein K, Stojanović SD, Dickel N, Fiedler J, Bauersachs J, Thum T, Kunz M, Tongers J. Artificial Intelligence Identifies an Urgent Need for Peripheral Vascular Intervention by Multiplexing Standard Clinical Parameters. Biomedicines 2021; 9:1456. [PMID: 34680572 PMCID: PMC8533252 DOI: 10.3390/biomedicines9101456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Peripheral artery disease (PAD) is a significant burden, particularly among patients with severe disease requiring invasive treatment. We applied a general Machine Learning (ML) workflow and investigated if a multi-dimensional marker set of standard clinical parameters can identify patients in need of vascular intervention without specialized intra-hospital diagnostics. METHODS This is a retrospective study involving patients with stable PAD (sPAD, Fontaine Class I and II, n = 38) and unstable PAD (unPAD, Fontaine Class III and IV, n = 18) in need of invasive therapeutic measures. ML algorithms such as Random Forest were utilized to evaluate a matrix consisting of multiple routinely clinically available parameters (age, complete blood count, inflammation, lipid, iron metabolism). RESULTS ML has enabled a generation of an Artificial Intelligence (AI) PAD score (AI-PAD) that successfully divided sPAD from unPAD patients (high AI-PAD in sPAD, low AI-PAD in unPAD, cutoff at 50 AI-PAD units). Furthermore, the probability score positively coincided with gold-standard intra-hospital mean ankle-brachial index (ABI). CONCLUSION AI-based tools may be promising to enable the correct identification of patients with unstable PAD by using existing clinical information, thus supplementing clinical decision making. Additional studies in larger prospective cohorts are necessary to determine the usefulness of this approach in comparison to standard diagnostic measures.
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Affiliation(s)
- Kristina Sonnenschein
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (S.D.S.); (J.F.); (T.T.)
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany; (J.B.); (J.T.)
| | - Stevan D. Stojanović
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (S.D.S.); (J.F.); (T.T.)
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany; (J.B.); (J.T.)
| | - Nicholas Dickel
- Chair of Medical Informatics, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91054 Erlangen, Germany; (N.D.); (M.K.)
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (S.D.S.); (J.F.); (T.T.)
- Fraunhofer Institute of Toxicology and Experimental Medicine, 30625 Hannover, Germany
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany; (J.B.); (J.T.)
- Center for Regenerative Translational Medicine, 30625 Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (S.D.S.); (J.F.); (T.T.)
- Fraunhofer Institute of Toxicology and Experimental Medicine, 30625 Hannover, Germany
- Center for Regenerative Translational Medicine, 30625 Hannover, Germany
| | - Meik Kunz
- Chair of Medical Informatics, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91054 Erlangen, Germany; (N.D.); (M.K.)
- Fraunhofer Institute of Toxicology and Experimental Medicine, 30625 Hannover, Germany
| | - Jörn Tongers
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany; (J.B.); (J.T.)
- Department of Internal Medicine III, Martin-Luther-University Halle-Wittenberg, 06097 Halle, Germany
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28
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MicroRNA-532-5p upregulation protects neurological deficits after ischemic stroke through inhibition of BTB and CNC homology 1. Int Immunopharmacol 2021; 100:108003. [PMID: 34464885 DOI: 10.1016/j.intimp.2021.108003] [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: 04/11/2021] [Revised: 06/23/2021] [Accepted: 07/18/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVE MicroRNA (miR)-532-5p has been reported to protect against ischemic stroke (IS), while the underlying mechanism of miR-532-5p targeting BTB and CNC homology 1 (BACH1) in IS remains unknown. Thus, we aim to detect the role of miR-532-5p in IS via targeting BACH1. METHODS Blood samples were collected from IS patients and healthy controls. Rat middle cerebral artery occlusion (MCAO) models were established and intracerebrally injected with altered miR-532-5p or BACH1 plasmid vectors to reveal their roles in neurological function, brain tissue pathology and inflammation in MCAO. Expression of miR-532-5p and BACH1 in patients' blood samples and rat brain tissues was assessed, and the targeting relationship between miR-532-5p and BACH1 was confirmed. RESULTS MiR-532-5p was downregulated and BACH1 was upregulated in IS. BACH1 was targeted by miR-532-5p. Restored miR-532-5p or inhibited BACH1 improved neurological function and inhibited inflammation and apoptosis in MCAO rats. On the contrary, miR-532-5p reduction or BACH1 overexpression had totally opposite effects on MCAO rats. The protective role of miR-532-5p for MCAO rats was reversed by upregulated BACH1. CONCLUSION MiR-532-5p upregulation protects against neurological deficits after IS through inhibition of BACH1.
