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Fakouri A, Razavi ZS, Mohammed AT, Hussein AHA, Afkhami H, Hooshiar MH. Applications of mesenchymal stem cell-exosome components in wound infection healing: new insights. BURNS & TRAUMA 2024; 12:tkae021. [PMID: 39139205 PMCID: PMC11319788 DOI: 10.1093/burnst/tkae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/12/2024] [Accepted: 04/22/2024] [Indexed: 08/15/2024]
Abstract
The healing process at a wound is made up of many types of cells, growth factors, the extracellular matrix, nerves and blood vessels all interacting with each other in complex and changing ways. Microbial colonization and proliferation are possible at the place of injury, which makes infection more likely. Because of this, any cut has a chance of getting an infection. Researchers have found that wound infections make patients more upset and cost the healthcare system a lot of money. Surgical site infections happen a lot to people who have recently had surgery. This study shows that such surgical infection is linked to a high rate of illness and death. This is shown by the fact that 25% of patients get serious sepsis and need to be transferred to an intensive care unit. In both animal models and people, mesenchymal stem cells (MSCs) play an active role in all stages of wound healing and have positive effects. Exosomes are one of the main things MSCs release. They have effects that are similar to those of the parent MSCs. Various effector proteins, messenger RNA and microRNAs can be transported by extracellular vesicles to control the activity of target cells. This has a big impact on the healing process. These results suggest that using MSC-exosomes as a new type of cell-free therapy could be a better and safer option than whole cell therapy. This review is mostly about how to use parts of MSC-exosomes to help wound infections heal.
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Affiliation(s)
- Arshia Fakouri
- Student Research Committee, USERN Office, Lorestan University of Medical Sciences, Khorramabad 6813833946, Iran
| | - Zahra-Sadat Razavi
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | | | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
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2
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Sharma R, Bisht P, Kesharwani A, Murti K, Kumar N. Epigenetic modifications in Parkinson's disease: A critical review. Eur J Pharmacol 2024; 975:176641. [PMID: 38754537 DOI: 10.1016/j.ejphar.2024.176641] [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: 01/29/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Parkinson's Disease (PD) is a progressive neurodegenerative disorder expected to increase by over 50% by 2030 due to increasing life expectancy. The disease's hallmarks include slow movement, tremors, and postural instability. Impaired protein processing is a major factor in the pathophysiology of PD, leading to the buildup of aberrant protein aggregates, particularly misfolded α-synuclein, also known as Lewy bodies. These Lewy bodies lead to inflammation and further death of dopaminergic neurons, leading to imbalances in excitatory and inhibitory neurotransmitters, causing excessive uncontrollable movements called dyskinesias. It was previously suggested that a complex interplay involving hereditary and environmental variables causes the specific death of neurons in PD; however, the exact mechanism of the association involving the two primary modifiers is yet unknown. An increasing amount of research points to the involvement of epigenetics in the onset and course of several neurological conditions, such as PD. DNA methylation, post-modifications of histones, and non-coding RNAs are the primary examples of epigenetic alterations, that is defined as alterations to the expression of genes and functioning without modifications in DNA sequence. Epigenetic modifications play a significant role in the development of PD, with genes such as Parkin, PTEN-induced kinase 1 (PINK1), DJ1, Leucine-Rich Repeat Kinase 2 (LRRK2), and alpha-synuclein associated with the disease. The aberrant epigenetic changes implicated in the pathophysiology of PD and their impact on the design of novel therapeutic approaches are the primary focus of this review.
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Affiliation(s)
- Ravikant Sharma
- Research Unit of Biomedicine and Internal Medicine, Faculty of Medicine, University of Oulu, Aapistie 5, 90220, Oulu, Finland
| | - Priya Bisht
- Department of Pharmacology and Toxicology, National Institution of Pharmaceutical Education and Research, Hajipur, Vaishali, 844102, Bihar, India
| | - Anuradha Kesharwani
- Department of Pharmacology and Toxicology, National Institution of Pharmaceutical Education and Research, Hajipur, Vaishali, 844102, Bihar, India
| | - Krishna Murti
- Department of Pharmacy Practice, National Institution of Pharmaceutical Education and Research, Hajipur, Vaishali, 844102, Bihar, India
| | - Nitesh Kumar
- Department of Pharmacology and Toxicology, National Institution of Pharmaceutical Education and Research, Hajipur, Vaishali, 844102, Bihar, India.
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3
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Hamidpour SK, Amiri M, Ketabforoush AHME, Saeedi S, Angaji A, Tavakol S. Unraveling Dysregulated Cell Signaling Pathways, Genetic and Epigenetic Mysteries of Parkinson's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04128-1. [PMID: 38573414 DOI: 10.1007/s12035-024-04128-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
Parkinson's disease (PD) is a prevalent and burdensome neurodegenerative disorder that has been extensively researched to understand its complex etiology, diagnosis, and treatment. The interplay between genetic and environmental factors in PD makes its pathophysiology difficult to comprehend, emphasizing the need for further investigation into genetic and epigenetic markers involved in the disease. Early diagnosis is crucial for optimal management of the disease, and the development of novel diagnostic biomarkers is ongoing. Although many efforts have been made in the field of recognition and interpretation of the mechanisms involved in the pathophysiology of the disease, the current knowledge about PD is just the tip of the iceberg. By scrutinizing genetic and epigenetic patterns underlying PD, new avenues can be opened for dissecting the pathology of the disorder, leading to more precise and efficient diagnostic and therapeutic approaches. This review emphasizes the importance of studying dysregulated cell signaling pathways and molecular processes associated with genes and epigenetic alterations in understanding PD, paving the way for the development of novel therapeutic strategies to combat this devastating disease.
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Affiliation(s)
- Shayesteh Kokabi Hamidpour
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Mobina Amiri
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | | | - Saeedeh Saeedi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Abdolhamid Angaji
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Shima Tavakol
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, 1449614535, Iran.
- Department of Research and Development, Tavakol BioMimetic Technologies Company, Tehran, Iran.
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4
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Mei Z, Huang L, Rao W. CircNUFIP2 overexpression induces GDF11 to ameliorate oxygen-glucose deprivation-induced hippocampal neuron cell apoptosis and oxidative stress after cerebral ischemia. Neurol Res 2023; 45:70-80. [PMID: 36328251 DOI: 10.1080/01616412.2022.2123172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Previous data have indicated the regulation of circular RNA (circRNA) toward cerebral ischemia. This study aims to reveal the effects of circNUFIP2 on cerebral ischemia and the underlying mechanism. Methods Oxygen-glucose deprivation (OGD) hippocampal neuron (HT22) cell model and middle cerebral artery occlusion (MCAO) mouse model were used for this study. The expression of circRNA nuclear FMR1 interacting protein 2 (circNUFIP2), microRNA-1224-5p (miR-1224-5p) and growth differentiation factor 11 (GDF11) was detected by quantitative real-time polymerase-chain reaction. Protein expression was checked by Western blotting. The binding relationships among circNUFIP2, miR-1224-5p and GDF11 were identified by dual-luciferase reporter assay, RNA pull-down assay, and RNA immunoprecipitation assay. Cell proliferation and apoptosis were investigated by 5-Ethynyl-29-deoxyuridine and flow cytometry analysis, respectively. Results CircNUFIP2 and GDF11 expression were decreased, but miR-1224-5p was increased in OGD-treated HT22 cells when compared with their expression in control groups. OGD treatment inhibited HT22 cell proliferation but induced cell apoptosis and oxidative stress; however, these effects were attenuated after circNUFIP2 overexpression. Also, circNUFIP2 upregulation assuaged the cerebral infarction of MCAO mice. Besides, circNUFIP2 bound to miR-1224-5p and mediated OGD-induced HT22 cell damage through miR-1224-5p. Meanwhile, knockdown of GDF11, a target gene of miR-1224-5p, relieved miR-1224-5p depletion-caused effects in OGD-treated HT22 cells. Furthermore, circNUFIP2 regulated GDF11 expression by interacting with miR-1224-5p. Conclusion CircNUFIP2 overexpression protected neuron cells against cerebral ischemia-induced damage, at least in part, by the miR-1224-5p/GDF11 pathway, providing a possible target for the therapy of cerebral ischemic stroke.
