Journal: Nature Communications

Article Title: Supercharging-enhanced nDIA-MS enables global profiling of drug-induced proteome solubility shifts

doi: 10.1038/s41467-026-69025-8

Figure Lengend Snippet: Volcano plots showing the comparisons of protein levels between MG132 vs vehicle, and MG132 + ML-792 vs ML-792 from ( A ) U2OS, ( B ) HeLa, and ( C ) HEK293A cells. Volcano plots showing the comparisons of protein levels between ML-792 vs vehicle, and MG132 + ML-792 vs MG132 from ( D ) U2OS, ( E ) HeLa, and ( F ) HEK293A cells. P -values were calculated using a two-tailed Student’s t-test. No adjustments for multiple comparisons were applied. G Venn diagram showing the overlaps of up- and down-regulated proteins obtained from three cancer cell lines following treatment of MG132. Differentially regulated proteins from two pairwise comparisons of MG132 vs vehicle and MG132 + ML-792 vs ML-792 were combined. H Venn diagram showing the overlaps of up- and down-regulated proteins obtained from three cancer cell lines following treatment of ML-792. I , J Heatmaps showing differential proteins modulated by MG132 ( I ) and ML792 ( J ), respectively. Only proteins dysregulated in at least two cell lines are displayed. Western blotting results of representative proteins modulated by MG132 or ML792, including C-FOS ( K ), EGR1 ( K ), CCN1/2 ( L ), HIF1A ( M ). Experiments were repeated at least three times, and similar results were obtained. Source data are provided as a Source Data file.

Article Snippet: U2OS cells were purchased from the ATCC (Manassas, VA) and maintained in McCoy’s 5 A (Modified) medium containing 10% fetal calf serum at 37 °C with 5% CO 2 .

Techniques: Two Tailed Test, Western Blot

Journal: Nature Communications

Article Title: Supercharging-enhanced nDIA-MS enables global profiling of drug-induced proteome solubility shifts

doi: 10.1038/s41467-026-69025-8

Figure Lengend Snippet: Volcano plots showing the comparisons of relative insolubility rates between MG132 vs vehicle, and MG132 + ML-792 vs ML-792 from ( A ) U2OS, ( B ) HeLa, and ( C ) HEK293A cells. P -values were calculated using a two-tailed Student’s t-test. No adjustments for multiple comparisons were applied. Venn diagram showing the overlaps of ( D ) up- and ( E ) down-regulated proteins obtained from three cancer cell lines. Differentially regulated proteins from two pairwise comparisons of MG132 vs vehicle and MG132 + ML-792 vs ML-792 were combined. Functional enrichment analysis of the proteins whose insolubility rates were consistently ( F ) up- and ( G ) down-regulated in at least two cell lines. Enrichment analysis was performed using DAVID with default settings. P-values were calculated using the modified Fisher’s exact test (EASE score). No adjustments for multiple comparisons were applied. H–J Heatmaps showing proteins modulated by MG132. K–M Western blotting result of representative proteins that modulated by MG132 or ML792, including BAG6, UBL4A, TEX264, HSF1, REV1, and ATR1. Experiments were repeated at least three times, and similar results were obtained. Source data are provided as a Source Data file.

Article Snippet: U2OS cells were purchased from the ATCC (Manassas, VA) and maintained in McCoy’s 5 A (Modified) medium containing 10% fetal calf serum at 37 °C with 5% CO 2 .

Techniques: Two Tailed Test, Functional Assay, Modification, Western Blot

Journal: Nature Communications

Article Title: Supercharging-enhanced nDIA-MS enables global profiling of drug-induced proteome solubility shifts

doi: 10.1038/s41467-026-69025-8

Figure Lengend Snippet: Volcano plots showing the comparisons of relative insolubility rates between ML-792 vs vehicle, and MG132 + ML-792 vs MG132 from ( A ) U2OS, ( B ) HeLa, and ( C ) HEK293A cells. P -values were calculated using a two-tailed Student’s t-test. No adjustments for multiple comparisons were applied. Venn diagram showing the overlaps of ( D ) up- and ( E ) down-regulated proteins obtained from three cancer cell lines. Differentially regulated proteins from two pairwise comparisons of ML-792 vs vehicle and MG132 + ML-792 vs MG132 were combined. F Functional enrichment analysis of the proteins whose insolubility rates were consistently up- and down-regulated in at least two cell lines. Enrichment analysis was performed using DAVID with default settings. P-values were calculated using the modified Fisher’s exact test (EASE score). No adjustments for multiple comparisons were applied. G–I Heatmaps showing proteins modulated by ML-792. J–L Western blotting result of representative proteins that modulated by MG132 or ML792, including FANCD2, POLR3G, SP100, and DAXX. Experiments were repeated at least three times, and similar results were obtained. Source data are provided as a Source Data file.

