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Vakili O, Adibi Sedeh P, Pourfarzam M. Metabolic biomarkers in irritable bowel syndrome diagnosis. Clin Chim Acta 2024; 560:119753. [PMID: 38821336 DOI: 10.1016/j.cca.2024.119753] [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: 04/14/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Irritable bowel syndrome (IBS) is a chronic gastrointestinal (GI) disorder characterized by altered bowel habits and abdominal discomfort during defecation. It significantly impacts life quality and work productivity for those affected. Global data suggests a slightly higher prevalence in females than in males. Today, unambiguous diagnosis of IBS remains challenging due to the absence of a specific biochemical, histopathological, or radiological test. Current diagnosis relies heavily on thorough symptom evaluation. Efforts by the Rome committees have established standardized diagnostic criteria (Rome I-IV), improving consistency and clinical applicability. Recent studies in this framework, seem to have successfully employed metabolomics techniques to identify distinct metabolite profiles in breath and stool samples of IBS patients, differentiating them from healthy controls and those with other functional GI disorders, such as inflammatory bowel disease (IBD). Building on this success, researchers are investigating the presence of similar metabolites in easily accessible biofluids such as urine, potentially offering a less invasive diagnostic approach. Accordingly, this review focuses on key metabolites specifically detected in IBS patients' biological specimens, with a focus on urinary metabolites, using various methods, particularly mass spectrometry (MS)-based techniques, including gas chromatography-MS (GC-MS), liquid chromatography-tandem MS (LC-MS/MS), and capillary electrophoresis-MS (CE-MS) metabolomics assays. These findings may make provision for a new set of non-invasive biomarkers for IBS diagnosis and management.
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Affiliation(s)
- Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Peyman Adibi Sedeh
- Gastroenterology and Hepatology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Morteza Pourfarzam
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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2
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Nguyen LT, Pollock CA, Saad S. Extraction of high quality and high yield RNA from frozen EDTA blood. Sci Rep 2024; 14:8628. [PMID: 38622175 PMCID: PMC11018810 DOI: 10.1038/s41598-024-58576-9] [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: 01/02/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Peripheral blood RNA profiling, which can reveal systemic changes in gene expression and immune responses to disease onset and progression, is a powerful tool for diagnosis and biomarker discovery. This technique usually requires high quality RNA, which is only obtainable from fresh blood, or frozen blood that has been collected in special RNA-stabilisation systems. The current study aimed to develop a novel protocol to extract high quality RNA from frozen blood that had been collected in the conventional EDTA tubes. We determined that thawing EDTA blood in the presence of cell lysis/RNA stabilisation buffers (Paxgene or Nucleospin) significantly improved RNA quality (RIN) from below 5 to above 7, which to date has not been shown possible. The EDTA-Nucleospin protocol resulted in 5 times higher yield than the EDTA-Paxgene-PreAnalytix method. The average RIN and mRNA expression levels of five different genes including 18 s, ACTB, MCP1, TNFa and TXNIP using this protocol were also indifferent to those from Paxgene blood, suggesting similar RNA quality and blood transcriptome. Moreover, the protocol allows DNA to be extracted simultaneously. In conclusion, we have developed a practical and efficient protocol to extract high quality, high yield RNA from frozen EDTA blood.
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Affiliation(s)
- Long T Nguyen
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia.
| | - Carol A Pollock
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia
| | - Sonia Saad
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia
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Liu X, Wang F, Fan X, Chen M, Xu X, Xu Q, Zhu H, Xu A, Pouladi MA, Xu X. CHCHD2 up-regulation in Huntington disease mediates a compensatory protective response against oxidative stress. Cell Death Dis 2024; 15:126. [PMID: 38341417 PMCID: PMC10858906 DOI: 10.1038/s41419-024-06523-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Huntington disease (HD) is a neurodegenerative disease caused by the abnormal expansion of a polyglutamine tract resulting from a mutation in the HTT gene. Oxidative stress has been identified as a significant contributing factor to the development of HD and other neurodegenerative diseases, and targeting anti-oxidative stress has emerged as a potential therapeutic approach. CHCHD2 is a mitochondria-related protein involved in regulating cell migration, anti-oxidative stress, and anti-apoptosis. Although CHCHD2 is highly expressed in HD cells, its specific role in the pathogenesis of HD remains uncertain. We postulate that the up-regulation of CHCHD2 in HD models represents a compensatory protective response against mitochondrial dysfunction and oxidative stress associated with HD. To investigate this hypothesis, we employed HD mouse striatal cells and human induced pluripotent stem cells (hiPSCs) as models to examine the effects of CHCHD2 overexpression (CHCHD2-OE) or knockdown (CHCHD2-KD) on the HD phenotype. Our findings demonstrate that CHCHD2 is crucial for maintaining cell survival in both HD mouse striatal cells and hiPSCs-derived neurons. Our study demonstrates that CHCHD2 up-regulation in HD serves as a compensatory protective response against oxidative stress, suggesting a potential anti-oxidative strategy for the treatment of HD.
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Affiliation(s)
- Xuanzhuo Liu
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
- Clinical Neuroscience Institute, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
- Department of Neurology, Taihe Hospital of Shiyan, Affiliated Hospital of Hubei Medical University, Shiyan, 442000, China
| | - Fang Wang
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
- Clinical Neuroscience Institute, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
| | - Xinman Fan
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
- Clinical Neuroscience Institute, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
| | - Mingyi Chen
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
- Clinical Neuroscience Institute, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
| | - Xiaoxin Xu
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
- Clinical Neuroscience Institute, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
| | - Qiuhong Xu
- Department of Plastic Surgery, The First Affiliated Hospital, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
| | - Huili Zhu
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
| | - Anding Xu
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
- Clinical Neuroscience Institute, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China
| | - Mahmoud A Pouladi
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Djavad Mowafaghian Centre for Brain Health, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, V5Z 4H4, Canada.
| | - Xiaohong Xu
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China.
- Clinical Neuroscience Institute, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong, 510632, China.
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4
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Chan SC, Tung CW, Lin CW, Tung YS, Wu PM, Cheng PH, Chen CM, Yang SH. miR-196a provides antioxidative neuroprotection via USP15/Nrf2 regulation in Huntington's disease. Free Radic Biol Med 2023; 209:292-300. [PMID: 37907121 DOI: 10.1016/j.freeradbiomed.2023.10.407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023]
Abstract
Huntington's disease (HD) is a devastating neurodegenerative disorder characterized by the accumulation of mutant Huntingtin protein (mHTT) and oxidative stress-induced neuronal damage. Based on previous reports, microRNA-196a (miR-196a) has emerged as a potential therapeutic target due to its neuroprotective effects in various neurodegenerative diseases. However, whether miR-196a functions through antioxidative effects is still unknown. In this study, we demonstrated that HD models, both in vitro and in vivo, exhibit elevated levels of reactive oxygen species (ROS) and increased neuronal death, and miR-196a mitigates ROS levels and reduces cell death in HD cells. Moreover, we elucidated that miR-196a facilitates the translocation of nuclear factor erythroid 2 (Nrf2) into the nucleus, enhancing the transcription of antioxidant genes, including heme oxygenase-1 (HO-1). We further identified ubiquitin-specific peptidase 15 (USP15), a direct target of miR-196a related to the Nrf2 pathway, and USP15 exacerbates mHTT aggregate formation while partially counteracting miR-196a-induced reductions in mHTT levels. Taken together, these findings shed light on the multifaceted role of miR-196a in HD, highlighting its potential as a therapeutic avenue for ameliorating oxidative stress and neurodegeneration in this debilitating disease.
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Affiliation(s)
- Siew Chin Chan
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chih-Wei Tung
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chia-Wei Lin
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yun-Shiuan Tung
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Po-Min Wu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Pei-Hsun Cheng
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chuan-Mu Chen
- Department of Life Sciences, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Shang-Hsun Yang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan.
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5
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O'Connell GC, Wang J, Smothers C. Donor white blood cell differential is the single largest determinant of whole blood gene expression patterns. Genomics 2023; 115:110708. [PMID: 37730167 PMCID: PMC10872590 DOI: 10.1016/j.ygeno.2023.110708] [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: 05/22/2023] [Revised: 08/18/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
It has become widely accepted that sample cellular composition is a significant determinant of the gene expression patterns observed in any transcriptomic experiment performed with bulk tissue. Despite this, many investigations currently performed with whole blood do not experimentally account for possible inter-specimen differences in cellularity, and often assume that any observed gene expression differences are a result of true differences in nuclear transcription. In order to determine how confounding of an assumption this may be, in this study, we recruited a large cohort of human donors (n = 138) and used a combination of next generation sequencing and flow cytometry to quantify and compare the underlying contributions of variance in leukocyte counts versus variance in other biological factors to overall variance in whole blood transcript levels. Our results suggest that the combination of donor neutrophil and lymphocyte counts alone are the primary determinants of whole blood transcript levels for up to 75% of the protein-coding genes expressed in peripheral circulation, whereas the other factors such as age, sex, race, ethnicity, and common disease states have comparatively minimal influence. Broadly, this infers that a majority of gene expression differences observed in experiments performed with whole blood are driven by latent differences in leukocyte counts, and that cell count heterogeneity must be accounted for to meaningfully biologically interpret the results.
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Affiliation(s)
- Grant C O'Connell
- Molecular Biomarker Core, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, Case Western Reserve University, Cleveland, OH, USA.
| | - Jing Wang
- Molecular Biomarker Core, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, Case Western Reserve University, Cleveland, OH, USA
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6
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Sharygin D, Koniaris LG, Wells C, Zimmers TA, Hamidi T. Role of CD14 in human disease. Immunology 2023; 169:260-270. [PMID: 36840585 PMCID: PMC10591340 DOI: 10.1111/imm.13634] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
The cell surface antigen CD14 is primarily understood to act as a co-receptor for toll-like receptors (TLRs) to activate innate immunity responses to pathogens and tissue injury in macrophages and monocytes. However, roles for CD14 are increasingly being uncovered in disease responses in epithelial and endothelial cells. Consistent with these broader functions, CD14 expression is altered in a variety of non-immune cell types in response to a several of disease states. Moreover, soluble CD14 activated by factors from both pathogens and tissue damage may initiate signalling in a variety of non-immune cells. This review examined the current understanding CD14 in innate immunity as well as its potential functions in nonimmune cells and associated human diseases.
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Affiliation(s)
- Daniel Sharygin
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Chemistry, Massachusetts institute of technology, Cambridge, MA, USA
| | - Leonidas G. Koniaris
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Clark Wells
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Teresa A. Zimmers
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN, USA
| | - Tewfik Hamidi
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
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7
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Qi D, Li J, Quarles CC, Fonkem E, Wu E. Assessment and prediction of glioblastoma therapy response: challenges and opportunities. Brain 2023; 146:1281-1298. [PMID: 36445396 PMCID: PMC10319779 DOI: 10.1093/brain/awac450] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
Glioblastoma is the most aggressive type of primary adult brain tumour. The median survival of patients with glioblastoma remains approximately 15 months, and the 5-year survival rate is <10%. Current treatment options are limited, and the standard of care has remained relatively constant since 2011. Over the last decade, a range of different treatment regimens have been investigated with very limited success. Tumour recurrence is almost inevitable with the current treatment strategies, as glioblastoma tumours are highly heterogeneous and invasive. Additionally, another challenging issue facing patients with glioblastoma is how to distinguish between tumour progression and treatment effects, especially when relying on routine diagnostic imaging techniques in the clinic. The specificity of routine imaging for identifying tumour progression early or in a timely manner is poor due to the appearance similarity of post-treatment effects. Here, we concisely describe the current status and challenges in the assessment and early prediction of therapy response and the early detection of tumour progression or recurrence. We also summarize and discuss studies of advanced approaches such as quantitative imaging, liquid biomarker discovery and machine intelligence that hold exceptional potential to aid in the therapy monitoring of this malignancy and early prediction of therapy response, which may decisively transform the conventional detection methods in the era of precision medicine.
