In vivo PDX CRISPR/Cas9 screens reveal mutual therapeutic targets to overcome heterogeneous acquired chemo-resistance

Abstract

Resistance towards cancer treatment represents a major clinical obstacle, preventing cure of cancer patients. To gain mechanistic insights, we developed a model for acquired resistance to chemotherapy by treating mice carrying patient derived xenografts (PDX) of acute lymphoblastic leukemia with widely-used cytotoxic drugs for 18 consecutive weeks. In two distinct PDX samples, tumors initially responded to treatment, until stable disease and eventually tumor re-growth evolved under therapy, at highly similar kinetics between replicate mice. Notably, replicate tumors developed different mutations in TP53 and individual sets of chromosomal alterations, suggesting independent parallel clonal evolution rather than selection, driven by a combination of stochastic and deterministic processes. Transcriptome and proteome showed shared dysregulations between replicate tumors providing putative targets to overcome resistance. In vivo CRISPR/Cas9 dropout screens in PDX revealed broad dependency on BCL2, BRIP1 and COPS2. Accordingly, venetoclax re-sensitized derivative tumors towards chemotherapy, despite genomic heterogeneity, demonstrating direct translatability of the approach. Hence, despite the presence of multiple resistance-associated genomic alterations, effective rescue treatment for polychemotherapy-resistant tumors can be identified using functional testing in preclinical models.

Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia

“…Enrichment analysis suggested that these target genes were associated with cell adhesion-related biological processes (Fig. 4e ), suggesting potential dysregulated interaction of leukemia cells and mesenchymal stromal cells in the bone marrow microenvironment, which was previously shown to be associated with chemoresistance of leukemia cells 34 , 35 .…”

Patient-derived xenograft models in cancer therapy: technologies and applications

“…They identified BCL2 and successfully recovered the tumor sensitivity toward chemotherapy. 124 Interestingly, Carlet et al used Cre-ERT2 inducible RNAi to mimic anti-cancer therapy and silence genes in PDX models, which combined the properties of the Cre-loxP system and RNAi techniques. 125 A DNA barcode sequence is a type of unique sequence which can track the exact cells or components that carry it.…”

Advancements in CRISPR screens for the development of cancer immunotherapy strategies

“…Notably, recent studies by Bahrami et al. 168 , 169 and Wirth et al. 168 , 169 have demonstrated the feasibility and potency of in vivo CRISPR-Cas9 functional screening in models of AML and chemoresistance, unveiling crucial genes such as BCL2 , BRIP1 , and COPS2 that govern therapeutic outcomes.…”