1
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Zou C, Zan X, Jia Z, Zheng L, Gu Y, Liu F, Han Y, Xu C, Wu A, Zhi Q. Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives. Clin Transl Med 2023; 13:e1479. [PMID: 37983927 PMCID: PMC10659771 DOI: 10.1002/ctm2.1479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/07/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD). METHODS Our review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next-generation sequencing (NGS) for AS events in IBD have been also discussed. RESULTS Available evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis-associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro-fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third-generation sequencing (TGS), single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), will be desired with great expectations. CONCLUSIONS To our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.
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Affiliation(s)
- Chentao Zou
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xinquan Zan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhenyu Jia
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Lu Zheng
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yijie Gu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Fei Liu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Ye Han
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chunfang Xu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Airong Wu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qiaoming Zhi
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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2
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Chan JNM, Sánchez-Vidaña DI, Anoopkumar-Dukie S, Li Y, Benson Wui-Man L. RNA-binding protein signaling in adult neurogenesis. Front Cell Dev Biol 2022; 10:982549. [PMID: 36187492 PMCID: PMC9523427 DOI: 10.3389/fcell.2022.982549] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
The process of neurogenesis in the brain, including cell proliferation, differentiation, survival, and maturation, results in the formation of new functional neurons. During embryonic development, neurogenesis is crucial to produce neurons to establish the nervous system, but the process persists in certain brain regions during adulthood. In adult neurogenesis, the production of new neurons in the hippocampus is accomplished via the division of neural stem cells. Neurogenesis is regulated by multiple factors, including gene expression at a temporal scale and post-transcriptional modifications. RNA-binding Proteins (RBPs) are known as proteins that bind to either double- or single-stranded RNA in cells and form ribonucleoprotein complexes. The involvement of RBPs in neurogenesis is crucial for modulating gene expression changes and posttranscriptional processes. Since neurogenesis affects learning and memory, RBPs are closely associated with cognitive functions and emotions. However, the pathways of each RBP in adult neurogenesis remain elusive and not clear. In this review, we specifically summarize the involvement of several RBPs in adult neurogenesis, including CPEB3, FXR2, FMRP, HuR, HuD, Lin28, Msi1, Sam68, Stau1, Smaug2, and SOX2. To understand the role of these RBPs in neurogenesis, including cell proliferation, differentiation, survival, and maturation as well as posttranscriptional gene expression, we discussed the protein family, structure, expression, functional domain, and region of action. Therefore, this narrative review aims to provide a comprehensive overview of the RBPs, their function, and their role in the process of adult neurogenesis as well as to identify possible research directions on RBPs and neurogenesis.
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Affiliation(s)
- Jackie Ngai-Man Chan
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - Dalinda Isabel Sánchez-Vidaña
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- Mental Health Research Centre, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | | | - Yue Li
- State Key Laboratory of Component-Based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lau Benson Wui-Man
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- Mental Health Research Centre, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- *Correspondence: Lau Benson Wui-Man,
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3
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Titus MB, Chang AW, Olesnicky EC. Exploring the Diverse Functional and Regulatory Consequences of Alternative Splicing in Development and Disease. Front Genet 2021; 12:775395. [PMID: 34899861 PMCID: PMC8652244 DOI: 10.3389/fgene.2021.775395] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a fundamental mechanism of eukaryotic RNA regulation that increases the transcriptomic and proteomic complexity within an organism. Moreover, alternative splicing provides a framework for generating unique yet complex tissue- and cell type-specific gene expression profiles, despite using a limited number of genes. Recent efforts to understand the negative consequences of aberrant splicing have increased our understanding of developmental and neurodegenerative diseases such as spinal muscular atrophy, frontotemporal dementia and Parkinsonism linked to chromosome 17, myotonic dystrophy, and amyotrophic lateral sclerosis. Moreover, these studies have led to the development of innovative therapeutic treatments for diseases caused by aberrant splicing, also known as spliceopathies. Despite this, a paucity of information exists on the physiological roles and specific functions of distinct transcript spliceforms for a given gene. Here, we will highlight work that has specifically explored the distinct functions of protein-coding spliceforms during development. Moreover, we will discuss the use of alternative splicing of noncoding exons to regulate the stability and localization of RNA transcripts.
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Affiliation(s)
- M Brandon Titus
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Adeline W Chang
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Eugenia C Olesnicky
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
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4
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Leung SK, Jeffries AR, Castanho I, Jordan BT, Moore K, Davies JP, Dempster EL, Bray NJ, O'Neill P, Tseng E, Ahmed Z, Collier DA, Jeffery ED, Prabhakar S, Schalkwyk L, Jops C, Gandal MJ, Sheynkman GM, Hannon E, Mill J. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. Cell Rep 2021; 37:110022. [PMID: 34788620 PMCID: PMC8609283 DOI: 10.1016/j.celrep.2021.110022] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 07/30/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community. There is widespread transcript diversity in the cortex and many novel transcripts Some genes display big differences in isoform number between human and mouse cortex There is evidence of differential transcript usage between human fetal and adult cortex There are many novel isoforms of genes associated with human brain disease
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Key Words
- isoform, transcript, expression, brain, cortex, mouse, human, adult, fetal, long-read sequencing, alternative splicing
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Affiliation(s)
| | | | - Isabel Castanho
- University of Exeter, Exeter, UK; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ben T Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | | | | | | | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | | | - Connor Jops
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; UVA Cancer Center, University of Virginia, Charlottesville, VA, USA
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5
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Zhang J, Chi Y, Feng L. The mechanism of degradation of alizarin red by a white-rot fungus Trametes gibbosa. BMC Biotechnol 2021; 21:64. [PMID: 34740358 PMCID: PMC8570020 DOI: 10.1186/s12896-021-00720-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Background Alizarin red (AR) is a typical anthraquinone dye, and the resulting wastewater is toxic and difficult to remove. A study showed that the white rot fungus Trametes gibbosa (T. gibbosa) can degrade dye wastewater by decolorization and has its own enzyme-producing traits. Methods In this study, transcriptome sequencing was performed after alizarin red treatment for 0, 3, 7, 10, and 14 h. The key pathways and key enzymes involved in alizarin red degradation were found to be through the analysis of KEGG and GO. The Glutathione S-transferase (GST), manganese peroxidase (MnP) and laccase activities of T. gibbosa treated with alizarin red for 0–14 h were detected. LC–MS and GC–MS analyses of alizarin red decomposition products after 7 h and 14 h were performed. Results The glutathione metabolic pathway ko00480, and the key enzymes GST, MnP, laccase and CYP450 were selected. Most of the genes encoding these enzymes were upregulated under alizarin red conditions. The GST activity increased 1.8 times from 117.55 U/mg prot at 0 h to 217.03 U/mg prot at 14 h. The MnP activity increased 2.9 times from 6.45 to 18.55 U/L. The laccase activity increased 3.7 times from 7.22 to 27.28 U/L. Analysis of the alizarin red decolourization rate showed that the decolourization rate at 14 h reached 20.21%. The main degradation intermediates were found to be 1,4-butene diacid, phthalic acid, 1,1-diphenylethylene, 9,10-dihydroanthracene, 1,2-naphthalene dicarboxylic acid, bisphenol, benzophenol-5,2-butene, acrylaldehyde, and 1-butylene, and the degradation process of AR was inferred. Overall, 1,4-butene diacid is the most important intermediate product produced by AR degradation. Conclusions The glutathione metabolic pathway was the key pathway for AR degradation. GST, MnP, laccase and CYP450 were the key enzymes for AR degradation. 1,4-butene diacid is the most important intermediate product. This study explored the process of AR biodegradation at the molecular and biochemical levels and provided a theoretical basis for its application in practical production. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00720-8.
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Affiliation(s)
- Jian Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Yujie Chi
- School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Lianrong Feng
- School of Forestry, Northeast Forestry University, Harbin, 150040, China.,Liaoning Provincial Institute of Poplar, Gaizhou, 115213, Liaoning, China
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6
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RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis. Int J Mol Sci 2021; 22:ijms222111870. [PMID: 34769301 PMCID: PMC8584444 DOI: 10.3390/ijms222111870] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/16/2021] [Accepted: 10/26/2021] [Indexed: 02/06/2023] Open
Abstract
The intrinsic cellular heterogeneity and molecular complexity of the mammalian nervous system relies substantially on the dynamic nature and spatiotemporal patterning of gene expression. These features of gene expression are achieved in part through mechanisms involving various epigenetic processes such as DNA methylation, post-translational histone modifications, and non-coding RNA activity, amongst others. In concert, another regulatory layer by which RNA bases and sugar residues are chemically modified enhances neuronal transcriptome complexity. Similar RNA modifications in other systems collectively constitute the cellular epitranscriptome that integrates and impacts various physiological processes. The epitranscriptome is dynamic and is reshaped constantly to regulate vital processes such as development, differentiation and stress responses. Perturbations of the epitranscriptome can lead to various pathogenic conditions, including cancer, cardiovascular abnormalities and neurological diseases. Recent advances in next-generation sequencing technologies have enabled us to identify and locate modified bases/sugars on different RNA species. These RNA modifications modulate the stability, transport and, most importantly, translation of RNA. In this review, we discuss the formation and functions of some frequently observed RNA modifications—including methylations of adenine and cytosine bases, and isomerization of uridine to pseudouridine—at various layers of RNA metabolism, together with their contributions to abnormal physiological conditions that can lead to various neurodevelopmental and neurological disorders.
