Laboratory of Xian-Ming Chen, MD

Mucosal surfaces, such as the gastrointestinal (GI), respiratory, and urogenital tracts, are a key portal of entry for the majority of medically relevant infectious diseases. Epithelial cells along the mucosal surface provide the front line of defense against luminal pathogen infection and are an important component of mucosal immunity. Dysfunction of epithelial immune functions contributes to the development of most of infectious diseases and causes a significant morbidity, mortality, and cost to the society. Pattern recognition receptors (PRRs) (e.g., Toll-like receptors) and their associated downstream signaling cascades (e.g., the NF-ĸB signaling pathway) are key to mucosal immune defense and have been implicated in secretion of antimicrobial peptides, release of cytokines/chemokines and exosomes to mobilize immune effector cells, and activation of adaptive immunity. Specifically, the PRR/NF-ĸB signaling carries out a finely controlled procedure that orchestrates the transactivation of immune genes “at the right place at the right time” in epithelial cells. Genomic research has revealed the existence of many non-coding RNAs (ncRNAs) in mammalian cells. Several classes of ncRNAs, including the long ncRNAs (lncRNAs), have been shown to play key regulatory roles in diverse biological functions, including development, maintenance of genome stability, regulation of cell signaling and proliferation in mammalian cells. Our general hypothesis is that ncRNAs participate in the regulation of defense responses in innate immune cells and mucosal epithelial cells; disorder of such regulation contributes to the pathogenesis of various inflammatory/infectious/malignant diseases (e.g., intestinal cryptosporidiosis) at the mucosal surfaces in humans; thus, ncRNAs may represent new targets for therapeutic interventions.

Our work

First, we are investigating the role of PRR-responsive lncRNAs in the regulation of inflammatory and defense responses in innate immune cells and intestinal epithelial cells, particularly transcriptional and posttranscriptional regulation of key inflammatory genes. It is well-recognized that PRRs and their associated downstream signaling cascades (e.g., the PRR/NF-ĸB signaling pathway) are key to mucosal immune defense. What remains unknown is the key cellular regulatory elements that determine PRR-mediated intestinal epithelial antimicrobial defense, and its association with the high susceptibility of infection in immunocompromised (AIDS) patients and in young children. We have identified a subclass of lncRNA genes that are expressed strictly in epithelial cells. Expression levels of several epithelial cell-derived lncRNAs are upregulated in GI epithelial cells following microbial infection through the PRR signaling pathway. Knockdown of selected epithelial cell-derived lncRNAs attenuated IFN-γ-mediated epithelial antimicrobial defense. Using complementary biochemical, molecular, and morphologic approaches, we are working to define the transcription of PRR-responsive and epithelial cell-derived lncRNA genes upon PRR signaling in GI epithelial cells following microbial infection, elucidate the molecular mechanisms by which epithelial cell-derived lncRNAs promote IFN-mediated epithelial defense, and decipher the roles of specific RNA-binding proteins in modulating IFN-mediated innate defense in GI epithelial cells through their interactions with epithelial cell-derived lncRNAs.

Second, we have conducted ground-breaking studies on the molecular mechanisms by which the protozoan parasite Cryptosporidium interacts with host epithelial cells and causes intestinal cryptosporidiosis. Cryptosporidium is a ubiquitous pathogen that infects the GI epithelium in humans and ruminants. This parasite is of great medical importance as infections in immunocompromised humans, including AIDS, cancer, and infections in transplant patients, often lead to life-threatening illness. A recent massive clinical and epidemiological study revealed that Cryptosporidium is one of the most common pathogens (second only after rotavirus) responsible for moderate-to-severe diarrhea in children under two years of age in developing countries. There is currently no fully effective therapy available for the infection. Using in vitro, ex vivo (enteroids) and in vivo models of cryptosporidiosis, we are investigating how Cryptosporidium invades host epithelial cells and the pathologic significance of delivery of specific parasite RNA molecules into host cells during and after internalization, including modulation of epigenetic gene regulation in infected host cells. We hypothesize that cryptosporidial infection induces epigenetic histone methylations in host cells through nuclear delivery of specific parasite RNAs, resulting in transcriptional suppression of genes in infected host epithelial cells. Moreover, Cryptosporidium infection also causes disturbances in intestinal homeostasis through its impact on intestinal stem cells, contributing to the long-lasting effects of infection in the gut.

In related studies focusing on the molecular signatures that may link mucosal inflammation to tumorigenesis and other infectious diseases, we are testing a potential role for lncRNAs and RNA methylations. Increasing evidence suggests that oncogenic PRR/NF-ĸB activation, as well as recently identified oncogenic RNA methylations, promotes epithelial tumor initiation and progression. We propose that oncogenic activation of PRR/NF-ĸB signaling may link chronic mucosal inflammation to the initiation and development of epithelial carcinoma through lncRNA-associated RNA methylations and epigenetic chromatin remodeling. Discerning the underpinning mechanisms of the link between inflammation and malignancy could advance the knowledge of tumor progression of GI epithelial carcinoma, as well as association between GI inflammation and the pathogenesis of diseases in other organs/systems.

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Technology and methods

  • RNA-DNA interaction measurement/assessment
  • RNA-protein interaction measurement/assessment
  • 3D enteroids and 2D enteroid/monolayers
  • Exosome purification and measurement/assessment

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Publications

Complete list of published work on PubMed

Complete list of published work on Scopus

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Funding

Current grants

Past grants

  • NIH U01-AI095532 : “Epithelial exosomes and TLR-mediated mucosal defense.”    Principal investigator: Dr. Chen    
  • NIH MIST_Pilot : “Epithelial lincRNAs in mucosal antimicrobial defense.” Principal investigator: Dr. Chen
  • DoD-PC121561 : “LincRNAs and AR reactivation in prostate cancer cells.” Principal investigator: Dr. Chen
  • NIH R01-DK057993: “Pathophysiology of Biliary Cryptosporidiosis.” Principal investigator: Dr. LaRusso; Co-Investigator: Dr. Chen
  • NIH R01-AI071321 : “microRNAs in Epithelial Innate Immunity to C. parvum.” Principal investigator: Dr. Chen

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Our team

Silu Deng, MD, Visiting PhD Graduate Student
Ai-Yu Gong, MD, MS, Research Scientist
Marion L. Graham, MS, PhD Candidate
Kanika Sharma, MS, Research Lab Tech 2
Zinat Sharmin, PhD, Postdoctoral Fellow
Shuhong Wang, MS, PhD Candidate

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Contact

Xian-Ming Chen, MD
Professor
Department of Microbial Pathogens and Immunity
Rush University Medical Center
1735 W. Harrison St.
Cohn Building, Suite 624
Chicago, IL 60612
Phone (office): (312) 563-1988
Phone (lab): (312) 942-3025 and (312) 942-3098
Email: xian_m_chen@rush.edu

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