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Sun M, Chang L, He L, Wang L, Jiang Z, Si Y, Yu J, Ma Y. Combining single-cell profiling and functional analysis explores the role of pseudogenes in human early embryonic development. J Genet Genomics 2024:S1673-8527(24)00189-9. [PMID: 39032861 DOI: 10.1016/j.jgg.2024.07.013] [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: 03/25/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
More and more studies have demonstrated that pseudogenes possess coding ability, and the functions of their transcripts in the development of diseases have been partially revealed. However, the role of pseudogenes in maintenance of normal physiological states and life activities has long been neglected. Here we identify pseudogenes that are dynamically expressed during human early embryogenesis, showing different expression pattern from that of adult tissues. We explore the expression correlation between pseudogenes and the parent genes, part due to their shared gene regulatory elements or the potential regulation network between them. The essential role of three pseudogenes, PI4KAP1, TMED10P1, and FBXW4P1, in maintaining self-renewal of human embryonic stem cells is demonstrated. We further find that the three pseudogenes might perform their regulatory functions by binding to proteins or microRNAs. The pseudogene-related single-nucleotide polymorphisms are significantly associated with human congenital disease, further illustrating their importance during early embryonic development. Overall, this study is an excavation and exploration of functional pseudogenes during early human embryonic development, suggesting that pseudogenes are not only capable of being specifically activated in pathological states, but also play crucial functions in the maintenance of normal physiological states.
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Affiliation(s)
- Mengyao Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China
| | - Le Chang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Liu He
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Li Wang
- Department of Obstetrics, Haidian District Maternity and Child Health Hospital, Beijing 100080, China
| | - Zhengyang Jiang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yanmin Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China.
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2
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Gustavsson EK, Sethi S, Gao Y, Brenton JW, García-Ruiz S, Zhang D, Garza R, Reynolds RH, Evans JR, Chen Z, Grant-Peters M, Macpherson H, Montgomery K, Dore R, Wernick AI, Arber C, Wray S, Gandhi S, Esselborn J, Blauwendraat C, Douse CH, Adami A, Atacho DAM, Kouli A, Quaegebeur A, Barker RA, Englund E, Platt F, Jakobsson J, Wood NW, Houlden H, Saini H, Bento CF, Hardy J, Ryten M. The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1. SCIENCE ADVANCES 2024; 10:eadk1296. [PMID: 38924406 PMCID: PMC11204300 DOI: 10.1126/sciadv.adk1296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 05/17/2024] [Indexed: 06/28/2024]
Abstract
Mutations in GBA1 cause Gaucher disease and are the most important genetic risk factor for Parkinson's disease. However, analysis of transcription at this locus is complicated by its highly homologous pseudogene, GBAP1. We show that >50% of short RNA-sequencing reads mapping to GBA1 also map to GBAP1. Thus, we used long-read RNA sequencing in the human brain, which allowed us to accurately quantify expression from both GBA1 and GBAP1. We discovered significant differences in expression compared to short-read data and identify currently unannotated transcripts of both GBA1 and GBAP1. These included protein-coding transcripts from both genes that were translated in human brain, but without the known lysosomal function-yet accounting for almost a third of transcription. Analyzing brain-specific cell types using long-read and single-nucleus RNA sequencing revealed region-specific variations in transcript expression. Overall, these findings suggest nonlysosomal roles for GBA1 and GBAP1 with implications for our understanding of the role of GBA1 in health and disease.
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Affiliation(s)
- Emil K. Gustavsson
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Siddharth Sethi
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - Yujing Gao
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - Jonathan W. Brenton
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sonia García-Ruiz
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David Zhang
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund, Sweden
| | - Regina H. Reynolds
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - James R. Evans
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Zhongbo Chen
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Melissa Grant-Peters
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Hannah Macpherson
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Kylie Montgomery
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Rhys Dore
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Anna I. Wernick
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Charles Arber
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Selina Wray
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Sonia Gandhi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Julian Esselborn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher H. Douse
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund, Sweden
| | - Diahann A. M. Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund, Sweden
| | - Antonina Kouli
- Wellcome-MRC Cambridge Stem Cell Institute and John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Annelies Quaegebeur
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Clinical Neurosciences, University of Cambridge, Clifford Albutt Building, Cambridge, UK
| | - Roger A. Barker
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Wellcome-MRC Cambridge Stem Cell Institute and John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Frances Platt
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Johan Jakobsson
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund, Sweden
| | - Nicholas W. Wood
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Harpreet Saini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - Carla F. Bento
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, UK
| | - John Hardy
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, UCL, London, UK
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, UCL, London, UK
- NIHR University College London Hospitals Biomedical Research Centre, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
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Gao G, McClellan J, Barbeira AN, Fiorica PN, Li JL, Mu Z, Olopade OI, Huo D, Im HK. A multi-tissue, splicing-based joint transcriptome-wide association study identifies susceptibility genes for breast cancer. Am J Hum Genet 2024; 111:1100-1113. [PMID: 38733992 PMCID: PMC11179262 DOI: 10.1016/j.ajhg.2024.04.010] [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: 10/09/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
Splicing-based transcriptome-wide association studies (splicing-TWASs) of breast cancer have the potential to identify susceptibility genes. However, existing splicing-TWASs test the association of individual excised introns in breast tissue only and thus have limited power to detect susceptibility genes. In this study, we performed a multi-tissue joint splicing-TWAS that integrated splicing-TWAS signals of multiple excised introns in each gene across 11 tissues that are potentially relevant to breast cancer risk. We utilized summary statistics from a meta-analysis that combined genome-wide association study (GWAS) results of 424,650 women of European ancestry. Splicing-level prediction models were trained in GTEx (v.8) data. We identified 240 genes by the multi-tissue joint splicing-TWAS at the Bonferroni-corrected significance level; in the tissue-specific splicing-TWAS that combined TWAS signals of excised introns in genes in breast tissue only, we identified nine additional significant genes. Of these 249 genes, 88 genes in 62 loci have not been reported by previous TWASs, and 17 genes in seven loci are at least 1 Mb away from published GWAS index variants. By comparing the results of our splicing-TWASs with previous gene-expression-based TWASs that used the same summary statistics and expression prediction models trained in the same reference panel, we found that 110 genes in 70 loci that are identified only by the splicing-TWASs. Our results showed that for many genes, expression quantitative trait loci (eQTL) did not show a significant impact on breast cancer risk, whereas splicing quantitative trait loci (sQTL) showed a strong impact through intron excision events.
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Affiliation(s)
- Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Julian McClellan
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Zepeng Mu
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Olufunmilayo I Olopade
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
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4
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Piergiorge RM, Vasconcelos ATRD, Santos-Rebouças CB. Understanding the (epi)genetic dysregulation in Parkinson's disease through an integrative brain competitive endogenous RNA network. Mech Ageing Dev 2024; 219:111942. [PMID: 38762037 DOI: 10.1016/j.mad.2024.111942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Parkinson's disease (PD) is a rapidly growing neurodegenerative disorder characterized by dopaminergic neuron loss in the substantia nigra pars compacta (SN) and aggregation of α-synuclein. Its aetiology involves a multifaceted interplay among genetic, environmental, and epigenetic factors. We integrated brain gene expression data from PD patients to construct a comprehensive regulatory network encompassing messenger RNAs (mRNAs), microRNAs (miRNAs), circular RNAs (circRNAs) and, for the first time, RNA binding proteins (RBPs). Expression data from the SN of PD patients and controls were systematically selected from public databases to identify combined differentially expressed genes (DEGs). Brain co-expression analysis revealed modules comprising significant DEGs that function cooperatively. The relationships among co-expressed DEGs, miRNAs, circRNAs, and RBPs revealed an intricate competitive endogenous RNA (ceRNA) network responsible for post-transcriptional dysregulation in PD. Many genes in the ceRNA network, including the TOMM20 and HMGCR genes, overlap with the most relevant genes in our previous Alzheimer's disease-associated ceRNA network, suggesting common underlying mechanisms between both conditions. Moreover, in the ceRNA subnetwork, the RBP Aly/REF export factor (ALYREF), which acts as an RNA 5-methylcytosine(m5C)-binding protein, stood out. Our data sheds new light on the potential role of brain ceRNA networks in PD pathogenesis.
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Affiliation(s)
- Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | | | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil.
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5
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Brümmer A, Bergmann S. Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs. Nat Commun 2024; 15:3786. [PMID: 38710690 DOI: 10.1038/s41467-024-48244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 04/23/2024] [Indexed: 05/08/2024] Open
Abstract
Expression quantitative trait loci (eQTL) studies typically consider exon expression of genes and discard intronic RNA sequencing reads despite their information on RNA metabolism. Here, we quantify genetic effects on exon and intron levels of genes and their ratio in lymphoblastoid cell lines, revealing thousands of cis-QTLs of each type. While genetic effects are often shared between cis-QTL types, 7814 (47%) are not detected as top cis-QTLs at exon levels. We show that exon levels preferentially capture genetic effects on transcriptional regulation, while exon-intron-ratios better detect those on co- and post-transcriptional processes. Considering all cis-QTL types substantially increases (by 71%) the number of colocalizing variants identified by genome-wide association studies (GWAS). It further allows dissecting the potential gene regulatory processes underlying GWAS associations, suggesting comparable contributions by transcriptional (50%) and co- and post-transcriptional regulation (46%) to complex traits. Overall, integrating intronic RNA sequencing reads in eQTL studies expands our understanding of genetic effects on gene regulatory processes.
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Affiliation(s)
- Anneke Brümmer
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland.
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
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6
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Kritika C. Transforming 'Junk' DNA into Cancer Warriors: The Role of Pseudogenes in Hepatocellular Carcinoma. CANCER DIAGNOSIS & PROGNOSIS 2024; 4:214-222. [PMID: 38707729 PMCID: PMC11062172 DOI: 10.21873/cdp.10311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 05/07/2024]
Abstract
In the dynamic landscape of hepatocellular carcinoma (HCC) or the liver cancer research, pseudogenes have emerged from the shadows of genetic obscurity to become central figures, significantly influencing the disease molecular development and clinical trajectory. This review explores a transformative shift in perspective, recognizing pseudogenes not as genetic remnants without function, but as critical regulators in the molecular underpinnings of HCC. Engaging in complex interactions such as microRNA sponging, gene expression modulation, and signaling pathway disruptions, pseudogenes orchestrate a part of the molecular complexity driving tumor genesis, progression, and drug resistance in the liver cancer. Their unique expression patterns in hepatoma tissues herald new opportunities for early HCC detection, offering insights into patient prognosis, and identifying novel targets for therapeutic intervention of this disease. Such advancements underscore the importance of pseudogenes in enriching our understanding and management of HCC, paving the way for more effective diagnostic strategies and targeted therapies in the ongoing battle against this challenging malignancy.
