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Buerger F, Salmanullah D, Liang L, Gauntner V, Krueger K, Qi M, Sharma V, Rubin A, Ball D, Lemberg K, Saida K, Merz LM, Sever S, Issac B, Sun L, Guerrero-Castillo S, Gomez AC, McNulty MT, Sampson MG, Al-Hamed MH, Saleh MM, Shalaby M, Kari J, Fawcett JP, Hildebrandt F, Majmundar AJ. Recessive variants in the intergenic NOS1AP-C1orf226 locus cause monogenic kidney disease responsive to anti-proteinuric treatment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.17.24303374. [PMID: 38562757 PMCID: PMC10984069 DOI: 10.1101/2024.03.17.24303374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In genetic disease, an accurate expression landscape of disease genes and faithful animal models will enable precise genetic diagnoses and therapeutic discoveries, respectively. We previously discovered that variants in NOS1AP , encoding nitric oxide synthase 1 (NOS1) adaptor protein, cause monogenic nephrotic syndrome (NS). Here, we determined that an intergenic splice product of N OS1AP / Nos1ap and neighboring C1orf226/Gm7694 , which precludes NOS1 binding, is the predominant isoform in mammalian kidney transcriptional and proteomic data. Gm7694 -/- mice, whose allele exclusively disrupts the intergenic product, developed NS phenotypes. In two human NS subjects, we identified causative NOS1AP splice variants, including one predicted to abrogate intergenic splicing but initially misclassified as benign based on the canonical transcript. Finally, by modifying genetic background, we generated a faithful mouse model of NOS1AP -associated NS, which responded to anti-proteinuric treatment. This study highlights the importance of intergenic splicing and a potential treatment avenue in a mendelian disorder.
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Filipek K, Deryło K, Michalec-Wawiórka B, Zaciura M, González-Ibarra A, Krokowski D, Latoch P, Starosta AL, Czapiński J, Rivero-Müller A, Wawiórka L, Tchórzewski M. Identification of a novel alternatively spliced isoform of the ribosomal uL10 protein. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194890. [PMID: 36328276 DOI: 10.1016/j.bbagrm.2022.194890] [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: 05/24/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Alternative splicing is one of the key mechanisms extending the complexity of genetic information and at the same time adaptability of higher eukaryotes. As a result, the broad spectrum of isoforms produced by alternative splicing allows organisms to fine-tune their proteome; however, the functions of the majority of alternatively spliced protein isoforms are largely unknown. Ribosomal protein isoforms are one of the groups for which data are limited. Here we report characterization of an alternatively spliced isoform of the ribosomal uL10 protein, named uL10β. The uL10 protein constitutes the core element of the ribosomal stalk structure within the GTPase associated center, which represents the landing platform for translational GTPases - trGTPases. The stalk plays an important role in the ribosome-dependent stimulation of GTP by trGTPases, which confer unidirectional trajectory for the ribosome, allosterically contributing to the speed and accuracy of translation. We have shown that the newly identified uL10β protein is stably expressed in mammalian cells and is primarily located within the nuclear compartment with a minor signal within the cytoplasm. Importantly, uL10β is able to bind to the ribosomal particle, but is mainly associated with 60S and 80S particles; additionally, the uL10β undergoes re-localization into the mitochondria upon endoplasmic reticulum stress induction. Our results suggest a specific stress-related dual role of uL10β, supporting the idea of existence of specialized ribosomes with an altered GTPase associated center.
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Affiliation(s)
- Kamil Filipek
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Barbara Michalec-Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Monika Zaciura
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Alan González-Ibarra
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Przemysław Latoch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Polish-Japanese Academy of Information Technology, Warsaw 02-008, Poland
| | - Agata L Starosta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Leszek Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
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Kim KS, Koo HY, Bok J. Alternative splicing in shaping the molecular landscape of the cochlea. Front Cell Dev Biol 2023; 11:1143428. [PMID: 36936679 PMCID: PMC10018040 DOI: 10.3389/fcell.2023.1143428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
The cochlea is a complex organ comprising diverse cell types with highly specialized morphology and function. Until now, the molecular underpinnings of its specializations have mostly been studied from a transcriptional perspective, but accumulating evidence points to post-transcriptional regulation as a major source of molecular diversity. Alternative splicing is one of the most prevalent and well-characterized post-transcriptional regulatory mechanisms. Many molecules important for hearing, such as cadherin 23 or harmonin, undergo alternative splicing to produce functionally distinct isoforms. Some isoforms are expressed specifically in the cochlea, while some show differential expression across the various cochlear cell types and anatomical regions. Clinical phenotypes that arise from mutations affecting specific splice variants testify to the functional relevance of these isoforms. All these clues point to an essential role for alternative splicing in shaping the unique molecular landscape of the cochlea. Although the regulatory mechanisms controlling alternative splicing in the cochlea are poorly characterized, there are animal models with defective splicing regulators that demonstrate the importance of RNA-binding proteins in maintaining cochlear function and cell survival. Recent technological breakthroughs offer exciting prospects for overcoming some of the long-standing hurdles that have complicated the analysis of alternative splicing in the cochlea. Efforts toward this end will help clarify how the remarkable diversity of the cochlear transcriptome is both established and maintained.