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Affiliation(s)
- Zhujun Mei
- Department of Neurology, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang City, Jiangxi Province, China
| | - LinLing Huang
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang City, Jiangxi Province, China
| | - Wei Rao
- Department of Neurology, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang City, Jiangxi Province, China
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5
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Partial Disturbance of Microprocessor Function in Human Stem Cells Carrying a Heterozygous Mutation in the DGCR8 Gene. Genes (Basel) 2022; 13:genes13111925. [DOI: 10.3390/genes13111925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 11/04/2022] Open
Abstract
Maturation of microRNAs (miRNAs) begins by the “Microprocessor” complex, containing the Drosha endonuclease and its partner protein, "DiGeorge Syndrome Critical Region 8" (DGCR8). Although the main function of the two proteins is to coordinate the first step of precursor miRNAs formation, several studies revealed their miRNA-independent functions in other RNA-related pathways (e.g., in snoRNA decay) or, for the DGCR8, the role in tissue development. To investigate the specific roles of DGCR8 in various cellular pathways, we previously established a human embryonic stem-cell (hESC) line carrying a monoallelic DGCR8 mutation by using the CRISPR-Cas9 system. In this study, we genetically characterized single-cell originated progenies of the cell line and showed that DGCR8 heterozygous mutation results in only a modest effect on the mRNA level but a significant decrease at the protein level. Self-renewal and trilineage differentiation capacity of these hESCs were not affected by the mutation. However, partial disturbance of the Microprocessor function could be revealed in pri-miRNA processing along the human chromosome 19 miRNA cluster in several clones. With all these studies, we can demonstrate that the mutant hESC line is a good model to study not only miRNA-related but also other “noncanonical” functions of the DGCR8 protein.
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Ma M, Li J, Zhang Z, Sun J, Liu Z, Zeng Z, Ouyang S, Kang W. The Role and Mechanism of microRNA-1224 in Human Cancer. Front Oncol 2022; 12:858892. [PMID: 35494023 PMCID: PMC9046935 DOI: 10.3389/fonc.2022.858892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/24/2022] Open
Abstract
microRNAs (miRNAs) are a type of small endogenous non-coding RNAs composed of 20-22 nucleotides, which can regulate the expression of a gene by targeting 3’ untranslated region (3’-UTR) of mRNA. Many studies have reported that miRNAs are involved in the occurrence and progression of human diseases, including malignant tumors. miR-1224 plays significant roles in different tumors, including tumor proliferation, metastasis, invasion, angiogenesis, biological metabolism, and drug resistance. Mostly, it serves as a tumor suppressor. With accumulating proofs of miR-1224, it can act as a potential bio-indicator in the diagnosis and prognosis of patients with cancer. In this article, we review the characteristics and research progress of miR-1224 and emphasize the regulation and function of miR-1224 in different cancer. Furthermore, we conclude the clinical implications of miR-1224. This review may provide new horizons for deeply understanding the role of miR-1224 as biomarkers and therapeutic targets in human cancer.
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Affiliation(s)
- Mingwei Ma
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Jie Li
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Zimu Zhang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Juan Sun
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Zhen Liu
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Ziyang Zeng
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Siwen Ouyang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Weiming Kang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
- *Correspondence: Weiming Kang,
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Han GD, Sun Y, Hui HX, Tao MY, Liu YQ, Zhu J. MiR-1224 Acts as a Prognostic Biomarker and Inhibits the Progression of Gastric Cancer by Targeting SATB1. Front Oncol 2021; 11:748896. [PMID: 34604093 PMCID: PMC8484804 DOI: 10.3389/fonc.2021.748896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/31/2021] [Indexed: 01/26/2023] Open
Abstract
Objective MiR-1224 has been reported to exhibit abnormal expression in several tumors. However, the expressing pattern and roles of miR-1224 in gastric cancer (GC) remain unclear. Our current research aimed to explore the potential involvement of miR-1224 in the GC progression. Materials and Methods The expression of miR-1224 was examined in tissue samples of 128 GC patients and cell lines by RT-PCR. Besides, the associations of miR-1224 expressions with clinicopathologic features and prognosis of GC patients were analyzed. Then, the possible influences of miR-1224 on cell proliferation and cell migration were determined. Afterward, the molecular target of miR-1224 was identified using bioinformatics assays and confirmed experimentally. Finally, RT-PCR and Western blot assays were performed to investigate the effect of the abnormal miR-1224 expression on the EMT and Wnt/β-catenin pathway. Results miR-1224 was lowly expressed in the GC specimens and cell lines due to T classification and TNM stage. Survival assays demonstrated that GC patients with low expressions of miR-1224 possessed poor overall survivals. Moreover, in vitro and in vivo assays revealed that the overexpression of miR-1224 inhibited cell proliferation, migration, and invasion in GC cells. SATB homeobox 1 (SATB1) was verified as a direct target of miR-1224 in GC. Furthermore, β-catenin and c-myc were significantly inhibited in miR-1224-overexpression cells. Conclusions Our findings highlight the potential of miR-1224 as a therapeutic target and novel biomarker for GC patients
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Affiliation(s)
- Guo-Dong Han
- Department of Orthopedics, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yuan Sun
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Hong-Xia Hui
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Ming-Yue Tao
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yang-Qing Liu
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Jing Zhu
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
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8
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Mirtron-mediated RNA knockdown/replacement therapy for the treatment of dominant retinitis pigmentosa. Nat Commun 2021; 12:4934. [PMID: 34400638 PMCID: PMC8368061 DOI: 10.1038/s41467-021-25204-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Rhodopsin (RHO) gene mutations are a common cause of autosomal dominant retinitis pigmentosa (ADRP). The need to suppress toxic protein expression together with mutational heterogeneity pose challenges for treatment development. Mirtrons are atypical RNA interference effectors that are spliced from transcripts as short introns. Here, we develop a novel mirtron-based knockdown/replacement gene therapy for the mutation-independent treatment of RHO-related ADRP, and demonstrate efficacy in a relevant mammalian model. Splicing and potency of rhodopsin-targeting candidate mirtrons are initially determined, and a mirtron-resistant codon-modified version of the rhodopsin coding sequence is validated in vitro. These elements are then combined within a single adeno-associated virus (AAV) and delivered subretinally in a RhoP23H knock-in mouse model of ADRP. This results in significant mouse-to-human rhodopsin RNA replacement and is associated with a slowing of retinal degeneration. This provides proof of principle that synthetic mirtrons delivered by AAV are capable of reducing disease severity in vivo.
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Posttranscriptional Regulation of the Human ABCG2 Multidrug Transporter Protein by Artificial Mirtrons. Genes (Basel) 2021; 12:genes12071068. [PMID: 34356084 PMCID: PMC8307164 DOI: 10.3390/genes12071068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/24/2022] Open
Abstract
ABCG2 is a membrane transporter protein that has been associated with multidrug resistance phenotype and tumor development. Additionally, it is expressed in various stem cells, providing cellular protection against endobiotics and xenobiotics. In this study, we designed artificial mirtrons to regulate ABCG2 expression posttranscriptionally. Applying EGFP as a host gene, we could achieve efficient silencing not only in luciferase reporter systems but also at the ABCG2 protein level. Moreover, we observed important new sequential-functional features of the designed mirtrons. Mismatch at the first position of the mirtron-derived small RNA resulted in better silencing than full complementarity, while the investigated middle and 3′ mismatches did not enhance silencing. These latter small RNAs operated most probably via non-seed specific translational inhibition in luciferase assays. Additionally, we found that a mismatch in the first position has not, but a second mismatch in the third position has abolished target mRNA decay. Besides, one nucleotide mismatch in the seed region did not impair efficient silencing at the protein level, providing the possibility to silence targets carrying single nucleotide polymorphisms or mutations. Taken together, we believe that apart from establishing an efficient ABCG2 silencing system, our designing pipeline and results on sequential-functional features are beneficial for developing artificial mirtrons for other targets.
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10
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Salim U, Kumar A, Kulshreshtha R, Vivekanandan P. Biogenesis, characterization, and functions of mirtrons. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1680. [PMID: 34155810 DOI: 10.1002/wrna.1680] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 01/18/2023]
Abstract
MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression. They base pair with the complementary target mRNA at the 3'UTR and modulate cellular processes by repressing the mRNA translation or degrading the mRNA. There are well-documented mechanisms of biogenesis of miRNA; however, a sizeable number of miRNAs are also produced by non-canonical pathways. Mirtrons represent a predominant class of non-canonical miRNAs. Mirtrons originate from intronic regions and are produced in a splicing-dependent and Drosha-independent manner. Mirtrons constitute about 15% of all miRNAs produced in a human body and have caught attention of researchers worldwide due to their unconventional origin, sequence characteristics, evolutionary dynamics, ability to regulate variety of cellular processes and their immense potential in disease therapeutics. In this comprehensive review we collate the research done in the past decade including biogenesis, sequence characteristics, regulation, and emerging therapeutic roles of mirtrons. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.
