Photoreceptor proliferation and dysregulation of cell cycle genes in early onset inherited retinal degenerations

Gardiner, Kristin L.; Downs, Louise; Berta-Antalics, Agnes I.; Santana, Evelyn; Aguirre, Gustavo D.; Genini, Sem

doi:10.1186/s12864-016-2477-9

Table 1 qRT-PCR retinal gene expression results in xlpra2, rcd1, and erd mutants compared to normal retinas

From: Photoreceptor proliferation and dysregulation of cell cycle genes in early onset inherited retinal degenerations

	Ages
Gene	3 wks	5 wks	7 wks	16 wks
Cell cycle: cyclins
CCNA1	n.s	n.s	n.s	+4.4x in rcd1
				+2.2x in xlpra2
				+3.0x in erd (11.9–14.1 w)
CCNA2	n.s	n.s	+2.0x in rcd1	n.s
			+2.2x in xlpra2
			+2.2x in erd (6.4 w)
			+3.2x in erd (8.3–9.9 w)
CCNB1	n.s	n.s	n.s	+3.3x in rcd1
CCNB1	n.s	n.s	n.s	+2.8x in xlpra2
CCND1	n.s	n.s	n.s	+2.4x in rcd1
CCND1	n.s	n.s	n.s	+2.7x in xlpra2
CCND3	n.s	n.s	n.s	+2.8x in rcd1
CCNE1	n.s	+2.4x in rcd1	+2.7x in rcd1	+5.5x in rcd1
			+4.1x in xlpra2	+5.1x in xlpra2
			+2.8x in erd (6.4 w)	+10x in erd (11.9–14.1 w)
			+5.7x in erd (8.3–9.9 w)	+10x in erd (11.9–14.1 w)
Cell cycle: cyclin-dependent kinases
CDK1	n.s	−2.1x in rcd1	−13.3x in rcd1	−2.2x in rcd1
			−10.2x in xlpra2	−3.4x in xlpra2
			−8.4x in erd (6.4 w)	−6.0x in erd (11.9–14.1 w)
			−6.9x in erd (8.3–9.9 w)	−6.0x in erd (11.9–14.1 w)
CDK2	+2.7x in rcd1	n.s	n.s	+3.4x in rcd1
CDK4	+2.2x in rcd1	n.s	n.s	+2.4x in rcd1
CDK6	+3.6x in rcd1	n.s	n.s	+2.9x in rcd1
CDK6	+2.5x in xlpra2	n.s	n.s	+2.1x in xlpra2
Cell division cycle phosphatases
CDC25A	n.s	n.s	n.s	n.s
CDC25B	n.s	n.s	n.s	n.s
CDC25C	n.s	n.s	n.s	+2.1x in rcd1
CDC25C	n.s	n.s	n.s	+2.7x in xlpra2
Cyclin-dependent kinase inhibitors
CDKN1A	n.s	n.s	n.s	n.s
CDKN1B	n.s	n.s	n.s	n.s
CDKN2A	−3.8x in rcd1	n.s	+3.0x in erd (8.3–9.9 w)	n.s
Cell cycle transcription regulators
BMI1	n.s	n.s	n.s	n.s
E2F1	+2.0x in rcd1	n.s	n.s	+6.2x in rcd1
	+2.6x in xlpra2			+6.2x in rcd1
	+2.6x in xlpra2			+3.7x in xlpra2
RB1	+2.1x in rcd1	n.s	n.s	n.s
RB1	+5.5x in xlpra2	n.s	n.s	n.s
Hippo signaling/NDR kinases
LATS1	n.s	n.s	n.s	+2.6x in erd (11.9–14.1 w)
LATS2	n.s	n.s	n.s	n.s
MOB1A	n.s	n.s	n.s	+2.5x in erd (11.9–14.1 w)
NDR1	n.s	n.s	n.s	+2.1x in erd (11.9–14.1 w)
STK38L (NDR2) (exons 4–5)	n.s	n.s	No expression in erd	No expression in erd
STK38L (NDR2) (exons 6–7)	n.s	n.s	n.s	n.s
Eye development regulation via proliferation/apoptosis
PAX6	n.s	n.s	−2.5x in erd (6.4 w)	+2.2x in rcd1
PCNA	n.s	n.s	n.s	n.s
PR function
GRK1	n.s	−2.0x in rcd1	−3.9x in rcd1	−3.3x in rcd1
GRK1	n.s	−2.0x in rcd1	−2.3x in xlpra2	−3.3x in rcd1
RBP3	n.s	n.s	n.s	n.s
RCVRN	n.s	n.s	−2.6x in rcd1	−2.4x in rcd1
				−2.2x in xlpra2
				−2.0x in erd (11.9–14.1 w)
PR development/structure
CRB1	n.s	n.s	n.s	n.s
NRL	n.s	−2.3x in rcd1	−2.0x in rcd1	−3.0x in rcd1
			−3.2x in erd (6.4 w)	−2.0x in xlpra2
			−3.7x in erd (8.3-9.9 w)	−5.8x in erd (11.9–14.1 w)
NR2E3	n.s	−2.0x in rcd1	−2.8x in erd (6.4 w)	n.s
RDS	n.s	−2.5x in rcd1	−2.0x in rcd1	−3.0x in rcd1

Statistically significant (p < 0.05 and FC > +/−2) differences in retinal gene expression are reported in comparison to normals at different ages (rcd1 and xlpra2: 3, 5, 7, 16 wks; erd: 6.4, 8.3–9.9, 11.9–14.1 wks). The examined genes are reported in alphabetical order within functional groups. The complete list of genes tested is available as Additional file 5. n.s = not statistically significant; + = up-regulated and - = down-regulated compared to normal

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