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7
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Jakubauskienė E, Kanopka A. Alternative Splicing and Hypoxia Puzzle in Alzheimer's and Parkinson's Diseases. Genes (Basel) 2021; 12:genes12081272. [PMID: 34440445 PMCID: PMC8394294 DOI: 10.3390/genes12081272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/08/2023] Open
Abstract
Alternative pre-mRNA splicing plays a very important role in expanding protein diversity as it generates numerous transcripts from a single protein-coding gene. Therefore, alterations lead this process to neurological human disorders, including Alzheimer’s and Parkinson’s diseases. Moreover, accumulating evidence indicates that the splicing machinery highly contributes to the cells’ ability to adapt to different altered cellular microenvironments, such as hypoxia. Hypoxia is known to have an effect on the expression of proteins involved in a multiple of biological processes, such as erythropoiesis, angiogenesis, and neurogenesis, and is one of the important risk factors in neuropathogenesis. In this review, we discuss the current knowledge of alternatively spliced genes, which, as it is reported, are associated with Alzheimer’s and Parkinson’s diseases. Additionally, we highlight the possible influence of cellular hypoxic microenvironment for the formation of mRNA isoforms contributing to the development of these neurodegenerative diseases.
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8
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Li D, McIntosh CS, Mastaglia FL, Wilton SD, Aung-Htut MT. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl Neurodegener 2021; 10:16. [PMID: 34016162 PMCID: PMC8136212 DOI: 10.1186/s40035-021-00240-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is a fundamental step in eukaryotic gene expression that systematically removes non-coding regions (introns) and ligates coding regions (exons) into a continuous message (mature mRNA). This process is highly regulated and can be highly flexible through a process known as alternative splicing, which allows for several transcripts to arise from a single gene, thereby greatly increasing genetic plasticity and the diversity of proteome. Alternative splicing is particularly prevalent in neuronal cells, where the splicing patterns are continuously changing to maintain cellular homeostasis and promote neurogenesis, migration and synaptic function. The continuous changes in splicing patterns and a high demand on many cis- and trans-splicing factors contribute to the susceptibility of neuronal tissues to splicing defects. The resultant neurodegenerative diseases are a large group of disorders defined by a gradual loss of neurons and a progressive impairment in neuronal function. Several of the most common neurodegenerative diseases involve some form of splicing defect(s), such as Alzheimer's disease, Parkinson's disease and spinal muscular atrophy. Our growing understanding of RNA splicing has led to the explosion of research in the field of splice-switching antisense oligonucleotide therapeutics. Here we review our current understanding of the effects alternative splicing has on neuronal differentiation, neuronal migration, synaptic maturation and regulation, as well as the impact on neurodegenerative diseases. We will also review the current landscape of splice-switching antisense oligonucleotides as a therapeutic strategy for a number of common neurodegenerative disorders.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Craig Stewart McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Frank Louis Mastaglia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Steve Donald Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia. .,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia.
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9
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Titus MB, Wright EG, Bono JM, Poliakon AK, Goldstein BR, Super MK, Young LA, Manaj M, Litchford M, Reist NE, Killian DJ, Olesnicky EC. The conserved alternative splicing factor caper regulates neuromuscular phenotypes during development and aging. Dev Biol 2021; 473:15-32. [PMID: 33508255 PMCID: PMC7987824 DOI: 10.1016/j.ydbio.2021.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/17/2022]
Abstract
RNA-binding proteins play an important role in the regulation of post-transcriptional gene expression throughout the nervous system. This is underscored by the prevalence of mutations in genes encoding RNA splicing factors and other RNA-binding proteins in a number of neurodegenerative and neurodevelopmental disorders. The highly conserved alternative splicing factor Caper is widely expressed throughout the developing embryo and functions in the development of various sensory neural subtypes in the Drosophila peripheral nervous system. Here we find that caper dysfunction leads to aberrant neuromuscular junction morphogenesis, as well as aberrant locomotor behavior during larval and adult stages. Despite its widespread expression, our results indicate that caper function is required to a greater extent within the nervous system, as opposed to muscle, for neuromuscular junction development and for the regulation of adult locomotor behavior. Moreover, we find that Caper interacts with the RNA-binding protein Fmrp to regulate adult locomotor behavior. Finally, we show that caper dysfunction leads to various phenotypes that have both a sex and age bias, both of which are commonly seen in neurodegenerative disorders in humans.
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Affiliation(s)
- M Brandon Titus
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Ethan G Wright
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Andrea K Poliakon
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Brandon R Goldstein
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Meg K Super
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Lauren A Young
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Melpomeni Manaj
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Morgan Litchford
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Noreen E Reist
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
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10
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Cheng Z, Shang Y, Xu X, Dong Z, Zhang Y, Du Z, Lu X, Zhang T. Presenilin 1 mutation likely contributes to U1 small nuclear RNA dysregulation and Alzheimer's disease-like symptoms. Neurobiol Aging 2021; 100:1-10. [PMID: 33450722 DOI: 10.1016/j.neurobiolaging.2020.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 12/15/2022]
Abstract
Previous studies showed that U1 small nuclear RNA (snRNA) was selectively enriched in the brain of individuals with familial Alzheimer's disease (AD), resulting in widespread changes in RNA splicing. Our study further reported that presenilin-1 (PSEN1) induced an increase in U1 snRNA expression, accompanied by changed amyloid precursor protein expression, β-amyloid level, and cell death in SH-SY5Y cells. However, the effect of U1 snRNA overexpression on learning and memory is still unclear. In the present study, we found that neuronal U1 snRNA overexpression could generate U1 snRNA aggregates in the nuclear, accompanied by the widespread alteration of RNA splicing, resulting in the impairments of synaptic plasticity and spatial memory. In addition, more U1 snRNAs is bound to the intron binding sites accompanied by an increased intracellular U1 snRNA level. This suggests that U1 snRNA overexpression regulates RNA splicing and gene expression in neurons by manipulating the recruitment of the U1 snRNA to the nascent transcripts. Using in situ hybridization staining of human central nervous system-type neurons, we identified nuclear aggregates of U1 snRNA in neurons by upregulating the U1 snRNA level. Quantitative polymerase chain reaction analysis showed U1 snRNA accumulation in the insoluble fraction of neurons with PSEN1 mutation neurons rather than other types of U snRNAs. These results show an independent function of U1 snRNA in regulating RNA splicing, suggesting that aberrant RNA processing may mediate neurodegeneration induced by PSEN1 mutation.
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Affiliation(s)
- Zhi Cheng
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Yingchun Shang
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Xinxin Xu
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Zhiqiang Dong
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Yongwang Zhang
- College of Pharmacy, Nankai University, Tianjin, PR China
| | - Zhanqiang Du
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Xinyi Lu
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China; College of Pharmacy, Nankai University, Tianjin, PR China
| | - Tao Zhang
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China.
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11
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Oh VKS, Li RW. Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data. Genes (Basel) 2021; 12:352. [PMID: 33673721 PMCID: PMC7997275 DOI: 10.3390/genes12030352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Dynamic studies in time course experimental designs and clinical approaches have been widely used by the biomedical community. These applications are particularly relevant in stimuli-response models under environmental conditions, characterization of gradient biological processes in developmental biology, identification of therapeutic effects in clinical trials, disease progressive models, cell-cycle, and circadian periodicity. Despite their feasibility and popularity, sophisticated dynamic methods that are well validated in large-scale comparative studies, in terms of statistical and computational rigor, are less benchmarked, comparing to their static counterparts. To date, a number of novel methods in bulk RNA-Seq data have been developed for the various time-dependent stimuli, circadian rhythms, cell-lineage in differentiation, and disease progression. Here, we comprehensively review a key set of representative dynamic strategies and discuss current issues associated with the detection of dynamically changing genes. We also provide recommendations for future directions for studying non-periodical, periodical time course data, and meta-dynamic datasets.
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Affiliation(s)
- Vera-Khlara S. Oh
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
- Department of Computer Science and Statistics, College of Natural Sciences, Jeju National University, Jeju City 63243, Korea
| | - Robert W. Li
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
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12
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Ishunina TA. Alternative splicing in aging and Alzheimer's disease: Highlighting the role of tau and estrogen receptor α isoforms in the hypothalamus. HANDBOOK OF CLINICAL NEUROLOGY 2021; 182:177-189. [PMID: 34266591 DOI: 10.1016/b978-0-12-819973-2.00012-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human genes show the highest efficacy of alternative splicing (AS) in the brain as compared to other tissues. Within the brain, a remarkably rich diversity of AS events was identified in the hypothalamus. The AS frequency is increased in the aging brain. Such AS events, as intron retention and accumulation of circular RNAs, were acknowledged as some of the main hallmarks of the aging brain. In Alzheimer's disease (AD) pivotal (tau gene, in particular), risk, candidate and other genes show significant alterations in AS. Therefore AD has been suggested to be a disease of dysregulated AS. One of the reported risk factors for AD is estrogen deficiency that may interfere with the extension of neurobrillary tangles. Mounting evidence suggests that estrogens may decrease hyperphosphorylated tau deposition in the brain. Furthermore, AS of estrogen receptor α (ERα) mRNA is decreased in AD brain areas with the highest tau load. These potential interactions among tau, estrogens, and ERα AS may be important for the development of therapeutic and preventive strategies for AD. The intriguing point is that the amount of splice variants of ERα in the hypothalamus and the hippocampus is increased in aging and decreased in AD, while ERα is one of the regulators of AS and is subject to AS itself.
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Affiliation(s)
- Tatjana A Ishunina
- Department of Histology, Embryology and Cytology, Kursk State Medical University, Kursk, Russia.
