Abstract 2072: Spatial genomic ISH predicts prognostic significance of retinal degeneration protein 3 (RD3) transcriptional loss in colon cancer

Abstract Our studies documented remarkable expression of Retinal degeneration protein 3 (RD3) in adult and fetal colon tissues and a significant loss in colon cancers. Further, in other solid cancers we recognized the function of RD3 in the disease pathogenesis. Here, we investigated the prognostic relevance of RD3 transcriptional loss in colorectal cancer, the second most common cause of cancer deaths. Additionally, we explored the real-time translational benefit of the spatial genomic ISH (RNAScope) as a tool for predicting the prognostic relevance and significance of RD3-loss in clinical outcomes. For this, tumor specimens (n=491) representing stage, primary/metastasis, diagnosis (Dx) or progressive disease (PD) from a test cohort of colon cancer patients (n=267) were assessed for RD3 status. Tissues in triplicate were custom archived in tissue microarrays (TMAs), and the spatiotemporal profiling of RD3 mRNA was performed using the chromogenic in situ hybridization (CISH) utilizing RNAScope with a custom designed target probe to human RD3 with PPIB and DapB (positive & negative) controls. Slides were scanned (40X, Zeiss Axio Scan) and group-analyzed for RD3 mRNA-specific positivity. Spatiotemporal distribution and quantitation of RD3 mRNA were performed using Halo image analysis configured to report copies per region of interest and probe copies per cell. RNAScope revealed significant fluctuations in RD3 transcription to cell and tissue-type, disease status (normal adjacent tissue to the tumor tissue), disease progression etc. Assessing the predictive relevance of RD3 transcription, our findings indicated a clear ‘low-is-worse’ association and RD3 profiling could serve as the independent variable (MANOVA) to predict disease aggression. The outcomes critically recognized that RD3 loss in cancers is significantly associated with the development of metastatic disease and could be designated as a prognostic marker for metastatic disease. Crucially, profiling RD3 transcription prior to and after therapy significantly recognized the anew loss of RD3 after the current first-line intensive multimodal clinical therapy. More importantly, a sizable low-is-worse correlation to the tumor recurrence, death, etc., Evidently, high levels of RD3 transcription exclusively displayed a significant association with better overall survival and showed that RD3 loss is an independent predictor of OS. Together, these results recognize transcriptional loss RD3 as an independent predictive biomarker for colon cancer progression and clinical outcomes. Further the results clearly imply that spatiotemporal RD3 RNAScope could serve as a clinical tool to predict disease evolution, that could lead to defined treatment stratification and better clinical outcomes in deadly colon cancer. Citation Format: Natarajan Aravindan, Poorvi Subramanaian, Sreenidhi Mohanvelu, Sheeja Aravindan. Spatial genomic ISH predicts prognostic significance of retinal degeneration protein 3 (RD3) transcriptional loss in colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2072.