Single-cell molecular analysis defines therapy response and immunophenotype of stem cell subpopulations in CML

Warfvinge, Rebecca; Geironson, Linda; Sommarin, Mikael; Lang, Stefan; Karlsson, Caroline; Roschupkina, Teona; Stenke, Leif; Stentoft, Jesper; Olsson‐Strömberg, Ulla; Hjorth‐Hansen, Henrik; Mustjoki, Satu; Soneji, Shamit; Richter, Johan; Karlsson, Göran

doi:10.1182/blood-2016-07-728873

Cited by 118 publications

(131 citation statements)

References 49 publications

(50 reference statements)

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“…We also recognized aberrant miR-21/TGF-b signalling activity in one of the JAK2-mutated patients whose disease subsequently transformed. This illustrates that single-cell analysis could eventually provide a golden opportunity in prognosticating the clinical course or predicting disease evolution, which echoes previous reports that demonstrated promising results in using scRNA-Seq to forecast therapy response in CML patients (Giustacchini et al, 2017;Warfvinge et al, 2017).…”

Section: Discussionsupporting

confidence: 80%

Molecular heterogeneity unravelled by single‐cell transcriptomics in patients with essential thrombocythaemia

et al. 2019

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Summary Significant phenotypic heterogeneity exists in patients with all subtypes of myeloproliferative neoplasms (MPN), including essential thrombocythaemia (ET). Single‐cell RNA sequencing (scRNA‐Seq) holds the promise of unravelling the biology of MPN at an unprecedented level of resolution. Herein we employed this approach to dissect the transcriptomes in the CD34+ cells from the peripheral blood of seven previously untreated ET patients and one healthy adult. The mutational profiles in these patients were as follows: JAK2 V617F in two, CALR in three (one type I and two type II) and triple‐negative (TN) in two. Our results reveal substantial heterogeneity within this enrolled cohort of patients. Activation of JAK/STAT signalling was recognized in discrepant progenitor lineages among different samples. Significantly disparate molecular profiling was identified in the comparison between ET patients and the control, between patients with different driver mutations (JAK2 V617F and CALR exon 9 indel), and even between patients harbouring the same driver. Intra‐individual clonal diversity was also found in the CD34+ progenitor population of a patient, possibly indicating the presence of multiple clones in this case. Estimation of subpopulation size based on cellular immunophenotyping suggested differentiation bias in all analysed samples. Furthermore, combining the transcriptomic information with data from targeted sequencing enabled us to unravel key somatic mutations that are molecularly relevant. To conclude, we demonstrated that scRNA‐Seq extended our knowledge of clonal diversity and inter‐individual heterogeneity in patients with ET. The obtained information could potentially leapfrog our efforts in the elucidation of the pathogenesis of the disease.

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Section: Discussionsupporting

confidence: 80%

Molecular heterogeneity unravelled by single‐cell transcriptomics in patients with essential thrombocythaemia

et al. 2019

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“…Early work on single cell sequencing initially focused on AML, using flow cytometry to separate single cells, and then performing targeted genotyping of a restricted panel of genes on each cell. 30 This was exhausting to both personnel and budgets. Recently, methods have been pioneered to perform automated sequencing by combining each cell with a synthetic pellet of barcoded primers.…”

Section: New Approaches To Detect Clonal Heterogeneitymentioning

confidence: 99%

Emerging translational science discoveries, clonal approaches, and treatment trends in chronic myeloproliferative neoplasms

Mughal

Pemmaraju

Radich

et al. 2019

Hematological Oncology

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The 60th American Society of Hematology (ASH) held in San Diego in December 2018 was followed by the 13th Post‐ASH chronic myeloproliferative neoplasms (MPNs) workshop on December 4 and 5, 2018. This closed annual workshop, first introduced in 2006 by Goldman and Mughal, was organized in collaboration with Alpine Oncology Foundation and allowed experts in preclinical and clinical research in the chronic MPNs to discuss the current scenario, including relevant presentations at ASH, and address pivotal open questions that impact translational research and clinical management. This review is based on the presentations and deliberations at this workshop, and rather than provide a resume of the proceedings, we have selected some of the important translational science and treatment issues that require clarity. We discuss the experimental and observational evidence to support the intimate interaction between aging, inflammation, and clonal evolution of MPNs, the clinical impact of the unfolding mutational landscape on the emerging targets and treatment of MPNs, new methods to detect clonal heterogeneity, the challenges in managing childhood and adolescent MPN, and reflect on the treatment of systemic mastocytosis (SM) following the licensing of midostaurin.

