Transcriptome profiling of mouse retina organoids at defined days in culture

Methods: Mouse retinal organoids (MRO) profiles at day 20, 22, 25, and 30 in culture under control conditions. MROs were generated using the previously established trisection protocol (Völkner et al. 2016, 2019). Single-end sequencing with 30 Mio reads per sample was performed at a length of 75 bases on HiSeq2500 (Illumina). The sequence reads that passed quality filters were analyzed at the transcripts level. Results: Our histologic studies indicate that MROs complete retinogenesis at day 20, and mature including development of a stratified structure with outer and inner plexiform layers and synapses within day 20 to 30. Further, immunostaining and ultrastructural studies showed that photoreceptors neurons mature, including nascent outer segment formation. However, MRO maturation is still incomplete and MRO start to undergo some pathologic changes starting at day 30 and progressing upon longer term culture. Transcriptome analysis support and extend this based on differential changes in temporal gene expression: For example. regulators of retinal development and proliferation cease over time. Further, genes involved in the formation of photoreceptor outer segments, synaptogenesis, and phototransduction machinery increase. Starting at day 30, gene involved in reactive gliosis and retinal neuroprotection are upregulated indicating pathologic changes at the molecular level. Conclusions: Transcriptome analysis of MROs support and extend our findings at the histological level, indicating that MROs reproducibly undergo several stages in culture, i.e. complete retinogenesis, mature on the cellular and molecular level, and develop some pathologic changes. Overall design: Mouse retinal organoids (MRO) profiles at day 20, 22, 25, and 30 in culture under control conditions (n=6 MRO per timepoint from N=1 independent experiment), generated on HiSeq2500 (Illumina).