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Affiliation(s)
- Uzma Salim
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Ashish Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
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11
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Findeiss E, Schwarz SC, Evsyukov V, Rösler TW, Höllerhage M, Chakroun T, Nykänen NP, Shen Y, Wurst W, Kohl M, Tost J, Höglinger GU. Comprehensive miRNome-Wide Profiling in a Neuronal Cell Model of Synucleinopathy Implies Involvement of Cell Cycle Genes. Front Cell Dev Biol 2021; 9:561086. [PMID: 33748099 PMCID: PMC7969723 DOI: 10.3389/fcell.2021.561086] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Growing evidence suggests that epigenetic mechanisms like microRNA-mediated transcriptional regulation contribute to the pathogenesis of parkinsonism. In order to study the influence of microRNAs (miRNAs), we analyzed the miRNome 2 days prior to major cell death in α-synuclein-overexpressing Lund human mesencephalic neurons, a well-established cell model of Parkinson’s disease (PD), by next-generation sequencing. The expression levels of 23 miRNAs were significantly altered in α-synuclein-overexpressing cells, 11 were down- and 12 upregulated (P < 0.01; non-adjusted). The in silico analysis of known target genes of these miRNAs was complemented by the inclusion of a transcriptome dataset (BeadChip) of the same cellular system, revealing the G0/G1 cell cycle transition to be markedly enriched. Out of 124 KEGG-annotated cell cycle genes, 15 were present in the miRNA target gene dataset and six G0/G1 cell cycle genes were found to be significantly altered upon α-synuclein overexpression, with five genes up- (CCND1, CCND2, and CDK4 at P < 0.01; E2F3, MYC at P < 0.05) and one gene downregulated (CDKN1C at P < 0.001). Additionally, several of these altered genes are targeted by miRNAs hsa-miR-34a-5p and hsa-miR-34c-5p, which also modulate α-synuclein expression levels. Functional intervention by siRNA-mediated knockdown of the cell cycle gene cyclin D1 (CCND1) confirmed that silencing of cell cycle initiation is able to substantially reduce α-synuclein-mediated cytotoxicity. The present findings suggest that α-synuclein accumulation induces microRNA-mediated aberrant cell cycle activation in post-mitotic dopaminergic neurons. Thus, the mitotic cell cycle pathway at the level of miRNAs might offer interesting novel therapeutic targets for PD.
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Affiliation(s)
- Elisabeth Findeiss
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sigrid C Schwarz
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany
| | - Valentin Evsyukov
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Neurology, Hannover Medical School, Hanover, Germany
| | - Thomas W Rösler
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matthias Höllerhage
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Neurology, Hannover Medical School, Hanover, Germany
| | - Tasnim Chakroun
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Niko-Petteri Nykänen
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Yimin Shen
- Laboratory for Epigenetics and Environment, Center National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, Munich, Germany.,Genome Engineering, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Michael Kohl
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Center National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Günter U Höglinger
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Neurology, Hannover Medical School, Hanover, Germany
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12
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Acharya S, Salgado-Somoza A, Stefanizzi FM, Lumley AI, Zhang L, Glaab E, May P, Devaux Y. Non-Coding RNAs in the Brain-Heart Axis: The Case of Parkinson's Disease. Int J Mol Sci 2020; 21:E6513. [PMID: 32899928 PMCID: PMC7555192 DOI: 10.3390/ijms21186513] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 02/08/2023] Open
Abstract
Parkinson's disease (PD) is a complex and heterogeneous disorder involving multiple genetic and environmental influences. Although a wide range of PD risk factors and clinical markers for the symptomatic motor stage of the disease have been identified, there are still no reliable biomarkers available for the early pre-motor phase of PD and for predicting disease progression. High-throughput RNA-based biomarker profiling and modeling may provide a means to exploit the joint information content from a multitude of markers to derive diagnostic and prognostic signatures. In the field of PD biomarker research, currently, no clinically validated RNA-based biomarker models are available, but previous studies reported several significantly disease-associated changes in RNA abundances and activities in multiple human tissues and body fluids. Here, we review the current knowledge of the regulation and function of non-coding RNAs in PD, focusing on microRNAs, long non-coding RNAs, and circular RNAs. Since there is growing evidence for functional interactions between the heart and the brain, we discuss the benefits of studying the role of non-coding RNAs in organ interactions when deciphering the complex regulatory networks involved in PD progression. We finally review important concepts of harmonization and curation of high throughput datasets, and we discuss the potential of systems biomedicine to derive and evaluate RNA biomarker signatures from high-throughput expression data.
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Affiliation(s)
- Shubhra Acharya
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
- Faculty of Science, Technology and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Antonio Salgado-Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Francesca Maria Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Andrew I. Lumley
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Lu Zhang
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg; (E.G.); (P.M.)
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg; (E.G.); (P.M.)
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
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13
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Nakamori M, Junn E, Mochizuki H, Mouradian MM. Nucleic Acid-Based Therapeutics for Parkinson's Disease. Neurotherapeutics 2019; 16:287-298. [PMID: 30756362 PMCID: PMC6554378 DOI: 10.1007/s13311-019-00714-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder that is diagnosed largely on clinical grounds due to characteristic motor manifestations that result from the loss of nigrostriatal dopaminergic neurons. While traditional pharmacological approaches to enhance dopamine levels, such as with L-dopa, can be very effective initially, the chronic use of this dopamine precursor is commonly plagued with motor response complications. Additionally, with advancing disease, non-motor manifestations emerge, including psychosis and dementia that compound patient disability. The pathology includes hallmark intraneuronal inclusions known as Lewy bodies and Lewy neurites that contain fibrillar α-synuclein aggregates. Evidence has also accumulated that these aggregates can propagate across synaptically connected brain regions, a phenomenon that can explain the progressive nature of the disease and the emergence of additional symptoms over time. The level of α-synuclein is believed to play a critical role in its fibrillization and aggregation. Accordingly, nucleic acid-based therapeutics for PD include strategies to deliver dopamine biosynthetic enzymes to boost dopamine production or modulate the basal ganglia circuitry in order to improve motor symptoms. Delivery of trophic factors that might enhance the survival of dopamine neurons is another strategy that has been attempted. These gene therapy approaches utilize viral vectors and are delivered stereotaxically in the brain. Alternative disease-modifying strategies focus on downregulating the expression of the α-synuclein gene using various techniques, including modified antisense oligonucleotides, short hairpin RNA, short interfering RNA, and microRNA. The latter approaches also have implications for dementia with Lewy bodies. Other PD genes can also be targeted using nucleic acids. In this review, we detail these various strategies that are still experimental, and discuss the challenges and opportunities of nucleic acid-based therapeutics for PD.
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Affiliation(s)
- Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Eunsung Junn
- Robert Wood Johnson Medical School Institute for Neurological Therapeutics, and Department of Neurology, Rutgers Biomedical and Health Sciences, Piscataway, NJ, 08854, USA
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - M Maral Mouradian
- Robert Wood Johnson Medical School Institute for Neurological Therapeutics, and Department of Neurology, Rutgers Biomedical and Health Sciences, Piscataway, NJ, 08854, USA.
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14
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MicroRNA-1224 Splicing CircularRNA-Filip1l in an Ago2-Dependent Manner Regulates Chronic Inflammatory Pain via Targeting Ubr5. J Neurosci 2019; 39:2125-2143. [PMID: 30651325 DOI: 10.1523/jneurosci.1631-18.2018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/10/2018] [Accepted: 12/26/2018] [Indexed: 12/20/2022] Open
Abstract
Dysfunctions of gene transcription and translation in the nociceptive pathways play the critical role in development and maintenance of chronic pain. Circular RNAs (circRNAs) are emerging as new players in regulation of gene expression, but whether and how circRNAs are involved in chronic pain remain elusive. We showed here that complete Freund's adjuvant-induced chronic inflammation pain significantly increased circRNA-Filip1l (filamin A interacting protein 1-like) expression in spinal neurons of mice. Blockage of this increase attenuated complete Freund's adjuvant-induced nociceptive behaviors, and overexpression of spinal circRNA-Filip1l in naive mice mimicked the nociceptive behaviors as evidenced by decreased thermal and mechanical nociceptive threshold. Furthermore, we found that mature circRNA-Filip1l expression was negatively regulated by miRNA-1224 via binding and splicing of precursor of circRNA-Filip1l (pre-circRNA-Filip1l) in the Argonaute-2 (Ago2)-dependent manner. Increase of spinal circRNA-Filip1l expression resulted from the decrease of miRNA-1224 expression under chronic inflammation pain state. miRNA-1224 knockdown or Ago2 overexpression induced nociceptive behaviors in naive mice, which was prevented by the knockdown of spinal circRNA-Filip1l. Finally, we demonstrated that a ubiquitin protein ligase E3 component n-recognin 5 (Ubr5), validated as a target of circRNA-Filip1l, plays a pivotal role in regulation of nociception by spinal circRNA-Filip1l. These data suggest that miRNA-1224-mediated and Ago2-dependent modulation of spinal circRNA-Filip1l expression regulates nociception via targeting Ubr5, revealing a novel epigenetic mechanism of interaction between miRNA and circRNA in chronic inflammation pain.SIGNIFICANCE STATEMENT circRNAs are emerging as new players in regulation of gene expression. Here, we found that the increase of circRNA-Filip1l mediated by miRNA-1224 in an Ago2-dependent way in the spinal cord is involved in regulation of nociception via targeting Ubr5 Our study reveals a novel epigenetic mechanism of interaction between miRNA and circRNA in chronic inflammation pain.
