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Newman JRB, Long SA, Speake C, Greenbaum CJ, Cerosaletti K, Rich SS, Onengut-Gumuscu S, McIntyre LM, Buckner JH, Concannon P. Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes. Commun Biol 2023; 6:988. [PMID: 37758901 PMCID: PMC10533491 DOI: 10.1038/s42003-023-05327-7] [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: 08/16/2022] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Genome-wide association studies have identified numerous loci with allelic associations to Type 1 Diabetes (T1D) risk. Most disease-associated variants are enriched in regulatory sequences active in lymphoid cell types, suggesting that lymphocyte gene expression is altered in T1D. Here we assay gene expression between T1D cases and healthy controls in two autoimmunity-relevant lymphocyte cell types, memory CD4+/CD25+ regulatory T cells (Treg) and memory CD4+/CD25- T cells, using a splicing event-based approach to characterize tissue-specific transcriptomes. Limited differences in isoform usage between T1D cases and controls are observed in memory CD4+/CD25- T-cells. In Tregs, 402 genes demonstrate differences in isoform usage between cases and controls, particularly RNA recognition and splicing factor genes. Many of these genes are regulated by the variable inclusion of exons that can trigger nonsense mediated decay. Our results suggest that dysregulation of gene expression, through shifts in alternative splicing in Tregs, contributes to T1D pathophysiology.
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Affiliation(s)
- Jeremy R B Newman
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, 32601, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32601, USA
| | - S Alice Long
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Carla J Greenbaum
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Karen Cerosaletti
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Lauren M McIntyre
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32601, USA
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, 32601, USA
| | - Jane H Buckner
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Patrick Concannon
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, 32601, USA.
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32601, USA.
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2
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González-Rodríguez P, Klionsky DJ, Joseph B. Autophagy regulation by RNA alternative splicing and implications in human diseases. Nat Commun 2022; 13:2735. [PMID: 35585060 PMCID: PMC9117662 DOI: 10.1038/s41467-022-30433-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Autophagy and RNA alternative splicing are two evolutionarily conserved processes involved in overlapping physiological and pathological processes. However, the extent of functional connection is not well defined. Here, we consider the role for alternative splicing and generation of autophagy-related gene isoforms in the regulation of autophagy in recent work. The impact of changes to the RNA alternative splicing machinery and production of alternative spliced isoforms on autophagy are reviewed with particular focus on disease relevance. The use of drugs targeting both alternative splicing and autophagy as well as the selective regulation of single autophagy-related protein isoforms, are considered as therapeutic strategies.
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Affiliation(s)
- Patricia González-Rodríguez
- Institute of Environmental Medicine, Toxicology Unit, Karolinska Institutet, Stockholm, Sweden
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Daniel J Klionsky
- Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Bertrand Joseph
- Institute of Environmental Medicine, Toxicology Unit, Karolinska Institutet, Stockholm, Sweden.
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3
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Does the Expression and Epigenetics of Genes Involved in Monogenic Forms of Parkinson’s Disease Influence Sporadic Forms? Genes (Basel) 2022; 13:genes13030479. [PMID: 35328033 PMCID: PMC8951612 DOI: 10.3390/genes13030479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Parkinson’s disease (PD) is a disorder characterized by a triad of motor symptoms (akinesia, rigidity, resting tremor) related to loss of dopaminergic neurons mainly in the Substantia nigra pars compacta. Diagnosis is often made after a substantial loss of neurons has already occurred, and while dopamine replacement therapies improve symptoms, they do not modify the course of the disease. Although some biological mechanisms involved in the disease have been identified, such as oxidative stress and accumulation of misfolded proteins, they do not explain entirely PD pathophysiology, and a need for a better understanding remains. Neurodegenerative diseases, including PD, appear to be the result of complex interactions between genetic and environmental factors. The latter can alter gene expression by causing epigenetic changes, such as DNA methylation, post-translational modification of histones and non-coding RNAs. Regulation of genes responsible for monogenic forms of PD may be involved in sporadic PD. This review will focus on the epigenetic mechanisms regulating their expression, since these are the genes for which we currently have the most information available. Despite technical challenges, epigenetic epidemiology offers new insights on revealing altered biological pathways and identifying predictive biomarkers for the onset and progression of PD.
