Cagan Laboratory

Research

Overview
Our laboratory develops disease models and novel lead therapeutics. Click the “+” at the right of each section to explore our different projects.  For a PubMed link to our work, check here.
Cancer Models

Our laboratory has developed a Drosophila model for Medullary Thyroid Carcinoma (MTC). Targeting oncogenic Ret to the eye, we phenocopied many aspects of the human syndrome. With this model in hand, we utilized a classical genetic modifier screen to identify 140 factors that function in the oncogenic process. More recently we have developed models for lung, breast, and colorectal cancers, exploring both the biology and therapeutics response for each tumor type.

Colorectal cancer models: Erdem, Sindhura, Tirtha, Delon, Dan

Targeting transgenes to the adult hindgut (e.g., byn>RAS[G12V]-P53[RNAi]-APC[RNAi]-PTEN[RNAi]) recapitulated several key aspects of tumorigenesis including multilayering, hyperproliferation, evasion of apoptosis and senescence,  SRC/MMP-dependent epithelial-to- mesenchymal transition (EMT), and metastasis-like migration of hindgut cells out of the epithelium to colonize distant sites within the body, recapitulating key aspects of metastasis (Figure). Using these models, we found that increased genetic complexity led to increased drug resistance that required drug combinations, a finding we validated in mouse xenograft models and, more recently, in patients in the CPCT.

We are currently building a collection of dozens of colorectal cancer ‘fly avatars’ to more deeply explore how to address genetic complexity in a whole animal context. This avatar collection will provide a unique opportunity to explore disease and to develop next generation therapeutics that are matched to patient biomarkers.

 

A RAS-APC-P53-PTEN cell leaving the hindgut

Thyroid and other RET-based cancer models: Renee, Marcos, Tirtha, Sara, Masa

Our laboratory has studied Medullary Thyroid Cancer for more than a decade. MTC is a rare, RET-driven cancer with a high metastasis and mortality rate. Using a fly RET MTC model, we characterized the RET cancer network through broad genetic screens. Through drug screening, we used our RET fly model to help identify/validate vandetanib as the first standard-of-care therapeutic for MTC; vandetinib was subsequently approved in 2011. More recently, we have used fly models to explore RET fusions including CCDC6-RET, NCOA4-RET, and KIF5B-RET, the latter linked primarily to lung cancers. Our fly lines demonstrated clear differences in the biology of transformation and in drug responses for each of the fusions, data that we subsequently validated in cell line models.

 Expressing oncogenic RET in the fly eye led to a ‘rough eye’phenotype that was rescued by APS6-45 (see drug discovery below)

References

  • Vidal, M., Larson, D. Read, R., and Cagan, R. (2006). Csk-deficient boundary cells are eliminated from normal Drosophila epithelia by exclusion, migration, and apoptosis. Developmental Cell, 10(1):33-44.
  • Vidal, M., Salavaggione, L., Ylagan, L., Wilkins, M., Watson, M., Weilbaecher, K., Cagan, R. (2010). A Role for the Epithelial Microenvironment at Tumor Boundaries: Evidence from Drosophila and Human Squamous Cell Carcinomas. Am J Pathol. 176(6):3007-14. PMC2877860
  • Das TK, Sangodkar J, Negre N, Narla G, and Cagan, R. (2012). Sin3a Acts through a Multi-Gene Module to Regulate Invasion in Drosophila and Human Tumors. Oncogene onc.2012.326. PMC3696049
  • Hirabayashi S. and Cagan R. (2015). Salt-inducible kinases mediate nutrient-sensing to link dietary sugar and tumorigenesis in Drosophila. eLife, doi: 10.7554/eLife.08501. PMC4643014
  • Bangi E., Murgia C., Teague A., Sansom O., and Cagan R. (2016). Functional exploration of colorectal cancer genomes using Drosophila. Nature Communications, doi: 10.1038/ncomms13615. PMC5141297
  • Das T, Cagan R (2017). KIF5B-RET Oncoprotein Signals Through a Multi-Kinase Signaling Hub. Cell Reports doi: 10.1016/j.celrep.2017.08.037
  • Das TK, Esernio J, Cagan R. (2018). Restraining Network Response to Targeted Cancer Therapies Improves Efficacy and Reduces Cellular Resistance. Cancer Res. doi: 10.1158/0008-5472.CAN-17-2001.
  • Bangi E, Ang C, Smibert P, Uzilov A, Teague A, Antipin Y, Chen R, Hecht C, Gruszczynski N, Yon W, Malyshev D, Laspina D, Selkridge I, Rainey H, Moe A, Lau CY, Taik P, Wilck E, Bhardwaj A, Sung M, Kim S, Yum K, Sebra R, Donovan M, Misiukiewicz K, Schadt E, Posner M, and Cagan R. (2019). A Personalized Platform Identifies Trametinib Plus Zoledronate For A Patient With KRAS-Mutant Metastatic Colorectal Cancer. Science Advances doi: 10.1126/sciadv.aav6528
Drug Discovery
A novel fly/chemistry platform: Tirtha, Masa in collaboration with Arvin Dar, Avner Schlessinger, Alex Scopton, and Peter Ung

