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Keuthan CJ, Karma S, Zack DJ. Alternative RNA Splicing in the Retina: Insights and Perspectives. Cold Spring Harb Perspect Med 2023; 13:a041313. [PMID: 36690463 PMCID: PMC10547393 DOI: 10.1101/cshperspect.a041313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Alternative splicing is a fundamental and highly regulated post-transcriptional process that enhances transcriptome and proteome diversity. This process is particularly important in neuronal tissues, such as the retina, which exhibit some of the highest levels of differentially spliced genes in the body. Alternative splicing is regulated both temporally and spatially during neuronal development, can be cell-type-specific, and when altered can cause a number of pathologies, including retinal degeneration. Advancements in high-throughput sequencing technologies have facilitated investigations of the alternative splicing landscape of the retina in both healthy and disease states. Additionally, innovations in human stem cell engineering, specifically in the generation of 3D retinal organoids, which recapitulate many aspects of the in vivo retinal microenvironment, have aided studies of the role of alternative splicing in human retinal development and degeneration. Here we review these advances and discuss the ongoing development of strategies for the treatment of alternative splicing-related retinal disease.
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Affiliation(s)
- Casey J Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Sadik Karma
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Donald J Zack
- Departments of Ophthalmology, Wilmer Eye Institute, Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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2
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Han N, Liu Z. Targeting alternative splicing in cancer immunotherapy. Front Cell Dev Biol 2023; 11:1232146. [PMID: 37635865 PMCID: PMC10450511 DOI: 10.3389/fcell.2023.1232146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Tumor immunotherapy has made great progress in cancer treatment but still faces several challenges, such as a limited number of targetable antigens and varying responses among patients. Alternative splicing (AS) is an essential process for the maturation of nearly all mammalian mRNAs. Recent studies show that AS contributes to expanding cancer-specific antigens and modulating immunogenicity, making it a promising solution to the above challenges. The organoid technology preserves the individual immune microenvironment and reduces the time/economic costs of the experiment model, facilitating the development of splicing-based immunotherapy. Here, we summarize three critical roles of AS in immunotherapy: resources for generating neoantigens, targets for immune-therapeutic modulation, and biomarkers to guide immunotherapy options. Subsequently, we highlight the benefits of adopting organoids to develop AS-based immunotherapies. Finally, we discuss the current challenges in studying AS-based immunotherapy in terms of existing bioinformatics algorithms and biological technologies.
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Affiliation(s)
- Nan Han
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoqi Liu
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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3
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Jiang C, Ge J, He B, Zhang Z, Hu Z, Li Y, Zeng B. Transcriptomic analysis reveals Aspergillus oryzae responds to temperature stress by regulating sugar metabolism and lipid metabolism. PLoS One 2022; 17:e0274394. [PMID: 36094945 PMCID: PMC9467314 DOI: 10.1371/journal.pone.0274394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/26/2022] [Indexed: 11/19/2022] Open
Abstract
Aspergillus oryzae is widely used in industrial applications, which always encounter changes within multiple environmental conditions during fermentation, such as temperature stress. However, the molecular mechanisms by which A. oryzae protects against temperature stress have not been elucidated. Therefore, this study aimed to characterize the fermentative behavior, transcriptomic profiles, and metabolic changes of A. oryzae in response to temperature stress. Both low and high temperatures inhibited mycelial growth and conidial formation of A. oryzae. Transcriptomic analysis revealed that most differentially expressed genes (DEGs) were involved in sugar metabolism and lipid metabolism under temperature stress. Specifically, the DEGs in trehalose synthesis and starch metabolism were upregulated under low-temperature stress, while high temperatures inhibited the expression of genes involved in fructose, galactose, and glucose metabolism. Quantitative analysis of intracellular sugar further revealed that low temperature increased trehalose accumulation, while high temperature increased the contents of intracellular trehalose, galactose, and glucose, consistent with transcriptome analysis. In addition, most DEGs involved in lipid metabolism were significantly downregulated under low-temperature stress. Furthermore, the metabolomic analysis revealed that linoleic acid, triacylglycerol, phosphatidylethanolamine, and phosphoribosyl were significantly decreased in response to low-temperature stress. These results increase our understanding of the coping mechanisms of A. oryzae in response to temperature stress, which lays the foundation for future improvements through genetic modification to enhance A. oryzae against extreme temperature stress.
