Tulpule Lab
Memorial Sloan Kettering Cancer Center
Research
The Tulpule Lab is interested in a long-standing question in cell biology: how do cells organize and compartmentalize critical cellular processes within the crowded and heterogeneous intracellular space? We focus on an emerging set of self-assembling, protein-based structures known as biomolecular condensates and their role in cancer, including a newly discovered pathogenic condensate – membraneless receptor tyrosine kinase (RTK) protein granules. Through interdisciplinary approaches combining cancer signaling, structural biology, biophysics, and high-resolution microscopy, we hope to understand how the compartmentalization of oncogenic fusion proteins can both co-opt and disrupt cellular condensates in order to drive cancer. We have two main areas of interest.
1. Oncogenic kinase fusions and signaling from RTK protein granules
Receptor tyrosine kinase (RTK)-mediated activation of downstream effector pathways such as the RAS/MAPK signaling cascade was thought to occur exclusively from lipid membrane compartments in mammalian cells and cancer. Yet the majority of chimeric (fusion) oncoproteins involving RTKs such as ALK or RET retain the intracellular kinase domain but lose the extracellular and transmembrane sequences, presenting fundamental questions as to how and where these oncoproteins organize RTK and RAS signaling in cells. We recently discovered that multiple prominent RTK fusion oncoproteins including EML4-ALK and CCDC6-RET do not localize to lipid membranes, but instead undergo de novo higher-order assembly into membraneless cytoplasmic protein granules that coordinate lipid-membrane independent RAS activation and MAPK signaling. These data establish a new pathogenic subcellular structure in cancer: membraneless RTK protein granules. Ongoing projects in the laboratory aim to (1) define the set of protein components in RTK fusion condensates and the rules of assembly, (2) determine how RAS and RAF are activated downstream of these membraneless compartments including a unique role for the ARAF isoform, and (3) identify and develop condensate “dissolvases” as a new therapeutic strategy for RTK fusion driven lung cancers.
While oncogenes promote cancer cell growth, unrestrained proliferation represents a significant stressor to cellular homeostasis networks such as the DNA damage response (DDR). To enable oncogene tolerance, many cancers disable tumor suppressive DDR signaling through genetic loss of DDR pathways and downstream effectors (e.g., ATM or p53 tumor suppressor mutations). Whether and how oncogenes can help “self-tolerize” by creating analogous functional deficiencies in physiologic DDR networks is not known. Our work focuses on the FET family of intrinsically disordered proteins (FUS, EWS, TAF15) that are frequent oncogenic fusion partners in a diversity of pediatric sarcomas and leukemias. Using Ewing sarcoma (ES) as a model of FET rearranged cancers, we recently discovered that the ES fusion oncoprotein EWSR1::FLI1 is recruited to sites of DNA damage and interferes with native FET protein function in activating the DNA damage sensor ATM. These data establish functional ATM defects as the principal DNA repair lesion in Ewing sarcoma and the compensatory ATR signaling axis as a collateral dependency and therapeutic target in multiple FET rearranged cancers. Our ongoing work on ES and other pediatric FET fusion sarcomas aims to (1) define how native FET proteins regulate the initial compartmentalization of DNA double-strand breaks (DSBs), (2) characterize the mechanisms by which FET fusion oncoproteins disrupt DNA repair with a focus on phase separation, and (3) test novel therapeutics to exploit the ATM defects in xenograft models and ultimately patients.
2. Oncogene disruption of cellular DNA repair networks
3. Clinical Translation
Lastly, we are working with Dr. Damon Reed and the Department of Pediatrics at MSKCC to launch new residual disease focused clinical trials in sarcoma that will incorporate our therapeutic findings. We are now able to characterize the poorly understood post-chemotherapy residual disease or “persister” state directly from patients using a unique clinical workflow that we developed in collaboration with our surgical and pathology colleagues. Our goal is to identify and test therapeutic hypotheses that specifically target the residual disease state first in PDX models and ultimately in patients.
