Journal: The FEBS journal

Article Title: Mapping the IMiD-dependent cereblon interactome using BioID-proximity labelling.

doi: 10.1111/febs.17196

Figure Lengend Snippet: Fig. 3. Bortezomib significantly perturbates the CRBN interactome. (A) Heatmap showing correlation between samples treated with DMSO, 10 nM bortezomib (Bort), 10 lM lenalidomide (Len), 2 lM pomalidomide (Pom), 2 lM iberdomide (Iber), and a combination of Bort and Len (BL), Bort and Pom (BP), and Bort and Iber (BI). (B) Heatmap showing proteins that are significantly more or less biotinylated by BioID2- CRBN in the presence of Bort (adj. P-value < 0.05). (C) Volcano plot displaying differential biotinylation of proteins in OPM2 cells expressing BioID2-CRBN that are treated with each Bort as compared to DMSO. Red dots represent proteins that are significant for adj. P-value < 0.05 and are more biotinylated in the presence of Bort. In blue, DVL1/2 proteins, in purple, proteins implicated in stress granule formation, in red, proteins involved in protein homeostasis.

Article Snippet: Lenalidomide (cat #S1029), Pomalidomide (cat #S1567) and Iberdomide (cat #S8760) were purchased from Selleckchem (Texas, USA).

Techniques: Expressing

Journal: The FEBS journal

Article Title: Mapping the IMiD-dependent cereblon interactome using BioID-proximity labelling.

doi: 10.1111/febs.17196

Figure Lengend Snippet: Fig. 3. Bortezomib significantly perturbates the CRBN interactome. (A) Heatmap showing correlation between samples treated with DMSO, 10 nM bortezomib (Bort), 10 lM lenalidomide (Len), 2 lM pomalidomide (Pom), 2 lM iberdomide (Iber), and a combination of Bort and Len (BL), Bort and Pom (BP), and Bort and Iber (BI). (B) Heatmap showing proteins that are significantly more or less biotinylated by BioID2- CRBN in the presence of Bort (adj. P-value < 0.05). (C) Volcano plot displaying differential biotinylation of proteins in OPM2 cells expressing BioID2-CRBN that are treated with each Bort as compared to DMSO. Red dots represent proteins that are significant for adj. P-value < 0.05 and are more biotinylated in the presence of Bort. In blue, DVL1/2 proteins, in purple, proteins implicated in stress granule formation, in red, proteins involved in protein homeostasis.

Article Snippet: Lenalidomide (cat #S1029), Pomalidomide (cat #S1567) and Iberdomide (cat #S8760) were purchased from Selleckchem (Texas, USA).

Techniques: Expressing

Journal: The FEBS journal

Article Title: Mapping the IMiD-dependent cereblon interactome using BioID-proximity labelling.

doi: 10.1111/febs.17196

Figure Lengend Snippet: Fig. 6. Analysis of previously published MS data reveals that IMiDs causes CRBN-MYH9 interaction, and that Len induces ubiquitination of MYH9. (A) Heatmaps generated from publicly available data in the work of Yamanaka et al. [24]. These heatmaps show the top 20 peptides with highest biotinylation by AirID-CRBN in MM.1S, HEK293T, HuH7, and IMR32 cells following treatment with thalidomide (Thal), lenalidomide (Len), pomalidomide (Pom) and the thalidomide metabolite 5-Hydroxythalidomide (5-HT). Peptides were filtered based on IMiD/ DMSO ratio values > 0 that was significant for P-value < 0.05 in at least one of the four IMiD/DMSO ratios. The heatmap was generated with log10 transformation of the ratios. Values between square brackets indicates the amino acid position of peptides in the protein of reference. MYH9 peptides are highlighted in bold characters. (B) Volcano plot, generated from publicly available data in the work of Kr€onke et al. [8]. This plot displays peptides containing ubiquitinated lysine in MM.1S cells treated with Len as compared to cells treated with DMSO. Blue dots represent ubiquitinated IKZF1 and IKZF3 peptides, violet dots represent ubiquitinated CK1a peptides, red dots represent ubiquitinated MYH9 peptides. The dashed line sets the P-value cut-off that corresponds to the P-value of the peptide with the largest adj. P- value that is < 0.05 (adj. P-value = 0.04971141).