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4
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Randhawa A, Kapila R, Schwartz RA. Leprosy: what is new. Int J Dermatol 2021; 61:733-738. [PMID: 34826151 DOI: 10.1111/ijd.15998] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 12/25/2022]
Abstract
Leprosy, also known as Hansen's disease, is an age-old chronic granulomatous infection characterized by prominent cutaneous and neurologic findings. Long known to be caused by Mycobacterium leprae, a new etiologic species was identified and linked in 2008, Mycobacterium lepromatosis. The BCG vaccine with highly variable efficacy may soon be replaced by the first leprosy-specific subunit vaccine LepVax, which has recently moved forward in human trials. Recent evidence supporting theories of zoonotic transmission from armadillos and the less-discussed Eurasian red squirrels has emerged. Knowledge on genetic polymorphisms that may increase leprosy susceptibility, such as the newly uncovered mitochondrial ribosomal protein S5 (MRPS5) polymorphism in the Chinese population, has provided a fresh perspective and direction. Further, we will delineate the latest information on leprosy, including the possible effects of leprosy coinfection with COVID-19, HIV, and HTLV-1, and the shift to newer leprosy therapies and treatment regimens.
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Affiliation(s)
- Avneet Randhawa
- Rutgers University New Jersey Medical School, New Jersey Medical School, Newark, NJ, USA
| | - Rajendra Kapila
- Rutgers University New Jersey Medical School, New Jersey Medical School, Newark, NJ, USA
| | - Robert A Schwartz
- Rutgers University New Jersey Medical School, New Jersey Medical School, Newark, NJ, USA
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5
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Murillo-González FE, García-Aguilar R, Vega L, Elizondo G. Regulation of Parkin expression as the key balance between neural survival and cancer cell death. Biochem Pharmacol 2021; 190:114650. [PMID: 34111426 DOI: 10.1016/j.bcp.2021.114650] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/25/2022]
Abstract
Parkin is a cytosolic E3 ubiquitin ligase that plays an important role in neuroprotection by targeting several proteins to be degraded by the 26S proteasome. Its dysfunction has been associated not only with Parkinson's disease (PD) but also with other neurodegenerative pathologies, such as Alzheimer's disease and Huntington's disease. More recently, Parkin has been identified as a tumor suppressor gene implicated in cancer development. Due to the important roles that this E3 ubiquitin ligase plays in cellular homeostasis, its expression, activity, and turnover are tightly regulated. Several reviews have addressed Parkin regulation; however, genetic and epigenetic regulation have been excluded. In addition to posttranslational modifications (PTMs), this review examines the regulatory mechanisms that control Parkin function through gene expression, epigenetic regulation, and degradation. Furthermore, the consequences of disrupting these regulatory processes on human health are discussed.
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Affiliation(s)
| | | | - Libia Vega
- Department of Toxicology, CINVESTAV-IPN, Av. IPN 2508, C.P. 07360 Mexico City, Mexico
| | - Guillermo Elizondo
- Department of Cellular Biology, CINVESTAV-IPN, Av. IPN 2508, C.P. 07360 Mexico City, Mexico.
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6
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The contribution of CNVs to the most common aging-related neurodegenerative diseases. Aging Clin Exp Res 2021; 33:1187-1195. [PMID: 32026430 DOI: 10.1007/s40520-020-01485-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
Alzheimer and Parkinson's diseases are neurodegenerative aging-related pathological conditions, mainly caused by the interplay of genetic and non-genetic factors and whose incidence rate is going to drastically increase given the growing life expectancy. To address these complex multifactorial traits, a systems biology strategy is needed to highlight genotype-phenotype correlations as well as overlapping gene signatures. Copy number variants (CNVs) are structural chromosomal imbalances that can have pathogenic nature causing or contributing to the disease onset or progression. Moreover, neurons affected by CNVs have been found to decline in number depending on age in healthy controls and may be selectively vulnerable to aging-related cell-death. In this review, we aim to update the reader on the role of these variations in the pathogenesis of Alzheimer and Parkinson diseases. To widen the comprehension of pathogenic mechanisms underlying them, we discuss variations detected from blood or brain specimens, as well as overlapped signatures between the two pathologies.