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Affiliation(s)
- Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
- * E-mail: (CJ); (BZ)
| | - Jinxin Ge
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Zhe Zhang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Zhihong Hu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yongkai Li
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
- * E-mail: (CJ); (BZ)
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4
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Liu L, Amorín R, Moriel P, DiLorenzo N, Lancaster PA, Peñagaricano F. Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle. BMC Genomics 2021; 22:780. [PMID: 34717556 PMCID: PMC8557564 DOI: 10.1186/s12864-021-08065-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/28/2021] [Indexed: 01/18/2023] Open
Abstract
Background The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively. Results Alternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons. Conclusions Overall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08065-4.
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Affiliation(s)
- Lihe Liu
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr, Madison, WI, 53706, USA
| | - Rocío Amorín
- University of Florida Genetics Institute, University of Florida, 32611, Gainesville, FL, USA
| | - Philipe Moriel
- Range Cattle Research and Education Center, University of Florida, 33865, Ona, FL, USA
| | - Nicolás DiLorenzo
- North Florida Research and Education Center, University of Florida, 32351, Marianna, FL, USA
| | - Phillip A Lancaster
- Department of Clinical Sciences, Kansas State University, 66506, Manhattan, KS, USA
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr, Madison, WI, 53706, USA.
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5
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Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief Bioinform 2021; 22:6330938. [PMID: 34329375 DOI: 10.1093/bib/bbab259] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
Significant innovations in next-generation sequencing techniques and bioinformatics tools have impacted our appreciation and understanding of RNA. Practical RNA sequencing (RNA-Seq) applications have evolved in conjunction with sequence technology and bioinformatic tools advances. In most projects, bulk RNA-Seq data is used to measure gene expression patterns, isoform expression, alternative splicing and single-nucleotide polymorphisms. However, RNA-Seq holds far more hidden biological information including details of copy number alteration, microbial contamination, transposable elements, cell type (deconvolution) and the presence of neoantigens. Recent novel and advanced bioinformatic algorithms developed the capacity to retrieve this information from bulk RNA-Seq data, thus broadening its scope. The focus of this review is to comprehend the emerging bulk RNA-Seq-based analyses, emphasizing less familiar and underused applications. In doing so, we highlight the power of bulk RNA-Seq in providing biological insights.
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Affiliation(s)
- Amarinder Singh Thind
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Isha Monga
- Columbia University, New York City, NY, USA
| | | | - Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | | | - Marie Ranson
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Bruce Ashford
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
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6
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Liu Z, Rabadan R. Computing the Role of Alternative Splicing in Cancer. Trends Cancer 2021; 7:347-358. [PMID: 33500226 PMCID: PMC7969404 DOI: 10.1016/j.trecan.2020.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022]
Abstract
Most human genes undergo alternative splicing (AS), and dysregulation of alternative splicing contributes to tumor initiation and progression. Computational analysis of genomic and transcriptomic data enables the systematic characterization of alternative splicing and its functional role in cancer. In this review, we summarize the latest computational approaches to studying alternative splicing in cancer and the current limitations of the most popular tools in this field. Finally, we describe some of the current computational challenges in the characterization of the role of alternative splicing in cancer.
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Affiliation(s)
- Zhaoqi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing 100101, China.
| | - Raul Rabadan
- Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA; Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY 10032, USA.
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7
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Merino GA, Fernández EA. Differential splicing analysis based on isoforms expression with NBSplice. J Biomed Inform 2020; 103:103378. [PMID: 31972288 DOI: 10.1016/j.jbi.2020.103378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/07/2019] [Accepted: 01/13/2020] [Indexed: 01/05/2023]
Abstract
Alternative splicing alterations have been widely related to several human diseases revealing the importance of their study for the success of translational medicine. Differential splicing (DS) occurrence has been mainly analyzed through exon-based approaches over RNA-seq data. Although these strategies allow identifying differentially spliced genes, they ignore the identity of the affected gene isoforms which is crucial to understand the underlying pathological processes behind alternative splicing changes. Moreover, despite several isoform quantification tools for RNA-seq data have been recently developed, DS tools have not taken advantage of them. Here, the NBSplice R package for differential splicing analysis by means of isoform expression data is presented. It estimates differences on relative expressions of gene transcripts between experimental conditions to infer changes in gene alternative splicing patterns. The developed tool was evaluated using a synthetic RNA-seq dataset with controlled differential splicing. NBSplice accurately predicted DS occurrence, outperforming current methods in terms of accuracy, sensitivity, F-score, and false discovery rate control. The usefulness of our development was demonstrated by the analysis of a real cancer dataset, revealing new differentially spliced genes that could be studied pursuing new colorectal cancer biomarkers discovery.
