Single-cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis

Identification and Exploration of Pyroptosis-Related Genes in Macrophage Cells Reveal Necrotizing Enterocolitis Heterogeneity Through Single-Cell and Bulk-Sequencing

Necrotizing enterocolitis (NEC) is an acute intestine dysfunction intestinal disorder characterized by inflammation and cell death, including pyroptosis. Previous studies have implicated pyroptosis, particularly via NLRP3 inflammatory activation, and contribute to the development of NEC. However, the genetic and molecular mechanisms underlying pyroptosis in NEC pathogenesis and sequelae remain unclear. Our study aimed to identify the pyroptosis-related cell populations and genes and explore potential therapeutic targets. Single-cell RNA sequencing (scRNA-seq) data were analyzed to identify the cell populations related to NEC and pyroptosis. Weighted gene correlation network analysis (WGCNA) of bulk RNA-seq was performed to identify gene modules associate with pyroptosis. Cell-cell communication was employed to investigate intercellular signaling networks. Gene Set Enrichment Analysis (GSEA) was conducted to compare the pathways enriched in the high and low TREM1-expressing subgroups. Immunofluorescence staining was performed to detect the TREM1+CD163+ macrophages in the intestines. PCR and Western blot were performed to detect the expression of mRNA and proteins in the intestine tissues and cells. scRNA-seq analysis revealed increased macrophage abundance in NEC, with one macrophage cluster (cluster 4) exhibiting a markedly elevated pyroptosis score. WGCNA identified a gene module (MEbrown) that positively correlated with pyroptosis. Five genes (TREM1, TLN1, NOTCH2, MPZL1, and ADA) within this module were identified as potential diagnostic markers of pyroptosis. Furthermore, we identified a novel macrophage subpopulation, TREM1+CD163+, in NEC. Cell-cell communication analysis suggested that TREM1+CD163+ macrophages interact with other cells primarily through the NAMPT/ITGA5/ITGB1 and CCL3/CCR1 pathways. GSEA revealed a significant association between high TREM1 expression and pathways related to pyroptosis, cell proliferation, and inflammation. In vivo and in vitro experiments confirmed an increase in TREM1+CD163+ macrophages in NEC-affected intestines. TREM1 inhibition in THP-1 cells significantly reduced the expression of pro-inflammatory cytokines and pyroptosis-related genes and proteins. We identified the TREM1+CD163+ macrophage population that plays a crucial role in pyroptosis during NEC progression. Our findings elucidate the biological functions and molecular mechanisms of TREM1, demonstrating its upregulation in vivo and pro-pyroptosis effects in vitro. These insights advance our understanding of the role of pyroptosis in NEC pathogenesis and suggest TREM1 is a potential therapeutic target for NEC.

Piezo1 promotes the progression of necrotizing enterocolitis by activating the Ca2(+)/CaMKII-dependent pathway

Necrotizing enterocolitis (NEC) is a devastating inflammatory bowel necrosis of preterm infants with limited therapeutic approaches. Mounting evidence supports the role of Piezo1, namely, a widely distributed mechanosensor in intestinal epithelial cells (IECs), in intestinal inflammation but its underlying mechanism in the development of NEC remains unexplored. In this study, we demonstrated that Piezo1 expression was higher in preterm infants with lower gestational age. C57BL/6J mice wherein Piezo1 was deleted in IECs (villin-specific Piezo1 knockout mice; Piezo1flox/floxVillinCre+) and Piezo1flox/flox littermates were subjected to induce NEC, and Piezo1 knockout regulated the intestinal barrier function, restricted cytokines secretion, and diminished the inflammatory response in NEC mouse models. Piezo1 elevated cytosolic Ca2+ levels and activated Ca2+/calmodulin-dependent protein kinase II (CaMKII) to promote the CaMKII/NF-κB interaction and NF-κB activation in vitro. Finally, the effects of a CaMKII inhibitor, KN93, were evaluated both in vitro and in vivo in NEC models, and the functions of Piezo1 in IECs were suppressed partially by KN93. In this study, we characterise the undefined role of Piezo1 in the development of NEC, which may partially be attributed to the differential role of calcium under pathophysiological conditions.