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7
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Perwez A, Wahabi K, Rizvi MA. Parkin: A targetable linchpin in human malignancies. Biochim Biophys Acta Rev Cancer 2021; 1876:188533. [PMID: 33785381 DOI: 10.1016/j.bbcan.2021.188533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/21/2021] [Accepted: 03/21/2021] [Indexed: 12/16/2022]
Abstract
Parkin, an E3 ubiquitin ligase has been found to be deregulated in a variety of human cancers. Our current understanding is endowed with strong evidences that Parkin plays crucial role in the pathogenesis of cancer by controlling/interfering with major hallmarks of cancer delineated till today. Consistent with the idea of mitophagy, the existing studies imitates the tumor suppressive potential of Parkin, resolved by its capacity to regulate cell proliferation, cell migration, angiogenesis, apoptosis and overall cellular survival. Dysfunction of Parkin has resulted in the loss of ubiquitination of cell cycle components followed by their accumulation leading to genomic instability, perturbed cell cycle and eventually tumor progression. In this review, we provide an overview of current knowledge about the critical role of Parkin in cancer development and progression and have focussed on its therapeutic implications highlighting the diagnostic and prognostic value of Parkin as a biomarker. We earnestly hope that an in-depth knowledge of Parkin will provide a linchpin to target in various cancers that will open a new door of clinical applications and therapeutics.
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Affiliation(s)
- Ahmad Perwez
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Khushnuma Wahabi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Moshahid A Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
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8
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Ahmed SAH, Ansari SA, Mensah-Brown EPK, Emerald BS. The role of DNA methylation in the pathogenesis of type 2 diabetes mellitus. Clin Epigenetics 2020; 12:104. [PMID: 32653024 PMCID: PMC7353744 DOI: 10.1186/s13148-020-00896-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Diabetes mellitus (DM) is a chronic condition characterised by β cell dysfunction and persistent hyperglycaemia. The disorder can be due to the absence of adequate pancreatic insulin production or a weak cellular response to insulin signalling. Among the three types of DM, namely, type 1 DM (T1DM), type 2 DM (T2DM), and gestational DM (GDM); T2DM accounts for almost 90% of diabetes cases worldwide. Epigenetic traits are stably heritable phenotypes that result from certain changes that affect gene function without altering the gene sequence. While epigenetic traits are considered reversible modifications, they can be inherited mitotically and meiotically. In addition, epigenetic traits can randomly arise in response to environmental factors or certain genetic mutations or lesions, such as those affecting the enzymes that catalyse the epigenetic modification. In this review, we focus on the role of DNA methylation, a type of epigenetic modification, in the pathogenesis of T2DM.
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Affiliation(s)
- Sanabil Ali Hassan Ahmed
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Suraiya Anjum Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Eric P K Mensah-Brown
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates.
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9
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Splicing Players Are Differently Expressed in Sporadic Amyotrophic Lateral Sclerosis Molecular Clusters and Brain Regions. Cells 2020; 9:cells9010159. [PMID: 31936368 PMCID: PMC7017305 DOI: 10.3390/cells9010159] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/23/2019] [Accepted: 01/04/2020] [Indexed: 12/12/2022] Open
Abstract
Splicing is a tightly orchestrated process by which the brain produces protein diversity over time and space. While this process specializes and diversifies neurons, its deregulation may be responsible for their selective degeneration. In amyotrophic lateral sclerosis (ALS), splicing defects have been investigated at the singular gene level without considering the higher-order level, involving the entire splicing machinery. In this study, we analyzed the complete spectrum (396) of genes encoding splicing factors in the motor cortex (41) and spinal cord (40) samples from control and sporadic ALS (SALS) patients. A substantial number of genes (184) displayed significant expression changes in tissue types or disease states, were implicated in distinct splicing complexes and showed different topological hierarchical roles based on protein–protein interactions. The deregulation of one of these splicing factors has a central topological role, i.e., the transcription factor YBX1, which might also have an impact on stress granule formation, a pathological marker associated with ALS.
