Paneth cells are specialized intestinal epithelial cells that are located at the base of small intestinal crypts and play a vital role in preserving the gut epithelium homeostasis. Paneth cells act as a safeguard from bacterial translocation across the epithelium and constitute the niche for intestinal stem cells in the small intestine by providing multiple niche signals. Recently, Paneth cells have become the focal point of investigations defining the mechanisms underlying the epithelium-microbiome interactions and pathogenesis of chronic gut mucosal inflammation and bacterial infection. Function of Paneth cells is tightly regulated by numerous factors at different levels, while Paneth cell defects have been widely documented in various gut mucosal diseases in humans. The post-transcription events, specific change in mRNA stability and translation by RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) are implicated in many aspects of gut mucosal physiology by modulating Paneth cell function. Deregulation of RBPs and ncRNAs and subsequent Paneth cell defects are identified as crucial elements of gut mucosal pathologies. Here, we overview the posttranscriptional regulation of Paneth cells by RBPs and ncRNAs, with a particular focus on the increasing evidence of RBP HuR and long ncRNA H19 in this process. We also discuss the involvement of Paneth cell dysfunction in altered susceptibility of the intestinal epithelium to chronic inflammation and bacterial infection following disrupted expression of HuR and H19.

Long noncoding RNA uc.173, transcribed from ultraconserved regions, modulates many cell processes central to human pathologies, but the mechanism underlying uc.173 in the homeostasis of the intestinal epithelium is underexplored. Here, we investigated the role of uc.173 in regulating mitochondrial metabolism and defined the implication of altered mitochondrial activity by uc.173 in renewal of the intestinal mucosa. Studies were conducted in CRISPR-Cas9 knock-in mice, primary enterocytes, and Caco-2 cells. Mitochondrial structure and function were elucidated by measuring mitochondria-associated proteins and mitochondrial respiratory capacity. Intestinal mucosal growth was measured by Ki67 immunostaining or BrdU incorporation assays. Transient and specific deletion of uc.173 in the intestinal epithelium of mice by CRISPR-Cas9 knock-in using small guide RNA decreased the levels of several mitochondria-associated proteins including PGC-1α, along with disrupted mucosal growth. Decreasing the levels of uc.173 in cultured intestinal epithelial cells also decreased mitochondrial proteins and caused defects in the mitochondrial respiratory capacity. Reinforcing mitochondrial activity by using a mitochondrial activator or by overexpressing PGC-1α rescued growth of uc.173-deficient intestinal organoids. Mechanistic studies revealed that uc.173 increased PGC-1α expression by acting as a molecular decoy for miR-29b, thereby preventing the repressive interaction of miR-29b with PGC-1α mRNA. These findings indicate that uc.173 is a novel regulator of mitochondrial metabolism in the intestinal epithelium and highlight a role of deregulation of uc.173, miR-29b, and PGC-1α in the suppressed renewal of intestinal mucosa in patients with critical illnesses.

Disruptions in the integrity of the intestinal epithelium occur commonly in inflammatory bowel disease (IBD) and critical surgical disorders, but the underlying mechanisms remain largely unknown. Here we identified long noncoding RNA GAS5 as a repressor of intestinal mucosal growth and the function of the gut epithelial barrier. The levels of tissue GAS5 / Gas5 increased in mouse intestinal mucosa after colitis and septic stress, as well as in human intestinal mucosa from patients with IBD. Transient and tissue-specific knockdown of Gas5 in mice using CRISPR/Cas9 enhanced the renewal of the mucosa of the small intestine, increased the levels of tight junction (TJ) proteins ZO-1, ZO-2, claudin-1, and claudin-2, and improved gut barrier function. Conversely, ectopic overexpression of GAS5 in intestinal organoids and in cultured intestinal epithelium cells decreased the levels of these TJ proteins and caused epithelial barrier dysfunction. Mechanistic studies revealed that GAS5 acted as a transcriptional enhancer of the gene encoding small noncoding vault RNAs (vtRNAs) and that GAS5 repressed TJ expression by increasing the levels of vtRNAs. Together, our results indicate that GAS5 disrupts the integrity of the intestinal epithelium by impairing mucosal growth and epithelial barrier function and that it represses TJ expression, at least in part, via vtRNAs.

