Extensive Research Description
A. Signaling Mechanisms of Receptor Tyrosine Kinases
A major focus of the Lemmon lab is to understand transmembrane signaling by growth factor receptor tyrosine kinases (RTKs), of which there are 58 in the human proteome – separated into 20 different families. Mutations in almost all of these RTKs – some activating, some inactivating – cause cancer or other diseases, and RTKs are important therapeutic targets. We are interested in understanding how these receptors signal, and – importantly – how RTK mutations seen in afflicted patients affect receptor activity. Understanding these mutations provides an important window into molecular mechanism, but also allows us to use our mechanistic understanding to advance development and application of targeted therapeutics. To achieve this, we combine cellular, biochemical, biophysical, and structural approaches – and collaborate closely with geneticists and clinical investigators. Our goal is to link detailed mechanistic understanding to biology in the intact organism (or patient). Although we are interested in all RTKs, and in RTK signaling in general – at the organismal, cellular, and molecular levels (and use a wide variety of approaches) – we are currently focused on the following families (or groups of families) or RTKs:
1. The Epidermal Growth Factor Receptor (EGFR) family
Often considered a ‘prototypic’ RTK, the EGFR has been a major focus of our work for the past decade or so. Combining crystallographic, cellular, and other approaches we have developed a sophisticated understanding of how growth factor binding promotes dimerization of the extracellular region of the receptor, how EGFR is regulated allosterically, and how its intracellular juxtamembrane region contributes to activation. We have also defined the molecular function of the extracellular EGFR inhibitor Argos, from which we hope to extract clues for developing new EGFR inhibitory approaches in cancer.
A second key area in our EGFR work is to understand how different activating ligands can promote distinct modes of signaling through this single receptor. EGF, TGF-alpha, betacellulin, HB-EGF, epiregulin, epigen, and amphiregulin all signal through EGFR - but with subtly different consequences. Our most recent work is revealing some unexpected structural origins for these differences that are impacting how we think about the EGFR.
2. Anaplastic Lymphoma Kinase (ALK)
Working with Dr. Yaël Mossé, a pediatric oncologist at the Children’s Hospital of Philadelphia, we are trying to understand how ALK – an orphan RTK – signals. Dr. Mossé discovered in 2008 that mutations in the tyrosine kinase domain of ALK cause a significant proportion of neuroblastomas, by promoting growth factor-independent signaling by the receptor. We have worked together to understand all ALK mutations seen in neuroblastoma patients, in terms of their signaling activity and response to available ALK inhibitors that are being used in the clinic. Working with Ravi Radhakrishnan in Penn Bioengineering, we are also trying to develop algorithms for predicting whether novel ALK mutations are activating and inhibitor-sensitive, which we hope will one day guide clinical treatment. We are now extending these approaches to mutations found in EGFR in lung cancer and glioblastoma.
3. RTKs that bind Wnt Ligands
It is now known that several orphan RTKs, namely PTK7/CCK4 (called Lemon in Hydra!), Ror1/2, Ryk, and MuSK are involved in ‘non-canonical’ Wnt signaling. This is a new arena for RTKs, and how they are involved remains unclear. Moreover, PTK7/CCK4, Ror1/2 and Ryk all have so-called pseudokinases in their intracellular region. That is, they look like RTKs, but appear to have ‘dead’ tyrosine kinases. We are working hard to understand how these unusual RTKs mediate signaling by these unexpected ligands, combining biochemical, cellular and structural studies with a collaboration with Peter Klein’s lab at Penn in Xenopus and Lee Fradkin in Drosophila. This work is likely to open new paradigms in RTK signaling and – we hope – to illuminate new therapeutic avenues. We also hope that these studies will shed new light on how pseudokinases function more broadly.
B. Binding of Protein Modules to Lipids and Other Targets: Conditional Membrane Proteins
The Lemmon lab has worked a great deal in the past on Pleckstrin Homology (PH), PX, FYVE, and other domains that bind phosphoinositides and other membrane lipids. We also recently described the kinase-associated (KA1) domain as another module that binds acidic phospholipids (Moravcevic et al. Cell 143, 966: 2010). We are now trying to understand how the KA1 contributes to activation of the kinases that harbor it. We are also interested in other targets for PH, F-BAR and other domains – which we study by combining yeast genetic studies with structural biology and biochemistry
EGFR ligands differentially stabilize receptor dimers to specify signaling kinetics
Freed DM, Bessman NJ, Kiyatkin A, Salazar-Cavazos E, Byrne PO, Moore JO, Valley CC, Ferguson KM, Leahy DJ, Lidke DS, Lemmon MA. (2017) Cell Oct 4, pii: S0092-8674(17)31066-8. doi: 10.1016/j.cell.2017.09.017. [Epub ahead of print]
Dimerization of Tie2 mediated by its membrane-proximal FNIII domains
Moore JO, Lemmon MA, Ferguson KM. (2017) Proc. Natl. Acad. Sci. USA 114, 432-4387
Molecular determinants of KA1 domain-mediated autoinhibition and phospholipid activation of MARK1 kinase.
Emptage RP, Lemmon MA, Ferguson KM. (2017) Biochem. J. 474, 385-398
Overcoming resistance to HER2 inhibitors through state-specific kinase binding
Novotny CJ, Pollari S, Park JH, Lemmon MA, Shen W, Shokat KM. (2016) Nature Chemical Biology 12, 923-930
The dark side of cell signaling: Positive roles for negative regulators.
Lemmon MA, Freed DM, Schlessinger J, Kiyatkin A. (2016) Cell 164, 1172-84
The ALK/ROS1 inhibitor PF-06463922 overcomes primary resistance to Crizotinib in ALK-driven neuroblastoma
Infarinato NR, Park JH, Krytska K, Ryles HT, Sano R, Szigety KM, Li Y, Zou HY, Lee NV, Smeal T, Lemmon MA, Mossé YP. (2016) Cancer Discovery 6, 96-107
Ligand regulation of a constitutively dimeric EGF receptor
Freed DM, Alvarado D, Lemmon MA. (2015) Nature Communications 6, 7380
Comparison of Saccharomyces cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site.
Moravcevic K, Alvarado D, Schmitz KR, Kenniston JA, Mendrola JM, Ferguson KM, Lemmon MA. (2015) Structure 23, 352-63
ALK mutations confer differential oncogenic activation and sensitivity to ALK inhibition therapy in neuroblastoma.
Bresler SC, Weiser DA, Huwe PJ, Park JH, Krytska K, Ryles H, Laudenslager M, Rappaport EF, Wood AC, McGrady PW, Hogarty MD, London WB, Radhakrishnan R, Lemmon MA, Mossé YP. (2014) Cancer Cell ,26 682-94.
Complex relationship between ligand binding and dimerization in the epidermal growth factor receptor.
Bessman NJ, Bagchi A, Ferguson KM, Lemmon MA. (2014) Cell Reports 9, 1306-17.