Mitophagy and immune cell interaction: insights into pathogenesis and potential targets for necrotizing enterocolitis

Background

Neonatal necrotizing enterocolitis (NEC) is a fatal disease in early life characterized by an inflammatory response or even necrosis of the bowel wall. NEC is one of the leading causes of preterm infant mortality. The pathogenesis of NEC is intricate and involves mitochondrial damage to intestinal cells and infiltration of immune cells. However, the specific functions of mitophagy and its association with immune cells in NEC remain unclear. The aim of this study was to explore the pivotal roles of mitophagy and the immune microenvironment in NEC and their potential interactions.

Methods

Microarray data (GSE46619) associated with NEC were obtained from the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI). Differentially expressed genes (DEGs) were screened by GEO2R. Mitophagy gene data were downloaded from the Pathway Unification database and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Consequently, mitophagy-related differentially expressed genes (MRDEGs) were obtained. To identify hub MRDEGs that are closely associated with NEC, we used CytoHubba, Molecular Complex Detection (MCODE) and Comparative Toxicogenomics Database (CTD) scores. Cytoscape and miRWalk databases were used to predict the transcription factors (TFs) and target microRNAs (miRNAs) of hub MRDEGs, respectively, and a regulatory network was established. The ImmuCellAI was used to analyze the pattern of immune infiltration, and the Spearman correlation was used to investigate the relationship between the hub MRDEGs and the abundance of infiltrating immune cells. Finally, the expression levels of the hub MRDEGs were verified by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting in NEC animal model.

Results

A total of 14 up-regulated and 22 down-regulated MRDEGs were identified, these genes exhibited enrichment in mitophagy, and inflammation-related pathways. Furthermore, 13 hub MRDEGs closely related to NEC were identified. The increased presence of immune cells such as neutrophils, M1 macrophages, and activated mast cells were observed while adaptive immune cells including B cells and various T-cell subsets exhibited reduced infiltration. Furthermore, up-regulated MRDEGs were positively correlated with the proinflammatory immune cell infiltration, and the down-regulated MRDEGs were positively correlated with the anti-inflammatory immune cell infiltration. In vivo experiments demonstrated that the expressions of four genes Hif-1a, Acsl4, Pck2, and Aifm1 were consistent with the bioinformatics analysis results.

Conclusions

The potential interplay of mitophagy and immune cells is crucial in the onset and progression of NEC. This perspective opens the door for deeper investigations into NEC pathogenesis, presenting a possible target for disease intervention.

Epigenetic Insights Into Necrotizing Enterocolitis: Unraveling Methylation-Regulated Biomarkers

Necrotizing enterocolitis (NEC) is a multifactorial gastrointestinal disease with high morbidity and mortality among premature infants. This study aimed to identify novel methylation-regulated biomarkers in NEC intestinal tissue through multiomics analysis. We analyzed DNA methylation and transcriptome datasets from ileum and colon tissues of patients with NEC. We identify methylation-related differential genes (MrDEGs) based on the rule that the degree of methylation in the promoter region is inversely proportional to RNA transcription. These MrDEGs included ADAP1, GUCA2A, BCL2L14, FUT3, MISP, USH1C, ITGA3, UNC93A and IL22RA1. Single-cell data revealed that MrDEGs were mainly located in the intestinal epithelial part of intestinal tissue. These MrDEGs were verified through Target gene bisulfite sequencing and RT-qPCR. We successfully identified and verified the ADAP1, GUCA2A, IL22RA1 and MISP, primarily expressed in intestinal epithelial villus cells through single-cell data. Through single-gene gene set enrichment analysis, we found that these genes participate mainly in the pathological process of T-cell differentiation and the suppression of intestinal inflammation in NEC. This study enhances our understanding of the pathogenesis of NEC and may promote the development of new precision medicine methods for NEC prediction and diagnosis.