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Affiliation(s)
- Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
| | - Jing Li
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Chad Quarles
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ekokobe Fonkem
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Medical Education, School of Medicine, Texas A&M University, Bryan, TX 77807, USA
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Medical Education, School of Medicine, Texas A&M University, Bryan, TX 77807, USA
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M University, College Station, TX 77843, USA
- Department of Oncology and LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
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Integrated Bioinformatics Analysis of Shared Genes, miRNA, Biological Pathways and Their Potential Role as Therapeutic Targets in Huntington's Disease Stages. Int J Mol Sci 2023; 24:ijms24054873. [PMID: 36902304 PMCID: PMC10003639 DOI: 10.3390/ijms24054873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Huntington's Disease (HD) is a progressive neurodegenerative disease caused by CAG repeat expansion in the huntingtin gene (HTT). The HTT gene was the first disease-associated gene mapped to a chromosome, but the pathophysiological mechanisms, genes, proteins or miRNAs involved in HD remain poorly understood. Systems bioinformatics approaches can divulge the synergistic relationships of multiple omics data and their integration, and thus provide a holistic approach to understanding diseases. The purpose of this study was to identify the differentially expressed genes (DEGs), HD-related gene targets, pathways and miRNAs in HD and, more specifically, between the pre-symptomatic and symptomatic HD stages. Three publicly available HD datasets were analysed to obtain DEGs for each HD stage from each dataset. In addition, three databases were used to obtain HD-related gene targets. The shared gene targets between the three public databases were compared, and clustering analysis was performed on the common shared genes. Enrichment analysis was performed on (i) DEGs identified for each HD stage in each dataset, (ii) gene targets from the public databases and (iii) the clustering analysis results. Furthermore, the hub genes shared between the public databases and the HD DEGs were identified, and topological network parameters were applied. Identification of HD-related miRNAs and their gene targets was obtained, and a miRNA-gene network was constructed. Enriched pathways identified for the 128 common genes revealed pathways linked to multiple neurodegeneration diseases (HD, Parkinson's disease, Spinocerebellar ataxia), MAPK and HIF-1 signalling pathways. Eighteen HD-related hub genes were identified based on network topological analysis of MCC, degree and closeness. The highest-ranked genes were FoxO3 and CASP3, CASP3 and MAP2 were found for betweenness and eccentricity and CREBBP and PPARGC1A were identified for the clustering coefficient. The miRNA-gene network identified eleven miRNAs (mir-19a-3p, mir-34b-3p, mir-128-5p, mir-196a-5p, mir-34a-5p, mir-338-3p, mir-23a-3p and mir-214-3p) and eight genes (ITPR1, CASP3, GRIN2A, FoxO3, TGM2, CREBBP, MTHFR and PPARGC1A). Our work revealed that various biological pathways seem to be involved in HD either during the pre-symptomatic or symptomatic stages of HD. This may offer some clues for the molecular mechanisms, pathways and cellular components underlying HD and how these may act as potential therapeutic targets for HD.
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Pradhan SS, Rao KR, Manjunath M, Saiswaroop R, Patnana DP, Phalguna KS, Choudhary B, Sivaramakrishnan V. Vitamin B 6, B 12 and folate modulate deregulated pathways and protein aggregation in yeast model of Huntington disease. 3 Biotech 2023; 13:96. [PMID: 36852176 PMCID: PMC9958225 DOI: 10.1007/s13205-023-03525-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Huntington's disease (HD) is an incurable and progressive neurodegenerative disease affecting the basal ganglia of the brain. HD is caused due to expansion of the polyglutamine tract in the protein Huntingtin resulting in aggregates. The increased PolyQ length results in aggregation of protein Huntingtin leading to neuronal cell death. Vitamin B6, B12 and folate are deficient in many neurodegenerative diseases. We performed an integrated analysis of transcriptomic, metabolomic and cofactor-protein network of vitamin B6, B12 and folate was performed. Our results show considerable overlap of pathways modulated by Vitamin B6, B12 and folate with those obtained from transcriptomic and metabolomic data of HD patients and model systems. Further, in yeast model of HD we showed treatment of B6, B12 or folate either alone or in combination showed impaired aggregate formation. Transcriptomic analysis of yeast model treated with B6, B12 and folate showed upregulation of pathways like ubiquitin mediated proteolysis, autophagy, peroxisome, fatty acid, lipid and nitrogen metabolism. Metabolomic analysis of yeast model shows deregulation of pathways like aminoacyl-tRNA biosynthesis, metabolism of various amino acids, nitrogen metabolism and glutathione metabolism. Integrated transcriptomic and metabolomic analysis of yeast model showed concordance in the pathways obtained. Knockout of Peroxisomal (PXP1 and PEX7) and Autophagy (ATG5) genes in yeast increased aggregates which is mitigated by vitamin B6, B12 and folate treatment. Taken together our results show a role for Vitamin B6, B12 and folate mediated modulation of pathways important for preventing protein aggregation with potential implications for HD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03525-y.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - K. Raksha Rao
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - R. Saiswaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Durga Prasad Patnana
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Kanikaram Sai Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
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Maszka P, Kwasniak-Butowska M, Cysewski D, Slawek J, Smolenski RT, Tomczyk M. Metabolomic Footprint of Disrupted Energetics and Amino Acid Metabolism in Neurodegenerative Diseases: Perspectives for Early Diagnosis and Monitoring of Therapy. Metabolites 2023; 13:metabo13030369. [PMID: 36984809 PMCID: PMC10057046 DOI: 10.3390/metabo13030369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
The prevalence of neurodegenerative diseases (NDs) is increasing due to the aging population and improved longevity. They are characterized by a range of pathological hallmarks, including protein aggregation, mitochondrial dysfunction, and oxidative stress. The aim of this review is to summarize the alterations in brain energy and amino acid metabolism in Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD). Based on our findings, we proposed a group of selected metabolites related to disturbed energy or mitochondrial metabolism as potential indicators or predictors of disease. We also discussed the hidden challenges of metabolomics studies in NDs and proposed future directions in this field. We concluded that biochemical parameters of brain energy metabolism disruption (obtained with metabolomics) may have potential application as a diagnostic tool for the diagnosis, prediction, and monitoring of the effectiveness of therapies for NDs. However, more studies are needed to determine the sensitivity of the proposed candidates. We suggested that the most valuable biomarkers for NDs studies could be groups of metabolites combined with other neuroimaging or molecular techniques. To attain clinically applicable results, the integration of metabolomics with other “omic” techniques might be required.
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Affiliation(s)
- Patrycja Maszka
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Magdalena Kwasniak-Butowska
- Division of Neurological and Psychiatric Nursing, Medical University of Gdansk, 80-211 Gdansk, Poland
- Department of Neurology, St. Adalbert Hospital, 80-462 Gdansk, Poland
| | - Dominik Cysewski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Jaroslaw Slawek
- Division of Neurological and Psychiatric Nursing, Medical University of Gdansk, 80-211 Gdansk, Poland
- Department of Neurology, St. Adalbert Hospital, 80-462 Gdansk, Poland
| | - Ryszard T. Smolenski
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdansk, Poland
- Correspondence: (R.T.S.); (M.T.)
| | - Marta Tomczyk
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdansk, Poland
- Correspondence: (R.T.S.); (M.T.)
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Shanker OR, Kumar S, Dixit AB, Banerjee J, Tripathi M, Sarat Chandra P. Epigenetics of neurological diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:165-184. [DOI: 10.1016/bs.pmbts.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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12
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Current Diagnostic Methods and Non-Coding RNAs as Possible Biomarkers in Huntington’s Disease. Genes (Basel) 2022; 13:genes13112017. [PMID: 36360254 PMCID: PMC9689996 DOI: 10.3390/genes13112017] [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: 08/28/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Whether as a cause or a symptom, RNA transcription is recurrently altered in pathologic conditions. This is also true for non-coding RNAs, with regulatory functions in a variety of processes such as differentiation, cell identity and metabolism. In line with their increasingly recognized roles in cellular pathways, RNAs are also currently evaluated as possible disease biomarkers. They could be informative not only to follow disease progression and assess treatment efficacy in clinics, but also to aid in the development of new therapeutic approaches. This is especially important for neurological and genetic disorders, where the administration of appropriate treatment during the disease prodromal stage could significantly delay, if not halt, disease progression. In this review we focus on the current status of biomarkers in Huntington’s Disease (HD), a fatal hereditary and degenerative disease condition. First, we revise the sources and type of wet biomarkers currently in use. Then, we explore the feasibility of different RNA types (miRNA, ncRNA, circRNA) as possible biomarker candidates, discussing potential advantages, disadvantages, sources of origin and the ongoing investigations on this topic.
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13
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Yang HI, Huang PY, Chan SC, Tung CW, Cheng PH, Chen CM, Yang SH. miR-196a enhances polymerization of neuronal microfilaments through suppressing IMP3 and upregulating IGF2 in Huntington's disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:286-299. [PMID: 36320323 PMCID: PMC9593307 DOI: 10.1016/j.omtn.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022]
Abstract
Huntington's disease (HD) is one of the inheritable neurodegenerative diseases, and these diseases share several similar pathological characteristics, such as abnormal neuronal morphology. miR-196a is a potential target to provide neuroprotective functions, and has been reported to enhance polymerization of neuronal microtubules in HD. While microtubules and microfilaments are two important components of the neuronal cytoskeleton, whether miR-196a improves neuronal microfilaments is still unknown. Here, we identify insulin-like growth factor 2 mRNA binding protein 3 (IMP3), and show that miR-196a directly suppresses IMP3 to increase neurite outgrowth in neurons. In addition, IMP3 disturbs neurite outgrowth in vitro and in vivo, and worsens the microfilament polymerization. Moreover, insulin-like growth factor-II (IGF2) is identified as the downstream target of IMP3, and miR-196a downregulates IMP3 to upregulate IGF2, which increases microfilamental filopodia numbers and activates Cdc42 to increase neurite outgrowth. Besides, miR-196a increases neurite outgrowth through IGF2 in different HD models. Finally, higher expression of IMP3 and lower expression IGF2 are observed in HD transgenic mice and patients, and increase the formation of aggregates in the HD cell model. Taken together, miR-196a enhances polymerization of neuronal microfilaments through suppressing IMP3 and upregulating IGF2 in HD, supporting the neuroprotective functions of miR-196a through neuronal cytoskeleton in HD.
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Affiliation(s)
- Han-In Yang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pin-Yu Huang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Siew Chin Chan
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chih-Wei Tung
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pei-Hsun Cheng
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chuan-Mu Chen
- Department of Life Sciences, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Shang-Hsun Yang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan,Corresponding author Shang-Hsun Yang, Ph.D., Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.
