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Albrecht E, Pelz K, Gress A, Trung HN, Kalinina OV, Kacprowski T, Baumbach J, List M, Tsoy O. DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders. Nucleic Acids Res 2025:gkaf384. [PMID: 40337913 DOI: 10.1093/nar/gkaf384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 04/11/2025] [Accepted: 04/25/2025] [Indexed: 05/09/2025] Open
Abstract
Changes in alternative splicing between groups or conditions contribute to protein-protein interaction rewiring, a consequence often neglected in data analysis. The web server and database DIGGER overcomes this limitation by augmenting a protein-protein interaction network with domain-domain interactions and splicing information. Here, we present DIGGER 2.0, which now features both experimental and newly added predicted domain-domain interactions. In addition to the human interactome, DIGGER 2.0 adds support for mouse as an important model organism. Additionally, we integrated the splicing analysis tool NEASE, which allows users to perform online splicing- and interactome-informed enrichment analysis on RNA-seq data. In two application cases (multiple sclerosis and mice models of cardiac diseases), we show the utility of DIGGER 2.0 for deeper exploration and functional interpretation of changes in alternative splicing in human and mouse disorders. DIGGER 2.0 is available at https://exbio.wzw.tum.de/digger/.
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Affiliation(s)
- Elias Albrecht
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
- Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
| | - Konstantin Pelz
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
| | - Alexander Gress
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Campus E1.3, 66123 Saarbrücken, Germany
| | - Hieu Nguyen Trung
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Drug Bioinformatics, Medical Faculty, Saarland University, Gebäude 15, 66421 Homburg, Germany
- Center for Bioinformatics, Saarland University, Campus E2.1, 66123 Saarbrücken, Germany
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Rebenring 56 Lower Saxony, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56 Lower Saxony, 38106 Braunschweig, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
- Institute of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Markus List
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
- Munich Data Science Institute (MDSI), Technical University of Munich, Walther-von-Dyck-Straße 10, 85748 Garching, Germany
| | - Olga Tsoy
- Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
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2
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Yuasa T, Tokuda Y, Nakano M, Tashiro K, Tourtas T, Schlötzer-Schrehardt U, Kruse F, Koizumi N, Okumura N. Comprehensive analysis of splicing variants in corneal endothelial cells of patients with Fuchs endothelial corneal dystrophy. Sci Rep 2025; 15:14664. [PMID: 40287469 PMCID: PMC12033338 DOI: 10.1038/s41598-025-92119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Accepted: 02/25/2025] [Indexed: 04/29/2025] Open
Abstract
Trinucleotide repeat (TNR) expansion in the transcription factor 4 (TCF4) gene represents the most prevalent genetic risk factor for Fuchs endothelial corneal dystrophy (FECD) and may cause dysfunction of splicing regulators. We investigated differential alternative splicing (DAS) events in corneal endothelial cells (CECs) from FECD patients with and without TCF4 TNR expansion through RNA-Seq analysis. We identified distinct splicing profiles among control subjects, FECD patients with TNR expansion, and FECD patients without TNR expansion. Skipped Exon events constituted approximately 50% of all DAS events across all comparisons, with the remaining events distributed among alternative 3' splice site, alternative 5' splice site, mutually exclusive exon, and retained intron categories. Motif analysis in FECD patients with TNR expansion revealed several RNA-binding proteins, including MBNL1, as potential regulators of these splicing alterations. Computational analysis demonstrated that 34% of Skipped Exon events in the TNR expansion group significantly impacted protein structure. This comprehensive analysis revealed distinct alternative splicing signatures in FECD, particularly in cases with TNR expansion, suggesting a crucial role for aberrant splicing in FECD pathogenesis.
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Affiliation(s)
- Taichi Yuasa
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Yuichi Tokuda
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Theofilos Tourtas
- Department of Ophthalmology, University of Erlangen-Nürnberg, Erlangen, Germany
| | | | - Friedrich Kruse
- Department of Ophthalmology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Noriko Koizumi
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Naoki Okumura
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan.