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13
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Qu W, Jin H, Chen BP, Liu J, Li R, Guo W, Tian H. CPEB3 regulates neuron-specific alternative splicing and involves neurogenesis gene expression. Aging (Albany NY) 2020; 13:2330-2347. [PMID: 33318303 PMCID: PMC7880327 DOI: 10.18632/aging.202259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022]
Abstract
In the mammalian brain, alternative pre-mRNA splicing is a fundamental mechanism that modifies neuronal function dynamically where secretion of different splice variants regulates neurogenesis, development, pathfinding, maintenance, migration, and synaptogenesis. Sequence-specific RNA-Binding Protein CPEB3 has distinctive isoform-distinct biochemical interactions and neuronal development assembly roles. Nonetheless, the mechanisms moderating splice isoform options remain unclear. To establish the modulatory trend of CPEB3, we cloned and excessively expressed CPEB3 in HT22 cells. We used RNA-seq to analyze CPEB3-regulated alternative splicing on control and CPEB3-overexpressing cells. Consequently, we used iRIP-seq to identify CPEB-binding targets. We additionally validated CPEB3-modulated genes using RT-qPCR. CPEB3 overexpression had insignificant effects on gene expression in HT22 cells. Notably, CPEB3 partially modulated differential gene splicing enhanced in the modulation of neural development, neuron cycle, neurotrophin, synapse, and specific development pathway, implying an alternative splicing regulatory mechanism associated with neurogenesis. Moreover, qRT-PCR verified the CPEB3-modulated transcription of neurogenesis genes LCN2 and NAV2, synaptogenesis gene CYLD, as well as neural development gene JADE1. Herein, we established that CPEB3 is a critical modulator of alternative splicing in neurogenesis, which remarkably enhances the current understanding of the CPEB3 mediated alternative pre-mRNA splicing.
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Affiliation(s)
- Wenrui Qu
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Hongjuan Jin
- Department of Plastic and Reconstructive Surgery, The First Hospital of Jilin University, Changchun, China
| | - Bing-Peng Chen
- Orthopedic Medical Center, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Jun Liu
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Rui Li
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Wenlai Guo
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Heng Tian
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin Province, China
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14
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Lyons LC, Chatterjee S, Vanrobaeys Y, Gaine ME, Abel T. Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq. Mol Brain 2020; 13:165. [PMID: 33272296 PMCID: PMC7713217 DOI: 10.1186/s13041-020-00702-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Sleep deprivation is a global health problem adversely affecting health as well as causing decrements in learning and performance. Sleep deprivation induces significant changes in gene transcription in many brain regions, with the hippocampus particularly susceptible to acute sleep deprivation. However, less is known about the impacts of sleep deprivation on post-transcriptional gene regulation. To identify the effects of sleep deprivation on the translatome, we took advantage of the RiboTag mouse line to express HA-labeled Rpl22 in CaMKIIα neurons to selectively isolate and sequence mRNA transcripts associated with ribosomes in excitatory neurons. We found 198 differentially expressed genes in the ribosome-associated mRNA subset after sleep deprivation. In comparison with previously published data on gene expression in the hippocampus after sleep deprivation, we found that the subset of genes affected by sleep deprivation was considerably different in the translatome compared with the transcriptome, with only 49 genes regulated similarly. Interestingly, we found 478 genes differentially regulated by sleep deprivation in the transcriptome that were not significantly regulated in the translatome of excitatory neurons. Conversely, there were 149 genes differentially regulated by sleep deprivation in the translatome but not in the whole transcriptome. Pathway analysis revealed differences in the biological functions of genes exclusively regulated in the transcriptome or translatome, with protein deacetylase activity and small GTPase binding regulated in the transcriptome and unfolded protein binding, kinase inhibitor activity, neurotransmitter receptors and circadian rhythms regulated in the translatome. These results indicate that sleep deprivation induces significant changes affecting the pool of actively translated mRNAs.
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Affiliation(s)
- Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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15
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Fazeli S, Motovali-Bashi M, Peymani M, Hashemi MS, Etemadifar M, Nasr-Esfahani MH, Ghaedi K. A compound downregulation of SRRM2 and miR-27a-3p with upregulation of miR-27b-3p in PBMCs of Parkinson's patients is associated with the early stage onset of disease. PLoS One 2020; 15:e0240855. [PMID: 33171483 PMCID: PMC7654768 DOI: 10.1371/journal.pone.0240855] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023] Open
Abstract
Parkinson’s disease (PD) is diagnosed when motor symptoms emerges, which almost 70% of dopamine neurons are lost. Therefore, early diagnosis of PD is crucial to prevent the progress of disease. Blood-based biomarkers, which are minimally invasive, potentially used for diagnosis of PD, including miRNAs. The aim of this study was to assess whether SRRM2 and miR-27a/b-3p could act as early diagnostic biomarkers for PD. Total RNAs from PBMCs of 30 PD’s patients and 14 healthy age and gender matched subjects was extracted. The expression levels of respective genes were assessed. Data were presented applying a two-tailed unpaired t-test and one-way ANOVA. We observed significant down-regulation of SRRM2 (p = 0.0002) and miR-27a-3p (p = 0.0001), and up-regulation of miR-27b-3p (p = 0.02) in PBMCs of Parkinson's patients. Down-regulation of miR-27a-3p is associated with increasing disease severity, whereas the up-regulation of miR-27b-3p was observed mostly at HY-1 and disease duration between 3–5 years. There was a negative correlation between SRRM2 and miR-27b-3p expressions, and miR-27a-3p positively was correlated with miR-27b-3p. Based on functional enrichment analysis, SRRM2 and miR-27a/b-3p acted on common functional pathways. miR-27a/b-3p could potentially predict the progression and severity of PD. Although both miRs had no similarity on expression, a positive correlation between both miRs was identified, supporting their potential role as biomarkers in clinical PD stages. Of note that SRRM2 and miR-27a-3p were able to distinguish PD patients from healthy individuals. Functional analysis of the similarity between genes associated with SRRM2 and miR-27a/b-3p indicates common functional pathways and their dysfunction correlates with molecular etiopathology mechanisms of PD onset.
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Affiliation(s)
- Soudabeh Fazeli
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Majid Motovali-Bashi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Islamic Azad University, Shahrekord, Iran
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
| | - Motahare-Sadat Hashemi
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Masoud Etemadifar
- Department of Neurology and Isfahan Neurosurgery Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
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16
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Li D, Mastaglia FL, Fletcher S, Wilton SD. Progress in the molecular pathogenesis and nucleic acid therapeutics for Parkinson's disease in the precision medicine era. Med Res Rev 2020; 40:2650-2681. [PMID: 32767426 PMCID: PMC7589267 DOI: 10.1002/med.21718] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/16/2022]
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders that manifest various motor and nonmotor symptoms. Although currently available therapies can alleviate some of the symptoms, the disease continues to progress, leading eventually to severe motor and cognitive decline and reduced life expectancy. The past two decades have witnessed rapid progress in our understanding of the molecular and genetic pathogenesis of the disease, paving the way for the development of new therapeutic approaches to arrest or delay the neurodegenerative process. As a result of these advances, biomarker‐driven subtyping is making it possible to stratify PD patients into more homogeneous subgroups that may better respond to potential genetic‐molecular pathway targeted disease‐modifying therapies. Therapeutic nucleic acid oligomers can bind to target gene sequences with very high specificity in a base‐pairing manner and precisely modulate downstream molecular events. Recently, nucleic acid therapeutics have proven effective in the treatment of a number of severe neurological and neuromuscular disorders, drawing increasing attention to the possibility of developing novel molecular therapies for PD. In this review, we update the molecular pathogenesis of PD and discuss progress in the use of antisense oligonucleotides, small interfering RNAs, short hairpin RNAs, aptamers, and microRNA‐based therapeutics to target critical elements in the pathogenesis of PD that could have the potential to modify disease progression. In addition, recent advances in the delivery of nucleic acid compounds across the blood–brain barrier and challenges facing PD clinical trials are also reviewed.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
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17
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Griswold AJ, Sivasankaran SK, Van Booven D, Gardner OK, Rajabli F, Whitehead PL, Hamilton-Nelson KL, Adams LD, Scott AM, Hofmann NK, Vance JM, Cuccaro ML, Bush WS, Martin ER, Byrd GS, Haines JL, Pericak-Vance MA, Beecham GW. Immune and Inflammatory Pathways Implicated by Whole Blood Transcriptomic Analysis in a Diverse Ancestry Alzheimer's Disease Cohort. J Alzheimers Dis 2020; 76:1047-1060. [PMID: 32597797 DOI: 10.3233/jad-190855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Significant work has identified genetic variants conferring risk and protection for Alzheimer's disease (AD), but functional effects of these variants is lacking, particularly in under-represented ancestral populations. Expression studies performed in easily accessible tissue, such as whole blood, can recapitulate some transcriptional changes occurring in brain and help to identify mechanisms underlying neurodegenerative processes. OBJECTIVE We aimed to identify transcriptional differences between AD cases and controls in a cohort of diverse ancestry. METHODS We analyzed the protein coding transcriptome using RNA sequencing from peripheral blood collected from 234 African American (AA) (115 AD, 119 controls) and 240 non-Hispanic Whites (NHW) (121 AD, 119 controls). To identify case-control differentially expressed genes and pathways, we performed stratified, joint, and interaction analyses using linear regression models within and across ancestral groups followed by pathway and gene set enrichment analyses. RESULTS Overall, we identified 418 (291 upregulated, 127 downregulated) and 488 genes (352 upregulated, 136 downregulated) differentially expressed in the AA and NHW datasets, respectively, with only 16 genes commonly differentially expressed in both ancestral groups. Joint analyses provided greater power to detect case-control differences and identified 1,102 differentially expressed genes between cases and controls (812 upregulated, 290 downregulated). Interaction analysis identified only 27 genes with different effects in AA compared to NHW. Pathway and gene-set enrichment analyses revealed differences in immune response-related pathways that were enriched across the analyses despite different underlying gene sets. CONCLUSION These results support the hypothesis of converging underlying pathophysiological processes in AD across ancestral groups.
