Normfinder analysis identified that
HPRT1 and
POLR2A were the most stable reference gene pair in this dataset, therefore the expressions of target genes were normalized to the geometric mean of
HPRT1 and
POLR2A. The results of ddPCR demonstrated that TZ cells cocultured with P-LMSCs expressed significantly higher levels of pluripotency gene
NANOG (0.0016 ± 0.0003 vs. 0.0007 ± 0.0002,
P = 0.034), neural crest genes
SOX9 (0.2326 ± 0.0048 vs. 0.1863 ± 0.0080,
P = 0.019), and
TFAP2A (0.7271 ± 0.0467 vs. 0.5601 ± 0.0509,
P = 0.048), and periocular mesenchyme gene
PITX2 (1.9485 ± 0.0350 vs. 1.5235 ± 0.1224,
P = 0.019) than the TZ only control (
Fig. 7). Moreover, the expression of neural crest gene
NESTIN in TZ cells cocultured with P-LMSCs was significantly higher than those cocultured with A-LMSCs (1.4644 ± 0.0714 vs. 1.1010 ± 0.0347,
P = 0.022) and showed an increasing trend compared to TZ cells without coculture (1.2286 ± 0.0829,
P = 0.064). The corneal endothelial gene
SLC4A11 in TZ cells was downregulated after coculturing with P-LMSCs (0.0220 ± 0.0003 vs. TZ control 0.0298 ± 0.0009,
P = 0.015). However, the corneal endothelial gene
AQP1 was upregulated after coculturing with A-LMSCs (1.3046 ± 0.0849 vs. TZ control 0.4168 ± 0.0512,
P = 0.004) and P-LMSCs (0.9759 ± 0.1566,
P = 0.015). Other corneal endothelial genes, such as
COL8A1,
TJP1, and
ATP1A1, did not show significant differences among TZ cells with and without coculture. Overall, pluripotency genes exhibited very low expressions compared to neural crest, periocular mesenchyme, and CEC genes.