The phenotype of necrotizing enterocolitis correlates with distinct changes of intestinal junctional proteins

Necrotizing enterocolitis (NEC) is a major cause of mortality in preterm infants. Its pathophysiology remains poorly understood but intestinal epithelial barrier dysfunction contributes to the disease. We characterized junctional proteins in intestinal specimens from preterm infants. Samples from 27 patients with NEC and 20 patients with focal intestinal perforation (FIP) from the center of the specimens (affected) or the macroscopically healthy resection margins whenever available (non-affected) were collected. NEC patients displayed higher mortality and more commonly occurrence of impaired glucose homeostasis, patent ductus arteriosus, anemia and antibiotic treatment compared to FIP patients. Discrimination between NEC and FIP was not possible in affected areas based on H.E. staining using a newly developed scoring system. Immunofluorescence revealed reduced Claudin-3 in affected NEC samples and decreased Claudin-4 in affected FIP and all NEC samples. E-cadherin and Desmoglein-2 were reduced in a subgroup of the affected NEC samples. Plakophilin-2 was decreased in intestine affected by FIP and unaffected intestine in patients with NEC. In affected areas of NEC, Plakophilin-2 was completely lost. Plakoglobin reduction in affected NEC samples correlated with poor survival. This study provides novel insights into changes of junctional proteins in NEC, suggesting Claudin-3 and Plakophilin-2 as diagnostic markers to differentiate FIP from NEC and reduced Plakoglobin as a prognostic marker.

The Human Milk-derived Peptide Drives Rapid Regulation of Macrophage Inflammation Responses in the Neonatal Intestine

BACKGROUND & AIMS

The interactions between human milk and the regulation of innate immune homeostasis in newborns, and their impact on intestinal health, are not fully understood. This study aimed to explore the role of peptides in human milk extracellular vesicles (EVs) in this process.

METHODS

A comprehensive screening of peptides within human milk EVs was performed, leading to the identification of a beta-casein-derived peptide (CASB135-150). The effects of CASB135-150 on intestinal injury were evaluated in a rat necrotizing enterocolitis (NEC) model. Immunofluorescence analysis was used to determine its distribution, and its impact on NF-κB signaling and inflammation was studied in bone marrow-derived macrophages (BMDMs) and intestinal macrophages. Protein-protein interaction (PPI) analysis, single-cell RNA-seq (scRNA-seq), and co-immunoprecipitation (co-IP) experiments were conducted to explore the mechanism underlying CASB135-150 function.

RESULTS

CASB135-150 significantly mitigated intestinal injury in the rat NEC model. Immunofluorescence analysis revealed that CASB135-150 could target intestinal macrophages and rapidly inhibited NF-κB signaling and reduced inflammation. ScRNA-seq analyses indicated a strong association between FHL2 and NEC development, and co-IP confirmed the interaction between CASB135-150 and FHL2. CASB135-150 disrupted the FHL2/TRAF6 complex, reducing TRAF6 protein levels. Mutation of key amino acids in CASB135-150 disrupted its interaction with FHL2 and abolished its ability to inhibit NF-κB signaling, which also prevented its protective effect in vivo. RNA-seq of intestinal tissue further highlighted the impact of CASB135-150 on the NF-κB signaling pathway.

CONCLUSIONS

Our study identifies CASB135-150, a novel peptide in human milk EVs, that rapidly regulates macrophage inflammatory responses and protects against NEC-induced intestinal injury. These findings provide new insights into the role of human milk in modulating the infant immune system and intestinal health.

Peripheral Lymphocyte Changes Associate With the Progression of Necrotizing Enterocolitis in Infants

INTRODUCTION

Immune factors are important antecedents in the pathophysiology of necrotizing enterocolitis (NEC). However, studies on the peripheral blood lymphocyte subsets changes in NEC patients among different Bell stages and in patients requiring surgery are scarce.

METHODS

34 infants with NEC and 33 age-matched controls were included. Peripheral blood was collected within 48 h after NEC diagnosis. Peripheral blood B and T lymphocytes subsets were detected by 12-color flow cytometry. Cell ratios were calculated, and their relationship to disease severity and their roles as indicators for surgery were assessed.