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15
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Rousset F, Salmon P, Bredl S, Cherpin O, Coelho M, Myburgh R, Alessandrini M, Perny M, Roccio M, Speck RF, Senn P, Krause KH. Optimizing Synthetic miRNA Minigene Architecture for Efficient miRNA Hairpin Concatenation and Multi-target Gene Knockdown. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:351-363. [PMID: 30665184 PMCID: PMC6350225 DOI: 10.1016/j.omtn.2018.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 12/20/2022]
Abstract
Synthetic microRNA (miRNA) minigenes (SMIGs) have a major potential for molecular therapy; however, their optimal architecture still needs to be determined. We have previously optimized the stem structure of miRNA hairpins for efficient gene knockdown. Here, we investigate the overall architecture of SMIGs driven by polymerase II-dependent promoters. When miRNA hairpins were placed directly behind the promoter, gene knockdown was inefficient as compared with constructs containing an intercalated sequence (“spacer”). Spacer sequence was relevant for knockdown efficiency and concatenation potential: GFP-based sequences (even when truncated or including stop codons) were particularly efficient. In contrast, a spacer of similar length based on a CD4 intronic sequence was entirely inefficient. Spacer sequences influenced miRNA steady-state levels without affecting transcript stability. We demonstrate that with an optimized spacer, up to five concatenated hairpins targeting two different genes are efficiently expressed and able to knock down their respective targets. Transplantation of hematopoietic stem cells containing a CCR5 knockdown SMIG demonstrated a sustained in vivo efficacy of our approach. In summary, we have defined features that optimize SMIG efficiency. Based on these results, optimized knockdown of genes of interest, such as the HIV co-receptor CCR5 and the NADPH oxidase subunit p22phox, was achieved.
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Affiliation(s)
- Francis Rousset
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| | - Patrick Salmon
- Department of Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Simon Bredl
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
| | - Ophélie Cherpin
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marta Coelho
- Department of Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Renier Myburgh
- Division of Hematology, University Hospital of Zurich, Zurich, Switzerland
| | - Marco Alessandrini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Michael Perny
- Department of Otorhinolaryngology, Inselspital and University of Bern, Bern, Switzerland
| | - Marta Roccio
- Department of Otorhinolaryngology, Inselspital and University of Bern, Bern, Switzerland
| | - Roberto F Speck
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
| | - Pascal Senn
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Department of Head and Neck Surgery, University Hospital of Geneva, Geneva, Switzerland
| | - Karl Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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16
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Taguchi YH, Wang H. Exploring MicroRNA Biomarkers for Parkinson's Disease from mRNA Expression Profiles. Cells 2018; 7:E245. [PMID: 30563060 PMCID: PMC6315543 DOI: 10.3390/cells7120245] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease (PD) is a chronic, progressive neurodegenerative disease characterized by both motor and nonmotor features. The diagnose of PD is based on a review of patients' signs and symptoms, and neurological and physical examinations. So far, no tests have been devised that can conclusively diagnose PD. In this study, we explore both microRNA and gene biomarkers for PD. Microarray gene expression profiles for PD patients and healthy control are analyzed using a principal component analysis (PCA)-based unsupervised feature extraction (FE). 244 genes are selected to be potential gene biomarkers for PD. In addition, we implement these genes into Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and find that the 15 microRNAs (miRNAs), hsa-miR-92a-3p, 16-5p, 615-3p, 877-3p, 100-5p, 320a, 877-5p, 23a-3p, 484, 23b-3p, 15a-5p, 324-3p, 19b-3p, 7b-5p and 505-3p, significantly target these 244 genes. These miRNAs are shown to be significantly related to PD. This reveals that both selected genes and miRNAs are potential biomarkers for PD.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, 1-13-27 Kasuga, Bunky-ku, Tokyo 112-8551, Japan.
| | - Hsiuying Wang
- Institute of Statistics, National Chiao Tung University, Hsinchu 30010, Taiwan.
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17
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Ahmed N, De Graaf JF, Ahmed N, Foss DV, Delcorde J, Schultz PG, Pezacki JP. Visualization of the Delivery and Release of Small RNAs Using Genetic Code Expansion and Unnatural RNA-Binding Proteins. Bioconjug Chem 2018; 29:3982-3986. [DOI: 10.1021/acs.bioconjchem.8b00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Noreen Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Joanna Fréderique De Graaf
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Nadine Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Dana V. Foss
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Julie Delcorde
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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18
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Pourshafie N, Lee PR, Chen KL, Harmison GG, Bott LC, Fischbeck KH, Rinaldi C. Systemic Delivery of MicroRNA Using Recombinant Adeno-associated Virus Serotype 9 to Treat Neuromuscular Diseases in Rodents. J Vis Exp 2018. [PMID: 30148479 PMCID: PMC6126683 DOI: 10.3791/55724] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RNA interference via the endogenous miRNA pathway regulates gene expression by controlling protein synthesis through post-transcriptional gene silencing. In recent years, miRNA-mediated gene regulation has shown potential for treatment of neurological disorders caused by a toxic gain of function mechanism. However, efficient delivery to target tissues has limited its application. Here we used a transgenic mouse model for spinal and bulbar muscular atrophy (SBMA), a neuromuscular disease caused by polyglutamine expansion in the androgen receptor (AR), to test gene silencing by a newly identified AR-targeting miRNA, miR-298. We overexpressed miR-298 using a recombinant adeno-associated virus (rAAV) serotype 9 vector to facilitate transduction of non-dividing cells. A single tail-vein injection in SBMA mice induced sustained and widespread overexpression of miR-298 in skeletal muscle and motor neurons and resulted in amelioration of the neuromuscular phenotype in the mice.
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Affiliation(s)
- Naemeh Pourshafie
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - Philip R Lee
- Section on Nervous System Development and Plasticity, The Eunice Kennedy Shriver National Institute of Child and Human Development, National Institutes of Health
| | - Ke-Lian Chen
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - George G Harmison
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - Laura C Bott
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - Carlo Rinaldi
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Department of Physiology, Anatomy and Genetics, University of Oxford;
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19
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Su L, Wang C, Zheng C, Wei H, Song X. A meta-analysis of public microarray data identifies biological regulatory networks in Parkinson's disease. BMC Med Genomics 2018; 11:40. [PMID: 29653596 PMCID: PMC5899355 DOI: 10.1186/s12920-018-0357-7] [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: 12/19/2017] [Accepted: 03/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a long-term degenerative disease that is caused by environmental and genetic factors. The networks of genes and their regulators that control the progression and development of PD require further elucidation. METHODS We examine common differentially expressed genes (DEGs) from several PD blood and substantia nigra (SN) microarray datasets by meta-analysis. Further we screen the PD-specific genes from common DEGs using GCBI. Next, we used a series of bioinformatics software to analyze the miRNAs, lncRNAs and SNPs associated with the common PD-specific genes, and then identify the mTF-miRNA-gene-gTF network. RESULT Our results identified 36 common DEGs in PD blood studies and 17 common DEGs in PD SN studies, and five of the genes were previously known to be associated with PD. Further study of the regulatory miRNAs associated with the common PD-specific genes revealed 14 PD-specific miRNAs in our study. Analysis of the mTF-miRNA-gene-gTF network about PD-specific genes revealed two feed-forward loops: one involving the SPRK2 gene, hsa-miR-19a-3p and SPI1, and the second involving the SPRK2 gene, hsa-miR-17-3p and SPI. The long non-coding RNA (lncRNA)-mediated regulatory network identified lncRNAs associated with PD-specific genes and PD-specific miRNAs. Moreover, single nucleotide polymorphism (SNP) analysis of the PD-specific genes identified two significant SNPs, and SNP analysis of the neurodegenerative disease-specific genes identified seven significant SNPs. Most of these SNPs are present in the 3'-untranslated region of genes and are controlled by several miRNAs. CONCLUSION Our study identified a total of 53 common DEGs in PD patients compared with healthy controls in blood and brain datasets and five of these genes were previously linked with PD. Regulatory network analysis identified PD-specific miRNAs, associated long non-coding RNA and feed-forward loops, which contribute to our understanding of the mechanisms underlying PD. The SNPs identified in our study can determine whether a genetic variant is associated with PD. Overall, these findings will help guide our study of the complex molecular mechanism of PD.