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Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | | | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Olivia K Gardner
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | | | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Aja M Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - William S Bush
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Goldie S Byrd
- Department of Public Health Sciences, Wake Forest University, Winston-Salem, NC, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
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18
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Xu M, Liu Y, Huang Y, Wang J, Yan J, Zhang L, Zhang C. Re-exploring the core genes and modules in the human frontal cortex during chronological aging: insights from network-based analysis of transcriptomic studies. Aging (Albany NY) 2019; 10:2816-2831. [PMID: 30341976 PMCID: PMC6224233 DOI: 10.18632/aging.101589] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/04/2018] [Indexed: 11/25/2022]
Abstract
Frontal cortical dysfunction is a fundamental pathology contributing to age-associated behavioral and cognitive deficits that predispose older adults to neurodegenerative diseases. It is established that aging increases the risk of frontal cortical dysfunction; however, the underlying molecular mechanism remains elusive. Here, we used an integrative meta-analysis to combine five frontal cortex microarray studies with a combined sample population of 161 younger and 155 older individuals. A network-based analysis was used to describe an outline of human frontal cortical aging to identify core genes whose expression changes with age and to reveal the interrelationships among these genes. We found that histone deacetylase 1 (HDAC1) and YES proto-oncogene 1 (YES1) are the two most upregulated genes, while cell division cycle 42 (CDC42) is the central regulatory gene decreased in the aged human frontal cortex. Quantitative PCR assays revealed corresponding changes in frontal cortical Hdac1, Yes1 and Cdc42 mRNA levels in an established aging mouse model. Moreover, analysis of the GSE48350 dataset confirmed similar changes in HDAC1, CDC42 and YES1 expression in Alzheimer's disease, thereby providing a molecular connection between aging and Alzheimer's disease (AD). This framework of network-based analysis could provide novel strategies for detecting and monitoring aging in the brain.
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Affiliation(s)
- Mulin Xu
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China
| | - Yu Liu
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China.,Department of Internal Medicine, University of Utah, Salt Lake City, Utah 84112, U.S.A
| | - Yi Huang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China
| | - Jinli Wang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China
| | - Jinhua Yan
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China
| | - Le Zhang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China
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19
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Zhang J, Harvey SE, Cheng C. A high-throughput screen identifies small molecule modulators of alternative splicing by targeting RNA G-quadruplexes. Nucleic Acids Res 2019; 47:3667-3679. [PMID: 30698802 PMCID: PMC6468248 DOI: 10.1093/nar/gkz036] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/08/2019] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
RNA secondary structures have been increasingly recognized to play an important regulatory role in post-transcriptional gene regulation. We recently showed that RNA G-quadruplexes, which serve as cis-elements to recruit splicing factors, play a critical role in regulating alternative splicing during the epithelial-mesenchymal transition. In this study, we performed a high-throughput screen using a dual-color splicing reporter to identify chemical compounds capable of regulating G-quadruplex-dependent alternative splicing. We identify emetine and its analog cephaeline as small molecules that disrupt RNA G-quadruplexes, resulting in inhibition of G-quadruplex-dependent alternative splicing. Transcriptome analysis reveals that emetine globally regulates alternative splicing, including splicing of variable exons that contain splice site-proximal G-quadruplexes. Our data suggest the use of emetine and cephaeline for investigating mechanisms of G-quadruplex-associated alternative splicing.
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Affiliation(s)
- Jing Zhang
- Lester & Sue Smith Breast Center, Department of Molecular & Human Genetics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Samuel E Harvey
- Lester & Sue Smith Breast Center, Department of Molecular & Human Genetics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chonghui Cheng
- Lester & Sue Smith Breast Center, Department of Molecular & Human Genetics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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20
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Yang J, Long Y, Xu DM, Zhu BL, Deng XJ, Yan Z, Sun F, Chen GJ. Age- and Nicotine-Associated Gene Expression Changes in the Hippocampus of APP/PS1 Mice. J Mol Neurosci 2019; 69:608-622. [PMID: 31399937 DOI: 10.1007/s12031-019-01389-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/18/2019] [Indexed: 12/17/2022]
Abstract
The etiology of Alzheimer's disease (AD) has been intensively studied. However, little is known about the molecular alterations in early-stage and late-stage AD. Hence, we performed RNA sequencing and assessed differentially expressed genes (DEGs) in the hippocampus of 18-month and 7-month-old APP/PS1 mice. Moreover, the DEGs induced by treatment with nicotine, the nicotinic acetylcholine receptor agonist that is known to improve cognition in AD, were also analyzed in old and young APP/PS1 mice. When comparing old APP/PS1 mice with their younger littermates, we found an upregulation in genes associated with calcium overload, immune response, cancer, and synaptic function; the transcripts of 14 calcium ion channel subtypes were significantly increased in aged mice. In contrast, the downregulated genes in aged mice were associated with ribosomal components, mitochondrial respiratory chain complex, and metabolism. Through comparison with DEGs in normal aging from previous reports, we found that changes in calcium channel genes remained one of the prominent features in aged APP/PS1 mice. Nicotine treatment also induced changes in gene expression. Indeed, nicotine augmented glycerolipid metabolism, but inhibited PI3K and MAPK signaling in young mice. In contrast, nicotine affected genes associated with cell senescence and death in old mice. Our study suggests a potential network connection between calcium overload and cellular signaling, in which additional nicotinic activation might not be beneficial in late-stage AD.
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Affiliation(s)
- Jie Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Yan Long
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - De-Mei Xu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Bing-Lin Zhu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Xiao-Juan Deng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - Fei Sun
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Guo-Jun Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China.
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21
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Weishäupl D, Schneider J, Peixoto Pinheiro B, Ruess C, Dold SM, von Zweydorf F, Gloeckner CJ, Schmidt J, Riess O, Schmidt T. Physiological and pathophysiological characteristics of ataxin-3 isoforms. J Biol Chem 2018; 294:644-661. [PMID: 30455355 DOI: 10.1074/jbc.ra118.005801] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/08/2018] [Indexed: 12/18/2022] Open
Abstract
Ataxin-3 is a deubiquitinating enzyme and the affected protein in the neurodegenerative disorder Machado-Joseph disease (MJD). The ATXN3 gene is alternatively spliced, resulting in protein isoforms that differ in the number of ubiquitin-interacting motifs. Additionally, nonsynonymous SNPs in ATXN3 cause amino acid changes in ataxin-3, and one of these polymorphisms introduces a premature stop codon in one isoform. Here, we examined the effects of different ataxin-3 isoforms and of the premature stop codon on ataxin-3's physiological function and on main disease mechanisms. At the physiological level, we show that alternative splicing and the premature stop codon alter ataxin-3 stability and that ataxin-3 isoforms differ in their enzymatic deubiquitination activity, subcellular distribution, and interaction with other proteins. At the pathological level, we found that the expansion of the polyglutamine repeat leads to a stabilization of ataxin-3 and that ataxin-3 isoforms differ in their aggregation properties. Interestingly, we observed a functional interaction between normal and polyglutamine-expanded ATXN3 allelic variants. We found that interactions between different ATXN3 allelic variants modify the physiological and pathophysiological properties of ataxin-3. Our findings indicate that alternative splicing and interactions between different ataxin-3 isoforms affect not only major aspects of ataxin-3 function but also MJD pathogenesis. Our results stress the importance of considering isoforms of disease-causing proteins and their interplay with the normal allelic variant as disease modifiers in MJD and autosomal-dominantly inherited diseases in general.
