Research & Projects

Overview

Motivated by both kinase VUSs observed in Apsel Winger’s clinical practice and the remarkable responses of molecularly targeted kinase inhibitors in patients with vascular anomalies and cancer, the lab’s long-term goal is to expand targeted therapy options for patients with kinase mutations. Our lab uses molecular and chemical biology techniques to understand the mechanism by which uncharacterized mutations in kinases impact function.

 

 

Characterizing the mechanism of mutant kinases in vascular anomalies

 

Vascular anomalies result from abnormal development of the vascular system and present as congenital soft tissue masses that can be highly disfiguring and cause significant morbidity including pain, infection, and even death. These patients have very limited treatment options. Historically, vascular anomalies were thought of as a completely separate disease from cancer, but we've learned that the same activating mutations found in cancer are also found in vascular anomalies. Our research seeks to understand the mechanisms by which mutant kinases drive the development of vascular anomalies with the goal of advancing kinase-directed therapy for these conditions. We develop tissue culture models of vascular anomalies expressing these mutant proteins to study the signaling and define new therapeutic targets for our patients. Our projects are directly informed by our patients and the mutations we find in their vascular anomalies.

One example is our recent discovery of the oncogenic kinase fusion EML4::ALK in a small cohort of children with lymphatic malformations. This is a highly oncogenic fusion, mice expressing EML4::ALK in lung epithelial cells develop many tumors in their lungs at a young age. Therefore, it was highly surprising to find this mutation in our patients with benign vascular anomalies. We are actively interrogating in the lab how this fusion, or any kinase fusion, can drive the development of vascular anomalies. This has major treatment implications as there are six approved drugs against EML4::ALK that could help treat these patients with otherwise limited treatment options.

Already, one of our patients with an EML4::ALK+ lymphatic malformation (LM) has responded to an ALK inhibitor suggesting EML4::ALK is in fact driving the disease phenotype. However the mechanism is entirely unknown. 

Characterizing kinase VUSs

An important focus of our lab is to identify activating, drug-sensitive mutations in kinases, thus we have partnered with the Jacobson Lab and the Mobley Lab to develop and implement a rigorous, quantitative computational method while the Apsel Winger lab carries out the experimental validation. This method will be based on molecular dynamics (MD), a computational method carried out by our collaborators that simulates the movement of atoms and molecules based on Newton’s laws of motion. Our goal is to create a new computational pipeline for predicting if kinase VUSs are activating and sensitive to kinase inhibitors. We are grateful to our funders in the Bachrach Family Foundation and TeamConnor Childhood Cancer Foundation for supporting this work.

We hypothesize that kinase-activating mutations can be identified based on free energy changes in MD simulations between wildtype and mutant kinases. Decades of research in statistical mechanics and computational biophysics has demonstrated that MD-based calculations can predict kinase activity, however this has never been applied to clinical mutations with the goal of improving patient care. Our lab specifically carries out the experimental validation of the Jacobson lab's and Mobley lab's molecular dynamics predictions.

We have demonstrated the feasibility of applying this method to patient-derived mutations. One of our teenage patients with refractory acute lymphoblastic leukemia had a VUS in the oncogenic kinase PDGFRA, PDGFRA D842N. We used MD-based free energy calculations to predict PDGFRA D842N was activating, guiding the decision to treat with a PDGFR inhibitor in combination with chemotherapy, which put this patient into remission (Paolino et al, 2023). We are expanding this type of work to characterize additional mutations in PDGFRA as well as mutations in other medically relevant kinases, such as FLT3, KIT, RET, and others (Sandoval-Perez et al, 2022).

Once we establish the workflow from VUS detection to prediction of effect, this method will be applied to other kinases and integrated into molecular tumor board and clinical care. This work will expand our mechanistic understanding of which mutations can lead to kinase activation and drug sensitivity which will ultimately expand targeted therapy options for pediatric cancer patients with genetic testing of their tumors.

Understanding the mechanism of gatekeeper mutations

There are many mechanisms by which gatekeeper mutations in kinases have been shown to impact kinase function and drug sensitivity. Based on our previous work in cancer research (see ATP-Competitive Inhibitors Midostaurin and Avapritinib Have Distinct Resistance Profiles in Exon 17–Mutant KIT), we hypothesize that gatekeeper mutations in the kinase KIT impact drug sensitivity through unique mechanisms involving conformational changes in portions of the kinase not previously described as being impacted by gatekeeper mutations, such as the P-loop. Using Ba/F3 cells we are interrogating how the chemistry of the residue at the gatekeeper position impacts kinase function. Based on these studies, we hope to learn about the mechanism by which gatekeeper mutations in KIT cause drug resistance to help inform future generations of KIT inhibitors.