Nearly optimal Bayesian Shrinkage for High Dimensional Regression

During the past decade, shrinkage priors have received much attention in Bayesian analysis of high-dimensional data. In this paper, we study the problem for high-dimensional linear regression models. We show that if the shrinkage prior has a heavy and flat tail, and allocates a sufficiently large probability mass in a very small neighborhood of zero, then its posterior properties are as good as those of the spike-and-slab prior. While enjoying its efficiency in Bayesian computation, the shrinkage prior can lead to a nearly optimal contraction rate and selection consistency as the spike-and-slab prior. Our numerical results show that under posterior consistency, Bayesian methods can yield much better results in variable selection than the regularization methods, such as Lasso and SCAD. We also establish a Bernstein von-Mises type results comparable to Castillo et al (2015), this result leads to a convenient way to quantify uncertainties of the regression coefficient estimates, which has been beyond the ability of regularization methods

Roles of Cytosolic Nucleic Acid Sensors in Cancer and Infection

Pattern recognition receptors are innate immune sensors that recognize pathogen-associated molecular patterns (PAMPs) and danger-associated molecular patterns (DAMPs) with crucial roles in host defense against microbial infection, autoimmune diseases and cancer. Cytosolic nucleic acids including DNA and RNA originate from pathogens or self-cells, which form major groups of PAMPs and DAMPs. A range of nucleic acid sensors have evolved to sense various types of nucleic acids. How different DNA-sensing pathways regulate microbial infection and cancer is the focus of this dissertation. Stimulator of IFN genes (STING) is a cytosolic innate immune sensor for cyclic dinucleotides that also serves a dual role as an adaptor molecule for a number of intracellular DNA receptors. A physiological role for STING in cancer was previously unknown. We showed that STING-deficient mice were highly susceptible to colitis-associated colorectal cancer. Colons of STING-deficient mice exhibited significant intestinal damage and overt proliferation with increased levels of pro-inflammatory cytokines during early stages of tumorigenesis, uncovering an unexpected and important role for STING in mediating protection against colorectal tumorigenesis. Absent in melanoma 2 (AIM2) forms an inflammasome with ASC and caspase-1 upon recognition of double-stranded DNA (dsDNA) in the cytosol leading to caspase-1 activation and caspase-1-dependent pyroptosis and release of cytokines IL-1 and IL-18. Mutations in AIM2 are frequently identified in patients with colorectal cancer, but how AIM2 modulates colonic tumorigenesis is unknown. We found that AIM2-deficient mice were hypersusceptible to colonic tumor development. While production of inflammasome-associated cytokines and other inflammatory mediators was largely intact in AIM2-deficient mice, intestinal stem cells lacking AIM2 were prone to uncontrolled proliferation. Aberrant Wnt signaling expanded a population of tumor-initiating stem cells in the absence of AIM2 driving the tumor development in AIM2-deficient mice. In addition to its role in cancer, AIM2 recognizes bacteria including Francisella tularensis subspecies novicida (F. novicida) and induces inflammasome responses. Type I interferon (IFN) signaling drives activation of AIM2 inflammasome in F. novicida-infected macrophages; however, the relative contribution of IFNs and inflammasome responses in host defense against F. novicida infection is less understood. We found intact AIM2 inflammasome responses in mice lacking type I IFN signaling during infection with F. novicida. Lack of type I IFN signaling conferred protection to F. novicida infection in contrast to the increased susceptibility in AIM2-deficient mice. Interestingly, mice lacking both AIM2 and IFNAR2 were protected against the infection indicating a dominant role for type I IFNs in mediating detrimental responses despite the protective AIM2 inflammasome responses. Gasdermin D (GSDMD) is activated by caspase-1 to generate pores on the plasma membrane to induce pyroptosis downstream of the AIM2 inflammasome. We also demonstrated that mice lacking GSDMD were highly susceptible to F. novicida infection. Interestingly, GSDMD is required for optimal caspase-1 activation during F. novicida infection, providing protection to the host during the infection. In addition, we identified differential mechanisms regulating expression of inflammasome-associated cytokines IL-1β and IL-18. IL-1β is only induced in response to inflammatory stimuli and its expression is not sustained during chronic treatment, while IL-18 is constitutively expressed and further induced after the stimulation in a type I IFN signaling-dependent manner. Overall, this dissertation addresses protective roles for cytosolic nucleic acid-sensing molecules, STING and AIM2, in colon cancer, uncovers an interplay between the AIM2 inflammasome and type IFN signaling during F. novicida infection, and demonstrates a novel function for GSDMD in regulating AIM2 inflammasome. The dissertation finally describes distinctive mechanisms governing inflammasome-associated cytokines IL-1β and IL-18