Hannah Carter, Associate Professor at UC San Diego, in collaboration with Prashant Mali. Mapping gene regulatory networks that are perturbed in cancer can reveal downstream genes that could serve as therapeutic targets. As gene expression changes propagate through complex networks, measuring changes to gene expression levels alone cannot distinguish between direct and indirect effects. Thus, approaches are needed to determine direct targets of key transcriptional regulators downstream of activated oncogenic pathways. The aim of this pilot project is to implement a joint experimental and computational framework capable of mapping direct targets of key transcriptional regulators that mediate neoplastic gene expression programs. This project will use strategic mutagenesis informed through computational modeling to perturb cancer-associated transcriptional regulators, followed by single cell RNA- and ATAC-seq to map cancer associated gene regulation. This project will use RUNX1, a master regulator of hematopoiesis that is frequently altered in leukemia and breast cancer, as a proof of concept. Our preliminary scRNA-seq study of 12 mutations shows the potential of this approach to dissect different regulatory circuits in which RUNX1 is involved.

Natalia Jura, Associate Professor at UCSF, in collaboration with Nevan Krogan, Jennifer Grandis and Silvio Gutkind. The receptor tyrosine kinase HER3 is a multi-site scaffold for the phosphoinositide-3 kinase (PI3K), whose downstream signaling to Akt constitutes one of the most frequently deregulated pathways in human cancer, including head and neck cancer. Recent studies in the Krogan and Grandis laboratories found that a subset of PI3KCA mutations present in head and neck cancer cells preferentially associate with HER3. Moreover, the Gutkind lab showed that these PI3KCA mutants are dependent on HER3 binding to elicit its oncogenic signaling. These exciting findings point to a unique mechanism by which HER3 activates PI3KCA, whose understanding will help develop personalized therapies for the affected patients. At present, the nature of this selectivity is unknown due to the lack of direct insights into the mechanism of PI3KCA/HER3 binding. This project seeks to address this gap through the biophysical and structural characterization of the PI3KCA/HER3 interaction and its modulation by the cancer mutations. We now routinely collect cryo-EM data sets on almost full-length preparations of HER receptors (including HER3) and are confident that obtaining structures of wild type and mutant PIK3CA complexes with HER3 fragments is feasible.