Article Snippet: Lenalidomide (cat #S1029), Pomalidomide (cat #S1567) and Iberdomide (cat #S8760) were purchased from Selleckchem (Texas, USA).

Techniques: Ubiquitin Proteomics, Generated, Transformation Assay

Journal: Nature Communications

Article Title: A degron-mimicking molecular glue drives CRBN homo-dimerization and degradation

doi: 10.1038/s41467-025-65094-3

Figure Lengend Snippet: a Chemical structure of MRT-31619, OUN20985 (CRBN homo-PROTAC) and Lenalidomide. b , c Global quantitative proteomics in Jurkat cells. Volcano plots show compound/DMSO protein abundance upon treatment with 1 μM of MRT-31619 or CRBN homo-PROTAC for 1 h, 3 h and 24 h, and with 10 μM of MRT-31619 or CRBN homo-PROTAC for 24 h. d HEK293T_HiBiT-CRBN cells were treated with MRT-31619 for 1 h. Bortezomib at 2 μM, MLN4924 at 2 μM, and lenalidomide at 20 μM were added 1 h prior to MRT-31619 treatment. Values were normalized to DMSO treatment. Four biological replicates were plotted as mean ± Standard Deviation (SD). e HEK293T_HiBiT-CRBN cells were treated with CRBN homo-PROTAC for 1 h. Bortezomib at 2 μM, MLN4924 at 2 μM, and lenalidomide at 20 μM were added 1 h prior to CRBN homo-PROTAC treatment. Values were normalized to DMSO treatment. Four biological replicates were plotted as mean ± SD. f NanoBRET assay for HaloTag-CRBN and CRBN-NanoLuc constructs upon MRT-31619 or lenalidomide treatment. In the double treatment condition, lenalidomide was added at 20 μM, 1 h prior to MRT-31619 treatment. Values were normalized to DMSO treatment. Three biological replicates were plotted as mean ± Standard Error of Measurement (SEM). g NanoBRET assay for HaloTag-CRBN and CRBN-NanoLuc (CRBN-Nluc) wild-type (WT) and W386A constructs upon MRT-31619 treatment. Values were normalized to DMSO treatment. Three biological replicates were plotted as mean ± SEM. Source data are provided as a Source Data file.

Article Snippet: When applicable, cells were pre-treated for 1 h with bortezomib (Selleckchem Cat#S1013), MLN4924 (Selleckchem Cat#S7109) or lenalidomide (Selleckchem Cat#S1029).

Techniques: Quantitative Proteomics, Standard Deviation, Construct

Journal: Leukemia

Article Title: Haploinsufficiency of miR-143 and miR-145 reveal targetable dependencies in resistant del(5q) myelodysplastic neoplasm.

doi: 10.1038/s41375-025-02537-2

Figure Lengend Snippet: Fig. 5 del(5q) MDS cells depleted of TP53 or RUNX1 are sensitive to Abl or MAPK inhibitors. GSEA enrichment plots based on miR-143 or miR-145 expression for the BIOCARTA_GLEEVEC (A), BIOCARTA_MAPK (B), and BIOCARTA_MTOR (C) pathways in MDS patient CD34+ bone marrow cells. D Imatinib dose-response curves for LEN-resistant and WT MDS-L cells following treatment for 48 h, as measured by AlamarBlue assay. E Proportion of apoptotic cells as measured by Annexin V staining for LEN-resistant and WT MDS-L cells following 144 h treatment with imatinib, LEN or vehicle (DMSO). F Colony output of LEN-resistant and WT MDS-L cells in the presence of imatinib (10 μM), LEN (1 μM) or vehicle (DMSO). Effect of inhibitors of pathways downstream of IGF-1R including everolimus (mTOR inhibitor, 0.1 μM), temsirolimus (mTOR inhibitor, 0.5 μM) and trametinib (MEK1/2 inhibitor, 0.03 μM) or LEN (1 μM) or vehicle (DMSO), on del(5q) cell lines: KG1a cells (G) and MDS-L (H). I Trametinib dose-response curves for LEN-resistant and WT MDS-L cells following treatment for 48 h, as measured by AlamarBlue assay. J Proportion of apoptotic cells as measured by Annexin V staining for LEN-resistant and WT MDS-L cells following 144 h treatment with trametinib (0.03 μM), LEN (1 μM) or vehicle (DMSO).