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Affiliation(s)
- Kwan Soo Kim
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hei Yeun Koo
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
- *Correspondence: Jinwoong Bok,
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4
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Vihinen M. Individual Genetic Heterogeneity. Genes (Basel) 2022; 13:genes13091626. [PMID: 36140794 PMCID: PMC9498725 DOI: 10.3390/genes13091626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden
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Bertini V, Milone R, Cristofani P, Cambi F, Bosetti C, Barbieri F, Bertelloni S, Cioni G, Valetto A, Battini R. Enhancing DLG2 Implications in Neuropsychiatric Disorders: Analysis of a Cohort of Eight Patients with 11q14.1 Imbalances. Genes (Basel) 2022; 13:genes13050859. [PMID: 35627244 PMCID: PMC9140951 DOI: 10.3390/genes13050859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/20/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are considered synaptopathies, as they are due to anomalies in neuronal connectivity during development. DLG2 is a gene involved insynaptic function; the phenotypic effect of itsalterations in NDDs has been underestimated since few cases have been thoroughly described.We report on eight patients with 11q14.1 imbalances involving DLG2, underlining its potential effects on clinical presentation and its contribution to NDD comorbidity by accurate neuropsychiatric data collection. DLG2 is a very large gene in 11q14.1, extending over 2.172 Mb, with alternative splicing that gives rise to numerous isoforms differentially expressed in brain tissues. A thorough bioinformatic analysis of the altered transcripts was conducted for each patient. The different expression profiles of the isoforms of this gene and their influence on the excitatory–inhibitory balance in crucial brain structures could contribute to the phenotypic variability related to DLG2 alterations. Further studies on patients would be helpful to enrich clinical and neurodevelopmental findings and elucidate the molecular mechanisms subtended to NDDs.
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Affiliation(s)
- Veronica Bertini
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
| | - Roberta Milone
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Paola Cristofani
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Francesca Cambi
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
| | - Chiara Bosetti
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Filippo Barbieri
- Mental Health Department, ASL Toscana Nordovest, 56100 Pisa, Italy;
| | - Silvano Bertelloni
- Pediatric Endocrinology, Department of Obstetrics, Gynecology and Pediatrics, Azienda Ospedaliero-Universitaria Pisana, Via Roma 57, 56100 Pisa, Italy;
| | - Giovanni Cioni
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56100 Pisa, Italy
| | - Angelo Valetto
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
- Correspondence:
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56100 Pisa, Italy
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Hao W, Yang Z, Sun Y, Li J, Zhang D, Liu D, Yang X. Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents. Biomolecules 2022; 12:biom12020154. [PMID: 35204660 PMCID: PMC8961525 DOI: 10.3390/biom12020154] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition.
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Affiliation(s)
- Wanjun Hao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Zewei Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Yuanlu Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Jiaxin Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Dongjie Zhang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
- Correspondence: (D.L.); (X.Y.); Tel.: +86-451-8667-7458 (D.L.); +86-451-5519-1738 (X.Y.)
| | - Xiuqin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
- Correspondence: (D.L.); (X.Y.); Tel.: +86-451-8667-7458 (D.L.); +86-451-5519-1738 (X.Y.)