RESULTS

NEC patients showed elevated percentages of unSwB cells (CD27+IgD+ unswitched memory/activated B cells)/B cells, SwB cells (CD27+IgD-switched memory B cells)/B cells, CD8+ T (CD3+CD8+ T cells)/T cells, Tem (CD45RA-CCR7-effector memory T cells)/CD4+ T cells, Tem/CD8+ T cells and decreased Bn (CD27-IgD+ naïve B cells)/B cells, CD4+T (CD3+CD4+ T cells)/T cells, CD45RA+ CCR7+ naïve T cells (CD45RA+CCR7+ naïve T cells)/CD8+T cells. Compared to NEC patients at BELL stage I + II, patients at BELL stage III showed increased percentages of SwB cells/B cells, antibody secreting cell (ASC, CD3-CD20-CD27high CD38high ASCs)/B cells and Tem/CD4+ T cells, and decreased percentages of CD45RA+CCR7+ naïve T cells/CD4+ T cells. The Receiver Operating Characteristic Curve analysis showed that the sensitivity of ASC/B cells ratio (0.52%) is 86.67% and the specificity of Tem/CD4+T ratio (5.22%) is 100%, indicating that NEC patients required surgery.

CONCLUSIONS

The severity of NEC exhibits codirectional changes with the maturation of B and T lymphocytes, especially CD4+ T cells. The increased ASC/B and Tem/CD4+ T cells could serve as potential indicators for NEC patients requiring surgery.

Single-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells

Proper development of mucosal immunity is critical for human health. Over the past decade, it has become evident that in humans, this process begins in utero. However, there are limited data on the unique features and functions of fetal mucosal immune cells. To address this gap, we integrated several single-cell ribonucleic acid sequencing datasets of the human small intestine (SI) to create an SI transcriptional atlas throughout the human life span, ranging from the first trimester to adulthood, with a focus on immune cells. Fetal SI displayed a complex immune landscape comprising innate and adaptive immune cells that exhibited distinct transcriptional programs from postnatal samples, especially compared with pediatric and adult samples. We identified shifts in myeloid populations across gestation and progression of memory T-cell states throughout the human lifespan. In particular, there was a marked shift of memory T cells from those with stem-like properties in the fetal samples to fully differentiated cells with a high expression of activation and effector function genes in adult samples, with neonatal samples containing both features. Finally, we demonstrate that the SI developmental atlas can be used to elucidate improper trajectories linked to mucosal diseases by implicating developmental abnormalities underlying necrotizing enterocolitis, a severe intestinal complication of prematurity. Collectively, our data provide valuable resources and important insights into intestinal immunity that will facilitate regenerative medicine and disease understanding.

A spatial expression atlas of the adult human proximal small intestine

The mouse small intestine shows profound variability in gene expression along the crypt-villus axis1,2. Whether similar spatial heterogeneity exists in the adult human gut remains unclear. Here we use spatial transcriptomics, spatial proteomics and single-molecule fluorescence in situ hybridization to reconstruct a comprehensive spatial expression atlas of the adult human proximal small intestine. We describe zonated expression and cell type representation for epithelial, mesenchymal and immune cell types. We find that migrating enterocytes switch from lipid droplet assembly and iron uptake at the villus bottom to chylomicron biosynthesis and iron release at the tip. Villus tip cells are pro-immunogenic, recruiting γδ T cells and macrophages to the tip, in contrast to their immunosuppressive roles in mouse. We also show that the human small intestine contains abundant serrated and branched villi that are enriched at the tops of circular folds. Our study presents a detailed resource for understanding the biology of the adult human small intestine.

Human Milk Supports Robust Intestinal Organoid Growth, Differentiation, and Homeostatic Cytokine Production

Background and Aims

Necrotizing enterocolitis is a severe gastrointestinal complication of prematurity. Using small intestinal organoids derived from fetal tissue of a gestational age similar to an extremely preterm infant, this study aims to assess the effect of diet on intestinal epithelial growth and differentiation to elucidate the role nutrition type plays in intestinal development and modifies the risk for necrotizing enterocolitis.

