Targeted protein degradation(TPD)has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell’s endogenous protein degradation machinery.However,the susceptibilit...Targeted protein degradation(TPD)has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell’s endogenous protein degradation machinery.However,the susceptibility of proteins for targeting by TPD approaches,termed“degradability”,is largely unknown.Here,we developed a machine learning model,model-free analysis of protein degradability(MAPD),to predict degradability from features intrinsic to protein targets.MAPD shows accurate performance in predicting kinases that are degradable by TPD compounds[with an area under the precision–recall curve(AUPRC)of 0.759 and an area under the receiver operating characteristic curve(AUROC)of 0.775]and is likely generalizable to independent non-kinase proteins.We found five features with statistical significance to achieve optimal prediction,with ubiquitination potential being the most predictive.By structural modeling,we found that E2-accessible ubiquitination sites,but not lysine residues in general,are particularly associated with kinase degradability.Finally,we extended MAPD predictions to the entire proteome to find964 disease-causing proteins(including proteins encoded by 278 cancer genes)that may be tractable to TPD drug development.展开更多
BRAF is a serine/threonine kinase that harbors activating mutations in^7%of human malignancies and^60%of melanomas.Despite initial clinical responses to BRAF inhibitors,patients frequently develop drug resistance.To i...BRAF is a serine/threonine kinase that harbors activating mutations in^7%of human malignancies and^60%of melanomas.Despite initial clinical responses to BRAF inhibitors,patients frequently develop drug resistance.To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma,we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAF inhibitors.To investigate the mechanisms and pathways enabling resistance to BRAF inhibitors in melanomas,we integrate expression,ATAC-seq,and CRISPR screen data.We identify the JUN family transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6,which together enable resistance to BRAF inhibitors in melanoma cells.Our findings reveal genes contributing to resistance to a selective BRAF inhibitor PLX4720,providing new insights into gene regulation in BRAF inhibitor resistant melanoma cells.展开更多
基金supported by grants from the Breast Cancer Research Foundation(Grant No.BCRF-19-100 to X.Shirley Liu)the Mark Foundation for Cancer Research(Mark Foundation Emerging Leader Award+5 种基金Grant No.19-001-ELA to Eric S.Fischer)the National Institutes of Health(NIHGrant Nos.R01CA218278 and R01CA214608 to Eric S.Fischer)Cancer Research Institute(Irvington Postdoctoral FellowshipGrant No.CRI 3442 to Shourya S.Roy Burman),USADamon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation,USA(Grant No.DRQ-04-20)。
文摘Targeted protein degradation(TPD)has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell’s endogenous protein degradation machinery.However,the susceptibility of proteins for targeting by TPD approaches,termed“degradability”,is largely unknown.Here,we developed a machine learning model,model-free analysis of protein degradability(MAPD),to predict degradability from features intrinsic to protein targets.MAPD shows accurate performance in predicting kinases that are degradable by TPD compounds[with an area under the precision–recall curve(AUPRC)of 0.759 and an area under the receiver operating characteristic curve(AUROC)of 0.775]and is likely generalizable to independent non-kinase proteins.We found five features with statistical significance to achieve optimal prediction,with ubiquitination potential being the most predictive.By structural modeling,we found that E2-accessible ubiquitination sites,but not lysine residues in general,are particularly associated with kinase degradability.Finally,we extended MAPD predictions to the entire proteome to find964 disease-causing proteins(including proteins encoded by 278 cancer genes)that may be tractable to TPD drug development.
基金supported by grants from the National Natural Science Foundation of China(Grant No.81872290)the National Key R&D Program of China(Grant No.2017YFC0908500)
文摘BRAF is a serine/threonine kinase that harbors activating mutations in^7%of human malignancies and^60%of melanomas.Despite initial clinical responses to BRAF inhibitors,patients frequently develop drug resistance.To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma,we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAF inhibitors.To investigate the mechanisms and pathways enabling resistance to BRAF inhibitors in melanomas,we integrate expression,ATAC-seq,and CRISPR screen data.We identify the JUN family transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6,which together enable resistance to BRAF inhibitors in melanoma cells.Our findings reveal genes contributing to resistance to a selective BRAF inhibitor PLX4720,providing new insights into gene regulation in BRAF inhibitor resistant melanoma cells.
