Research

Emerging research highlights the surprising finding that mRNA transcript levels predict less than half of protein abundance, which is the prime determinant of the functional cellular response. Post-transcriptional control mechanisms enable cancer cells to precisely and rapidly respond to changing cell state, such as oncogenic transformation, unchecked proliferation, and metastasis. In particular, the functional interactions between specific RNA binding proteins (RBPs) and select target genes, have remained elusive, emphasizing the need for new perspectives and technologies. To fill this gap, our lab takes a systems-level strategy that integrates functional transcriptome-wide sequencing approaches, RNA structure probing, and proteomics to illuminate the hidden RNA regulatory code that maintains cell homeostasis and is dysregulated in cancer. Like transcriptional control, where a defined set of factors binds to specific DNA elements to drive selective transcription, how does a repertoire of RBPs act in trans to selectively regulate gene expression?

Identifying novel regulators of post-transcriptional control of oncogenic transformation.

A fundamental unsolved question is how cells maintain the expression of select target genes to cope with stress when overall protein synthesis is reduced. We utilize an approach developed by Dr. Kovalski that couples a fluorescent selective translation reporter system with CRISPRi screening to unveil the logic of post-transcriptional control across a spectrum of cancer signaling pathways and cell stress states like drug treatments. Our goal is to decipher novel selective regulators of pro-tumorigenic gene expression to identify new therapeutic targets.

How functional mRNA structures mediate expression of the oncogenic proteome.

How RNA structures drive changes in protein abundance to alter cellular functions, such as proliferation, metabolic rewiring, or change in cell state, is largely unknown. RNA sequence and the binding of RBPs shape RNA structure, generating a new level of gene expression regulation missed by classic genomic techniques. We utilize in-cell mutation and mapping techniques coupled with functional assays to validate the RNA structures and characterize the functional consequences. Ultimately, through endogenous DNA editing, we can conduct tumorigenesis studies in mouse models. We seek to illuminate how diverse cellular stressors can selectively remodel RNA structures to modulate protein abundance and functionally impact the cellular response.

Mapping novel dynamic RNA binding protein interaction networks.

How do cancer cells rewire select RNA binding protein networks to promote tumorigenesis? We are only beginning to appreciate the highly dynamic and interconnected functions of canonical and novel RNA binding proteins. We and others have observed the relocalization of RBPs during the process of oncogenic transformation. We employ proteomic approaches to identify RBP protein-protein interaction networks across different cell states and specific subcellular compartments. Our approach also reveals candidates not previously implicated in RNA binding processes. We use functional assays such as CLIP-sequencing, RNA stability, splicing alterations, and polysome-sequencing to determine the mechanisms by which these multifunctional RBPs maintain cellular homeostasis yet can be hijacked to drive tumorigenesis. These studies will uncover new functional mechanisms by which specific RBPs connect diverse cellular processes to sustain tumorigenesis.

Cracking the RNA code

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