Context-specific pathway dependencies for nuclear envelope proteins in brain cancer

About This Grant

PROJECT SUMMARY It is clear that the early, simplistic view that the nuclear envelope (NE) serves only as a barrier between the genome and the cytoplasm is not accurate. The NE is a dynamic signaling interface from which both biophysical and biochemical inputs are transmitted to affect a multitude of cellular processes. The complexity of NE functions is reflected in the variety of human cancers and tissue-specific diseases caused by mutations in NE proteins. These proteins are differentially expressed and have multiple binding partners to perform distinct biochemical functions. The molecular and phenotypic pleiotropy of NE-associated proteins and their context-specific roles poses a major challenge in determining direct phenotypic effects resulting from mutations in NE genes and mechanistically defining functions for NE proteins. We addressed this by capitalizing on the hundreds of cellular contexts in large-scale human cancer cell fitness screens to define signaling and functional networks of NE proteins. In particular, we used an analysis framework, called Webster, that accounts for molecular pleiotropy by assessing high variance gene effects across diverse cellular contexts. Webster discriminates biological functions for multifunctional proteins and ranks relevant contexts (cancer cell line models) for each pathway. Important to this proposal, Webster identified independent functional groupings for pleiotropic NE proteins particularly in central nervous system cancers. Aims 1 and 2 investigate context-specific nuclear mechanosensing and TGFb/BMP signaling functions identified by Webster for the NE-associated protein phosphatase CTDNEP1 and its binding partner NEP1R1 in brain cancer cell lineages. Aim 1 will determine the mechanistic relationship of CTDNEP1 in regulating NE lipids and nucleo-cytoskeletal linkages to cell-matrix adhesions transmitting force on the NE, with a focus on glioblastoma cell models. Aim 2 will build on prior work establishing CTDNEP1 and the integral NE protein LEMD3 as inhibitors of TGFb/BMP signaling to determine their functional connection to cancer, with a focus on medulloblastomas. Loss-of-function mutations in the CTDNEP1 gene are highly recurrent in group 3 medulloblastomas making it an important disease candidate to parse individual NE functions. In Aim 3, we use preliminary data we generated from an improved Webster platform which better captures NE protein pleiotropy. We focus on distinct functional groupings for the NE protein LEMD2 and its binding partner CHMP7, critical to NE repair. We will validate that these Webster-defined functional groupings reflect pleiotropic, cell cycle specific NE repair pathways, and begin to delineate the mechanistic underpinnings of their context-specific requirements in cancer models. Using animal and human tissue-derived models (tumor neurospheres) as well as clinical data will ensure our studies recapitulate the physiological complexity of human tissues and are relevant for human cancers. Together, by leveraging distinct dependencies of cancer cell models, we aim to advance mechanistic understanding of NE proteins, with a long-term goal of uncovering targets for selective therapeutics.