Poster Presentation 35th Lorne Cancer Conference 2023

Using CRISPR activation CROP-seq techniques to mimic signals from the microenvironment that mediate resistance to venetoclax in aggressive lymphomas (#347)

Gaoyuan Wang 1 2 , Johannes Wichmann 1 2 , Hongke Peng 1 2 , Yexuan Deng 1 2 , Andrew Kueh 1 2 , Lin Tai 1 , Sarah T Diepstraten 1 2 , Gemma L Kelly 1 2 , Marco J Herold 1 2
  1. Walter and Eliza Hall Institute of Medical Research, North Melbourne, VIC, Australia
  2. Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia

Venetoclax is a BCL-2-specific BH3-mimetic drug that is FDA approved for the treatment of Chronic Lymphocytic Leukemia (CLL) and Acute Myeloid Leukemia (AML). While initial treatment success was very high, recent reports suggest relapse of patients being treated with venetoclax. Hence, identifying resistance factors to venetoclax therapy is an area of great clinical relevance. Therefore, our lab has recently established a novel mouse model of aggressive lymphoma that expresses high MYC and BCL-2, resembling double hit lymphoma (DHL). The murine DHLs are highly sensitive to treatment with venetoclax. This model provides an excellent tool to identify venetoclax therapy resistance factors. While a plethora of resistance mechanisms have been described, we are particularly interested in signals provided by the tumour micro-environment that mediate drug resistance of haematopoietic cancers. It is known that the upregulation of BCL-2 family proteins, for example, results from microenvironmental signals that can help cancer cells evade apoptosis. We designed a CRISPR droplet sequencing (CROP-seq) based transcriptional activation library to upregulate genes that mimic signals from the microenvironment (~30 genes; 5sgRNAs/gene). The CROP-seq method allows detection of each cell’s sgRNA along with its single cell transcriptomic landscape, providing gene expression signatures for individual gene perturbations. We have introduced this library into our DHL cell lines, that already express the CRISPR activation machinery, and treated the cells with venetoclax or DMSO. To identify the sgRNAs mediating survival post-venetoclax treatment, samples were collected for both bulk sequencing and single-cell RNAseq. The enrichment of sgRNAs targeting the pro-survival Bcl-2 family genes could be detected in the venetoclax treated samples by both DNA amplicon sequencing and by CROP-seq analysis. The CROPseq method revealed the efficiency of CRISPR activation and the performance of each sgRNA, and differential gene expression analysis between venetoclax treated and untreated samples identified some potential venetoclax resistance mechanisms. The ultimate goal of this project is to obtain more insight into the pathways mediating venetoclax resistance and use this information to target synergistic pathways increasing the treatment response to venetoclax in blood cancer patients.