Biology subjects

Ayyagari, R.

Publications and source records attributed to Ayyagari, R..

3 recordsLinked to original sources

bioRxiv2025

Multi-omic analysis of photoreceptor alterations during early-onset retinal degeneration in Mfrp-/- mice

Loss-of-function mutations in the membrane frizzled-related protein (MFRP) gene are associated with autosomal recessive ocular disorders such as nanophthalmos, posterior microphthalmia, and retinitis pigmentosa, yet the molecular mechanisms underlying MFRP-related retinal degeneration remain poorly defined. To investigate these mechanisms, we generated and characterized Mfrp-/- mice and conducted an integrated multi-omic analysis to map the onset and progression of transcriptional changes during retinal degeneration. Using longitudinal in vivo imaging, histological and immunohistochemical analysis, qRT-PCR, single-nucleus RNA sequencing (snRNA-seq), snATAC seq (single-nucleus Assay for Transposase-Accessible Chromatin using sequencing) and spatial transcriptomics (GeoMx DSP), we identified early and progressive photoreceptor loss in Mfrp-/- mice, beginning by 28d. Retinal thinning and autofluorescent deposits in Mfrp-/- mice were accompanied by decreased expression of rod and cone opsins. Transcriptomic profiling by snRNA-seq revealed distinct, photoreceptor-specific gene expression changes, including early upregulation of inflammatory and stress-related genes and later downregulation of genes involved in chromatin remodeling, synaptic function, and neurodevelopment. Spatial transcriptomic analysis of the outer nuclear layer (ONL) revealed disruptions in mitochondrial function, mTORC1 signaling, and G protein-coupled receptor pathways. These findings define a temporally and spatially coordinated program of degeneration triggered by Mfrp loss and demonstrate that Mfrp is required for the maintenance of photoreceptor integrity and gene regulatory homeostasis during retinal development. Our work establishes Mfrp-/- mice as a robust model for dissecting photoreceptor vulnerability and provides a transcriptomic atlas of disease progression with potential relevance for therapeutic development in MFRP-associated retinal dystrophies.

genomics↗

bioRxiv2024

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE)/choroid. We identified 420,824 unique candidate regulatory elements and characterized their chromatin states in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells further revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina and relevant diseases.

genomics↗

bioRxiv2018

Human iPSC-derived retinal pigment epithelium: a model system for identifying and functionally characterizing causal variants at AMD risk loci

We evaluate whether human induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells can be used to prioritize and functionally characterize causal variants at age-related macular degeneration (AMD) risk loci. We generated iPSC-RPE from six subjects and show that they have morphological and molecular characteristics similar to native RPE. We generated RNA-seq, ATAC-seq, and H3K27ac ChIP-seq data and observe high similarity in gene expression and enriched transcription factor motif profiles between iPSC-RPE and human fetal-RPE. We performed fine-mapping of AMD risk loci by integrating molecular data from the iPSC-RPE, adult retina, and adult RPE, which identified rs943080 as the probable causal variant at VEGFA. We show that rs943080 is associated with altered chromatin accessibility of a distal ATAC-seq peak, decreased overall gene expression of VEGFA, and allele specific expression of a non-coding transcript. These results provide insight into the mechanism underlying the association of the VEGFA locus with AMD.

genetics↗