Optimization of a single cell multi-omic analysis platform for circulating and therapeutic immune cells

The National Institutes of Health National Cancer Institute awarded The Medical University of South Carolina $211,778 on September 1, 2026, under the Cancer Detection and Diagnosis Research program (CFDA 93.394) to optimize a single-cell multi-omics analysis platform for circulating and therapeutic immune cells.

The funded work develops and standardizes analyte profiles detectable in CD4, CD8, CD14, CD19, CD16, and CD56 immune cells isolated from cancer-associated peripheral blood mononuclear cells, including proteomic and glycoproteomic data. The platform captures single cells using cell-type-specific antibodies or lectins on a glass slide and analyzes them by MALDI mass spectrometry at a rate of approximately six cells per second, generating data for over 5,000 cells in 15 minutes. Robust workflows detect lipids sequentially followed by N-glycans, glycogen, and peptides. The project also applies the platform to CAR-T cell preparations from ongoing cancer clinical trials, combining antibody arrays, single-cell isolation, and imaging mass spectrometry to characterize immune cell populations in patient samples. Associated software, SOLOCell, was created to support the analytical workflow.

Work is performed in Charleston, South Carolina. The project period runs from September 1, 2026, through August 31, 2029.

Abstract

A single cell multi-omics platform has been created that allows thousands of single cells to be captured, localized, visualized and serially analyzed by maldi mass spectrometry.to detect multiple analytes. A software package, solocell, was created specifically for this workflow. At an analysis rate of 6 cells per second, data for over 5000 cells in 15 minutes is obtained, which is then repeated for the next analyte. The platform is particularly useful for characterization of immune cells, which are captured singly using either cell type specific antibodies to CD8, CD4, CD19 and CD14 markers, or lectins, bound to a glass slide. Peripheral blood mononuclear cells (PBMC) from cancer patients and cancer therapeutic car-T cells will be evaluated. Robust workflows were developed to detect lipids first, followed sequentially by N-glycans, glycogen and peptides. The approach is in essence a form of solid-state flow cytometry that can be used to phenotype each individual cell by immunostaining for cell surface receptors. This allows cellular phenotypes to be aligned with single cell analyte data from essentially any ionizable analyte. The goals of this proposal are three-fold: 1. Define and standardize the analyte profiles detectable in CD4, CD8, CD14, CD19, CD16 and CD56 immune cells from cancer associated pbmcs, including proteomic and glycoproteomic data. 2. Apply the platform to a cohort of car- T cell preparations used in ongoing cancer clinical trials; this innovative technology combines the power of antibody arrays, single-cell isolation, and imaging mass spectrometry to provide researchers with an unprecedented tool for unraveling the complexities of immune cell populations in car-T trial patient samples.