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Affiliation(s)
- Gabriela Alejandra Merino
- Instituto de Investigación y Desarrollo en Bioingeniería y Bioinformática (IBB), Universidad Nacional de Entre Ríos, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta 11 Km 10.5, E3100XAD Oro Verde, Argentina; Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE), Universidad Católica de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Armada Argentina 3555, X5016DHK Córdoba, Argentina.
| | - Elmer Andrés Fernández
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE), Universidad Católica de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Armada Argentina 3555, X5016DHK Córdoba, Argentina; Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield 1611, X5016GCA Córdoba, Argentina.
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8
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Mehmood A, Laiho A, Venäläinen MS, McGlinchey AJ, Wang N, Elo LL. Systematic evaluation of differential splicing tools for RNA-seq studies. Brief Bioinform 2019; 21:2052-2065. [PMID: 31802105 PMCID: PMC7711265 DOI: 10.1093/bib/bbz126] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 08/26/2019] [Accepted: 09/03/2019] [Indexed: 12/22/2022] Open
Abstract
Differential splicing (DS) is a post-transcriptional biological process with critical, wide-ranging effects on a plethora of cellular activities and disease processes. To date, a number of computational approaches have been developed to identify and quantify differentially spliced genes from RNA-seq data, but a comprehensive intercomparison and appraisal of these approaches is currently lacking. In this study, we systematically evaluated 10 DS analysis tools for consistency and reproducibility, precision, recall and false discovery rate, agreement upon reported differentially spliced genes and functional enrichment. The tools were selected to represent the three different methodological categories: exon-based (DEXSeq, edgeR, JunctionSeq, limma), isoform-based (cuffdiff2, DiffSplice) and event-based methods (dSpliceType, MAJIQ, rMATS, SUPPA). Overall, all the exon-based methods and two event-based methods (MAJIQ and rMATS) scored well on the selected measures. Of the 10 tools tested, the exon-based methods performed generally better than the isoform-based and event-based methods. However, overall, the different data analysis tools performed strikingly differently across different data sets or numbers of samples.
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Affiliation(s)
- Arfa Mehmood
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Department of Physiology, University of Turku, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Mikko S Venäläinen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Aidan J McGlinchey
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Ning Wang
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
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9
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Nazarie FW, Shih B, Angus T, Barnett MW, Chen SH, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M, Dongen SV, Enright AJ, Freeman TC. Visualization and analysis of RNA-Seq assembly graphs. Nucleic Acids Res 2019; 47:7262-7275. [PMID: 31305886 PMCID: PMC6698738 DOI: 10.1093/nar/gkz599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/31/2019] [Accepted: 07/10/2019] [Indexed: 01/20/2023] Open
Abstract
RNA-Seq is a powerful transcriptome profiling technology enabling transcript discovery and quantification. Whilst most commonly used for gene-level quantification, the data can be used for the analysis of transcript isoforms. However, when the underlying transcript assemblies are complex, current visualization approaches can be limiting, with splicing events a challenge to interpret. Here, we report on the development of a graph-based visualization method as a complementary approach to understanding transcript diversity from short-read RNA-Seq data. Following the mapping of reads to a reference genome, a read-to-read comparison is performed on all reads mapping to a given gene, producing a weighted similarity matrix between reads. This is used to produce an RNA assembly graph, where nodes represent reads and edges similarity scores between them. The resulting graphs are visualized in 3D space to better appreciate their sometimes large and complex topology, with other information being overlaid on to nodes, e.g. transcript models. Here we demonstrate the utility of this approach, including the unusual structure of these graphs and how they can be used to identify issues in assembly, repetitive sequences within transcripts and splice variants. We believe this approach has the potential to significantly improve our understanding of transcript complexity.
