Patient Cohort

CML patients were classified into three categories broadly based on recommendations by the European LeukemiaNet (ELN). Group A Patients (n = 9) who either achieved major molecular response (MMR) after imatinib treatment within 12 months and/or deep molecular response (DMR) (MR4.5, MR5.0) were classified as ‘good responders’. Group B Patients (n = 9) who did not meet benchmark molecular (6/9) and/or cytogenetic (3/9) response benchmarks until 18 months of imatinib treatment but responded optimally to 2nd/3rd line TKI were classified as ‘imatinib failures’. Group C Patients (n = 6), who failed TKI therapy and progressed from chronic phase (CP) to the blast crisis (BC) stage of the disease was classified as ‘poor responders’.

Group A: P145, P625, P631, P654, P677, P685, P713, P735, P742

Group B: P157, P160, P464, P170, P189, P312, P387, P489, P687

Group C: BM157, LEU9, P147, P309, P430, P605

Healthy/normal bone marrow (NBM): NBM90369, NBM90222, NBM40316, NBM80350, NBM250267

BM157, P430 and P605 transformed into lymphoid blast crisis, while LEU9, P147 and P309 transformed into myeloid blast crisis.

The toggle “Group” can be used to select the prognostic group. The toggle “Simplified Group” can be used to compare healthy against CML samples.

Experimental design

CD34+ and CD34- cells were purified and subjected to scRNA-seq separately. The scRNA-seq data for the 2 fractions were merged at the time of data analysis. Thus, cell type proportions should be plotted after using the “CD” toggle. The toggle “CD” allows the user to determine whether the cells originated from the CD34+ or the CD34- tube. Please note that we did not get high-quality scRNA-seq data for the CD34+ fraction of P631, and CD34- fractions of P687 and NBM90222, hence these cells are missing from the dataset.

Cell type annotations

The toggle “MajorCellType” refers to the grouping of cells into the four broad groups: B, myeloid, progenitor and the T/NK cells. The toggle “MinorCellType” refers to further annotation into individual cell types. Of these the Stem and Progenitor cell types are hematopoietic stem cell (HSC), immature megakaryocyte progenitor (iMKP), megakaryocyte progenitor (MKP), erythroid progenitor (ERP), eosinophil-basophil mast cell progenitor (EOBM), immature neutrophil progenitor (iNeP), neutrophil progenitor (NeP) and lymphoid progenitor (Lyp). The differentiated cell types are CD4+ T central memory (CD4+ TCM), CD8+ T effector memory expressing CD45RA (CD8+ TEMRA), classical dendritic cells (cDC2), classical monocytes (C Mono), γδ T cells (gd T cells), inflammatory monocytes (I Mono), myeloid-derived suppressor cells- monocyte type (Mo-MDSC), monocye-T (Mono-T), natural killer (NK) cells, plasmacytoid dendritic cell (pDC).

Important note

The information contained within this site is to be used for research purposes only, and not for any patient-related management decisions. We kindly request that authors who use any data acknowledge this website (http://scdbm.ddnetbio.com/) and the original publication (Krishnan et al. A Single-cell Atlas Identifies Pretreatment Features of Primary Imatinib Resistance in Chronic Myeloid Leukemia. Blood 2023).