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29
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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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Fehlmann T, Kern F, Laham O, Backes C, Solomon J, Hirsch P, Volz C, Müller R, Keller A. miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale. Nucleic Acids Res 2021; 49:W397-W408. [PMID: 33872372 PMCID: PMC8262700 DOI: 10.1093/nar/gkab268] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 01/19/2023] Open
Abstract
Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Omar Laham
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jeffrey Solomon
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Carsten Volz
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
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Yuen SC, Liang X, Zhu H, Jia Y, Leung SW. Prediction of differentially expressed microRNAs in blood as potential biomarkers for Alzheimer's disease by meta-analysis and adaptive boosting ensemble learning. Alzheimers Res Ther 2021; 13:126. [PMID: 34243793 PMCID: PMC8272278 DOI: 10.1186/s13195-021-00862-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 06/17/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Blood circulating microRNAs that are specific for Alzheimer's disease (AD) can be identified from differentially expressed microRNAs (DEmiRNAs). However, non-reproducible and inconsistent reports of DEmiRNAs hinder biomarker development. The most reliable DEmiRNAs can be identified by meta-analysis. To enrich the pool of DEmiRNAs for potential AD biomarkers, we used a machine learning method called adaptive boosting for miRNA disease association (ABMDA) to identify eligible candidates that share similar characteristics with the DEmiRNAs identified from meta-analysis. This study aimed to identify blood circulating DEmiRNAs as potential AD biomarkers by augmenting meta-analysis with the ABMDA ensemble learning method. METHODS Studies on DEmiRNAs and their dysregulation states were corroborated with one another by meta-analysis based on a random-effects model. DEmiRNAs identified by meta-analysis were collected as positive examples of miRNA-AD pairs for ABMDA ensemble learning. ABMDA identified similar DEmiRNAs according to a set of predefined criteria. The biological significance of all resulting DEmiRNAs was determined by their target genes according to pathway enrichment analyses. The target genes common to both meta-analysis- and ABMDA-identified DEmiRNAs were collected to construct a network to investigate their biological functions. RESULTS A systematic database search found 7841 studies for an extensive meta-analysis, covering 54 independent comparisons of 47 differential miRNA expression studies, and identified 18 reliable DEmiRNAs. ABMDA ensemble learning was conducted based on the meta-analysis results and the Human MicroRNA Disease Database, which identified 10 additional AD-related DEmiRNAs. These 28 DEmiRNAs and their dysregulated pathways were related to neuroinflammation. The dysregulated pathway related to neuronal cell cycle re-entry (CCR) was the only statistically significant pathway of the ABMDA-identified DEmiRNAs. In the biological network constructed from 1865 common target genes of the identified DEmiRNAs, the multiple core ubiquitin-proteasome system, that is involved in neuroinflammation and CCR, was highly connected. CONCLUSION This study identified 28 DEmiRNAs as potential AD biomarkers in blood, by meta-analysis and ABMDA ensemble learning in tandem. The DEmiRNAs identified by meta-analysis and ABMDA were significantly related to neuroinflammation, and the ABMDA-identified DEmiRNAs were related to neuronal CCR.
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Affiliation(s)
- Sze Chung Yuen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Xiaonan Liang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Hongmei Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Yongliang Jia
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan China
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Siu-wai Leung
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, China
- Edinburgh Bayes Centre for AI Research in Shenzhen, College of Science and Engineering, University of Edinburgh, Edinburgh, Scotland, UK
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Wu D, Ding Y, Fan J. Bioinformatics Analysis of Autophagy-related lncRNAs in Esophageal Carcinoma. Comb Chem High Throughput Screen 2021; 25:1374-1384. [PMID: 34170806 DOI: 10.2174/1386207324666210624143452] [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: 01/19/2021] [Revised: 04/01/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Esophageal carcinoma (ESCA) is a malignant tumor with high invasiveness and mortality. Autophagy has multiple roles in the development of cancer; however, there are limited data on autophagy genes associated with long non-coding RNAs (lncRNAs) in ESCA. The purpose of this study was to screen potential diagnostic and prognostic molecules and to identify gene co-expression networks associated with autophagy in ESCA. METHODS We downloaded transcriptome expression profiles from The Cancer Genome Atlas and autophagy-related gene data from the Human Autophagy Database and analyzed the co-expression of mRNAs and lncRNAs. In addition, the diagnostic and prognostic value of autophagy-related lncRNAs was analyzed by multivariate Cox regression. Furthermore, Kyoto Encyclopedia of Genes and Genomes analysis was carried out for high-risk patients, and enriched pathways were analyzed by gene set enrichment analysis. RESULTS The results showed that genes of high-risk patients were enriched in protein export and spliceosome. Based on Cox stepwise regression and survival analysis, we identified seven autophagy-related lncRNAs with prognostic and diagnostic value, with the potential to be used as a combination to predict the prognosis of patients with ESCA. Finally, a co-expression network related to autophagy was constructed. CONCLUSION These results suggest that autophagy-related lncRNAs and the spliceosome play important parts in the pathogenesis of ESCA. Our findings provide new insight into the molecular mechanism of ESCA and suggest a new method for improving its treatment.