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Affiliation(s)
- Fahmi W Nazarie
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Barbara Shih
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tim Angus
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Mark W Barnett
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sz-Hau Chen
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Kim M Summers
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK.,Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba QLD 4102, Australia
| | - Karsten Klein
- Life Science Informatics Group, Department of Computer Science, Konstanz University, 78457 Konstanz, Germany
| | - Geoffrey J Faulkner
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba QLD 4102, Australia
| | - Harpreet K Saini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, UK
| | - Mick Watson
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Stijn van Dongen
- Cellular Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Anton J Enright
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Tom C Freeman
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
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10
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Merino GA, Conesa A, Fernández EA. A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies. Brief Bioinform 2019; 20:471-481. [PMID: 29040385 DOI: 10.1093/bib/bbx122] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/20/2017] [Indexed: 12/16/2022] Open
Abstract
Over the last few years, RNA-seq has been used to study alterations in alternative splicing related to several diseases. Bioinformatics workflows used to perform these studies can be divided into two groups, those finding changes in the absolute isoform expression and those studying differential splicing. Many computational methods for transcriptomics analysis have been developed, evaluated and compared; however, there are not enough reports of systematic and objective assessment of processing pipelines as a whole. Moreover, comparative studies have been performed considering separately the changes in absolute or relative isoform expression levels. Consequently, no consensus exists about the best practices and appropriate workflows to analyse alternative and differential splicing. To assist the adequate pipeline choice, we present here a benchmarking of nine commonly used workflows to detect differential isoform expression and splicing. We evaluated the workflows performance over different experimental scenarios where changes in absolute and relative isoform expression occurred simultaneously. In addition, the effect of the number of isoforms per gene, and the magnitude of the expression change over pipeline performances were also evaluated. Our results suggest that workflow performance is influenced by the number of replicates per condition and the conditions heterogeneity. In general, workflows based on DESeq2, DEXSeq, Limma and NOISeq performed well over a wide range of transcriptomics experiments. In particular, we suggest the use of workflows based on Limma when high precision is required, and DESeq2 and DEXseq pipelines to prioritize sensitivity. When several replicates per condition are available, NOISeq and Limma pipelines are indicated.
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Affiliation(s)
| | - Ana Conesa
- Microbiology and Cell Sciences Department of the University of Florida at Gainesville, FL, USA
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11
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Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Haplosaurus computes protein haplotypes for use in precision drug design. Nat Commun 2018; 9:4128. [PMID: 30297836 PMCID: PMC6175845 DOI: 10.1038/s41467-018-06542-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/07/2018] [Indexed: 01/08/2023] Open
Abstract
Selecting the most appropriate protein sequences is critical for precision drug design. Here we describe Haplosaurus, a bioinformatic tool for computation of protein haplotypes. Haplosaurus computes protein haplotypes from pre-existing chromosomally-phased genomic variation data. Integration into the Ensembl resource provides rapid and detailed protein haplotypes retrieval. Using Haplosaurus, we build a database of unique protein haplotypes from the 1000 Genomes dataset reflecting real-world protein sequence variability and their prevalence. For one in seven genes, their most common protein haplotype differs from the reference sequence and a similar number differs on their most common haplotype between human populations. Three case studies show how knowledge of the range of commonly encountered protein forms predicted in populations leads to insights into therapeutic efficacy. Haplosaurus and its associated database is expected to find broad applications in many disciplines using protein sequences and particularly impactful for therapeutics design.
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Affiliation(s)
- William Spooner
- Eagle Genomics Ltd., Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 3DR UK
- Genomics England, QMUL Dawson Hall, London, EC1M 6BQ UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | | | - Robin Butler
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | - David Rider
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | | | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
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12
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Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth. BMC Microbiol 2018; 18:12. [PMID: 29444636 PMCID: PMC5813417 DOI: 10.1186/s12866-018-1158-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/09/2018] [Indexed: 11/16/2022] Open
Abstract
Background The gene expression profile and metabolic pathways of Aspergillus oryzae underlying the anatomical and morphological differentiation across different growth stages have not been fully characterized. The rapid development of next-generation sequencing technologies provides advanced knowledge of the genomic organization of A. oryzae. Results In this study, we characterized the growth and development of A. oryzae at different growth stages, including the adaptive phase, logarithmic phase, and stationary phase. Our results revealed that A. oryzae undergoes physiological and morphological differentiation across the different stages. RNA-seq was employed to analyze the three stages of A. oryzae, which generated more than 27 million high-quality reads per sample. The analysis of differential gene expression showed more genes expressed differentially upon transition from the adaptive phase to the logarithmic and stationary phases, while relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase. GO classification of the differentially expressed genes among different growth stages revealed that most of these genes were enriched for single-organism process, metabolic process, and catalytic activity. These genes were then subjected to a clustering analysis. The results showed that the cluster with the majority of genes with increased expression upon transition from the adaptive phase to the logarithmic phase, and steady expression from the logarithmic phase to the stationary phase was mainly involved in the carbohydrate and amino acid metabolism. Conclusion Our results provide a foundation for identifying developmentally important genes and understanding the biological processes across various growth stages. Electronic supplementary material The online version of this article (10.1186/s12866-018-1158-z) contains supplementary material, which is available to authorized users.