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Saha S, Soliman A, Rajasekaran S. A robust and stable gene selection algorithm based on graph theory and machine learning. Hum Genomics 2021; 15:66. [PMID: 34753514 PMCID: PMC8579680 DOI: 10.1186/s40246-021-00366-9] [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: 06/30/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nowadays we are observing an explosion of gene expression data with phenotypes. It enables us to accurately identify genes responsible for certain medical condition as well as classify them for drug target. Like any other phenotype data in medical domain, gene expression data with phenotypes also suffer from being a very underdetermined system. In a very large set of features but a very small sample size domain (e.g. DNA microarray, RNA-seq data, GWAS data, etc.), it is often reported that several contrasting feature subsets may yield near equally optimal results. This phenomenon is known as instability. Considering these facts, we have developed a robust and stable supervised gene selection algorithm to select a set of robust and stable genes having a better prediction ability from the gene expression datasets with phenotypes. Stability and robustness is ensured by class and instance level perturbations, respectively. RESULTS We have performed rigorous experimental evaluations using 10 real gene expression microarray datasets with phenotypes. They reveal that our algorithm outperforms the state-of-the-art algorithms with respect to stability and classification accuracy. We have also performed biological enrichment analysis based on gene ontology-biological processes (GO-BP) terms, disease ontology (DO) terms, and biological pathways. CONCLUSIONS It is indisputable from the results of the performance evaluations that our proposed method is indeed an effective and efficient supervised gene selection algorithm.
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Affiliation(s)
- Subrata Saha
- Irving Medical Center, Columbia University, New York, NY, 10032, USA
| | - Ahmed Soliman
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Sanguthevar Rajasekaran
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA.
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8
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Rose KWJ, Taye N, Karoulias SZ, Hubmacher D. Regulation of ADAMTS Proteases. Front Mol Biosci 2021; 8:701959. [PMID: 34268335 PMCID: PMC8275829 DOI: 10.3389/fmolb.2021.701959] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023] Open
Abstract
A disintegrin and metalloprotease with thrombospondin type I motifs (ADAMTS) proteases are secreted metalloproteinases that play key roles in the formation, homeostasis and remodeling of the extracellular matrix (ECM). The substrate spectrum of ADAMTS proteases can range from individual ECM proteins to entire families of ECM proteins, such as the hyalectans. ADAMTS-mediated substrate cleavage is required for the formation, remodeling and physiological adaptation of the ECM to the needs of individual tissues and organ systems. However, ADAMTS proteases can also be involved in the destruction of tissues, resulting in pathologies such as arthritis. Specifically, ADAMTS4 and ADAMTS5 contribute to irreparable cartilage erosion by degrading aggrecan, which is a major constituent of cartilage. Arthritic joint damage is a major contributor to musculoskeletal morbidity and the most frequent clinical indication for total joint arthroplasty. Due to the high sequence homology of ADAMTS proteases in their catalytically active site, it remains a formidable challenge to design ADAMTS isotype-specific inhibitors that selectively inhibit ADAMTS proteases responsible for tissue destruction without affecting the beneficial functions of other ADAMTS proteases. In vivo, proteolytic activity of ADAMTS proteases is regulated on the transcriptional and posttranslational level. Here, we review the current knowledge of mechanisms that regulate ADAMTS protease activity in tissues including factors that induce ADAMTS gene expression, consequences of posttranslational modifications such as furin processing, the role of endogenous inhibitors and pharmacological approaches to limit ADAMTS protease activity in tissues, which almost exclusively focus on inhibiting the aggrecanase activity of ADAMTS4 and ADAMTS5.
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Affiliation(s)
| | | | | | - Dirk Hubmacher
- Orthopaedic Research Laboratories, Leni and Peter W. May Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Pozo F, Martinez-Gomez L, Walsh TA, Rodriguez JM, Di Domenico T, Abascal F, Vazquez J, Tress ML. Assessing the functional relevance of splice isoforms. NAR Genom Bioinform 2021; 3:lqab044. [PMID: 34046593 PMCID: PMC8140736 DOI: 10.1093/nargab/lqab044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/22/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Alternative splicing of messenger RNA can generate an array of mature transcripts, but it is not clear how many go on to produce functionally relevant protein isoforms. There is only limited evidence for alternative proteins in proteomics analyses and data from population genetic variation studies indicate that most alternative exons are evolving neutrally. Determining which transcripts produce biologically important isoforms is key to understanding isoform function and to interpreting the real impact of somatic mutations and germline variations. Here we have developed a method, TRIFID, to classify the functional importance of splice isoforms. TRIFID was trained on isoforms detected in large-scale proteomics analyses and distinguishes these biologically important splice isoforms with high confidence. Isoforms predicted as functionally important by the algorithm had measurable cross species conservation and significantly fewer broken functional domains. Additionally, exons that code for these functionally important protein isoforms are under purifying selection, while exons from low scoring transcripts largely appear to be evolving neutrally. TRIFID has been developed for the human genome, but it could in principle be applied to other well-annotated species. We believe that this method will generate valuable insights into the cellular importance of alternative splicing.
