Journal: Cell & Bioscience

Article Title: Transcriptionally imprinted glycomic signatures of acute myeloid leukemia

doi: 10.1186/s13578-023-00981-0

Figure Lengend Snippet: Overview of the conducted study. AML glycosylation was explored on the level of glycomics (GPST datasets) and transcriptomics (GSE and DepMap datasets). Based on the depicted datasets originating from cell lines and primary cells we sought to explore cellular glycosylation, involved GSTs, and responsible TFs

Article Snippet: AML cell line transcriptomics data was obtained from the depmap portal (Expression 22Q2 Public; Broad Institute, Cambridge, MA, USA) [ ].

Techniques: Glycoproteomics

Journal: Cell & Bioscience

Article Title: Transcriptionally imprinted glycomic signatures of acute myeloid leukemia

doi: 10.1186/s13578-023-00981-0

Figure Lengend Snippet: Glycomic overview of various AML cell lines. a PCA of glycosylation features derived from glycomics data of 19 AML cell lines. Individual cell lines are annotated and colored by their FAB classifications as assigned earlier . b The associated score plot depicts considered glycan features, which are linked to their respective glycan class ( N -, O -, and GSL) by color (purple, orange, and green) and symbol (triangle, square, and circle). In addition, arrows indicate features that are linked to a specific type of fucosylation. c Radar plots are showing the differences in glycosylation features between AML classes M5 and M6. Again, these features are subdivided into their respective classes based on color and symbols. Data on all AML cell lines were z-transformed prior to visualizing differences between FAB classes in these radar plots. d Spearman correlation of selected glycosylation features between the different glycan classes. Thick connective lines indicate a good correlation whereas thin connective lines show less correlation. Correlation values are depicted

Article Snippet: AML cell line transcriptomics data was obtained from the depmap portal (Expression 22Q2 Public; Broad Institute, Cambridge, MA, USA) [ ].

Techniques: Glycoproteomics, Derivative Assay, Transformation Assay

Journal: Cell & Bioscience

Article Title: Transcriptionally imprinted glycomic signatures of acute myeloid leukemia

doi: 10.1186/s13578-023-00981-0

Figure Lengend Snippet: Correlation of glycosylation features of N -, O -, and GSL-glycans with the expression of selected TFs in AML cell lines. Correlation coefficients were obtained by Spearman analysis and are indicated by color as indicated in the legend. Of note, due to rather weak correlations of ST6GALs and glycomics data, we did not include these GSTs in our overview. Significant values are marked with * (p ≤ 0.05), ** (p ≤ 0.01,) and *** (p ≤ 0.001). Correlation coefficients and p-values are listed in the Additional file : Table S9

Article Snippet: AML cell line transcriptomics data was obtained from the depmap portal (Expression 22Q2 Public; Broad Institute, Cambridge, MA, USA) [ ].

Techniques: Glycoproteomics, Expressing

Journal: Cell & Bioscience

Article Title: Transcriptionally imprinted glycomic signatures of acute myeloid leukemia

doi: 10.1186/s13578-023-00981-0

Figure Lengend Snippet: Differences in glycan signatures of M5 and M6 AML cell lines as well as corresponding GST and TF expression. M5 and M6 classes are presented as grey and brown rectangles, respectively. GSTs displayed in the figure present a positive correlation with the corresponding glycosylation feature. The underlined TFs correlate with the glycosylation features. The underlined TFs colored in red are positively correlated with GSTs

Article Snippet: AML cell line transcriptomics data was obtained from the depmap portal (Expression 22Q2 Public; Broad Institute, Cambridge, MA, USA) [ ].

Techniques: Glycoproteomics, Expressing

Journal: Cell & Bioscience

Article Title: Transcriptionally imprinted glycomic signatures of acute myeloid leukemia

doi: 10.1186/s13578-023-00981-0

Figure Lengend Snippet: GST and TF expression in primary AML cells. a Determination of the matrix correlation coefficient RV2 (0.49) between expression patterns observed in cell lines and primary samples. b Spearman correlation of selected GSTs with TFs in AML cell lines (left) and primary AML cells (right). c Comparison of the expression of selected GSTs and TFs in primary AML cells grouped by FAB classification. Significances were assessed by one-way ANOVA followed by a Tukey post-hoc test. Significant values are marked with * (p ≤ 0.05), ** (p ≤ 0.01), *** (p ≤ 0.001), and **** (p ≤ 0.0001)

Article Snippet: AML cell line transcriptomics data was obtained from the depmap portal (Expression 22Q2 Public; Broad Institute, Cambridge, MA, USA) [ ].