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14
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Pradhan SS, Thota SM, Rajaratnam S, Bhagavatham SKS, Pulukool SK, Rathnakumar S, Phalguna KS, Dandamudi RB, Pargaonkar A, Joseph P, Joshy EV, Sivaramakrishnan V. Integrated multi-omics analysis of Huntington disease identifies pathways that modulate protein aggregation. Dis Model Mech 2022; 15:dmm049492. [PMID: 36052548 PMCID: PMC10655815 DOI: 10.1242/dmm.049492] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disease associated with polyglutamine expansion in the protein huntingtin (HTT). Although the length of the polyglutamine repeat correlates with age at disease onset and severity, psychological, cognitive and behavioral complications point to the existence of disease modifiers. Mitochondrial dysfunction and metabolic deregulation are both associated with the HD but, despite multi-omics characterization of patients and model systems, their mechanisms have remained elusive. Systems analysis of multi-omics data and its validation by using a yeast model could help to elucidate pathways that modulate protein aggregation. Metabolomics analysis of HD patients and of a yeast model of HD was, therefore, carried out. Our analysis showed a considerable overlap of deregulated metabolic pathways. Further, the multi-omics analysis showed deregulated pathways common in human, mice and yeast model systems, and those that are unique to them. The deregulated pathways include metabolic pathways of various amino acids, glutathione metabolism, longevity, autophagy and mitophagy. The addition of certain metabolites as well as gene knockouts targeting the deregulated metabolic and autophagy pathways in the yeast model system showed that these pathways do modulate protein aggregation. Taken together, our results showed that the modulation of deregulated pathways influences protein aggregation in HD, and has implications for progression and prognosis. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sai S. Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sai M. Thota
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Saiswaroop Rajaratnam
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sai K. S. Bhagavatham
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sujith K. Pulukool
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sriram Rathnakumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Kanikaram S. Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Rajesh B. Dandamudi
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515 134, India
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru 560048, India
| | - Prasanth Joseph
- Application Division, Agilent Technologies Ltd., Bengaluru 560048, India
| | - E. V. Joshy
- Department of Neurology, Sri Sathya Sai Institute of Higher Medical Sciences, Whitefield, Bengaluru, Karnataka 560066, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
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15
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Pupak A, Singh A, Sancho-Balsells A, Alcalá-Vida R, Espina M, Giralt A, Martí E, Ørom UAV, Ginés S, Brito V. Altered m6A RNA methylation contributes to hippocampal memory deficits in Huntington's disease mice. Cell Mol Life Sci 2022; 79:416. [PMID: 35819730 PMCID: PMC9276730 DOI: 10.1007/s00018-022-04444-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/07/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022]
Abstract
N6-methyladenosine (m6A) regulates many aspects of RNA metabolism and is involved in learning and memory processes. Yet, the impact of a dysregulation of post-transcriptional m6A editing on synaptic impairments in neurodegenerative disorders remains unknown. Here we investigated the m6A methylation pattern in the hippocampus of Huntington’s disease (HD) mice and the potential role of the m6A RNA modification in HD cognitive symptomatology. m6A modifications were evaluated in HD mice subjected to a hippocampal cognitive training task through m6A immunoprecipitation sequencing (MeRIP-seq) and the relative levels of m6A-modifying proteins (FTO and METTL14) by subcellular fractionation and Western blot analysis. Stereotaxic CA1 hippocampal delivery of AAV-shFTO was performed to investigate the effect of RNA m6A dysregulation in HD memory deficits. Our results reveal a m6A hypermethylation in relevant HD and synaptic related genes in the hippocampal transcriptome of Hdh+/Q111 mice. Conversely, m6A is aberrantly regulated in an experience-dependent manner in the HD hippocampus leading to demethylation of important components of synapse organization. Notably, the levels of RNA demethylase (FTO) and methyltransferase (METTL14) were modulated after training in the hippocampus of WT mice but not in Hdh+/Q111 mice. Finally, inhibition of FTO expression in the hippocampal CA1 region restored memory disturbances in symptomatic Hdh+/Q111 mice. Altogether, our results suggest that a differential RNA methylation landscape contributes to HD cognitive symptoms and uncover a role of m6A as a novel hallmark of HD.
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Affiliation(s)
- Anika Pupak
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Ankita Singh
- Department for Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Anna Sancho-Balsells
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Rafael Alcalá-Vida
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, Strasbourg, France
| | - Marc Espina
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Albert Giralt
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | - Silvia Ginés
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain. .,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
| | - Verónica Brito
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain. .,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
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16
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Martí-Martínez S, Valor LM. A Glimpse of Molecular Biomarkers in Huntington's Disease. Int J Mol Sci 2022; 23:ijms23105411. [PMID: 35628221 PMCID: PMC9142992 DOI: 10.3390/ijms23105411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022] Open
Abstract
Huntington's disease (HD) is a devastating neurodegenerative disorder that is caused by an abnormal expansion of CAG repeats in the Huntingtin (HTT) gene. Although the main symptomatology is explained by alterations at the level of the central nervous system, predominantly affecting the basal ganglia, a peripheral component of the disease is being increasingly acknowledged. Therefore, the manifestation of the disease is complex and variable among CAG expansion carriers, introducing uncertainty in the appearance of specific signs, age of onset and severity of disease. The monogenic nature of the disorder allows a precise diagnosis, but the use of biomarkers with prognostic value is still needed to achieve clinical management of the patients in an individual manner. In addition, we need tools to evaluate the patient's response to potential therapeutic approaches. In this review, we provide a succinct summary of the most interesting molecular biomarkers that have been assessed in patients, mostly obtained from body fluids such as cerebrospinal fluid, peripheral blood and saliva.
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Affiliation(s)
- Silvia Martí-Martínez
- Servicio de Neurología, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain;
| | - Luis M. Valor
- Laboratorio de Apoyo a la Investigación, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
- Correspondence: ; Tel.: +34-965-913-988
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17
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Golub VM, Reddy DS. Post-Traumatic Epilepsy and Comorbidities: Advanced Models, Molecular Mechanisms, Biomarkers, and Novel Therapeutic Interventions. Pharmacol Rev 2022; 74:387-438. [PMID: 35302046 PMCID: PMC8973512 DOI: 10.1124/pharmrev.121.000375] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Post-traumatic epilepsy (PTE) is one of the most devastating long-term, network consequences of traumatic brain injury (TBI). There is currently no approved treatment that can prevent onset of spontaneous seizures associated with brain injury, and many cases of PTE are refractory to antiseizure medications. Post-traumatic epileptogenesis is an enduring process by which a normal brain exhibits hypersynchronous excitability after a head injury incident. Understanding the neural networks and molecular pathologies involved in epileptogenesis are key to preventing its development or modifying disease progression. In this article, we describe a critical appraisal of the current state of PTE research with an emphasis on experimental models, molecular mechanisms of post-traumatic epileptogenesis, potential biomarkers, and the burden of PTE-associated comorbidities. The goal of epilepsy research is to identify new therapeutic strategies that can prevent PTE development or interrupt the epileptogenic process and relieve associated neuropsychiatric comorbidities. Therefore, we also describe current preclinical and clinical data on the treatment of PTE sequelae. Differences in injury patterns, latency period, and biomarkers are outlined in the context of animal model validation, pathophysiology, seizure frequency, and behavior. Improving TBI recovery and preventing seizure onset are complex and challenging tasks; however, much progress has been made within this decade demonstrating disease modifying, anti-inflammatory, and neuroprotective strategies, suggesting this goal is pragmatic. Our understanding of PTE is continuously evolving, and improved preclinical models allow for accelerated testing of critically needed novel therapeutic interventions in military and civilian persons at high risk for PTE and its devastating comorbidities.
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Affiliation(s)
- Victoria M Golub
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas
| | - Doodipala Samba Reddy
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas
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18
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Deng X, Li M, Deng S, Wang L. Hybrid gene selection approach using XGBoost and multi-objective genetic algorithm for cancer classification. Med Biol Eng Comput 2022; 60:663-681. [PMID: 35028863 DOI: 10.1007/s11517-021-02476-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
Microarray gene expression data are often accompanied by a large number of genes and a small number of samples. However, only a few of these genes are relevant to cancer, resulting in significant gene selection challenges. Hence, we propose a two-stage gene selection approach by combining extreme gradient boosting (XGBoost) and a multi-objective optimization genetic algorithm (XGBoost-MOGA) for cancer classification in microarray datasets. In the first stage, the genes are ranked using an ensemble-based feature selection using XGBoost. This stage can effectively remove irrelevant genes and yield a group comprising the most relevant genes related to the class. In the second stage, XGBoost-MOGA searches for an optimal gene subset based on the most relevant genes' group using a multi-objective optimization genetic algorithm. We performed comprehensive experiments to compare XGBoost-MOGA with other state-of-the-art feature selection methods using two well-known learning classifiers on 14 publicly available microarray expression datasets. The experimental results show that XGBoost-MOGA yields significantly better results than previous state-of-the-art algorithms in terms of various evaluation criteria, such as accuracy, F-score, precision, and recall.
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Affiliation(s)
- Xiongshi Deng
- School of Information Engineering, Nanchang Institute of Technology, Jiangxi, 330099, People's Republic of China.,Jiangxi Province Key Laboratory of Water Information Cooperative Sensing and Intelligent Processing, Jiangxi, 330099, People's Republic of China
| | - Min Li
- School of Information Engineering, Nanchang Institute of Technology, Jiangxi, 330099, People's Republic of China. .,Jiangxi Province Key Laboratory of Water Information Cooperative Sensing and Intelligent Processing, Jiangxi, 330099, People's Republic of China.
| | - Shaobo Deng
- School of Information Engineering, Nanchang Institute of Technology, Jiangxi, 330099, People's Republic of China.,Jiangxi Province Key Laboratory of Water Information Cooperative Sensing and Intelligent Processing, Jiangxi, 330099, People's Republic of China
| | - Lei Wang
- School of Information Engineering, Nanchang Institute of Technology, Jiangxi, 330099, People's Republic of China.,Jiangxi Province Key Laboratory of Water Information Cooperative Sensing and Intelligent Processing, Jiangxi, 330099, People's Republic of China
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19
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Nuclear and cytoplasmic huntingtin inclusions exhibit distinct biochemical composition, interactome and ultrastructural properties. Nat Commun 2021; 12:6579. [PMID: 34772920 PMCID: PMC8589980 DOI: 10.1038/s41467-021-26684-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/11/2021] [Indexed: 12/20/2022] Open
Abstract
Despite the strong evidence linking the aggregation of the Huntingtin protein (Htt) to the pathogenesis of Huntington's disease (HD), the mechanisms underlying Htt aggregation and neurodegeneration remain poorly understood. Herein, we investigated the ultrastructural properties and protein composition of Htt cytoplasmic and nuclear inclusions in mammalian cells and primary neurons overexpressing mutant exon1 of the Htt protein. Our findings provide unique insight into the ultrastructural properties of cytoplasmic and nuclear Htt inclusions and their mechanisms of formation. We show that Htt inclusion formation and maturation are complex processes that, although initially driven by polyQ-dependent Htt aggregation, also involve the polyQ and PRD domain-dependent sequestration of lipids and cytoplasmic and cytoskeletal proteins related to HD dysregulated pathways; the recruitment and accumulation of remodeled or dysfunctional membranous organelles, and the impairment of the protein quality control and degradation machinery. We also show that nuclear and cytoplasmic Htt inclusions exhibit distinct biochemical compositions and ultrastructural properties, suggesting different mechanisms of aggregation and toxicity.
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20
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Wang F, Ma XR, Wu Y, Xu YC, Gu HM, Wang DX, Dong ZJ, Li HL, Wang LB, Zhao JW. Neutralization of Hv1/HVCN1 With Antibody Enhances Microglia/Macrophages Myelin Clearance by Promoting Their Migration in the Brain. Front Cell Neurosci 2021; 15:768059. [PMID: 34744634 PMCID: PMC8570284 DOI: 10.3389/fncel.2021.768059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 01/09/2023] Open
Abstract
Microglia dynamically monitor the microenvironment of the central nervous system (CNS) by constantly extending and retracting their processes in physiological conditions, and microglia/macrophages rapidly migrate into lesion sites in response to injuries or diseases in the CNS. Consequently, their migration ability is fundamentally important for their proper functioning. However, the mechanisms underlying their migration have not been fully understood. We wonder whether the voltage-gated proton channel HVCN1 in microglia/macrophages in the brain plays a role in their migration. We show in this study that in physiological conditions, microglia and bone marrow derived macrophage (BMDM) express HVCN1 with the highest level among glial cells, and upregulation of HVCN1 in microglia/macrophages is presented in multiple injuries and diseases of the CNS, reflecting the overactivation of HVCN1. In parallel, myelin debris accumulation occurs in both the focal lesion and the site where neurodegeneration takes place. Importantly, both genetic deletion of the HVCN1 gene in cells in vitro and neutralization of HVCN1 with antibody in the brain in vivo promotes migration of microglia/macrophages. Furthermore, neutralization of HVCN1 with antibody in the brain in vivo promotes myelin debris clearance by microglia/macrophages. This study uncovers a new role of HVCN1 in microglia/macrophages, coupling the proton channel HVCN1 to the migration of microglia/macrophages for the first time.