The mammalian intestinal epithelium is a rapid self-renewal tissue in the body, serving as a critical interface between the host and the external environment. Maintaining the intestinal epithelium homeostasis requires precise coordination of cellular processes, including proliferation, migration, differentiation, autophagy, and cell-to-cell interaction. An increasing body of evidence has unveiled circular RNAs (circRNAs) as abundant and stable regulatory molecules that play pivotal roles in the intestinal epithelial biology and are intimately involved in many aspects of gut mucosal pathologies. Unlike linear RNAs, circRNAs form covalently closed loop structures through back-splicing events, conferring remarkable stability and resistance to exonucleolytic degradation. circRNAs regulate the growth of the intestinal mucosa, injury-induced epithelial regeneration, and gut barrier function via diverse mechanisms, including interactions with microRNAs and RNA-binding proteins. Deregulated circRNAs are implicated in the pathogenesis of various gut mucosal disorders such as inflammatory bowel disease and malignancies. In this review, we highlight pathobiological functions and mechanisms of intestinal epithelium-enriched circRNAs, particularly circHIPK3, Cdrlas, and circPABPN1, in the epithelium homeostasis and pathologies and also discuss potential clinical application of circRNAs as diagnostic biomarkers and therapeutic targets in patients with critical diseases.

The mammalian intestinal epithelium is a rapid self-renewing tissue that functions as a physical barrier against a wide array of noxious substances and the gut microbiome that inhabit the intestinal lumen. Homeostasis of the intestinal epithelium is tightly regulated via well-controlled mechanisms and depends on rapid gene expression pattern alterations to effectively regulate cell survival, adapt to stress, and keep epithelial integrity in stressful environments. Vault RNAs (vtRNAs) are small noncoding RNAs that are highly expressed in the intestinal epithelium and involved in many cellular processes essential for healthy and pathological states. In this review, we provide a broad discussion of vtRNA biogenesis, the roles of vtRNAs in intestinal mucosal renewal and gut barrier function regulation, and the interactions of vtRNAs with RNA-binding proteins in modulating mRNA stability and translation. We also highlight the implications of vtRNAs in human gut mucosal disorders and point out vtRNAs as potential biomarkers and/or novel targets for developing new diagnostic and/or therapeutic modalities for identifying and preserving the integrity of the intestinal epithelial lining in patients with critical disorders.

Background/Objectives: Intestinal mucosal function relies on the integrated contribution of multiple cell lineages, including secretory cells. Long noncoding RNA H19 modulates many cell processes essential for human pathologies. Here, we investigated the role of H19 in development and function of secretory lineage cells and elucidated the implication of altered ATOH1 by H19 in dysfunction of the secretory cells. Methods: Studies were conducted in H19-transgenic (H19-Tg) and H19-knockout (H19^−/−) mice, intestinal organoids, and Caco-2 cells. Secretory lineage cells were examined by fluorescent immunostaining with their specific cell markers, including Lysozyme, Mucin2, DCLK1, and Chromogranin A. Intestinal mucosal growth was measured by BrdU incorporation, and intestinal permeability was detected by paracellular tracer flux assay using FITC-Dextran. Single cell RNA-sequence, quantitative real-time PCR, and Western immunoblotting analyses were used to monitor changes in gene expression. Results: Tissue-specific transgenic expression of H19 in the intestinal epithelium caused defects in Paneth, goblet, tuft, and enteroendocrine cells in mice, whereas targeted deletion of the H19 gene increased the function of secretory lineage cells. Locally increasing the levels of H19 in the epithelium impaired gut barrier function in H19-Tg mice, although it failed to alter mucosal growth. The intestinal mucosal tissues of H19-Tg mice exhibited a remarkable decrease in the levels of differentiation-associated transcription factors including ATOH1. Ectopically expressed ATOH1 in the H19-enriched intestinal organoids derived from H19-Tg mice rescued development of the secretory lineage cells. Mechanistically, H19 inhibited ATOH1 expression via inhibition of its translation. Conclusions: These findings indicate that H19 functions as a negative regulator of differentiation and function of secretory lineage cells in the intestinal mucosa at least partially via the inhibition of ATOH1 translation.