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10
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La Cognata V, Morello G, Gentile G, Cavalcanti F, Cittadella R, Conforti FL, De Marco EV, Magariello A, Muglia M, Patitucci A, Spadafora P, D’Agata V, Ruggieri M, Cavallaro S. NeuroArray: A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders. Curr Genomics 2018; 19:431-443. [PMID: 30258275 PMCID: PMC6128384 DOI: 10.2174/1389202919666180404105451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases. METHODS In this report, we comprehensively describe the design method, the procedures, validation, and implementation of an exon-centric customized aCGH (NeuroArray 1.0), tailored to detect both single and multi-exon deletions or duplications in a large set of multi- and monogenic neurological diseases. This focused platform enables a targeted measurement of structural imbalances across the human genome, targeting the clinically relevant genes at exon-level resolution. CONCLUSION An increasing use of the NeuroArray platform may offer new insights in investigating potential overlapping gene signatures among neurological conditions and defining genotype-phenotype relationships.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sebastiano Cavallaro
- Address correspondence to this author at the Institute of Neurological Sciences, National Research Council, Via Paolo Gaifami 18, 95125, Catania, Italy; Tel: +39-095-7338111; E-mail:
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11
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Abstract
Osteosarcoma (OS) is the most common primary malignant bone tumor mainly occurring in children and adolescents. In past decades, studies revealed that PARK2 was a vital tumor suppressor gene in many malignant solid tumors. However, the role of PARK2 in OS remains largely unclear. Therefore, we assessed PARK2 expression in OS tissue and adjacent non-tumor tissues by immunohistochemical (IHC) analysis, and evaluated PARK2 mRNA expression in OS cell lines by real-time PCR analysis. The HOS and U2OS cell lines were employed to establish a PARK2 overexpression model. Using this model, we investigated the potential role of PARK2 in OS and explored the underlying molecular mechanisms. Our study showed PARK2 was downregulated in OS tissue and cell lines, which was significantly associated with higher tumor stage (P < 0.05). Overexpression of PARK2 arrested the cell cycle, inhibited cell proliferation, migration, and invasion, induced cell apoptosis, and reduced tube formation in vitro. Moreover, overexpression of PARK2 significantly suppressed tumor growth and angiogenesis in vivo. Additionally, PARK2 negatively regulated OS development through the JAK2/STAT3/VEGF pathway. Our findings demonstrate that PARK2 is a tumor suppressor gene that may negatively affect OS growth and angiogenesis via partly inhibiting the JAK2/STAT3/VEGF signaling pathway.
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12
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Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Res 2018; 28:396-411. [PMID: 29440222 PMCID: PMC5848618 DOI: 10.1101/gr.222976.117] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 01/08/2018] [Indexed: 01/15/2023]
Abstract
High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, resulting more frequently in novel ORFs than novel UTRs, and are enriched in both general metabolic and neural-specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read-based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases, we find that alternative isoforms are elusive to proteogenomics detection. SQANTI allows the user to maximize the analytical outcome of long-read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes.
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Affiliation(s)
- Manuel Tardaguila
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Lorena de la Fuente
- Genomics of Gene Expression Laboratory, Centro de Investigaciones Principe Felipe (CIPF), 46012 Valencia, Spain
| | - Cristina Marti
- Genomics of Gene Expression Laboratory, Centro de Investigaciones Principe Felipe (CIPF), 46012 Valencia, Spain
| | - Cécile Pereira
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | | | - Hector Del Risco
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Marc Ferrell
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | | | - Marissa Macchietto
- Department of Developmental and Cell Biology, University of California, Irvine, California 92617, USA
| | - Kenneth Verheggen
- VIB-UGent Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Mariola Edelmann
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Iakes Ezkurdia
- Centro Nacional de Investigaciones Cardiovasculares CNIC, 28029 Madrid, Spain
| | - Jesus Vazquez
- Centro Nacional de Investigaciones Cardiovasculares CNIC, 28029 Madrid, Spain
| | - Michael Tress
- Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, California 92617, USA
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Susana Rodriguez-Navarro
- Gene Expression and mRNA Metabolism Laboratory, CSIC, IBV, 46010 Valencia, Spain
- Gene Expression and mRNA Metabolism Laboratory, CIPF, 46012 Valencia, Spain
| | | | - Ana Conesa
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
- Genomics of Gene Expression Laboratory, Centro de Investigaciones Principe Felipe (CIPF), 46012 Valencia, Spain
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13
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Bejar R. Splicing Factor Mutations in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 907:215-28. [PMID: 27256388 DOI: 10.1007/978-3-319-29073-7_9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many cancers demonstrate aberrant splicing patterns that contribute to their development and progression. Recently, recurrent somatic mutations of genes encoding core subunits of the spliceosome have been identified in several different cancer types. These mutations are most common in hematologic malignancies like the myelodysplastic syndromes (MDS), acute myeloid leukemia, and chronic lymphocytic leukemia, but also in occur in several solid tumors at lower frequency. The most frequent mutations occur in SF3B1, U2AF1, SRSF2, and ZRSR2 and are largely exclusive of each other. Mutations in SF3B1, U2AF1, and SRSF2 acquire heterozygous missense mutations in specific codons, resembling oncogenes. ZRSR2 mutations include clear loss-of-function variants, a pattern more common to tumor suppressor genes. These splicing factors are associated with distinct clinical phenotypes and patterns of mutation in different malignancies. Mutations have both diagnostic and prognostic relevance. Splicing factor mutations appear to affect only a minority of transcripts which show little overlap by mutation type. How differences in splicing caused by somatic mutations of spliceosome subunits lead to oncogenesis is not clear and may involve different targets in each disease type. However, cells with mutated splicing machinery may be particularly vulnerable to further disruption of the spliceosome suggesting a novel strategy for the targeted therapy of cancers.