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13
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Hojny J, Zemankova P, Lhota F, Sevcik J, Stranecky V, Hartmannova H, Hodanova K, Mestak O, Pavlista D, Janatova M, Soukupova J, Vocka M, Kleibl Z, Kleiblova P. Multiplex PCR and NGS-based identification of mRNA splicing variants: Analysis of BRCA1 splicing pattern as a model. Gene 2017; 637:41-49. [PMID: 28919163 DOI: 10.1016/j.gene.2017.09.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/26/2017] [Accepted: 09/13/2017] [Indexed: 02/08/2023]
Abstract
Alternative pre-mRNA splicing increases transcriptome plasticity by forming naturally-occurring alternative splicing variants (ASVs). Alterations of splicing processes, caused by DNA mutations, result in aberrant splicing and the formation of aberrant mRNA isoforms. Analyses of hereditary cancer predisposition genes reveal many DNA variants with unknown clinical significance (VUS) that potentially affect pre-mRNA splicing. Therefore, a comprehensive description of ASVs is an essential prerequisite for the interpretation of germline VUS in high-risk individuals. To identify ASVs in a gene of interest, we have proposed an approach based on multiplex PCR (mPCR) amplification of all theoretically possible exon-exon junctions and subsequent characterization of size-selected and pooled mPCR products by next-generation sequencing (NGS). The efficiency of this method is illustrated by a comprehensive analysis of BRCA1 ASVs in human leukocytes, normal mammary, and adipose tissues and stable cell lines. We revealed 94 BRCA1 ASVs, including 29 variants present in all tested samples. While differences in the qualitative expression of BRCA1 ASVs among the analyzed human tissues were minor, larger differences were detected between tissue and cell line samples. Compared with other ASV analysis methods, this approach represents a highly sensitive and rapid alternative for the identification of ASVs in any gene of interest.
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Affiliation(s)
- Jan Hojny
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague 12853, Czech Republic
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague 12853, Czech Republic
| | - Filip Lhota
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague 12853, Czech Republic
| | - Jan Sevcik
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague 12853, Czech Republic
| | - Viktor Stranecky
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Hana Hartmannova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Katerina Hodanova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Ondrej Mestak
- Department of Plastic Surgery, First Faculty of Medicine, Charles University and Na Bulovce Hospital, Prague 180 81, Czech Republic
| | - David Pavlista
- Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague 12853, Czech Republic
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague 12853, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague 12853, Czech Republic
| | - Petra Kleiblova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague 12853, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic.
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14
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Leshkowitz D, Feldmesser E, Friedlander G, Jona G, Ainbinder E, Parmet Y, Horn-Saban S. Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools. PLoS One 2016; 11:e0153782. [PMID: 27100792 PMCID: PMC4839710 DOI: 10.1371/journal.pone.0153782] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 04/04/2016] [Indexed: 11/25/2022] Open
Abstract
One of the key applications of next-generation sequencing (NGS) technologies is RNA-Seq for transcriptome genome-wide analysis. Although multiple studies have evaluated and benchmarked RNA-Seq tools dedicated to gene level analysis, few studies have assessed their effectiveness on the transcript-isoform level. Alternative splicing is a naturally occurring phenomenon in eukaryotes, significantly increasing the biodiversity of proteins that can be encoded by the genome. The aim of this study was to assess and compare the ability of the bioinformatics approaches and tools to assemble, quantify and detect differentially expressed transcripts using RNA-Seq data, in a controlled experiment. To this end, in vitro synthesized mouse spike-in control transcripts were added to the total RNA of differentiating mouse embryonic bodies, and their expression patterns were measured. This novel approach was used to assess the accuracy of the tools, as established by comparing the observed results versus the results expected of the mouse controlled spiked-in transcripts. We found that detection of differential expression at the gene level is adequate, yet on the transcript-isoform level, all tools tested lacked accuracy and precision.
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Affiliation(s)
- Dena Leshkowitz
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- * E-mail:
| | - Ester Feldmesser
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gilgi Friedlander
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ghil Jona
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Elena Ainbinder
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yisrael Parmet
- Industrial Engineering and Management Department, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Shirley Horn-Saban
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
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