Fig. 2: Discovery of novel neosubstrates in Huh-7 cells.

a Scatter plot illustrating newly identified CRBN neosubstrates in Huh-7 cells. The plot displays all proteins that showed significant downregulation following treatment with 10 µM MGD for 6 h (x-axis) alongside their corresponding fold-changes under co-treatment with 5 µM MLN4924 (y-axis). Proteins regulated in a neddylation-dependent manner are highlighted in blue, while those regulated in a neddylation-independent manner are indicated in red. b Volcano plots depicting protein (left) and ubiquitinated peptide (right) quantifications for the KDM4B degrader SJ41564 (10 µM), with log₂ fold-change on the x-axis and standard error on the y-axis (log₁₀ scale). Significant up- and downregulations of proteins (LIMMA⁶⁹, FDR = 1%) or ubiquitination sites (LIMMA⁶⁹, FDR = 5%) are colored in blue and red, respectively. c Summary of proteome (x-axis) and ubiquitinome (y-axis) t-statistic comparisons for all newly validated neosubstrates in Huh-7 cells. T-statistics for ubiquitination sites mapped to the same protein were averaged, and only significantly upregulated sites were included in the analysis. Volcano plots of protein quantifications for SJ42101 (d) and SJ06986 (e) after 24 h of treatment. Significantly up- and downregulated proteins (LIMMA⁶⁹, FDR = 1%) are colored in blue and red, respectively. The proteome (x-axis) and ubiquitinome (y-axis) t-statistic comparison plots are shown (bottom). Statistically significant up- and downregulations in the proteome (LIMMA⁶⁹, FDR = 1%) and the ubiquitinome (LIMMA⁶⁹, FDR = 5%) are colored in blue and red, respectively. P-value adjustments were made for multiple comparisons using the Benjamini-Hochberg procedure. Proteins that are both significantly downregulated after a 24-h compound treatment and harbor upregulated ubiquitination sites at 30 min of compound treatment are colored in turquoise. n.s. not significant. Source Data are provided as a Source Data file.