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Affiliation(s)
- Dan Wu
- Department of Anesthesiology, Shanxi Medical University, Taiyuan 030000, Shanxi Province, China
| | - Yi Ding
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - JunBai Fan
- Department of Anesthesiology, Second Hospital of Shanxi Medical University, Taiyuan 030000, Shanxi Province, China
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A Novel Autophagy-Related lncRNA Gene Signature to Improve the Prognosis of Patients with Melanoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8848227. [PMID: 34250091 PMCID: PMC8238568 DOI: 10.1155/2021/8848227] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 05/20/2021] [Indexed: 01/04/2023]
Abstract
Objective Autophagy and long noncoding RNAs (lncRNAs) have been the focus of research on the pathogenesis of melanoma. However, the autophagy network of lncRNAs in melanoma has not been reported. The purpose of this study was to investigate the lncRNA prognostic markers related to melanoma autophagy and predict the prognosis of patients with melanoma. Methods We downloaded RNA sequencing data and clinical information of melanoma from the Cancer Genome Atlas. The coexpression of autophagy-related genes (ARGs) and lncRNAs was analyzed. The risk model of autophagy-related lncRNAs was established by univariate and multivariate Cox regression analyses, and the best prognostic index was evaluated combined with clinical data. Finally, gene set enrichment analysis was performed on patients in the high- and low-risk groups. Results According to the results of the univariate Cox analysis, only the overexpression of LINC00520 was associated with poor overall survival, unlike HLA-DQB1-AS1, USP30-AS1, AL645929, AL365361, LINC00324, and AC055822. The results of the multivariate Cox analysis showed that the overall survival of patients in the high-risk group was shorter than that recorded in the low-risk group (p < 0.001). Moreover, in the receiver operating characteristic curve of the risk model we constructed, the area under the curve (AUC) was 0.734, while the AUC of T and N was 0.707 and 0.658, respectively. The Gene Ontology was mainly enriched with the positive regulation of autophagy and the activation of the immune system. The results of the Kyoto Encyclopedia of Genes and Genomes enrichment were mostly related to autophagy, immunity, and melanin metabolism. Conclusion The positive regulation of autophagy may slow the transition from low-risk patients to high-risk patients in melanoma. Furthermore, compared with clinical information, the autophagy-related lncRNA risk model may better predict the prognosis of patients with melanoma and provide new treatment ideas.
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Wang J, Xu F, Zhu X, Li X, Li Y, Li J. Targeting microRNAs to Regulate the Integrity of the Blood-Brain Barrier. Front Bioeng Biotechnol 2021; 9:673415. [PMID: 34178963 PMCID: PMC8226126 DOI: 10.3389/fbioe.2021.673415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
The blood-brain barrier (BBB) is a highly specialized neurovascular unit that protects the brain from potentially harmful substances. In addition, the BBB also engages in the exchange of essential nutrients between the vasculature and brain parenchyma, which is critical for brain homeostasis. Brain diseases, including neurological disorders and cerebrovascular diseases, are often associated with disrupted BBB integrity, evidenced by increased permeability. Therefore, defining the mechanisms underlying the regulation of BBB integrity is crucial for the development of novel therapeutics targeting brain diseases. MicroRNAs (miRNA), a type of small non-coding RNAs, are emerging as an important regulator of BBB integrity. Here we review recent developments related to the role of miRNAs in regulating BBB integrity.
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Affiliation(s)
- Juntao Wang
- School of Nuclear Technology and Chemistry and Biology, Hubei University of Science and Technology, Xianning, China
- Hubei Key Laboratory of Radiation Chemistry and Functional Materials, Hubei University of Science and Technology, Xianning, China
| | - Fang Xu
- School of Nuclear Technology and Chemistry and Biology, Hubei University of Science and Technology, Xianning, China
- Hubei Key Laboratory of Radiation Chemistry and Functional Materials, Hubei University of Science and Technology, Xianning, China
| | - Xiaoming Zhu
- School of Nuclear Technology and Chemistry and Biology, Hubei University of Science and Technology, Xianning, China
- Hubei Key Laboratory of Radiation Chemistry and Functional Materials, Hubei University of Science and Technology, Xianning, China
| | - Xianghua Li
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
| | - Yankun Li
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
- Hubei Key Laboratory of Cardiovascular, Cerebrovascular, and Metabolic Disorders, Hubei University of Science and Technology, Xianning, China
| | - Jia Li
- Centre for Motor Neuron Disease, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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Piscopo P, Bellenghi M, Manzini V, Crestini A, Pontecorvi G, Corbo M, Ortona E, Carè A, Confaloni A. A Sex Perspective in Neurodegenerative Diseases: microRNAs as Possible Peripheral Biomarkers. Int J Mol Sci 2021; 22:ijms22094423. [PMID: 33922607 PMCID: PMC8122918 DOI: 10.3390/ijms22094423] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
Sex is a significant variable in the prevalence and incidence of neurological disorders. Sex differences exist in neurodegenerative disorders (NDs), where sex dimorphisms play important roles in the development and progression of Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis. In the last few years, some sex specific biomarkers for the identification of NDs have been described and recent studies have suggested that microRNA (miRNA) could be included among these, as influenced by the hormonal and genetic background. Failing to consider the possible differences between males and females in miRNA evaluation could introduce a sex bias in studies by not considering some of these sex-related biomarkers. In this review, we recapitulate what is known about the sex-specific differences in peripheral miRNA levels in neurodegenerative diseases. Several studies have reported sex-linked disparities, and from the literature analysis miR-206 particularly has been shown to have a sex-specific involvement. Hopefully, in the near future, patient stratification will provide important additional clues in diagnosis, prognosis, and tailoring of the best therapeutic approaches for each patient. Sex-specific biomarkers, such as miRNAs, could represent a useful tool for characterizing subgroups of patients.
