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Cellular milieu of the neural retina informs complement immune regulation

ABSTRACT: Cellular milieu of the neural retina informs complement immune regulation

PROVIDER: PRJNA483791 | ENA |

REPOSITORIES: ENA

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Cellular milieu of the neural retina informs complement immune regulation [Hs]

Project description:Cellular milieu of the neural retina informs complement immune regulation [Hs]

| PRJNA483793 | ENA

Cellular milieu of the neural retina informs complement immune regulation [Hs]

Project description:Purpose: We present a comprehensive map of the human retinal complement expression at a single-cell resolution, spanning 11 cell types. Methods: Retinal mRNA profiles from were generated by scRNA sequencing (10x Genomics) from a healthy human donor immediately within 4 hours of death. The data was normalized using Seurat. Results: Using an optimized data analysis workflow, we found novel patterns of complement expression in the retina Conclusions: Our landmark atlas provides crucial mechanistic insights in complement immunology

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Cellular milieu of the neural retina informs complement immune regulation

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Project description:The human neural retina is enriched for alternative splicing, and it is estimated that more than 10% of variants associated with inherited retinal diseases (IRDs) alter splicing. Previous research mainly used short-read RNA-sequencing techniques to investigate retina-specific splicing and splicing factors. However, this technique provides limited information about transcript isoforms. To gain a deeper understanding of the human neural retina and its isoforms, we generated a proteogenomic atlas that combined PacBio long-read RNA-sequencing data with mass-spectrometry and whole-genome sequencing data from three healthy human neural retina samples. RNA-sequencing revealed that one-third of all transcripts were novel, and for IRD-associated genes, even 43% were novel. The most common novel elements of these transcripts were alternative poly(A) sites, exon elongation, and intron retention. Some novel elements affect the non-coding region but for more than 50% of the novel transcripts a novel open reading frame was predicted. Using proteomics, ten novel peptides confirmed novel isoforms in five genes. Additionally, we found novel isoforms of IMPDH1, an IRD-associated gene, with supporting peptide evidence. This study provides a comprehensive overview of the transcript and protein isoforms expressed in the healthy human neural retina. Moreover, it highlights the importance of studying tissue specific transcriptomes in greater detail to better understand tissue-specific regulation and to identify disease-causing variants.

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