Alfredo Dueñas Rey

Retina-specific long non-coding RNAs associated with inherited retinal disease genes

Emma Delanote, Karla Alejandra Ruiz-Ceja, Alfredo Dueñas Rey, Dalila Capasso et autres

Long non‑coding RNAs (lncRNAs) are increasingly recognized as important regulatory molecules, yet their roles remain largely unexplored in many tissues. This study aimed to identify and characterize lncRNAs involved in human retinal biology and inherited retinal disease (IRD), a leading cause of …

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Generation of two iPSC lines (UGENTi003 and UGENTi004) from patients with intermediate rod-cone dystrophy carrying the c.[-123C>T;701G>A];[806_810del] variants in the RDH12 gene

Manon Bouckaert, Filip Van den Broeck, Mehrnaz Ghazvini, Alfredo Dueñas Rey et autres

Biallelic variants in RDH12 are associated with early-onset retinal dystrophy and Leber congenital amaurosis. RDH12 plays a role in the phototransduction cascade by converting all-trans retinal into all-trans retinol in the photoreceptor inner segments. Induced pluripotent stem cells (iPSCs) were generated and …

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DA.Vra1-congenic rats display increased gene expression and Schwann cell apoptosis but unaffected nerve regeneration compared to parental DA rats after sciatic nerve injury and repair

Lena Stenberg, Michael Jewett, Alfredo Dueñas Rey, Maria Swanberg et autres

Introduction The rat Vra1 locus, containing glutathione S-transferase alpha 4 (Gsta4), regulates the degeneration of central nervous system (CNS) neurons in toxin-, protein-, and injury-based models. We hypothesize that Piebald Virol Glaxo.1AV1 (PVG) alleles in Vra1 confer protection and increased axonal outgrowth …

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Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches

Merel Stemerdink, Tabea Riepe, Nick Zomer, Renee Salz et autres

Sequencing technologies have long limited the comprehensive investigation of large transcripts associated with inherited retinal diseases (IRDs) like Usher syndrome, which involves 11 associated genes with transcripts up to 19.6 kb. To address this, we used PacBio long-read mRNA isoform sequencing (Iso-Seq) …

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A proteogenomic atlas of the human neural retina

Tabea Riepe, Merel Stemerdink, Renee Salz, Alfredo Dueñas Rey et autres

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 …

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Pushing the limits of single molecule transcript sequencing to uncover the largest disease-associated transcript isoforms in the human neural retina

Merel Stemerdink, Tabea Riepe, Nick Zomer, Renee Salz et autres

ABSTRACT Sequencing technologies have long limited the comprehensive investigation of large transcripts associated with inherited retinal diseases (IRDs) like Usher syndrome, which involves 11 associated genes with transcripts up to 19.6 kb. To address this, we used PacBio long-read mRNA isoform sequencing …

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A proteogenomic atlas of the human neural retina

Tabea Riepe, Merel Stemerdink, Renee Salz, Alfredo Dueñas Rey et autres

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 …

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Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci

Eva D’haene, Víctor López-Soriano, Pedro Manuel Martínez‐García, Soraya Kalayanamontri et autres

BACKGROUND: Vision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory …

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Author Correction: Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci

Víctor López-Soriano, Alfredo Dueñas Rey, Rajarshi Mukherjee, Chris F. Inglehearn et autres

The original version of this Article contained an error in the Acknowledgements, which incorrectly omitted the following: ‘This publication is part of the Human Cell Atlas - www.humancellatlas.org/publications (HCA-51)’. This has been corrected in both the PDF and HTML versions of the …

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Autozygome‐guided exome‐first study in a consanguineous cohort with early‐onset retinal disease uncovers an isolated RIMS2 phenotype and a retina‐enriched RIMS2 isoform

Marta Del Pozo‐Valero, Basamat Almoallem, Alfredo Dueñas Rey, Quinten Mahieu et autres

Leber congenital amaurosis (LCA) and early-onset retinal degeneration (EORD) are inherited retinal diseases (IRD) characterized by early-onset vision impairment. Herein, we studied 15 Saudi families by whole exome sequencing (WES) and run-of-homozygosity (ROH) detection via AutoMap in 12/15 consanguineous families. This revealed …

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Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci

Víctor López-Soriano, Alfredo Dueñas Rey, Rajarshi Mukherjee, Chris F. Inglehearn et autres

Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) …

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Author response for "Autozygome‐guided exome‐first study in a consanguineous cohort with early‐onset retinal disease uncovers an isolated RIMS2 phenotype and a retina‐enriched RIMS2 isoform"

Marta Del Pozo‐Valero, Basamat Almoallem, Alfredo Dueñas Rey, Quinten Mahieu et autres