In this KO1 proposal, we attempt to deeply interrogate the role of molecular recognition and structure in a receptor-ligand system, type I Interferons (IFNs), that has fundamental implications for basic receptor signaling biology as well as human health. We intend to elucidate the structure- functional relationships of IFN induced signaling and to enhance IFN functions through combinatorial, computational, and structural biology. The training and research proposal describes a five year mentored program under the guidance of Dr. K. Christopher Garcia designed to build upon Dr. Mendoza's previous training in order to further expertise in combinatorial, computational, and structural biology. This will establish Dr. Mendoza as an independent multi-disciplinary scientist with a powerful set of tools to give him the experimental range to tackle problems in cytokine engineering for cancer biology. We will attempt to understand how IFN cytokines mediate a wide range of physiological processes through their effects on cell growth, differentiation, and proliferation. Type I IFNs have anti-proliferative properties important for the surveillance and control of malignant cells. Upon engagement of their receptor extracellular regions, IFNs differentially activate intracellular JAK/STAT signaling cascades. Members of the type I IFN family elicit different signaling responses despite binding to a common pair of receptors, IFN?R1 and IFN?R2. Fundamentally, the specificity of cytokine signaling is largely determined by the composition of receptor chains within the signaling complex. While much is known about cytokine-activated intracellular signaling pathways, we know much less about how extracellular structural changes induced by ligand binding translates into signaling events. The experiments proposed will provide more clarity to this question. The potential translational and cancer therapeutic applications are based on a pioneering study published more than ten years ago suggesting that IFN diversification through in vitro evolution could yield molecules with enhanced functional properties. Now, armed with powerful new methodologies, we wish to revisit this concept to create IFNs with diverse functional properties, but also to provide a structural and mechanistic rationale for these altered activities in a way that could inform strategies to engineer IFNs for cancer therapy in the future. We will achieve this by 1) in vitro evolution of IFN?1, 2) identification of variants with altered function using in vitro anti-viral and anti-proliferative assays, 3) structural characterization of the ternary complexes of the evolved IFNs to correlate structure with function, and 4) the computational design and in vitro evolution of chimeric cytokines with distinct and novel signaling and functional outputs. By understanding the molecular basis of cytokine/receptor interactions with correlated function, the results from this work may be able to guide the future development of cytokines as therapeutics as well as expand the capabilities and diversity of receptor mediated signaling, functional activities, and therapeutic properties.

Public Health Relevance

The Type I Interferon family of cytokines and receptors has powerful immunomodulatory functions, and are clinically used for a variety of cancers, immune and viral diseases. We propose to use the techniques of biochemistry, computational and structural biology to evolve and visualize the three-dimensional shapes of engineered interferon cytokines bound to their cellular receptors, and understand how this binding event is communicated across the cell membrane to elicit distinct anti-viral versus anti-cancer effects. These studies will give us insight into basic receptor signaling mechanisms, as well as test the concept that cytokine diversification could be an approach to generate new, potentially improved molecules for basic research and therapeutic development in cancer biology.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Scientist Development Award - Research & Training (K01)
Project #
5K01CA175127-05
Application #
9326170
Study Section
Subcommittee I - Transistion to Independence (NCI)
Program Officer
Soyombo-Shoola, Abigail Adebisi
Project Start
2013-09-18
Project End
2018-11-30
Budget Start
2017-09-01
Budget End
2018-11-30
Support Year
5
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Stanford University
Department
Biophysics
Type
Schools of Medicine
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94304
Illing, Patricia T; Pymm, Phillip; Croft, Nathan P et al. (2018) HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome. Nat Commun 9:4693
Gee, Marvin H; Han, Arnold; Lofgren, Shane M et al. (2018) Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes. Cell 172:549-563.e16
Gee, Marvin H; Sibener, Leah V; Birnbaum, Michael E et al. (2018) Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro. Proc Natl Acad Sci U S A 115:E7369-E7378
Riley, Timothy P; Hellman, Lance M; Gee, Marvin H et al. (2018) T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability. Nat Chem Biol 14:934-942
Mendoza, Juan L; Schneider, William M; Hoffmann, Hans-Heinrich et al. (2017) The IFN-?-IFN-?R1-IL-10R? Complex Reveals Structural Features Underlying Type III IFN Functional Plasticity. Immunity 46:379-392
Moraga, Ignacio; Spangler, Jamie B; Mendoza, Juan L et al. (2017) Synthekines are surrogate cytokine and growth factor agonists that compel signaling through non-natural receptor dimers. Elife 6:
Hilton, Hugo G; McMurtrey, Curtis P; Han, Alex S et al. (2017) The Intergenic Recombinant HLA-B?46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands. Cell Rep 19:1394-1405
Ng, Cherie T; Mendoza, Juan L; Garcia, K Christopher et al. (2016) Alpha and Beta Type 1 Interferon Signaling: Passage for Diverse Biologic Outcomes. Cell 164:349-52
Spangler, Jamie B; Moraga, Ignacio; Mendoza, Juan L et al. (2015) Insights into cytokine-receptor interactions from cytokine engineering. Annu Rev Immunol 33:139-67
Birnbaum, Michael E; Mendoza, Juan L; Sethi, Dhruv K et al. (2014) Deconstructing the peptide-MHC specificity of T cell recognition. Cell 157:1073-87