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Affiliation(s)
- Rafael Bejar
- Division of Hematology and Oncology, UC San Diego Moores Cancer Center, La Jolla, CA, USA.
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14
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La Cognata V, Maugeri G, D'Amico AG, Saccone S, Federico C, Cavallaro S, D'Agata V. Differential expression of PARK2 splice isoforms in an in vitro model of dopaminergic-like neurons exposed to toxic insults mimicking Parkinson's disease. J Cell Biochem 2017; 119:1062-1073. [PMID: 28688199 DOI: 10.1002/jcb.26274] [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] [Received: 05/29/2017] [Accepted: 07/07/2017] [Indexed: 12/16/2022]
Abstract
Mutations in PARK2 (or parkin) are responsible for 50% of cases of autosomal-recessive juvenile-onset Parkinson's disease (PD). To date, 21 alternative splice variants of the human gene have been cloned. Yet most studies have focused on the full-length protein, whereas the spectrum of the parkin isoforms expressed in PD has never been investigated. In this study, the role of parkin proteins in PD neurodegeneration was explored for the first time by analyzing their expression profile in an in vitro model of PD. To do so, undifferentiated and all-trans-retinoic-acid (RA)-differentiated SH-SY5Y cells (which thereby acquire a PD-like phenotype) were exposed to PD-mimicking neurotoxins: 1-methyl-4-phenylpyridinium (MPP+ ) and 6-hydroxydopamine (6-OHDA) are widely used in PD models, whereas carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and carbobenzoxy-Leu-Leu-leucinal (MG132) interfere, respectively, with mitochondrial mitophagy and proteasomal degradation. Following treatment with each neurotoxin H1, the first parkin isoform to be cloned, was down-regulated compared to the respective controls both in undifferentiated and RA-differentiated cells. In contrast, the expression pattern of the minor splice isoforms varied as a function of the compound used: it was largely unchanged in both cell cultures (eg, H21-H6, H12, XP isoform) or it showed virtually opposite alterations in undifferentiated and RA-differentiated cells (eg, H20 and H3 isoform). This complex picture suggests that up- or down-regulation may be a direct effect of toxin exposure, and that the different isoforms may exert different actions in neurodegeneration via modulation of different molecular pathways.
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Affiliation(s)
- Valentina La Cognata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Institute of Neurological Sciences, National Research Council, Catania, Italy
| | - Grazia Maugeri
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Agata Grazia D'Amico
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Department of Human Science and Promotion of Quality of Life, San Raffaele Open University of Rome, Rome, Italy
| | - Salvatore Saccone
- Section of Animal Biology, Department of Biological, Geological, and Environmental Sciences, University of Catania, Catania, Italy
| | - Concetta Federico
- Section of Animal Biology, Department of Biological, Geological, and Environmental Sciences, University of Catania, Catania, Italy
| | | | - Velia D'Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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D'Amico AG, Maugeri G, Reitano R, Cavallaro S, D'Agata V. Proteomic Analysis of Parkin Isoforms Expression in Different Rat Brain Areas. Protein J 2017; 35:354-362. [PMID: 27601173 DOI: 10.1007/s10930-016-9679-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PARK2 gene's mutations are related to the familial form of juvenile Parkinsonism, also known as the autosomic recessive juvenile Parkinsonism. This gene encodes for parkin, a 465-amino acid protein. To date, a large number of parkin isoforms, generated by an alternative splicing mechanism, have been described. Currently, Gene Bank lists 27 rat PARK2 transcripts, which matches to 20 exclusive parkin alternative splice variants. Despite the existence of these isoforms, most of the studies carried out so far, have been focused only on the originally cloned parkin. In this work we have analyzed the expression profile of parkin isoforms in some rat brain areas including prefrontal cortex, hippocampus, substantia nigra and cerebellum. To discriminate among these isoforms, we detected their localization through the use of two antibodies that are able to identify different domains of the parkin canonical sequence. Our analysis has revealed that at least fourteen parkin isoforms are expressed in rat brain with a various distribution in the regions analyzed. Our study might help to elucidate the pathophysiological role of these proteins in the central nervous system.