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Affiliation(s)
- Daniel Weishäupl
- From the Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany.,the Center for Rare Diseases, 72076 Tübingen, Germany.,the NGS Competence Center, 72076 Tübingen, Germany.,the Graduate Training Center of Neuroscience, 72074 Tübingen, Germany
| | - Juliane Schneider
- From the Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany.,the Center for Rare Diseases, 72076 Tübingen, Germany.,the NGS Competence Center, 72076 Tübingen, Germany
| | - Barbara Peixoto Pinheiro
- From the Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany.,the Center for Rare Diseases, 72076 Tübingen, Germany.,the NGS Competence Center, 72076 Tübingen, Germany
| | - Corinna Ruess
- From the Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany.,the Center for Rare Diseases, 72076 Tübingen, Germany.,the NGS Competence Center, 72076 Tübingen, Germany
| | - Sandra Maria Dold
- From the Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany.,the Center for Rare Diseases, 72076 Tübingen, Germany.,the NGS Competence Center, 72076 Tübingen, Germany
| | - Felix von Zweydorf
- the German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany, and
| | - Christian Johannes Gloeckner
- the German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany, and.,the Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, 72076 Tübingen, Germany
| | - Jana Schmidt
- From the Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany.,the Center for Rare Diseases, 72076 Tübingen, Germany.,the NGS Competence Center, 72076 Tübingen, Germany
| | - Olaf Riess
- From the Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany.,the Center for Rare Diseases, 72076 Tübingen, Germany.,the NGS Competence Center, 72076 Tübingen, Germany
| | - Thorsten Schmidt
- From the Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany, .,the Center for Rare Diseases, 72076 Tübingen, Germany.,the NGS Competence Center, 72076 Tübingen, Germany
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22
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Kim A, Nigmatullina R, Zalyalova Z, Soshnikova N, Krasnov A, Vorobyeva N, Georgieva S, Kudrin V, Narkevich V, Ugrumov M. Upgraded Methodology for the Development of Early Diagnosis of Parkinson's Disease Based on Searching Blood Markers in Patients and Experimental Models. Mol Neurobiol 2018; 56:3437-3450. [PMID: 30128652 DOI: 10.1007/s12035-018-1315-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023]
Abstract
Numerous attempts to develop an early diagnosis of Parkinson's disease (PD) by searching biomarkers in biological fluids were unsuccessful. The drawback of this methodology is searching markers in patients at the clinical stage without guarantee that they are also characteristic of either preclinical stage or prodromal stage (preclinical-prodromal stage). We attempted to upgrade this methodology by selecting only markers that are found both in patients and in PD animal models. HPLC and RT-PCR were used to estimate the concentration of amino acids, catecholamines/metabolites in plasma and gene expression in lymphocytes in 36 untreated early-stage PD patients and 52 controls, and in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice at modeling the clinical ("symptomatic") stage and preclinical-prodromal ("presymptomatic") stage of PD. It was shown that among 13 blood markers found in patients, 7 markers are characteristic of parkinsonian symptomatic mice and 3 markers of both symptomatic and presymptomatic mice. According to our suggestion, the detection of the same marker in patients and symptomatic animals indicates adequate reproduction of pathogenesis along the corresponding metabolic pathway, whereas the detection of the same marker in presymptomatic animals indicates its specificity for preclinical-prodromal stage. This means that the minority of markers found in patients-decreased concentration of L-3,4-dihydroxyphenylalanine (L-DOPA) and dihydroxyphenylacetic acid (DOPAC) and increased dopamine D3 receptor gene expression-are specific for preclinical-prodromal stage and are suitable for early diagnosis of PD. Thus, we upgraded a current methodology for development of early diagnosis of PD by searching blood markers not only in patients but also in parkinsonian animals.
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Affiliation(s)
- Alexander Kim
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Razina Nigmatullina
- Kazan State Medical University, Ministry of Health of the Russian Federation, Kazan, Russia
| | - Zuleikha Zalyalova
- Kazan State Medical University, Ministry of Health of the Russian Federation, Kazan, Russia
- Kazan Hospital for War Veterans, Ministry of Health of the Republic of Tatarstan, Kazan, Russia
| | | | - Alexey Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Sofia Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Michael Ugrumov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.
- National Research University Higher School of Economics, Moscow, Russia.
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23
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Olesnicky EC, Wright EG. Drosophila as a Model for Assessing the Function of RNA-Binding Proteins during Neurogenesis and Neurological Disease. J Dev Biol 2018; 6:E21. [PMID: 30126171 PMCID: PMC6162566 DOI: 10.3390/jdb6030021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 12/16/2022] Open
Abstract
An outstanding question in developmental neurobiology is how RNA processing events contribute to the regulation of neurogenesis. RNA processing events are increasingly recognized as playing fundamental roles in regulating multiple developmental events during neurogenesis, from the asymmetric divisions of neural stem cells, to the generation of complex and diverse neurite morphologies. Indeed, both asymmetric cell division and neurite morphogenesis are often achieved by mechanisms that generate asymmetric protein distributions, including post-transcriptional gene regulatory mechanisms such as the transport of translationally silent messenger RNAs (mRNAs) and local translation of mRNAs within neurites. Additionally, defects in RNA splicing have emerged as a common theme in many neurodegenerative disorders, highlighting the importance of RNA processing in maintaining neuronal circuitry. RNA-binding proteins (RBPs) play an integral role in splicing and post-transcriptional gene regulation, and mutations in RBPs have been linked with multiple neurological disorders including autism, dementia, amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Fragile X syndrome (FXS), and X-linked intellectual disability disorder. Despite their widespread nature and roles in neurological disease, the molecular mechanisms and networks of regulated target RNAs have been defined for only a small number of specific RBPs. This review aims to highlight recent studies in Drosophila that have advanced our knowledge of how RBP dysfunction contributes to neurological disease.
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Affiliation(s)
- Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
| | - Ethan G Wright
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
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24
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Verheijen J, Sleegers K. Understanding Alzheimer Disease at the Interface between Genetics and Transcriptomics. Trends Genet 2018; 34:434-447. [PMID: 29573818 DOI: 10.1016/j.tig.2018.02.007] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/20/2018] [Accepted: 02/26/2018] [Indexed: 12/21/2022]
Abstract
Over 25 genes are known to affect the risk of developing Alzheimer disease (AD), the most common neurodegenerative dementia. However, mechanistic insights and improved disease management remains limited, due to difficulties in determining the functional consequences of genetic associations. Transcriptomics is increasingly being used to corroborate or enhance interpretation of genetic discoveries. These approaches, which include second and third generation sequencing, single-cell sequencing, and bioinformatics, reveal allele-specific events connecting AD risk genes to expression profiles, and provide converging evidence of pathophysiological pathways underlying AD. Simultaneously, they highlight brain region- and cell-type-specific expression patterns, and alternative splicing events that affect the straightforward relation between a genetic variant and AD, re-emphasizing the need for an integrated approach of genetics and transcriptomics in understanding AD.
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Affiliation(s)
- Jan Verheijen
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, B-2610, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, B-2610, Belgium
| | - Kristel Sleegers
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, B-2610, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, B-2610, Belgium.
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25
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Whole transcriptome profiling of Late-Onset Alzheimer's Disease patients provides insights into the molecular changes involved in the disease. Sci Rep 2018. [PMID: 29523845 PMCID: PMC5844946 DOI: 10.1038/s41598-018-22701-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alzheimer’s Disease (AD) is the most common cause of dementia affecting the elderly population worldwide. We have performed a comprehensive transcriptome profiling of Late-Onset AD (LOAD) patients using second generation sequencing technologies, identifying 2,064 genes, 47 lncRNAs and 4 miRNAs whose expression is specifically deregulated in the hippocampal region of LOAD patients. Moreover, analyzing the hippocampal, temporal and frontal regions from the same LOAD patients, we identify specific sets of deregulated miRNAs for each region, and we confirm that the miR-132/212 cluster is deregulated in each of these regions in LOAD patients, consistent with these miRNAs playing a role in AD pathogenesis. Notably, a luciferase assay indicates that miR-184 is able to target the 3’UTR NR4A2 - which is known to be involved in cognitive functions and long-term memory and whose expression levels are inversely correlated with those of miR-184 in the hippocampus. Finally, RNA editing analysis reveals a general RNA editing decrease in LOAD hippocampus, with 14 recoding sites significantly and differentially edited in 11 genes. Our data underline specific transcriptional changes in LOAD brain and provide an important source of information for understanding the molecular changes characterizing LOAD progression.
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26
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Wang B, Lo UG, Wu K, Kapur P, Liu X, Huang J, Chen W, Hernandez E, Santoyo J, Ma SH, Pong RC, He D, Cheng YQ, Hsieh JT. Developing new targeting strategy for androgen receptor variants in castration resistant prostate cancer. Int J Cancer 2017; 141:2121-2130. [PMID: 28722220 PMCID: PMC5777133 DOI: 10.1002/ijc.30893] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/09/2017] [Accepted: 07/03/2017] [Indexed: 01/05/2023]
Abstract
The presence of androgen receptor variant 7 (AR-V7) variants becomes a significant hallmark of castration-resistant prostate cancer (CRPC) relapsed from hormonal therapy and is associated with poor survival of CRPC patients because of lacking a ligand-binding domain. Currently, it still lacks an effective agent to target AR-V7 or AR-Vs in general. Here, we showed that a novel class of agents (thailanstatins, TSTs and spliceostatin A analogs) can significantly suppress the expression of AR-V7 mRNA and protein but in a less extent on the full-length AR expression. Mechanistically, TST-D is able to inhibit AR-V7 gene splicing by interfering the interaction between U2AF65 and SAP155 and preventing them from binding to polypyrimidine tract located between the branch point and the 3' splice site. In vivo, TST-D exhibits a potent tumor inhibitory effect on human CRPC xenografts leading to cell apoptosis. The machinery associated with AR gene splicing in CRPC is a potential target for drugs. Based on their potency in the suppression of AR-V7 responsible for the growth/survival of CRPC, TSTs representing a new class of anti-AR-V agents warrant further development into clinical application.
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Affiliation(s)
- Bin Wang
- Department of Urology, The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - U-Ging Lo
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kaijie Wu
- Department of Urology, The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Jun Huang
- Department of Urology, The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth Hernandez
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John Santoyo
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shi-Hong Ma
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rey-Chen Pong
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dalin He
- Department of Urology, The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Jer-Tsong Hsieh
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Graduate Institute of Cancer Biology, China Medical University Hospital, Taichung 40447, Taiwan
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27
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Yahara M, Kitamura A, Kinjo M. U6 snRNA expression prevents toxicity in TDP-43-knockdown cells. PLoS One 2017; 12:e0187813. [PMID: 29125873 PMCID: PMC5681290 DOI: 10.1371/journal.pone.0187813] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022] Open
Abstract
Depletion of amyotrophic lateral sclerosis (ALS)-associated transactivation response (TAR) RNA/DNA-binding protein 43 kDa (TDP-43) alters splicing efficiency of multiple transcripts and results in neuronal cell death. TDP-43 depletion can also disturb expression levels of small nuclear RNAs (snRNAs) as spliceosomal components. Despite this knowledge, the relationship between cell death and alteration of snRNA expression during TDP-43 depletion remains unclear. Here, we knocked down TDP-43 in murine neuroblastoma Neuro2A cells and found a time lag between efficient TDP-43 depletion and appearance of cell death, suggesting that several mechanisms mediate between these two events. The amount of U6 snRNA was significantly decreased during TDP-43 depletion prior to increase of cell death, whereas that of U1, U2, and U4 snRNAs was not. Downregulation of U6 snRNA led to cell death, whereas transient exogenous expression of U6 snRNA counteracted the effect of TDP-43 knockdown on cell death, and slightly decreased the mis-splicing rate of Dnajc5 and Sortilin 1 transcripts, which are assisted by TDP-43. These results suggest that regulation of the U6 snRNA expression level by TDP-43 is a key factor in the increase in cell death upon TDP-43 loss-of-function.