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Affiliation(s)
- Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Laura Martinez-Gomez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Thomas A Walsh
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - José Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Tomas Di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Federico Abascal
- Somatic Evolution Group, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Jesús Vazquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Michael L Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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Montero-Calle A, Barderas R. Analysis of Protein-Protein Interactions by Protein Microarrays. Methods Mol Biol 2021; 2344:81-97. [PMID: 34115353 DOI: 10.1007/978-1-0716-1562-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The analysis of the proteome and the interactome would be useful for a better understanding of the pathophysiology of several disorders, allowing the identification of potential specific markers for early diagnosis and prognosis, as well as potential targets of intervention. Among different proteomic approaches, high-density protein microarrays have become an interesting tool for the screening of protein-protein interactions and the interactome definition of disease-associated dysregulated proteins. This information might contribute to the identification of altered signaling pathways and protein functions involved in the pathogenesis of a disease. Remarkably, protein microarrays have been already satisfactorily employed for the study of protein-protein interactions in cancer, allergy, or neurodegenerative diseases. Here, we describe the utilization of recombinant protein microarrays for the identification of protein-protein interactions to help in the definition of disease-specific dysregulated interactomes.
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Affiliation(s)
- Ana Montero-Calle
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, Madrid, Spain.
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11
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Qin G, Liu Z, Xie L. Multiple Omics Data Integration. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11508-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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12
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Vihinen M. Functional effects of protein variants. Biochimie 2020; 180:104-120. [PMID: 33164889 DOI: 10.1016/j.biochi.2020.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
Genetic and other variations frequently affect protein functions. Scientific articles can contain confusing descriptions about which function or property is affected, and in many cases the statements are pure speculation without any experimental evidence. To clarify functional effects of protein variations of genetic or non-genetic origin, a systematic conceptualisation and framework are introduced. This framework describes protein functional effects on abundance, activity, specificity and affinity, along with countermeasures, which allow cells, tissues and organisms to tolerate, avoid, repair, attenuate or resist (TARAR) the effects. Effects on abundance discussed include gene dosage, restricted expression, mis-localisation and degradation. Enzymopathies, effects on kinetics, allostery and regulation of protein activity are subtopics for the effects of variants on activity. Variation outcomes on specificity and affinity comprise promiscuity, specificity, affinity and moonlighting. TARAR mechanisms redress variations with active and passive processes including chaperones, redundancy, robustness, canalisation and metabolic and signalling rewiring. A framework for pragmatic protein function analysis and presentation is introduced. All of the mechanisms and effects are described along with representative examples, most often in relation to diseases. In addition, protein function is discussed from evolutionary point of view. Application of the presented framework facilitates unambiguous, detailed and specific description of functional effects and their systematic study.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22 184, Lund, Sweden.
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13
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Rodriguez JM, Pozo F, di Domenico T, Vazquez J, Tress ML. An analysis of tissue-specific alternative splicing at the protein level. PLoS Comput Biol 2020; 16:e1008287. [PMID: 33017396 PMCID: PMC7561204 DOI: 10.1371/journal.pcbi.1008287] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 10/15/2020] [Accepted: 08/25/2020] [Indexed: 01/09/2023] Open
Abstract
The role of alternative splicing is one of the great unanswered questions in cellular biology. There is strong evidence for alternative splicing at the transcript level, and transcriptomics experiments show that many splice events are tissue specific. It has been suggested that alternative splicing evolved in order to remodel tissue-specific protein-protein networks. Here we investigated the evidence for tissue-specific splicing among splice isoforms detected in a large-scale proteomics analysis. Although the data supporting alternative splicing is limited at the protein level, clear patterns emerged among the small numbers of alternative splice events that we could detect in the proteomics data. More than a third of these splice events were tissue-specific and most were ancient: over 95% of splice events that were tissue-specific in both proteomics and RNAseq analyses evolved prior to the ancestors of lobe-finned fish, at least 400 million years ago. By way of contrast, three in four alternative exons in the human gene set arose in the primate lineage, so our results cannot be extrapolated to the whole genome. Tissue-specific alternative protein forms in the proteomics analysis were particularly abundant in nervous and muscle tissues and their genes had roles related to the cytoskeleton and either the structure of muscle fibres or cell-cell connections. Our results suggest that this conserved tissue-specific alternative splicing may have played a role in the development of the vertebrate brain and heart. We manually curated a set of 255 splice events detected in a large-scale tissue-based proteomics experiment and found that more than a third had evidence of significant tissue-specific differences. Events that were significantly tissue-specific at the protein level were highly conserved; almost 75% evolved over 400 million years ago. The tissues in which we found most evidence for tissue-specific splicing were nervous tissues and cardiac tissues. Genes with tissue-specific events in these two tissues had functions related to important cellular structures in brain and heart tissues. These splice events may have been essential for the development of vertebrate heart and muscle. However, our data set may not be representative of alternative exons as a whole. We found that most tissue specific splicing was strongly conserved, but just 5% of annotated alternative exons in the human gene set are ancient. More than three quarters of alternative exons are primate-derived. Although the analysis does not provide a definitive answer to the question of the functional role of alternative splicing, our results do indicate that alternative splice variants may have played a significant part in the evolution of brain and heart tissues in vertebrates.