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Affiliation(s)
- Agata Grazia D'Amico
- San Raffaele Open University of Rome, Rome, Italy.,Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia, 87, 95123, Catania, Italy
| | - Grazia Maugeri
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia, 87, 95123, Catania, Italy
| | - Rita Reitano
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia, 87, 95123, Catania, Italy
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences, Italian National Research Council, Catania, Italy
| | - Velia D'Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia, 87, 95123, Catania, Italy.
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16
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WT1 Alternative Splicing: Role of Its Isoforms in Neuroblastoma. J Mol Neurosci 2017; 62:131-141. [DOI: 10.1007/s12031-017-0930-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/08/2017] [Indexed: 02/07/2023]
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17
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Annalora AJ, Marcus CB, Iversen PL. Alternative Splicing in the Cytochrome P450 Superfamily Expands Protein Diversity to Augment Gene Function and Redirect Human Drug Metabolism. Drug Metab Dispos 2017; 45:375-389. [DOI: 10.1124/dmd.116.073254] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022] Open
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18
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Copy number variability in Parkinson's disease: assembling the puzzle through a systems biology approach. Hum Genet 2016; 136:13-37. [PMID: 27896429 PMCID: PMC5214768 DOI: 10.1007/s00439-016-1749-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
Abstract
Parkinson’s disease (PD), the second most common progressive neurodegenerative disorder of aging, was long believed to be a non-genetic sporadic origin syndrome. The proof that several genetic loci are responsible for rare Mendelian forms has represented a revolutionary breakthrough, enabling to reveal molecular mechanisms underlying this debilitating still incurable condition. While single nucleotide polymorphisms (SNPs) and small indels constitute the most commonly investigated DNA variations accounting for only a limited number of PD cases, larger genomic molecular rearrangements have emerged as significant PD-causing mutations, including submicroscopic Copy Number Variations (CNVs). CNVs constitute a prevalent source of genomic variations and substantially participate in each individual’s genomic makeup and phenotypic outcome. However, the majority of genetic studies have focused their attention on single candidate-gene mutations or on common variants reaching a significant statistical level of acceptance. This gene-centric approach is insufficient to uncover the genetic background of polygenic multifactorial disorders like PD, and potentially masks rare individual CNVs that all together might contribute to disease development or progression. In this review, we will discuss literature and bioinformatic data describing the involvement of CNVs on PD pathobiology. We will analyze the most frequent copy number changes in familiar PD genes and provide a “systems biology” overview of rare individual rearrangements that could functionally act on commonly deregulated molecular pathways. Assessing the global genome-wide burden of CNVs in PD patients may reveal new disease-related molecular mechanisms, and open the window to a new possible genetic scenario in the unsolved PD puzzle.
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19
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A customized high-resolution array-comparative genomic hybridization to explore copy number variations in Parkinson's disease. Neurogenetics 2016; 17:233-244. [PMID: 27637465 PMCID: PMC5566182 DOI: 10.1007/s10048-016-0494-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022]
Abstract
Parkinson’s disease (PD), the second most common progressive neurodegenerative disorder, was long believed to be a non-genetic sporadic syndrome. Today, only a small percentage of PD cases with genetic inheritance patterns are known, often complicated by reduced penetrance and variable expressivity. The few well-characterized Mendelian genes, together with a number of risk factors, contribute to the major sporadic forms of the disease, thus delineating an intricate genetic profile at the basis of this debilitating and incurable condition. Along with single nucleotide changes, gene-dosage abnormalities and copy number variations (CNVs) have emerged as significant disease-causing mutations in PD. However, due to their size variability and to the quantitative nature of the assay, CNV genotyping is particularly challenging. For this reason, innovative high-throughput platforms and bioinformatics algorithms are increasingly replacing classical CNV detection methods. Here, we report the design strategy, development, validation and implementation of NeuroArray, a customized exon-centric high-resolution array-based comparative genomic hybridization (aCGH) tailored to detect single/multi-exon deletions and duplications in a large panel of PD-related genes. This targeted design allows for a focused evaluation of structural imbalances in clinically relevant PD genes, combining exon-level resolution with genome-wide coverage. The NeuroArray platform may offer new insights in elucidating inherited potential or de novo structural alterations in PD patients and investigating new candidate genes.