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Affiliation(s)
- Chugh Kritika
- Graduate Student, School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, TX, U.S.A
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Yarkova ES, Grigor’eva EV, Medvedev SP, Tarasevich DA, Pavlova SV, Valetdinova KR, Minina JM, Zakian SM, Malakhova AA. Detection of ER Stress in iPSC-Derived Neurons Carrying the p.N370S Mutation in the GBA1 Gene. Biomedicines 2024; 12:744. [PMID: 38672099 PMCID: PMC11047942 DOI: 10.3390/biomedicines12040744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Endoplasmic reticulum (ER) stress is involved in the pathogenesis of many human diseases, such as cancer, type 2 diabetes, kidney disease, atherosclerosis and neurodegenerative diseases, in particular Parkinson's disease (PD). Since there is currently no treatment for PD, a better understanding of the molecular mechanisms underlying its pathogenesis, including the mechanisms of the switch from adaptation in the form of unfolded protein response (UPR) to apoptosis under ER stress conditions, may help in the search for treatment methods. Genetically encoded biosensors based on fluorescent proteins are suitable tools that facilitate the study of living cells and visualization of molecular events in real time. The combination of technologies to generate patient-specific iPSC lines and genetically encoded biosensors allows the creation of cell models with new properties. Using CRISPR-Cas9-mediated homologous recombination at the AAVS1 locus of iPSC with the genetic variant p.N370S (rs76763715) in the GBA1 gene, we created a cell model designed to study the activation conditions of the IRE1-XBP1 cascade of the UPR system. The cell lines obtained have a doxycycline-dependent expression of the genetically encoded biosensor XBP1-TagRFP, possess all the properties of human pluripotent cells, and can be used to test physical conditions and chemical compounds that affect the development of ER stress, the functioning of the UPR system, and in particular, the IRE1-XBP1 cascade.
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Affiliation(s)
- Elena S. Yarkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena V. Grigor’eva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Sergey P. Medvedev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Denis A. Tarasevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sophia V. Pavlova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Kamila R. Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Julia M. Minina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Suren M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Anastasia A. Malakhova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
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8
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Jia K, Shen J. Transcriptome-wide association studies associated with Crohn's disease: challenges and perspectives. Cell Biosci 2024; 14:29. [PMID: 38403629 PMCID: PMC10895848 DOI: 10.1186/s13578-024-01204-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
Crohn's disease (CD) is regarded as a lifelong progressive disease affecting all segments of the intestinal tract and multiple organs. Based on genome-wide association studies (GWAS) and gene expression data, transcriptome-wide association studies (TWAS) can help identify susceptibility genes associated with pathogenesis and disease behavior. In this review, we overview seven reported TWASs of CD, summarize their study designs, and discuss the key methods and steps used in TWAS, which affect the prioritization of susceptibility genes. This article summarized the screening of tissue-specific susceptibility genes for CD, and discussed the reported potential pathological mechanisms of overlapping susceptibility genes related to CD in a certain tissue type. We observed that ileal lipid-related metabolism and colonic extracellular vesicles may be involved in the pathogenesis of CD by performing GO pathway enrichment analysis for susceptibility genes. We further pointed the low reproducibility of TWAS associated with CD and discussed the reasons for these issues, strategies for solving them. In the future, more TWAS are needed to be designed into large-scale, unified cohorts, unified analysis pipelines, and fully classified databases of expression trait loci.
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Affiliation(s)
- Keyu Jia
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Nephrology department, Shanghai Jiao Tong University, 1058 Huanzhen Northroad, Shanghai, 200444, China
| | - Jun Shen
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Nephrology department, Shanghai Jiao Tong University, 1058 Huanzhen Northroad, Shanghai, 200444, China.
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Research Center, Ren Ji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China.
- NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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9
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Firdaus Z, Li X. Unraveling the Genetic Landscape of Neurological Disorders: Insights into Pathogenesis, Techniques for Variant Identification, and Therapeutic Approaches. Int J Mol Sci 2024; 25:2320. [PMID: 38396996 PMCID: PMC10889342 DOI: 10.3390/ijms25042320] [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: 01/18/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic abnormalities play a crucial role in the development of neurodegenerative disorders (NDDs). Genetic exploration has indeed contributed to unraveling the molecular complexities responsible for the etiology and progression of various NDDs. The intricate nature of rare and common variants in NDDs contributes to a limited understanding of the genetic risk factors associated with them. Advancements in next-generation sequencing have made whole-genome sequencing and whole-exome sequencing possible, allowing the identification of rare variants with substantial effects, and improving the understanding of both Mendelian and complex neurological conditions. The resurgence of gene therapy holds the promise of targeting the etiology of diseases and ensuring a sustained correction. This approach is particularly enticing for neurodegenerative diseases, where traditional pharmacological methods have fallen short. In the context of our exploration of the genetic epidemiology of the three most prevalent NDDs-amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, our primary goal is to underscore the progress made in the development of next-generation sequencing. This progress aims to enhance our understanding of the disease mechanisms and explore gene-based therapies for NDDs. Throughout this review, we focus on genetic variations, methodologies for their identification, the associated pathophysiology, and the promising potential of gene therapy. Ultimately, our objective is to provide a comprehensive and forward-looking perspective on the emerging research arena of NDDs.
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Affiliation(s)
- Zeba Firdaus
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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10
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Xia J, Bu C, Zhang B, Wang X, Chen Y, Li T. The emerging role of microRNA-22 in the Leukemia: experimental and clinical implications. Mol Biol Rep 2023; 51:12. [PMID: 38085373 DOI: 10.1007/s11033-023-08922-3] [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: 07/21/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs, approximately 20-24 nucleotides long that negatively regulate gene expression by either inhibiting translation or cleaving complementary mRNA to participate in various biological processes. Accumulating evidence has indicated that miRNAs are widely present in hematological cancers, particularly leukemia, exhibiting either upregulation or downregulation in leukemia patients compared with healthy controls. These miRNAs have a pivotal role in the development, progression and metastasis of leukemia, as well as in the prognosis and/or relapse of patients. miR-22 is one of the abnormally expressed miRNAs in a variety of leukemia diseases, and is considered to be one of the few cancer suppressors. Recent research has demonstrated that miR-22 is involved in the regulation of leukemia cell proliferation, differentiation and apoptosis, and could be a promising biomarker and prognostic indicator for leukemia. Here, we summarize all relevant findings that carry out experimental investigation and clinical analyses, aiming to elucidate the comprehensive implications of miR-22 in various types of leukemia for the development of new therapeutic and prognostic strategies and new drug targets for the treatment of leukemia.
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Affiliation(s)
- Jing Xia
- Department of Hematology, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, 214023, Jiangsu, China
| | - Chaozhi Bu
- State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China
| | - Bing Zhang
- Department of Gynaecology, Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China
| | - Xingqing Wang
- Department of Hematology, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, 214023, Jiangsu, China
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Yuejuan Chen
- State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China
| | - Tianyu Li
- Department of Hematology, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, 214023, Jiangsu, China.
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11
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Liu R, Yin G, Tuo H, Guo Y, Zhu Y, Zhang L, Yang W, Liu Q, Wang Y. METTL3-induced lncRNA GBAP1 promotes hepatocellular carcinoma progression by activating BMP/SMAD pathway. Biol Direct 2023; 18:53. [PMID: 37658413 PMCID: PMC10472583 DOI: 10.1186/s13062-023-00409-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/19/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common and challenging cancers in the world. N6-methyladenosine (m6A) modification and long non-coding RNAs (lncRNAs) play critical roles in the progression of HCC. However, there are few reports on genome-wide screening and functional annotations of m6A-methylated lncRNAs in HCC. METHODS The expression levels of m6A methyltransferase METTL3 and the association with the prognosis in HCC were determined by RT-qPCR, public dataset platforms. Then, RNA-seq, Pearson correlation analysis, MeRIP-qPCR, RNA half-life assay, gene site-directed mutation, RIP assay and RT-qPCR analysis were employed to determine the downstream target of METTL3 in HCC. Subsequently, the expression levels and roles of lncRNA glucosylceramidase beta pseudogene 1 (GBAP1) in HCC were determined by Kaplan-meier curves, RT-qPCR, in vitro functional experiments and in vivo tumorigenesis and lung metastasis models. Then, the downstream target and pathway of GBAP1 were explored by GO biological process, KEGG pathway enrichment, luciferase reporter assay, RIP assay and rescue experiments and so on. RESULTS METTL3 was upregulated in HCC and closely related to HCC prognosis. And METTL3 induced GBAP1 expression by acting as the m6A writer of GBAP1 and IGF2BP2 worked as its m6A reader. Clinically, GBAP1 expression was significantly associated with tumor size, venous infiltration, TNM stage and prognosis of HCC, Functionally, GBAP1 promoted HCC metastasis and growth both in vitro and in vivo. Furthermore, GBAP1 acted as the molecular sponge for miR-22-3p to increase the expression of bone morphogenetic protein receptor type 1A (BMPR1A), which then activated BMP/SMAD pathway in HCC cells. CONCLUSIONS Our findings demonstrated that METTL3-induced GBAP1 promoted migration, invasion and proliferation of HCC cells via GBAP1/miR-22-3p/BMPR1A/SMAD axis. GBAP1 could be a potential prognosis indicator and therapeutic target for HCC.
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Affiliation(s)
- Runkun Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Guozhi Yin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Hang Tuo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Yixian Guo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Yifeng Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Lei Zhang
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Wei Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Qingguang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
| | - Yufeng Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
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12
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Russo T, Kolisnyk B, Aswathy BS, Wan Kim T, Martin J, Plessis-Belair J, Ni J, Pearson JA, Park EJ, Sher RB, Studer L, Riessland M. The SATB1-MIR22-GBA axis mediates glucocerebroside accumulation inducing a cellular senescence-like phenotype in dopaminergic neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549710. [PMID: 37503189 PMCID: PMC10370136 DOI: 10.1101/2023.07.19.549710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Idiopathic Parkinson's Disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta, which is associated with neuroinflammation and reactive gliosis. The underlying cause of PD and the concurrent neuroinflammation are not well understood. In this study, we utilized human and murine neuronal lines, stem cell-derived dopaminergic neurons, and mice to demonstrate that three previously identified genetic risk factors for PD, namely SATB1, MIR22HG, and GBA, are components of a single gene regulatory pathway. Our findings indicate that dysregulation of this pathway leads to the upregulation of glucocerebrosides (GluCer), which triggers a cellular senescence-like phenotype in dopaminergic neurons. Specifically, we discovered that downregulation of the transcriptional repressor SATB1 results in the derepression of the microRNA miR-22-3p, leading to decreased GBA expression and subsequent accumulation of GluCer. Furthermore, our results demonstrate that an increase in GluCer alone is sufficient to impair lysosomal and mitochondrial function, thereby inducing cellular senescence dependent on S100A9 and stress factors. Dysregulation of the SATB1-MIR22-GBA pathway, observed in both PD patients and normal aging, leads to lysosomal and mitochondrial dysfunction due to the GluCer accumulation, ultimately resulting in a cellular senescence-like phenotype in dopaminergic neurons. Therefore, our study highlights a novel pathway involving three genetic risk factors for PD and provides a potential mechanism for the senescence-induced neuroinflammation and reactive gliosis observed in both PD and normal aging.