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Affiliation(s)
- Paola Piscopo
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (V.M.); (A.C.); (A.C.)
- Correspondence: ; Tel.: +39-064-990-3538
| | - Maria Bellenghi
- Center of Gender Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.B.); (G.P.); (E.O.); (A.C.)
| | - Valeria Manzini
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (V.M.); (A.C.); (A.C.)
| | - Alessio Crestini
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (V.M.); (A.C.); (A.C.)
| | - Giada Pontecorvi
- Center of Gender Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.B.); (G.P.); (E.O.); (A.C.)
| | - Massimo Corbo
- Department of Neurorehabilitation Sciences, Casa Cura Policlinico, Via Dezza 48, 20144 Milano, Italy;
| | - Elena Ortona
- Center of Gender Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.B.); (G.P.); (E.O.); (A.C.)
| | - Alessandra Carè
- Center of Gender Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.B.); (G.P.); (E.O.); (A.C.)
| | - Annamaria Confaloni
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (V.M.); (A.C.); (A.C.)
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Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson’s disease progression. ACTA ACUST UNITED AC 2021; 1:309-322. [PMID: 37118411 DOI: 10.1038/s43587-021-00042-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Noncoding RNAs have diagnostic and prognostic importance in Parkinson's disease (PD). We studied circulating small noncoding RNAs (sncRNAs) in two large-scale longitudinal PD cohorts (Parkinson's Progression Markers Initiative (PPMI) and Luxembourg Parkinson's Study (NCER-PD)) and modeled their impact on the transcriptome. Sequencing of sncRNAs in 5,450 blood samples of 1,614 individuals in PPMI yielded 323 billion reads, most of which mapped to microRNAs but covered also other RNA classes such as piwi-interacting RNAs, ribosomal RNAs and small nucleolar RNAs. Dysregulated microRNAs associated with disease and disease progression occur in two distinct waves in the third and seventh decade of life. Originating predominantly from immune cells, they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. Profiling 1,553 samples from 1,024 individuals in the NCER-PD cohort validated biomarkers and main findings by an independent technology. Finally, network analysis of sncRNA and transcriptome sequencing from PPMI identified regulatory modules emerging in patients with progressing PD.
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Li Y, Fehlmann T, Borcherding A, Drmanac S, Liu S, Groeger L, Xu C, Callow M, Villarosa C, Jorjorian A, Kern F, Grammes N, Meese E, Jiang H, Drmanac R, Ludwig N, Keller A. CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing. Nucleic Acids Res 2021; 49:e10. [PMID: 33290507 PMCID: PMC7826284 DOI: 10.1093/nar/gkaa1122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/02/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.
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Affiliation(s)
- Yongping Li
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | | | - Sophie Liu
- Complete Genomics Incorporated, San Jose, CA 95134, USA
| | - Laura Groeger
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Chongjun Xu
- MGI, BGI-Shenzhen, Shenzhen 518083, China
- Complete Genomics Incorporated, San Jose, CA 95134, USA
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | | | | | | | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nadja Grammes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Hui Jiang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Radoje Drmanac
- MGI, BGI-Shenzhen, Shenzhen 518083, China
- Complete Genomics Incorporated, San Jose, CA 95134, USA
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Neurology and Neurological Sciences, Stanford UniversitySchool of Medicine, Stanford, CA 94304, USA
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Boscher E, Goupil C, Petry S, Keraudren R, Loiselle A, Planel E, Hébert SS. MicroRNA-138 Overexpression Alters Aβ42 Levels and Behavior in Wildtype Mice. Front Neurosci 2021; 14:591138. [PMID: 33519353 PMCID: PMC7840584 DOI: 10.3389/fnins.2020.591138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/21/2020] [Indexed: 11/30/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by changes in cognitive and behavioral functions. With the exception or rare mutations in PSEN and APP genes causing early-onset autosomal dominant AD (EOADAD), little is known about the genetic factors that underlie the vast majority (>95%) of early onset AD (EOAD) cases. We have previously identified copy number variations (CNVs) in microRNA genes in patients with EOAD, including a duplication of the MIR-138-2 gene. Overexpression of miR-138 in cultured cells increased Aβ production and tau phosphorylation, similar to what is seen in AD brain. In this study, we sought to determine if miR-138 overexpression could recapitulate certain features of disease in vivo in non-transgenic mice. A mild overexpression of pre-miR-138 in the brain of C57BL/6J wildtype mice altered learning and memory in a novel object recognition test and in the Barnes Maze. Increased levels of anxiety were also observed in the open-field test. MiR-138 upregulation in vivo caused an increase in endogenous Aβ42 production as well as changes in synaptic and inflammation markers. Tau expression was significantly lower with no overt effects on phosphorylation. We finally observed that Sirt1, a direct target of miR-138 involved in Aβ production, learning and memory as well as anxiety, is decreased following miR-138 overexpression. In sum, this study further strengthens a role for increased gene dosage of MIR-138-2 gene in modulating AD risk, possibly by acting on different biological pathways. Further studies will be required to better understand the role of CNVs in microRNA genes in AD and related neurodegenerative disorders.
