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Published on: February 18, 2020
CRISPR/Cas9 Screen in Gastric Cancer Patient-Derived Organoids Reveals KDM1A-NDRG1 Axis as a Targetable Vulnerability
Jovan Mircetic1,2, Aylin Camgöz3,4,5,6,7, Moustafa Abohawya1
1German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany.
Abstract:
Viability CRISPR screens have proven indispensable in parsing genome function. However, their application in new, more physiologically relevant culturing systems like patient-derived organoids (PDOs) has been much slower. To probe epigenetic contribution to gastric cancer (GC), the third leading cause of cancer-related deaths worldwide, the first negative selection CRISPR screen in GC PDOs that faithfully preserve primary tumor characteristics is performed. Extensive quality control measurements showing feasibility of CRISPR screens in primary organoid culture are provided. The screen reveals the histone lysine demethylase-1A (KDM1A) to constitute a GC vulnerability. Both genetic and pharmacological inhibition of KDM1A cause organoid growth retardation. Further, it is shown that most of KDM1A cancer-supporting functions center on repression of N-myc downstream regulates gene-1 (NDRG1). De-repression of NDRG1 by KDM1A inhibitors (KDM1Ai) causes inhibition of Wnt signaling and a strong G1 cell cycle arrest. Finally, by profiling 20 GC PDOs, it is shown that NDRG1 upregulation predicts KDM1Ai response with 100% sensitivity and 82% specificity in the tested cohort. Thus, this work pioneers the use of negative selection CRISPR screens in patient-derived organoids, identifies a marker of KDM1Ai response, and accordingly a cohort of patients who may benefit from such therapy.
Insights
This study pioneers CRISPR screens in patient-derived organoids for gastric cancer, identifying histone lysine demethylase-1A (KDM1A) as a therapeutic target and NDRG1 as a predictive biomarker for KDM1A inhibitor response.
Area of Science:
- Oncology
- Genomics
- Epigenetics
Background:
- CRISPR screens are vital for understanding genome function but challenging in patient-derived organoids (PDOs).
- Gastric cancer (GC) is a leading cause of cancer mortality, necessitating novel therapeutic strategies.
- Epigenetic mechanisms in GC remain underexplored in physiologically relevant models.
Purpose of the Study:
- To establish and validate negative selection CRISPR screens in GC PDOs.
- To identify epigenetic vulnerabilities in gastric cancer.
- To discover biomarkers predicting response to targeted therapies.
Main Methods:
- Performed the first negative selection CRISPR screen in gastric cancer patient-derived organoids (GC PDOs).
- Conducted extensive quality control for CRISPR screening in organoid cultures.
- Utilized genetic and pharmacological inhibition of histone lysine demethylase-1A (KDM1A).
- Assessed N-myc downstream regulated gene-1 (NDRG1) expression and its correlation with KDM1A inhibition.
Main Results:
- Demonstrated the feasibility of CRISPR screens in primary organoid cultures.
- Identified KDM1A as a critical vulnerability in gastric cancer.
- KDM1A inhibition led to organoid growth retardation by repressing NDRG1.
- NDRG1 de-repression by KDM1A inhibitors caused Wnt signaling inhibition and G1 cell cycle arrest.
- NDRG1 upregulation predicted KDM1A inhibitor response in 20 GC PDOs with high sensitivity and specificity.
Conclusions:
- Pioneered negative selection CRISPR screens in patient-derived organoids for gastric cancer.
- Identified KDM1A as a therapeutic target and NDRG1 as a predictive biomarker for KDM1A inhibitor therapy.
- This work paves the way for personalized treatment strategies in gastric cancer based on epigenetic markers.