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Affiliation(s)
- Jose Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Calle Melchor Fernandez, Madrid, Spain
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
| | - Tomas di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
| | - Jesus Vazquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Calle Melchor Fernandez, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Michael L. Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
- * E-mail:
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14
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Abstract
Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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15
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Sulakhe D, D'Souza M, Wang S, Balasubramanian S, Athri P, Xie B, Canzar S, Agam G, Gilliam TC, Maltsev N. Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. Brief Bioinform 2020; 20:1754-1768. [PMID: 29931155 DOI: 10.1093/bib/bby047] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
In recent years, the emphasis of scientific inquiry has shifted from whole-genome analyses to an understanding of cellular responses specific to tissue, developmental stage or environmental conditions. One of the central mechanisms underlying the diversity and adaptability of the contextual responses is alternative splicing (AS). It enables a single gene to encode multiple isoforms with distinct biological functions. However, to date, the functions of the vast majority of differentially spliced protein isoforms are not known. Integration of genomic, proteomic, functional, phenotypic and contextual information is essential for supporting isoform-based modeling and analysis. Such integrative proteogenomics approaches promise to provide insights into the functions of the alternatively spliced protein isoforms and provide high-confidence hypotheses to be validated experimentally. This manuscript provides a survey of the public databases supporting isoform-based biology. It also presents an overview of the potential global impact of AS on the human canonical gene functions, molecular interactions and cellular pathways.
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Affiliation(s)
- Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
| | - Mark D'Souza
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA
| | - Sheng Wang
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, USA
| | - Sandhya Balasubramanian
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Genentech, Inc. 1 DNA Way, Mail Stop: 35-6J, South San Francisco, CA, USA
| | - Prashanth Athri
- Department of Computer Science and Engineering, Amrita School of Engineering, Bengaluru, Amrita Vishwa Vidyapeetham, Kasavanahalli, Carmelaram P.O., Bengaluru, Karnataka, India
| | - Bingqing Xie
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA
| | - Stefan Canzar
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, USA.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gady Agam
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA
| | - T Conrad Gilliam
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
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16
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Hatje K, Mühlhausen S, Simm D, Kollmar M. The Protein-Coding Human Genome: Annotating High-Hanging Fruits. Bioessays 2019; 41:e1900066. [PMID: 31544971 DOI: 10.1002/bies.201900066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/07/2019] [Indexed: 12/19/2022]
Abstract
The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.
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Affiliation(s)
- Klas Hatje
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstr. 124, 4070, Basel, Switzerland
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Goldschmidtstr. 7, 37077, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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17
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Chen Y, Yuan X, Cang X. Population-based incremental learning for the prediction of Homo sapiens’ protein secondary structure. INT J BIOMATH 2019. [DOI: 10.1142/s1793524519500177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Protein structure prediction is the prediction of the 3D structure of a protein based on its amino acid sequence. It is a key component in disciplines such as medicine, biology, and biochemistry. The prediction of the protein secondary structure of Homo sapiens is one of the more important domains. Many methods have been used to feed forward neural networks or SVMs combined with a sliding window. This method’s mechanisms are too complex to be able to extract clear and straightforward physical meanings from it. This paper explores population-based incremental learning (PBIL), which is a method that combines the mechanisms of a generational genetic algorithm with simple competitive learning. The result shows that its accuracies are particularly associated with the Homo species. This new perspective reveals a number of different possibilities for the purposes of performance improvements.