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Affiliation(s)
- Emmanuelle Boscher
- Centre de Recherche du CHU de Québec - Université Laval, CHUL, Axe Neurosciences, Quebec City, QC, Canada.,Faculté de Médecine, Département de Psychiatrie et de Neurosciences, Université Laval, Quebec City, QC, Canada
| | - Claudia Goupil
- Centre de Recherche du CHU de Québec - Université Laval, CHUL, Axe Neurosciences, Quebec City, QC, Canada
| | - Serena Petry
- Centre de Recherche du CHU de Québec - Université Laval, CHUL, Axe Neurosciences, Quebec City, QC, Canada.,Faculté de Médecine, Département de Psychiatrie et de Neurosciences, Université Laval, Quebec City, QC, Canada
| | - Rémi Keraudren
- Centre de Recherche du CHU de Québec - Université Laval, CHUL, Axe Neurosciences, Quebec City, QC, Canada.,Faculté de Médecine, Département de Psychiatrie et de Neurosciences, Université Laval, Quebec City, QC, Canada
| | - Andréanne Loiselle
- Centre de Recherche du CHU de Québec - Université Laval, CHUL, Axe Neurosciences, Quebec City, QC, Canada
| | - Emmanuel Planel
- Centre de Recherche du CHU de Québec - Université Laval, CHUL, Axe Neurosciences, Quebec City, QC, Canada.,Faculté de Médecine, Département de Psychiatrie et de Neurosciences, Université Laval, Quebec City, QC, Canada
| | - Sébastien S Hébert
- Centre de Recherche du CHU de Québec - Université Laval, CHUL, Axe Neurosciences, Quebec City, QC, Canada.,Faculté de Médecine, Département de Psychiatrie et de Neurosciences, Université Laval, Quebec City, QC, Canada
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Schmartz GP, Kern F, Fehlmann T, Wagner V, Fromm B, Keller A. Encyclopedia of tools for the analysis of miRNA isoforms. Brief Bioinform 2020; 22:6032629. [PMID: 33313643 DOI: 10.1093/bib/bbaa346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/15/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
RNA sequencing data sets rapidly increase in quantity. For microRNAs (miRNAs), frequently dozens to hundreds of billion reads are generated per study. The quantification of annotated miRNAs and the prediction of new miRNAs are leading computational tasks. Now, the increased depth of coverage allows to gain deeper insights into the variability of miRNAs. The analysis of isoforms of miRNAs (isomiRs) is a trending topic, and a range of computational tools for the analysis of isomiRs has been developed. We provide an overview on 27 available computational solutions for the analysis of isomiRs. These include both stand-alone programs (17 tools) and web-based solutions (10 tools) and span a publication time range from 2010 to 2020. Seven of the tools were published in 2019 and 2020, confirming the rising importance of the topic. While most of the analyzed tools work for a broad range of organisms or are completely independent of a reference organism, several tools have been tailored for the analysis of human miRNA data or for plants. While 14 of the tools are general analysis tools of miRNAs, and isomiR analysis is one of their features, the remaining 13 tools have specifically been developed for isomiR analysis. A direct comparison on 20 deep sequencing data sets for selected tools provides insights into the heterogeneity of results. With our work, we provide users a comprehensive overview on the landscape of isomiR analysis tools and in that support the selection of the most appropriate tool for their respective research task.
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Affiliation(s)
| | | | | | | | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Andreas Keller
- Saarland Center for Bioinformatics and Chair for Clinical Bioinformatics, Saarland University Building E2.1, 66123 Saarbrücken, Germany
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Kern F, Fehlmann T, Solomon J, Schwed L, Grammes N, Backes C, Van Keuren-Jensen K, Craig DW, Meese E, Keller A. miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems. Nucleic Acids Res 2020; 48:W521-W528. [PMID: 32374865 PMCID: PMC7319446 DOI: 10.1093/nar/gkaa309] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/06/2020] [Accepted: 04/22/2020] [Indexed: 01/01/2023] Open
Abstract
Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.