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Affiliation(s)
- Fan Wang
- Department of Pathology and Department of Human Anatomy, Histology and Embryology, Sir Run Run Shaw Hospital, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Ru Ma
- Department of Pathology and Department of Human Anatomy, Histology and Embryology, Sir Run Run Shaw Hospital, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Wu
- Department of Pathology and Department of Human Anatomy, Histology and Embryology, Sir Run Run Shaw Hospital, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong-Cheng Xu
- Department of Pathology and Department of Human Anatomy, Histology and Embryology, Sir Run Run Shaw Hospital, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui-Min Gu
- Department of Pathology and Department of Human Anatomy, Histology and Embryology, Sir Run Run Shaw Hospital, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Di-Xian Wang
- Department of Pathology and Department of Human Anatomy, Histology and Embryology, Sir Run Run Shaw Hospital, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhao-Jun Dong
- Department of Pathology and Department of Human Anatomy, Histology and Embryology, Sir Run Run Shaw Hospital, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui-Liang Li
- Division of Medicine, Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Li-Bin Wang
- The General Hospital of Ningxia Medical University, Yinchuan, China
| | - Jing-Wei Zhao
- Department of Pathology and Department of Human Anatomy, Histology and Embryology, Sir Run Run Shaw Hospital, System Medicine Research Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
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21
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Malla B, Guo X, Senger G, Chasapopoulou Z, Yildirim F. A Systematic Review of Transcriptional Dysregulation in Huntington's Disease Studied by RNA Sequencing. Front Genet 2021; 12:751033. [PMID: 34721539 PMCID: PMC8554124 DOI: 10.3389/fgene.2021.751033] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
Huntington's disease (HD) is a chronic neurodegenerative disorder caused by an expansion of polyglutamine repeats in exon 1 of the Huntingtin gene. Transcriptional dysregulation accompanied by epigenetic alterations is an early and central disease mechanism in HD yet, the exact mechanisms and regulators, and their associated gene expression programs remain incompletely understood. This systematic review investigates genome-wide transcriptional studies that were conducted using RNA sequencing (RNA-seq) technology in HD patients and models. The review protocol was registered at the Open Science Framework (OSF). The biomedical literature and gene expression databases, PubMed and NCBI BioProject, Array Express, European Nucleotide Archive (ENA), European Genome-Phenome Archive (EGA), respectively, were searched using the defined terms specified in the protocol following the PRISMA guidelines. We conducted a complete literature and database search to retrieve all RNA-seq-based gene expression studies in HD published until August 2020, retrieving 288 articles and 237 datasets from PubMed and the databases, respectively. A total of 27 studies meeting the eligibility criteria were included in this review. Collectively, comparative analysis of the datasets revealed frequent genes that are consistently dysregulated in HD. In postmortem brains from HD patients, DNAJB1, HSPA1B and HSPB1 genes were commonly upregulated across all brain regions and cell types except for medium spiny neurons (MSNs) at symptomatic disease stage, and HSPH1 and SAT1 genes were altered in expression in all symptomatic brain datasets, indicating early and sustained changes in the expression of genes related to heat shock response as well as response to misfolded proteins. Specifically in indirect pathway medium spiny neurons (iMSNs), mitochondria related genes were among the top uniquely dysregulated genes. Interestingly, blood from HD patients showed commonly differentially expressed genes with a number of brain regions and cells, with the highest number of overlapping genes with MSNs and BA9 region at symptomatic stage. We also found the differential expression and predicted altered activity of a set of transcription factors and epigenetic regulators, including BCL6, EGR1, FOSL2 and CREBBP, HDAC1, KDM4C, respectively, which may underlie the observed transcriptional changes in HD. Altogether, our work provides a complete overview of the transcriptional studies in HD, and by data synthesis, reveals a number of common and unique gene expression and regulatory changes across different cell and tissue types in HD. These changes could elucidate new insights into molecular mechanisms of differential vulnerability in HD. Systematic Review Registration: https://osf.io/pm3wq.
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Affiliation(s)
- Bimala Malla
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xuanzong Guo
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gökçe Senger
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Zoi Chasapopoulou
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ferah Yildirim
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
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22
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Sun Y, Yang Y, Luo Y, Chen M, Wang L, Huang Y, Yang Y, Dong M. Lack of MECP2 gene transcription on the duplicated alleles of two related asymptomatic females with Xq28 duplications and opposite X-chromosome inactivation skewing. Hum Mutat 2021; 42:1429-1442. [PMID: 34273908 DOI: 10.1002/humu.24262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/23/2021] [Accepted: 07/14/2021] [Indexed: 11/10/2022]
Abstract
Xq28 duplication syndrome (MIM# 300815) is a severe neurodevelopmental disorder in males due to MeCP2 overexpression. Most females with MECP2 duplication are asymptomatic carriers, but there are phenotypic heterogeneities. Skewed X-chromosome inactivation (XCI) can protect females from exhibiting clinical phenotypes. Herein we reported two asymptomatic females (mother and grandmother) with interstitial Xq28 duplication. AR and RP2 assays showed that both had extremely skewed XCI, the Xq28 duplicated chromosome was inactivated in the mother, but was surprisingly activated in the grandmother. Interestingly, by combining RNA sequencing and whole-exome sequencing, we confirmed that XIST only expressed in the Xq28 duplication chromosomes of the two females, indicating that the Xq28 duplication chromosomes were inactive. Meanwhile, MECP2 and most XCI genes in the duplicated X-chromosomes were not transcriptionally expressed or upregulated, precluding major clinical phenotypes in the two females, especially the grandmother. We showed that XCI status detected using RNA sequencing was more relevant for establishing the clinical phenotype of MECP2 duplication in females. It suggested that there were other factors maintaining the XCI status in addition to DNA methylation, a possible additional inhibition mechanism occurred at the transcriptional level in the unmethylated X-chromosome, counter balancing the MECP2 duplication's detrimental phenotype effects.
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Affiliation(s)
- Yixi Sun
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yali Yang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yuqin Luo
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Min Chen
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Liya Wang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yingzhi Huang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yanmei Yang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Minyue Dong
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, China
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23
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Seefelder M, Kochanek S. A meta-analysis of transcriptomic profiles of Huntington's disease patients. PLoS One 2021; 16:e0253037. [PMID: 34111223 PMCID: PMC8191979 DOI: 10.1371/journal.pone.0253037] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
Description of robust transcriptomic alterations in Huntington’s disease is essential to identify targets for biochemical studies and drug development. We analysed publicly available transcriptome data from the brain and blood of 220 HD patients and 241 healthy controls and identified 737 and 661 genes with robustly altered mRNA levels in the brain and blood of HD patients, respectively. In the brain, a subnetwork of 320 genes strongly correlated with HD and was enriched in transport-related genes. Bioinformatical analysis of this subnetwork highlighted CDC42, PAK1, YWHAH, NFY, DLX1, HMGN3, and PRMT3. Moreover, we found that CREB1 can regulate 78.0% of genes whose mRNA levels correlated with HD in the blood of patients. Alterations in protein transport, metabolism, transcriptional regulation, and CDC42-mediated functions are likely central features of HD. Further our data substantiate the role of transcriptional regulators that have not been reported in the context of HD (e.g. DLX1, HMGN3 and PRMT3) and strongly suggest dysregulation of NFY and its target genes across tissues. A large proportion of the identified genes such as CDC42 were also altered in Parkinson’s (PD) and Alzheimer’s disease (AD). The observed dysregulation of CDC42 and YWHAH in samples from HD, AD and PD patients indicates that those genes and their upstream regulators may be interesting therapeutic targets.
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Affiliation(s)
- Manuel Seefelder
- Department of Gene Therapy, Ulm University, Ulm, Germany
- * E-mail:
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24
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de Castro IJ, Toner B, Xie SQ, Swingland J, Hodges A, Tabrizi SJ, Turkheimer F, Pombo A, Khalil A. Altered nuclear architecture in blood cells from Huntington's disease patients. Neurol Sci 2021; 43:379-385. [PMID: 33974169 DOI: 10.1007/s10072-021-05289-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/26/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cell nuclear architecture has been explored in cancer and laminopathies but not in neurodegenerative disorders. Huntington's disease (HD) is a neurodegenerative disorder that leads to neuronal death. Chromosome-wide changes in gene expression have been reported in HD, not only in the brain but also in peripheral blood cells, but whether this translates into nuclear and chromosome architecture alterations has not yet been studied. METHODS We investigate nuclear structure and chromosome organization in HD blood cells using fluorescence in situ hybridization in ultrathin cryosections (cryoFISH), coupled with machine learning image analysis to evaluate size, distribution, and morphology of nuclei and chromosomes. Four chromosomes were analyzed based on up- or downregulation of gene expression in HD. RESULTS We show that blood cells from HD patients display increased nuclear size and filamentary shape, increased size of gene-rich chromosome 19, decreased filamentary shape of gene-rich chromosome 22, and a more radially centralized position for chromosome 19, whereas chromosomes 4 and 5 do not show detectable differences. CONCLUSIONS We identify gross changes in nuclear architecture and chromosome organization associated with HD in blood. This adds a new layer of information onto disrupting mechanisms in HD and increases the potential of using blood to survey HD.
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Affiliation(s)
- Inês J de Castro
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK. .,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany. .,Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, Im Neuenheimer Feld 344, Heidelberg, 69120, Germany.
| | - Brian Toner
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Sheila Q Xie
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Chromatin and Development Group, MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - James Swingland
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,GRIP AI, London, EC2A 3AZ, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Angela Hodges
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Sarah J Tabrizi
- UCL Institute of Neurology, Box 104, National Hospital for Neurology and Neurosurgery Queen Square, University College London, London, WC1N 3BG, UK
| | - Federico Turkheimer
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK.,Huntington's Disease Centre, Department of Neurodegenerative Disease, University College London (UCL) Queen Square Institute of Neurology and the UK Dementia Research Institute, UCL, London, UK
| | - Ana Pombo
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - André Khalil
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA.
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25
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Andrade-Navarro MA, Mühlenberg K, Spruth EJ, Mah N, González-López A, Andreani T, Russ J, Huska MR, Muro EM, Fontaine JF, Amstislavskiy V, Soldatov A, Nietfeld W, Wanker EE, Priller J. RNA Sequencing of Human Peripheral Blood Cells Indicates Upregulation of Immune-Related Genes in Huntington's Disease. Front Neurol 2020; 11:573560. [PMID: 33329316 PMCID: PMC7731869 DOI: 10.3389/fneur.2020.573560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/06/2020] [Indexed: 11/13/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominantly inherited neurodegenerative disorder caused by a trinucleotide repeat expansion in the Huntingtin gene. As disease-modifying therapies for HD are being developed, peripheral blood cells may be used to indicate disease progression and to monitor treatment response. In order to investigate whether gene expression changes can be found in the blood of individuals with HD that distinguish them from healthy controls, we performed transcriptome analysis by next-generation sequencing (RNA-seq). We detected a gene expression signature consistent with dysregulation of immune-related functions and inflammatory response in peripheral blood from HD cases vs. controls, including induction of the interferon response genes, IFITM3, IFI6 and IRF7. Our results suggest that it is possible to detect gene expression changes in blood samples from individuals with HD, which may reflect the immune pathology associated with the disease.