Methods

Organoids were cultured for 5 days in growth media and 5 days in differentiation media supplemented 1:40 with 4 different diets: parental milk, donor human milk, standard formula, or extensively hydrolyzed formula. Images were captured daily and organoids were quantified. Organoids were preserved for RNA sequencing and immunofluorescence staining with Ki67, cleaved caspase 3, and chromogranin-A. Media was saved for cytokine/chemokine and growth factor analysis.

Results

Human milk supplementation improved growth and differentiation of intestinal organoids generating larger organoids during the growth phase and organoids with longer and wider buds during differentiation compared to formula. Ki67 staining confirmed the proliferative nature of milk-supplemented organoids and chromogranin A staining proved that MM-supplemented organoids induced highest enteroendocrine differentiation. Human milk supplementation also upregulated genes involved in Wnt signaling and fatty acid metabolism pathways and promoted a homeostatic immune landscape, including via increased secretion of tumor necrosis factor-related apoptosis-inducing ligand among other cytokines. Conversely, organoids supplemented with formula had a downregulation of cell-cycle-promoting genes and a more inflammatory immune signature, including a reduced level of leukemia inhibitory factor.

Conclusion

Our results demonstrate that parental milk, and to a lesser extent donor human milk, support robust intestinal epithelial proliferation, differentiation, and homeostatic cytokine production, suggesting a critical role for factors enriched in human milk in intestinal epithelial health.

I-FABP protein/mRNA and IL-6 as biomarkers of intestinal barrier dysfunction in neonates with necrotizing enterocolitis and SPF BALB/c mouse models

OBJECTIVE

Neonatal necrotizing enterocolitis (NEC) is a serious intestinal inflammatory disease. We investigated intestinal fatty acid binding protein (I-FABP), I-FABP mRNA, and interleukin-6 (IL-6) as potential diagnostic biomarkers in NEC.

METHODS

Forty mice were subjected to hypoxic-ischemic intestinal injury, and then serum I-FABP protein and mRNA levels were quantified. Ileal tissue pathological scores were determined by hematoxylin and eosin staining. I-FABP expression levels and translocation in these tissues were detected using western blotting and immunofluorescence, respectively. Samples from 30 human neonates with NEC and 30 healthy neonates had serum I-FABP protein/mRNA and IL-6 levels measured.

RESULTS

The mouse ileal tissue pathological score and I-FABP levels, as well as serum I-FABP and I-FABP mRNA levels, were significantly higher in the model group than in the control group. Serum I-FABP, I-FABP mRNA, and IL-6 levels were significantly higher in human neonates with NEC than in the healthy group. Logistic regression and receiver operating curve analyses revealed that I-FABP protein/mRNA and IL-6 levels could be diagnostic biomarkers for NEC.

CONCLUSIONS

I-FABP protein/mRNA and IL-6 levels are useful biomarkers of intestinal ischemic injury in neonates with NEC. The combined detection of I-FABP protein/mRNA and IL-6 is recommended rather than using a single biomarker.

More than nutrition: Therapeutic potential and mechanism of human milk oligosaccharides against necrotizing enterocolitis

Human milk is the most valuable source of nutrition for infants. The structure and function of human milk oligosaccharides (HMOs), which are key components of human milk, have long been attracting particular research interest. Several recent studies have found HMOs to be efficacious in the prevention and treatment of necrotizing enterocolitis (NEC). Additionally, they could be developed in the future as non-invasive predictive markers for NEC. Based on previous findings and the well-defined functions of HMOs, we summarize potential protective mechanisms of HMOs against neonatal NEC, which include: modulating signal receptor function, promoting intestinal epithelial cell proliferation, reducing apoptosis, restoring intestinal blood perfusion, regulating microbial prosperity, and alleviating intestinal inflammation. HMOs supplementation has been demonstrated to be protective against NEC in both animal studies and clinical observations. This calls for mass production and use of HMOs in infant formula, necessitating more research into the safety of industrially produced HMOs and the appropriate dosage in infant formula.