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Affiliation(s)
- Ye Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221008, P. R. China
| | - Xiaoping Yuan
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221008, P. R. China
| | - Xiaohui Cang
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, P. R. China
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18
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Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G. Translatomics: The Global View of Translation. Int J Mol Sci 2019; 20:ijms20010212. [PMID: 30626072 PMCID: PMC6337585 DOI: 10.3390/ijms20010212] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/01/2023] Open
Abstract
In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the other “omics”-methods, translatomics investigates the totality of the components in the translation process, including but not limited to translating mRNAs, ribosomes, tRNAs, regulatory RNAs and nascent polypeptide chains. Technical advances in recent years have brought breakthroughs in the investigation of these components at global scale, both for their composition and dynamics. These methods have been applied in a rapidly increasing number of studies to reveal multifaceted aspects of translation control. The process of translation is not restricted to the conversion of mRNA coding sequences into polypeptide chains, it also controls the composition of the proteome in a delicate and responsive way. Therefore, translatomics has extended its unique and innovative power to many fields including proteomics, cancer research, bacterial stress response, biological rhythmicity and plant biology. Rational design in translation can enhance recombinant protein production for thousands of times. This brief review summarizes the main state-of-the-art methods of translatomics, highlights recent discoveries made in this field and introduces applications of translatomics on basic biological and biomedical research.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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19
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Li D, Mastaglia FL, Fletcher S, Wilton SD. Precision Medicine through Antisense Oligonucleotide-Mediated Exon Skipping. Trends Pharmacol Sci 2018; 39:982-994. [PMID: 30282590 DOI: 10.1016/j.tips.2018.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/30/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022]
Abstract
Clinical implementation of two recently approved antisense RNA therapeutics - Exondys51® to treat Duchenne muscular dystrophy (Duchenne MD) and Spinraza® as a treatment for spinal muscular atrophy (SMA) - highlights the therapeutic potential of antisense oligonucleotides (ASOs). As shown in the Duchenne and Becker cases, the identification and specific removal of 'dispensable' exons by exon-skipping ASOs could potentially bypass lethal mutations in other genes and bring clinical benefits to affected individuals carrying amenable mutations. In this review, we discuss the potential of therapeutic alternative splicing, with a particular focus on targeted exon skipping using Duchenne MD as an example, and speculate on new applications for other inherited rare diseases where redundant or dispensable exons may be amenable to exon-skipping ASO intervention as precision medicine.
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Affiliation(s)
- Dunhui Li
- Centre for Comparative Genomics, Murdoch University, Perth 6050, Australia; Perron Institute for Neurological and Translational Science, University of Western Australia, Perth 6000, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, University of Western Australia, Perth 6000, Australia
| | - Sue Fletcher
- Centre for Comparative Genomics, Murdoch University, Perth 6050, Australia; Perron Institute for Neurological and Translational Science, University of Western Australia, Perth 6000, Australia
| | - Steve D Wilton
- Centre for Comparative Genomics, Murdoch University, Perth 6050, Australia; Perron Institute for Neurological and Translational Science, University of Western Australia, Perth 6000, Australia.
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20
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de Bruin RG, Rabelink TJ, van Zonneveld AJ, van der Veer EP. Emerging roles for RNA-binding proteins as effectors and regulators of cardiovascular disease. Eur Heart J 2018; 38:1380-1388. [PMID: 28064149 DOI: 10.1093/eurheartj/ehw567] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/02/2016] [Indexed: 12/18/2022] Open
Abstract
The cardiovascular system comprises multiple cell types that possess the capacity to modulate their phenotype in response to acute or chronic injury. Transcriptional and post-transcriptional mechanisms play a key role in the regulation of remodelling and regenerative responses to damaged cardiovascular tissues. Simultaneously, insufficient regulation of cellular phenotype is tightly coupled with the persistence and exacerbation of cardiovascular disease. Recently, RNA-binding proteins such as Quaking, HuR, Muscleblind, and SRSF1 have emerged as pivotal regulators of these functional adaptations in the cardiovascular system by guiding a wide-ranging number of post-transcriptional events that dramatically impact RNA fate, including alternative splicing, stability, localization and translation. Moreover, homozygous disruption of RNA-binding protein genes is commonly associated with cardiac- and/or vascular complications. Here, we summarize the current knowledge on the versatile role of RNA-binding proteins in regulating the transcriptome during phenotype switching in cardiovascular health and disease. We also detail existing and potential DNA- and RNA-based therapeutic approaches that could impact the treatment of cardiovascular disease in the future.
