A host cell long noncoding RNA NR_033736 regulates type I interferon-mediated gene transcription and modulates intestinal epithelial anti-Cryptosporidium defense

Author summary Intestinal epithelial cells are an important component of gastrointestinal mucosal immunity. They generate various types of barriers to protect the intestinal mucosa from commensal microbes or invading pathogenic microorganisms. Upon microbial infection, intestinal epithelial cells quickly initiate a series of innate immune reactions, including production of antimicrobial molecules and release of inflammatory chemokines and cytokines. These chemokines and cytokines of epithelial cell origin may mobilize and activate immune effector cells to the infection sites. One family of these cytokines are type I IFNs (e.g., IFN-alpha/beta), which not only activate other immune effector cells at gastrointestinal mucosa but also stimulate epithelial function through ligation of receptors expressed on intestinal epithelial cells themselves in an autocrine manner. Cryptosporidium is an important opportunistic pathogen in AIDS patients and a common cause of diarrhea in young children in developing countries. Recent advances in Cryptosporidium research have revealed a strong type I IFN response in infected intestinal epithelium. In this study, we provide data demonstrating an important role for long noncoding RNAs (lncRNAs) in regulating type I IFN signaling in intestinal epithelial cells in response to Cryptosporidium infection. LncRNAs are recently identified long non-coding transcripts (>200 nt) that are not translated into protein. We found that upregulation of one host cell lncRNA, NR_033736, displays a significant suppressive effect on type I IFN-controlled gene transcription in intestinal epithelial cells following infection, contributing to the fine-tuning of epithelial anti-Cryptosporidium defense. Our data suggest a new arm of feedback regulation for type I IFN signaling through lncRNA-mediated gene transcription, contributing to fine-tuning of epithelial innate defense against microbial infection in the gastrointestinal tract. The gastrointestinal epithelium guides the immune system to differentiate between commensal and pathogenic microbiota, which relies on intimate links with the type I IFN signal pathway. Epithelial cells along the epithelium provide the front line of host defense against pathogen infection in the gastrointestinal tract. Increasing evidence supports the regulatory potential of long noncoding RNAs (lncRNAs) in immune defense but their role in regulating intestinal epithelial antimicrobial responses is still unclear. Cryptosporidium, a protozoan parasite that infects intestinal epithelial cells, is an important opportunistic pathogen in AIDS patients and a common cause of diarrhea in young children in developing countries. Recent advances in Cryptosporidium research have revealed a strong type I IFN response in infected intestinal epithelial cells. We previously identified a panel of host cell lncRNAs that are upregulated in murine intestinal epithelial cells following microbial challenge. One of these lncRNAs, NR_033736, is upregulated in intestinal epithelial cells following Cryptosporidium infection and displays a significant suppressive effect on type I IFN-controlled gene transcription in infected host cells. NR_033736 can be assembled into the ISGF3 complex and suppresses type I IFN-mediated gene transcription. Interestingly, upregulation of NR_033736 itself is triggered by the type I IFN signaling. Moreover, NR_033736 modulates epithelial anti-Cryptosporidium defense. Our data suggest that upregulation of NR_033736 provides negative feedback regulation of type I IFN signaling through suppression of type I IFN-controlled gene transcription, and consequently, contributing to fine-tuning of epithelial innate defense against microbial infection.