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Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jeffrey Solomon
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Louisa Schwed
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nadja Grammes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | - David Wesley Craig
- Institute of Translational Genomics, University of Southern California, Los Angeles, CA 90033, USA
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,School of Medicine Office, Stanford University, Stanford, CA 94305, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA
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Varma-Doyle AV, Lukiw WJ, Zhao Y, Lovera J, Devier D. A hypothesis-generating scoping review of miRs identified in both multiple sclerosis and dementia, their protein targets, and miR signaling pathways. J Neurol Sci 2020; 420:117202. [PMID: 33183778 DOI: 10.1016/j.jns.2020.117202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/26/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
Cognitive impairment (CI) is a frequent complication affecting people with multiple sclerosis (MS). The causes of CI in MS are not fully understood. Besides MRI measures, few other biomarkers exist to help us predict the development of CI and understand its biology. MicroRNAs (miRs) are relatively stable, non-coding RNA molecules about 22 nucleotides in length that can serve as biomarkers and possible therapeutic targets in several autoimmune and neurodegenerative diseases, including the dementias. In this review, we identify dysregulated miRs in MS that overlap with dysregulated miRs in cognitive disorders and dementia and explore how these overlapping miRs play a role in CI in MS. MiR-15, miR-21, miR-128, miR-132, miR-138, miR-142, miR-146a, miR-155, miR-181, miR-572, and let-7 are known to contribute to various forms of dementia and show abnormal expression in MS. These overlapping miRs are involved in pathways related to apoptosis, neuroinflammation, glutamate toxicity, astrocyte activation, microglial burst activity, synaptic dysfunction, and remyelination. The mechanisms of action suggest that these miRs may be related to CI in MS. From our review, we also delineated miRs that could be neuroprotective in MS, namely miR-23a, miR-219, miR-214, and miR-22. Further studies can help clarify if these miRs are responsible for CI in MS, leading to potential therapeutic targets.
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Affiliation(s)
- Aditi Vian Varma-Doyle
- Louisiana State University Health Sciences Center -New Orleans School of Medicine, Department of Neurology, New Orleans, United States of America
| | - Walter J Lukiw
- Louisiana State University Health Sciences Center -New Orleans School of Medicine, Department of Neurology, New Orleans, United States of America; Louisiana State University Health Sciences Center - New Orleans Neuroscience Center, United States of America; Louisiana State University Health Sciences Center - New Orleans Department of Ophthalmology, United States of America
| | - Yuhai Zhao
- Louisiana State University Health Sciences Center - New Orleans Department of Cell Biology and Anatomy, United States of America; Louisiana State University Health Sciences Center - New Orleans Neuroscience Center, United States of America
| | - Jesus Lovera
- Louisiana State University Health Sciences Center -New Orleans School of Medicine, Department of Neurology, New Orleans, United States of America.
| | - Deidre Devier
- Louisiana State University Health Sciences Center -New Orleans School of Medicine, Department of Neurology, New Orleans, United States of America; Louisiana State University Health Sciences Center - New Orleans Department of Cell Biology and Anatomy, United States of America.
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Kern F, Amand J, Senatorov I, Isakova A, Backes C, Meese E, Keller A, Fehlmann T. miRSwitch: detecting microRNA arm shift and switch events. Nucleic Acids Res 2020; 48:W268-W274. [PMID: 32356893 PMCID: PMC7319450 DOI: 10.1093/nar/gkaa323] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 12/27/2022] Open
Abstract
Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.
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Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jeremy Amand
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Ilya Senatorov
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,School of Medicine Office, Stanford University, Stanford, CA 94305, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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A blood miRNA signature associates with sporadic Creutzfeldt-Jakob disease diagnosis. Nat Commun 2020; 11:3960. [PMID: 32769986 PMCID: PMC7414116 DOI: 10.1038/s41467-020-17655-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/09/2020] [Indexed: 01/07/2023] Open
Abstract
Sporadic Creutzfeldt-Jakob disease (sCJD) presents as a rapidly progressive dementia which is usually fatal within six months. No clinical blood tests are available for diagnosis or disease monitoring. Here, we profile blood microRNA (miRNA) expression in sCJD. Sequencing of 57 sCJD patients, and healthy controls reveals differential expression of hsa-let-7i-5p, hsa-miR-16-5p, hsa-miR-93-5p and hsa-miR-106b-3p. Downregulation of hsa-let-7i-5p, hsa-miR-16-5p and hsa-miR-93-5p replicates in an independent cohort using quantitative PCR, with concomitant upregulation of four mRNA targets. Absence of correlation in cross-sectional analysis with clinical phenotypes parallels the lack of association between rate of decline in miRNA expression, and rate of disease progression in a longitudinal cohort of samples from 21 patients. Finally, the miRNA signature shows a high level of accuracy in discriminating sCJD from Alzheimer’s disease. These findings highlight molecular alterations in the periphery in sCJD which provide information about differential diagnosis and improve mechanistic understanding of human prion diseases. Sporadic Creutzfeldt-Jakob disease (sCJD) is a rapidly progressive dementia. No clinical blood tests are available for diagnosis. The authors identified three miRNAs in whole-blood that are downregulated in sCJD patients, and discriminate sCJD from Alzheimer’s disease patients and healthy controls.
