Rapid identification of comprehensive multi-omic protein and RNA biomarkers on a single FFPE tissue section using a novel integrated nCounter® workflow

Background: Biomarker detection approaches capable of rapid identification and quantification of both transcriptomic and proteomic datasets from the same tissue section have become increasingly valuable for investigating the highly complex biology of tumors. Unfortunately, today, the main challenges of true multi-omic analysis of protein and RNA on e.g. FFPE slides are the degradation and cross-linking of molecules from formalin fixation and storage, leading to variable and low-quality nucleic acids and proteins. This degradation, combined with inherent sample heterogeneity, makes it difficult to extract high yields of molecules and requires sophisticated bioinformatic methods to integrate resulting complex and often noisy multi-omics data. To address this need, we have developed and validated a novel workflow using the nCounter® Analysis System that enables simultaneous quantification of mRNA and protein targets from the same slide. This ‘multiomics made simple' approach is uniquely enabled by Bruker Spatial Biology's streamlined workflow and direct hybridization chemistry, now accessible and validated through NeoGenomics. Methods: The core innovation of this workflow lies in its ability to measure both mRNA and protein signal from a single FFPE slide as part of a simple 3-step protocol. Specifically, the assay leverages the harmonization of traditional nCounter mRNA Panels such as the PanCancer IO 360™ panel that measures up to 800 gene expression targets alongside newly designed and optimized Protein Panels capable of analyzing up to 800 proteins within a unified protocol. To validate performance specifications, NeoGenomics, a leading clinical research organization, evaluated this multi-omics application across diverse FFPE sample types, including breast, lung, colorectal, bladder, and urothelial tumors. Results: Across all tissue types, the streamlined assay demonstrated high specificity, strong correlation between replicate runs, and excellent dynamic range for both mRNA and protein analytes. These results confirm the platform's utility across a wide range of tumor biology contexts and support its adoption for biomarker discovery, target validation, and mechanism-of-action studies. By delivering combined mRNA and protein profiling from a single tissue section, the nCounter platform enables rapid identification of tumor-specific signatures, strengthening biological interpretation and simplifying translational workflow complexity. Conclusions: This newly validated application, now available through NeoGenomics, empowers research teams to unlock the synergistic power of true tissue multiomics through a simple, scalable, and reproducible workflow-making same-slide mRNA+Protein analysis from FFPE tissue a practical reality for pharma and translational research.