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Updated: Apr 19, 2026
Dual CRISPR-Interference Strategy for Targeting Synthetic Lethal Interactions Between Non-Coding RNAs in Cancer Cells
Published on: May 30, 2025
Identification of synthetic lethality of PRKDC in MYC-dependent human cancers by pooled shRNA screening
Zongxiang Zhou, Manishha Patel, Nicholas Ng
1Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA. jliu@gnf.org.
Background:
MYC family members are among the most frequently deregulated oncogenes in human cancers, yet direct therapeutic targeting of MYC in cancer has been challenging thus far. Synthetic lethality provides an opportunity for therapeutic intervention of MYC-driven cancers.
Methods:
A pooled kinase shRNA library screen was performed and next-generation deep sequencing efforts identified that PRKDC was synthetically lethal in cells overexpressing MYC. Genes and proteins of interest were knocked down or inhibited using RNAi technology and small molecule inhibitors, respectively. Quantitative RT-PCR using TaqMan probes examined mRNA expression levels and cell viability was assessed using CellTiter-Glo (Promega). Western blotting was performed to monitor different protein levels in the presence or absence of RNAi or compound treatment. Statistical significance of differences among data sets were determined using unpaired t test (Mann-Whitney test) or ANOVA.
Results:
Inhibition of PRKDC using RNAi (RNA interference) or small molecular inhibitors preferentially killed MYC-overexpressing human lung fibroblasts. Moreover, inducible PRKDC knockdown decreased cell viability selectively in high MYC-expressing human small cell lung cancer cell lines. At the molecular level, we found that inhibition of PRKDC downregulated MYC mRNA and protein expression in multiple cancer cell lines. In addition, we confirmed that overexpression of MYC family proteins induced DNA double-strand breaks; our results also revealed that PRKDC inhibition in these cells led to an increase in DNA damage levels.
Conclusions:
Our data suggest that the synthetic lethality between PRKDC and MYC may in part be due to PRKDC dependent modulation of MYC expression, as well as MYC-induced DNA damage where PRKDC plays a key role in DNA damage repair.
Insights
Targeting PRKDC shows synthetic lethality in MYC-driven cancers. PRKDC inhibition reduces MYC expression and increases DNA damage, offering a new therapeutic strategy for MYC-overexpressing cancers.
Area of Science:
- Oncology
- Molecular Biology
- Cancer Genetics
Background:
- MYC oncogenes are frequently deregulated in human cancers.
- Targeting MYC directly has proven challenging.
- Synthetic lethality offers a promising therapeutic strategy for MYC-driven cancers.
Purpose of the Study:
- To identify therapeutic targets for MYC-driven cancers using a synthetic lethality approach.
- To investigate the role of PRKDC in MYC-overexpressing cancer cells.
Main Methods:
- Conducted a pooled kinase shRNA library screen to identify synthetically lethal interactions with MYC.
- Utilized RNA interference (RNAi) and small molecule inhibitors to target PRKDC.
- Assessed cell viability, mRNA expression (TaqMan probes), and protein levels (Western blotting).
Main Results:
- PRKDC inhibition preferentially killed MYC-overexpressing human lung fibroblasts and small cell lung cancer cells.
- PRKDC knockdown downregulated MYC mRNA and protein expression.
- PRKDC inhibition increased DNA damage levels in cells with MYC overexpression.
Conclusions:
- Synthetic lethality between PRKDC and MYC is partly mediated by PRKDC's modulation of MYC expression.
- PRKDC plays a crucial role in repairing MYC-induced DNA damage.
- PRKDC inhibition represents a potential therapeutic strategy for MYC-driven cancers.