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Ke L, Liu J, Feng G, Li X, Zhang Y, Zhang S, Ma X, Di Q. Effects of acute PM 2.5 purification on cognitive function and underlying mechanisms: Evidence from integrating alternative splicing into multi-omics. JOURNAL OF HAZARDOUS MATERIALS 2025; 487:137214. [PMID: 39823879 DOI: 10.1016/j.jhazmat.2025.137214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 01/07/2025] [Accepted: 01/12/2025] [Indexed: 01/20/2025]
Abstract
The relationship between fine particulate matter (PM2.5) and cognition has been extensively investigated. However, the causal impact of acute PM2.5 purification on cognition improvement and the underlying biological mechanisms remain relatively opaque. Our double-blinded randomized controlled trial assessed the impact of acute PM2.5 purification on executive function, underpinned by multi-omics approaches including alternative splicing (AS) analysis. A total of 93 participants experienced a two-hour exposure to either reduced and normal PM2.5 levels. We measured the cognition of healthy young adults, collected peripheral blood before and after intervention, and performed multi-omics analysis including transcriptomics, metabolomics, and proteomics. Results indicated that reducing PM2.5 by 1 μg/m3 was associated with a 0.10 % (95 % CI: [0.18 %, 0.01 %]; p = 0.031) improvement in executive function. Notably, we identified 96 AS events without concurrent transcriptional amount alterations. Multi-layered omics analyses revealed disrupted pathways in hypoxia, mitochondrial function and energy metabolism, and immune responses, validated by ELISA and biochemical assay. These findings demonstrated short-term improvements of cognition following PM2.5 purification and provide mechanistic understandings of PM2.5-induced cognition alterations. This study underscores the significance of incorporating AS in the molecular framework of multi-omics research by exploring variable exon splicing, which could enrich multi-omics analysis methodologies and expose to broader audience.
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Affiliation(s)
- Limei Ke
- School of Medicine, Tsinghua University, Beijing 100084, China; School of Biomedical Engineering, Tsinghua University, Beijing 100084, China.
| | - Jianxiu Liu
- Division of Sports Science & Physical Education, Tsinghua University, Beijing 100084, China.
| | - Guoqing Feng
- School of Medicine, Tsinghua University, Beijing 100084, China; School of Biomedical Engineering, Tsinghua University, Beijing 100084, China.
| | - Xingtian Li
- Division of Sports Science & Physical Education, Tsinghua University, Beijing 100084, China.
| | - Yao Zhang
- Division of Sports Science & Physical Education, Tsinghua University, Beijing 100084, China; Soochow College, Soochow University, Suzhou 215006, China.
| | - Shiqi Zhang
- Division of Sports Science & Physical Education, Tsinghua University, Beijing 100084, China.
| | - Xindong Ma
- Division of Sports Science & Physical Education, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
| | - Qian Di
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China; Institute for Healthy China, Tsinghua University, Beijing 100084, China.
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4
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Monzó C, Liu T, Conesa A. Transcriptomics in the era of long-read sequencing. Nat Rev Genet 2025:10.1038/s41576-025-00828-z. [PMID: 40155769 DOI: 10.1038/s41576-025-00828-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2025] [Indexed: 04/01/2025]
Abstract
Transcriptome sequencing revolutionized the analysis of gene expression, providing an unbiased approach to gene detection and quantification that enabled the discovery of novel isoforms, alternative splicing events and fusion transcripts. However, although short-read sequencing technologies have surpassed the limited dynamic range of previous technologies such as microarrays, they have limitations, for example, in resolving full-length transcripts and complex isoforms. Over the past 5 years, long-read sequencing technologies have matured considerably, with improvements in instrumentation and analytical methods, enabling their application to RNA sequencing (RNA-seq). Benchmarking studies are beginning to identify the strengths and limitations of long-read RNA-seq, although there remains a need for comprehensive resources to guide newcomers through the intricacies of this approach. In this Review, we provide a comprehensive overview of the long-read RNA-seq workflow, from library preparation and sequencing challenges to core data processing, downstream analyses and emerging developments. We present an extensive inventory of experimental and analytical methods and discuss current challenges and prospects.
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Affiliation(s)
- Carolina Monzó
- Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain.
| | - Tianyuan Liu
- Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain.
