Oakes Lab


Protein Misfolding, ER Stress and Disease

The endoplasmic reticulum (ER) is the major site within the cell for folding, modification, and trafficking of proteins. Various physiological events (e.g., secretory cell differentiation) and pathological conditions (e.g., hypoxia, nutrient deprivation, sustained demands on the secretory pathway or somatic mutations in its client proteins) can overwhelm the protein folding capacity of the ER. Initially, the stress placed on the ER by an abundance of misfolded protein activates an evolutionarily conserved signal transduction pathway called the unfolded protein response (UPR). The ER-resident transmembrane sensors IRE1α, PERK, and ATF6 are the major effectors of the UPR in mammalian cells, and initially expand the ER network, upregulate chaperones and arrest global translation in order to restore homeostasis. However, if the ER damage is extensive or prolonged, ER stressed cells can become dysfunctional and ultimately die. Mounting evidence suggests that cell dysfunction triggered by excessive stress on the protein folding capacity of the ER contributes to pathological cell loss in many common human degenerative diseases, including Alzheimer’s, Parkinson’s, retinal degeneration, Amyotrophic Lateral Sclerosis, type 2 diabetes, and liver cirrhosis. A key focus in our lab is on discovering how protein misfolding leads to the dysfunction and death of the affected cells in these diseases.

Developing Drugs to Treat Protein Folding Disorders

Our ultimate goal is translate the mechanistic knowledge we gain from studying how cells respond to protein misfolding into new therapies to help patients with protein folding disorders (PFD). With our longstanding collaborator Feroz Papa at UCSF, we have designed rigorous in vitro assays and mouse models to identify and monitor the pro-survival and pro-death signals sent from the master UPR regulator IRE1α-an ER transmembrane kinase/RNase. Through building and testing a series of chemical-genetic IRE1α tools, our labs discovered that mammalian IRE1α has binary outputs that determine either homeostasis (Adaptive UPR) or apoptosis (Terminal UPR) depending on the strength of upstream ER stress. In collaboration with Feroz Papa, Dustin Maly (UWash), and Brad Backes (UCSF), we recently developed a novel class of IRE1α inhibitors (KIRAs for Kinase Inhibiting RNase Attenuators) that shuts down its RNase allosterically through the adjacent kinase domain, and showed that they have cytoprotective benefits in acute models of retinal degeneration and diabetes. We are testing KIRAs and other UPR modulators in a wide range of preclinical models of disease.

Cell Suicide

All multicellular organisms have evolved mechanisms to silence or eliminate rogue cells that threaten the survival of the majority. As such, human cells are genetically programmed to actively commit “suicide” through a process called apoptosis when they become harmful, superfluous or irreversibly damaged. The final executioners in the apoptotic pathway are a family of proteins called caspases that ultimately digest the cell from the inside out. While great strides have been made in identifying the core apoptotic machinery that dismantles the cell, we still know relatively little about how the process begins. In particular, we are largely ignorant of how cells sense internal damage (say in response to misfolded proteins), determine if the damage is lethal, and then relay this information to the apoptotic machinery. We have several projects ongoing to discover the signaling pathways and components that cells employ to commit suicide in response to internal damage so that we can find new targets to intervene.

When Cancer Cells Refuse to Die

Neuroendocrine tumors (e.g. carcinoids) are one class of solid tumor that may be particularly sensitive to protein folding stress due to their high protein secretory activity. Derived from professional secretory cells, neuroendocrine tumors can arise in many sites (e.g. gastro-intestinal tract, lung), but these tumors universally hypersecrete one or more peptide hormone(s). For the nearly 12,000 Americans diagnosed with a neuroendocrine tumor each year, surgery is the only potentially curative treatment. Unfortunately, the five year survival is extremely low for the ~25% of patients who develop metastatic disease.

We have compelling evidence that the adaptive UPR is upregulated and required for the growth of pancreatic neuroendocrine tumors (PanNETs), a representative model for this class of secretory solid tumors. We are using a variety of genetic, chemical-genetic, and pharmacological tools developed in our laboratory to selectively activate or disable the UPR master regulators in preclinical models of PanNETs with the hope of identifying new therapies for patients with this cancer.