Transcriptomic Profiling of Small Molecule Atf6 Modulators in the Retina

The Unfolded Protein Response (UPR) maintains endoplasmic reticulum (ER) homeostasis and is essential for retinal health. Activating Transcription Factor 6 (ATF6) controls a key UPR branch and upregulates genes that mitigate ER stress. Small molecule modulators of ATF6 have been characterized in cell culture models that increase or decrease the amount of the cleaved, transcriptional activator domain of ATF6 generated from the full-length precursor. However, the effects of these small molecule ATF6 modulators remains unclear in vivo, in part because of the lack of antibodies that robustly detect the cleaved, activated form of ATF6 in model organisms like mice. Here, we used targeted RNA sequencing (RNA-seq) to assess the transcriptional response to intraocular delivery of Ceapin-A7 (an ATF6 inhibitor) and AA147 (an ATF6 activator) in the mouse retina. Using this strategy, we demonstrate that Ceapin-A7 significantly suppressed ATF6 transcriptional targets, whereas AA147 induced ATF6-regulated genes in retinal tissue of the eye. We also show that neither small molecule ATF6 modulator caused retinal cell death, compromised vision, or triggered ER stress by histology, functional testing, and transcriptional analysis. These results identify a transcriptional strategy to sensitively detect and quantify Ceapin-A7 and AA147 modulation of ATF6 in vivo. These findings also identify non-toxic conditions for further in vivo evaluation of small molecule ATF6 modulators in mouse vision loss disease models linked to ER stress. Overall design: Two small molecule proteostasis modulators were investigated: Ceapin-A7 (ATF6 inhibitor) and AA147 (ATF6 activator), with Tunicamycin as a positive control. At postnatal day 30, C57BL/6J mice were intravitreally injected with each compound (10 µM). For the control treatment, both eyes of each animal were injected with 1 µL of saline containing 0.05–0.1% DMSO. Eyes were collected at 24 hours, 3 days, and 7 days post-injection for safety and efficacy tests. Retinal tissues were analyzed using immunohistochemistry, TUNEL staining, and electroretinography, and Bulk-RNA sequencing.