We found that active
Caspase 3 was abundantly expressed in the RGC layer in
hND6 bilateral injected mice 15 months after injection (
Figs. 4H, 4I). These mice had 61% cells in the RGC layer positive for active CASPASE 3 staining (
Fig. 4L), while the control mice only had 16% positive cells (
P = 3.74E-5,
Figs. 4L–4N). Ultrastructural analysis showed cells in the RGC layer of
hND6T14484C-injected mice had condensation of the cytoplasm and nuclear chromatin consistent with apoptosis (
Fig. 4M). Whole transcriptome sequencing (also known as RNA-seq) was performed using total RNA extracted from mouse optic nerve, the RGC's axons, at 1 month after the injection of
hND6T14484C (
n = 3) or
mCherry (
n = 3). The sequencing showed an increase in the expression of 277 transcripts and a decrease in the expression of 104 transcripts in
hND6-injected mice in comparison to
mCherry-injected mice (
Supplementary Fig. S1). Closer inspection of the RNA-seq data shows several increased transcripts are related to the regulation of oxidative stress and apoptosis. These transcripts include
SOD1 (superoxide dismutase 1),
PRDX1 (peroxiredoxin 1),
TMBIM6 (
BAX inhibitor 1),
PINK1 (
PTEN-induced kinase 1),
ROMO1 (reactive oxygen species modulator 1), and so on. Their expression increased by 28% to 73% in
hND6-injected mice compared to
mCherry-injected mice, suggesting this increase might be due to the elevated reactive oxygen species (ROS) level in the cell (
Supplementary Table S2,
Supplementary Table S3). Meanwhile, using EnrichR with the list of genes upregulated in
hND6 compared to
mCherry, an overrepresentation of genes was found in the pathway “cellular response to oxidative stress” (GO:0034599, adjusted
P = 0.0011) and in the Gene Ontology pathway “positive regulation of intrinsic apoptotic signaling pathway” (GO: 2001244, adjusted
P = 0.00128).
37,38 This same finding was confirmed using gene set enrichment analysis, an enrichment analysis method that uses ranking of genes rather than proportions tests (adjusted
P = 0.018 and 0.023,
Figs. 4N, 4O).
39,40 Taken together, these findings indicate that apoptosis rates were increased in the RGCs and optic nerve of
hND6T14484C-injected mice in comparison to control mice.