Abstract 81: High-resolution monitoring of B cell isotype switching for biomarker analysis of adenosine pathway inhibition immunotherapy
Authors: Ramadevi Prathapam, Kristen Champion, Anne Burkhardt, Chelsey L. Smith, Rajesh Singh, Timothy J. Looney
Journal: Cancer Research (2024)

Abstract Background B cell isotype switching gives rise to IgG-, IgA-, and IgE-expressing B cells and is an essential step in generating effective humoral responses to antigen challenge. Within the tumor microenvironment, extracellular adenosine may contribute to cancer immune evasion by inhibiting isotype switching through interaction with A2aR, a possibility that has driven investigation of adenosine pathway inhibition as an immunotherapeutic modality. In this context, methods to quantify isotype switching may provide insight into the pharmacodynamics of candidate agent activity and serve as a source of predictive biomarkers of response. We recently clinically validated the Oncomine IGH-LR assay for the measurement of CLL somatic hypermutation (SHM). Given that this assay also detects isotype switching events, we retrospectively analyzed our validation dataset to determine the suitability of the assay as a potential tool for biomarker analysis of adenosine pathway inhibition immunotherapy. Methods The Oncomine IGH-LR assay determines B cell SHM and isotype through targeted next-generation sequencing of IGH chains from RNA. The assay software organizes detected IGH chains into B cell clonal lineages, of which a subset may comprise multi-isotype lineages indicative of isotype switching events. The software further reports secondary repertoire features such as clonality/evenness. Total RNA was extracted from peripheral blood mononuclear cells or bone marrow aspirates from patients identified as having &amp;gt;10% monoclonal B-cell population by flow cytometry. Intra-assay precision was evaluated by processing RNA from 7 samples in triplicate and sequencing in the same run. Inter-assay precision was evaluated by having different operators process 10 samples on different days with different sequencing barcodes. Dominant clone isotype and clonal lineage assignment, total isotype abundance, and repertoire clonality were evaluated across replicates. Results Overall, 100% concordance was achieved for dominant clone isotype and clonal lineage calls for both intra- and inter-assay studies. Intra-assay and inter-assay median coefficient of variation (CV) for reported isotype frequencies ranged from 0.10-0.16 and 0.15-0.28, respectively. Intra-assay and inter-assay median CV for clonality (1 - Normalized Shannon Entropy) was 0.06 and 0.04, respectively. Conclusions We observe high reproducibility and repeatability of the IGH-LR assay for B cell isotyping, clonal lineage analysis, and clonality assessment. Multi-isotype clonal lineages are automatically reported by the software and provide a means to directly monitor isotype switching events in the context of antigen challenge or immunomodulation. Taken together, we anticipate this assay to be a useful tool for biomarker analysis of adenosine pathway inhibition immunotherapy. Citation Format: Ramadevi Prathapam, Kristen Champion, Anne Burkhardt, Chelsey L. Smith, Rajesh Singh, Timothy J. Looney. High-resolution monitoring of B cell isotype switching for biomarker analysis of adenosine pathway inhibition immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 81.