Article Snippet: Growth, survival, and proliferation assays The IGF-1R small molecule inhibitor BMS-536924 (cat #S1012), Lenalidomide (cat #S1029), Imatinib (cat #S2475), Trametinib (cat #S2673), Temsirolimus (cat #S1044) and Everolimus (cat #sS1120) were purchased from Selleck Chemicals (Houston, TX, USA) and resuspended in DMSO.

Techniques: Expressing, Alamar Blue Assay, Staining

Journal: Leukemia

Article Title: Haploinsufficiency of miR-143 and miR-145 reveal targetable dependencies in resistant del(5q) myelodysplastic neoplasm.

doi: 10.1038/s41375-025-02537-2

Figure Lengend Snippet: Fig. 6 LEN-resistant MDS is sensitive to Abl and MEK inhibitors. Viability of bone marrow cells from del(5q) MDS patients (A), or normal CD34+ HSPC (B), following treatment with Imatinib (10 μM), Trametinib (0.015 μM), LEN (1 μM), or vehicle (DMSO) for 48 h, as measured by Annexin V/7AAD staining.

Article Snippet: Growth, survival, and proliferation assays The IGF-1R small molecule inhibitor BMS-536924 (cat #S1012), Lenalidomide (cat #S1029), Imatinib (cat #S2475), Trametinib (cat #S2673), Temsirolimus (cat #S1044) and Everolimus (cat #sS1120) were purchased from Selleck Chemicals (Houston, TX, USA) and resuspended in DMSO.

Techniques: Staining

Journal: Leukemia

Article Title: Haploinsufficiency of miR-143 and miR-145 reveal targetable dependencies in resistant del(5q) myelodysplastic neoplasm.

doi: 10.1038/s41375-025-02537-2

Figure Lengend Snippet: Fig. 5 del(5q) MDS cells depleted of TP53 or RUNX1 are sensitive to Abl or MAPK inhibitors. GSEA enrichment plots based on miR-143 or miR-145 expression for the BIOCARTA_GLEEVEC (A), BIOCARTA_MAPK (B), and BIOCARTA_MTOR (C) pathways in MDS patient CD34+ bone marrow cells. D Imatinib dose-response curves for LEN-resistant and WT MDS-L cells following treatment for 48 h, as measured by AlamarBlue assay. E Proportion of apoptotic cells as measured by Annexin V staining for LEN-resistant and WT MDS-L cells following 144 h treatment with imatinib, LEN or vehicle (DMSO). F Colony output of LEN-resistant and WT MDS-L cells in the presence of imatinib (10 μM), LEN (1 μM) or vehicle (DMSO). Effect of inhibitors of pathways downstream of IGF-1R including everolimus (mTOR inhibitor, 0.1 μM), temsirolimus (mTOR inhibitor, 0.5 μM) and trametinib (MEK1/2 inhibitor, 0.03 μM) or LEN (1 μM) or vehicle (DMSO), on del(5q) cell lines: KG1a cells (G) and MDS-L (H). I Trametinib dose-response curves for LEN-resistant and WT MDS-L cells following treatment for 48 h, as measured by AlamarBlue assay. J Proportion of apoptotic cells as measured by Annexin V staining for LEN-resistant and WT MDS-L cells following 144 h treatment with trametinib (0.03 μM), LEN (1 μM) or vehicle (DMSO).

