Chronic myelomonocytic leukaemia stem cell transcriptomes anticipate disease morphology and outcome

Abstract

Background Chronic myelomonocytic leukaemia (CMML) is a clinically heterogeneous stem cell malignancy with overlapping features of myelodysplasia and myeloproliferation. Over 90% of patients carry mutations in epigenetic and/or splicing genes, typically detectable in the Lin − CD34 + CD38 − immunophenotypic stem cell compartment in which the leukaemia-initiating cells reside. Transcriptional dysregulation at the stem cell level is likely fundamental to disease onset and progression. Methods We performed single-cell RNA sequencing on 6826 Lin − CD34 + CD38 − stem cells from CMML patients and healthy controls using the droplet-based, ultra-high-throughput 10x platform. Findings We found substantial inter- and intra-patient heterogeneity, with CMML stem cells displaying distinctive transcriptional programs. Compared with normal controls, CMML stem cells exhibited transcriptomes characterized by increased expression of myeloid-lineage and cell cycle genes, and lower expression of genes selectively expressed by normal haematopoietic stem cells. Neutrophil-primed progenitor genes and a MYC transcription factor regulome were prominent in stem cells from CMML-1 patients, whereas CMML-2 stem cells exhibited strong expression of interferon-regulatory factor regulomes, including those associated with IRF1, IRF7 and IRF8. CMML-1 and CMML-2 stem cells (stages distinguished by proportion of downstream blasts and promonocytes) differed substantially in both transcriptome and pseudotime, indicating fundamentally different biology underpinning these disease states. Gene expression and pathway analyses highlighted potentially tractable therapeutic vulnerabilities for downstream investigation. Importantly, CMML patients harboured variably-sized subpopulations of transcriptionally normal stem cells, indicating a potential reservoir to restore functional haematopoiesis. Interpretation Our findings provide novel insights into the CMML stem cell compartment, revealing an unexpected degree of heterogeneity and demonstrating that CMML stem cell transcriptomes anticipate disease morphology, and therefore outcome. Funding Project funding was supported by Oglesby Charitable Trust, Cancer Research UK, Blood Cancer UK, and UK Medical Research Council.

Inflammatory Regulation by TNF-α-Activated Adipose-Derived Stem Cells in the Human Bladder Cancer Microenvironment

“…This effect was more obvious after 96 h of TNF-α treatment than 24 h. The findings also indicated that some transcription factors, including CEBPB, NFKB1, JUN, RELA, and EGR1, mediated the TNF-α-induced differentiation of ADSCs into mononuclear leukocytes. These included regulons centered on NFKB1, IRF8, RELA, RELB, IRF7, and other transcription factors that are strongly associated with monocytic lineage differentiation and whose interaction may be relevant to myeloid cell survival and development [ 29 , 30 ]. Thus, these results suggest that TNF-α treatment would enhance the potential of ADSCs to differentiate into immune cells.…”

Single-cell technologies and analyses in hematopoiesis and hematological malignancies

“…This technique also revealed considerable interpatient heterogeneity in myelofibrosis with respect to their different patterns of clonal evolution [55]. Regarding chronic myelomonocytic leukemia (CMML), transcriptome profiling of single cells identified CMML stem cells that transcriptionally resembled normal HSCs and differentiated between CMML-1 and CMML-2 stem cells, which can be distinguished clinically only by the percentages of their blasts and promonocytes [113]. Likewise, samples from patients with MDS del(5q) were assessed by scDNA-seq before and after lenalidomide treatment to infer their clonal architecture and found to have a high degree of intratumoral heterogeneity [114].…”

Tracking chronic myelomonocytic leukaemia diversity at the single cell level

“…The fraction of bone marrow blast cells distinguishes CMML-0, CMML-1 and CMML-2, the latter category being defined by a fraction of blast cells between 10% and 20% of bone marrow cells and the worst outcome. Comparing single cell gene expression in CMML-0/1 and CMML-2, Wiseman et al [4] identify striking segregation of CMML-2 CD34 + CD38 À cells, which is nicely illustrated by pseudotime ordering analysis. Interestingly, such a transcriptome-based dichotomy was not observed between dysplastic and proliferative CMML, the other distinctive categories identified by the WHO.…”

“…In this issue of EBioMedicine, Wiseman et al [4] analyze gene expression at the single cell level to track CMML diversity within and between individual patients. They focus on sorted bone marrow Lin À CD34 + CD38 À cells, a cell population enriched in disease initiating cells.…”

“…Behind these common features, Wiseman et al [4] observe that CMML samples demonstrate a striking inter-individual heterogeneity, each of the studied samples clustering separately on two-dimensional visualization of highly variable genes by the non-linear technique named t-Distributed Stochastic Neighbor Embedding (t-SNE algorithm). This diversity was confirmed by unsupervised iterative clustering of differentially expressed genes, which generated 17 clusters.…”