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Affiliation(s)
- Miguel A Andrade-Navarro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Katja Mühlenberg
- Neuroproteomics, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Eike J Spruth
- Department of Neuropsychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nancy Mah
- Charité-Universitätsmedizin Berlin, Virchow-Klinikum, Berlin-Brandenburger Centrum für Regenerative Therapien, Berlin, Germany
| | - Adrián González-López
- Klinik f. Anästhesiologie m.S. operative Intensivmedizin, Virchow Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tommaso Andreani
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jenny Russ
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Matthew R Huska
- Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Enrique M Muro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jean-Fred Fontaine
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Alexei Soldatov
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | | | - Erich E Wanker
- Neuroproteomics, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.,German Centre for Neurodegenerative Diseases, Berlin Institute of Health, Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Centre for Neurodegenerative Diseases, Berlin Institute of Health, Berlin, Germany.,Centre for Clinical Brain Sciences, UK Dementia Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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26
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Mitchell CT, Krier I, Arjomand J, Borowsky B, Tabrizi SJ, Leavitt BR, Luthi-Carter R. Longitudinal expression changes are weak correlates of disease progression in Huntington's disease. Brain Commun 2020; 2:fcaa172. [PMID: 33305259 PMCID: PMC7713990 DOI: 10.1093/braincomms/fcaa172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 08/31/2020] [Accepted: 09/16/2020] [Indexed: 11/15/2022] Open
Abstract
Huntington's disease is a severe but slowly progressive hereditary illness for which only symptomatic treatments are presently available. Clinical measures of disease progression are somewhat subjective and may require years to detect significant change. There is a clear need to identify more sensitive, objective and consistent measures to detect disease progression in Huntington's disease clinical trials. Whereas Huntington's disease demonstrates a robust and consistent gene expression signature in the brain, previous studies of blood cell RNAs have lacked concordance with clinical disease stage. Here we utilized longitudinally collected samples from a well-characterized cohort of control, Huntington's disease-at-risk and Huntington's disease subjects to evaluate the possible correlation of gene expression and disease status within individuals. We interrogated these data in both cross-sectional and longitudinal analyses. A number of changes in gene expression showed consistency within this study and as compared to previous reports in the literature. The magnitude of the mean disease effect over 2 years' time was small, however, and did not track closely with motor symptom progression over the same time period. We therefore conclude that while blood-derived gene expression indicators can be of value in understanding Huntington's disease pathogenesis, they are insufficiently sensitive to be of use as state biomarkers.
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Affiliation(s)
- Christopher T Mitchell
- University of Leicester, University Road, Leicester LE1 7RH, UK
- School of Medicine, King's College London, London, UK
| | - Irina Krier
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | | | - Sarah J Tabrizi
- UCL Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Dementia Research Institute at UCL, Huntington's Disease Centre, London WC1N 3BG, UK
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada 75Z 4H4
| | - Ruth Luthi-Carter
- University of Leicester, University Road, Leicester LE1 7RH, UK
- School of Medicine, King's College London, London, UK
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27
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Xiang C, Cong S, Liang B, Cong S. Bioinformatic gene analysis for potential therapeutic targets of Huntington's disease in pre-symptomatic and symptomatic stage. J Transl Med 2020; 18:388. [PMID: 33054835 PMCID: PMC7559361 DOI: 10.1186/s12967-020-02549-9] [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: 12/19/2019] [Accepted: 09/27/2020] [Indexed: 01/18/2023] Open
Abstract
Background Huntington’s disease (HD) is a neurodegenerative disorder characterized by psychiatric symptoms, serious motor and cognitive deficits. Certain pathological changes can already be observed in pre-symptomatic HD (pre-HD) patients; however, the underlying molecular pathogenesis is still uncertain and no effective treatments are available until now. Here, we reanalyzed HD-related differentially expressed genes from the GEO database between symptomatic HD patients, pre-HD individuals, and healthy controls using bioinformatics analysis, hoping to get more insight in the pathogenesis of both pre-HD and HD, and shed a light in the potential therapeutic targets of the disease. Methods Pre-HD and symptomatic HD differentially expressed genes (DEGs) were screened by bioinformatics analysis Gene Expression Omnibus (GEO) dataset GSE1751. A protein–protein interaction (PPI) network was used to select hub genes. Subsequently, Gene Ontology (GO) enrichment analysis of DEGs and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of hub genes were applied. Dataset GSE24250 was downloaded to verify our hub genes by the Kaplan–Meier method using Graphpad Prism 5.0. Finally, target miRNAs of intersected hub genes involved in pre-HD and symptomatic HD were predicted. Results A total of 37 and 985 DEGs were identified in pre-HD and symptomatic HD, respectively. The hub genes, SIRT1, SUZ12, and PSMC6, may be implicated in pre-HD, and the hub genes, FIS1, SIRT1, CCNH, SUZ12, and 10 others, may be implicated in symptomatic HD. The intersected hub genes, SIRT1 and SUZ12, and their predicted target miRNAs, in particular miR-22-3p and miR-19b, may be significantly associated with pre-HD. Conclusion The PSMC6, SIRT1, and SUZ12 genes and their related ubiquitin-mediated proteolysis, transcriptional dysregulation, and histone metabolism are significantly associated with pre-HD. FIS1, CCNH, and their related mitochondrial disruption and transcriptional dysregulation processes are related to symptomatic HD, which might shed a light on the elucidation of potential therapeutic targets in HD.
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Affiliation(s)
- Chunchen Xiang
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Shengri Cong
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Bin Liang
- Bioinformatics of Department, School of Life Sciences, China Medical University, Shenyang, China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China.
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28
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Christodoulou CC, Zachariou M, Tomazou M, Karatzas E, Demetriou CA, Zamba-Papanicolaou E, Spyrou GM. Investigating the Transition of Pre-Symptomatic to Symptomatic Huntington's Disease Status Based on Omics Data. Int J Mol Sci 2020; 21:ijms21197414. [PMID: 33049985 PMCID: PMC7582902 DOI: 10.3390/ijms21197414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Huntington’s disease is a rare neurodegenerative disease caused by a cytosine–adenine–guanine (CAG) trinucleotide expansion in the Huntingtin (HTT) gene. Although Huntington’s disease (HD) is well studied, the pathophysiological mechanisms, genes and metabolites involved in HD remain poorly understood. Systems bioinformatics can reveal synergistic relationships among different omics levels and enables the integration of biological data. It allows for the overall understanding of biological mechanisms, pathways, genes and metabolites involved in HD. The purpose of this study was to identify the differentially expressed genes (DEGs), pathways and metabolites as well as observe how these biological terms differ between the pre-symptomatic and symptomatic HD stages. A publicly available dataset from the Gene Expression Omnibus (GEO) was analyzed to obtain the DEGs for each HD stage, and gene co-expression networks were obtained for each HD stage. Network rewiring, highlights the nodes that change most their connectivity with their neighbors and infers their possible implication in the transition between different states. The CACNA1I gene was the mostly highly rewired node among pre-symptomatic and symptomatic HD network. Furthermore, we identified AF198444 to be common between the rewired genes and DEGs of symptomatic HD. CNTN6, DEK, LTN1, MST4, ZFYVE16, CEP135, DCAKD, MAP4K3, NUPL1 and RBM15 between the DEGs of pre-symptomatic and DEGs of symptomatic HD and CACNA1I, DNAJB14, EPS8L3, HSDL2, SNRPD3, SOX12, ACLY, ATF2, BAG5, ERBB4, FOCAD, GRAMD1C, LIN7C, MIR22, MTHFR, NABP1, NRG2, OTC, PRAMEF12, SLC30A10, STAG2 and Y16709 between the rewired genes and DEGs of pre-symptomatic HD. The proteins encoded by these genes are involved in various biological pathways such as phosphatidylinositol-4,5-bisphosphate 3-kinase activity, cAMP response element-binding protein binding, protein tyrosine kinase activity, voltage-gated calcium channel activity, ubiquitin protein ligase activity, adenosine triphosphate (ATP) binding, and protein serine/threonine kinase. Additionally, prominent molecular pathways for each HD stage were then obtained, and metabolites related to each pathway for both disease stages were identified. The transforming growth factor beta (TGF-β) signaling (pre-symptomatic and symptomatic stages of the disease), calcium (Ca2+) signaling (pre-symptomatic), dopaminergic synapse pathway (symptomatic HD patients) and Hippo signaling (pre-symptomatic) pathways were identified. The in silico metabolites we identified include Ca2+, inositol 1,4,5-trisphosphate, sphingosine 1-phosphate, dopamine, homovanillate and L-tyrosine. The genes, pathways and metabolites identified for each HD stage can provide a better understanding of the mechanisms that become altered in each disease stage. Our results can guide the development of therapies that may target the altered genes and metabolites of the perturbed pathways, leading to an improvement in clinical symptoms and hopefully a delay in the age of onset.
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Affiliation(s)
- Christiana C. Christodoulou
- Bioinformatics Department; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus; (C.C.C.); (M.Z.); (M.T.)
- Neurology Clinic D; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus;
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - Margarita Zachariou
- Bioinformatics Department; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus; (C.C.C.); (M.Z.); (M.T.)
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - Marios Tomazou
- Bioinformatics Department; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus; (C.C.C.); (M.Z.); (M.T.)
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - Evangelos Karatzas
- Department of Informatics and Telecommunications, University of Athens, 157 72 Athens, Greece;
| | - Christiana A. Demetriou
- Department of Primary Care and Population Health, University of Nicosia, 2417 Nicosia, Cyprus;
| | - Eleni Zamba-Papanicolaou
- Neurology Clinic D; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus;
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - George M. Spyrou
- Bioinformatics Department; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus; (C.C.C.); (M.Z.); (M.T.)
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
- Correspondence:
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29
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Comprehensive relative importance analysis and its applications to high dimensional gene expression data analysis. Knowl Based Syst 2020. [DOI: 10.1016/j.knosys.2020.106120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Song S, Li B, Jia Z, Guo L. Sirtuin 3 mRNA Expression is Downregulated in the Brain Tissues of Alzheimer's Disease Patients: A Bioinformatic and Data Mining Approach. Med Sci Monit 2020; 26:e923547. [PMID: 32747616 PMCID: PMC7427349 DOI: 10.12659/msm.923547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Emerging experimental evidence has shown that sirtuin 3 (SIRT3), which is a class III histone deacetylase, participates in the pathological process of Alzheimer’s disease (AD). However, data mining of current gene expression databases, such as Gene Expression Omnibus (GEO), has not been previously performed to determine whether SIRT3 expression is upregulated or downregulated in the brain tissues of AD patients. Material/Methods Eight RNA expression chip datasets of AD brains in the GEO database were selected, and GEO2R analysis was conducted to identify the differentially expressed genes (DEGs) between the AD and control groups. Furthermore, the SIRT3 mRNA levels between the AD and control groups and their relationships with the DEGs and diagnosis of AD were evaluated. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of both the AD-related DEGs and the SIRT3-related DEGs were conducted. Results The SIRT3 mRNA levels were downregulated in 7 of 8 databases and were related to the diagnosis of AD in 7 databases, with an area under the curve (AUC) of the receiver operating characteristic curve (ROC curve) greater than 50%. Additionally, GO and KEGG analyses showed that SIRT3 downregulation could affect neuroactive ligand-receptor interactions, the MAPK signaling pathway, long-term potentiation, the calcium signaling pathway and axon guidance in AD patients. Conclusions SIRT3 mRNA is downregulated in the brain tissues of AD patients, promoting the progression of AD.
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Affiliation(s)
- Shuang Song
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland).,Key Laboratory of Hebei Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland)
| | - Bin Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland).,Key Laboratory of Hebei Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland)
| | - Zhen Jia
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland).,Key Laboratory of Hebei Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland)
| | - Li Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland).,Key Laboratory of Hebei Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland)
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31
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Li WX, Li GH, Tong X, Yang PP, Huang JF, Xu L, Dai SX. Systematic metabolic analysis of potential target, therapeutic drug, diagnostic method and animal model applicability in three neurodegenerative diseases. Aging (Albany NY) 2020; 12:9882-9914. [PMID: 32461378 PMCID: PMC7288927 DOI: 10.18632/aging.103253] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/20/2020] [Indexed: 01/10/2023]
Abstract
Considerable evidence suggests that metabolic abnormalities are associated with neurodegenerative diseases. This study aimed to conduct a systematic metabolic analysis of Alzheimer’s disease (AD), Parkinson’s disease (PD) and Huntington’s disease (HD). Human and mouse model microarray datasets were downloaded from the Gene Expression Omnibus database. The metabolic genes and pathways were collected from the Recon 3D human metabolic model. Drug and target information was obtained from the DrugBank database. This study identified ATP1A1, ATP6V1G2, GOT1, HPRT1, MAP2K1, PCMT1 and PLK2 as key metabolic genes that were downregulated in AD, PD and HD. We screened 57 drugs that target these genes, such as digoxin, ouabain and diazoxide. This study constructed multigene diagnostic models for AD, PD and HD by using metabolic gene expression profiles in blood, all models showed high accuracy (AUC > 0.8) both in the experimental and validation sets. Furthermore, analysis of animal models showed that there was almost no consistency among the metabolic changes between mouse models and human diseases. This study systematically revealed the metabolic damage among AD, PD, and HD and uncovered the differences between animal models and human diseases. This information may be helpful for understanding the metabolic mechanisms and drug development for neurodegenerative diseases.
