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Ascensão-Ferreira M, Martins-Silva R, Saraiva-Agostinho N, Barbosa-Morais NL. betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions. RNA (NEW YORK, N.Y.) 2024; 30:337-353. [PMID: 38278530 PMCID: PMC10946425 DOI: 10.1261/rna.079764.123] [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: 07/06/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Next-generation RNA sequencing allows alternative splicing (AS) quantification with unprecedented resolution, with the relative inclusion of an alternative sequence in transcripts being commonly quantified by the proportion of reads supporting it as percent spliced-in (PSI). However, PSI values do not incorporate information about precision, proportional to the respective AS events' read coverage. Beta distributions are suitable to quantify inclusion levels of alternative sequences, using reads supporting their inclusion and exclusion as surrogates for the two distribution shape parameters. Each such beta distribution has the PSI as its mean value and is narrower when the read coverage is higher, facilitating the interpretability of its precision when plotted. We herein introduce a computational pipeline, based on beta distributions accurately modeling PSI values and their precision, to quantitatively and visually compare AS between groups of samples. Our methodology includes a differential splicing significance metric that compromises the magnitude of intergroup differences, the estimation uncertainty in individual samples, and the intragroup variability, being therefore suitable for multiple-group comparisons. To make our approach accessible and clear to both noncomputational and computational biologists, we developed betAS, an interactive web app and user-friendly R package for visual and intuitive differential splicing analysis from read count data.
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Affiliation(s)
- Mariana Ascensão-Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Rita Martins-Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Nuno Saraiva-Agostinho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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Sapio MR, King DM, Staedtler ES, Maric D, Jahanipour J, Kurochkina NA, Manalo AP, Ghetti A, Mannes AJ, Iadarola MJ. Expression pattern analysis and characterization of the hereditary sensory and autonomic neuropathy 2 A (HSAN2A) gene with no lysine kinase (WNK1) in human dorsal root ganglion. Exp Neurol 2023; 370:114552. [PMID: 37793538 DOI: 10.1016/j.expneurol.2023.114552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/20/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
Abstract
Inherited painless neuropathies arise due to genetic insults that either block the normal signaling of or destroy the sensory afferent neurons in the dorsal root ganglion (DRG) responsible for transducing noxious stimuli. Complete loss of these neurons leads to profound insensitivity to all sensory modalities including pain. Hereditary sensory and autonomic neuropathy type 2 (HSNAII) is a rare genetic neuropathy characterized by a progressive distal early onset sensory loss. This syndrome is caused by autosomal recessive mutations in the with-no-lysine protein kinase 1 (WNK1) serine-threonine kinase gene. Of interest, disease-associated mutations are found in the large exon, termed "HSN2," which encodes a 498 amino acid domain C-terminal to the kinase domain. These mutations lead to truncation of the HSN2-containing proteins through the addition of an early stop codon (nonsense mutation) leading to loss of the C-terminal domains of this large protein. The present study evaluates the transcripts, gene structure, and protein structure of HSN2-containing WNK1 splice variants in DRG and spinal cord in order to establish the basal expression patterns of WNK1 and HSN2-containing WNK1 splice variants using multiplex fluorescent situ hybridization. We hypothesized that these transcripts would be enriched in pain-sensing DRG neurons, and, potentially, that enrichment in nociceptive neurons was responsible for the painless phenotypes observed. However, our in-depth analyses revealed that the HSN2-WNK1 splice variants were ubiquitously expressed but were not enriched in tachykinin 1-expressing C-fiber neurons, a class of neurons with a highly nociceptive character. We subsequently identified other subpopulations of DRG neurons with higher levels of HSN2-WNK1 expression, including mechanosensory large fibers. These data are inconsistent with the hypothesis that this transcript is enriched in nociceptive fibers, and instead suggest it may be related to general axon maintenance, or that nociceptive fibers are more sensitive to the genetic insult. These findings clarify the molecular and cellular expression pattern of this painless neuropathy gene in human tissue.
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Affiliation(s)
- Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diana M King
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ellen S Staedtler
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dragan Maric
- National Institute of Neurological Disorders and Stroke, Flow and Imaging Cytometry Core Facility, Bethesda, MD 20892, USA
| | - Jahandar Jahanipour
- National Institute of Neurological Disorders and Stroke, Flow and Imaging Cytometry Core Facility, Bethesda, MD 20892, USA
| | | | - Allison P Manalo
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Andrew J Mannes
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA.
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Gallego-Paez LM, Edwards WJS, Chanduri M, Guo Y, Koorman T, Lee CY, Grexa N, Derksen P, Yan J, Schwartz MA, Mauer J, Goult BT. TLN1 contains a cancer-associated cassette exon that alters talin-1 mechanosensitivity. J Cell Biol 2023; 222:213923. [PMID: 36880935 PMCID: PMC9997659 DOI: 10.1083/jcb.202209010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/08/2023] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Talin-1 is the core mechanosensitive adapter protein linking integrins to the cytoskeleton. The TLN1 gene is comprised of 57 exons that encode the 2,541 amino acid TLN1 protein. TLN1 was previously considered to be expressed as a single isoform. However, through differential pre-mRNA splicing analysis, we discovered a cancer-enriched, non-annotated 51-nucleotide exon in TLN1 between exons 17 and 18, which we refer to as exon 17b. TLN1 is comprised of an N-terminal FERM domain, linked to 13 force-dependent switch domains, R1-R13. Inclusion of exon 17b introduces an in-frame insertion of 17 amino acids immediately after Gln665 in the region between R1 and R2 which lowers the force required to open the R1-R2 switches potentially altering downstream mechanotransduction. Biochemical analysis of this isoform revealed enhanced vinculin binding, and cells expressing this variant show altered adhesion dynamics and motility. Finally, we showed that the TGF-β/SMAD3 signaling pathway regulates this isoform switch. Future studies will need to consider the balance of these two TLN1 isoforms.
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Affiliation(s)
| | | | - Manasa Chanduri
- Departments of Internal Medicine (Cardiology) and Yale Cardiovascular Research Center , New Haven, CT, USA
| | - Yanyu Guo
- Mechanobiology Institute, National University of Singapore , Singapore, Singapore
| | - Thijs Koorman
- Department of Pathology, University Medical Center Utrecht , Utrecht, Netherlands
| | | | - Nina Grexa
- Biomed X Institute (GmbH) , Heidelberg, Germany
| | - Patrick Derksen
- Department of Pathology, University Medical Center Utrecht , Utrecht, Netherlands
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore , Singapore, Singapore.,Department of Physics, National University of Singapore , Singapore, Singapore
| | - Martin A Schwartz
- Departments of Internal Medicine (Cardiology) and Yale Cardiovascular Research Center , New Haven, CT, USA.,Departments of Cell Biology and Biomedical Engineering, Yale School of Medicine , New Haven, CT, USA
| | - Jan Mauer
- Biomed X Institute (GmbH) , Heidelberg, Germany.,Department of Immunology, Novartis Institutes for BioMedical Research, Basel, Switzerland
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