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Affiliation(s)
- Taylor Russo
- Department of Neurobiology and Behavior; Stony Brook University, Stony Brook, NY 11794, USA
- Center for Nervous System Disorders; Stony Brook University, Stony Brook, NY 11794, USA
| | - Benjamin Kolisnyk
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - BS Aswathy
- Department of Neurobiology and Behavior; Stony Brook University, Stony Brook, NY 11794, USA
- Center for Nervous System Disorders; Stony Brook University, Stony Brook, NY 11794, USA
| | - Tae Wan Kim
- Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA
| | - Jacqueline Martin
- Department of Neurobiology and Behavior; Stony Brook University, Stony Brook, NY 11794, USA
- Center for Nervous System Disorders; Stony Brook University, Stony Brook, NY 11794, USA
| | - Jonathan Plessis-Belair
- Department of Neurobiology and Behavior; Stony Brook University, Stony Brook, NY 11794, USA
- Center for Nervous System Disorders; Stony Brook University, Stony Brook, NY 11794, USA
| | - Jason Ni
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Jordan A. Pearson
- Medical Scientist Training Program, Stony Brook University Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Emily J. Park
- Stem Cells and Regenerative Medicine, Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Roger B. Sher
- Department of Neurobiology and Behavior; Stony Brook University, Stony Brook, NY 11794, USA
- Center for Nervous System Disorders; Stony Brook University, Stony Brook, NY 11794, USA
| | - Lorenz Studer
- Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA
| | - Markus Riessland
- Department of Neurobiology and Behavior; Stony Brook University, Stony Brook, NY 11794, USA
- Center for Nervous System Disorders; Stony Brook University, Stony Brook, NY 11794, USA
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13
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Chen R, Zhao M, An Y, Liu D, Tang Q. GBAP1 functions as a tumor promotor in hepatocellular carcinoma via the PI3K/AKT pathway. BMC Cancer 2023; 23:628. [PMID: 37407932 DOI: 10.1186/s12885-023-11107-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 06/23/2023] [Indexed: 07/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is common worldwide, and novel therapeutic targets and biomarkers are needed to improve outcomes. In this study, bioinformatics analyses combined with in vitro and in vivo assays were used to identify the potential therapeutic targets. Differentially expressed genes (DEG) in HCC were identified by the intersection between The Cancer Genome Atlas and International Cancer Genome Consortium data. The DEGs were evaluated by a gene set enrichment analysis as well as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. A protein interaction network, univariate Cox regression, and Lasso regression were used to screen out hub genes correlated with survival. Increased expression of the long noncoding RNA GBAP1 in HCC was confirmed in additional datasets and its biological function was evaluated in HCC cell lines and nude mice. Among 121 DEGs, GBAP1 and PRC1 were identified as hub genes with significant prognostic value. Overexpression of GBAP1 in HCC was confirmed in 21 paired clinical tissues and liver cancer or normal cell lines. The inhibition of GBAP1 expression reduced HCC cell proliferation and promoted apoptosis by inactivating the PI3K/AKT pathway in vitro and in vivo. Therefore, GBAP1 has a pro-oncogenic function in HCC and is a candidate prognostic biomarker and therapeutic target.
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Affiliation(s)
- Rong Chen
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu Province, China.
| | - Meng Zhao
- Medical college, Henan University of Traditional Chinese Medicine, 450001, Henan Province, China
| | - Yanli An
- Jiangsu Provincial Laboratory of Molecular and Functional Imaging, Department of Radiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu Province, China
| | - Dongfang Liu
- Jiangsu Provincial Laboratory of Molecular and Functional Imaging, Department of Radiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu Province, China
| | - Qiusha Tang
- Medical School of Southeast University, Nanjing, 210009, Jiangsu Province, China
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14
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Muraleedharan A, Vanderperre B. The endo-lysosomal system in Parkinson's disease: expanding the horizon. J Mol Biol 2023:168140. [PMID: 37148997 DOI: 10.1016/j.jmb.2023.168140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease, and its prevalence is increasing with age. A wealth of genetic evidence indicates that the endo-lysosomal system is a major pathway driving PD pathogenesis with a growing number of genes encoding endo-lysosomal proteins identified as risk factors for PD, making it a promising target for therapeutic intervention. However, detailed knowledge and understanding of the molecular mechanisms linking these genes to the disease are available for only a handful of them (e.g. LRRK2, GBA1, VPS35). Taking on the challenge of studying poorly characterized genes and proteins can be daunting, due to the limited availability of tools and knowledge from previous literature. This review aims at providing a valuable source of molecular and cellular insights into the biology of lesser-studied PD-linked endo-lysosomal genes, to help and encourage researchers in filling the knowledge gap around these less popular genetic players. Specific endo-lysosomal pathways discussed range from endocytosis, sorting, and vesicular trafficking to the regulation of membrane lipids of these membrane-bound organelles and the specific enzymatic activities they contain. We also provide perspectives on future challenges that the community needs to tackle and propose approaches to move forward in our understanding of these poorly studied endo-lysosomal genes. This will help harness their potential in designing innovative and efficient treatments to ultimately re-establish neuronal homeostasis in PD but also other diseases involving endo-lysosomal dysfunction.
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Affiliation(s)
- Amitha Muraleedharan
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois and Biological Sciences Department, Université du Québec à Montréal
| | - Benoît Vanderperre
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois and Biological Sciences Department, Université du Québec à Montréal
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15
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Extracellular vesicles: Critical bilateral communicators in periphery-brain crosstalk in central nervous system disorders. Biomed Pharmacother 2023; 160:114354. [PMID: 36753954 DOI: 10.1016/j.biopha.2023.114354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Growing evidence shows that there is a comorbid mechanism between the central nervous system (CNS) and the peripheral organs. The bilateral transmission of signal molecules in periphery-brain crosstalk plays an important role in the underlying mechanism, which result from complex networks of neurohumoral circuits. Secreted by almost all cells and considered innovative information transport systems, extracellular vesicles (EVs) encapsulate and deliver nucleic acids, proteins, lipids, and various other bioactive regulators. Moreover, EVs can cross the blood-brain barrier (BBB), they are also identified primarily as essential communicators between the periphery and the CNS. In addition to transporting molecules under physiological or pathological conditions, EVs also show novel potential in targeted drug delivery. In this review, we discuss the mechanisms implicated in the transport of EVs in crosstalk between the peripheral and the central immune systems as well as in crosstalk between the peripheral organs and the brain in CNS disorders, especially in neurodegenerative diseases, stroke, and trauma. This work will help in elucidating the contributions of EVs to brain health and disorders, and promote the development of new strategies for minimally invasive treatment.
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16
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Grigor’eva EV, Kopytova AE, Yarkova ES, Pavlova SV, Sorogina DA, Malakhova AA, Malankhanova TB, Baydakova GV, Zakharova EY, Medvedev SP, Pchelina SN, Zakian SM. Biochemical Characteristics of iPSC-Derived Dopaminergic Neurons from N370S GBA Variant Carriers with and without Parkinson's Disease. Int J Mol Sci 2023; 24:ijms24054437. [PMID: 36901867 PMCID: PMC10002967 DOI: 10.3390/ijms24054437] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 03/12/2023] Open
Abstract
GBA variants increase the risk of Parkinson's disease (PD) by 10 times. The GBA gene encodes the lysosomal enzyme glucocerebrosidase (GCase). The p.N370S substitution causes a violation of the enzyme conformation, which affects its stability in the cell. We studied the biochemical characteristics of dopaminergic (DA) neurons generated from induced pluripotent stem cells (iPSCs) from a PD patient with the GBA p.N370S mutation (GBA-PD), an asymptomatic GBA p.N370S carrier (GBA-carrier), and two healthy donors (control). Using liquid chromatography with tandem mass spectrometry (LC-MS/MS), we measured the activity of six lysosomal enzymes (GCase, galactocerebrosidase (GALC), alpha-glucosidase (GAA), alpha-galactosidase (GLA), sphingomyelinase (ASM), and alpha-iduronidase (IDUA)) in iPSC-derived DA neurons from the GBA-PD and GBA-carrier. DA neurons from the GBA mutation carrier demonstrated decreased GCase activity compared to the control. The decrease was not associated with any changes in GBA expression levels in DA neurons. GCase activity was more markedly decreased in the DA neurons of GBA-PD patient compared to the GBA-carrier. The amount of GCase protein was decreased only in GBA-PD neurons. Additionally, alterations in the activity of the other lysosomal enzymes (GLA and IDUA) were found in GBA-PD neurons compared to GBA-carrier and control neurons. Further study of the molecular differences between the GBA-PD and the GBA-carrier is essential to investigate whether genetic factors or external conditions are the causes of the penetrance of the p.N370S GBA variant.
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Affiliation(s)
- Elena V. Grigor’eva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alena E. Kopytova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina 188300, Russia
- Department of Molecular Genetic and Nanobiological Technologies, Scientific and Research Centre, Pavlov First Saint-Petersburg State Medical University, Saint-Petersburg 197022, Russia
| | - Elena S. Yarkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sophia V. Pavlova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Diana A. Sorogina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anastasia A. Malakhova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Tuyana B. Malankhanova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | | | - Sergey P. Medvedev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sofia N. Pchelina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina 188300, Russia
- Department of Molecular Genetic and Nanobiological Technologies, Scientific and Research Centre, Pavlov First Saint-Petersburg State Medical University, Saint-Petersburg 197022, Russia
| | - Suren M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Correspondence:
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17
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Asadi MR, Abed S, Kouchakali G, Fattahi F, Sabaie H, Moslehian MS, Sharifi-Bonab M, Hussen BM, Taheri M, Ghafouri-Fard S, Rezazadeh M. Competing endogenous RNA (ceRNA) networks in Parkinson's disease: A systematic review. Front Cell Neurosci 2023; 17:1044634. [PMID: 36761351 PMCID: PMC9902725 DOI: 10.3389/fncel.2023.1044634] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Parkinson's disease (PD) is a distinctive clinical syndrome with several causes and clinical manifestations. Aside from an infectious cause, PD is a rapidly developing neurological disorder with a global rise in frequency. Notably, improved knowledge of molecular pathways and the developing novel diagnostic methods may result in better therapy for PD patients. In this regard, the amount of research on ceRNA axes is rising, highlighting the importance of these axes in PD. CeRNAs are transcripts that cross-regulate one another via competition for shared microRNAs (miRNAs). These transcripts may be either coding RNAs (mRNAs) or non-coding RNAs (ncRNAs). This research used a systematic review to assess validated loops of ceRNA in PD. The Prisma guideline was used to conduct this systematic review, which entailed systematically examining the articles of seven databases. Out of 309 entries, forty articles met all criteria for inclusion and were summarized in the appropriate table. CeRNA axes have been described through one of the shared vital components of the axes, including lncRNAs such as NEAT1, SNHG family, HOTAIR, MALAT1, XIST, circRNAs, and lincRNAs. Understanding the multiple aspects of this regulatory structure may aid in elucidating the unknown causal causes of PD and providing innovative molecular therapeutic targets and medical fields.
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Affiliation(s)
- Mohammad Reza Asadi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Samin Abed
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ghazal Kouchakali
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fateme Fattahi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marziyeh Sadat Moslehian
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mirmohsen Sharifi-Bonab
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department of Biomedical Sciences, Cihan University-Erbil, Erbil, Iraq
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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The Consequences of GBA Deficiency in the Autophagy-Lysosome System in Parkinson's Disease Associated with GBA. Cells 2023; 12:cells12010191. [PMID: 36611984 PMCID: PMC9818455 DOI: 10.3390/cells12010191] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/27/2022] [Accepted: 12/31/2022] [Indexed: 01/05/2023] Open
Abstract
GBA gene variants were the first genetic risk factor for Parkinson's disease. GBA encodes the lysosomal enzyme glucocerebrosidase (GBA), which is involved in sphingolipid metabolism. GBA exhibits a complex physiological function that includes not only the degradation of its substrate glucosylceramide but also the metabolism of other sphingolipids and additional lipids such as cholesterol, particularly when glucocerebrosidase activity is deficient. In the context of Parkinson's disease associated with GBA, the loss of GBA activity has been associated with the accumulation of α-synuclein species. In recent years, several hypotheses have proposed alternative and complementary pathological mechanisms to explain why lysosomal enzyme mutations lead to α-synuclein accumulation and become important risk factors in Parkinson's disease etiology. Classically, loss of GBA activity has been linked to a dysfunctional autophagy-lysosome system and to a subsequent decrease in autophagy-dependent α-synuclein turnover; however, several other pathological mechanisms underlying GBA-associated parkinsonism have been proposed. This review summarizes and discusses the different hypotheses with a special focus on autophagy-dependent mechanisms, as well as autophagy-independent mechanisms, where the role of other players such as sphingolipids, cholesterol and other GBA-related proteins make important contributions to Parkinson's disease pathogenesis.
