Abstract 7661: Integrated multiomics profiling of lysates using nCounter® protein and RNA panels for comprehensive oncology insights.

Abstract Multiomic approaches combining transcriptomic and proteomic data are critical for understanding complex biological systems in oncology. The nCounter® platform enables simultaneous quantification of RNA and protein targets from the same sample, reducing variability and maximizing biological insight. This innovation builds upon the demonstrated clinical utility of classic nCounter mRNA assays in translational and clinical research, including Prosigna®(FDA-cleared), Lymph2Cx, and Merck’s Tumor Inflammation Signature (TIS). Lysates were prepared from eight different cancer cell lines (HT-29, Daudi, PC-3, U-937, LNCaP, HeLa, PANC-1, MCF-7) following optimized protocols for nCounter multiomics. Protein targets were profiled using the new nCounter Tumor Signaling Panel plus Immune Pathways (500+ Abcam RabMab monoclonal antibodies) and combined with IO360 gene expression panel for integrated analysis. Using 5,000 - 20,000 lysed cells, we find high reproducibility between replicate lysate, with low coefficient of variation (CV) for RNA and protein across replicates. Sensitivity of detection was maintained down to 50 ng of RNA and 200 ng protein per lysate. As expected median Pearson correlation between RNA and protein expression for overlapping markers was R 0.5, highlighting the high multiomics assay information content. In addition, integrated analysis of transcript and protein levels uncovered concordant activated pathways, including key post-translational modifications (PTMs). This study demonstrates the feasibility and utility of lysate-based multiomics using nCounter panels for oncology research. The approach provides a streamlined workflow for comprehensive molecular profiling, supporting translational studies and biomarker discovery. Citation Format: Brian Filanoski, Lori Hamanishi, Giang Ong, Terence C. Theisen, Erin Piazza, Christina Bailey, Prajan Divakar, Margaret L. Hoang, Joseph M. Beechem, . Integrated multiomics profiling of lysates using nCounter® protein and RNA panels for comprehensive oncology insights abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7661.