Prof. Michael B Yaffe

When cells encounter stress or injury such DNA damage, they activate complex signaling networks that regulate their ability to recover, repair the damage, and return to a homeostatic equilibrium. These networks must integrate a wide variety of signals from inside and outside the cell, transduced through protein kinase and lipid signaling pathways, to ultimately control cell cycle arrest or progression, coordinately regulate specific patterns of gene expression and/or initiate programmed cell death. Mutations in, or dysfunction of, protein kinase signaling pathways that normally respond to DNA damage, for example, play critical roles in tumor development and progression, while intentional targeting of these pathways can enhance the ability of commonly used DNA damaging chemotherapy and radiation to cure cancer.

DNA damage signaling pathways are intimately interconnected with pathways involved in cell growth, RNA processing and cytokine signaling, but how these pathways are integrated together at the systems level is poorly understood. Similarly, cells and tissues subjected to other types of injuries and/or infection by pathogens activate many of the same pathways involved in the DNA damage response. Inappropriate activity of these pathways cause auto-inflammatory tissue damage and multiple organ failure in states of overwhelming infection and sepsis as a result of mis-regulation of cytokine feedback loops, dysfunction of the blood clotting cascade, and uncontrolled activity of neutrophils, macophages and lymphocytes.

How are the signals from individual pathways integrated at the molecular level to control the phenotypic response of cells to infection, stress and DNA damage? What are the key pathways and molecules that are involved in these cellular events, and how are their activities and their interactions regulated by protein phosphorylation? How can these pathways be therapeutically manipulated using combination chemotherapies to re-wire tumor cells for optimal killing, or to limit cytokine-mediated inflammation and death? Our lab uses a broad range of technologies to decode how these cell signaling pathways are “wired” into functional networks through proteomic methods, high- and medium-throughput signaling assays, RNAi-based screens using high-content imaging, and computational/bioinformatics approaches, together with more traditional techniques from cell biology, physical biochemistry, structural biology and mouse genetics. We also have a long history of inventing new chemical, biochemical, and computational methods to study signaling, including peptide library-based screens and motif-based bioinformatics tools for building signaling networks in silico.

Current projects in the lab are examining:

(1) How phosphoserine/threonine-binding modules (Polo-box domains, 14-3-3 proteins, BRCT domains, and FHA domains) work together with specific protein kinases to form signaling circuits that control DNA damage signaling and cell cycle progression, how these networks are perturbed during tumor progression, and how these networks can be therapeutically targeted to enhance the ability of chemotherapy and radiation to kill tumor cells.
(2) How growth factor signaling pathways cross-talk with DNA damage signaling pathways to control tumor cell responses, and how combination chemotherapy can be intelligently used to re-wire signaling networks in tumor cells for optimal tumor killing using a ‘systems pharmacology’ approach.
(3) How MAP kinase pathways, cytokine feedback loops, and DNA damage signaling pathways are wired together, with a particularly strong focus on the role of the p38MAPK/MAPKAP Kinase-2 pathway in cell cycle control and cytokine signaling. Ongoing work in the lab suggests that this pathway plays a critical role in stress responses through the post-transcriptional control of gene expression by regulating mRNA splicing, stability and translation of cytokines and cell cycle regulatory molecules that are responsible, on one hand for tumor development and resistance to chemotherapy, and on the other hand for pathological inflammation and apoptotic responses seen during sepsis and infection.
(4) How protein kinase pathways work together with lipid signaling molecules, to control the extent to which phagocytic and immune cells either kill pathogens and/or damage host tissues through ROS production by the NADPH oxidase. Our most recent data suggests a molecular basis through which distinct lipid signaling pathways and protein kinase pathways converge to control oxidase activity, and implicates pathologic dysregulation of the blood clotting cascade as a significant contributor to inappropriate ROS-mediated inflammation during injury, infection, and sepsis.