Loss-of-function SLC30A2 mutants are associated with gut dysbiosis and alterations in intestinal gene expression in preterm infants

Abstract

Loss of Paneth cell (PC) function is implicated in intestinal dysbiosis, mucosal inflammation, and numerous intestinal disorders, including necrotizing enterocolitis (NEC). Studies in mouse models show that zinc transporter ZnT2 ( SLC30A2 ) is critical for PC function, playing a role in granule formation, secretion, and antimicrobial activity; however, no studies have investigated whether loss of ZnT2 function is associated with dysbiosis, mucosal inflammation, or intestinal dysfunction in humans. SLC30A2 was sequenced in healthy preterm infants (26–37 wks; n = 75), and structural analysis and functional assays determined the impact of mutations. In human stool samples, 16S rRNA sequencing and RNAseq of bacterial and human transcripts were performed. Three ZnT2 variants were common (>5%) in this population: H 346 Q, f = 19%; L 293 R, f = 7%; and a previously identified compound substitution in Exon7, f = 16%). H 346 Q had no effect on ZnT2 function or beta-diversity. Exon7 impaired zinc transport and was associated with a fractured gut microbiome. Analysis of microbial pathways suggested diverse effects on nutrient metabolism, glycan biosynthesis and metabolism, and drug resistance, which were associated with increased expression of host genes involved in tissue remodeling. L 293 R caused profound ZnT2 dysfunction and was associated with overt gut dysbiosis. Microbial pathway analysis suggested effects on nucleotide, amino acid and vitamin metabolism, which were associated with the increased expression of host genes involved in inflammation and immune response. In addition, L 293 R was associated with reduced weight gain in the early postnatal period. This implicates ZnT2 as a novel modulator of mucosal homeostasis in humans and suggests that genetic variants in ZnT2 may affect the risk of mucosal inflammation and intestinal disease.

ZnT2 Is Critical for TLR4-Mediated Cytokine Expression in Colonocytes and Modulates Mucosal Inflammation in Mice

“…A role for ZnT2 in intestinal health in humans has been previously proposed as genetic variants in ZnT2 have been associated with alterations in the gut microbiome and gene expression in the intestinal exfoliome [ 11 ]. A compound substitution in the C-terminus (Exon 7) [ 35 ] impairs Zn transport and is associated with enrichment of nosocomial bacteria and enrichment in intestinal genes associated with cell proliferation and remodeling [ 11 ].…”

“…A role for ZnT2 in intestinal health in humans has been previously proposed as genetic variants in ZnT2 have been associated with alterations in the gut microbiome and gene expression in the intestinal exfoliome [ 11 ]. A compound substitution in the C-terminus (Exon 7) [ 35 ] impairs Zn transport and is associated with enrichment of nosocomial bacteria and enrichment in intestinal genes associated with cell proliferation and remodeling [ 11 ]. A second ZnT2 variant (L 293 R) also predicted to impair Zn transport is associated with profound gut dysbiosis, changes in intestinal gene expression consistent with inflammation, and poor growth in preterm infants [ 11 ].…”

“…Numerous genetic variants in human ZnT2 that result in loss-of-function (LOF) have been identified [ 10 ] which underpins the need to understand the function of ZnT2 in the intestine. In fact, we recently identified two ZnT2 variants, one of which (Exon 7) is associated with enrichment of nosocomial bacteria in the gut and changes in intestinal gene expression consistent with mucosal proliferation and remodeling, while the other (L 293 R) is associated with profound gut dysbiosis, changes in intestinal gene expression consistent with inflammation, and poor growth in preterm infants [ 11 ]. Collectively, this suggests ZnT2 function in the host intestinal epithelium plays an important role in maintaining mucosal homeostasis and is critical for robust response to infectious colitis.…”

Effect of the Microbiome on Intestinal Innate Immune Development in Early Life and the Potential Strategy of Early Intervention

“…PCs are housed in the crypt of the intestine and secrete antimicrobial peptides (AMPs), which are known to defend against pathogen infection ( 36 , 37 ). Furthermore, PCs also play an essential role in intestinal homeostasis and microbiome colonization; for example, loss of PC function is implicated in microbiome dysbiosis and NEC in early life ( 38 , 39 ). It has been found that Cdk5rap3 (a gene that serves a vital role in intestinal PC development and maintenance) knockout resulted in early embryonic lethality, which indicated that embryonic PC function may determine the embryo fate ( 40 ).…”

Myostatin gene deletion alters gut microbiota stimulating fast-twitch glycolytic muscle growth

“…Genetic variation can reshape the structure of the gut microbiota. Mutation in human SLC30A2 leads to reduced intestinal zinc transport and increased Clostridiales and Bacteroidales abundance, causing mucosal inflammation and intestinal dysfunction (Kelleher et al, 2022). Moreover, the gut GLUT1 gene deletion altered the abundances of Barnesiella intestinis and Faecalibaculum rodentium , promoted fat accumulation, and impaired sugar tolerance (He et al, 2022).…”