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20
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Maugeri G, D'Amico AG, Reitano R, Saccone S, Federico C, Cavallaro S, D'Agata V. Parkin modulates expression of HIF-1α and HIF-3α during hypoxia in gliobastoma-derived cell lines in vitro. Cell Tissue Res 2016; 364:465-474. [PMID: 26742768 DOI: 10.1007/s00441-015-2340-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/28/2015] [Accepted: 12/02/2015] [Indexed: 12/11/2022]
Abstract
Mutation of the Parkin gene causes an autosomal recessive juvenile-onset form of Parkinson's disease. However, recently, it has been also linked to a wide variety of malignancies, including glioblastoma multiforme (GBM). In this pathology, Parkin exhibits a tumor suppressor role by mitigating the proliferation rate in both in vitro and in vivo models. However, Parkin involvement in the hypoxic process has not as yet been investigated. GBM is the most common and aggressive primary brain tumor in adults and is characterized by hypoxic areas. The low oxygen supply causes the expression of hypoxia-inducible factors (HIFs) leading to an accumulation of pro-angiogenic factors and tumoral invasiveness. We assess the relationship between Parkin and two HIFs expressed during hypoxic conditions, namely HIF-1α and HIF-3α. Our data show that Parkin is downregulated under hypoxia and that it interferes with HIF expression based on cellular oxygen tension. These results suggest a role for the involvement of Parkin in GBM, although further studies will be needed to understand the mechanism by which it modulates HIF-1α and HIF-3α expression.
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Affiliation(s)
- Grazia Maugeri
- Sections of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia 87, 95123, Catania, Italy
| | - Agata Grazia D'Amico
- Sections of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia 87, 95123, Catania, Italy
- San Raffaele Telematic University of Rome, Rome, Italy
| | - Rita Reitano
- Sections of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia 87, 95123, Catania, Italy
| | - Salvatore Saccone
- Section of Animal Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Concetta Federico
- Section of Animal Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Sebastiano Cavallaro
- Functional Genomics Unit, Institute of Neurological Sciences, Italian National Research Council, Catania, Italy
| | - Velia D'Agata
- Sections of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, Via S.Sofia 87, 95123, Catania, Italy.
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21
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MAUGERI GRAZIA, D'AMICO AGATAGRAZIA, MAGRO GAETANO, SALVATORELLI LUCIA, BARBAGALLO GIUSEPPEM, SACCONE SALVATORE, DRAGO FILIPPO, CAVALLARO SEBASTIANO, D'AGATA VELIA. Expression profile of parkin isoforms in human gliomas. Int J Oncol 2015; 47:1282-92. [DOI: 10.3892/ijo.2015.3105] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/12/2015] [Indexed: 11/05/2022] Open
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22
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Luft FC. Aberrant transcriptional regulation could explain phenotypic variability in autosomal recessive polycystic kidney disease. J Mol Med (Berl) 2015; 92:1011-4. [PMID: 25096485 DOI: 10.1007/s00109-014-1197-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Friedrich C Luft
- Experimental and Clinical Research Center, Charité Medical Faculty, Berlin, Germany,
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23
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Splicing: is there an alternative contribution to Parkinson's disease? Neurogenetics 2015; 16:245-63. [PMID: 25980689 PMCID: PMC4573652 DOI: 10.1007/s10048-015-0449-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 05/04/2015] [Indexed: 12/21/2022]
Abstract
Alternative splicing is a crucial mechanism of gene expression regulation that enormously increases the coding potential of our genome and represents an intermediate step between messenger RNA (mRNA) transcription and protein posttranslational modifications. Alternative splicing occupies a central position in the development and functions of the nervous system. Therefore, its deregulation frequently leads to several neurological human disorders. In the present review, we provide an updated overview on the impact of alternative splicing in Parkinson's disease (PD), the second most common neurodegenerative disorder worldwide. We will describe the alternative splicing of major PD-linked genes by collecting the current evidences about this intricate and not carefully explored aspect. Assessing the role of this mechanism on PD pathobiology may represent a central step toward an improved understanding of this complex disease.