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Affiliation(s)
- Ruben G de Bruin
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Ton J Rabelink
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Anton Jan van Zonneveld
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Eric P van der Veer
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
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21
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Zhang SJ, Wang C, Yan S, Fu A, Luan X, Li Y, Sunny Shen Q, Zhong X, Chen JY, Wang X, Chin-Ming Tan B, He A, Li CY. Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events. Mol Biol Evol 2017; 34:2453-2468. [PMID: 28957512 PMCID: PMC5850651 DOI: 10.1093/molbev/msx212] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recent RNA-seq technology revealed thousands of splicing events that are under rapid evolution in primates, whereas the reliability of these events, as well as their combination on the isoform level, have not been adequately addressed due to its limited sequencing length. Here, we performed comparative transcriptome analyses in human and rhesus macaque cerebellum using single molecule long-read sequencing (Iso-seq) and matched RNA-seq. Besides 359 million RNA-seq reads, 4,165,527 Iso-seq reads were generated with a mean length of 14,875 bp, covering 11,466 human genes, and 10,159 macaque genes. With Iso-seq data, we substantially expanded the repertoire of alternative RNA processing events in primates, and found that intron retention and alternative polyadenylation are surprisingly more prevalent in primates than previously estimated. We then investigated the combinatorial mode of these alternative events at the whole-transcript level, and found that the combination of these events is largely independent along the transcript, leading to thousands of novel isoforms missed by current annotations. Notably, these novel isoforms are selectively constrained in general, and 1,119 isoforms have even higher expression than the previously annotated major isoforms in human, indicating that the complexity of the human transcriptome is still significantly underestimated. Comparative transcriptome analysis further revealed 502 genes encoding selectively constrained, lineage-specific isoforms in human but not in rhesus macaque, linking them to some lineage-specific functions. Overall, we propose that the independent combination of alternative RNA processing events has contributed to complex isoform evolution in primates, which provides a new foundation for the study of phenotypic difference among primates.
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Affiliation(s)
- Shi-Jian Zhang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Chenqu Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Science, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shouyu Yan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Aisi Fu
- Wuhan Institute of Biotechnology, Wuhan, Hubei, China
| | - Xuke Luan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Science, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yumei Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiaoming Zhong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jia-Yu Chen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences College of Medicine, Tao-Yuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chuan-Yun Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
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22
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Reggiani C, Coppens S, Sekhara T, Dimov I, Pichon B, Lufin N, Addor MC, Belligni EF, Digilio MC, Faletra F, Ferrero GB, Gerard M, Isidor B, Joss S, Niel-Bütschi F, Perrone MD, Petit F, Renieri A, Romana S, Topa A, Vermeesch JR, Lenaerts T, Casimir G, Abramowicz M, Bontempi G, Vilain C, Deconinck N, Smits G. Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability. Genome Med 2017; 9:67. [PMID: 28724449 PMCID: PMC5518101 DOI: 10.1186/s13073-017-0452-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/20/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. METHODS Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play. RESULTS Integrating genomics, transcriptomics, and epigenomics data, we describe two novel DLG2 promoters and coding first exons expressed in human fetal brain. Their murine conservation and protein-level evidence allowed us to produce new DLG2 gene models for human and mouse. These new genic elements are deleted in 90% of 29 patients (public and in-house) showing partial deletion of the DLG2 gene. The patients' clinical characteristics expand the neurodevelopmental phenotypic spectrum linked to DLG2 gene disruption to cognitive and behavioral categories. CONCLUSIONS While protein-coding genes are regarded as well known, our work shows that integration of multiple omics datasets can unveil novel coding elements. From a clinical perspective, our work demonstrates that two new DLG2 promoters and exons are crucial for the neurodevelopmental phenotypes associated with this gene. In addition, our work brings evidence for the lack of cross-annotation in human versus mouse reference genomes and nucleotide versus protein databases.
