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Journal: Molecular & Cellular Proteomics : MCP
Article Title: LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance
doi: 10.1016/j.mcpro.2026.101514
Figure Lengend Snippet: Proteome and phosphoproteome alterations associated with imatinib resistance. A – C , the ImR clone exhibited resistance to imatinib ( A ), dasatinib ( B ), and ponatinib ( C ), as demonstrated by relative proliferation of K562 and ImR cells following 72 h inhibitor treatment (mean ± SEM, n = 3 biological replicates). D , volcano plot illustrating differential protein expression between ImR and parental K562 cells. E , GSEA revealed oncogenic signatures enriched in ImR ( red ) or K562 ( blue ) cells. F , volcano plot showing significantly increased ( red ) or decreased ( blue ) phosphosites in ImR compared to K562. G , PhosphoSitePlus (PSP) regulatory site enrichment analysis of upregulated phosphosites in ImR cells. For all volcano plots, significance thresholds were set at a Benjamini–Hochberg (BH)-corrected p value <0.05 and minimum fold change of 1.3. All data were obtained from cells cultured in drug-free conditions. GSEA, Gene Set Enrichment Analysis; ImR, imatinib resistance.
Article Snippet: For pharmacological studies, cells were treated with inhibitors to various kinases, including
Techniques: Expressing, Cell Culture
Journal: Molecular & Cellular Proteomics : MCP
Article Title: LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance
doi: 10.1016/j.mcpro.2026.101514
Figure Lengend Snippet: Kinome reprogramming in imatinib-resistant cells. A , protein–protein interaction network of kinases significantly over-expressed in ImR compared to K562 at the proteome level. B , interaction network of kinases showing significantly increased phosphorylation in ImR versus K562, with collapsed fold-changes of detected phosphosites. Networks were created using StringApp in Cytoscape, with node color intensity representing fold-change and edge thickness indicating interaction confidence score. C , box plots showing representative TKs with a significant increase in both abundance and activity-regulatory site phosphorylation in ImR relative to K562. D , box plots demonstrating significant suppression of the ABL1-STAT5A signaling axis by imatinib treatment. E , box plots showing activation of the BCR-ABL downstream effector A-Raf in ImR cells. Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01, ∗∗∗ p < 0.001 (Student t test). BCR, breakpoint cluster region; ImR, imatinib resistance.
Article Snippet: For pharmacological studies, cells were treated with inhibitors to various kinases, including
Techniques: Phospho-proteomics, Activity Assay, Activation Assay
Journal: Molecular & Cellular Proteomics : MCP
Article Title: LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance
doi: 10.1016/j.mcpro.2026.101514
Figure Lengend Snippet: A signaling network nucleated by AKT and p70S6K underlies imatinib resistance. A and B , kinase activity predictions for ( A ) STKs/TKs by KSEA and ( B ) STKs by Kinase Library analysis. Activated kinases in ImR relative to K562 are shown in red , suppressed kinases in blue . C – E , substrates of AKT1, RPS6KA3, or RPS6KB1 demonstrating phosphoproteomic changes (log 2 fold change >1 or < -1) between ImR and K562 cells. F , protein-protein interaction network centered on AKT1/AKT2 with upstream regulators and downstream effectors, constructed using Omics Visualizer and StringApp in Cytoscape. Inner and outer circles display protein expression and phosphorylation changes (ImR versus K562), respectively, with line thickness representing interaction confidence. Asterisks indicate phosphosites validated by western blot. G , schematic of AKT-p70S6K (RPS6K) signaling pathways promoting protein translation. H and I , treatment with either ( H ) AKT1/2 inhibitor (ATKi-1/2) or ( I ) rapamycin, alone or combined with 100 nM imatinib, significantly restored imatinib sensitivity in ImR. ImR, imatinib resistance; KSEA, kinase substrate enrichment analysis; STK, Ser/Thr kinase; TK, tyrosine kinase.