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Affiliation(s)
- Wen-Xing Li
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Xin Tong
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Peng-Peng Yang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Jing-Fei Huang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Lin Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China.,Centre for Excellence in Brain Science and Intelligent Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shao-Xing Dai
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
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Mitochondrial Dysfunctions: A Red Thread across Neurodegenerative Diseases. Int J Mol Sci 2020; 21:ijms21103719. [PMID: 32466216 PMCID: PMC7279270 DOI: 10.3390/ijms21103719] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria play a central role in a plethora of processes related to the maintenance of cellular homeostasis and genomic integrity. They contribute to preserving the optimal functioning of cells and protecting them from potential DNA damage which could result in mutations and disease. However, perturbations of the system due to senescence or environmental factors induce alterations of the physiological balance and lead to the impairment of mitochondrial functions. After the description of the crucial roles of mitochondria for cell survival and activity, the core of this review focuses on the "mitochondrial switch" which occurs at the onset of neuronal degeneration. We dissect the pathways related to mitochondrial dysfunctions which are shared among the most frequent or disabling neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's, Amyotrophic Lateral Sclerosis, and Spinal Muscular Atrophy. Can mitochondrial dysfunctions (affecting their morphology and activities) represent the early event eliciting the shift towards pathological neurobiological processes? Can mitochondria represent a common target against neurodegeneration? We also review here the drugs that target mitochondria in neurodegenerative diseases.
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Shen L, Yin Q. Data maximum dispersion classifier in projection space for high-dimension low-sample-size problems. Knowl Based Syst 2020. [DOI: 10.1016/j.knosys.2019.105420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Rahman MH, Peng S, Hu X, Chen C, Rahman MR, Uddin S, Quinn JM, Moni MA. A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17031035. [PMID: 32041280 PMCID: PMC7037290 DOI: 10.3390/ijerph17031035] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 12/21/2022]
Abstract
Neurological diseases (NDs) are progressive disorders, the progression of which can be significantly affected by a range of common diseases that present as comorbidities. Clinical studies, including epidemiological and neuropathological analyses, indicate that patients with type 2 diabetes (T2D) have worse progression of NDs, suggesting pathogenic links between NDs and T2D. However, finding causal or predisposing factors that link T2D and NDs remains challenging. To address these problems, we developed a high-throughput network-based quantitative pipeline using agnostic approaches to identify genes expressed abnormally in both T2D and NDs, to identify some of the shared molecular pathways that may underpin T2D and ND interaction. We employed gene expression transcriptomic datasets from control and disease-affected individuals and identified differentially expressed genes (DEGs) in tissues of patients with T2D and ND when compared to unaffected control individuals. One hundred and ninety seven DEGs (99 up-regulated and 98 down-regulated in affected individuals) that were common to both the T2D and the ND datasets were identified. Functional annotation of these identified DEGs revealed the involvement of significant cell signaling associated molecular pathways. The overlapping DEGs (i.e., seen in both T2D and ND datasets) were then used to extract the most significant GO terms. We performed validation of these results with gold benchmark databases and literature searching, which identified which genes and pathways had been previously linked to NDs or T2D and which are novel. Hub proteins in the pathways were identified (including DNM2, DNM1, MYH14, PACSIN2, TFRC, PDE4D, ENTPD1, PLK4, CDC20B, and CDC14A) using protein-protein interaction analysis which have not previously been described as playing a role in these diseases. To reveal the transcriptional and post-transcriptional regulators of the DEGs we used transcription factor (TF) interactions analysis and DEG-microRNAs (miRNAs) interaction analysis, respectively. We thus identified the following TFs as important in driving expression of our T2D/ND common genes: FOXC1, GATA2, FOXL1, YY1, E2F1, NFIC, NFYA, USF2, HINFP, MEF2A, SRF, NFKB1, USF2, HINFP, MEF2A, SRF, NFKB1, PDE4D, CREB1, SP1, HOXA5, SREBF1, TFAP2A, STAT3, POU2F2, TP53, PPARG, and JUN. MicroRNAs that affect expression of these genes include mir-335-5p, mir-16-5p, mir-93-5p, mir-17-5p, mir-124-3p. Thus, our transcriptomic data analysis identifies novel potential links between NDs and T2D pathologies that may underlie comorbidity interactions, links that may include potential targets for therapeutic intervention. In sum, our neighborhood-based benchmarking and multilayer network topology methods identified novel putative biomarkers that indicate how type 2 diabetes (T2D) and these neurological diseases interact and pathways that, in the future, may be targeted for treatment.
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Affiliation(s)
- Md Habibur Rahman
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; (M.H.R.); (S.P.); (X.H.); (C.C.)
- University of Chinese Academy of Sciences, Beijing 100190, China
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Silong Peng
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; (M.H.R.); (S.P.); (X.H.); (C.C.)
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiyuan Hu
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; (M.H.R.); (S.P.); (X.H.); (C.C.)
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Chen Chen
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; (M.H.R.); (S.P.); (X.H.); (C.C.)
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, Khwaja Yunus Ali University, Enayetpur, Sirajgonj 6751, Bangladesh;
| | - Shahadat Uddin
- Complex Systems Research Group & Project Management Program, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Julian M.W. Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Correspondence:
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Rawat C, Kushwaha S, Srivastava AK, Kukreti R. Peripheral blood gene expression signatures associated with epilepsy and its etiologic classification. Genomics 2020; 112:218-224. [DOI: 10.1016/j.ygeno.2019.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/23/2019] [Accepted: 01/26/2019] [Indexed: 01/19/2023]
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36
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Gallardo-Orihuela A, Hervás-Corpión I, Hierro-Bujalance C, Sanchez-Sotano D, Jiménez-Gómez G, Mora-López F, Campos-Caro A, Garcia-Alloza M, Valor LM. Transcriptional correlates of the pathological phenotype in a Huntington's disease mouse model. Sci Rep 2019; 9:18696. [PMID: 31822756 PMCID: PMC6904489 DOI: 10.1038/s41598-019-55177-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/25/2019] [Indexed: 02/07/2023] Open
Abstract
Huntington disease (HD) is a fatal neurodegenerative disorder without a cure that is caused by an aberrant expansion of CAG repeats in exon 1 of the huntingtin (HTT) gene. Although a negative correlation between the number of CAG repeats and the age of disease onset is established, additional factors may contribute to the high heterogeneity of the complex manifestation of symptoms among patients. This variability is also observed in mouse models, even under controlled genetic and environmental conditions. To better understand this phenomenon, we analysed the R6/1 strain in search of potential correlates between pathological motor/cognitive phenotypical traits and transcriptional alterations. HD-related genes (e.g., Penk, Plk5, Itpka), despite being downregulated across the examined brain areas (the prefrontal cortex, striatum, hippocampus and cerebellum), exhibited tissue-specific correlations with particular phenotypical traits that were attributable to the contribution of the brain region to that trait (e.g., striatum and rotarod performance, cerebellum and feet clasping). Focusing on the striatum, we determined that the transcriptional dysregulation associated with HD was partially exacerbated in mice that showed poor overall phenotypical scores, especially in genes with relevant roles in striatal functioning (e.g., Pde10a, Drd1, Drd2, Ppp1r1b). However, we also observed transcripts associated with relatively better outcomes, such as Nfya (CCAAT-binding transcription factor NF-Y subunit A) plus others related to neuronal development, apoptosis and differentiation. In this study, we demonstrated that altered brain transcription can be related to the manifestation of HD-like symptoms in mouse models and that this can be extrapolated to the highly heterogeneous population of HD patients.
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Affiliation(s)
- Andrea Gallardo-Orihuela
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Irati Hervás-Corpión
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Carmen Hierro-Bujalance
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Área de Fisiología, Facultad de Medicina, Universidad de Cádiz, Plaza Fragela, 11003, Cádiz, Spain
| | - Daniel Sanchez-Sotano
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Área de Fisiología, Facultad de Medicina, Universidad de Cádiz, Plaza Fragela, 11003, Cádiz, Spain
| | - Gema Jiménez-Gómez
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Francisco Mora-López
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Servicio de Inmunología, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Antonio Campos-Caro
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Monica Garcia-Alloza
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Área de Fisiología, Facultad de Medicina, Universidad de Cádiz, Plaza Fragela, 11003, Cádiz, Spain
| | - Luis M Valor
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain. .,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain.
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Silajdžić E, Björkqvist M. A Critical Evaluation of Wet Biomarkers for Huntington's Disease: Current Status and Ways Forward. J Huntingtons Dis 2019; 7:109-135. [PMID: 29614689 PMCID: PMC6004896 DOI: 10.3233/jhd-170273] [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] [Indexed: 01/04/2023]
Abstract
There is an unmet clinical need for objective biomarkers to monitor disease progression and treatment response in Huntington's disease (HD). The aim of this review is, therefore, to provide practical advice for biomarker discovery and to summarise studies on biofluid markers for HD. A PubMed search was performed to review literature with regard to candidate saliva, urine, blood and cerebrospinal fluid biomarkers for HD. Information has been organised into tables to allow a pragmatic approach to the discussion of the evidence and generation of practical recommendations for future studies. Many of the markers published converge on metabolic and inflammatory pathways, although changes in other analytes representing antioxidant and growth factor pathways have also been found. The most promising markers reflect neuronal and glial degeneration, particularly neurofilament light chain. International collaboration to standardise assays and study protocols, as well as to recruit sufficiently large cohorts, will facilitate future biomarker discovery and development.
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Affiliation(s)
- Edina Silajdžić
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Maria Björkqvist
- Department of Experimental Medical Science, Brain Disease Biomarker Unit, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
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38
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Malondkar A, Corizzo R, Kiringa I, Ceci M, Japkowicz N. Spark-GHSOM: Growing Hierarchical Self-Organizing Map for large scale mixed attribute datasets. Inf Sci (N Y) 2019. [DOI: 10.1016/j.ins.2018.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Min B, Park M, Jeon K, Park JS, Seo H, Jeong S, Kang YK. Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription. Aging (Albany NY) 2019; 10:789-807. [PMID: 29706608 PMCID: PMC5940109 DOI: 10.18632/aging.101428] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/20/2018] [Indexed: 02/03/2023]
Abstract
This study addressed the question of how well the quantitative transcriptome structure established in early life is maintained and how consistently it appears with increasing age, and if there is age-associated alteration of gene expression (A3GE), how much influence the Huntington’s disease (HD) genotype exerts on it. We examined 285 exonic sequences of 175 genes using targeted PCR sequencing in skeletal muscle, brain, and splenic CD4+ T cells of wild-type and HD mice. In contrast to the muscle and brain, T cells exhibited large A3GE, suggesting a strong contribution to functional decline of the organism. This A3GE was markedly intensified in age-matched HD T cells, which exhibited accelerated aging as determined by reduced telomere length. Regression analysis suggested that gene expression levels change at a rate of approximately 3% per month with age. We found a bimodal relationship in A3GE in T cells in that weakly expressed genes in young mice were increasingly transcribed in older animals whereas highly expressed genes in the young were decreasingly expressed with age. This bimodal transcriptional drift in the T cell transcriptome data causes the differences in transcription rate between genes to progressively reduce with age.
