frozen human bone marrow mononuclear cells stem cell  (STEMCELL Technologies Inc)

Journal: Cancer cell

Article Title: Extensive Remodeling of the Immune Microenvironment in B-cell Acute Lymphoblastic Leukemia

doi: 10.1016/j.ccell.2020.04.015

Figure Lengend Snippet: A, Representative flow cytometry of primary healthy and CD19+CD10+ B-ALL diagnosis bone marrow. B, UMAP visualization of 53,447 individual cells from eleven individual primary thawed mononuclear bone marrow samples taken from healthy donors (n = 4), as well as ETV6/RUNX1 (ETV, n = 5) and Ph+ (PH, n = 2) B-ALL patients. C, Marker-based cell type identification analysis allowed prediction of six broad immune cell types across all profiled single cells. D, Gene expression heatmap of top-10 cell type-specific marker genes as measured by Wilcoxon rank-sum test. E, Expression levels of lineage-specific genes overlaid on the UMAP representation. F, Heatmap showing pair-wise distribution density ratio of the UMAP projections of diagnosis and healthy bone marrow cells. G, Boxplot showing fraction of HSPC, Myeloid and T/NK cells in the non-B cell, non-erythrocytic fraction of individual patients. Wilcoxon rank-sum test performed to measure differences in representation between healthy (H) and diagnosis (D) groups, with p value indicated on plots. Horizontal lines in the boxplots represent the median, the lower and upper hinges correspond to the first and third quartiles, and the whiskers extend from the hinge up to 1.5 times the interquartile range from the hinge. H, Significantly-enriched MSigDB Hallmark gene sets in healthy versus diagnosis cells within each of the immune cell types. Normalized enrichment score (NES) denoted by shade of color highlighted in legend.

Article Snippet: Frozen primary human whole bone marrow mononuclear cells were obtained from Lonza (Catalogue #125C), Weill Cornell (courtesy of Giorgio Inghirami.

Techniques: Flow Cytometry, Marker, Expressing

Journal: Cancer cell

Article Title: Extensive Remodeling of the Immune Microenvironment in B-cell Acute Lymphoblastic Leukemia

doi: 10.1016/j.ccell.2020.04.015

Figure Lengend Snippet: A, UMAP visualization of 10,480 individual Myeloid cells of four primary B-ALL patients with mononuclear bone marrow samples taken at diagnosis, remission and relapse B-ALL samples. B, Five transcriptionally distinct Myeloid cell clusters overlaid on the UMAP representation. C, Expression levels of CD14/CD14 and FCGR3A/CD16 across Myeloid cells overlaid on the UMAP representation, and based on mRNA and CITE-Seq antibody measurements. D, Heatmap showing select CITE-Seq antibodies and their corresponding mRNA allowing cell type subpopulation identification, scaled independently. E, Representative immunofluorescence microscopy analysis of primary bone marrow sections from independent B-ALL patients at disease diagnosis and relapse, with scale bars and fluorescent markers indicated for all sections. F, Representative flow cytometry of CD45CD19CD3CD56’ CX3CR1+ gate comparing CD 14 and CD 16 expression of primary healthy and B-ALL diagnosis bone marrow. G, Quantification of fraction of classical (CD14+CD16dim), intermediate (CD14+ CD16+) and non-classical monocytes (CD14dimCD16+) within the CD45+CD19−CD3−CD56− gate of bone marrow (top) and peripheral blood (bottom) of healthy donors and individual B-ALL patients at diagnosis or relapse. Diagnosis and relapse samples are not matched, and relapse samples were not analyzed for peripheral blood. Gating strategy adapted from (Cassetta et al., 2019). Statistical analysis performed using unpaired t-test. Error bars represent mean ± SEM, *P< 0.05, ***P< 0.001.

Article Snippet: Frozen primary human whole bone marrow mononuclear cells were obtained from Lonza (Catalogue #125C), Weill Cornell (courtesy of Giorgio Inghirami.

Techniques: Expressing, Immunofluorescence, Microscopy, Flow Cytometry

Journal: Cancer cell

Article Title: Extensive Remodeling of the Immune Microenvironment in B-cell Acute Lymphoblastic Leukemia

doi: 10.1016/j.ccell.2020.04.015

Figure Lengend Snippet: A, UMAP visualization of 7,122 individual Myeloid cells from eleven individual primary thawed mononuclear bone marrow samples taken from healthy donors and B-ALL patients. B, Six transcriptionally distinct Myeloid cell clusters overlaid on the UMAP representation. Cluster abbreviations, for example, HD-M1 is based on Healthy/Diagnosis Myeloid cluster L C, Relative expression of top Myeloid cluster-specific marker genes. D, Expression levels of CD14, FCGR3A and CSF1R in the Myeloid cells overlaid on the UMAP representation. E, Heatmap showing pair-wise distribution density ratio of the UMAP projections of diagnosis and healthy Myeloid cells. F, Boxplot showing fraction of Myeloid clusters in the Myeloid fraction of individual patients. Wilcoxon rank-sum test performed to measure differences in representation between healthy (H) and diagnosis (D) groups, with p value indicated on plots. Horizontal lines in the boxplots represent the median, the lower and upper hinges correspond to the first and third quartiles, and the whiskers extend from the hinge up to 1.5 times the interquartile range from the hinge. G, Diffusion map of Myeloid cells, highlighting putative cluster cell type identity. H, GSVA gene set enrichment scores of myeloid cluster expression profiles based on established human blood monocyte and dendritic cell gene signatures (Villani et al., 2017). I. Heatmap of select differentially-expressed genes (based on KEGG pathways for leukocyte migration, chemotaxis, cytokines, antigen processing) distinguishing diagnosis and healthy non-classical monocytes (HD-M5).

Article Snippet: Frozen primary human whole bone marrow mononuclear cells were obtained from Lonza (Catalogue #125C), Weill Cornell (courtesy of Giorgio Inghirami.

Techniques: Expressing, Marker, Diffusion-based Assay, Migration, Chemotaxis Assay