Article Snippet: U2OS cells were purchased from the ATCC (Manassas, VA) and maintained in McCoy’s 5 A (Modified) medium containing 10% fetal calf serum at 37 °C with 5% CO 2 .

Techniques: Two Tailed Test, Functional Assay, Modification, Western Blot

Journal: Cell reports

Article Title: Uncovering genetic interactions in the DNA repair network in response to endogenous damage and ionizing radiation

doi: 10.1016/j.celrep.2025.116850

Figure Lengend Snippet: (A) Distribution of the observed phenotypes depleted in the basal screen results, indicating where the MRE11A-UBR5 gene pair falls relative to other depleted interactions. (B) Ranked observed phenotypes from the basal screen for both UBR5 and MRE11A . Blue/red regions highlight significantly enriched/depleted UBR5 -gene and MRE11A -gene interactions, respectively. Blue and red regions highlight gene combinations that are enriched above (blue) or depleted below (red) one standard deviation (+0.6981 and −0.7791) of the mean of all basal interactions and possess a Fisher-combined p < 0.05. (C) Time-lapse images of growth from Dox-induced dual-guide vectors with NT-1 x UBR5 -g2 or NT-1 x NT-2 in nuclear-EGFP-expressing cells co-cultured with nuclear-RFP-expressing cells grown in DMSO or 6.25 μM mirin (+mirin). Images are from one well per condition over the first 72 h of growth. Scale bar: 100 μM. (D) Measurements are calculated as the log 2 fold change (log 2 FC) of Dox induced over uninduced growth for the labeled condition, relative to the growth of co-cultured RFP+ cells, as seen in (C). Data represent mean ± SEM of 3 biological repliactes. The gray bar indicates the 72 h of growth shown in (C), though imaging continued. (E) Comparative growth differences at 96 h of two separate, inducible UBR5 guides from experiments performed similarly to those shown in (C) and (D). Bars are only shown for Dox-treated conditions but are normalized to uninduced, DMSO-treated control wells for each genotype and replicate. Mirin: 5 μM. Blue prediction bars are calculated from an additive model assuming no interaction, with the average effect of mirin on NT cells plus the average effect of UBR5 depletion for each guide and replicate. Data represent mean ± SEM of 2 biological replicates, and statistics represent a two-way ANOVA with Dunnett multiple comparisons test; p = 0.0277. (F) Western blot depicting robust UBR5 KO in two selected HT1080-6TG clones. (G) Dose curve of HT1080-6TG clones shown in (F) grown in increasing doses of mirin in a colony formation assay. IC50 was calculated from a sigmoidal interpolation of all datasets. Error bars: ± SEM from three biological replicates. Statistics match in color the clone they reference, relative to NT cells. Statistics: a two-way ANOVA with Dunnett’s multiple comparisons test between NT-treated cells and UBR5 -KO clones at each concentration; * p < 0.01 and **** p < 0.0001. (H) Western blot showing UBR5 depletion in U2-OS cells electroporated with either an sgNT-RNP or an sg UBR5 -RNP. (I) Log 2 of the relative confluence over time (relative to DMSO) for sgNT-RNP- or sg UBR5 -RNP-treated U2-OS cells from (H), grown with 25 μM mirin over 120 h. The shaded area around each solid line indicates the SEM from three biological replicates. Statistics: a two-way ANOVA at 120 h with Šídák’s multiple comparisons test; p = 0.0317. See also .

Article Snippet: U2-OS , ATCC , HTB-96.

Techniques: Standard Deviation, Expressing, Cell Culture, Labeling, Imaging, Control, Western Blot, Clone Assay, Colony Assay, Concentration Assay