Abstract LB-036: A genome wide functional genomics screen for co-driver mutations of mutant TP53 promoting cellular heterogeneity during breast cancer progression

Abstract

Abstract Breast tumors present a high degree of heterogeneity. The major tumor suppressor TP53 is mutated in 30% of all breast tumors and 80% in basal subtype co-existing with numerous other somatic mutations. We hypothesized that combination neo-morphic functions of specific TP53 driver mutations and combination of unique ‘co-drivers' result in inter-tumor heterogeneity. We observed a broad spectrum of phenotypic changes in hallmarks of cancer like cell survival, resistance to apoptosis and anoikis, cell migration and invasion among a panel of 10 mutant p53 expressing mammary epithelial cell lines compared to those with WT p53. Integrated analysis from ChIP-seq and RNA-seq revealed distinct promoter binding profiles of the different mutant p53 proteins, implying non-canonical transcriptional activity contributing to the possible phenotypic heterogeneity in TP53-mutated tumors. The phenotypic heterogeneity of seen in TP53 mutated breast tumors can be attributed to both altered DNA binding properties resulting in expression changes of canonical or mutant-specific target genes and functional crosstalk with distinct co-existing somatic mutations or co-drivers. For the proof-of-concept of co-drivers of mutant p53, when PTEN was deleted using CRISPR in non-invasive p53 mutant Y234C expressing cells a remarkable increase in cell invasion was observed. A genome wide CRISPR based pooled library screen maintained at low MOI on two distinct p53 mutant Y234C and R273C cells followed by bulk sequencing identified completely different candidate co-driver mutations that promoted cell invasion, the initiating step for tumor cell metastasis. The top co-driver candidates included unique genes associated with cytoskeletal and apoptosis resistance pathways and some known mutated genes reported in breast cancer patients harboring TP53 mutations. These invasive pooled library transduced cells when injected in a xenograft mouse model failed to form any mammary tumors. Interestingly, primary tumors appeared in mice injected with pooled library cells transduced at high MOI along with overexpression of MYC. Such results reinstated the importance of functional crosstalk between genes and specific gene combinations driving tumorigenesis. We are currently optimizing a single-cell sequencing platform to capture the combinatorial co-drivers of mutant TP53 promoting the mice primary tumors. This combined approach of deep molecular profiling and functional genomic screen powered the identification of distinct mutant TP53 driver and co-driver gene sets that may contribute to heterogeneous cellular phenotypes and promote aggressive behavior which can guide the development of novel targeted therapies. Citation Format: Anasuya Pal, Chenxi Xu, Jin Park, Joshua LaBaer. A genome wide functional genomics screen for co-driver mutations of mutant TP53 promoting cellular heterogeneity during breast cancer progression [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-036.