Project 09
Evaluation by RNA-seq-based approaches of the global role of microRNAs and of other noncoding RNAs in the human and mouse retina in both physiological and pathological conditions (Inherited Retinal Disease).
Inherited retinal diseases are a heterogeneous group of conditions that include many different clinical subtypes.
Inherited retinal diseases are a heterogeneous group of conditions that include many different clinical subtypes, such as RP, LCA, Stargardt disease and others, which differ in primary retinal cell target, severity and age of onset. The main outcome of IRDs is usually represented by photoreceptor/retinal pigment epithelium cell death. IRDs are caused by mutations in >250 genes, but the underlying molecular mechanisms are still unclear.
In particular, the role of microRNAs (miRNAs) as well as of other types on noncoding RNAs, such as long noncoding RNAs (lncRNAs) remain elusive. We previously generated the most comprehensive expression atlas of miRNAs in the human retina, which allowed us to reconstruct the general architecture of the miRNome in normal conditions (Karali et al, 2016). Here, we plan to perform systematic expression analyses of miRNAs and lncRNAs by Next Generation Sequencing (NGS)-based approaches including RNA-seq and small RNA-seq in murine models of IRDs at different clinically relevant timepoints, including 1) a pre-clinical stage (i.e., before the onset of degeneration), 2) an “acute” stage (i.e., the peak of degeneration) and 3) a post-degeneration stage, in which rod PRs, i.e., the primary cell targets in most IRD forms are completely degenerated but cone PRs are still present but undergoing secondary death. We plan to do this both by using bulk as well as single cell procedures. We will also aim at carrying out similar approaches in human IRD models, namely retinal organoids harboring genotypes responsible for IRDs. The results generated in this project should lead to a better understanding of the role of noncoding RNAs in pathogenesis and progression of IRDs.
Expected results
- Assessment of global expression profiles of miRNAs across the main pathogenic stages of IRDs and their relations with mRNAs
- Assessment of global expression profiles of lncRNAs across the main pathogenic stages of IRDs and their relations with protein coding genes
- In silico identification of key pathways regulated by noncoding RNAs during the main phases of retinal cell degeneration and initial insight into their potential therapeutic exploitation as mutation-independent approaches
Planned secondments
- B2, supervisor: Zohreh Hosseizadeh
Purpose: generation of retinal organoids from patients - AP7, supervisor: Beatriz Llamusí
Purpose: business training - B1, supervisor: Javier Sancho-Pelluz
Purpose: extraction and characterisation during degeneration of exosome from the retina - B6, supervisor: Jan Wijnholds
Purpose: use of RNA-based therapies - B7, supervisor: Aileen Murphy
Purpose: economic training