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19
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Xia J, Xu D, Qin Y, Wan F, Ren Y, Bu C, Li T. Meta-analysis of the Prognostic Value of microRNA-22 in Leukemia Patients. Technol Cancer Res Treat 2023; 22:15330338231212309. [PMID: 37942522 PMCID: PMC10637174 DOI: 10.1177/15330338231212309] [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: 05/02/2023] [Revised: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Objective: The pathogenesis of leukemia is complex and there are no effective diagnostic and prognostic indicators. Previous studies showed that microRNA-22 (miR-22) has altered expression level in multiple leukemia subtypes, which is associated with the survival outcomes of leukemia. Methods: According to the constituted retrieval strategy, eligible studies were included from January 2010 to November 2022 by searching database. The pooled Risk Ratio (RR) and 95% confidence intervals (CI) were used to study the relationship between miR-22 and survival. Stata12.0 was used for meta-analysis. Differential expression analysis was conducted based on expression profile of miRNA. Results: Four English articles were included containing a total of 215 leukemia patients. Data showed that the pooled RR for overall survival (OS) was 1.558 (95% CI: 1.197-2.028, P < .01). Subgroup analysis for OS of acute myeloid leukemia patients and the RFS of plasma cell leukemia patients were statistically significant with different expression levels of miR-22 (RR:1.495, 95%CI:1.141-1.958, P < .01 and RR:1.517, 95%CI:1.114-2.065, P < .01, respectively). Moreover, all data included had no significant heterogeneity and publication bias. Conclusions: miR-22 is associated with the survival outcome of leukemia patients suggesting that miR-22 may be a promising prognostic biomarker for this patient population, and the expression level of miR-22 in ALL patients down-regulated.
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Affiliation(s)
- Jing Xia
- Department of Hematology, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China
| | - Daming Xu
- Department of Hematology, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China
| | - Yuanling Qin
- Department of Hematology, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China
- Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi Children's Hospital, Wuxi, China
| | - Faguang Wan
- Department of Ultrasound Medicine, Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, China
| | - Yongwei Ren
- State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, China
| | - Chaozhi Bu
- State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, China
| | - Tianyu Li
- Department of Hematology, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China
- Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi Children's Hospital, Wuxi, China
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20
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Riboldi GM, Vialle RA, Navarro E, Udine E, de Paiva Lopes K, Humphrey J, Allan A, Parks M, Henderson B, Astudillo K, Argyrou C, Zhuang M, Sikder T, Oriol Narcis J, Kumar SD, Janssen W, Sowa A, Comi GP, Di Fonzo A, Crary JF, Frucht SJ, Raj T. Transcriptome deregulation of peripheral monocytes and whole blood in GBA-related Parkinson's disease. Mol Neurodegener 2022; 17:52. [PMID: 35978378 PMCID: PMC9386994 DOI: 10.1186/s13024-022-00554-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic mutations in beta-glucocerebrosidase (GBA) represent the major genetic risk factor for Parkinson's disease (PD). GBA participates in both the endo-lysosomal pathway and the immune response, two important mechanisms involved in the pathogenesis of PD. However, modifiers of GBA penetrance have not yet been fully elucidated. METHODS We characterized the transcriptomic profiles of circulating monocytes in a population of patients with PD and healthy controls (CTRL) with and without GBA variants (n = 23 PD/GBA, 13 CTRL/GBA, 56 PD, 66 CTRL) and whole blood (n = 616 PD, 362 CTRL, 127 PD/GBA, 165 CTRL/GBA). Differential expression analysis, pathway enrichment analysis, and outlier detection were performed. Ultrastructural characterization of isolated CD14+ monocytes in the four groups was also performed through electron microscopy. RESULTS We observed hundreds of differentially expressed genes and dysregulated pathways when comparing manifesting and non-manifesting GBA mutation carriers. Specifically, when compared to idiopathic PD, PD/GBA showed dysregulation in genes involved in alpha-synuclein degradation, aging and amyloid processing. Gene-based outlier analysis confirmed the involvement of lysosomal, membrane trafficking, and mitochondrial processing in manifesting compared to non-manifesting GBA-carriers, as also observed at the ultrastructural levels. Transcriptomic results were only partially replicated in an independent cohort of whole blood samples, suggesting cell-type specific changes. CONCLUSIONS Overall, our transcriptomic analysis of primary monocytes identified gene targets and biological processes that can help in understanding the pathogenic mechanisms associated with GBA mutations in the context of PD.
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Affiliation(s)
- Giulietta Maria Riboldi
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, 222 East 41st street, New York, NY, 10017, USA
| | - Ricardo A Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA.,Department of Biochemistry and Molecular Biology (Universidad Complutense de Madrid) & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Evan Udine
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Amanda Allan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Madison Parks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Brooklyn Henderson
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, 222 East 41st street, New York, NY, 10017, USA
| | - Kelly Astudillo
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, 222 East 41st street, New York, NY, 10017, USA
| | - Charalambos Argyrou
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Maojuan Zhuang
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Tamjeed Sikder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15th Floor, New York, NY, 10029, USA.,Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 9-22, New York, NY, 10029, USA
| | - J Oriol Narcis
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA
| | - Shilpa Dilip Kumar
- Microscopy Core and Advanced Bioimaging Center at the Icahn School of Medicine at Mount Sinai Center, 1468 Madison Avenue, Room 18-250, New York, NY, 10029, USA
| | - William Janssen
- Microscopy Core and Advanced Bioimaging Center at the Icahn School of Medicine at Mount Sinai Center, 1468 Madison Avenue, Room 18-250, New York, NY, 10029, USA
| | - Allison Sowa
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15th Floor, New York, NY, 10029, USA
| | - Giacomo P Comi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy.,Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 35, 20122, Milano, MI, Italy
| | - Alessio Di Fonzo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy.,Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 35, 20122, Milano, MI, Italy
| | - John F Crary
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15th Floor, New York, NY, 10029, USA.,Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 9-22, New York, NY, 10029, USA
| | - Steven J Frucht
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, 222 East 41st street, New York, NY, 10017, USA
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1137, New York, NY, 10029, USA. .,Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, ICAHN 10-70E, New York, NY, 10029-6574, USA.
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21
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Miyoshi K, Hagita H, Horiguchi T, Tanimura A, Noma T. Redefining GBA gene structure unveils the ability of Cap-independent, IRES-dependent gene regulation. Commun Biol 2022; 5:639. [PMID: 35831491 PMCID: PMC9279297 DOI: 10.1038/s42003-022-03577-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Glucosylceramide is the primary molecule of glycosphingolipids, and its metabolic regulation is crucial for life. Defects in the catabolizing enzyme, glucocerebrosidase (GCase), cause a lysosomal storage disorder known as Gaucher disease. However, the genetic regulation of GCase has not been fully understood. Here we show the redefined structure of the GCase coding gene (GBA), and clarify the regulatory mechanisms of its transcription and translation. First, alternative uses of the two GBA gene promoters were identified in fibroblasts and HL60-derived macrophages. Intriguingly, both GBA transcripts and GCase activities were induced in macrophages but not in neutrophils. Second, we observed cap-independent translation occurs via unique internal ribosome entry site activities in first promoter-driven GBA transcripts. Third, the reciprocal expression was observed in GBA and miR22-3p versus GBAP1 transcripts before and after HL60-induced macrophage differentiation. Nevertheless, these findings clearly demonstrate novel cell-type-specific GBA gene expression regulatory mechanisms, providing new insights into GCase biology. The cell type-specific expression of the glucocerebrosidase gene, associated with the lysosomal storage disorder called Gaucher disease, is linked to cis- and trans-regulatory transcriptional and translational mechanisms.
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Affiliation(s)
- Keiko Miyoshi
- Department of Oral Bioscience, Tokushima University Graduate School of Biomedical Sciences, Tokushima, 770-8504, Japan.
| | - Hiroko Hagita
- Department of Oral Bioscience, Tokushima University Graduate School of Biomedical Sciences, Tokushima, 770-8504, Japan
| | - Taigo Horiguchi
- Department of Oral Bioscience, Tokushima University Graduate School of Biomedical Sciences, Tokushima, 770-8504, Japan
| | - Ayako Tanimura
- Division of Food & Health Sciences, Department of Environmental and Symbiotic Sciences, Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto, 862-8502, Japan
| | - Takafumi Noma
- Department of Nutrition and Health Promotion, Faculty of Human Life Studies, Hiroshima Jogakuin University, 4-13-1 Ushita-higashi, Higashi-ku, Hiroshima, 732-0063, Japan
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22
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Guo JN, Guan M, Jiang N, Li N, Li YJ, Zhang J, Ma D. Establishment and Phenotypic Analysis of the Novel Gaucher Disease Mouse Model With the Partially Humanized Gba1 Gene and F213I Mutation. Front Genet 2022; 13:892457. [PMID: 35711931 PMCID: PMC9196271 DOI: 10.3389/fgene.2022.892457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 12/02/2022] Open
Abstract
Gaucher disease (GD) is an autosomal recessive lysosomal storage disorder caused by mutations in the GBA1 gene, which produces the glucocerebrosidase (GCase) protein. There are more than 500 mutations reported in GBA1, among which L444P (p.Leu444Pro) and F213I (p.Phe213Ile) are the most common in the Chinese population, while the function of F213I mutation remains elusive. This study aims to establish the GD mouse model of partially humanized Gba1 gene with F213I mutation. In vitro GCase activity assays showed that the product of partially humanized Gba1 gene, in which the mouse exons 5-7 were replace by the corresponding human exons, displayed similar activity with the wild-type mouse Gba1, while the F213I mutation in the humanized Gba1 led to significant decrease in enzyme activity. ES cell targeting was used to establish the mice expressing the partially humanized Gba1-F213I. Gba1F213I/+ mice did not show obviously abnormal phenotypes, but homozygous Gba1F213I/F213I mice died within 24 h after birth, whose epidermal stratum corneum were abnormal from the wild-type. The GCase activity in Gba1F213I/F213I mice greatly decreased. In conclusion, our results showed that the partially humanized GD mouse model with the F213I mutation was developed and homozygous F213I mutation is lethal for newborn mice.
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Affiliation(s)
- Jia-Ni Guo
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Huashan Hospital, Fudan University, Shanghai, China
| | - Ming Guan
- Huashan Hospital, Fudan University, Shanghai, China
| | - Nan Jiang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Na Li
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Jun Li
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Children's Hospital, Fudan University, Shanghai, China
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23
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Xiao Y, Chen H, Liao J, Zhang Q, He H, Lei J, Huang J, Ouyang Q, Shen Y, Wang J. The Potential Circular RNAs Biomarker Panel and Regulatory Networks of Parkinson's Disease. Front Neurosci 2022; 16:893713. [PMID: 35645729 PMCID: PMC9136065 DOI: 10.3389/fnins.2022.893713] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease. It has been reported that circular RNAs (circRNAs) play important roles in several neurological diseases. However, the role and regulatory networks of circRNAs in PD are still largely unclear. In this study, we first compared the global expression level of circRNAs from patients with PD and controls using microarray, then the candidate circRNAs were validated in another PD cohort. The possible functions of these candidate circRNAs were analyzed using Gene Ontology (GO) analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and the regulatory networks of these candidate circRNAs were constructed through circRNA-miRNA-mRNA regulatory networks, protein-protein interaction (PPI) networks, and transcription factor-circRNA networks. The results indicated that hsa_circRNA_101275, hsa_circRNA_103730, and hsa_circRNA_038416 were significantly more highly expressed in patients with PD, while hsa_circRNA_102850 was lower expressed in patients with PD when compared with controls. A circRNA panel combining the four differentially expressed circRNA showed a high diagnostic ability to distinguish patients with PD from controls (AUC = 0.938). Furthermore, GO and KEGG analysis showed these candidate circRNAs were enriched in PI3K-Akt and MAPK signaling pathways. We established circRNA-miRNA-mRNA regulatory networks and identified 10 hub genes (ESR1, PTEN, SHC1, IGF1R, SMAD2, KRAS, MDM2, HIF1A, BMP4, and ACVR2B) were closely related to PD by using PPI network analysis. Besides, these circRNAs were predicted to be regulated through tyrosine hydroxylase (TH)-relevant transcription factors such as GATA2 and GATA3. In conclusion, our results suggest that the circRNA panel and the established circRNA-miRNA-mRNA regulation networks might provide potential novel biomarkers and therapeutic targets for PD.