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“…Rather, additional molecular lesions and hits are required for full transformation of clonal pre-leukemic (stem) cells into fully malignant leukemic (stem) cells. Correspondingly, singlecell gene expression analysis revealed great heterogeneity within LSC populations 10,12 . Their normal counterparts, HSC, also constitute a heterogeneous population, and individual HSC exhibit certain properties related to their stem cell nature: self-renewal, quiescence, repopulation capacity, and differentiation potential 13,14 .…”

Section: Introductionmentioning

confidence: 99%

“…One report has shown the involvement of microRNAs in TKI sensitivity in CML LSC 21 . Recent advances in the characterization of aberrant expression of surface markers have allowed the prospective isolation of LSC and HSC from CML patients 12,22 . In this work, we aimed to characterize the miRNome of LSC and HSC isolated by fluorescence-activated cell sorting (FACS) from CML patients at diagnosis by small RNA-Next-Generation Sequencing (NGS), in order to identify differential molecular mechanisms that contribute to unravel LSC biology, and the possible therapeutic implications of such differences.…”

Section: Introductionmentioning

confidence: 99%

miRNome profiling of clonal stem cells in Ph⁺CML

Ruiz

Sánchez

Bonecker

et al. 2020

Preprint

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Chronic myeloid leukemia (CML) is a myeloid stem cell neoplasm characterized by an expansion of myeloid progenitor cells and the presence of BCR-ABL1 oncoprotein. Since the introduction of specific BCR-ABL1 tyrosine kinase inhibitors (TKI), overall survival has improved significantly. However, under long-term therapy patients may have residual disease that originates from TKI-resistant leukemic stem cells (LSC). In this work, we analyzed the miRNome of CML LSC, normal hematopoietic stem cells (HSC) obtained from the same CML patients, and stem and progenitor cells obtained from healthy donors (HD) by next-generation sequencing. We detected a global decrease of microRNA levels in LSC and HSC from CML patients, and decreased levels of microRNAs and snoRNAs from a genomic cluster in chromosome 14, suggesting a mechanism of silencing of multiple non-coding RNAs. Surprisingly, HSC from CML patients, despite the absence of BCR-ABL1 expression, showed an altered miRNome. In silico analysis revealed an association between validated microRNAs and multiple metabolic pathways, suggesting that these molecules may be mediators of the previously reported dysregulation of LSC metabolism. This is the first report of the LSC miRNome that distinguishes between BCR-ABL1 + LSC and their BCR-ABL1counterparts, providing valuable data for future studies.

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Single-cell molecular analysis defines therapy response and immunophenotype of stem cell subpopulations in CML

Abstract: Key Points Single-cell gene expression analysis reveals CML stem cell heterogeneity and changes imposed by TKI therapy. A subpopulation with primitive, quiescent signature and increased survival to therapy can be high-purity captured as CD45RA−cKIT−CD26+.

Cited by 118 publications

References 49 publications

Molecular heterogeneity unravelled by single‐cell transcriptomics in patients with essential thrombocythaemia

Molecular heterogeneity unravelled by single‐cell transcriptomics in patients with essential thrombocythaemia

Emerging translational science discoveries, clonal approaches, and treatment trends in chronic myeloproliferative neoplasms

miRNome profiling of clonal stem cells in Ph⁺CML

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Single-cell molecular analysis defines therapy response and immunophenotype of stem cell subpopulations in CML

Abstract: Key Points Single-cell gene expression analysis reveals CML stem cell heterogeneity and changes imposed by TKI therapy. A subpopulation with primitive, quiescent signature and increased survival to therapy can be high-purity captured as CD45RA−cKIT−CD26+.

Cited by 118 publications

References 49 publications

Molecular heterogeneity unravelled by single‐cell transcriptomics in patients with essential thrombocythaemia

Molecular heterogeneity unravelled by single‐cell transcriptomics in patients with essential thrombocythaemia

Emerging translational science discoveries, clonal approaches, and treatment trends in chronic myeloproliferative neoplasms

miRNome profiling of clonal stem cells in Ph+CML

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miRNome profiling of clonal stem cells in Ph⁺CML