Cell lines as quality controls for Quantitative Continuous Scoring (QCS) of IHC stained samples

Background: Effectively measuring therapeutic target expression is critical in oncology for precise and accurate patient selection. Target expression is often measured by immunohistochemistry (IHC) using visual pathology scoring; however, digital pathology-based Quantitative Continuous Scoring (QCS) has emerged as a more precise and accurate alternative 1 . Given that IHC assays and whole slide image (WSI) scanners have known variability, we designed a proof-of-concept study to evaluate the applicability of using cell lines as quality controls for QCS scoring of IHC stained samples. Methods: A panel of cell lines (N=10) were selected to represent a broad range of target expression and cultured as cell pellets into a Formalin-Fixed Paraffin Embedded (FFPE) Cell Micro Array (CMA) for downstream IHC analysis with QCS. The CMA was sectioned (4 µm) and stained with a target antibody according to standard protocols. The stained slides were scanned at 40x, and images were analyzed using a trained QCS deep-learning based QCS model that quantifies membrane staining intensity (SI). Results: Cell line controls showed highly consistent QCS staining intensity (SI) scores through the entire CMA block (n=40 sections). SI from triplicates run on the same day were compared among each other or across days with a coefficient of variation (CV) <10% for each cell line, demonstrating a high level of precision and reproducibility through the entire cell line pellet. Additionally, cell density was also consistent throughout the FFPE block. Moreover, we observed highly significant correlation (R=0.98) between QCS SI and mass-spectrometry results, thus demonstrating specificity for assessing target expression in cell lines. Finally, early experiments with contrived assay variability showed the ability of cell lines to track the 32% contrived variability observed in tissue and correct that variability to 7%, thus supporting the use of cell lines to potentially improve IHC/QCS precision and reproducibility. Conclusion: These data support the feasibility of using cell lines as qualitative controls for QCS scoring of IHC stained samples. Given that heterogeneity of expression is not a significant factor like it is in tissue, cell lines provide consistent expression throughout the entire block with a high degree of precision and reproducibility. These data thus support the potential for integrating cell line controls into the quality assurance pipeline for QCS-based IHC measurements in the laboratory setting. Further, cell line quality controls could also be used for bridging and comparability, thus enabling efficient and robust development of QCS assays. 1 Kapil et al. “HER2 quantitative continuous scoring for accurate patient selection in HER2 negative trastuzumab deruxtecan treated breast cancer”. Nature Sci Rep. 2024 May 27;14(1):12129.