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Targa A, Dakterzada F, Benítez ID, de Gonzalo-Calvo D, Moncusí-Moix A, López R, Pujol M, Arias A, de Batlle J, Sánchez-de-la-Torre M, Barbé F, Piñol-Ripoll G. Circulating MicroRNA Profile Associated with Obstructive Sleep Apnea in Alzheimer's Disease. Mol Neurobiol 2020; 57:4363-4372. [PMID: 32720075 DOI: 10.1007/s12035-020-02031-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/22/2020] [Indexed: 11/29/2022]
Abstract
The diagnosis of obstructive sleep apnea (OSA) in Alzheimer's disease (AD) by polysomnography (PSG) is challenging due to the required collaboration of the patients. In addition, screening questionnaires have demonstrated limited usefulness with this subpopulation. Considering this, we investigated the circulating microRNA (miRNA) profile associated with OSA in AD patients. This study included a carefully selected cohort of females with mild-moderate AD confirmed by biological evaluation (n = 29). The individuals were submitted to one-night PSG to diagnose OSA (apnea-hypopnea index ≥ 15/h) and the blood was collected in the following morning. The plasma miRNA profile was evaluated using RT-qPCR. The patients had a mean (SD) age of 75.8 (5.99) years old with a body mass index of 28.6 (3.83) kg m-2. We observed a subset of 15 miRNAs differentially expressed between OSA and non-OSA patients, of which 10 were significantly correlated with the severity of OSA. Based on this, we built a prediction model that generated an AUC (95% CI) of 0.95 (0.88-1.00) including 5 of the differentially expressed miRNAs that correlated with OSA severity: miR-26a-5p, miR-30a-3p, miR-374a-5p, miR-377-3p, and miR-545-3p. Our preliminary results suggest a plasma miRNA signature associated with the presence of OSA in AD patients. Further studies will be necessary to validate these findings.
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Affiliation(s)
- A Targa
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, IRBLleida, Lleida, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - F Dakterzada
- Unitat Trastorns Cognitius, Clinical Neuroscience Research, Santa Maria University Hospital, IRBLleida, Rovira Roure n° 44, 25198, Lleida, Spain
| | - I D Benítez
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, IRBLleida, Lleida, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - D de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, IRBLleida, Lleida, Spain
| | - A Moncusí-Moix
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, IRBLleida, Lleida, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - R López
- Unitat Trastorns Cognitius, Clinical Neuroscience Research, Santa Maria University Hospital, IRBLleida, Rovira Roure n° 44, 25198, Lleida, Spain
| | - M Pujol
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, IRBLleida, Lleida, Spain
| | - A Arias
- Unitat Trastorns Cognitius, Clinical Neuroscience Research, Santa Maria University Hospital, IRBLleida, Rovira Roure n° 44, 25198, Lleida, Spain
| | - J de Batlle
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, IRBLleida, Lleida, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - M Sánchez-de-la-Torre
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Group of Precision Medicine in Chronic Diseases, Hospital Universitari Arnau de Vilanova-Santa Maria, IRBLleida, Lleida, Spain
| | - F Barbé
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, IRBLleida, Lleida, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Gerard Piñol-Ripoll
- Unitat Trastorns Cognitius, Clinical Neuroscience Research, Santa Maria University Hospital, IRBLleida, Rovira Roure n° 44, 25198, Lleida, Spain.
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Najm R, Zalocusky KA, Zilberter M, Yoon SY, Hao Y, Koutsodendris N, Nelson M, Rao A, Taubes A, Jones EA, Huang Y. In Vivo Chimeric Alzheimer's Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons. Cell Rep 2020; 32:107962. [PMID: 32726626 PMCID: PMC7430173 DOI: 10.1016/j.celrep.2020.107962] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/15/2020] [Accepted: 07/03/2020] [Indexed: 02/08/2023] Open
Abstract
Despite its clear impact on Alzheimer's disease (AD) risk, apolipoprotein (apo) E4's contributions to AD etiology remain poorly understood. Progress in answering this and other questions in AD research has been limited by an inability to model human-specific phenotypes in an in vivo environment. Here we transplant human induced pluripotent stem cell (hiPSC)-derived neurons carrying normal apoE3 or pathogenic apoE4 into human apoE3 or apoE4 knockin mouse hippocampi, enabling us to disentangle the effects of apoE4 produced in human neurons and in the brain environment. Using single-nucleus RNA sequencing (snRNA-seq), we identify key transcriptional changes specific to human neuron subtypes in response to endogenous or exogenous apoE4. We also find that Aβ from transplanted human neurons forms plaque-like aggregates, with differences in localization and interaction with microglia depending on the transplant and host apoE genotype. These findings highlight the power of in vivo chimeric disease modeling for studying AD.