Techniques: Expressing, Comparison

Journal: Journal of Proteome Research

Article Title: Glycosphingolipid-Glycan Signatures of Acute Myeloid Leukemia Cell Lines Reflect Hematopoietic Differentiation

doi: 10.1021/acs.jproteome.1c00911

Figure Lengend Snippet: PGC-nanoLC-MS/MS analysis of GSL glycans of an AML cell line without (A) and with α2–3 neuraminidase S treatment (B). EICs represent the non-sialylated GSL glycan (H4N2; m / z 1073.39; yellow trace) and sialylated GSL glycans (H4N2S1; m / z 1364.48; pink trace). Fragmentation spectra of the two isomeric species at 57.3 and 67.0 min are illustrated in panel (C) (H4N2S1 2,6 ) and (D) (H4N2S1 2,3 ), respectively. MS/MS spectra of the doubly ( m / z 681.742 – ) and singly charged ( m / z 1364.48 – ) precursor ion are shown. “*” indicates an analyte with m / z 1365.55 – .

Article Snippet: AML cell lines were grown at the Department of Immunopathology of Sanquin Research (Amsterdam, The Netherlands).

Techniques: Tandem Mass Spectroscopy, Glycoproteomics

Journal: Journal of Proteome Research

Article Title: Glycosphingolipid-Glycan Signatures of Acute Myeloid Leukemia Cell Lines Reflect Hematopoietic Differentiation

doi: 10.1021/acs.jproteome.1c00911

Figure Lengend Snippet: GSL glycan profiles of two exemplary AML cell lines. (A) GSL glycan profile of cell line AML 193 expresses gangliosides, and high diversity of (neo)lacto-series including linear and branched GSL glycans, with a high expression of I antigen, no globosides detected. (B) Cell line M07e reveals high abundance of gangliosides, some globosides, and (neo)lacto-series, but less diversity and no I branching expressed. The background in blue, yellow, and pink represents the gangliosides, globosides, and (neo)lacto-series glycans, respectively. Symbols of monosaccharide residues from the Symbol Nomenclature for Glycans system were used.

Article Snippet: AML cell lines were grown at the Department of Immunopathology of Sanquin Research (Amsterdam, The Netherlands).

Techniques: Glycoproteomics, Expressing

Journal: Journal of Proteome Research

Article Title: Glycosphingolipid-Glycan Signatures of Acute Myeloid Leukemia Cell Lines Reflect Hematopoietic Differentiation

doi: 10.1021/acs.jproteome.1c00911

Figure Lengend Snippet: PCA of GSL glycan structural features and their relative abundance (%) in AML cell lines. (A) PCA scores plot of PC1 against PC2. (B) PCA loadings plot indicates the contribution of each glycosylation trait to the PCA model. The top two PCs explain 57.33% of the variation within the data. Technical replicates were averaged for each cell line. AML cell lines are color-coded based upon the FAB classification.

Article Snippet: AML cell lines were grown at the Department of Immunopathology of Sanquin Research (Amsterdam, The Netherlands).

Techniques: Glycoproteomics

Journal: Journal of Proteome Research

Article Title: Glycosphingolipid-Glycan Signatures of Acute Myeloid Leukemia Cell Lines Reflect Hematopoietic Differentiation

doi: 10.1021/acs.jproteome.1c00911

Figure Lengend Snippet: Associations of GSL glycan structural features with gene expression of GTs and hematopoietic TFs. The clustered heat map of the canonical model illustrates the correlation between glycosylation features and gene expression of corresponding GTs and TFs. The canonical correlation analysis was conducted based on the dataset of relative quantification of the glycosylation features (right) in 17 AML cell lines and the dataset of gene expression of relevant GTs and TFs (bottom) which were extracted from the CCLE. The correlation is indicated at the top legend (blue: negative correlation; red: positive correlation).

Article Snippet: AML cell lines were grown at the Department of Immunopathology of Sanquin Research (Amsterdam, The Netherlands).

Techniques: Glycoproteomics, Gene Expression, Quantitative Proteomics