To develop new therapeutic leads that improve on vandetanib for MTC—a similarly rare and deadly disease that is inherited in 25% of patients—we used a fly model to identify the FDA approved drug sorafenib as showing moderate efficacy. We then used a new platform developed by the Dar and Cagan laboratories to create sorafenib analogs (‘sorafelogs’) that (i) show excellent preclinical efficacy while (ii) retaining the druggable properties of sorafenib.

A key effort in the laboratory is developing new generation lead therapeutic compounds. Our initial focus is on cancer, where we are working with Arvin Dar and Avner Schlessinger and their teams to develop a novel fly/chemistry drug development platform.

Example- sorafenib analogs: To identify a kinase inhibitor as a starting point for RET-dependent Medullary Thyroid Carcinoma (MTC), we began by screening most FDA approved kinase inhibitors for rescue of a RET[M955T] fly cancer model: sorafenib improved survival to adulthood from 0% to 5%. We then used genetic screening of the fly kinome to identify ‘pro-targets’ (new targets that would improve sorafenib therapeutic index) and ‘anti-targets’ (sorafenib targets that are liabilities, either by reducing activity in the tumor or promoting whole body toxicity).

Computational modeling and chemical evolution studies were then used to add pro-targets and remove anti-targets from sorafenib’s cap structure. For example, removing the anti-target MKNK1 from sorafenib led to reduced whole body sorafenib toxicity. The eventual result was a new set of sorafenib analogs that showed improved efficacy in fly and mouse xenograft models (Figure); our initial mammalian ADME studies indicate that these ‘Tissue Calibrated Inhibitors’ (TCIs) retained many or most of the drug-like properties of sorafenib. Importantly, we moved these sorafelogs into novel chemical space, permitting us to file for the patent protection required to bring them into clinical trials. We are currently working to move APS6-45 sister compounds through IND-enabling studies.

 

Summary of chemical evolution from sorafenib (5% fly viability rescue) to APS6-45 (85% rescue).

 

 

 

Next steps: We are currently focused on advancing our platform to other diseases including other cancers (liver, lung) and inherited diseases (RASopathies, Tauopathy). This platform develops leads that are different than most other leads: the compounds are tuned to the whole body and can act anywhere including multiple points along the body and along the cancer network.

References

  • Vidal, M., Wells, S., Ryan, A., and Cagan, R. (2005). ZD6474 suppresses oncogenic Ret isoforms in a Drosophila model for Type 2 Multiple Endocrine Neoplasia Syndromes and Papillary Thyroid Carcinoma. Cancer Research 65(9), 3538-41. PMC5867345
  • *Dar AC, *Das T, Shokat KM, and Cagan R. (2012). Chemical Genetic Discovery of Targets and Anti-targets for Polypharmacological Treatment of Cancer. Nature 486(7401):80-4. *Co-first author.
  • Levine B and Cagan R. Drosophila Lung Cancer Models Identify Trametinib Plus A Statin as a Candidate Therapeutic (2016). Cell Reports, doi: 10.1016/j.celrep.2015.12.105. PMC4904304
  • *Sonoshita, M., *Scopton, A., Ung, P., Murray, M., Silber, L., Maldonado, A., Real, A., Schlessinger, A., **Cagan, R., **Dar, A. (2017). A Whole Animal Platform to Advance A Clinical Kinase Inhibitor Into New Disease Space. Nature Chem Biol 2018 Mar;14(3):291-298. *Co-first author; **co-corresponding.
RASopathies
Fly RASopathy models: Jared, Tirtha in collaboration with Bruce Gelb and colleagues

     The RASopathies are a collection of inherited disorders that are characterized by mutations that elevate activity of the RAS/ERK signaling network. Patients present with a broad palette of developmental defects as well as those that emerge postnatally. In addition to reducing quality of life, most patients with these traits encounter some RASopathy-associated morbidities such as hypertrophic cardiomyopathy (HCM), which can be life-threatening. Currently, only symptomatic care is available for affected individuals.