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Affiliation(s)
- Masao Yahara
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Akira Kitamura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
- * E-mail:
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28
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Cheng Z, Shang Y, Gao S, Zhang T. Overexpression of U1 snRNA induces decrease of U1 spliceosome function associated with Alzheimer's disease. J Neurogenet 2017; 31:337-343. [PMID: 29098922 DOI: 10.1080/01677063.2017.1395425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We recently reported that presenilin-1 (PS1) induced an increase of U1 snRNA expression accompanied with the change of amyloid precursor protein expression, β-amyloid level and cell death. In the present study, our data showed that both overexpression and knockdown of U1 snRNA could cause the loss in the function of U1 snRNA and resulted in PCPA as well as the same downstream phenomena including the expression changes of genes specific to AD, tau hyperphosphorylation on the site of Thr212, the decrease of acetylated α-tubulin, the reduction of cell viability and upregulation of RIPK1, RIPK3 and caspase8. These findings not only helped researchers better understand the functions of U1 snRNA, but also paved the way to reveal the mechanisms of AD from a different point of view and may find a new therapeutic target for the disease.
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Affiliation(s)
- Zhi Cheng
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Yingchun Shang
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Shan Gao
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Tao Zhang
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
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29
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Sánchez-Hernández N, Prieto-Sánchez S, Moreno-Castro C, Muñoz-Cobo JP, El Yousfi Y, Boyero-Corral S, Suñé-Pou M, Hernández-Munain C, Suñé C. Targeting proteins to RNA transcription and processing sites within the nucleus. Int J Biochem Cell Biol 2017; 91:194-202. [DOI: 10.1016/j.biocel.2017.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022]
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30
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van Vliet EA, Puhakka N, Mills JD, Srivastava PK, Johnson MR, Roncon P, Das Gupta S, Karttunen J, Simonato M, Lukasiuk K, Gorter JA, Aronica E, Pitkänen A. Standardization procedure for plasma biomarker analysis in rat models of epileptogenesis: Focus on circulating microRNAs. Epilepsia 2017; 58:2013-2024. [PMID: 28960286 DOI: 10.1111/epi.13915] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2017] [Indexed: 12/21/2022]
Abstract
The World Health Organization estimates that globally 2.4 million people are diagnosed with epilepsy each year. In nearly 30% of these cases, epilepsy cannot be properly controlled by antiepileptic drugs. More importantly, treatments to prevent or modify epileptogenesis do not exist. Therefore, novel therapies are urgently needed. In this respect, it is important to identify which patients will develop epilepsy and which individually tailored treatment is needed. However, currently, we have no tools to identify the patients at risk, and diagnosis of epileptogenesis remains as a major unmet medical need, which relates to lack of diagnostic biomarkers for epileptogenesis. As the epileptogenic process in humans is typically slow, the use of animal models is justified to speed up biomarker discovery. We aim to summarize recommendations for molecular biomarker research and propose a standardized procedure for biomarker discovery in rat models of epileptogenesis. The potential of many phylogenetically conserved circulating noncoding small RNAs, including microRNAs (miRNAs), as biomarkers has been explored in various brain diseases, including epilepsy. Recent studies show the feasibility of detecting miRNAs in blood in both experimental models and human epilepsy. However, the analysis of circulating miRNAs in rodent models is challenging, which relates both to the lack of standardized sampling protocols and to analysis of miRNAs. We will discuss the issues critical for preclinical plasma biomarker discovery, such as documentation, blood and brain tissue sampling and collection, plasma separation and storage, RNA extraction, quality control, and RNA detection. We propose a protocol for standardization of procedures for discovery of circulating miRNA biomarkers in rat models of epileptogenesis. Ultimately, we hope that the preclinical standardization will facilitate clinical biomarker discovery for epileptogenesis in man.
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Affiliation(s)
- Erwin A van Vliet
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Noora Puhakka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - James D Mills
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, United Kingdom
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, United Kingdom
| | - Paolo Roncon
- Division of Neuroscience, University Vita-Salute San Raffaele, Milan, Italy
| | - Shalini Das Gupta
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jenni Karttunen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Michele Simonato
- Division of Neuroscience, University Vita-Salute San Raffaele, Milan, Italy.,University of Ferrara, Ferrara, Italy
| | - Katarzyna Lukasiuk
- Laboratory of Epileptogenesis, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Jan A Gorter
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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31
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Systematic review and meta-analysis of differentially expressed miRNAs in experimental and human temporal lobe epilepsy. Sci Rep 2017; 7:11592. [PMID: 28912503 PMCID: PMC5599629 DOI: 10.1038/s41598-017-11510-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/25/2017] [Indexed: 01/08/2023] Open
Abstract
Temporal lobe epilepsy (TLE) is a common chronic neurological disease in humans. A number of studies have demonstrated differential expression of miRNAs in the hippocampus of humans with TLE and in animal models of experimental epilepsy. However, the dissimilarities in experimental design have led to largely discordant results across these studies. Thus, a comprehensive comparison is required in order to better characterize miRNA profiles obtained in various post-status epilepticus (SE) models. We therefore created a database and performed a meta-analysis of differentially expressed miRNAs across 3 post-SE models of epileptogenesis (electrical stimulation, pilocarpine and kainic acid) and human TLE with hippocampal sclerosis (TLE-HS). The database includes data from 11 animal post-SE studies and 3 human TLE-HS studies. A total of 378 differentially expressed miRNAs were collected (274 up-regulated and 198 down-regulated) and analyzed with respect to the post-SE model, time point and animal species. We applied the novel robust rank aggregation method to identify consistently differentially expressed miRNAs across the profiles. It highlighted common and unique miRNAs at different stages of epileptogenesis. The pathway analysis revealed involvement of these miRNAs in key pathogenic pathways underlying epileptogenesis, including inflammation, gliosis and deregulation of the extracellular matrix.
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32
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江 海, 李 平, 张 梅, 张 锋, 苏 丽. RNA-Seq技术及其在胃肠肿瘤研究中的应用现状. Shijie Huaren Xiaohua Zazhi 2017; 25:1564-1571. [DOI: 10.11569/wcjd.v25.i17.1564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
转录组是特定的细胞或组织在特定的时间或状态下转录出来的RNA集合, 转录组研究能够从整体水平研究基因功能以及基因结构, 并能很好的显示处于表达状态的基因数量和活跃程度. 作为转录组学新一代高通量测序技术之一, RNA-Seq技术能够更为快速、准确地为人们提供更多的生物体转录信息, 在生物医学研究中已经得到广泛应用. 随着全球胃肠肿瘤发病率的逐年提高, RNA-Seq技术在胃肠肿瘤研究领域进行全转录组测序分析的应用越来越多, 并取得了一些新的进展. 本文将就RNA-Seq技术原理、优势及其在胃肠肿瘤研究中的具体应用进行论述.
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33
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Kunkle B, Carney R, Kohli M, Naj A, Hamilton-Nelson K, Whitehead P, Wang L, Lang R, Cuccaro M, Vance J, Byrd G, Beecham G, Gilbert J, Martin E, Haines J, Pericak-Vance M. Targeted sequencing of ABCA7 identifies splicing, stop-gain and intronic risk variants for Alzheimer disease. Neurosci Lett 2017; 649:124-129. [DOI: 10.1016/j.neulet.2017.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/07/2017] [Indexed: 12/30/2022]
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34
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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35
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Martin G, Selcuklu SD, Schouest K, Nembaware V, McKeown PC, Seoighe C, Spillane C. Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells. Gene 2017; 598:107-112. [PMID: 27826023 DOI: 10.1016/j.gene.2016.11.004] [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: 07/09/2016] [Revised: 10/16/2016] [Accepted: 11/03/2016] [Indexed: 10/20/2022]
Abstract
Allele-specific splicing is the production of different RNA isoforms from different alleles of a gene. Altered splicing patterns such as exon skipping can have a dramatic effect on the final protein product yet have traditionally proven difficult to predict. We investigated the splicing effects of a set of nine single nucleotide polymorphisms (SNPs) which are predicted to have a direct impact on mRNA splicing, each in a different gene. Predictions were based on SNP location relative to splice junctions and intronic/exonic splicing elements, combined with an analysis of splice isoform expression data from public sources. Of the nine genes tested, six SNPs led to direct impacts on mRNA splicing as determined by the splicing reporter minigene assay and RT-PCR in human HeLa cells, of which four were allele-specific effects. These included previously unreported alternative splicing patterns in the genes ZNF419 and DKKL1. Notably, the SNP in ZNF419, a transcription factor, leads to the deletion of a DNA-binding domain from the protein and is associated with an expression QTL, while the SNP in DKKL1 leads to shortened transcripts predicted to produce a truncated protein. We conclude that the impact of SNP mutations on mRNA splicing, and its biological relevance, can be predicted by integrating SNP position with available data on relative isoform abundance in human cell lines.