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Affiliation(s)
- Lining Su
- Department of Biology of Basic Medical Science College, Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Chunjie Wang
- Department of Basic Medicine, Zhangjiakou University, Zhangjiakou, 75000, Hebei, China
| | - Chenqing Zheng
- Shenzhen RealOmics (Biotech) Co., Ltd, Shenzhen, 518081, Guangdong, China
| | - Huiping Wei
- Department of Biology of Basic Medical Science College, Hebei North University, Zhangjiakou, 075000, Hebei, China.
| | - Xiaoqing Song
- Department of Biology of Basic Medical Science College, Hebei North University, Zhangjiakou, 075000, Hebei, China
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20
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Krauskopf J, Caiment F, van Veldhoven K, Chadeau-Hyam M, Sinharay R, Chung KF, Cullinan P, Collins P, Barratt B, Kelly FJ, Vermeulen R, Vineis P, de Kok TM, Kleinjans JC. The human circulating miRNome reflects multiple organ disease risks in association with short-term exposure to traffic-related air pollution. ENVIRONMENT INTERNATIONAL 2018; 113:26-34. [PMID: 29421404 DOI: 10.1016/j.envint.2018.01.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/17/2018] [Accepted: 01/17/2018] [Indexed: 05/24/2023]
Abstract
Traffic-related air pollution is a complex mixture of particulate matter (PM) and gaseous pollutants, such as nitrogen dioxide (NO2). PM exposure contributes to the pathogenesis of many diseases including several types of cancer, as well as pulmonary, cardiovascular and neurodegenerative diseases. Also exposure to NO2 has been related to increased cardiovascular mortality. In search of an early diagnostic biomarker for improved air pollution-associated health risk assessment, recent human studies have shown that certain circulating miRNAs are altered upon exposure to traffic-related air pollutants. Here, we present for the first time a global analysis of the circulating miRNA genome in an experimental cross-over study of a human population exposed to traffic-related air pollution. By utilizing next-generation sequencing technology and detailed real-time exposure measurements we identified 54 circulating miRNAs to be dose- and pollutant species-dependently associated with PM10, PM2.5, black carbon, ultrafine particles and NO2 already after 2 h of exposure. Bioinformatics analysis suggests that these circulating miRNAs actually reflect the adverse consequences of traffic pollution-induced toxicity in target tissues including the lung, heart, kidney and brain. This study shows the strong potential of circulating miRNAs as novel biomarkers for environmental health risk assessment.
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Affiliation(s)
- Julian Krauskopf
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Karin van Veldhoven
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Marc Chadeau-Hyam
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Rudy Sinharay
- National Heart and Lung Institute, Imperial College London, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, UK
| | - Paul Cullinan
- National Heart and Lung Institute, Imperial College London, UK
| | - Peter Collins
- National Heart and Lung Institute, Imperial College London, UK
| | - Benjamin Barratt
- MRC-PHE Centre for Environment and Health, Analytical & Environmental Sciences, King's College London, UK
| | - Frank J Kelly
- MRC-PHE Centre for Environment and Health, Analytical & Environmental Sciences, King's College London, UK
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Theo M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Jos C Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
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21
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Mo M, Xiao Y, Huang S, Cen L, Chen X, Zhang L, Luo Q, Li S, Yang X, Lin X, Xu P. MicroRNA expressing profiles in A53T mutant alpha-synuclein transgenic mice and Parkinsonian. Oncotarget 2018; 8:15-28. [PMID: 27965467 PMCID: PMC5352072 DOI: 10.18632/oncotarget.13905] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/01/2016] [Indexed: 12/23/2022] Open
Abstract
α-synuclein gene mutations can cause α-synuclein protein aggregation in the midbrain of Parkinson's disease (PD) patients. MicroRNAs (miRNAs) play a key role in the metabolism of α-synuclein but the mechanism involved in synucleinopathy remains unclear. In this study, we investigated the miRNA profiles in A53T-α-synuclein transgenic mice and analyzed the candidate miRNAs in the cerebrospinal fluid (CSF) of PD patients. The 12-month A53T-transgenic mouse displayed hyperactive movement and anxiolytic-like behaviors with α-synuclein aggregation in midbrain. A total of 317,759 total and 289,207 unique small RNA sequences in the midbrain of mice were identified by high-throughput deep sequencing. We found 644 miRNAs were significantly changed in the transgenic mice. Based on the conserved characteristic of miRNAs, we selected 11 candidates from the 40 remarkably expressed miRNAs and explored their expression in 44 CSF samples collected from PD patients. The results revealed that 11 microRNAs were differently expressed in CSF, emphatically as miR-144-5p, miR-200a-3p and miR-542-3p, which were dramatically up-regulated in both A53T-transgenic mice and PD patients, and had a helpful accuracy for the PD prediction. The ordered logistic regression analysis showed that the severity of PD has strong correlation with an up-expression of miR-144-5p, miR-200a-3p and miR-542-3p in CSF. Taken together, our data suggested that miRNAs in CSF, such as miR-144-5p, miR-200a-3p and miR-542-3p, may be useful to the PD diagnosis as potential biomarkers.
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Affiliation(s)
- Mingshu Mo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Yousheng Xiao
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Shuxuan Huang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Luan Cen
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Xiang Chen
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Limin Zhang
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Qin Luo
- Department of Neurology, The Third Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shaomin Li
- Ann Romney Center for Neurologic Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinling Yang
- Department of Neurology, The Third Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xian Lin
- Department of Anatomy & Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong, China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
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22
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Lu J, Xu Y, Quan Z, Chen Z, Sun Z, Qing H. Dysregulated microRNAs in neural system: Implication in pathogenesis and biomarker development in Parkinson’s disease. Neuroscience 2017; 365:70-82. [DOI: 10.1016/j.neuroscience.2017.09.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/03/2023]
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23
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Zhou F, Zhang C, Guan Y, Chen Y, Lu Q, Jie L, Gao H, Du H, Zhang H, Liu Y, Wang X. Screening the expression characteristics of several miRNAs in G93A-SOD1
transgenic mouse: altered expression of miRNA-124 is associated with astrocyte differentiation by targeting Sox2 and Sox9. J Neurochem 2017; 145:51-67. [DOI: 10.1111/jnc.14229] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/18/2017] [Accepted: 09/23/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Fenghua Zhou
- Department of Pathology; Weifang Medical University; Weifang Shandong China
| | - Caixia Zhang
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
| | - Yingjun Guan
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
| | - Yanchun Chen
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
- Department of Neurosurgery; Brigham and Women's Hospital; Harvard Medical School; Boston Massachusetts USA
| | - Qiang Lu
- Department of Pathology; Weifang Medical University; Weifang Shandong China
| | - Linlin Jie
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
| | - Hailing Gao
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
| | - Hongmei Du
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
| | - Haoyun Zhang
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
| | - Yongxin Liu
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
| | - Xin Wang
- Department of Histology and Embryology; Weifang Medical University; Weifang Shandong China
- Department of Neurosurgery; Brigham and Women's Hospital; Harvard Medical School; Boston Massachusetts USA
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Wu Q, Xu T, Liu Y, Li Y, Yuan J, Yao W, Xu Q, Yan W, Ni C. miR-1224-5p Mediates Mitochondrial Damage to Affect Silica-Induced Pulmonary Fibrosis by Targeting BECN1. Int J Mol Sci 2017; 18:ijms18112357. [PMID: 29112159 PMCID: PMC5713326 DOI: 10.3390/ijms18112357] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 12/20/2022] Open
Abstract
Silicosis is associated with fibroblast proliferation and extracellular matrix deposition in lung tissues. The dysregulation of miR-1224-5p has been implicated in several human cancers; however, the expression and function of miR-1224-5p in silicosis is unknown. The mitochondrial dysfunctions play critical roles in some diseases, but how these processes are regulated in silicosis remains limited. Here, we explored the role of miR-1224-5p in a mouse model of silicosis. We showed that the expression of miR-1224-5p is increased both in lung tissues of silica-induced pulmonary fibrosis and fibroblasts exposed to TGF-β1. Repression of miR-1224-5p expression attenuated silica-induced fibrotic progression in vivo and TGF-β1-induced myofibroblast differentiation in vitro. Additionally, we demonstrated that miR-1224-5p facilitated silica-induced pulmonary fibrosis primarily by repressing one of target genes, BECN1, thereby blocking PARK2 translocation to mitochondria and inducing the accumulation of damaged mitochondria. Furthermore, the activation of PDGFR signal mediated by mitochondrial damage and insufficient mitophagy resulted in myofibroblast differentiation. Collectively, these data indicated that miR-1224-5p exerts key functions in silica-induced pulmonary fibrosis and may represent a potential therapeutic target for silicosis.
