Innate Immunity and Bacterial Pathogenesis

All living things must defend themselves against infection — this is the job of the immune system. In the Vance Lab, we focus on the initial events that occur upon the first encounter between a host and a pathogen. In particular, we are interested in answering two fundamental questions: (1) how does the innate immune system detect pathogens? and (2) how are pathogen infections distinguished from benign encounters with harmless microbes?

We study a diversity of different infection models and use a variety of experimental techniques, from structural biology to biochemistry to genetics to in vivo studies. Despite our varied experimental approach, several themes recur in our studies. For example, we focus primarily on bacterial infections. We are also particularly interested in pathogen sensors that are situated in the cytosol of host cells. And lastly, we are interested in how the immune system detects pathogen-encoded activities, what we have termed “patterns of pathogenesis“.

Currently the lab is working in several areas:

Inflammasomes: guardians of the host cell cytosol

Cryo-EM structure of the NAIP5/NLRC4 inflammasome

Inflammasomes are multi-protein complexes that assemble in the cytosol of host cells upon detection of various noxious or infectious stimuli. Once assembled, inflammasomes serve as a scaffold for the dimerization and activation of inflammatory caspases, most notably, Caspase-1. Cells express several different inflammasomes, each of which is responsive to distinct stimuli. The Vance Lab has focused primarily on two inflammasomes: the NAIP/NLRC4 inflammasome that detects bacterial proteins such as flagellin; and the NLRP1 inflammasome that detects pathogen-derived toxins and enzymes.

NAIP5/NLRC4: In collaboration with the Nogales Lab on campus, we recently solved the structure the NAIP/NLRC4 inflammasome bound to flagellin (pictured above). Our paper provides insights into how flagellin is detected and why pathogens cannot easily mutate flagellin to escape detection. We have also recently studied the function of the NAIP5/NLRC4 inflammasome in defense against Salmonella infection, and in auto-inflammatory disease.

NLRP1: The NLRP1 inflammasome provides resistance against infection with Bacillus anthracis, the causative agent of anthrax, but the mechanism by which NLRP1 is activated has been mysterious. We showed that proteolytic cleavage of NLRP1 results in its activation. In a recent preprint, we provide evidence for a surprising mechanism of NLRP1 activation in which NLRP1 becomes activated as a consequence of its proteasome-mediated degradation.

We are continuing structural and functional studies of inflammasomes. We want to better understand their roles during infection and adaptive immune responses.

Cytosolic sensing of cyclic-di-nucleotides and nucleic acids

Structure of STING from the sea anemone Nematostella vectensis

A series of fortuitous observations led us to discover that bacterial molecules called cyclic-di-nucleotides stimulate a specific innate immune response characterized by the production of type I interferons. By using random chemical mutagenesis of mice, we discovered that a host protein called STING is essential for the cytosolic interferon response to cyclic-di-nucleotides. We further showed that STING is a direct cytosolic receptor for cyclic-di-nucleotides. It was subsequently shown by the Chen lab that cyclic-di-nucleotides are not unique to bacteria but are also produced by a cytosolic DNA sensor protein called cGAS. We then showed that the cyclic-di-nucleotides produced by cGAS have a unique chemical structure that allows them to potently stimulate human STING.

We have recently become particularly interested in the evolutionary origins of the STING protein. We were surprised to discover that even sea anemone, organisms that diverged from humans more than 500 million years ago, encode a functional STING protein that binds cyclic-di-nucleotides (pictured above). Sea anemone lack type I interferons, so an important question we are currently pursuing is: what is the evolutionarily ancient function of STING? and is this function conserved in mammalian STING?

Legionella pneumophila: detection of  pathogen-encoded activities

Legionella pneumophila (transmission EM stylized in photoshop)

L. pneumophila is a bacterium that is the causative agent of a severe pneumonia called Legionnaires’ Disease. We are interested in how the innate immune system detects L. pneumophila. In fact, our initial studies on L. pneumophila were what led us to identify the NAIP/NLRC4 inflammasome as an important sensor of flagellin. Our work on L. pneumophila also led to our interest in cyclic-di-nucleotides. More recently, we showed that additional innate sensing pathways also contribute to immune recognition of L. pneumophila. For example, we discovered an unusual immune response that is triggered upon blockade of host protein synthesis by L. pneumophila. This response appears to be critical for the initial immune response to L. pneumophila in the lung. We used ribosome profiling to show that this response depends upon a dramatic transcriptional superinduction of specific alarm signals called cytokines.

One of the most remarkable aspects of L. pneumophila is that its natural host cells are freshwater amoebae, yet L. pneumophila is still able to cause disease in humans. The broad host range of L. pneumophila has been attributed to its large arsenal of ‘effector’ proteins, enzymes that the bacterium secretes into host cells. In fact, L. pneumophila encodes over 300 such effectors, comprising approximately 10% of its protein-coding capacity. Most of the effectors are of unknown function, but one of our recent papers demonstrated that several L. pneumophila effectors appear to modulate host cell metabolism, and in particular, affect the function of the master metabolic regulator mTOR. We speculate that modulation of mTOR by L. pneumophila is part of the strategy this pathogen uses to obtain nutrients from host cells.

Mycobacterium tuberculosis

Recently, we have become particularly interested in applying our knowledge of innate immunity to an important globally significant pathogen. Mycobacterium tuberculosis, the causative agent of tuberculosis, is the single pathogen responsible for more human deaths than any other viral, bacterial or protozoan pathogen. M. tuberculosis was discovered by Robert Koch in 1882, but we remain largely ignorant about fundamental aspects of its microbiology and immunopathogenesis. Our current studies on M. tuberculosis were stimulated by a sabbatical visit from Heran Darwin. In addition, we are lucky to have two great colleagues at Berkeley, Jeff Cox and Sarah Stanley, who have helped us cope with the technical challenges of working with this BSL3 organism. We are attempting to utilize mouse genetic approaches to identify critical host factors that mediate susceptibility and resistance to M. tuberculosis.