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Affiliation(s)
- Grace Martin
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - S Duygu Selcuklu
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Katherine Schouest
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Victoria Nembaware
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Private Bag, Rondebosch, 7700 Cape Town, South Africa
| | - Peter C McKeown
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Charles Spillane
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland.
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36
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Pfau T, Pacheco MP, Sauter T. Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. Brief Bioinform 2016; 17:1060-1069. [PMID: 26615025 PMCID: PMC5142010 DOI: 10.1093/bib/bbv100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Genome-scale metabolic network reconstructions provide a basis for the investigation of the metabolic properties of an organism. There are reconstructions available for multiple organisms, from prokaryotes to higher organisms and methods for the analysis of a reconstruction. One example is the use of flux balance analysis to improve the yields of a target chemical, which has been applied successfully. However, comparison of results between existing reconstructions and models presents a challenge because of the heterogeneity of the available reconstructions, for example, of standards for presenting gene-protein-reaction associations, nomenclature of metabolites and reactions or selection of protonation states. The lack of comparability for gene identifiers or model-specific reactions without annotated evidence often leads to the creation of a new model from scratch, as data cannot be properly matched otherwise. In this contribution, we propose to improve the predictive power of metabolic models by switching from gene-protein-reaction associations to transcript-isoform-reaction associations, thus taking advantage of the improvement of precision in gene expression measurements. To achieve this precision, we discuss available databases that can be used to retrieve this type of information and point at issues that can arise from their neglect. Further, we stress issues that arise from non-standardized building pipelines, like inconsistencies in protonation states. In addition, problems arising from the use of non-specific cofactors, e.g. artificial futile cycles, are discussed, and finally efforts of the metabolic modelling community to unify model reconstructions are highlighted.
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Ita K. Recent trends in the transdermal delivery of therapeutic agents used for the management of neurodegenerative diseases. J Drug Target 2016; 25:406-419. [PMID: 27701893 DOI: 10.1080/1061186x.2016.1245310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
With the increasing proportion of the global geriatric population, it becomes obvious that neurodegenerative diseases will become more widespread. From an epidemiological standpoint, it is necessary to develop new therapeutic agents for the management of Alzheimer's disease, Parkinson's disease, multiple sclerosis and other neurodegenerative disorders. An important approach in this regard involves the use of the transdermal route. With transdermal drug delivery systems (TDDS), it is possible to modulate the pharmacokinetic profiles of these medications and improve patient compliance. Transdermal drug delivery has also been shown to be useful for drugs with short half-life and low or unpredictable bioavailability. In this review, several transdermal drug delivery enhancement technologies are being discussed in relation to the delivery of medications used for the management of neurodegenerative disorders.
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Affiliation(s)
- Kevin Ita
- a College of Pharmacy, Touro University , Mare Island-Vallejo , CA , USA
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38
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Takenaka K, Chen BJ, Modesitt SC, Byrne FL, Hoehn KL, Janitz M. The emerging role of long non-coding RNAs in endometrial cancer. Cancer Genet 2016; 209:445-455. [PMID: 27810073 DOI: 10.1016/j.cancergen.2016.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/19/2016] [Accepted: 09/08/2016] [Indexed: 12/22/2022]
Abstract
The human genome is pervasively transcribed and approximately 98% of the genome is non-coding. Long non-coding RNAs (lncRNAs) are a heterogeneous group of RNA transcripts that are >200 nucleotides in length with minimal to no protein-coding potential. Similar to proteins, lncRNAs have important biological functions in both normal cells and disease states including many types of cancer. This review summarizes recent advances in our understanding of lncRNAs in cancer biology and highlights the potential for lncRNA as diagnostic biomarkers and therapeutics. Herein we focus on the poorly understood role of lncRNAs in endometrial cancer, the most common gynecologic malignancy in the developed world.
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Affiliation(s)
- Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Susan C Modesitt
- Division of Gynecologic Oncology, Obstetrics and Gynecology Department, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Frances L Byrne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kyle L Hoehn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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39
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Kanduc D. Role of codon usage and tRNA changes in rat cytomegalovirus latency and (re)activation. J Basic Microbiol 2016; 56:617-26. [DOI: 10.1002/jobm.201500621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/27/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics; University of Bari; Bari 70126 Italy
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40
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Castrillo JI, Oliver SG. Alzheimer's as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks. Methods Mol Biol 2016; 1303:3-48. [PMID: 26235058 DOI: 10.1007/978-1-4939-2627-5_1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD), and many neurodegenerative disorders, are multifactorial in nature. They involve a combination of genomic, epigenomic, interactomic and environmental factors. Progress is being made, and these complex diseases are beginning to be understood as having their origin in altered states of biological networks at the cellular level. In the case of AD, genomic susceptibility and mechanisms leading to (or accompanying) the impairment of the central Amyloid Precursor Protein (APP) processing and tau networks are widely accepted as major contributors to the diseased state. The derangement of these networks may result in both the gain and loss of functions, increased generation of toxic species (e.g., toxic soluble oligomers and aggregates) and imbalances, whose effects can propagate to supra-cellular levels. Although well sustained by empirical data and widely accepted, this global perspective often overlooks the essential roles played by the main counteracting homeostatic networks (e.g., protein quality control/proteostasis, unfolded protein response, protein folding chaperone networks, disaggregases, ER-associated degradation/ubiquitin proteasome system, endolysosomal network, autophagy, and other stress-protective and clearance networks), whose relevance to AD is just beginning to be fully realized. In this chapter, an integrative perspective is presented. Alzheimer's disease is characterized to be a result of: (a) intrinsic genomic/epigenomic susceptibility and, (b) a continued dynamic interplay between the deranged networks and the central homeostatic networks of nerve cells. This interplay of networks will underlie both the onset and rate of progression of the disease in each individual. Integrative Systems Biology approaches are required to effect its elucidation. Comprehensive Systems Biology experiments at different 'omics levels in simple model organisms, engineered to recapitulate the basic features of AD may illuminate the onset and sequence of events underlying AD. Indeed, studies of models of AD in simple organisms, differentiated cells in culture and rodents are beginning to offer hope that the onset and progression of AD, if detected at an early stage, may be stopped, delayed, or even reversed, by activating or modulating networks involved in proteostasis and the clearance of toxic species. In practice, the incorporation of next-generation neuroimaging, high-throughput and computational approaches are opening the way towards early diagnosis well before irreversible cell death. Thus, the presence or co-occurrence of: (a) accumulation of toxic Aβ oligomers and tau species; (b) altered splicing and transcriptome patterns; (c) impaired redox, proteostatic, and metabolic networks together with, (d) compromised homeostatic capacities may constitute relevant 'AD hallmarks at the cellular level' towards reliable and early diagnosis. From here, preventive lifestyle changes and tailored therapies may be investigated, such as combined strategies aimed at both lowering the production of toxic species and potentiating homeostatic responses, in order to prevent or delay the onset, and arrest, alleviate, or even reverse the progression of the disease.
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Affiliation(s)
- Juan I Castrillo
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK,
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41
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Chen BJ, Mills JD, Janitz C, Janitz M. RNA-Sequencing to Elucidate Early Patterns of Dysregulation Underlying the Onset of Alzheimer's Disease. Methods Mol Biol 2016; 1303:327-347. [PMID: 26235077 DOI: 10.1007/978-1-4939-2627-5_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
With its ability to perform rapid transcriptome profiling and profound transcriptomic analysis powered by high-throughput sequencing at a high resolution with deep coverage, the advent of RNA sequencing technology, RNA-Seq, outperforms other methods in the field, such as microarrays, and has changed our way of performing transcriptomic investigation. Protocols for preparing libraries for RNA-Seq using the Illumina and Roche 454 sequencing platforms are included in this chapter. Common steps for library preparation in both platforms include RNA fragmentation, cDNA synthesis, adaptor ligation, and PCR amplification of cDNA strands. Illumina adopts solid-phase bridge PCR amplification, while 454 uses water-in-oil emulsion-based PCR amplification. Despite differences in the PCR amplification step, both platforms employ the same sequencing-by-synthesis technology for the sequencing process. Application of the RNA-Seq technique in the context of dysregulation of the transcriptome in Alzheimer's disease is also discussed.
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Affiliation(s)
- Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
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42
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Wehrspaun CC, Haerty W, Ponting CP. Microglia recapitulate a hematopoietic master regulator network in the aging human frontal cortex. Neurobiol Aging 2015; 36:2443.e9-2443.e20. [PMID: 26002684 PMCID: PMC4503803 DOI: 10.1016/j.neurobiolaging.2015.04.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/18/2015] [Accepted: 04/17/2015] [Indexed: 12/11/2022]
Abstract
Microglia form the immune system of the brain. Previous studies in cell cultures and animal models suggest altered activation states and cellular senescence in the aged brain. Instead, we analyzed 3 transcriptome data sets from the postmortem frontal cortex of 381 control individuals to show that microglia gene markers assemble into a transcriptional module in a gene coexpression network. These markers predominantly represented M1 and M1/M2b activation phenotypes. Expression of genes in this module generally declines over the adult life span. This decrease was more pronounced in microglia surface receptors for microglia and/or neuron crosstalk than in markers for activation state phenotypes. In addition to these receptors for exogenous signals, microglia are controlled by brain-expressed regulatory factors. We identified a subnetwork of transcription factors, including RUNX1, IRF8, PU.1, and TAL1, which are master regulators (MRs) for the age-dependent microglia module. The causal contributions of these MRs on the microglia module were verified using publicly available ChIP-Seq data. Interactions of these key MRs were preserved in a protein-protein interaction network. Importantly, these MRs appear to be essential for regulating microglia homeostasis in the adult human frontal cortex in addition to their crucial roles in hematopoiesis and myeloid cell-fate decisions during embryogenesis.
