research image Zaki Lab

Zaki Lab's research focuses on the the study of gastrointestinal inflammation and cancer.

Recognition of pathogens and danger signals by the host immune system represents an important physiological event that is critically important for host defense against infectious diseases as well as non-infectious diseases, including inflammation and tumorigenesis.  A classic example of maintenance of immune homeostasis and regulation of diseases by host-pathogen interaction is the gastrointestinal system where trillions of microorganisms reside. While interactions of intestinal immune and epithelial cell population with the commensal bacteria and their products ensures an immune homeostasis, a defect in the host’s pathogen recognition system leads to various disorders such as gastrointestinal infections, inflammatory bowel disease (IBD), and gastric and colorectal cancer. Therefore, understanding the physiological functions of pathogen recognition receptors and exploring the role of those receptors in the pathogenesis of intestinal inflammatory disease and cancer is cutting edge.

There are several dedicated pathogen recognition receptors in biological systems, including membrane-bound Toll-like Receptors (TLRs), and cytosolic NOD-like Receptors (NLRs), RIG-I like receptors (RLR) and C-type lectine like receptors (CTLR). Our research is primarily focused on characterizing the functions of NLRs in infection, inflammation, and cancer of the gastrointestinal system. More than 20 NLRs have been identified which have multiple biological functions, including activation of NF-kB and MAPK, activation of inflammasome, and inhibition of inflammatory signaling pathways (Fig 1).

At least three different NLRs (NLRP3, NLRP1, and NLRC4) form the scaffolding complex called inflammasome in association with an adapter molecule ASC and caspase-1. Inflammasome-mediated activation of caspase-1 is essential for cleavage and secretion of IL-1b and IL-18, which play central roles in inflammation and immunity. Several other NLRs such as NLRP12, NLRC5, NLRX1, and NLRP6 have been shown to regulate multiple diseases, but the precise mechanism through which these NLRs exert their physiological functions is not well understood.

The major focus of my laboratory is to characterize the cellular and molecular mechanisms of NLR-mediated regulation of intestinal inflammation and cancer.

Research Projects

    We previously demonstrated that NLR family members NLRP3 and NLRP12 play important roles in host defense against colorectal tumorigenesis. A role for other NLRs such as NOD2 and NLRP6 in the pathogenesis of colorectal cancer has also been described. However, detailed mechanisms of NLRs-mediated protection against colorectal tumorigenesis are largely unknown. Colorectal tumorigenesis is a multistep process, which is initiated by mutations in several cancer suppressor genes such as b-catenin, p53, and KRAS, and facilitated by production of inflammatory mediators in the tumor microenvironment. Hence, we are interested in exploring the role of NLRs in regulating cancer signaling pathways and tumor microenvironment. The following questions are being addressed in our research:

    • Do defects in NLR signaling increase mutational frequency in cancer suppressor genes in colorectal cancer stem cells?
    • Do NLRs interact with molecules in cancer signaling pathways?
    • How do different NLRs regulate the tumor microenvironment in the colon?
    • How do NLRs regulate cellular proliferation and cell cycle progression?

    We are using both in vivo animal models and in vitro cell culture-based approaches to address these concerns.

    IBD and other intestinal inflammatory disorders are initiated with an aberrant immune response to intestinal microbiota and their products. Mounting evidence suggests that the presence of certain bacterial species, e.g. Prevotellaceae, TM7, BacteriodsClostridium difficile, etc., predisposes IBD susceptibility and enhances the severity of the disease. A major concern in IBD research is how the host immune system regulates the microbial ecology in the gut. Studies from our laboratory and others have demonstrated the development of altered microbiota in several NLR-deficient mice. However, how NLRs regulate the microbial ecology is less understood. A major focus of our laboratory is to study the relationship between NLRs and gut microbiota. In particular, we will address the following issues:

    • Do NLRs regulate gut microbiota?
    • What is the mechanism of NLR-mediated regulation of gut microbiota?
    • How do microbiota shape mucosal immune response?
    • Does dysbiosis in NLR-deficient mice contribute to the IBD pathogenesis?

      The intestinal epithelial barrier segregates commensal bacteria from mucosal tissue and provides the first line of defense against intestinal inflammation. A dysfunction in intestinal epithelium leads to a compromised host defense against colonization and invasion of commensal flora into lamina propia, triggering exuberant inflammatory responses. We previously showed that the NLRP3 inflammasome is a critical regulator of the intestinal epithelial barrier. However, the molecular mechanism of how the NLRP3 inflammasome regulates the intestinal epithelial barrier is not clearly understood.

      Our current research is investigating how NLRP3 and other inflammasomes regulate epithelial cell proliferation and function. To address this issue, we will take advantage of an in vitro epithelial crypt culture system, which we have established in our laboratory. By investigating the mechanism of NLR-mediated regulation of epithelial barrier permeability, we may identify treatment measures for the inflammatory ailments of the gastrointestinal tract. 

      Since their discovery more than a decade ago, several members of the NLR family have been genetically linked with multiple inflammatory diseases. Experimental studies also have provided mounting evidence of critical roles NLRs play in health and diseases. However, among 22 human NLRs, only a few have been characterized so far. A major challenge in this field is to explore the precise biological role of these NLRs.

      Our laboratory is particularly interested in dissecting the physiological function of NLR member NLRP12. We recently demonstrated that mice deficient in NLRP12 are highly susceptible to colitis and colitis-associated colorectal tumorigenesis. Increased inflammation in the colon of NLRP12-deficient mice was associated with increased NF-kB activation, which was further supported by in vitro study showing increased activation of NF-kB in LPS-stimulated NLRP12-deficient macrophages compared to that in wild-type. We, therefore, hypothesize that NLRP12 is a negative regulator of NF-kB signaling pathway. We are now investigating the molecular mechanism of NLRP12-mediated regulation of NF-kB activation.

      Toward this goal, we have developed stable macrophage cell lines expressing NLRP12. Using biochemical and proteomic approaches, we will identify the molecular partners of NLRP12 and explore the physiological function of NLRP12. This study will help to design drugs to treat IBD, colorectal cancer, and other inflammatory disease via manipulation of the NLRP12 signaling pathway.

      Join Our Lab

      Be part of the great impact we're having on science.

      To learn more about opportunities available at Zaki Lab, please reach out to us below with your information.