Leveraging cancer-specific defects in nuclear integrity to inform novel synthetic lethal strategies

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Summary Altered nuclear shape and appearance has long been known to be pathognomonic for cellular transformation; as a consequence, it is a critical parameter used in cancer diagnosis and tumor grading. Despite an increasingly mechanistic understanding of oncogenic and tumor suppressor pathways, as well as burgeoning genomic data that heralds the possibility of personalized treatments, we still lack a firm understanding of the relationship between nuclear architecture and cancer. In particular, it has yet to be defined if changes in the nucleus are causal or simply a consequence of transformation. Here, we sidestep this question, and instead ask: can the changes in nuclear architecture typical of cancer cells be exploited as a liability? Altered nuclear shape is intimately tied to mechanical defects of the nuclear envelope; recently, such defects have been linked to either transient or catastrophic losses of nuclear integrity, which can lead to cell death through two potential mechanisms. First, permanent losses of nuclear integrity are incompatible with cellular viability. Second, even transient losses of the nuclear barrier expose the DNA to cytoplasmic DNA sensors such as cGAS, which can drive a STING-dependent innate immune response that, at least in some cases, is sufficient to drive cell- autonomous death. In the latter case, loss of nuclear integrity also boosts the immune response to the tumor. Importantly, pathways that recognize and “heal” ruptures of the nuclear envelope have also been recently defined; perhaps not surprisingly, these repair mechanisms become critical for cell viability in contexts where nuclear integrity is compromised. Taken together, these new insights make a strong case that further weakening nuclear integrity in tumor cells can be exploited to drive cell death and immune system recognition. Here, in Aim 1, we propose to leverage an unbiased, genome-wide CRISPR dropout screen to identify synthetic lethal interactions of 1) normal cells with either weakened nuclear integrity or defective nuclear repair mechanisms or 2) cancer cell lines, with and without further compromise of their nuclear integrity pathways. In Aim 2, we will apply systems level approaches to organize the resulting context-dependent fitness genes into functional nodes. Beyond the strength of the genetic interaction, targets for in depth analysis will be further prioritized based on the availability of chemical inhibitors and representation in The Cancer Genome Atlas. Mechanistic experiments will explicitly examine these high priority synthetic genetic relationships in the context of nuclear shape, nuclear ruptures, and innate immune pathway activation. Completion of these two Aims will lead to the development of novel targets that exploit a key pathognomonic structure for cancer.