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Dery KJ, Wong Z, Wei M, Kupiec-Weglinski JW. Mechanistic Insights into Alternative Gene Splicing in Oxidative Stress and Tissue Injury. Antioxid Redox Signal 2024; 41:890-909. [PMID: 37776178 PMCID: PMC11631805 DOI: 10.1089/ars.2023.0437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
Abstract
Significance: Oxidative stress (OS) and inflammation are inducers of tissue injury. Alternative splicing (AS) is an essential regulatory step for diversifying the eukaryotic proteome. Human diseases link AS to OS; however, the underlying mechanisms must be better understood. Recent Advances: Genome‑wide profiling studies identify new differentially expressed genes induced by OS-dependent ischemia/reperfusion injury. Overexpression of RNA-binding protein RBFOX1 protects against inflammation. Hypoxia-inducible factor-1α directs polypyrimidine tract binding protein 1 to regulate mouse carcinoembryonic antigen-related cell adhesion molecule 1 (Ceacam1) AS under OS conditions. Heterogeneous nuclear ribonucleoprotein L variant 1 contains an RGG/RG motif that coordinates with transcription factors to influence human CEACAM1 AS. Hypoxia intervention involving short interfering RNAs directed to long-noncoding RNA 260 polarizes M2 macrophages toward an anti-inflammatory phenotype and alleviates OS by inhibiting IL-28RA gene AS. Critical Issues: Protective mechanisms that eliminate reactive oxygen species (ROS) are important for resolving imbalances that lead to chronic inflammation. Defects in AS can cause ROS generation, cell death regulation, and the activation of innate and adaptive immune factors. We propose that AS pathways link redox regulation to the activation or suppression of the inflammatory response during cellular stress. Future Directions: Emergent studies using molecule-mediated RNA splicing are being conducted to exploit the immunogenicity of AS protein products. Deciphering the mechanisms that connect misspliced OS and pathologies should remain a priority. Controlled release of RNA directly into cells with clinical applications is needed as the demand for innovative nucleic acid delivery systems continues to be demonstrated.
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Affiliation(s)
- Kenneth J. Dery
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Zeriel Wong
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Megan Wei
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jerzy W. Kupiec-Weglinski
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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6
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Kiseleva OI, Arzumanian VA, Kurbatov IY, Poverennaya EV. In silico and in cellulo approaches for functional annotation of human protein splice variants. BIOMEDITSINSKAIA KHIMIIA 2024; 70:315-328. [PMID: 39324196 DOI: 10.18097/pbmc20247005315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
The elegance of pre-mRNA splicing mechanisms continues to interest scientists even after over a half century, since the discovery of the fact that coding regions in genes are interrupted by non-coding sequences. The vast majority of human genes have several mRNA variants, coding structurally and functionally different protein isoforms in a tissue-specific manner and with a linkage to specific developmental stages of the organism. Alteration of splicing patterns shifts the balance of functionally distinct proteins in living systems, distorts normal molecular pathways, and may trigger the onset and progression of various pathologies. Over the past two decades, numerous studies have been conducted in various life sciences disciplines to deepen our understanding of splicing mechanisms and the extent of their impact on the functioning of living systems. This review aims to summarize experimental and computational approaches used to elucidate the functions of splice variants of a single gene based on our experience accumulated in the laboratory of interactomics of proteoforms at the Institute of Biomedical Chemistry (IBMC) and best global practices.
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Affiliation(s)
- O I Kiseleva
- Institute of Biomedical Chemistry, Moscow, Russia
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7
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Tan C, Sim D, Zhen Y, Tian H, Koh J, Roca X. PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation. Nucleic Acids Res 2024; 52:8800-8814. [PMID: 38943321 PMCID: PMC11347146 DOI: 10.1093/nar/gkae557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024] Open
Abstract
We characterized the regulatory mechanisms and role in human myeloid cell survival and differentiation of PRPF40A, a splicing factor lacking a canonical RNA Binding Domain. Upon PRPF40A knockdown, HL-60 cells displayed increased cell death, decreased proliferation and slight differentiation phenotype with upregulation of immune activation genes. Suggestive of both redundant and specific functions, cell death but not proliferation was rescued by overexpression of its paralog PRPF40B. Transcriptomic analysis revealed the predominant role of PRPF40A as an activator of cassette exon inclusion of functionally relevant splicing events. Mechanistically, the exons exclusively upregulated by PRPF40A are flanked by short and GC-rich introns which tend to localize to nuclear speckles in the nucleus center. These PRPF40A regulatory features are shared with other splicing regulators such as SRRM2, SON, PCBP1/2, and to a lesser extent TRA2B and SRSF2, as a part of a functional network that regulates splicing partly via co-localization in the nucleus.