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Affiliation(s)
- Qiuyun Wu
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, China.
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Tiantian Xu
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Yi Liu
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Yan Li
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Jiali Yuan
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Wenxi Yao
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Qi Xu
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Weiwen Yan
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Chunhui Ni
- Department of Occupational Medicine and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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Curtis HJ, Seow Y, Wood MJA, Varela MA. Knockdown and replacement therapy mediated by artificial mirtrons in spinocerebellar ataxia 7. Nucleic Acids Res 2017; 45:7870-7885. [PMID: 28575281 PMCID: PMC5569705 DOI: 10.1093/nar/gkx483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 05/26/2017] [Indexed: 12/13/2022] Open
Abstract
We evaluate a knockdown-replacement strategy mediated by mirtrons as an alternative to allele-specific silencing using spinocerebellar ataxia 7 (SCA7) as a model. Mirtrons are introns that form pre-microRNA hairpins after splicing, producing RNAi effectors not processed by Drosha. Mirtron mimics may therefore avoid saturation of the canonical processing pathway. This method combines gene silencing mediated by an artificial mirtron with delivery of a functional copy of the gene such that both elements of the therapy are always expressed concurrently, minimizing the potential for undesirable effects and preserving wild-type function. This mutation- and single nucleotide polymorphism-independent method could be crucial in dominant diseases that feature both gain- and loss-of-function pathologies or have a heterogeneous genetic background. Here we develop mirtrons against ataxin 7 with silencing efficacy comparable to shRNAs, and introduce silent mutations into an ataxin 7 transgene such that it is resistant to their effect. We successfully express the transgene and one mirtron together from a single construct. Hence, we show that this method can be used to silence the endogenous allele of ataxin 7 and replace it with an exogenous copy of the gene, highlighting the efficacy and transferability across patient genotypes of this approach.
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Affiliation(s)
- Helen J Curtis
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK.,Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford OX2 6GG, UK
| | - Yiqi Seow
- Molecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Singapore
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Miguel A Varela
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
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26
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Recent developments in circulating biomarkers in Parkinson’s disease: the potential use of miRNAs in a clinical setting. Bioanalysis 2016; 8:2497-2518. [DOI: 10.4155/bio-2016-0166] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder, affecting 5% of the elderly population. PD diagnosis is still based on the identification of neuromotor symptoms although nonmotor manifestations emerge years prior to diagnosis. The discovery of biomarkers at the earliest stages of PD is of extreme interest. miRNAs have been considered potential biomarkers for neurodegenerative diseases, but only a limited number have been found to be PD related. This review focuses on the current findings in the field of circulating miRNAs in PD and the challenges surrounding clinical utility and validation. We briefly describe the more established circulating biomarkers in PD and provide a more thorough review of miRNAs differentially expressed in PD. We highlight their potential for being considered as biomarkers for diagnosis while emphasizing the challenges for adequate validation of the findings and how miRNAs can be envisioned in a clinical setting satisfying regulatory bodies.
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Bofill-De Ros X, Gu S. Guidelines for the optimal design of miRNA-based shRNAs. Methods 2016; 103:157-66. [PMID: 27083402 PMCID: PMC4921303 DOI: 10.1016/j.ymeth.2016.04.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 03/28/2016] [Accepted: 04/04/2016] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is an extremely useful tool for inhibiting gene expression. It can be triggered by transfected synthetic small interfering RNA (siRNA) or by expressed small hairpin RNA (shRNA). The cellular machinery processes the latter into siRNA in vivo. shRNA is preferred or required in genetic screens and specific RNAi approaches in gene therapy settings. Despite its many successes, the field of shRNAs faces many challenges. Insufficient knockdowns and off-target effects become obstacles for shRNA usage in many applications. Numerous failures are triggered by pitfalls in shRNA design that is often associated with impoverished biogenesis. Here, based on current understanding of the miRNA maturation pathway, we discuss the principles of different shRNA design (pre-miRNA-like, pri-miRNA-like and Ago-shRNA) with an emphasis on the RNA structure. We also provide detailed instructions for an optimal design of pre-miRNA-like shRNA.
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Affiliation(s)
- Xavier Bofill-De Ros
- Gene Regulation and Chromosome Biology Laboratory, Center For Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Shuo Gu
- Gene Regulation and Chromosome Biology Laboratory, Center For Cancer Research, National Cancer Institute, Frederick, MD, United States.
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28
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Butkytė S, Čiupas L, Jakubauskienė E, Vilys L, Mocevicius P, Kanopka A, Vilkaitis G. Splicing-dependent expression of microRNAs of mirtron origin in human digestive and excretory system cancer cells. Clin Epigenetics 2016; 8:33. [PMID: 27019673 PMCID: PMC4807562 DOI: 10.1186/s13148-016-0200-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/18/2016] [Indexed: 11/17/2022] Open
Abstract
Background An abundant class of intronic microRNAs (miRNAs) undergoes atypical Drosha-independent biogenesis in which the spliceosome governs the excision of hairpin miRNA precursors, called mirtrons. Although nearly 500 splicing-dependent miRNA candidates have been recently predicted via bioinformatic analysis of human RNA-Seq datasets, only a few of them have been experimentally validated. The detailed mechanism of miRNA processing by the splicing machinery and the roles of mirtronic miRNAs in cancer are yet to be uncovered. Methods We experimentally examined whether biogenesis of certain miRNAs is under a splicing control by analyzing their expression levels in response to alterations in the 5′- and 3′-splice sites of a series of intron-containing minigenes carrying appropriate miRNAs. The expression levels of the miRNAs processed from mirtrons were determined by quantitative real-time PCR in five digestive tract (pancreas PANC-1, SU.86.86, T3M4, stomach KATOIII, colon HCT116) and two excretory system (kidney CaKi-1, 786-O) carcinoma cell lines as well as in pancreatic, stomach, and colorectal tumors. Transiently expressed SRSF1 and SRSF2 splicing factors were quantified by western blotting in the nuclear fractions of HCT116 cells. Results We found that biogenesis of the human hsa-miR-1227-3p, hsa-miR-1229-3p, and hsa-miR-1236-3p is splicing-dependent; therefore, these miRNAs can be assigned to the class of miRNAs processed by a non-canonical mirtron pathway. The expression analysis revealed a differential regulation of human mirtronic miRNAs in various cancer cell lines and tumors. In particular, hsa-miR-1229-3p is selectively upregulated in the pancreatic and stomach cancer cell lines derived from metastatic sites. Compared with the healthy controls, the expression of hsa-miR-1226-3p was significantly higher in stomach tumors but extensively downregulated in colorectal tumors. Furthermore, we provided evidence that overexpression of SRSF1 or SRSF2 can upregulate the processing of individual mirtronic miRNAs in HCT116 cells. Conclusions An interplay of different splicing factors, such as SRSF1 or SRSF2, may alter the levels of miRNAs of mirtron origin in a cell. Our findings underline the specific expression profiles of mirtronic miRNAs in colorectal, stomach, and pancreatic cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0200-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stasė Butkytė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Laurynas Čiupas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Eglė Jakubauskienė
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Laurynas Vilys
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Paulius Mocevicius
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Arvydas Kanopka
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Giedrius Vilkaitis
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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29
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Hoss AG, Labadorf A, Beach TG, Latourelle JC, Myers RH. microRNA Profiles in Parkinson's Disease Prefrontal Cortex. Front Aging Neurosci 2016; 8:36. [PMID: 26973511 PMCID: PMC4772525 DOI: 10.3389/fnagi.2016.00036] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/10/2016] [Indexed: 01/17/2023] Open
Abstract
Objective: The goal of this study was to compare the microRNA (miRNA) profile of Parkinson's disease (PD) frontal cortex with normal control brain, allowing for the identification of PD specific signatures as well as study the disease-related phenotypes of onset age and dementia. Methods: Small RNA sequence analysis was performed from prefrontal cortex for 29 PD samples and 33 control samples. After sample QC, normalization and batch correction, linear regression was employed to identify miRNAs altered in PD, and a PD classifier was developed using weighted voting class prediction. The relationship of miRNA levels to onset age and PD with dementia (PDD) was also characterized in case-only analyses. Results: One twenty five miRNAs were differentially expressed in PD at a genome-wide level of significance (FDR q < 0.05). A set of 29 miRNAs classified PD from non-diseased brain (93.9% specificity, 96.6% sensitivity). The majority of differentially expressed miRNAs (105/125) showed an ordinal relationship from control, to PD without dementia (PDN), to PDD. Among PD brains, 36 miRNAs classified PDD from PDN (sensitivity = 81.2%, specificity = 88.9%). Among differentially expressed miRNAs, miR-10b-5p had a positive association with onset age (q = 4.7e-2). Conclusions: Based on cortical miRNA levels, PD brains were accurately classified from non-diseased brains. Additionally, the PDD miRNA profile exhibited a more severe pattern of alteration among those differentially expressed in PD. To evaluate the clinical utility of miRNAs as potential clinical biomarkers, further characterization and testing of brain-related miRNA alterations in peripheral biofluids is warranted.
