Defining an Optimized Workflow for Enriching and Analyzing Residual Tumor Populations Using Intracellular Markers

Abstract

Tumor relapse is well-recognized to arise from treatment-resistant residual populations. Strategies enriching such populations for in-depth downstream analyses focus on tumor-specific surface markers; however, enrichment using intracellular biomarkers remains challenging. Using B-cell lymphoma as an exemplar, we demonstrate feasibility to enrich BCL2high populations, a surrogate marker for t(14;18)+ lymphomas, for use in downstream applications. Different fixation protocols were assessed for impact on antibody expression and RNA integrity; glyoxal fixation demonstrated superior results regarding minimal effects on surface and intracellular expression, and RNA quality, compared to alternative fixatives evaluated. Furthermore, t(14;18)+ B-cells were effectively detected using intracellular BCL2 over-expression to facilitate tumor cell enrichment. Tumor cell populations were enriched using the cellenONE F1.4 single cell sorting platform, which detected and dispensed BCL2high-expressing cells directly into library preparation reagents for transcriptome analyses. Sorted glyoxal-fixed cells generated good quality sequencing libraries, with high concordance between live and fixed single cell transcriptomic profiles, discriminating cell populations predominantly on B-cell biology. Overall, we successfully develop a proof-of-concept workflow employing a robust cell preparation protocol for intracellular markers combined with cell enrichment using the cellenONE platform, providing an alternative to droplet-based technologies when cellular input is low or requires prior enrichment to detect rare populations. This workflow has wider prognostic and therapeutic potential to study residual cells in a pan-cancer setting.