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Affiliation(s)
- Cheryl Weiqi Tan
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Donald Yuhui Sim
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Yashu Zhen
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Haobo Tian
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Jace Koh
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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8
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Arora C, De Oliveira Rosa N, Matic M, Cascone M, Miglionico P, Raimondi F. EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics. BIOINFORMATICS ADVANCES 2023; 3:vbad135. [PMID: 37810457 PMCID: PMC10560094 DOI: 10.1093/bioadv/vbad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023]
Abstract
Summary EXPANSION (https://expansion.bioinfolab.sns.it/) is an integrated web-server to explore the functional consequences of protein-coding alternative splice variants. We combined information from Differentially Expressed (DE) protein-coding transcripts from cancer genomics, together with domain architecture, protein interaction network, and gene enrichment analysis to provide an easy-to-interpret view of the effects of protein-coding splice variants. We retrieved all the protein-coding Ensembl transcripts and mapped Interpro domains and post-translational modifications on canonical sequences to identify functionally relevant splicing events. We also retrieved isoform-specific protein-protein interactions and binding regions from IntAct to uncover isoform-specific functions via gene-set over-representation analysis. Through EXPANSION, users can analyze precalculated or user-inputted DE transcript datasets, to easily gain functional insights on any protein spliceform of interest. Availability and Implementation EXPANSION is freely available at http://expansion.bioinfolab.sns.it/. The code of the scripts used for EXPASION is available at: https://github.com/raimondilab/expansion. Datasets associated to this resource are available at the following URL: https://doi.org/10.5281/zenodo.8229120. The web-server was developed using Apache2 (https://https.apache.org/) and Flask (v2.0.2) (http://flask.pocoo.org/) for the web frontend and for the internal pipeline to handle back-end processes. We additionally used the following Python and JavaScript libraries at both back- and front-ends: D3 (v4), jQuery (v3.2.1), DataTables (v2.3.2), biopython (v1.79), gprofiler-officia l(v1.0.0), Mysql-connector-python (v8.0.31). To construct the API, Fast API library (v0.95.1) was used.
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Affiliation(s)
- Chakit Arora
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Natalia De Oliveira Rosa
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Marin Matic
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Mariastella Cascone
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Pasquale Miglionico
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Francesco Raimondi
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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9
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Hackl LM, Fenn A, Louadi Z, Baumbach J, Kacprowski T, List M, Tsoy O. Alternative splicing impacts microRNA regulation within coding regions. NAR Genom Bioinform 2023; 5:lqad081. [PMID: 37705830 PMCID: PMC10495541 DOI: 10.1093/nargab/lqad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that bind to target sites in different gene regions and regulate post-transcriptional gene expression. Approximately 95% of human multi-exon genes can be spliced alternatively, which enables the production of functionally diverse transcripts and proteins from a single gene. Through alternative splicing, transcripts might lose the exon with the miRNA target site and become unresponsive to miRNA regulation. To check this hypothesis, we studied the role of miRNA target sites in both coding and non-coding regions using six cancer data sets from The Cancer Genome Atlas (TCGA) and Parkinson's disease data from PPMI. First, we predicted miRNA target sites on mRNAs from their sequence using TarPmiR. To check whether alternative splicing interferes with this regulation, we trained linear regression models to predict miRNA expression from transcript expression. Using nested models, we compared the predictive power of transcripts with miRNA target sites in the coding regions to that of transcripts without target sites. Models containing transcripts with target sites perform significantly better. We conclude that alternative splicing does interfere with miRNA regulation by skipping exons with miRNA target sites within the coding region.
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Affiliation(s)
- Lena Maria Hackl
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
| | - Amit Fenn
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Zakaria Louadi
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Campusvej 50, 5230 Odense, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Olga Tsoy
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
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10
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Gjerga E, Naarmann-de Vries IS, Dieterich C. Characterizing alternative splicing effects on protein interaction networks with LINDA. Bioinformatics 2023; 39:i458-i464. [PMID: 37387163 DOI: 10.1093/bioinformatics/btad224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Alternative RNA splicing plays a crucial role in defining protein function. However, despite its relevance, there is a lack of tools that characterize effects of splicing on protein interaction networks in a mechanistic manner (i.e. presence or absence of protein-protein interactions due to RNA splicing). To fill this gap, we present Linear Integer programming for Network reconstruction using transcriptomics and Differential splicing data Analysis (LINDA) as a method that integrates resources of protein-protein and domain-domain interactions, transcription factor targets, and differential splicing/transcript analysis to infer splicing-dependent effects on cellular pathways and regulatory networks. RESULTS We have applied LINDA to a panel of 54 shRNA depletion experiments in HepG2 and K562 cells from the ENCORE initiative. Through computational benchmarking, we could show that the integration of splicing effects with LINDA can identify pathway mechanisms contributing to known bioprocesses better than other state of the art methods, which do not account for splicing. Additionally, we have experimentally validated some of the predicted splicing effects that the depletion of HNRNPK in K562 cells has on signalling.
