A multi-omic investigation of molecular pathogenesis, cellular phenotypes, and therapeutic vulnerabilities of Blast Phase Chronic Myelomonocytic Leukaemia

Abstract

Chronic myelomonocytic leukaemia (CMML) is a clonal myeloid malignancy with heterogenous clinical presentation and frequent acute leukaemic transformation (LT) into blast-phase (BP) CMML (BP-CMML). Prognosis of BP-CMML patients is poor and the dynamics of LT are not understood. Investigating disease propagating blasts cells, and the molecular dynamics leading to LT may enable formulation of effective therapeutic and preventive treatments. To this end, we collected multiparametric data for 42 BP-CMML patients, including blood counts, clinical metadata, genotype, immunophenotype and transcriptome. Using unsupervised clustering via RandomForest we identified two homogenous BP-CMML subgroups C1 and C2, reflective of differences in blast count, and maturation state both transcriptionally and immunophenotypically. C1 (Immature) and C2 (Mature), scored differently to mined signatures of drug response/resistance. We validated these drug response/resistance signatures on patient samples ex vivo. To identify novel molecular vulnerabilities and potential preventive therapies, we leveraged the use of single-cell technologies to define the longitudinal changes occurring throughout LT via Single-cell CITEseq and Single-cell DNA + Protein (ADT) sequencing. After validating a custom based computational approach for semi-supervised cell type annotation based solely on ADT data, we were able to solve the clonal architecture of 17 CMML and BP-CMML samples, highlighting variable clonal distribution across cell types. Further, our analysis demonstrated that BP-CMML with immature or mature type blasts, present expansions of HSC/MPP and myelomonocytic cells respectively. Longitudinal analysis in 3 paired sample sets reported both linear and branching evolution, with/without acquisition of new mutations. Parallel transcriptome analysis demonstrated BP-CMML LT is initiated with the expansion of pre-existing blast-like cells at CMML stage. Ex vivo drug testing studies based on commonly up-regulated pathways during transformation revealed dose-dependent additive toxicity to Merestinib (MKNK1 inhibitor) and Triciribine (AKT inhibitor). In summary, this project contributed to the understanding of the biology of BP-CMML at and throughout transformation, and to the identification of effective novel or repurposed drugs.

Date of Award	31 Dec 2023
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Tim Somervaille (Supervisor), Kiran Batta (Supervisor) & Daniel Wiseman (Supervisor)