Models: To address this continuing unmet need, we are collaborating with the Gelb laboratory to identify new lead therapeutics through a novel approach: using Drosophila RASopathy models as whole animal screening platforms. We generated 14 new RASopathy models by expressing human disease isoforms of KRAS, RAF1, BRAF, and PTPN11 in flies: the result is a series of phenotypes that related to altered RAS pathway activity. We found that different disease isoforms can show significantly different phenotypes (Figure). In addition, different mutations can act both cell autonomously and—in some cases—non-autonomously to affect RAS signaling at a distance.

Drug discovery and development: Taking advantage of our set of fly RASopathy models, we have embarked on an extensive drug development effort using a rescue-from-lethality assay. Screening ~80 FDA approved drugs led to several candidate therapeutics including RAS pathway inhibitors but also drugs that act more broadly. Screening a library of 14,400 novel compounds, we are developing new chemical entities tuned to RASopathies. We currently have four ‘pharmacophores’ that show initial activity in at least one fly RASopathy model.

Different RASopathy mutations direct different defects. Top: Expressing hRAF1[L613V] led to ectopic wing vein material (arrows) but mostly normal eye, notum. Mutations sites are shown above. Middle: Expressing a different allele, hRAF1[D486G], led to normal wings, abnormal eye, ‘split’ thorax (arrow). Bottom: PTPN11[D61G] only affected the eye.

Collaboration: The Gelb lab is assessing the most promising of these therapeutic candidates in iPSC-derived cardiomyocytes; HCM represents a measurable parameter for future clinical trials. Together, this represents one of the most extensive RASopathy therapeutic efforts to date.

Tauopathies
Fly model of Tauopathy: Masa, Alex, Angelique in collaboration with Alison Goate and Kat Bowles

Tauopathies are a set of complex diseases that result in loss of nervous system tissue including brain function. In the 30 years since Tau was first identified as a key constituent of neurofibrillary tangles—and subsequently a causative agent of neurodegeneration—the Tauopathy field has made important strides in understanding how abnormal forms of Tau protein lead to damage. Tau interacts in complex ways with other cellular constituents and with surrounding cells within the brain, making Tauopathy therapeutics challenging.

Using previously developed fly TAU and TAU[R406W] models, we showed/confirmed that expressing human TAU in the fly eye led to its appropriate phosphorylation–indicating flies properly process the protein. Expressing TAU and especially the disease form TAU[R406W] also led to degeneration of the eye, a model for neurodegeneration (Figure). Our genetic screens identified several kinases that either enhance or suppress this degeneration (Figure), establishing a ‘Tauopathy’ functional network as well as candidate therapeutic targets.

Top: Validating human Tau[R406W] expression by protein expression and phosphorylation in retinal cells (rc) and associated axons (a) into the optic stalk (os). Bottom: The resulting reduced eye field—due to cell loss—was enhanced by reducing ryk gene dosage and suppressed by reducing aurora kinase A gene dosage.

Early drug hits: Based on a drug screen of TAU[R406W] flies, we have identified several candidate therapeutics including novel and FDA approved drugs. We are now working with Alison and Kat to test these leads in iPSC-derived human neurons.

Mt. Sinai Pilot Center for Precision Disease Modeling
Drosophila provides an excellent companion to mammalian models, and this is certainly true of our efforts with model building and drug design. We received a U54 grant from the National Institutes of Health (NIH-U54OD020353) to further build a fly-chemistry-mammal platform to better explore biology and develop therapeutics. For more details including our large team, please see our Mount Sinai Pilot Center for Precision Disease Modeling website.
Center for Personalized Cancer Therapeutics

Based on the work from many laboratories including our own, we are testing the concept that drug response predictions would be improved in a real world setting if genomic complexity were more completely captured in a whole animal setting. We have recently published our first fly-to-bedside paper (PMID: 31131321). For more details of our fly-to-bedside clinical trial, please go to the CPCT web site.