Multilayered control of retinal stem/progenitor cell fate in the single-cell and organoid era: Developmental blueprints and regenerative opportunities

Table 2 Atlas-to-engineering toolkit - multi-omics reference types, inference outputs, and what they enable experimentally

Reference/method class	What it quantifies (output)	“Control objects” you can engineer	Best validation experiment	Key pitfalls you should flag in text
scRNA/snRNA atlases	Cell states; trajectories; GRNs	TF modules; lineage branch points	Perturb TFs; scRNA readout + reference mapping	Marker mimicry; stress-induced pseudo-states
Multiome (RNA + ATAC)	State + chromatin accessibility	Competence windows; enhancer permission space	Time-gated TF pulses aligned to accessibility shifts	Accessibility ≠ activity; batch effects
3D genome/enhancer-promoter maps	Regulatory architecture	Cis-regulatory nodes; enhancer hubs	dCas9 recruitment/CRISPRi to specific enhancers	Context dependence; cell-type specificity required
Spatial multi-omics	Niche-positioned states	Layer-aware targets; microenvironment coupling	Perturb niche cues + spatial readouts	Resolution limits; deconvolution artifacts
CellRank/fate probability	Decision regions; fate bias	“Threshold tuning” at branchpoints	Perturb node then compare fate probabilities	Velocity assumptions; sampling density
CellChat/LR inference	Niche signaling network	Immune/niche gating; permissive vs restrictive cues	Ligand blockade/receptor editing + readouts	LR inference is probabilistic, not causal
Cross-species mapping	Conserved vs divergent programs	Identify why mammalian competence is lost	Match intervention nodes across species	Orthology mismatch; latent space alignment bias
Reference mapping benchmarks	Congruence to fetal tissue	Quantitative maturity score	Iterative differentiation optimization loop	Overfitting to reference; missing rare subtypes

scRNA: Single-cell RNA; snRNA: Single-nucleus RNA; GRNs: Gene regulatory networks; TF: Transcription factor; ATAC: Assay for transposase-accessible chromatin; 3D: Three-dimensional; dCas9: Catalytically dead Cas9; CRISPRi: CRISPR interference; LR: Ligand-receptor.