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Affiliation(s)
- Yousheng Xiao
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hongchang Chen
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Neurology, Minzu Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jiajia Liao
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qinxin Zhang
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Honghu He
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiang Lei
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinjun Huang
- Department of Rehabilitation, Guiping People’s Hospital, Guiping, China
| | - Qiang Ouyang
- Department of Neurology, Minzu Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yuefei Shen
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jin Wang
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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24
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Ren S, Lee W, Han K. Predicting lymph node metastasis and prognosis of individual cancer patients based on miRNA-mediated RNA interactions. BMC Med Genomics 2022; 15:87. [PMID: 35430805 PMCID: PMC9014599 DOI: 10.1186/s12920-022-01231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Lymph node metastasis is usually detected based on the images obtained from clinical examinations. Detecting lymph node metastasis from clinical examinations is a direct way of diagnosing metastasis, but the diagnosis is done after lymph node metastasis occurs.
Results
We developed a new method for predicting lymph node metastasis based on differential correlations of miRNA-mediated RNA interactions in cancer. The types of RNAs considered in this study include mRNAs, lncRNAs, miRNAs, and pseudogenes. We constructed cancer patient-specific networks of miRNA mediated RNA interactions and identified key miRNA–RNA pairs from the network. A prediction model using differential correlations of the miRNA–RNA pairs of a patient as features showed a much higher performance than other methods which use gene expression data. The key miRNA–RNA pairs were also powerful in predicting prognosis of an individual patient in several types of cancer.
Conclusions
Differential correlations of miRNA–RNA pairs identified from patient-specific networks of miRNA mediated RNA interactions are powerful in predicting lymph node metastasis in cancer patients. The key miRNA–RNA pairs were also powerful in predicting prognosis of an individual patient of solid cancer.
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25
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Does the Expression and Epigenetics of Genes Involved in Monogenic Forms of Parkinson’s Disease Influence Sporadic Forms? Genes (Basel) 2022; 13:genes13030479. [PMID: 35328033 PMCID: PMC8951612 DOI: 10.3390/genes13030479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Parkinson’s disease (PD) is a disorder characterized by a triad of motor symptoms (akinesia, rigidity, resting tremor) related to loss of dopaminergic neurons mainly in the Substantia nigra pars compacta. Diagnosis is often made after a substantial loss of neurons has already occurred, and while dopamine replacement therapies improve symptoms, they do not modify the course of the disease. Although some biological mechanisms involved in the disease have been identified, such as oxidative stress and accumulation of misfolded proteins, they do not explain entirely PD pathophysiology, and a need for a better understanding remains. Neurodegenerative diseases, including PD, appear to be the result of complex interactions between genetic and environmental factors. The latter can alter gene expression by causing epigenetic changes, such as DNA methylation, post-translational modification of histones and non-coding RNAs. Regulation of genes responsible for monogenic forms of PD may be involved in sporadic PD. This review will focus on the epigenetic mechanisms regulating their expression, since these are the genes for which we currently have the most information available. Despite technical challenges, epigenetic epidemiology offers new insights on revealing altered biological pathways and identifying predictive biomarkers for the onset and progression of PD.
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Duan X, Shan L, Shi S, Xu B, Chen X, Di J, Chen B, Li X, Liu S, Wang Y, Yang W. GBAP1 polymorphisms (rs140081212, rs1057941 and rs2990220) contribute to reduced risk of gastric cancer. Future Oncol 2022; 18:1861-1872. [PMID: 35156841 DOI: 10.2217/fon-2021-0973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study was designed to evaluate the contribution of GBAP1 variants to gastric cancer (GC) risk in a Chinese Han population. Methods: The genotypes of GBAP1 polymorphisms were detected using the Agena MassARRAY platform. Logistic regression analysis was used to calculate odds ratios (ORs) and 95% CIs. Results: GBAP1 rs140081212 (OR = 0.51, p = 4.50 × 10-07), rs1057941 (OR = 0.48, p = 1.19 × 10-08) and rs2990220 (OR = 0.46, p = 7.34 × 10-09) contribute to reduced GC risk, especially gastric adenocarcinoma. Interestingly, the contribution of GBAP1 variants to GC susceptibility was associated with age, sex, BMI, smoking and drinking. Conclusion: This research suggested that GBAP1 polymorphisms might provide a protective effect against GC occurrence in a Chinese Han population.
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Affiliation(s)
- Xianglong Duan
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, XizangMinzu University, Xianyang, Shaanxi, 712082, China.,Department of Rehabilitation Medicine, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Liang Shan
- Department of Rehabilitation Medicine, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Shuai Shi
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Boyu Xu
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Xin Chen
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Jinqin Di
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Bopeng Chen
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Xiaoqing Li
- Department of Dermatology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Sida Liu
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Yuhe Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, XizangMinzu University, Xianyang, Shaanxi, 712082, China
| | - Wei Yang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, XizangMinzu University, Xianyang, Shaanxi, 712082, China
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Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs of 17-22 nucleotides in length with a critical function in posttranscriptional gene regulation. These master regulators are themselves subject to regulation both transcriptionally and posttranscriptionally. Recently, miRNA function has been shown to be modulated by exogenous RNA molecules that function as miRNA sponges. Interestingly, endogenous transcripts such as transcribed pseudogenes, long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and mRNAs may serve as natural miRNA sponges. These transcripts, which bind to miRNAs and competitively sequester them away from their targets, are naturally existing endogenous miRNA sponges, called competing endogenous RNAs (ceRNAs). Here we present a historical background of miRNAs, exogenous and endogenous miRNA sponges as well as some examples of endogenous miRNA sponges involved in regulatory mechanisms associated with various diseases, developmental stages, and other cellular processes.
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Affiliation(s)
- Ayşe Hale Alkan
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Bünyamin Akgül
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey.
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Mahmoud M, Doddapaneni H, Timp W, Sedlazeck FJ. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol 2021; 22:268. [PMID: 34521442 PMCID: PMC8442460 DOI: 10.1186/s13059-021-02486-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/02/2021] [Indexed: 12/11/2022] Open
Abstract
Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive insight into the sample and thus enables novel findings in biology or medicine. PRINCESS is a structured workflow that takes raw sequence reads and generates a fully phased SNV, SV, and methylation call set within a few hours. PRINCESS achieves high accuracy and long phasing even on low coverage datasets and can resolve repetitive, complex medical relevant genes that often escape detection. PRINCESS is publicly available at https://github.com/MeHelmy/princess under the MIT license.
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Affiliation(s)
- Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | | | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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Current State-of-the-Art and Unresolved Problems in Using Human Induced Pluripotent Stem Cell-Derived Dopamine Neurons for Parkinson's Disease Drug Development. Int J Mol Sci 2021; 22:ijms22073381. [PMID: 33806103 PMCID: PMC8037675 DOI: 10.3390/ijms22073381] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
Human induced pluripotent stem (iPS) cells have the potential to give rise to a new era in Parkinson's disease (PD) research. As a unique source of midbrain dopaminergic (DA) neurons, iPS cells provide unparalleled capabilities for investigating the pathogenesis of PD, the development of novel anti-parkinsonian drugs, and personalized therapy design. Significant progress in developmental biology of midbrain DA neurons laid the foundation for their efficient derivation from iPS cells. The introduction of 3D culture methods to mimic the brain microenvironment further expanded the vast opportunities of iPS cell-based research of the neurodegenerative diseases. However, while the benefits for basic and applied studies provided by iPS cells receive widespread coverage in the current literature, the drawbacks of this model in its current state, and in particular, the aspects of differentiation protocols requiring further refinement are commonly overlooked. This review summarizes the recent data on general and subtype-specific features of midbrain DA neurons and their development. Here, we review the current protocols for derivation of DA neurons from human iPS cells and outline their general weak spots. The associated gaps in the contemporary knowledge are considered and the possible directions for future research that may assist in improving the differentiation conditions and increase the efficiency of using iPS cell-derived neurons for PD drug development are discussed.
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Wang T, Liang D, Yang H. SNHG15 facilitated malignant behaviors of oral squamous cell carcinoma through targeting miR-188-5p/DAAM1. J Oral Pathol Med 2021; 50:681-691. [PMID: 33742497 DOI: 10.1111/jop.13169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 02/10/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Long non-coding RNA (lncRNA) small nucleolar RNA host gene 15 (SNHG15) has been discovered and demonstrated to have significant function in multiple cancers. Nevertheless, how it participates in the progression of oral squamous cell carcinoma (OSCC) and its potential regulatory system are still unclear. METHODS RT-qPCR detected the expression of SNHG15, miR-188-5p, and DAAM1. RNA pull down, RT-qPCR, and bioinformatics were used for finding and selecting downstream targets of SNHG15. RESULTS SNHG15 presented a high expression in OSCC cells. Moreover, inhibition of SNHG15 exhibited repressive influence on proliferative, migrated, and invasive abilities but induce apoptosis of OSCC cells. Through the search of bioinformatics and RNA pull down assays, we confirmed that miR-188-5p was one target of SNHG15 in OSCC cells. Additionally, miR-188-5p could hamper the growth of OSCC cells. Moreover, it was manifested that DAAM1 was down-regulated by miR-188-5p. DAAM1 was up-regulated in OSCC cells. Furthermore, it exerted oncogenic function in the course of OSCC. Eventually, overexpression of DAAM1 offsets the effects of down-regulation of SNHG15 on the development of OSCC. CONCLUSION To summarize, our study certified that SNHG15 contributed to the process of OSCC via sponging miR-188-5p to elevate DAAM1 expression. SNHG15 might offer novel sight to improve the results of treatment for OSCC.
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Affiliation(s)
- Tongwu Wang
- Department of Stomatology, First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China
| | - Dong Liang
- Department of Stomatology, Lianyungang Municipal Oriental Hospital, Lianyungang, Jiangsu, China
| | - Hongyu Yang
- Department of Stomatology, First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China
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Modelling Parkinson's Disease: iPSCs towards Better Understanding of Human Pathology. Brain Sci 2021; 11:brainsci11030373. [PMID: 33799491 PMCID: PMC8000082 DOI: 10.3390/brainsci11030373] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023] Open
Abstract
Parkinson’s Disease (PD) is a chronic neurodegenerative disorder characterized by motor and non-motor symptoms, among which are bradykinesia, rigidity, tremor as well as mental symptoms such as dementia. The underlying cause of Parkinson disease is degeneration of dopaminergic neurons. It has been challenging to develop an efficient animal model to accurately represent the complex phenotypes found with PD. However, it has become possible to recapitulate the myriad of phenotypes underlying the PD pathology by using human induced pluripotent stem cell (iPSC) technology. Patient-specific iPSC-derived dopaminergic neurons are available and present an opportunity to study many aspects of the PD phenotypes in a dish. In this review, we report the available data on iPSC-derived neurons derived from PD patients with identified gene mutations. Specifically, we will report on the key phenotypes of the generated iPSC-derived neurons from PD patients with different genetic background. Furthermore, we discuss the relationship these cellular phenotypes have to PD pathology and future challenges and prospects for iPSC modelling and understanding of the pathogenesis of PD.
