The cancer microenvironment plays an important role in the disease emergence, development, recurrence, and treatment resistance. For human myeloid malignancies, the bone marrow microenvironment contains a complex structure with a number of different cell types. The sophisticated interaction network between myeloid leukemia and the microenvironment adds great challenges to elucidating the pathogenesis of the disease, and discovering novel therapeutic mechanisms. Over the last few years, CRISPR-Cas9 genome editing technology has risen as a powerful tool for identifying essential genes for cancer growth. Our lab has further developed an advanced CRISPR-Cas9 screening approach that uses pooled sgRNAs targeting functional protein domains to significantly improve screening efficiency. In contrast to the massive amount of in vitroCRISPR-Cas9 screening studies, very few studies have focused on developing an in vivoCRISPR-Cas9 screening approach. Compared to in vitroscreening, a huge advantage of in vivoscreening is that it allows cancer cells in direct contact with the native microenvironment, which would lead to the identification of essential signalings for cancer development in vivo. In this study, we developed an effective and efficient in vivo domain-targeting CRISPR-Cas9 screening approach with a human acute myeloid leukemia (AML) xenograft model. We designed and constructed a number of domain-targeting sgRNA libraries covering different cellular functions, including G-protein coupled receptors, ion channels, solute carriers, membrane associated proteins, kinases, phosphatases, glycosylation pathway proteins, proteases, transcription factors, and chromatin regulators. We performed the CRISPR-Cas9 screens both in vivo and in vitro at the same time to identify in vivo specific essential genes for AML. With the focused-size libraries, we are able to achieve high screening quality and to nominate high confident in vivo specific targets. Among them, we re-captured the in vivo specific essentialities of the CXCR4 and CD47 genes, which have been well studied for their critical connections with bone marrow microenvironment. In addition, we identified and validated several in vivo specific targets associate with glycosylation pathway, integrin linked pathways, and chromatin regulators. Our preliminary results have demonstrated this approach can effectively identify essential genes for cancer microenvironment, which in vitroscreening is incapable of. We aim to use this approach to further identify in vivo specific targets in other pathways; and to understand their mechanism connecting to the cancer microenvironment; and to identify small molecules with therapeutic potency that could disrupt these connections.

Citation Format: Yiliang Wei, Christopher Vakoc. Probing leukemia vulnerabilitiesin vivousing domain-focused CRISPR screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5161.