Role of innate T cells in necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a destructive gastrointestinal disease primarily affecting preterm babies. Despite advancements in neonatal care, NEC remains a significant cause of morbidity and mortality in neonatal intensive care units worldwide and the etiology of NEC is still unclear. Risk factors for NEC include prematurity, very low birth weight, feeding with formula, intestinal dysbiosis and bacterial infection. A review of the literature would suggest that supplementation of prebiotics and probiotics prevents NEC by altering the immune responses. Innate T cells, a highly conserved subpopulation of T cells that responds quickly to stimulation, develops differently from conventional T cells in neonates. This review aims to provide a succinct overview of innate T cells in neonates, encompassing their phenotypic characteristics, functional roles, likely involvement in the pathogenesis of NEC, and potential therapeutic implications.

High-dimensional mass cytometry reveals systemic and local immune signatures in necrotizing enterocolitis

Objective

Patients with necrotizing enterocolitis display severe gastrointestinal complications of prematurity, but the mechanism driving this clinical profile remains unknown. We used mass cytometry time-of-flight to characterize and compare immune cell populations in the blood and intestine tissue from patients with and without (controls) necrotizing enterocolitis at single-cell resolution.

Methods

We completed a deep mapping of the immune system of the peripheral blood mononuclear cells and intestinal mucosa tissue using mass cytometry to evaluate immune cell types, which revealed global immune dysregulation characteristics underlying necrotizing enterocolitis.

Results

Compared with controls, natural killer cells display signs of heightened activation and increased cytotoxic potential in the peripheral blood and mucosa of patients with necrotizing enterocolitis. Furthermore, CD4+ T effector memory cells, non-classical monocytes, active dendritic cells, and neutrophils were specifically enriched in the mucosa, suggesting trafficking from the periphery to areas of inflammation. Moreover, we mapped the systemic and local distinct immune signatures suggesting patterns of cell localization in necrotizing enterocolitis.

Conclusion

We used mass cytometry time-of-flight technology to identify immune cell populations specific to the peripheral blood and intestinal mucosa tissue from patients with necrotizing enterocolitis and controls. This information might be used to develop precise diagnosis and therapies that target specific cell populations in patients with necrotizing enterocolitis.

Vancomycin-induced gut microbial dysbiosis alters enteric neuron-macrophage interactions during a critical period of postnatal development

Vancomycin is a broad-spectrum antibiotic widely used in cases of suspected sepsis in premature neonates. While appropriate and potentially lifesaving in this setting, early-life antibiotic exposure alters the developing microbiome and is associated with an increased risk of deadly complications, including late-onset sepsis (LOS) and necrotizing enterocolitis (NEC). Recent studies show that neonatal vancomycin treatment disrupts postnatal enteric nervous system (ENS) development in mouse pups, which is in part dependent upon neuroimmune interactions. This suggests that early-life antibiotic exposure could disrupt these interactions in the neonatal gut. Notably, a subset of tissue-resident intestinal macrophages, muscularis macrophages, has been identified as important contributors to the development of postnatal ENS. We hypothesized that vancomycin-induced neonatal dysbiosis impacts postnatal ENS development through its effects on macrophages. Using a mouse model, we found that exposure to vancomycin in the first 10 days of life, but not in adult mice, resulted in an expansion of pro-inflammatory colonic macrophages by increasing the recruitment of bone-marrow-derived macrophages. Single-cell RNA sequencing of neonatal colonic macrophages revealed that early-life vancomycin exposure was associated with an increase in immature and inflammatory macrophages, consistent with an influx of circulating monocytes differentiating into macrophages. Lineage tracing confirmed that vancomycin significantly increased the non-yolk-sac-derived macrophage population. Consistent with these results, early-life vancomycin exposure did not expand the colonic macrophage population nor decrease enteric neuron density in CCR2-deficient mice. Collectively, these findings demonstrate that early-life vancomycin exposure alters macrophage number and phenotypes in distinct ways compared with vancomycin exposure in adult mice and results in altered ENS development.