As specialized and secretory IECs in the small intestinal mucosa, Paneth cells produce a variety of antimicrobial peptides and proteins [25,30]. Because the surfaces of the small intestinal mucosa are constantly awash with bacteria and their products, Paneth cells continuously synthesize and release antimicrobials at a baseline rate via granule secretion mechanism, with increased amounts secreted on maximum stimulation. In response to bacterial infection, for example, these antimicrobial-rich granules in Paneth cells are released into the crypt lumen, where increased accumulations of antimicrobials prevent bacterial invasion of the crypt and protect the epithelium against infections by enteric pathogens [37,40]. Many antimicrobial proteins/peptides destroy their target bacteria by impairing integrity of the membrane, but some peptides/proteins specifically repress bacterial cell wall synthesis through the association with lipid II [41]. Defensins are a major family of antimicrobial peptides in mammals, and Paneth cells produce many antimicrobial peptides and proteins that are evolutionally related to α-defensins. The α-defensins are only expressed in Paneth cells in mice and contributes to the enteric innate immunity [25,26]. Availability of enteric α-defensins and its impact on epithelial defense are markedly linked to Paneth cell function and homeostasis. Mice overexpressing the Defa5/6 gene exhibit Paneth cell dysfunction, along with a significant alteration in the composition of resident ileal microbiota, similar to those observed in IBD patients [28]. As altered microflora in human is implicated in pathogenesis of IBD, the quantity and the repertoire of Paneth cell α-defensins and other-related genetic products in such condition alter gut mucosal defense and affect the epithelial integrity by constituting a healthy microbiota or by increasing risk to inflammation and infections in genetically predisposed individuals [28,29,37,40].

Several studies have demonstrated the necessity of autophagy in Paneth cells, including formation of secretory granules, secretion of antimicrobial peptides and/or proteins, and control of host immunity [10,11,13,26,27]. As a conserved intracellular pathway, autophagy sequesters the cytoplasmic structures and pathogens involved in the process of degradation [31,42]. Autophagy is required for maintaining normal structure and function of various cellular organelles such as ER and mitochondria in Paneth cells, while lysozyme secretion by Paneth cells is mediated via secretory autophagy to limit intestinal bacterial infection [26,31]. Mutation of the autophagy-related genes (Atgs) leads to dysfunctional mitochondria and ER and subsequent defects in Paneth cells, thus enhancing the release of inflammatory cytokines in dextran sulfate sodium-induced colitis in mice and other pathological conditions [31,32,37,40,43]. Mice with hypomorphic IBD-associated allele Atg16L1 exhibit reduced Paneth cells, which is associated with an inhibition of secretory granule formation, a decrease in lysozyme synthesis, and an increase in inflammatory cytokines by macrophages [32,33]. The Atg16L1 deletion in mice causes abnormal alterations such as Paneth cell number, organoid assembly, granule structure, and secretion of antimicrobial peptides [4,29,32]. Loss of Atg4B, Atg5, or Atg7 genes also results in Paneth cell defects; all these findings suggest that autophagy plays a critical role in the control of Paneth cell function [22,32].

The human small intestinal epithelium undergoes ~10¹¹ mitoses/day and this rapid and dynamic turnover rate is driven by ISCs, which are tightly regulated by multiple factors at different levels [16,33]. ISCs divide daily and produce bipotent progenitors amplifying and differentiating into absorptive or secretory lineages [12,33]. Paneth cells create the niche for ISCs in the crypts and provide many secreted as well as surfaced-bound niche signals [11,12]. The Paneth cell niche is the microenvironment in which ISCs both reside and receive stimulations that determine their fate in vivo. Emerging evidence indicates that interactions between Paneth cells and ISCs in the intestinal crypts are essential for continuous and rapid intestinal epithelial renewal under various pathophysiological conditions [27,44]. Coculturing of sorted Paneth cells with ISCs dramatically enhances intestinal organoid formation and growth [12], whereas Paneth cell defects results in ISC dysfunction and leads to an inhibition of intestinal mucosal growth [12,27]. In the case of Paneth cell ablation, enteroendocrine and Tuft cells and intestinal stromal cells can also support ISC function [11,45,46].