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Affiliation(s)
- Claudio Reggiani
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, 1050 Belgium
| | - Sandra Coppens
- Department of Neurology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
- Neuropediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
| | - Tayeb Sekhara
- Neuropediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
- Present address: Neuropediatrics, Clinique Saint-Anne Saint-Rémy - CHIREC, Brussels, 1070 Belgium
| | - Ivan Dimov
- Faculté de Médecine, Université Libre de Bruxelles, Brussels, 1070 Belgium
| | - Bruno Pichon
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
| | - Nicolas Lufin
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
| | - Marie-Claude Addor
- Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois CHUV, Lausanne, 1011 Switzerland
| | - Elga Fabia Belligni
- Department of Public Health and Pediatrics, University of Torino, Turin, 10126 Italy
| | | | - Flavio Faletra
- S.C. Medical Genetics, Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, Trieste, 34137 Italy
| | | | - Marion Gerard
- Laboratory of Medical Genetics, CHU de Caen - Hôpital Clémenceau, Caen, 14033 Caen Cedex, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, 44093 Nantes Cedex 1, France
| | - Shelagh Joss
- West of Scotland Clinical Genetics Service, South Glasgow University Hospitals, Glasgow, G51 4TF UK
| | - Florence Niel-Bütschi
- Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois CHUV, Lausanne, 1011 Switzerland
| | - Maria Dolores Perrone
- S.C. Medical Genetics, Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, Trieste, 34137 Italy
- Present address: Assisted Fertilization Department, Casa di Cura Città di Udine, Udine, 33100 Italy
| | - Florence Petit
- Service de Génétique, CHRU de Lille - Hôpital Jeanne de Flandre, Lille, 59000 France
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, 53100 Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, 53100 Italy
| | - Serge Romana
- Service d’Histologie Embryologie Cytogénétique, Hôpital Necker Enfants Malades, Paris, 75015 France
- Université Paris Descartes - Institut IMAGINE, Paris, 75015 France
| | - Alexandra Topa
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, 413 45 Sweden
| | | | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, 1050 Belgium
- AI lab, Vrije Universiteit Brussel, Brussels, 1050 Belgium
| | - Georges Casimir
- Pediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
| | - Marc Abramowicz
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, 1050 Belgium
| | - Catheline Vilain
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
- Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
| | - Nicolas Deconinck
- Neuropediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
- Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
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23
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Wu W, Zong J, Wei N, Cheng J, Zhou X, Cheng Y, Chen D, Guo Q, Zhang B, Feng Y. CASH: a constructing comprehensive splice site method for detecting alternative splicing events. Brief Bioinform 2017; 19:905-917. [DOI: 10.1093/bib/bbx034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/03/2023] Open
Affiliation(s)
- Wenwu Wu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Hangzhou, China
| | - Jie Zong
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Ning Wei
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jian Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xuexia Zhou
- Tianjin Medical University General Hospital, China
| | - Yuanming Cheng
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Dai Chen
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Qinghua Guo
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Bo Zhang
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Ying Feng
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
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24
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Tress ML, Abascal F, Valencia A. Alternative Splicing May Not Be the Key to Proteome Complexity. Trends Biochem Sci 2016; 42:98-110. [PMID: 27712956 DOI: 10.1016/j.tibs.2016.08.008] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/19/2016] [Accepted: 08/15/2016] [Indexed: 12/21/2022]
Abstract
Alternative splicing is commonly believed to be a major source of cellular protein diversity. However, although many thousands of alternatively spliced transcripts are routinely detected in RNA-seq studies, reliable large-scale mass spectrometry-based proteomics analyses identify only a small fraction of annotated alternative isoforms. The clearest finding from proteomics experiments is that most human genes have a single main protein isoform, while those alternative isoforms that are identified tend to be the most biologically plausible: those with the most cross-species conservation and those that do not compromise functional domains. Indeed, most alternative exons do not seem to be under selective pressure, suggesting that a large majority of predicted alternative transcripts may not even be translated into proteins.
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Affiliation(s)
- Michael L Tress
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Federico Abascal
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain; Human Genetics Department, Sandhu Group, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alfonso Valencia
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain; National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain.
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25
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Haas CT, Roe JK, Pollara G, Mehta M, Noursadeghi M. Diagnostic 'omics' for active tuberculosis. BMC Med 2016; 14:37. [PMID: 27005907 PMCID: PMC4804573 DOI: 10.1186/s12916-016-0583-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/08/2016] [Indexed: 12/12/2022] Open
Abstract
The decision to treat active tuberculosis (TB) is dependent on microbiological tests for the organism or evidence of disease compatible with TB in people with a high demographic risk of exposure. The tuberculin skin test and peripheral blood interferon-γ release assays do not distinguish active TB from a cleared or latent infection. Microbiological culture of mycobacteria is slow. Moreover, the sensitivities of culture and microscopy for acid-fast bacilli and nucleic acid detection by PCR are often compromised by difficulty in obtaining samples from the site of disease. Consequently, we need sensitive and rapid tests for easily obtained clinical samples, which can be deployed to assess patients exposed to TB, discriminate TB from other infectious, inflammatory or autoimmune diseases, and to identify subclinical TB in HIV-1 infected patients prior to commencing antiretroviral therapy. We discuss the evaluation of peripheral blood transcriptomics, proteomics and metabolomics to develop the next generation of rapid diagnostics for active TB. We catalogue the studies published to date seeking to discriminate active TB from healthy volunteers, patients with latent infection and those with other diseases. We identify the limitations of these studies and the barriers to their adoption in clinical practice. In so doing, we aim to develop a framework to guide our approach to discovery and development of diagnostic biomarkers for active TB.
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Affiliation(s)
- Carolin T Haas
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Jennifer K Roe
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Gabriele Pollara
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Meera Mehta
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK.
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