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Exploring the secrets of brain transcriptional regulation: developing methodologies, recent significant findings, and perspectives. Brain Struct Funct 2021; 226:313-322. [PMID: 33547496 DOI: 10.1007/s00429-021-02230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
Exploring and revealing the secret of the function of the human brain has been the dream of mankind and science. Delineating brain transcriptional regulation has been extremely challenging, but recent technological advances have facilitated a deeper investigation of molecular processes in the brain. Tracing the molecular regulatory mechanisms of different gene expression profiles in the brain is divergent and has made it possible to connect spatial and temporal variations in gene expression to distributed properties of brain structure and function. Here, we review the molecular diversity of the brain among rodents, non-human primates and humans. We also discuss the molecular mechanism of non-coding DNA/RNA at the transcriptional/post-transcriptional level based on recent technical advances to highlight an improved understanding of the complex transcriptional network in the brain. Spatiotemporal and single-cell transcriptomics have attempted to gain novel insight into the development and evolution of the brain as well as the progression of human diseases. Although it is clear that the field is developing and challenges remain to be resolved, the impressive recent progress provides a solid foundation to better understand the brain and evidence-based recommendations for the diagnosis and treatment of brain diseases.
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Pawliński Ł, Polus A, Tobór E, Sordyl M, Kopka M, Solnica B, Kieć-Wilk B. MiRNA Expression in Patients with Gaucher Disease Treated with Enzyme Replacement Therapy. Life (Basel) 2020; 11:life11010002. [PMID: 33375048 PMCID: PMC7822051 DOI: 10.3390/life11010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 11/29/2022] Open
Abstract
Aims: The aim of the work was to establish potential biomarkers or drug targets by analysing changes in miRNA concentration among patients with Gaucher disease (GD) compared to in healthy subjects. Methods: This study was an observational, cross-sectional analysis of 30 adult participants: 10 controls and 20 adults with GD type 1. Patients with GD type 1 were treated with enzyme replacement therapy (ERT) for at least two years. The control group was composed of healthy volunteers, unrelated to the patients, adjusted with age, sex and body mass index (BMI). The miRNA alteration between these groups was examined. After obtaining preliminary results on a group of six GD patients by the high-output method (TaqMan low-density array (TLDA)), potential miRNAs were selected for confirming the results by using the qRT-PCR method. With Diane Tools, we analysed miRNAs of which differential expression is most significant and their potential role in GD pathophysiology. We also determined the essential pathways these miRNAs are involved in. Results: 266 dysregulated miRNAs were found among 753 tested. Seventy-eight miRNAs were downregulated, and 188 were upregulated. Thirty miRNAs were significantly altered; all of them were upregulated. The analysis of pathways regulated by the selected miRNAs showed an effect on bone development, inflammation or regulation of axonal transmission in association with Parkinson’s disease. Conclusions: We revealed few miRNAs, like miR-26-5p, which are highly altered and fit the GD pathophysiological model, might be considered as novel biomarkers of disease progression but need further evaluation.
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Affiliation(s)
- Łukasz Pawliński
- Clinical Department of Metabolic Diseases and Diabetology, University Hospital in Krakow, 30-688 Kraków, Poland; (Ł.P.); (E.T.); (M.K.)
- European Reference Network for Hereditary Metabolic Disorders (MetabERN), 31-501 Kraków, Poland
| | - Anna Polus
- Department of Clinical Biochemistry, Jagiellonian University Medical College, 30-688 Kraków, Poland; (A.P.); (M.S.); (B.S.)
| | - Ewa Tobór
- Clinical Department of Metabolic Diseases and Diabetology, University Hospital in Krakow, 30-688 Kraków, Poland; (Ł.P.); (E.T.); (M.K.)
| | - Maria Sordyl
- Department of Clinical Biochemistry, Jagiellonian University Medical College, 30-688 Kraków, Poland; (A.P.); (M.S.); (B.S.)
| | - Marianna Kopka
- Clinical Department of Metabolic Diseases and Diabetology, University Hospital in Krakow, 30-688 Kraków, Poland; (Ł.P.); (E.T.); (M.K.)
| | - Bogdan Solnica
- Department of Clinical Biochemistry, Jagiellonian University Medical College, 30-688 Kraków, Poland; (A.P.); (M.S.); (B.S.)
| | - Beata Kieć-Wilk
- Clinical Department of Metabolic Diseases and Diabetology, University Hospital in Krakow, 30-688 Kraków, Poland; (Ł.P.); (E.T.); (M.K.)
- European Reference Network for Hereditary Metabolic Disorders (MetabERN), 31-501 Kraków, Poland
- Department of Metabolic Diseases and Diabetology, Jagiellonian University Medical College, 30-688 Kraków, Poland
- Correspondence:
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34
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Competing Endogenous RNA Networks as Biomarkers in Neurodegenerative Diseases. Int J Mol Sci 2020; 21:ijms21249582. [PMID: 33339180 PMCID: PMC7765627 DOI: 10.3390/ijms21249582] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
Protein aggregation is classically considered the main cause of neuronal death in neurodegenerative diseases (NDDs). However, increasing evidence suggests that alteration of RNA metabolism is a key factor in the etiopathogenesis of these complex disorders. Non-coding RNAs are the major contributor to the human transcriptome and are particularly abundant in the central nervous system, where they have been proposed to be involved in the onset and development of NDDs. Interestingly, some ncRNAs (such as lncRNAs, circRNAs and pseudogenes) share a common functionality in their ability to regulate gene expression by modulating miRNAs in a phenomenon known as the competing endogenous RNA mechanism. Moreover, ncRNAs are found in body fluids where their presence and concentration could serve as potential non-invasive biomarkers of NDDs. In this review, we summarize the ceRNA networks described in Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and spinocerebellar ataxia type 7, and discuss their potential as biomarkers of these NDDs. Although numerous studies have been carried out, further research is needed to validate these complex interactions between RNAs and the alterations in RNA editing that could provide specific ceRNET profiles for neurodegenerative disorders, paving the way to a better understanding of these diseases.
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Gjorgjieva M, Sobolewski C, Ay AS, Abegg D, Correia de Sousa M, Portius D, Berthou F, Fournier M, Maeder C, Rantakari P, Zhang FP, Poutanen M, Picard D, Montet X, Nef S, Adibekian A, Foti M. Genetic Ablation of MiR-22 Fosters Diet-Induced Obesity and NAFLD Development. J Pers Med 2020; 10:jpm10040170. [PMID: 33066497 PMCID: PMC7711493 DOI: 10.3390/jpm10040170] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
miR-22 is one of the most abundant miRNAs in the liver and alterations of its hepatic expression have been associated with the development of hepatic steatosis and insulin resistance, as well as cancer. However, the pathophysiological roles of miR-22-3p in the deregulated hepatic metabolism with obesity and cancer remains poorly characterized. Herein, we observed that alterations of hepatic miR-22-3p expression with non-alcoholic fatty liver disease (NAFLD) in the context of obesity are not consistent in various human cohorts and animal models in contrast to the well-characterized miR-22-3p downregulation observed in hepatic cancers. To unravel the role of miR-22 in obesity-associated NAFLD, we generated constitutive Mir22 knockout (miR-22KO) mice, which were subsequently rendered obese by feeding with fat-enriched diet. Functional NAFLD- and obesity-associated metabolic parameters were then analyzed. Insights about the role of miR-22 in NAFLD associated with obesity were further obtained through an unbiased proteomic analysis of miR-22KO livers from obese mice. Metabolic processes governed by miR-22 were finally investigated in hepatic transformed cancer cells. Deletion of Mir22 was asymptomatic when mice were bred under standard conditions, except for an onset of glucose intolerance. However, when challenged with a high fat-containing diet, Mir22 deficiency dramatically exacerbated fat mass gain, hepatomegaly, and liver steatosis in mice. Analyses of explanted white adipose tissue revealed increased lipid synthesis, whereas mass spectrometry analysis of the liver proteome indicated that Mir22 deletion promotes hepatic upregulation of key enzymes in glycolysis and lipid uptake. Surprisingly, expression of miR-22-3p in Huh7 hepatic cancer cells triggers, in contrast to our in vivo observations, a clear induction of a Warburg effect with an increased glycolysis and an inhibited mitochondrial respiration. Together, our study indicates that miR-22-3p is a master regulator of the lipid and glucose metabolism with differential effects in specific organs and in transformed hepatic cancer cells, as compared to non-tumoral tissue.
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Affiliation(s)
- Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Anne-Sophie Ay
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA; (D.A.); (A.A.)
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Dorothea Portius
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Flavien Berthou
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Pia Rantakari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Fu-Ping Zhang
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Didier Picard
- Department of Cell Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland;
| | - Xavier Montet
- Department of Radiology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Serge Nef
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA; (D.A.); (A.A.)
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
- Diabetes Center, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Correspondence: ; Tel.: +41-22-37-95-204; Fax: +41-22-37-95-260
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Abstract
Glycosylation is a sophisticated informational system that controls specific biological functions at the cellular and organismal level. Dysregulation of glycosylation may underlie some of the most complex and common diseases of the modern era. In the past 5 years, microRNAs have come to the forefront as a critical regulator of the glycome. Herein, we review the current literature on miRNA regulation of glycosylation and how this work may point to a new way to identify the biological importance of glycosylation enzymes.
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Affiliation(s)
- Chu T Thu
- Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Lara K Mahal
- Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States
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Menozzi E, Schapira AHV. Enhancing the Activity of Glucocerebrosidase as a Treatment for Parkinson Disease. CNS Drugs 2020; 34:915-923. [PMID: 32607746 DOI: 10.1007/s40263-020-00746-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mutations in the glucocerebrosidase (GBA1) gene are the most common genetic risk factor for Parkinson disease (PD). Homozygous or compound heterozygous GBA1 mutations cause the lysosomal storage disorder Gaucher disease (GD), characterized by deficient activity of the glucocerebrosidase enzyme (GCase). Both individuals with GD type I and heterozygous carriers of pathogenic variants of GBA1 have an increased risk of developing PD, by approximately ten- to 20-fold compared to non-carriers. GCase activity is also reduced in PD patients without GBA1 mutations, suggesting that the GCase lysosomal pathway might be involved in PD pathogenesis. Available evidence indicates that GCase can affect α-synuclein pathology in different ways. Misfolded GCase proteins are retained in the endoplasmic reticulum, altering the lysosomal trafficking of the enzyme and disrupting protein trafficking. Also, deficient GCase leads to accumulation of substrates that in turn may bind α-synuclein and promote pathological formation of aggregates. Furthermore, α-synuclein itself can lower the enzymatic activity of GCase, indicating that a bidirectional interaction exists between GCase and α-synuclein. Targeted therapies aimed at enhancing GCase activity, augmenting the trafficking of misfolded GCase proteins by small molecule chaperones, or reducing substrate accumulation, have been tested in preclinical and clinical trials. This article reviews the molecular mechanisms linking GCase to α-synuclein and discusses the therapeutic drugs that by targeting the GCase pathway can influence PD progression.