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Affiliation(s)
- Byungkuk Min
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, South Korea
| | - Myungsun Park
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, South Korea
| | - Kyuheum Jeon
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, South Korea
| | - Hyemyung Seo
- Department of Molecular and Life Sciences, Hanyang University, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea
| | - Sangkyun Jeong
- Mibyeong Research Center, Korea Institute of Oriental Medicine (KIOM), Daejeon 305-811, Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, South Korea
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Abstract
Dementia is an overarching term which describes a group of symptoms that result in long-term decline in cognitive functioning that is significant enough to affect daily function. It is caused by a number of different diseases, the most common of which is Alzheimer's disease. Currently, there are no definitive biomarkers for preclinical or diagnostic use, or which differentiate between underlying disease types. The purpose of this review is to highlight several important areas of research on blood-based biomarkers of dementia, with a specific focus on epigenetic biomarkers. A systematic search of the literature identified 77 studies that compared blood DNA methylation between individuals with dementia and controls and 45 studies that measured microRNA. Very few studies were identified that focused on histone modifications. There were many promising findings from studies in the field of blood-based epigenetic biomarkers of dementia, however, a lack of consistency in study design, technologies, and platforms used for the biomarker measurement, as well as statistical analysis methods, have hampered progress. To date, there are very few findings that have been independently replicated across more than one study, indicating a preponderance of false-positive findings and the field has likely been plagued by positive publication bias. Here, we highlight and discuss several of the limitations of existing studies and provide recommendations for how these could be overcome in future research. A robust framework should be followed to enable development of the most valid and reproducible biomarkers with the strongest clinical utility. Defining a series of biomarkers that may be complimentary to each other could permit a stronger multifactorial biomarker to be developed that would allow for not only accurate dementia diagnosis but preclinical detection.
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Affiliation(s)
- Peter D Fransquet
- Department of Epidemiology and Preventive Medicine, Monash University , Melbourne , Australia.,Disease Epigenetics, Murdoch Children's Research Institute , Parkville , Australia
| | - Joanne Ryan
- Department of Epidemiology and Preventive Medicine, Monash University , Melbourne , Australia.,Disease Epigenetics, Murdoch Children's Research Institute , Parkville , Australia
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41
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Byrne A, Supple MA, Volden R, Laidre KL, Shapiro B, Vollmers C. Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear ( Ursus maritimus). Front Genet 2019; 10:643. [PMID: 31379921 PMCID: PMC6658610 DOI: 10.3389/fgene.2019.00643] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/18/2019] [Indexed: 11/26/2022] Open
Abstract
Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result, long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9-based depletion method (depletion of abundant sequences by hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion, we discovered ∼6,000 high-confidence isoforms and a number of novel genes. This indicates that there is a high diversity of gene isoforms within U. maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.
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Affiliation(s)
- Ashley Byrne
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA, United States
- Genomics Institute, University of California, Santa Cruz, CA, United States
| | - Megan A. Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Roger Volden
- Genomics Institute, University of California, Santa Cruz, CA, United States
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Kristin L. Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, United States
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Christopher Vollmers
- Genomics Institute, University of California, Santa Cruz, CA, United States
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
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42
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Wang Y, Li Z. RNA-seq analysis of blood of valproic acid-responsive and non-responsive pediatric patients with epilepsy. Exp Ther Med 2019; 18:373-383. [PMID: 31258675 PMCID: PMC6566089 DOI: 10.3892/etm.2019.7538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 04/09/2019] [Indexed: 12/13/2022] Open
Abstract
Epilepsy is the most common chronic neurological disorder, affecting ~70 million individuals worldwide. However, approximately one-third of the patients are refractory to epilepsy medication. Of note, 100% of patients with genetic epilepsy who are resistant to the traditional drug, valproic acid (VPA), are also refractory to the other anti-epileptic drugs. The aim of the present study was to compare the transcriptomes in VPA responders and non-responders, to explore the mechanism of action of VPA and identify possible biomarkers to predict VPA resistance. Thus, RNA-seq was employed for transcriptomic analysis, differentially expressed genes (DEGs) were analyzed using Cuffdiff software and the DAVID database was used to infer the functions of the DEGs. A protein-protein interaction network was obtained using STRING and visualized with Cytoscape. A total of 389 DEGs between VPA-responsive and non-responsive pediatric patients were identified. Of these genes, 227 were upregulated and 162 were downregulated. The upregulated DEGs were largely associated with cytokines, chemokines and chemokine receptor-binding factors, whereas the downregulated DEGs were associated with cation channels, iron ion binding proteins, and immunoglobulin E receptors. In the pathway analysis, the toll-like receptor signaling pathway, pathways in cancer, and cytokine-cytokine receptor interaction were mostly enriched by the DEGs. Furthermore, three modules were identified by protein-protein interaction analysis, and the potential hub genes, chemokine (C-C motif) ligand 3 and 4, chemokine (C-X-C motif) ligand 9, tumor necrosis factor-α and interleukin-1β, which are known to be closely associated with epilepsy, were identified. These specific chemokines may participate in processes associated with VPA resistance and may be potential biomarkers for monitoring the efficacy of VPA.
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Affiliation(s)
- Yan Wang
- Department of Pharmacy, Children's Hospital of Fudan University, Shanghai 201102, P.R. China.,Hainan Provincial Key Lab of R&D of Tropical Herbs, College of Pharmacy, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Zhiping Li
- Department of Pharmacy, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
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Sayad A, Taheri M, Azari I, Oskoei VK, Ghafouri-Fard S. PIAS genes as disease markers in bipolar disorder. J Cell Biochem 2019; 120:12937-12942. [PMID: 30861611 DOI: 10.1002/jcb.28564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/16/2018] [Accepted: 01/10/2019] [Indexed: 11/11/2022]
Abstract
The protein inhibitors of activated STAT (PIAS) are involved in regulation of many transcription factors and signaling pathways that contribute to the pathogenesis of bipolar disease (BD). In the current study, we evaluated the expression of four PIAS genes (PIAS1-4) in peripheral blood of BD patients and healthy subjects to explore their contribution in the pathogenesis of BD and their suitability as peripheral biomarkers for this disorder. All PIAS genes were significantly upregulated in total BD patients compared with total controls. The sex-based analysis confirmed upregulation of PIAS1-4 genes in male BD patients compared with male controls (P < 0.001). However, PIAS1 was significantly downregulated in female patients compared with female controls (P = 0.02). Expression levels of other PIAS genes were not significantly different between female patients and female controls. There were no significant correlations between expression levels of PIAS genes and any of the clinical data of study participants after adjustment of the effects of the sex. On the basis of the area under the curve (AUC) values in receiver operating characteristic curves, PIAS4 had the best performance in the differentiation of disease status between study participants (AUC = 0.81). PIAS3 and PIAS4 genes had the best sensitivity and specificity values, respectively. Combination of expression levels of four genes resulted in the improvement of diagnostic power (AUC = 0.82). The current data implies the role of PIAS genes in the pathogenesis of BD and denotes their suitability as peripheral markers for this disorder.
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Affiliation(s)
- Arezou Sayad
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Iman Azari
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Kholghi Oskoei
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Zadel M, Maver A, Kovanda A, Peterlin B. Transcriptomic Biomarkers for Huntington's Disease: Are Gene Expression Signatures in Whole Blood Reliable Biomarkers? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:283-294. [PMID: 29652574 DOI: 10.1089/omi.2017.0206] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Huntington's disease (HD) is a severe neurodegenerative disorder manifesting as progressive impairment of motor function, cognitive decline, psychiatric symptoms, and immunological and endocrine dysfunction. We explored the consistency of blood transcriptomic biomarkers in HD based on a novel Slovene patient cohort and expert review of previous studies. HumanHT-12 v4 BeadChip microarrays were performed on the whole blood samples of a cohort of 23 HD mutation carriers and 23 controls to identify differentially expressed (DE) transcripts. In addition, we performed an expert review of DE transcripts identified in comparable HD studies from whole blood, to identify any consistent signature of HD. In the Slovene cohort, we identified 740 DE transcripts (p < 0.01 and a false discovery rate (FDR) of <0.1) of which 414 were downregulated and 326 were upregulated. Pathway analyses of DE transcripts showed enrichment for pathways involved in systemic, rather than neural processes in HD. With an expert review of comparable studies, we have further identified 15 DE transcripts shared by 3 studies. We suggest transcriptomic changes in blood reflect systemic changes in HD pathogenesis, rather than being a direct result of the neuropathological processes in the central nervous system during HD progression, and thus, have limited value as disease biomarkers.
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Affiliation(s)
- Maja Zadel
- 1 Community Health Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- 2 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Anja Kovanda
- 2 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Borut Peterlin
- 2 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
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Yen GS, Fujimoto BS, Schneider T, Kreutz JE, Chiu DT. Statistical Analysis of Nonuniform Volume Distributions for Droplet-Based Digital PCR Assays. J Am Chem Soc 2019; 141:1515-1525. [PMID: 30605325 DOI: 10.1021/jacs.8b09073] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present a method to determine the concentration of nucleic acids in a sample by partitioning it into droplets with a nonuniform volume distribution. This digital PCR method requires no special equipment for partitioning, unlike other methods that require nearly identical volumes. Droplets are generated by vortexing a sample in an immiscible oil to create an emulsion. PCR is performed, and droplets in the emulsion are imaged. Droplets with one or more copies of a nucleic acid are identified, and the nucleic acid concentration of the sample is determined. Numerical simulations of droplet distributions were used to estimate measurement error and dynamic range and to examine the effects of the total volume of droplets imaged and the shape of the droplet size distribution on measurement accuracy. The ability of the method to resolve 1.5- and 3-fold differences in concentration was assessed by using simulations of statistical power. The method was validated experimentally; droplet shrinkage and fusion during amplification were also assessed experimentally and showed negligible effects on measured concentration.
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Affiliation(s)
- Gloria S Yen
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
| | - Bryant S Fujimoto
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
| | - Thomas Schneider
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
| | - Jason E Kreutz
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
| | - Daniel T Chiu
- Department of Chemistry , University of Washington , Seattle , Washington 98195-1700 , United States
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47
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Schrag A, Martino D, Apter A, Ball J, Bartolini E, Benaroya-Milshtein N, Buttiglione M, Cardona F, Creti R, Efstratiou A, Gariup M, Georgitsi M, Hedderly T, Heyman I, Margarit I, Mir P, Moll N, Morer A, Müller N, Müller-Vahl K, Münchau A, Orefici G, Plessen KJ, Porcelli C, Paschou P, Rizzo R, Roessner V, Schwarz MJ, Steinberg T, Tagwerker Gloor F, Tarnok Z, Walitza S, Dietrich A, Hoekstra PJ. European Multicentre Tics in Children Studies (EMTICS): protocol for two cohort studies to assess risk factors for tic onset and exacerbation in children and adolescents. Eur Child Adolesc Psychiatry 2019; 28:91-109. [PMID: 29982875 PMCID: PMC6349795 DOI: 10.1007/s00787-018-1190-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/28/2018] [Indexed: 12/22/2022]
Abstract
Genetic predisposition, autoimmunity and environmental factors [e.g. pre- and perinatal difficulties, Group A Streptococcal (GAS) and other infections, stress-inducing events] might interact to create a neurobiological vulnerability to the development of tics and associated behaviours. However, the existing evidence for this relies primarily on small prospective or larger retrospective population-based studies, and is therefore still inconclusive. This article describes the design and methodology of the EMTICS study, a longitudinal observational European multicentre study involving 16 clinical centres, with the following objectives: (1) to investigate the association of environmental factors (GAS exposure and psychosocial stress, primarily) with the onset and course of tics and/or obsessive-compulsive symptoms through the prospective observation of at-risk individuals (ONSET cohort: 260 children aged 3-10 years who are tic-free at study entry and have a first-degree relative with a chronic tic disorder) and affected individuals (COURSE cohort: 715 youth aged 3-16 years with a tic disorder); (2) to characterise the immune response to microbial antigens and the host's immune response regulation in association with onset and exacerbations of tics; (3) to increase knowledge of the human gene pathways influencing the pathogenesis of tic disorders; and (4) to develop prediction models for the risk of onset and exacerbations of tic disorders. The EMTICS study is, to our knowledge, the largest prospective cohort assessment of the contribution of different genetic and environmental factors to the risk of developing tics in putatively predisposed individuals and to the risk of exacerbating tics in young individuals with chronic tic disorders.
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Affiliation(s)
- Anette Schrag
- 0000000121901201grid.83440.3bDepartment of Clinical Neurosciences, UCL Institute of Neurology, University College London, London, UK
| | - Davide Martino
- 0000 0004 1936 7697grid.22072.35Department of Clinical Neurosciences, University of Calgary, Calgary, Canada
| | - Alan Apter
- 0000 0004 1937 0546grid.12136.37Child and Adolescent Psychiatry Department, Schneider Children’s Medical Center of Israel, Affiliated to Sackler Faculty of Medicine, Tel Aviv University, Petah-Tikva, Israel
| | - Juliane Ball
- 0000 0004 1937 0650grid.7400.3Clinic of Child and Adolescent Psychiatry and Psychotherapy, University of Zurich, Zurich, Switzerland
| | | | - Noa Benaroya-Milshtein
- 0000 0004 1937 0546grid.12136.37Child and Adolescent Psychiatry Department, Schneider Children’s Medical Center of Israel, Affiliated to Sackler Faculty of Medicine, Tel Aviv University, Petah-Tikva, Israel
| | - Maura Buttiglione
- 0000 0001 0120 3326grid.7644.1Department of Biological Sciences and Human Oncology, Medical School, University of Bari “Aldo Moro”, Bari, Italy
| | - Francesco Cardona
- grid.7841.aDepartment of Human Neurosciences, University La Sapienza of Rome, Rome, Italy
| | - Roberta Creti
- 0000 0000 9120 6856grid.416651.1Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Androulla Efstratiou
- 0000 0004 5909 016Xgrid.271308.fWHO Global Collaborating Centre for Reference and Research on Diphtheria and Streptococcal Infections, Reference Microbiology, Directorate National Infection Service, Public Health England, London, UK
| | - Maria Gariup
- 0000 0004 1937 0247grid.5841.8University of Barcelona, Barcelona, Spain ,Intensive Inpatient Unit, Copenhagen Psychiatric Center, Copenhagen, Denmark
| | - Marianthi Georgitsi
- 0000 0001 2170 8022grid.12284.3dDepartment of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece ,0000000109457005grid.4793.9Department of Medicine, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Tammy Hedderly
- 0000 0004 5345 7223grid.483570.dEvelina London Children’s Hospital GSTT, Kings Health Partners AHSC, London, UK
| | - Isobel Heyman
- 0000000121901201grid.83440.3bGreat Ormond Street Hospital for Children, UCL Institute of Child Health, London, UK
| | | | - Pablo Mir
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clinica, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Seville, Spain
| | - Natalie Moll
- 0000 0004 1936 973Xgrid.5252.0Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Astrid Morer
- 0000 0000 9635 9413grid.410458.cDepartment of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic Universitari, Barcelona, Spain ,grid.10403.36Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ,0000 0000 9314 1427grid.413448.eCentro de Investigacion en Red de Salud Mental (CIBERSAM), Instituto Carlos III, Madrid, Spain
| | - Norbert Müller
- 0000 0004 1936 973Xgrid.5252.0Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany ,Marion von Tessin Memory-Zentrum gGmbH, Munich, Germany
| | - Kirsten Müller-Vahl
- 0000 0000 9529 9877grid.10423.34Clinic of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Alexander Münchau
- 0000 0001 0057 2672grid.4562.5Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Graziella Orefici
- 0000 0000 9120 6856grid.416651.1Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Kerstin J. Plessen
- Child and Adolescent Mental Health Center, Mental Health Services, Capital Region of Denmark and University of Copenhagen, Copenhagen, Denmark ,0000 0001 2165 4204grid.9851.5Service of Child and Adolescent Psychiatry, Department of Psychiatry, University Medical Center, University of Lausanne, Lausanne, Switzerland
| | - Cesare Porcelli
- Azienda Sanitaria Locale di Bari, Mental Health Department, Child and Adolescent Neuropsychiatry Service of Bari Metropolitan Area, Bari, Italy
| | - Peristera Paschou
- 0000 0004 1937 2197grid.169077.eDepartment of Biological Sciences, Purdue University, West Lafayette, USA
| | - Renata Rizzo
- 0000 0004 1757 1969grid.8158.4Child Neuropsychiatry Section, Department of Clinical and Experimental Medicine, School of Medicine, Catania University, Catania, Italy
| | - Veit Roessner
- 0000 0001 2111 7257grid.4488.0Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Markus J. Schwarz
- 0000 0004 1936 973Xgrid.5252.0Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Tamar Steinberg
- 0000 0004 1937 0546grid.12136.37Child and Adolescent Psychiatry Department, Schneider Children’s Medical Center of Israel, Affiliated to Sackler Faculty of Medicine, Tel Aviv University, Petah-Tikva, Israel
| | - Friederike Tagwerker Gloor
- 0000 0004 1937 0650grid.7400.3Clinic of Child and Adolescent Psychiatry and Psychotherapy, University of Zurich, Zurich, Switzerland
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Susanne Walitza
- 0000 0004 1937 0650grid.7400.3Clinic of Child and Adolescent Psychiatry and Psychotherapy, University of Zurich, Zurich, Switzerland
| | - Andrea Dietrich
- 0000 0004 0407 1981grid.4830.fDepartment of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Pieter J. Hoekstra
- 0000 0004 0407 1981grid.4830.fDepartment of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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Wang Y, Xu Z, Wang X. miRNA-373 promotes urinary bladder cancer cell proliferation, migration and invasion through upregulating epidermal growth factor receptor. Exp Ther Med 2018; 17:1190-1195. [PMID: 30679992 PMCID: PMC6327664 DOI: 10.3892/etm.2018.7061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/10/2018] [Indexed: 01/07/2023] Open
Abstract
MicroRNA (miRNA)-373 has been demonstrated to be involved in several types of cancer, whereas its involvement in urinary bladder cancer and the mechanism of its function remains poorly understood. The present study aimed to investigate the functionality of miRNA-373 in urinary bladder cancer. Tumor tissues and adjacent healthy tissues were collected from patients with urinary bladder cancer (n=55), and blood samples were collected from patients with urinary bladder cancer and healthy controls (n=45). The expression of miRNA-373 in these tissues was detected by reverse transcription quantitative polymerase chain reaction. The diagnostic value of serum miRNA-373 for urinary bladder cancer was investigated by receiver operating characteristic curve analysis and survival curve analysis, respectively. miRNA-373 mimics were transfected into urinary bladder cancer cells, and the effects on cancer cell proliferation, migration and invasion, and on epidermal growth factor receptor (EGFR) expression was assessed by Cell Counting kit-8 assay, Transwell migration and invasion assays, and western blot analysis. It was identified that the miRNA-373 expression level was increased in tumor tissues compared with adjacent healthy tissues. The serum level of miRNA-373 was increased in patients with cancer compared with the healthy controls. Serum miRNA-373 may be used to accurately predict urinary bladder cancer. miRNA-373 overexpression promoted tumor cell proliferation, migration and invasion, and resulted in upregulated EGFR expression in urinary bladder cancer cells. It was concluded that miRNA-373 overexpression may promote urinary bladder cancer cell proliferation, migration and invasion by upregulating EGFR.
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Affiliation(s)
- Yibing Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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49
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Denis HL, Lamontagne-Proulx J, St-Amour I, Mason SL, Weiss A, Chouinard S, Barker RA, Boilard E, Cicchetti F. Platelet-derived extracellular vesicles in Huntington's disease. J Neurol 2018; 265:2704-2712. [PMID: 30209650 DOI: 10.1007/s00415-018-9022-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 01/09/2023]
Abstract
The production and release of extracellular vesicles (EV) is a property shared by all eukaryotic cells and a phenomenon frequently exacerbated in pathological conditions. The protein cargo of EV, their cell type signature and availability in bodily fluids make them particularly appealing as biomarkers. We recently demonstrated that platelets, among all types of blood cells, contain the highest concentrations of the mutant huntingtin protein (mHtt)-the genetic product of Huntington's disease (HD), a neurodegenerative disorder which manifests in adulthood with a complex combination of motor, cognitive and psychiatric deficits. Herein, we used a cohort of 59 HD patients at all stages of the disease, including individuals in pre-manifest stages, and 54 healthy age- and sex-matched controls, to evaluate the potential of EV derived from platelets as a biomarker. We found that platelets of pre-manifest and manifest HD patients do not release more EV even if they are activated. Importantly, mHtt was not found within EV derived from platelets, despite them containing high levels of this protein. Correlation analyses also failed to reveal an association between the number of platelet-derived EV and the age of the patients, the number of CAG repeats, the Unified Huntington Disease Rating Scale total motor score, the Total Functional Capacity score or the Burden of Disease score. Our data would, therefore, suggest that EV derived from platelets with HD is not a valuable biomarker in HD.
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Affiliation(s)
- Hélèna L Denis
- Centre de Recherche du CHU de Québec, Québec, QC, Canada
| | | | | | - Sarah L Mason
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
| | | | - Sylvain Chouinard
- Centre Hospitalier de l'Université de Montréal et Centre de recherche du Centre Hospitalier de l'Université de Montréal, Département de médecine, Hôpital Notre-Dame, Université de Montréal, Montréal, QC, Canada
| | - Roger A Barker
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
| | - Eric Boilard
- Centre de Recherche du CHU de Québec, Québec, QC, Canada. .,Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, QC, Canada.
| | - Francesca Cicchetti
- Centre de Recherche du CHU de Québec, Québec, QC, Canada. .,Département de psychiatrie et neurosciences, Université Laval, Québec, QC, Canada.
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50
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De Felice B, Manfellotto F, Fiorentino G, Annunziata A, Biffali E, Pannone R, Federico A. Wide-Ranging Analysis of MicroRNA Profiles in Sporadic Amyotrophic Lateral Sclerosis Using Next-Generation Sequencing. Front Genet 2018; 9:310. [PMID: 30154826 PMCID: PMC6102490 DOI: 10.3389/fgene.2018.00310] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNA (miRNA) has emerged as an important regulator of gene expression in neurodegenerative disease as amyotrophic lateral sclerosis (ALS). In the nervous system, dysregulation in miRNA-related pathways is subordinated to neuronal damage and cell death, which contributes to the expansion of neurodegenerative disorders, such as ALS. In the present research, we aimed to profile dysregulation of miRNAs in ALS blood and neuromuscular junction as well as healthy blood control by next-generation sequencing (NGS). The expression of three upregulated miRNAs, as miR-338-3p, miR-223-3p, and miR-326, in the ALS samples compared to healthy controls, has been validated by qRT-PCR in a cohort of 45 samples collected previously. Bioinformatics tools were used to perform ALS miRNAs target analysis and to predict novel miRNAs secondary structure. The analysis of the NGS data identified 696 and 49 novel miRNAs which were differentially expressed in ALS tissues. In particular, in neuromuscular junction the differential expression of miR-338-3p, which we previously found upregulated in different types of ASL tissues, miR-223-3p, and miR-326 was elevated compared to normal control. ALS miRNAs gene target were significantly involved in neuronal related pathway as BDFN1 and HIF-1genes. This study presents the direct experimental evidence that, overall, miR-338-3p is highly expressed in ALS tissues including neuromuscular junction characterizing ALS from normal tissues. Beside, our analysis identified, for the first time, novel miRNAs highly expressed in ALS tissues. In conclusion, the results indicate that miRNAs has an important role in the diagnosis and treatment of ALS.
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Affiliation(s)
- Bruna De Felice
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Francesco Manfellotto
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | | | - Anna Annunziata
- Division of Physiopathology, Monaldi Hospital, Naples, Italy
| | | | | | - Antonio Federico
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", National Research Council, Naples, Italy
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