Abstract 4614: Differential PD-L1 expression by IHC between matched samples obtained from FFPE blocks versus frozen blocks
Authors: Rebeeca Bascom, Paige Nelson, Jacob Harris, David Booker, Ken Dixon, Jared James Barrott
Journal: Cancer Research (2025)

Abstract Introduction: Personalized cancer treatment is crucial for improving patient outcomes, yet the standard preservation methods for clinical tissue samples may not fully support this goal. Currently, most cancer tissue samples are preserved as formalin-fixed and paraffin-embedded (FFPE), which recent studies suggest compromise DNA quality and quantity. In this study, we extended previous research by comparing the protein expression of PD-L1, a significant biomarker associated with cancer cell evasion of immune response, between FFPE and cryopreserved (frozen) tissues from 37 patients with various types of cancer. We hypothesized that cryopreserved samples would exhibit higher and more accurate PD-L1 levels than FFPE samples. Methods: The first step in our research was to confirm the presence of cancer in 37 patient tissue samples through standard hematoxylin and eosin (H&amp;E) staining. Next, we stained both the FFPE and cryopreserved samples using immunohistochemistry (IHC) protocols to visualize PD-L1 expression. The FFPE protocol involved dewaxing, antigen retrieval, incubation with primary and secondary antibodies, and staining. The protocol for the cryopreserved tissues was similar, with slight changes by eliminating the dewaxing and antigen retrieval steps. DAB was used to stain PD-L1 (identified in brown) and hematoxylin was used to stain cell nuclei (identified in blue). Positive controls were included in each stain to ensure reliability and minimize overstaining. Once each sample was stained in both its FFPE and cryopreserved forms, samples were sent to a board certified pathologist for further analysis and comparison. Results: Our research results indicated a trend towards increased PD-L1 expression in cryopreserved samples, supporting our hypothesis that FFPE tissue exhibits a weaker PD-L1 signal compared to cryopreserved tissue. We have seen a significant difference between the FFPE and cryopreserved tissue samples-a result that was corroborated by a board-certified pathologist. Among the FFPE samples, less than 6% were found to be positive for PD-L1. Conversely, the cryopreserved samples exhibited a 64% rate for positive PD-L1 expression. Discussion: This study highlights the impact of tissue preservation methods on the accuracy of cancer diagnostics through an analysis of protein preservation. The personalization of treatment strategies in a clinical setting depends on data such as these, underscoring the need for more accurate analysis. This data, along with previous and future studies, will advocate for a shift towards cryopreservation in clinical settings, leading to better personalized treatment and results for the patient. Citation Format: Rebeeca Bascom, Paige Nelson, Jacob Harris, David Booker, Ken Dixon, Jared James Barrott. Differential PD-L1 expression by IHC between matched samples obtained from FFPE blocks versus frozen blocks [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 4614.