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Affiliation(s)
- Elisa Menozzi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
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Ravanidis S, Bougea A, Papagiannakis N, Koros C, Simitsi AM, Pachi I, Breza M, Stefanis L, Doxakis E. Validation of differentially expressed brain-enriched microRNAs in the plasma of PD patients. Ann Clin Transl Neurol 2020; 7:1594-1607. [PMID: 32860338 PMCID: PMC7480914 DOI: 10.1002/acn3.51146] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
Objective There is a pressing need to identify and validate, minimally invasive, molecular biomarkers that will complement current practices and increase the diagnostic accuracy in Parkinson’s disease (PD). Brain‐enriched miRNAs regulate all aspects of neuron development and function; importantly, they are secreted by neurons in amounts that can be readily detected in the plasma. Τhe aim of the present study was to validate a set of previously identified brain‐enriched miRNAs with diagnostic potential for idiopathic PD and recognize the molecular pathways affected by these deregulated miRNAs. Methods RT‐qPCR was performed in the plasma of 92 healthy controls and 108 idiopathic PD subjects. Statistical and in silico analyses were used to validate deregulated miRNAs and pathways in PD, respectively. Results miR‐22‐3p, miR‐124‐3p, miR‐136‐3p, miR‐154‐5p, and miR‐323a‐3p levels were found to be differentially expressed between healthy controls and PD patients. miR‐330‐5p, miR‐433‐3p, and miR‐495‐3p levels were overall higher in male subjects. Most of these miRNAs are clustered at Chr14q32 displaying CREB1, CEBPB, and MAZ transcription factor binding sites. Gene Ontology annotation analysis of deregulated miRNA targets revealed that “Protein modification,” “Transcription factor activity,” and “Cell death” terms were over‐represented. Kyoto Encyclopedia of Genes and Genome analysis revealed that “Long‐term depression,” “TGF‐beta signaling,” and “FoxO signaling” pathways were significantly affected. Interpretation We validated a panel of brain‐enriched miRNAs that can be used along with other measures for the detection of PD, revealed molecular pathways targeted by these deregulated miRNAs, and identified upstream transcription factors that may be directly implicated in PD pathogenesis.
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Affiliation(s)
- Stylianos Ravanidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece
| | - Anastasia Bougea
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece.,Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Nikolaos Papagiannakis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Christos Koros
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Athina Maria Simitsi
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Ioanna Pachi
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Marianthi Breza
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece
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The LGMN pseudogene promotes tumor progression by acting as a miR-495-3p sponge in glioblastoma. Cancer Lett 2020; 490:111-123. [PMID: 32711096 DOI: 10.1016/j.canlet.2020.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022]
Abstract
Pseudogenes, which are long noncoding RNAs that originate from protein-coding genes, have been suggested to play important roles in disease. Although studies have revealed high expression of legumain (LGMN) in many types of tumors, the regulation of LGMN remains largely unknown. Here, we found that a novel LGMN pseudogene (LGMNP1) was upregulated in glioblastoma (GBM) tissues and high LGMNP1 expression in GBM cells enhanced proliferation and invasion. Biochemical analysis showed that cytoplasmic LGMNP1 functionally targeted miR-495-3p in a manner involving an RNA-induced silencing complex. Dual-luciferase reporter assays demonstrated that LGMN was a target of miR-495-3p, and LGMN was upregulated and positively correlated with LGMNP1 in GBM. Moreover, miR-495-3p was downregulated and negatively correlated with LGMNP1 in GBM tissues. Notably, the tumor-promoting effects of LGMNP1 upregulation could be alleviated by miR-495-3p mimics. Furthermore, GBM cells overexpressing LGMNP1 exhibited more aggressive tumor progression and elevated LGMN expression in vivo. Thus, our data illustrate that LGMNP1 exerts its oncogenic activity, at least in part, as a competitive endogenous RNA (ceRNA) that elevates LGMN expression by sponging miR-495-3p. CeRNA-mediated miRNA sequestration might be a novel therapeutic strategy in GBM.
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Zou J, Guo Y, Wei L, Yu F, Yu B, Xu A. Long Noncoding RNA POU3F3 and α-Synuclein in Plasma L1CAM Exosomes Combined with β-Glucocerebrosidase Activity: Potential Predictors of Parkinson's Disease. Neurotherapeutics 2020; 17:1104-1119. [PMID: 32236821 PMCID: PMC7609611 DOI: 10.1007/s13311-020-00842-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are implicated in the autophagic-lysosomal pathway (ALP) and are closely linked to Parkinson's disease (PD) pathology. β-Glucocerebrosidase (GCase) has also been reported to be correlated with α-synuclein (α-syn) proteostasis. However, lncRNAs and α-syn in neural-derived L1CAM exosomes and GCase activity in the plasma of PD patients have not been studied. This study used an ultrasensitive methodology, fluorescence nanoparticle tracking analysis (NTA), to measure plasma L1CAM exosomes and Quanterix Simoa to measure α-syn concentrations in L1CAM exosomes. Eighty-five healthy controls and 93 PD patients were enrolled, and several scales were used to rate the severity of PD. Receiver operating characteristic (ROC) curves were applied to map the diagnostic accuracy of categorizing PD patients and healthy subjects. We found increased Linc-POU3F3 and α-syn concentrations in L1CAM exosomes and decreased GCase activity in PD patients compared with controls. The three biomarkers displayed obvious differences among PD patients based on gender, H-Y stage, and UPDRS-III distribution. Interestingly, Linc-POU3F3 was significantly positively correlated with α-syn in L1CAM exosomes and inversely correlated with GCase activity in PD patients. Significant correlations were observed among L1CAM exosomal Linc-POU3F3 levels, GCase activity, and PD severity, including motor/cognitive dysfunction. Additionally, the combination of Linc-POU3F3 and α-syn in L1CAM exosomes and GCase activity could discriminate PD patients from controls. These results suggest that L1CAM exosomal Linc-POU3F3, L1CAM exosomal α-syn, and GCase activity may shed light on the mechanism underlying the autophagic-lysosomal system in the pathogenesis of PD and could be used to assess the severity of PD.
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Affiliation(s)
- Jing Zou
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, Guangdong, People's Republic of China
- Clinical Neuroscience Institute of Jinan University, Guangzhou, 510630, Guangdong, People's Republic of China
| | - Yue Guo
- Key Laboratory of Assisted Circulation, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, People's Republic of China
- NHC Key Laboratory of Assisted Circulation, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Lei Wei
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, Guangdong, People's Republic of China
| | - Fang Yu
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213, USA
| | - Bo Yu
- Department of Medicine, Lincoln Medical Center, Bronx, New York, 10451, USA
| | - Anding Xu
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, Guangdong, People's Republic of China.
- Clinical Neuroscience Institute of Jinan University, Guangzhou, 510630, Guangdong, People's Republic of China.
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Zhao Y, Chen X, Jiang J, Wan X, Wang Y, Xu P. Epigallocatechin gallate reverses gastric cancer by regulating the long noncoding RNA LINC00511/miR-29b/KDM2A axis. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165856. [PMID: 32512188 DOI: 10.1016/j.bbadis.2020.165856] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/20/2020] [Accepted: 05/30/2020] [Indexed: 12/31/2022]
Abstract
Epigallocatechin gallate (EGCG), as one of the main ingredients of green tea, has been reported to have potential prevention on a variety of solid tumors. However, the system-wide molecular mechanisms targeted to EGCG's anti-tumor effect have not been illustrated. Here, AGS and SGC7901 GC cells were used to investigate the EGCG-mediated change of gene expression. Our data showed that EGCG retarded cell growth and promoted cell death of GC in dose-dependent manner. Analyses based on transcription, translation as well as function were performed to explore the elusive anticancer role of EGCG. Of them, cell cycle was probably implicated key pathway of EGCG. Besides, our data revealed numerous LncRNAs activated after EGCG treatment. In this study, LINC00511 was discovered to be suppressed by EGCG and highly expressed in GC cells and tissues. Knockdown of LINC00511 inhibited cell growth and promoted cell death ratio in GC. Additionally, our data suggested LINC00511 could decrease the expression of miR-29b, followed by inducing GC development. Knockdown of miR-29b recovered the effects of LINC00511 silencing. In addition, we found overexpression of KDM2A, a target of miR-29b, would rescue the level of LINC00511. All the data showed that the LINC00511/miR-29b/KDM2A axis can be used as a diagnostic and therapeutic target for GC.
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Affiliation(s)
- Yueling Zhao
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Xiangbo Chen
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Jun Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xuechao Wan
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuefei Wang
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Ping Xu
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China.
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Abstract
PURPOSE OF REVIEW GBA1 mutations, which result in the lysosomal disorder Gaucher disease, are the most common known genetic risk factor for Parkinson disease and Dementia with Lewy Bodies (DLB). The pathogenesis of this association is not fully understood, but further elucidation of this link could lead to new therapeutic options. RECENT FINDINGS The characteristic clinical phenotype of GBA1-PD resembles sporadic Parkinson disease, but with an earlier onset and more severe course. Many different GBA1 mutations increase the risk of Parkinson disease, some primarily detected in specific populations. Glucocerebrosidase deficiency appears to be associated with increased α-synuclein aggregation and accumulation, mitochondrial dysfunction because of impaired autophagy, and increased endoplasmic reticulum stress. SUMMARY As our understanding of GBA1-associated Parkinson disease increases, new treatment opportunities emerge. MicroRNA profiles are providing examples of both up-regulated and down-regulated proteins related to GBA1 and may provide new therapeutic targets. Chaperone therapy, directed at either misfolded glucocerebrosidase or α-synuclein aggregation, is currently under development and there are several early clinical trials ongoing. Substrate reduction therapy, aimed at lowering the accumulation of metabolic by-products, especially glucosylsphingosine, is also being explored. Basic science insights from the rare disorder Gaucher disease are serving to catapult drug discovery for parkinsonism.
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43
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Autophagy lysosomal pathway dysfunction in Parkinson's disease; evidence from human genetics. Parkinsonism Relat Disord 2020; 73:60-71. [DOI: 10.1016/j.parkreldis.2019.11.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023]
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44
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Lou W, Ding B, Fu P. Pseudogene-Derived lncRNAs and Their miRNA Sponging Mechanism in Human Cancer. Front Cell Dev Biol 2020; 8:85. [PMID: 32185172 PMCID: PMC7058547 DOI: 10.3389/fcell.2020.00085] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/30/2020] [Indexed: 12/28/2022] Open
Abstract
Pseudogenes, abundant in the human genome, are traditionally considered as non-functional “junk genes.” However, recent studies have revealed that pseudogenes act as key regulators at DNA, RNA or protein level in diverse human disorders (including cancer), among which pseudogene-derived long non-coding RNA (lncRNA) transcripts are extensively investigated and has been reported to be frequently dysregulated in various types of human cancer. Growing evidence demonstrates that pseudogene-derived lncRNAs play important roles in cancer initiation and progression by serving as competing endogenous RNAs (ceRNAs) through competitively binding to shared microRNAs (miRNAs), thus affecting both their cognate genes and unrelated genes. Herein, we retrospect those current findings about expression, functions and potential ceRNA mechanisms of pseudogene-derived lncRNAs in human cancer, which may provide us with some crucial clues in developing potential targets for cancer therapy in the future.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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45
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Hanss Z, Boussaad I, Jarazo J, Schwamborn JC, Krüger R. Quality Control Strategy for CRISPR-Cas9-Based Gene Editing Complicated by a Pseudogene. Front Genet 2020; 10:1297. [PMID: 31998363 PMCID: PMC6961559 DOI: 10.3389/fgene.2019.01297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 11/25/2019] [Indexed: 12/02/2022] Open
Abstract
CRISPR-Cas9 mediated gene editing in induced pluripotent stem cells became an efficient tool to investigate biological mechanisms underlying genetic-driven diseases while accounting for the respective genetic background. This technique relies on the targeting of a specific nucleotide sequence present in the gene of interest. Therefore, the gene editing of some genes can be complicated by non-coding pseudogenes presenting a high homology of sequence with their respective genes. Among them, GBA is raising special interest because of its implication as the most common genetic risk factor for Parkinson’s disease. In this study, we present an easy-to-use CRISPR-Cas9 gene editing strategy allowing for specific editing of point mutations in a gene without genetic alteration of its pseudogene exemplified by the correction or insertion of the common N370S mutation in GBA. A quality control strategy by combined fluorescence and PCR-based screening allows the early identification of correctly edited clones with unambiguous identification of the status of its pseudogene, GBAP1. Successful gene editing was confirmed by functional validation. Our work presents the first CRISPR-Cas9 based editing of a point mutation in GBA and paves the way for technically demanding gene engineering due to the presence of pseudogenes.