Article Snippet: Growth, survival, and proliferation assays The IGF-1R small molecule inhibitor BMS-536924 (cat #S1012), Lenalidomide (cat #S1029), Imatinib (cat #S2475), Trametinib (cat #S2673), Temsirolimus (cat #S1044) and Everolimus (cat #sS1120) were purchased from Selleck Chemicals (Houston, TX, USA) and resuspended in DMSO.

Techniques: Expressing, Alamar Blue Assay, Staining

Journal: Leukemia

Article Title: Haploinsufficiency of miR-143 and miR-145 reveal targetable dependencies in resistant del(5q) myelodysplastic neoplasm.

doi: 10.1038/s41375-025-02537-2

Figure Lengend Snippet: Fig. 5 del(5q) MDS cells depleted of TP53 or RUNX1 are sensitive to Abl or MAPK inhibitors. GSEA enrichment plots based on miR-143 or miR-145 expression for the BIOCARTA_GLEEVEC (A), BIOCARTA_MAPK (B), and BIOCARTA_MTOR (C) pathways in MDS patient CD34+ bone marrow cells. D Imatinib dose-response curves for LEN-resistant and WT MDS-L cells following treatment for 48 h, as measured by AlamarBlue assay. E Proportion of apoptotic cells as measured by Annexin V staining for LEN-resistant and WT MDS-L cells following 144 h treatment with imatinib, LEN or vehicle (DMSO). F Colony output of LEN-resistant and WT MDS-L cells in the presence of imatinib (10 μM), LEN (1 μM) or vehicle (DMSO). Effect of inhibitors of pathways downstream of IGF-1R including everolimus (mTOR inhibitor, 0.1 μM), temsirolimus (mTOR inhibitor, 0.5 μM) and trametinib (MEK1/2 inhibitor, 0.03 μM) or LEN (1 μM) or vehicle (DMSO), on del(5q) cell lines: KG1a cells (G) and MDS-L (H). I Trametinib dose-response curves for LEN-resistant and WT MDS-L cells following treatment for 48 h, as measured by AlamarBlue assay. J Proportion of apoptotic cells as measured by Annexin V staining for LEN-resistant and WT MDS-L cells following 144 h treatment with trametinib (0.03 μM), LEN (1 μM) or vehicle (DMSO).

Article Snippet: Growth, survival, and proliferation assays The IGF-1R small molecule inhibitor BMS-536924 (cat #S1012), Lenalidomide (cat #S1029), Imatinib (cat #S2475), Trametinib (cat #S2673), Temsirolimus (cat #S1044) and Everolimus (cat #sS1120) were purchased from Selleck Chemicals (Houston, TX, USA) and resuspended in DMSO.

Techniques: Expressing, Alamar Blue Assay, Staining

Journal: Leukemia

Article Title: Haploinsufficiency of miR-143 and miR-145 reveal targetable dependencies in resistant del(5q) myelodysplastic neoplasm.

doi: 10.1038/s41375-025-02537-2

Figure Lengend Snippet: Fig. 6 LEN-resistant MDS is sensitive to Abl and MEK inhibitors. Viability of bone marrow cells from del(5q) MDS patients (A), or normal CD34+ HSPC (B), following treatment with Imatinib (10 μM), Trametinib (0.015 μM), LEN (1 μM), or vehicle (DMSO) for 48 h, as measured by Annexin V/7AAD staining.

Article Snippet: Growth, survival, and proliferation assays The IGF-1R small molecule inhibitor BMS-536924 (cat #S1012), Lenalidomide (cat #S1029), Imatinib (cat #S2475), Trametinib (cat #S2673), Temsirolimus (cat #S1044) and Everolimus (cat #sS1120) were purchased from Selleck Chemicals (Houston, TX, USA) and resuspended in DMSO.

Techniques: Staining