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24
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Lal D, Ruppert AK, Trucks H, Schulz H, de Kovel CG, Kasteleijn-Nolst Trenité D, Sonsma ACM, Koeleman BP, Lindhout D, Weber YG, Lerche H, Kapser C, Schankin CJ, Kunz WS, Surges R, Elger CE, Gaus V, Schmitz B, Helbig I, Muhle H, Stephani U, Klein KM, Rosenow F, Neubauer BA, Reinthaler EM, Zimprich F, Feucht M, Møller RS, Hjalgrim H, De Jonghe P, Suls A, Lieb W, Franke A, Strauch K, Gieger C, Schurmann C, Schminke U, Nürnberg P, Sander T. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies. PLoS Genet 2015; 11:e1005226. [PMID: 25950944 PMCID: PMC4423931 DOI: 10.1371/journal.pgen.1005226] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/16/2015] [Indexed: 01/06/2023] Open
Abstract
Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
- EPICURE Consortium
| | - Ann-Kathrin Ruppert
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Holger Trucks
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Herbert Schulz
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Carolien G. de Kovel
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Anja C. M. Sonsma
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P. Koeleman
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Lindhout
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- SEIN Epilepsy Institute in the Netherlands, Hoofddorp, The Netherlands
| | - Yvonne G. Weber
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Holger Lerche
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Kapser
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Christoph J. Schankin
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Wolfram S. Kunz
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Rainer Surges
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Christian E. Elger
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Verena Gaus
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
| | - Bettina Schmitz
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
- Department of Neurology, Vivantes Humboldt-Klinikum, Berlin, Germany
| | - Ingo Helbig
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Hiltrud Muhle
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Ulrich Stephani
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Karl M. Klein
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Rosenow
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Eva M. Reinthaler
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Fritz Zimprich
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martha Feucht
- EPICURE Consortium
- Department of Pediatrics and Neonatology, Medical University of Vienna, Vienna, Austria
| | - Rikke S. Møller
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Helle Hjalgrim
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Peter De Jonghe
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, and Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University, Greifswald, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, Ernst Moritz Arndt University, Greifswald, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- EPICURE Consortium
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Thomas Sander
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
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25
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D’Amico AG, Maugeri G, Magro G, Salvatorelli L, Drago F, D’Agata V. Expression pattern of parkin isoforms in lung adenocarcinomas. Tumour Biol 2015; 36:5133-41. [DOI: 10.1007/s13277-015-3166-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/26/2015] [Indexed: 10/24/2022] Open
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26
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Alternative splicing generates different parkin protein isoforms: evidences in human, rat, and mouse brain. BIOMED RESEARCH INTERNATIONAL 2014; 2014:690796. [PMID: 25136611 PMCID: PMC4124806 DOI: 10.1155/2014/690796] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/30/2014] [Indexed: 11/17/2022]
Abstract
Parkinson protein 2, E3 ubiquitin protein ligase (PARK2) gene mutations are the most frequent causes of autosomal recessive early onset Parkinson's disease and juvenile Parkinson disease. Parkin deficiency has also been linked to other human pathologies, for example, sporadic Parkinson disease, Alzheimer disease, autism, and cancer. PARK2 primary transcript undergoes an extensive alternative splicing, which enhances transcriptomic diversification. To date several PARK2 splice variants have been identified; however, the expression and distribution of parkin isoforms have not been deeply investigated yet. Here, the currently known PARK2 gene transcripts and relative predicted encoded proteins in human, rat, and mouse are reviewed. By analyzing the literature, we highlight the existing data showing the presence of multiple parkin isoforms in the brain. Their expression emerges from conflicting results regarding the electrophoretic mobility of the protein, but it is also assumed from discrepant observations on the cellular and tissue distribution of parkin. Although the characterization of each predicted isoforms is complex, since they often diverge only for few amino acids, analysis of their expression patterns in the brain might account for the different pathogenetic effects linked to PARK2 gene mutations.
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