With the goal of studying the gene expression profile of RPE cells and subretinal MG/MΦ in chCfhTg mice, we used a recently published method
39 to isolate RPE cells. This method allows us to perform simultaneous RPE cell isolation and RNA stabilization (SRIRS), and generates high-quality RNA that has very little contamination from conjunctiva, sclera, choroid, or retina. It does contain, in addition to the RNA from RPE cells, the RNA from the subretinal MG/MΦ that is normally adhered to the RPE layer. A preliminary Illumina microarray (San Diego, CA, USA) analysis on SRIRS-generated RNA isolates (individual eyes from 2-year-old chCfhTg [
n = 3] and B6 [
n = 3] mice) yielded low signals. Still, interestingly, analysis of the results with Ingenuity Pathway Analysis software (Qiagen, Redwood City, CA, USA) revealed that the top three biological functions affected in chCfhTg mice compared to B6 mice were inflammatory response, hypersensitivity response, and immunologic disease (
Supplementary Table S4). Gene expression analysis by qPCR (
Figs. 6A,
6B) was then performed on a larger number of SRIRS-generated RNA samples from 2-year-old mice (no pooling of samples;
n = 15–17 eyes/group, except
NLRP3, which included 10 eyes/group). The data demonstrated that chCfhTg mice had an increased expression of
CD68 (marker of activated MG/MΦ,
56–59 P = 0.02), and
TREM2 (a microglial gene that is increased in activated microglia,
60–63 P = 0.004). We also found a significant increase in
IP-10 (CXCL10, a chemoattractant
64 for monocytes and lymphocytes that has been found to be increased in the aqueous humor, serum, and RPE of AMD patients
65,66 (
P = 0.008); and
NLRP3 (the NLRP3 inflammasome plays a key role in innate immunity
67 by initiating inflammatory signals
68 and priming/activating microglia
69,70; it has been recently proposed to be an important, although still ill-defined, player in AMD pathogenesis,
71–73 P = 0.032). These findings were corroborated on a subset of genes in a separate experiment using 1-year-old chCfhTg versus age-matched B6 mice (six eyes/group;
Fig. 6C). Furthermore, immunohistochemistry of retinal sections demonstrated that subretinal microglia from chCfhTg mice (
Figs. 6H–K), but not B6 mice (
Figs. 6D–G), were positive for IP-10 and NLRP3.