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Affiliation(s)
- Andrew G Hoss
- Department of Neurology, Boston University School of MedicineBoston, MA, USA; Graduate Program in Genetics and Genomics, Boston University School of MedicineBoston, MA, USA
| | - Adam Labadorf
- Department of Neurology, Boston University School of MedicineBoston, MA, USA; Bioinformatics Program, Boston UniversityBoston, MA, USA
| | | | - Jeanne C Latourelle
- Department of Neurology, Boston University School of Medicine Boston, MA, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of MedicineBoston, MA, USA; Graduate Program in Genetics and Genomics, Boston University School of MedicineBoston, MA, USA; Bioinformatics Program, Boston UniversityBoston, MA, USA; Genome Science Institute, Boston University School of MedicineBoston, MA, USA
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30
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MiR-298 Counteracts Mutant Androgen Receptor Toxicity in Spinal and Bulbar Muscular Atrophy. Mol Ther 2016; 24:937-45. [PMID: 26755334 PMCID: PMC4881766 DOI: 10.1038/mt.2016.13] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/04/2016] [Indexed: 01/18/2023] Open
Abstract
Spinal and bulbar muscular atrophy (SBMA) is a currently untreatable adult-onset neuromuscular disease caused by expansion of a polyglutamine repeat in the androgen receptor (AR). In SBMA, as in other polyglutamine diseases, a toxic gain of function in the mutant protein is an important factor in the disease mechanism; therefore, reducing the mutant protein holds promise as an effective treatment strategy. In this work, we evaluated a microRNA (miRNA) to reduce AR expression. From a list of predicted miRNAs that target human AR, we selected microRNA-298 (miR-298) for its ability to downregulate AR mRNA and protein levels when transfected in cells overexpressing wild-type and mutant AR and in SBMA patient-derived fibroblasts. We showed that miR-298 directly binds to the 3'-untranslated region of the human AR transcript, and counteracts AR toxicity in vitro. Intravenous delivery of miR-298 with adeno-associated virus serotype 9 vector resulted in efficient transduction of muscle and spinal cord and amelioration of the disease phenotype in SBMA mice. Our findings support the development of miRNAs as a therapeutic strategy for SBMA and other neurodegenerative disorders caused by toxic proteins.
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31
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Zhang Q, Kim YC, Narayanan NS. Disease-modifying therapeutic directions for Lewy-Body dementias. Front Neurosci 2015; 9:293. [PMID: 26347604 PMCID: PMC4542461 DOI: 10.3389/fnins.2015.00293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/04/2015] [Indexed: 12/26/2022] Open
Abstract
Dementia with Lewy bodies (DLB) is the second leading cause of dementia following Alzheimer's disease (AD) and accounts for up to 25% of all dementia. DLB is distinct from AD in that it involves extensive neuropsychiatric symptoms as well as motor symptoms, leads to enormous societal costs in terms of direct medical care and is associated with high financial and caregiver costs. Although, there are no disease-modifying therapies for DLB, we review several new therapeutic directions in treating DLB. We discuss progress in strategies to decrease the level of alpha-synuclein, to prevent the cell to cell transmission of misfolded alpha-synuclein, and the potential of brain stimulation in DLB.
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Affiliation(s)
- Qiang Zhang
- Department of Neurology, University of Iowa Iowa City, IA, USA ; Physician Scientist Training Program, University of Iowa Iowa City, IA, USA
| | - Young-Cho Kim
- Department of Neurology, University of Iowa Iowa City, IA, USA
| | - Nandakumar S Narayanan
- Department of Neurology, University of Iowa Iowa City, IA, USA ; Aging Mind and Brain Initiative, Carver College of Medicine, University of Iowa Iowa City, IA, USA
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32
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Kock KH, Kong KW, Hoon S, Seow Y. Functional VEGFA knockdown with artificial 3'-tailed mirtrons defined by 5' splice site and branch point. Nucleic Acids Res 2015; 43:6568-78. [PMID: 26089392 PMCID: PMC4513878 DOI: 10.1093/nar/gkv617] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/02/2015] [Indexed: 11/28/2022] Open
Abstract
Mirtrons are introns that form pre-miRNA hairpins after splicing to produce RNA interference (RNAi) effectors distinct from Drosha-dependent intronic miRNAs, and will be especially useful for co-delivery of coding genes and RNAi. A specific family of mirtrons – 3′-tailed mirtrons – has hairpins precisely defined on the 5′ end by the 5′ splice site and 3′ end by the branch point. Here, we present design principles for artificial 3′-tailed mirtrons and demonstrate, for the first time, efficient gene knockdown with tailed mirtrons within eGFP coding region. These artificial tailed mirtrons, unlike canonical mirtrons, have very few sequence design restrictions. Tailed mirtrons targeted against VEGFA mRNA, the misregulation of which is causative of several disorders including cancer, achieved significant levels of gene knockdown. Tailed mirtron-mediated knockdown was further shown to be splicing-dependent, and at least as effective as equivalent artificial intronic miRNAs, with the added advantage of very defined cleavage sites for generation of mature miRNA guide strands. Further development and exploitation of this unique mirtron biogenesis pathway for therapeutic RNAi coupled into protein-expressing genes can potentially enable the development of precisely controlled combinatorial gene therapy.
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Affiliation(s)
- Kian Hong Kock
- Molecular Engineering Laboratory, Biomedical Medical Sciences Institutes, 61 Biopolis Drive Proteos #03-13 Singapore 138673
| | - Kiat Whye Kong
- Molecular Engineering Laboratory, Biomedical Medical Sciences Institutes, 61 Biopolis Drive Proteos #03-13 Singapore 138673
| | - Shawn Hoon
- Molecular Engineering Laboratory, Biomedical Medical Sciences Institutes, 61 Biopolis Drive Proteos #03-13 Singapore 138673 School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yiqi Seow
- Molecular Engineering Laboratory, Biomedical Medical Sciences Institutes, 61 Biopolis Drive Proteos #03-13 Singapore 138673
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Targeting alpha-synuclein with a microRNA-embedded silencing vector in the rat substantia nigra: positive and negative effects. Brain Res 2014; 1550:47-60. [PMID: 24463035 DOI: 10.1016/j.brainres.2014.01.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/16/2013] [Accepted: 01/10/2014] [Indexed: 12/31/2022]
Abstract
BACKGROUND Alpha-synuclein (SNCA) downregulation shows therapeutic potential for synucleinopathies, including Parkinson's disease (PD). Previously we showed that human (h)SNCA gene silencing using a short hairpin (sh)RNA in rat substantia nigra (SN) protects against a hSNCA-induced forelimb deficit, but not dopamine (DA) neuron loss. Furthermore, the shRNA increases cell death in vitro, but the same target sequence embedded in a microRNA30 transcript (mir30-hSNCA) does not. OBJECTIVE Examine hSNCA gene silencing using mir30-hSNCA in vivo. METHODS Rats were stereotaxically injected into one SN with adeno-associated virus serotype 2/8 (AAV)-hSNCA, AAV-hSNCA plus AAV-mir30-SNCA or AAV-hSNCA plus a control non-silencing mir30-embedded siRNA and DA neuron markers and associated behavior were examined. RESULTS AAV2/8-mediated SN hSNCA expression induces a forelimb deficit and tyrosine hydroxylase-immunoreactive (TH-IR) neuron loss. hSNCA gene silencing using mir30-hSNCA protects against this forelimb deficit at 2 m and ameliorates TH-IR neuron loss. Striatal (ST) TH-IR fiber density and DA markers, assessed by western blot, are unaffected by AAV-hSNCA alone. Co-expression of either silencing vector reduces ST TH-IR fibers, panTH in SN and Ser40 phosphorylated TH in SN and ST, but does not affect vesicular monoamine transporter-2. However, hSNCA gene silencing promotes partial TH-IR fiber recovery by 2 m. Co-expression of either silencing vector also induces SN inflammation, although some recovery was observed by 2 m in hSNCA-silenced SN. CONCLUSION hSNCA gene silencing with AAV-mir30-hSNCA has positive effects on forelimb behavior and SN DA neurons, which are compromised by inflammation and reduced TH expression, suggesting that AAV2/8-mir30-hSNCA-mediated gene silencing, although promising in vitro, is not a candidate for therapeutic translation for PD.
