Frontiers in Genetics (Sep 2024)
A proteogenomic atlas of the human neural retina
- Tabea V. Riepe,
- Tabea V. Riepe,
- Tabea V. Riepe,
- Tabea V. Riepe,
- Merel Stemerdink,
- Renee Salz,
- Alfredo Dueñas Rey,
- Alfredo Dueñas Rey,
- Suzanne E. de Bruijn,
- Suzanne E. de Bruijn,
- Erica Boonen,
- Erica Boonen,
- Erica Boonen,
- Tomasz Z. Tomkiewicz,
- Tomasz Z. Tomkiewicz,
- Tomasz Z. Tomkiewicz,
- Michael Kwint,
- Jolein Gloerich,
- Hans J. C. T. Wessels,
- Emma Delanote,
- Emma Delanote,
- Elfride De Baere,
- Elfride De Baere,
- Filip van Nieuwerburgh,
- Sarah De Keulenaer,
- Barbara Ferrari,
- Stefano Ferrari,
- Frauke Coppieters,
- Frauke Coppieters,
- Frauke Coppieters,
- Frans P. M. Cremers,
- Frans P. M. Cremers,
- Frans P. M. Cremers,
- Erwin van Wyk,
- Susanne Roosing,
- Susanne Roosing,
- Susanne Roosing,
- Erik de Vrieze,
- Peter A. C. ‘t Hoen
Affiliations
- Tabea V. Riepe
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, Netherlands
- Tabea V. Riepe
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Tabea V. Riepe
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Tabea V. Riepe
- Maastricht University Medical Center+, Maastricht, Netherlands
- Merel Stemerdink
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Renee Salz
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, Netherlands
- Alfredo Dueñas Rey
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Suzanne E. de Bruijn
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Erica Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Erica Boonen
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Erica Boonen
- Maastricht University Medical Center+, Maastricht, Netherlands
- Tomasz Z. Tomkiewicz
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Tomasz Z. Tomkiewicz
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Tomasz Z. Tomkiewicz
- Maastricht University Medical Center+, Maastricht, Netherlands
- Michael Kwint
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Jolein Gloerich
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Hans J. C. T. Wessels
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Emma Delanote
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Emma Delanote
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Filip van Nieuwerburgh
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Sarah De Keulenaer
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Barbara Ferrari
- 0Fondazione Banca degli Occhi del Veneto, Venice, Italy
- Stefano Ferrari
- 0Fondazione Banca degli Occhi del Veneto, Venice, Italy
- Frauke Coppieters
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Frauke Coppieters
- 1Department of Pharmaceutics, Ghent University, Ghent, Belgium
- Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Frans P. M. Cremers
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Frans P. M. Cremers
- Maastricht University Medical Center+, Maastricht, Netherlands
- Erwin van Wyk
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Susanne Roosing
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Susanne Roosing
- Maastricht University Medical Center+, Maastricht, Netherlands
- Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Gelderland, Netherlands
- Peter A. C. ‘t Hoen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, Netherlands
- DOI
- https://doi.org/10.3389/fgene.2024.1451024
- Journal volume & issue
-
Vol. 15
Abstract
The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNA-sequencing methods have been used for understanding retina-specific splicing but have limitations in detailing transcript isoforms. To address this, we generated a proteogenomic atlas that combines PacBio long-read RNA-sequencing data with mass spectrometry and whole genome sequencing data of three healthy human neural retina samples. We identified nearly 60,000 transcript isoforms, of which approximately one-third are novel. Additionally, ten novel peptides confirmed novel transcript isoforms. For instance, we identified a novel IMPDH1 isoform with a novel combination of known exons that is supported by peptide evidence. Our research underscores the potential of in-depth tissue-specific transcriptomic analysis to enhance our grasp of tissue-specific alternative splicing. The data underlying the proteogenomic atlas are available via EGA with identifier EGAD50000000101, via ProteomeXchange with identifier PXD045187, and accessible through the UCSC genome browser.
Keywords