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Affiliation(s)
- Enio Gjerga
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg 69120, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Isabel S Naarmann-de Vries
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg 69120, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg 69120, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
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11
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Cimmino G, Conte S, Palumbo D, Sperlongano S, Torella M, Della Corte A, Golino P. The Novel Role of Noncoding RNAs in Modulating Platelet Function: Implications in Activation and Aggregation. Int J Mol Sci 2023; 24:7650. [PMID: 37108819 PMCID: PMC10144470 DOI: 10.3390/ijms24087650] [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: 03/12/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
It is currently believed that plaque complication, with the consequent superimposed thrombosis, is a key factor in the clinical occurrence of acute coronary syndromes (ACSs). Platelets are major players in this process. Despite the considerable progress made by the new antithrombotic strategies (P2Y12 receptor inhibitors, new oral anticoagulants, thrombin direct inhibitors, etc.) in terms of a reduction in major cardiovascular events, a significant number of patients with previous ACSs treated with these drugs continue to experience events, indicating that the mechanisms of platelet remain largely unknown. In the last decade, our knowledge of platelet pathophysiology has improved. It has been reported that, in response to physiological and pathological stimuli, platelet activation is accompanied by de novo protein synthesis, through a rapid and particularly well-regulated translation of resident mRNAs of megakaryocytic derivation. Although the platelets are anucleate, they indeed contain an important fraction of mRNAs that can be quickly used for protein synthesis following their activation. A better understanding of the pathophysiology of platelet activation and the interaction with the main cellular components of the vascular wall will open up new perspectives in the treatment of the majority of thrombotic disorders, such as ACSs, stroke, and peripheral artery diseases before and after the acute event. In the present review, we will discuss the novel role of noncoding RNAs in modulating platelet function, highlighting the possible implications in activation and aggregation.
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Affiliation(s)
- Giovanni Cimmino
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy (A.D.C.)
- Cardiology Unit, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Piazza Miraglia, 80138 Naples, Italy
| | - Stefano Conte
- Department of Translational Medical Sciences, Section of Lung Diseases, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Domenico Palumbo
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy (A.D.C.)
| | - Simona Sperlongano
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy (A.D.C.)
- Cardiology Unit, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Piazza Miraglia, 80138 Naples, Italy
| | - Michele Torella
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy (A.D.C.)
| | - Alessandro Della Corte
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy (A.D.C.)
| | - Paolo Golino
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy (A.D.C.)
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12
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Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023; 24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
Abstract
The removal of introns from mRNA precursors and its regulation by alternative splicing are key for eukaryotic gene expression and cellular function, as evidenced by the numerous pathologies induced or modified by splicing alterations. Major recent advances have been made in understanding the structures and functions of the splicing machinery, in the description and classification of physiological and pathological isoforms and in the development of the first therapies for genetic diseases based on modulation of splicing. Here, we review this progress and discuss important remaining challenges, including predicting splice sites from genomic sequences, understanding the variety of molecular mechanisms and logic of splicing regulation, and harnessing this knowledge for probing gene function and disease aetiology and for the design of novel therapeutic approaches.
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Affiliation(s)
- Malgorzata Ewa Rogalska
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Vivori
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- The Francis Crick Institute, London, UK
| | - Juan Valcárcel
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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13
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Lio CT, Grabert G, Louadi Z, Fenn A, Baumbach J, Kacprowski T, List M, Tsoy O. Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics 2022; 39:6965022. [PMID: 36579860 PMCID: PMC9831059 DOI: 10.1093/bioinformatics/btac846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. RESULTS Here, we propose Spycone, a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection. AVAILABILITY AND IMPLEMENTATION The Spycone package is available as a PyPI package. The source code of Spycone is available under the GPLv3 license at https://github.com/yollct/spycone and the documentation at https://spycone.readthedocs.io/en/latest/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chit Tong Lio
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Gordon Grabert
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig 38106, Germany,Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig 38106, Germany
| | - Zakaria Louadi
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Amit Fenn
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Institute of Mathematics and Computer Science, University of Southern Denmark, Odense 5000, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig 38106, Germany,Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig 38106, Germany
| | | | - Olga Tsoy
- To whom correspondence should be addressed.
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