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Douglas MR. Gene therapy for Parkinson's disease: state-of-the-art treatments for neurodegenerative disease. Expert Rev Neurother 2014; 13:695-705. [PMID: 23739006 DOI: 10.1586/ern.13.58] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pharmacological and surgical treatments offer symptomatic benefits to patients with Parkinson's disease; however, as the condition progresses, patients experience gradual worsening in symptom control, with the development of a range of disabling complications. In addition, none of the currently available therapies have convincingly shown disease-modifying effects - either in slowing or reversing the disease. These problems have led to extensive research into the possible use of gene therapy as a treatment for Parkinson's disease. Several treatments have reached human clinical trial stages, providing important information on the risks and benefits of this novel therapeutic approach, and the tantalizing promise of improved control of this currently incurable neurodegenerative disorder.
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Affiliation(s)
- Michael R Douglas
- School of Clinical and Experimental Medicine, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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35
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Goodall EF, Heath PR, Bandmann O, Kirby J, Shaw PJ. Neuronal dark matter: the emerging role of microRNAs in neurodegeneration. Front Cell Neurosci 2013; 7:178. [PMID: 24133413 PMCID: PMC3794211 DOI: 10.3389/fncel.2013.00178] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 09/21/2013] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small, abundant RNA molecules that constitute part of the cell's non-coding RNA “dark matter.” In recent years, the discovery of miRNAs has revolutionised the traditional view of gene expression and our understanding of miRNA biogenesis and function has expanded. Altered expression of miRNAs is increasingly recognized as a feature of many disease states, including neurodegeneration. Here, we review the emerging role for miRNA dysfunction in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis (ALS) and Huntington's disease pathogenesis. We emphasize the complex nature of gene regulatory networks and the need for systematic studies, with larger sample cohorts than have so far been reported, to reveal the most important miRNA regulators in disease. Finally, miRNA diversity and their potential to target multiple pathways, offers novel clinical applications for miRNAs as biomarkers and therapeutic agents in neurodegenerative diseases.
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Affiliation(s)
- Emily F Goodall
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield Sheffield, UK
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36
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Nielsen TT, Nielsen JE. Antisense gene silencing: therapy for neurodegenerative disorders? Genes (Basel) 2013; 4:457-84. [PMID: 24705213 PMCID: PMC3924827 DOI: 10.3390/genes4030457] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/11/2013] [Accepted: 08/13/2013] [Indexed: 01/17/2023] Open
Abstract
Since the first reports that double-stranded RNAs can efficiently silence gene expression in C. elegans, the technology of RNA interference (RNAi) has been intensively exploited as an experimental tool to study gene function. With the subsequent discovery that RNAi could also be applied to mammalian cells, the technology of RNAi expanded from being a valuable experimental tool to being an applicable method for gene-specific therapeutic regulation, and much effort has been put into further refinement of the technique. This review will focus on how RNAi has developed over the years and how the technique is exploited in a pre-clinical and clinical perspective in relation to neurodegenerative disorders.
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Affiliation(s)
- Troels T Nielsen
- Danish Dementia Research Centre, Neurogenetics Clinic, Department of Neurology, Section 6702, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark.
| | - Jørgen E Nielsen
- Danish Dementia Research Centre, Neurogenetics Clinic, Department of Neurology, Section 6702, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
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37
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Zhou F, Guan Y, Chen Y, Zhang C, Yu L, Gao H, Du H, Liu B, Wang X. miRNA-9 expression is upregulated in the spinal cord of G93A-SOD1 transgenic mice. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2013; 6:1826-1838. [PMID: 24040447 PMCID: PMC3759489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/03/2013] [Indexed: 06/02/2023]
Abstract
The pathogenesis of amyotrophic lateral sclerosis (ALS) remains unclear. Accumulating evidence indicates that various miRNAs expressed in a spatially and temporally controlled manner in the nervous system have an important function in the development of neurodegenerative diseases. The present study aimed to determine the expression and cellular distribution of miRNA-9 in the spinal cord of G93A-SOD1 mutant mice at different time points (post-natal 95, 108 and 122 d). miRNA expression was evaluated by microarray analysis; differentially expressed miRNAs were validated by RT-qPCR. The cellular distribution of miRNA-9 was analyzed by in-situ hybridization. Microarray results indicated for the first time that various miRNAs were differentially expressed between the G93A-SOD1 mutant mice and the littermate control mice. miRNA-9 expression was upregulated at 95, 108, and 122 d as validated by microarray analysis, RT-qPCR, and ISH. ISH results also showed that the miRNA-9-positive cells mainly expressed in the cytoplasm were located in the dorsal horn and the ventral horn of the spinal cord. The majority of miRNA-9-positive cells were located in the ventral horn of the gray matter, the locus of neurodegeneration. These results indicated that the differential expression of miRNA-9 may have an important function in the pathogenesis of G93A-SOD1 transgenic mice.
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Affiliation(s)
- Fenghua Zhou
- Department of Pathology, Weifang Medical UniversityWeifang, Shandong, P. R. China
| | - Yingjun Guan
- Department of Histology and Embryology, Weifang Medical UniversityWeifang, Shandong, P. R. China
| | - Yanchun Chen
- Department of Histology and Embryology, Weifang Medical UniversityWeifang, Shandong, P. R. China
| | - Caixia Zhang
- Department of Histology and Embryology, Weifang Medical UniversityWeifang, Shandong, P. R. China
| | - Li Yu
- Department of Histology and Embryology, Weifang Medical UniversityWeifang, Shandong, P. R. China
| | - Hailing Gao
- Department of Histology and Embryology, Weifang Medical UniversityWeifang, Shandong, P. R. China
| | - Hongmei Du
- Department of Histology and Embryology, Weifang Medical UniversityWeifang, Shandong, P. R. China
| | - Bing Liu
- Department of Histology and Embryology, Weifang Medical UniversityWeifang, Shandong, P. R. China
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical SchoolBoston, MA, USA
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Ramachandran PS, Keiser MS, Davidson BL. Recent advances in RNA interference therapeutics for CNS diseases. Neurotherapeutics 2013; 10:473-85. [PMID: 23589092 PMCID: PMC3701762 DOI: 10.1007/s13311-013-0183-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Over the last decade, RNA interference technology has shown therapeutic promise in rodent models of dominantly inherited brain diseases, including those caused by polyglutamine repeat expansions in the coding region of the affected gene. For some of these diseases, proof-of concept studies in model organisms have transitioned to safety testing in larger animal models, such as the nonhuman primate. Here, we review recent progress on RNA interference-based therapies in various model systems. We also highlight outstanding questions or concerns that have emerged as a result of an improved (and ever advancing) understanding of the technologies employed.
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Affiliation(s)
| | - Megan S. Keiser
- />Interdisciplinary program in Neuroscience, University of Iowa, Iowa City, IA USA
| | - Beverly L. Davidson
- />Interdisciplinary program in Genetics, University of Iowa, Iowa City, IA 52242 USA
- />Interdisciplinary program in Neuroscience, University of Iowa, Iowa City, IA USA
- />Department of Internal Medicine, University of Iowa, Iowa City, USA
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