Article Snippet: For pharmacological studies, cells were treated with inhibitors to various kinases, including
Techniques: Activity Assay, Construct, Expressing, Phospho-proteomics, Western Blot, Protein-Protein interactions
Journal: Molecular & Cellular Proteomics : MCP
Article Title: LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance
doi: 10.1016/j.mcpro.2026.101514
Figure Lengend Snippet: Essential role for LIN28A in imatinib resistance. A , proteomic and phosphoproteomic analyses reveal altered expression and phosphorylation of LIN28A interactors/regulators in the let-7-independent pathway. B , significant upregulation of DIS3L2, a negative regulator of let-7, in ImR cells. C , RT-PCR analysis demonstrating reduced abundance of let-7 family miRNAs in ImR cells compared to K562, with or without 1 μM imatinib treatment (mean ± SEM; n = 3 biological replicates). D , increased abundance of let-7 target proteins in ImR cells, as shown by GSEA normalized enrichment score. E , western blot validation of LIN28A overexpression in K562-LIN28A OE cells and depletion in ImR-LIN28A KD cells. F , growth curves showing cell proliferation in 500 nM imatinib over time (mean ± SEM; n = 3–5 independent experiments). Statistical significance: ∗, p < 0.05; ∗∗, p < 0.01; ∗∗∗, p < 0.001; ∗∗∗, p < 0.001; ∗∗∗∗, p < 0.0001 (one-way ANOVA with Tukey’s post hoc test). GSEA, Gene Set Enrichment Analysis; ImR, imatinib resistance.
Article Snippet: For pharmacological studies, cells were treated with inhibitors to various kinases, including
Techniques: Expressing, Phospho-proteomics, Reverse Transcription Polymerase Chain Reaction, Western Blot, Biomarker Discovery, Over Expression
Journal: Molecular & Cellular Proteomics : MCP
Article Title: LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance
doi: 10.1016/j.mcpro.2026.101514
Figure Lengend Snippet: LIN28A regulates the protein translation machinery via AKT-RPS6K signaling. A , heatmap displaying differentially expressed proteins (DEPs) between K562-LIN28A OE and empty vector control cells. B , volcano plot showing differentially phosphorylated proteins (DPPs) in K562-LIN28A OE versus control cells. C , heatmap of significant DEPs between ImR-LIN28 KD and control cells. D , volcano plot showing significant DPPs in ImR-LIN28 KD versus control cells. E , interaction network centered on AKT, RSP6K, and LIN28A, with inner and outer circles representing DEPs and DPPs (Log2 fold change, ImR/ImR-LIN28 KD ) based on MS data. F , western blot analysis of AKT-mTOR pathway proteins in cells with LIN28A overexpression or knockdown, treated with 1 mM imatinib or vehicle for 24 h. ImR, imatinib resistance; MS, mass spectrometry.
Article Snippet: For pharmacological studies, cells were treated with inhibitors to various kinases, including
Techniques: Plasmid Preparation, Control, Western Blot, Over Expression, Knockdown, Mass Spectrometry
Journal: Molecular & Cellular Proteomics : MCP
Article Title: LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance
doi: 10.1016/j.mcpro.2026.101514
Figure Lengend Snippet: LIN28A-mediated reprogramming of an STK network promotes imatinib resistance. A , Z-score of STKs predicted by KSEA to be activated ( red ) in ImR and K562-LIN28 OE cells and suppressed ( blue ) in ImR-LIN28A KD cells. Asterisks (∗) indicate significant prediction (FDR<0.05). B , signaling network centered on PRKCD (PKCd), showing differential protein expression ( inner circle ) and phosphorylation ( outer circle ) in ImR versus ImR-LIN28A KD cells (Omics Visualizer and StringApp in Cytoscape). Color scale represents log2 fold changes from MS data. C , relative proliferation of the indicated cells treated with midostaurin (1 μM, PKC inhibitor), GSK650394 (1 μM, SGK1 inhibitor), or AKTi (1 μM), with or without 500 nM imatinib. Cell viability was assessed by WST-8 assay after 72 h. Data are normalized to vehicle (DMSO) or imatinib-only controls (mean ± SEM; ∗ p < 0.05, one-way ANOVA with Tukey's post hoc test). AKTi, AKT inhibition; DMSO, dimethyl sulfoxide; FDR, false discovery rate; ImR, imatinib resistance; KSEA, kinase substrate enrichment analysis; STK, Ser/Thr kinase; WST-8, water-soluble tetrazolium 8.
Article Snippet: For pharmacological studies, cells were treated with inhibitors to various kinases, including
Techniques: Expressing, Phospho-proteomics, Inhibition
Journal: Molecular & Cellular Proteomics : MCP
Article Title: LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance
doi: 10.1016/j.mcpro.2026.101514
Figure Lengend Snippet: Proposed model of LIN28A-regulated kinase signaling in imatinib resistance .
Article Snippet: For pharmacological studies, cells were treated with inhibitors to various kinases, including
Techniques: