Abstract 5467: Single-cell analysis of CD34-enriched blood cells reveals early prognostic markers of myelodysplastic syndromes

Abstract

Abstract Myelodysplastic Syndromes (MDS) are a group of blood malignancies characterized by aberrant differentiation of hematopoietic stem and progenitor cells (HSPC) in the bone marrow that results in inefficient hematopoiesis and high risk of transformation to acute myeloid leukemia. In order to detect aberrant HSC differentiation in blood samples sensitively and accurately, we explored the use of scRNA-seq of CD34-enriched cells from peripheral blood in identifying differentiation trajectories that are abnormal in patient samples versus expected normal development. A total of 685,000 CD34-enriched PBMCs from 93 samples were analyzed using 10X 3’ v3 scRNA-seq library preparation. For increased efficiency, the samples were multiplexed in groups of 5 individuals and were later identified based on individual natural genetic variation using a custom genotyping assay or low-pass WGS. We then sequenced these 24 libraries on a UG100 sequencer to yield an average of 20,000 reads per cell. Six of these libraries were also sequenced on a NovaSeq. Comparison between scRNA profiles generated on the two different sequencers yielded highly similar results, including a similar ability to demultiplex the patient samples using genetic markers, accurately quantify gene modules and determine cell populations.To analyze the scRNA data, we used a novel computational framework, Metacell, to reconstruct metacell modules for both healthy and disease samples allowing us to find variability in the differentiation process between the disease samples and the normal baseline state. Two patients with MDS which had transformed to acute myelogenous leukemia (AML) demonstrated unique and distinct metacell clusters that were significantly separate from normal HSPC differentiation patterns, demonstrating distinct clusters with elevated levels of BCL2 which is an existing therapy target in secondary AML. Our results demonstrate that scRNA-seq analysis of peripheral blood HSPCs samples can be used to detect aberrations in HSC development in MDS patients and serve as a prognostic tool for stratification of patients with aggressive disease and drug response. Given the cost-efficiency of the entire process, we believe this is one of the first examples of the potential practical utility of single-cell analysis in a clinical setting. Citation Format: Eti Meiri, Nili Saar-Furer, Nimrod Rappoport, Sarah Pollock, Gila Lithwick-Yanai, Zohar Shipony, Nika Iremadze, Doron Lipson, Amos Tanay, Liran Shlush. Single-cell analysis of CD34-enriched blood cells reveals early prognostic markers of myelodysplastic syndromes. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5467.