Fig. 7: HT-HRO model transcriptomics indicates distinct pathologic processes and candidate regulators. | Nature Communications

Fig. 7: HT-HRO model transcriptomics indicates distinct pathologic processes and candidate regulators.

From: HBEGF-TNF induce a complex outer retinal pathology with photoreceptor cell extrusion in human organoids

Fig. 7

a Experimental design: RNA-seq was performed on individual HROs after daily treatment with HBEGF-TNF (HT) for 10 days or with no treatment (CTRL), and at three different organoid ages. b Principal component (PC) analysis of the rlog-transformed count data. c Volcano plot shows statistical significance (−log10 of the adjusted P values) in the magnitude of change (log2FC values) of the differentially- (DEG; red and blue) and non-differentially (black) expressed genes between HT and CTRL (D210, FDR 0.01). d Graphs depicting the 1st PC of the log2-fold change in CTRL and HT-HROs (D210) for custom-made genes-of-interest (GOI) lists based on published data (Supplementary Data 4), representing retinal cell types (photoreceptors and Müller glia (MG)), cell-extrusion regulators, and gliosis (marker for pan-gliosis, A1 and A2 states). e Heatmaps depict Z-scores of rlog-transformed counts of genes expressed at D210 selected from the specified GOIs that are differentially expressed in HT versus CTRL HROs. f Ensemble of Gene Set Enrichment Analysis (EGSEA): selected examples of significantly enriched terms (e.g., biological functions or signaling pathways) in the HT-HRO model (Supplementary Data 5a) overlap with gene sets previously reported in relation to AMD (references indicated). The Z-score (red, up; blue, down) states how many standard deviations a given score deviates from the population’s mean. Data have been deposited on Gene Expression Omnibus.

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