SFPQ-ABL1 and BCR-ABL1 activate distinct signaling networks. (A) Viability analysis of Ba/F3 cells expressing MSCV (empty vector control), BCR-ABL1, BCR-ABL1 – SH2/SH3, SFPQ-ABL1, or SFPQ-ABL1 + SH2/SH3, after 48-hour IL-3 withdrawal. Viability was determined by propidium iodide (PI) exclusion, measured by flow cytometry (n = 3). (B) Proliferation analysis of Ba/F3 cells expressing ABL1 fusions after 48-hour withdrawal. Proliferation was measured by luminescence relative to MSCV empty vector control, using the CellTiter-Glo 2.0 reagent (n = 3). (C) Multidimensional scaling plot of label-free quantification phosphoproteomics data. Data were normalized, and missing peptide values were imputed by using a method based on low-rank decomposition. Data were corrected via Surrogate Variable Analysis to remove unwanted variation. Samples are colored according to the key in the top left corner of the plot. (D) Heat map showing top differentially phosphorylated sites between BCR-ABL1– and SFPQ-ABL1–expressing cells in DPE analysis. Expression for 16 samples (z score; scaled log2-intensity), including 4 biological repeats for each cell line, MSCV, BCR-ABL1, SFPQ-ABL1, and SFPQ-ABL1 + SH2/SH3, is shown (colored according to key, n = 4). Gene names and phosphorylation sites (in parentheses) are given on the right side of the heat map. (E) Differentially expressed KEGG pathways between SFPQ-ABL1– and BCR-ABL1–expressing cells. Sime’s adjustment was applied to peptide P values to obtain protein level P values. limma was used to test for enriched KEGG terms. (F) Barcode plot of KEGG cell cycle proteins identified in DPE analysis. (G) Venn diagram of cell cycle proteins identified in phosphoproteomics analysis. Proteins were determined as differentially expressed if Sime’s adjusted P value was < .05. logFC, log fold change.