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Affiliation(s)
- Zoé Hanss
- Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Ibrahim Boussaad
- Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Javier Jarazo
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Jens C Schwamborn
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.,Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
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Chen Z, Wu H, Zhang Z, Li G, Liu B. LINC00511 accelerated the process of gastric cancer by targeting miR-625-5p/NFIX axis. Cancer Cell Int 2019; 19:351. [PMID: 31889903 PMCID: PMC6933746 DOI: 10.1186/s12935-019-1070-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/12/2019] [Indexed: 01/26/2023] Open
Abstract
Background Gastric cancer (GC) is a common-sighted cancer which is hard to cure over the world. Substantial researches revealed that long non-coding RNAs (lncRNAs) were fundamental regulators in the process of cancers. Nevertheless, the biological function of LINC00511 and how LINC00511 was involved in the regulatory system in GC remained unclear. Methods RIP assays and luciferase reporter assays were performed to illustrate combination between LINC00511 and miR-625-5p. Loss-of-function assays were applied for identifying LINC00511 function in GC. Results In our study, LINC00511 was discovered significantly high in expression in GC tissues and cell lines. Moreover, LINC00511 showed a strong expression in I/II and III/IV stage. Knockdown of LINC00511 could inhibit the cell proliferation while enhanced cell apoptosis rate in GC. We used nuclear–cytoplasmic fractionation to judge the subcellular localization of LINC00511. Furthermore, miR-625-5p was found to have binding sites for LINC00511 and negatively regulated by LINC00511. Overexpression of miR-625-5p repressed the course of GC. And knockdown of miR-625-5p could recover the effects of LINC00511 silence. Besides, NFIX was discovered as a downstream target of miR-625-5p and overexpression of NFIX could offset the influence of LINC00511 silence. The results of vivo studies manifested that down-regulation of LINC00511 could reduce the Ki67 expression and NFIX while lifted the expression of miR-625-5p. Conclusion Overall, the results from our study demonstrated that LINC00511 could function as a tumor promoter by targeting miR-625-5p NFIX axis, suggesting LINC00511 could be considered as a target for GC treatment.
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Affiliation(s)
- Zhaosheng Chen
- Department of Gastroenterology, The Second Hospital of Shandong University, No. 247, Beiyuan Street, Ji Nan, 250033 Shandong China
| | - Honglei Wu
- Department of Gastroenterology, The Second Hospital of Shandong University, No. 247, Beiyuan Street, Ji Nan, 250033 Shandong China
| | - Zhen Zhang
- Department of Gastroenterology, The Second Hospital of Shandong University, No. 247, Beiyuan Street, Ji Nan, 250033 Shandong China
| | - Guangchun Li
- Department of Gastroenterology, The Second Hospital of Shandong University, No. 247, Beiyuan Street, Ji Nan, 250033 Shandong China
| | - Bin Liu
- Department of Gastroenterology, The Second Hospital of Shandong University, No. 247, Beiyuan Street, Ji Nan, 250033 Shandong China
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Ravanidis S, Bougea A, Papagiannakis N, Maniati M, Koros C, Simitsi AM, Bozi M, Pachi I, Stamelou M, Paraskevas GP, Kapaki E, Moraitou M, Michelakakis H, Stefanis L, Doxakis E. Circulating Brain-enriched MicroRNAs for detection and discrimination of idiopathic and genetic Parkinson's disease. Mov Disord 2019; 35:457-467. [PMID: 31799764 DOI: 10.1002/mds.27928] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/13/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A minimally invasive test for early detection and monitoring of Parkinson's disease (PD) is a highly unmet need for drug development and planning of patient care. Blood plasma represents an attractive source of biomarkers. MicroRNAs (miRNAs) are conserved noncoding RNA molecules that serve as posttranscriptional regulators of gene expression. As opposed to ubiquitously expressed miRNAs that control house-keeping processes, brain-enriched miRNAs regulate diverse aspects of neuron development and function. These include neuron-subtype specification, axonal growth, dendritic morphogenesis, and spine density. Backed by a large number of studies, we now know that the differential expression of neuron-enriched miRNAs leads to brain dysfunction. OBJECTIVES The aim was to identify subsets of brain-enriched miRNAs with diagnostic potential for familial and idiopathic PD as well as specify the molecular pathways deregulated in PD. METHODS Initially, brain-enriched miRNAs were selected based on literature review and validation studies in human tissues. Subsequently, real-time reverse transcription polymerase chain reaction was performed in the plasma of 100 healthy controls and 99 idiopathic and 53 genetic (26 alpha-synucleinA53T and 27 glucocerebrosidase) patients. Statistical and bioinformatics analyses were carried out to pinpoint the diagnostic biomarkers and deregulated pathways, respectively. RESULTS An explicit molecular fingerprint for each of the 3 PD cohorts was generated. Although the idiopathic PD fingerprint was different from that of genetic PD, the molecular pathways deregulated converged between all PD subtypes. CONCLUSIONS The study provides a group of brain-enriched miRNAs that may be used for the detection and differentiation of PD subtypes. It has also identified the molecular pathways deregulated in PD. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Stylianos Ravanidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Anastasia Bougea
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Nikolaos Papagiannakis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Matina Maniati
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Christos Koros
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece.,2nd Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Athina-Maria Simitsi
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Maria Bozi
- 2nd Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Ioanna Pachi
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Maria Stamelou
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece.,Parkinson's disease and Movement disorders department, HYGEIA Hospital, Athens, Greece
| | - George P Paraskevas
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Elisabeth Kapaki
- 1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Marina Moraitou
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - Helen Michelakakis
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,1st Department of Neurology, National and Kapodistrian University of Athens Medical School, Eginition Hospital, Athens, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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Ren C, Wang F, Guan LN, Cheng XY, Zhang CY, Geng DQ, Liu CF. A compendious summary of Parkinson's disease patient-derived iPSCs in the first decade. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:685. [PMID: 31930086 PMCID: PMC6944564 DOI: 10.21037/atm.2019.11.16] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/10/2019] [Indexed: 12/23/2022]
Abstract
The number of Parkinson's disease (PD) patients increases with aging, which brings heavy burden to families and society. The emergence of patient-derived induced pluripotent stem cells (iPSCs) has brought hope to the current situation of lacking new breakthroughs in diagnosis and treatment of PD. In this article, we reviewed and analyzed the current researches related to PD patient-derived iPSCs, in order to provide solid theoretical basis for future study of PD. In 2008, successful iPSCs derived from PD patients were reported. The current iPSCs research in PD mostly focused on the establishment of specific iPSCs models of PD patients carrying susceptible genes. The main source of PD patient-derived iPSCs is skin fibroblasts and the mainstream reprogramming methodology is the mature "four-factor" method, which introduces four totipotent correlation factors Oct4, Sox2, Klf4 and c-Myc into somatic cells. The main sources of iPSCs are patients with non-pedigrees and there have been no studies involving both PD patients and unaffected carriers within the same family. Most of the existing studies of PD patient-derived iPSCs started with the induction method for obtaining dopaminergic neurons in the first instance, but therapeutic applications are being increased. Although it is not the ultimate panacea, and there are still some unsolved problems (e.g., whether the mutated genes should be corrected or not), a better understanding of iPSCs may be a good gift for both PD patients and doctors due to their advantages in diagnosis and treatment of PD.
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Affiliation(s)
- Chao Ren
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
- Department of Neurology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou 215123, China
| | - Fen Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou 215123, China
| | - Li-Na Guan
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
- Department of Neurosurgical Intensive Care Unit, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, China
| | - Xiao-Yu Cheng
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Cai-Yi Zhang
- Department of Emergency, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221006, China
| | - De-Qin Geng
- Department of Neurology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221006, China
| | - Chun-Feng Liu
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou 215123, China
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Nuzziello N, Liguori M. The MicroRNA Centrism in the Orchestration of Neuroinflammation in Neurodegenerative Diseases. Cells 2019; 8:cells8101193. [PMID: 31581723 PMCID: PMC6829202 DOI: 10.3390/cells8101193] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with a unique ability to regulate the transcriptomic profile by binding to complementary regulatory RNA sequences. The ability of miRNAs to enhance (proinflammatory miRNAs) or restrict (anti-inflammatory miRNAs) inflammatory signalling within the central nervous system is an area of ongoing research, particularly in the context of disorders that feature neuroinflammation, including neurodegenerative diseases (NDDs). Furthermore, the discovery of competing endogenous RNAs (ceRNAs) has led to an increase in the complexity of miRNA-mediated gene regulation, with a paradigm shift from a unidirectional to a bidirectional regulation, where miRNA acts as both a regulator and is regulated by ceRNAs. Increasing evidence has revealed that ceRNAs, including long non-coding RNAs, circular RNAs, and pseudogenes, can act as miRNA sponges to regulate neuroinflammation in NDDs within complex cross-talk regulatory machinery, which is referred to as ceRNA network (ceRNET). In this review, we discuss the role of miRNAs in neuroinflammatory regulation and the manner in which cellular and vesicular ceRNETs could influence neuroinflammatory dynamics in complex multifactorial diseases, such as NDDs.
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Affiliation(s)
- Nicoletta Nuzziello
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy.
| | - Maria Liguori
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy.
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de Boni L, Wüllner U. Epigenetic Analysis in Human Neurons: Considerations for Disease Modeling in PD. Front Neurosci 2019; 13:276. [PMID: 31024227 PMCID: PMC6460245 DOI: 10.3389/fnins.2019.00276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/08/2019] [Indexed: 12/28/2022] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder next to Alzheimer’s disease. Most PD cases are considered to be sporadic and despite considerable scientific effort, the underlying cause(s) still remain(s) enigmatic. In particular, it is unknown to which extent epigenetic alterations contribute to the pathophysiology of this devastating disorder. This is partly due to the fact that appropriate PD models are not yet available. Moreover, epigenetic patterns and mechanisms are species specific and murine systems reflect only a few of the idiosyncrasies of human neurons. For several years now, patient-specific stem cell-derived neural and non-neural cells have been employed to overcome this limitation allowing the analysis and establishment of humanized disease models for PD. Thus, several studies tried to dissect epigenetic alterations such as aberrant DNA methylation or microRNA patterns using lund human mesencephalic cell lines or neurons derived from (patient-specific) induced pluripotent stem cells. These studies demonstrate that human neurons have the potential to be used as model systems for the study of epigenetic modifications in PD such as characterizing epigenetic changes, correlating epigenetic changes to gene expression alterations and hopefully using these insights for the development of novel therapeutics. However, more research is required to define the epigenetic (age-associated) landscape of human in vitro neurons and compare these to native neurons before they can be established as suitable models for epigenetic studies in PD. In this review, we summarize the knowledge about epigenetic studies performed on human neuronal PD models, and we discuss advantages and current limitations of these (stem cell-derived) neuronal models for the study of epigenetic alterations in PD.
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Affiliation(s)
- Laura de Boni
- Dementia Research Institute, University College London, London, United Kingdom
| | - Ullrich Wüllner
- Department of Neurology, University Hospital Bonn, German Center for Neurologic Diseases, Bonn, Germany
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