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Affiliation(s)
- Ramsey Najm
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kelly A Zalocusky
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA
| | - Misha Zilberter
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Seo Yeon Yoon
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Yanxia Hao
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA
| | - Nicole Koutsodendris
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Maxine Nelson
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Antara Rao
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alice Taubes
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily A Jones
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Neurology and Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.
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Arisan ED, Dart A, Grant GH, Arisan S, Cuhadaroglu S, Lange S, Uysal-Onganer P. The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities. Viruses 2020; 12:v12060614. [PMID: 32512929 PMCID: PMC7354481 DOI: 10.3390/v12060614] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a member of the betacoronavirus family, which causes COVID-19 disease. SARS-CoV-2 pathogenicity in humans leads to increased mortality rates due to alterations of significant pathways, including some resulting in exacerbated inflammatory responses linked to the “cytokine storm” and extensive lung pathology, as well as being linked to a number of comorbidities. Our current study compared five SARS-CoV-2 sequences from different geographical regions to those from SARS, MERS and two cold viruses, OC43 and 229E, to identify the presence of miR-like sequences. We identified seven key miRs, which highlight considerable differences between the SARS-CoV-2 sequences, compared with the other viruses. The level of conservation between the five SARS-CoV-2 sequences was identical but poor compared with the other sequences, with SARS showing the highest degree of conservation. This decrease in similarity could result in reduced levels of transcriptional control, as well as a change in the physiological effect of the virus and associated host-pathogen responses. MERS and the milder symptom viruses showed greater differences and even significant sequence gaps. This divergence away from the SARS-CoV-2 sequences broadly mirrors the phylogenetic relationships obtained from the whole-genome alignments. Therefore, patterns of mutation, occurring during sequence divergence from the longer established human viruses to the more recent ones, may have led to the emergence of sequence motifs that can be related directly to the pathogenicity of SARS-CoV-2. Importantly, we identified 7 key-microRNAs (miRs 8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) with significant links to KEGG pathways linked to viral pathogenicity and host responses. According to Bioproject data (PRJNA615032), SARS-CoV-2 mediated transcriptomic alterations were similar to the target pathways of the selected 7 miRs identified in our study. This mechanism could have considerable significance in determining the symptom spectrum of future potential pandemics. KEGG pathway analysis revealed a number of critical pathways linked to the seven identified miRs that may provide insight into the interplay between the virus and comorbidities. Based on our reported findings, miRNAs may constitute potential and effective therapeutic approaches in COVID-19 and its pathological consequences.
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Affiliation(s)
- Elif Damla Arisan
- Institute of Biotechnology, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey;
| | - Alwyn Dart
- Institute of Medical and Biomedical Education, St George’s University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK;
| | - Guy H. Grant
- School of Life Sciences, University of Bedfordshire, Park Square, Luton LU1 3JU, UK;
| | - Serdar Arisan
- Department of Urology, Şişli Hamidiye Etfal Research and Training Hospital, 34360 Istanbul, Turkey;
| | - Songul Cuhadaroglu
- Thoracic Surgery Clinic, Memorial Hospital Sisli, Kaptanpasa Mah. Piyalepasa Bulvarı, 434385 Istanbul, Turkey;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK;
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
- Correspondence: ; Tel.: +44-(0)207-911-5151 (ext. 64581)
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Amand J, Fehlmann T, Backes C, Keller A. DynaVenn: web-based computation of the most significant overlap between ordered sets. BMC Bioinformatics 2019; 20:743. [PMID: 31888436 PMCID: PMC6937821 DOI: 10.1186/s12859-019-3320-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 12/16/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND In many research disciplines, ordered lists are compared. One example is to compare a subset of all significant genes or proteins in a primary study to those in a replication study. Often, the top of the lists are compared using Venn diagrams, ore more precisely Euler diagrams (set diagrams showing logical relations between a finite collection of different sets). If different cohort sizes, different techniques or algorithms for evaluation were applied, a direct comparison of significant genes with a fixed threshold can however be misleading and approaches comparing lists would be more appropriate. RESULTS We developed DynaVenn, a web-based tool that incrementally creates all possible subsets from two or three ordered lists and computes for each combination a p-value for the overlap. Respectively, dynamic Venn diagrams are generated as graphical representations. Additionally an animation is generated showing how the most significant overlap is reached by backtracking. We demonstrate the improved performance of DynaVenn over an arbitrary cut-off approach on an Alzheimer's Disease biomarker set. CONCLUSION DynaVenn combines the calculation of the most significant overlap of different cohorts with an intuitive visualization of the results. It is freely available as a web service at http://www.ccb.uni-saarland.de/dynavenn.
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Affiliation(s)
- Jérémy Amand
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany.
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Qu H, Lei H, Fang X. Big Data and the Brain: Peeking at the Future. GENOMICS, PROTEOMICS & BIOINFORMATICS 2019; 17:333-336. [PMID: 31809865 PMCID: PMC6943752 DOI: 10.1016/j.gpb.2019.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/09/2019] [Accepted: 11/25/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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