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Affiliation(s)
- Claudia C Wehrspaun
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Section on Neuropathology, Clinical Brain Disorders Branch, Genes, Cognition and Psychosis Program, IRP, NIMH, NIH, Bethesda, MD, USA.
| | - Wilfried Haerty
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, UK
| | - Chris P Ponting
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, UK
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43
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Md. SSG, Diego-Álvarez D, Buades C, Romera-López A, Pérez-Cabornero L, Valero-Hervás D, Cantalapiedra D, Bioinformatics, Felipe-Ponce V, Hernández-Poveda G, José Roca M, Casañs C, Fernández-Pedrosa V, M. CC, C. ÁA, P. JCT, C. ÓR, Marco G, Gil M, Miñambres R, Ballester A. DIAGNÓSTICO MOLECULAR DE ENFERMEDADES GENÉTICAS: DEL DIAGNÓSTICO GENÉTICO AL DIAGNÓSTICO GENÓMICO CON LA SECUENCIACIÓN MASIVA. REVISTA MÉDICA CLÍNICA LAS CONDES 2015. [DOI: 10.1016/j.rmclc.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Cui H, Dhroso A, Johnson N, Korkin D. The variation game: Cracking complex genetic disorders with NGS and omics data. Methods 2015; 79-80:18-31. [PMID: 25944472 DOI: 10.1016/j.ymeth.2015.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/27/2015] [Accepted: 04/17/2015] [Indexed: 12/14/2022] Open
Abstract
Tremendous advances in Next Generation Sequencing (NGS) and high-throughput omics methods have brought us one step closer towards mechanistic understanding of the complex disease at the molecular level. In this review, we discuss four basic regulatory mechanisms implicated in complex genetic diseases, such as cancer, neurological disorders, heart disease, diabetes, and many others. The mechanisms, including genetic variations, copy-number variations, posttranscriptional variations, and epigenetic variations, can be detected using a variety of NGS methods. We propose that malfunctions detected in these mechanisms are not necessarily independent, since these malfunctions are often found associated with the same disease and targeting the same gene, group of genes, or functional pathway. As an example, we discuss possible rewiring effects of the cancer-associated genetic, structural, and posttranscriptional variations on the protein-protein interaction (PPI) network centered around P53 protein. The review highlights multi-layered complexity of common genetic disorders and suggests that integration of NGS and omics data is a critical step in developing new computational methods capable of deciphering this complexity.
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Affiliation(s)
- Hongzhu Cui
- Department of Computer Science, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States
| | - Andi Dhroso
- Department of Computer Science, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States
| | - Nathan Johnson
- Department of Computer Science, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States
| | - Dmitry Korkin
- Department of Computer Science, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States; Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States
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45
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Singh NN, Lee BM, Singh RN. Splicing regulation in spinal muscular atrophy by an RNA structure formed by long-distance interactions. Ann N Y Acad Sci 2015; 1341:176-87. [PMID: 25727246 PMCID: PMC4651915 DOI: 10.1111/nyas.12727] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Humans carry two copies of the survival motor neuron gene: SMN1 and SMN2. Loss of SMN1 coupled with skipping of SMN2 exon 7 causes spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. Our discovery of intronic splicing silencer N1 (ISS-N1) is a promising target, currently in a phase III clinical trial, for an antisense oligonucleotide-mediated splicing correction in SMA. We have recently shown that the first residue of ISS-N1 is locked in a unique RNA structure that we term ISTL1 (internal stem through long-distance interaction-1). Complementary strands of ISTL1 are separated from each other by 279 nucleotides. Using site-specific mutations and chemical structure probing, we confirmed the formation and functional significance of ISTL1. Located in the middle of intron 7, the 3' strand of ISTL1 falls within an inhibitory region that we term ISS-N2. We demonstrate that an antisense oligonucleotide-mediated sequestration of ISS-N2 fully corrects SMN2 exon 7 splicing and restores high levels of SMN in SMA patient cells. These results underscore the therapeutic potential of the regulatory information present in a secondary and high-order RNA structure of a human intron.
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Affiliation(s)
- Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa
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46
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Nussbacher JK, Batra R, Lagier-Tourenne C, Yeo GW. RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci 2015; 38:226-36. [PMID: 25765321 PMCID: PMC4403644 DOI: 10.1016/j.tins.2015.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/02/2015] [Accepted: 02/09/2015] [Indexed: 12/13/2022]
Abstract
As critical players in gene regulation, RNA binding proteins (RBPs) are taking center stage in our understanding of cellular function and disease. In our era of bench-top sequencers and unprecedented computational power, biological questions can be addressed in a systematic, genome-wide manner. Development of high-throughput sequencing (Seq) methodologies provides unparalleled potential to discover new mechanisms of disease-associated perturbations of RNA homeostasis. Complementary to candidate single-gene studies, these innovative technologies may elicit the discovery of unexpected mechanisms, and enable us to determine the widespread influence of the multifunctional RBPs on their targets. Given that the disruption of RNA processing is increasingly implicated in neurological diseases, these approaches will continue to provide insights into the roles of RBPs in disease pathogenesis.
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Affiliation(s)
- Julia K Nussbacher
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Ranjan Batra
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
| | - Gene W Yeo
- Department of Cellular and Molecule Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Department of Physiology, National University of Singapore, Singapore.
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47
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Chen J, Mills JD, Halliday GM, Janitz M. The role of transcriptional control in multiple system atrophy. Neurobiol Aging 2015; 36:394-400. [DOI: 10.1016/j.neurobiolaging.2014.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/29/2014] [Accepted: 08/12/2014] [Indexed: 12/15/2022]
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Na D, Son H, Gsponer J. Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity. BMC Genomics 2014; 15:1091. [PMID: 25495442 PMCID: PMC4298957 DOI: 10.1186/1471-2164-15-1091] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Communalities between large sets of genes obtained from high-throughput experiments are often identified by searching for enrichments of genes with the same Gene Ontology (GO) annotations. The GO analysis tools used for these enrichment analyses assume that GO terms are independent and the semantic distances between all parent-child terms are identical, which is not true in a biological sense. In addition these tools output lists of often redundant or too specific GO terms, which are difficult to interpret in the context of the biological question investigated by the user. Therefore, there is a demand for a robust and reliable method for gene categorization and enrichment analysis. RESULTS We have developed Categorizer, a tool that classifies genes into user-defined groups (categories) and calculates p-values for the enrichment of the categories. Categorizer identifies the biologically best-fit category for each gene by taking advantage of a specialized semantic similarity measure for GO terms. We demonstrate that Categorizer provides improved categorization and enrichment results of genetic modifiers of Huntington's disease compared to a classical GO Slim-based approach or categorizations using other semantic similarity measures. CONCLUSION Categorizer enables more accurate categorizations of genes than currently available methods. This new tool will help experimental and computational biologists analyzing genomic and proteomic data according to their specific needs in a more reliable manner.
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Affiliation(s)
| | | | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Centre for High-throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada.
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49
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Mills JD, Kim WS, Halliday GM, Janitz M. Transcriptome analysis of grey and white matter cortical tissue in multiple system atrophy. Neurogenetics 2014; 16:107-22. [PMID: 25370810 DOI: 10.1007/s10048-014-0430-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/20/2014] [Indexed: 01/02/2023]
Abstract
Multiple system atrophy (MSA) is a distinct member of a group of neurodegenerative diseases known as α-synucleinopathies, which are characterized by the presence of aggregated α-synuclein in the brain. MSA is unique in that the principal site for α-synuclein deposition is in the oligodendrocytes rather than neurons. The cause of MSA is unknown, and the pathogenesis of MSA is still largely speculative. Brain transcriptome perturbations during the onset and progression of MSA are mostly unknown. Using RNA sequencing, we performed a comparative transcriptome profiling analysis of the grey matter (GM) and white matter (WM) of the frontal cortex of MSA and control brains. The transcriptome sequencing revealed increased expression of the alpha and beta haemoglobin genes in MSA WM, decreased expression of the transthyretin (TTR) gene in MSA GM and numerous region-specific long intervening non-coding RNAs (lincRNAs). In contrast, we observed only moderate changes in the expression patterns of the α-synuclein (SNCA) gene, which confirmed previous observations by other research groups. Our study suggests that at the transcriptional level, MSA pathology may be related to increased iron levels in WM and perturbations of the non-coding fraction of the transcriptome.
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Affiliation(s)
- James D Mills
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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50
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Siva K, Covello G, Denti MA. Exon-skipping antisense oligonucleotides to correct missplicing in neurogenetic diseases. Nucleic Acid Ther 2014; 24:69-86. [PMID: 24506781 DOI: 10.1089/nat.2013.0461] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alternative splicing is an important regulator of the transcriptome. However, mutations may cause alteration of splicing patterns, which in turn leads to disease. During the past 10 years, exon skipping has been looked upon as a powerful tool for correction of missplicing in disease and progress has been made towards clinical trials. In this review, we discuss the use of antisense oligonucleotides to correct splicing defects through exon skipping, with a special focus on diseases affecting the nervous system, and the latest stage achieved in its progress.
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Affiliation(s)
- Kavitha Siva
- 1 Center for Integrative Biology (CIBIO), University of Trento , Trento, Italy
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