Abstract 5646: Spatial transcriptomic profiling of the human and mouse retina prepared with CryoJane Tape Transfer System using GeoMx and CosMx spatial analysis

Abstract The goal of this study is to identify key transcriptomic markers within layers of the retina by individually profiling layers using cellular and subcellular spatial transcriptomics, additionally, comparing the results between each level. Both human and mouse retina samples, prepared fresh frozen and fixed frozen, are analyzed using the GeoMx® Digital Spatial Profiler (DSP) and CosMx® Spatial Molecular Imager (SMI) using the whole mouse transcriptome atlas and 1000-plex mouse neuro panel, respectively. Samples are fixed using Cryo-Jane Taper Transfer system. Samples are mounted on to adhesive coated slides as well as adhesive tape to mount samples to glass slides. This method is used to secure fragile frozen tissue, such as the retina. Human and mouse samples were stained using immunofluorescent microscopy targeting neurofilament H (NF-H), glial fibrillary acidic protein (GFAP) and NeuN on DSP and 18s rRNA, amyloid-beta and GFAP on SMI. Staining allows for identification of structural layers in the retina. Simultaneously, regions of interest (ROI) for spatial profiling are selected based on immunofluorescent stains. On DSP, each sample had 3x ROIs in the photoreceptor layer, inner nuclear layer and ganglion cell layer, then, oligonucleotides were collected and sequenced. Finally, raw counts were Q3 normalized for analysis. For SMI data analysis, 6 field of views (FOVs) were put on each section to cover most regions with multiple layers. ~8000 genes were detected on human retina samples using DSP. Around 500 unique genes were detected between the photoreceptor and inner nuclear layer using DSP. Preliminary SMI results show we were able to identify cell types (amacrine, horizontal cell, biopolar cell, ganglion cell, etc) and cell specific markers for outer nuclear layer, inner nuclear layer and ganglion cell layer. Data between DSP and SMI showed high concordance with one another, identifying many genes in each layer. Citation Format: Charles Glaser, Su Ma, Wei Yang, Yan Liang, Joeseph Beechem, Vera L. Bonilha, Sujata Rao, William Horrigan, Bela Anand-Apte. Spatial transcriptomic profiling of the human and mouse retina prepared with CryoJane Tape Transfer System using GeoMx and CosMx spatial analysis. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5646.