NAD+ Metabolism and Immune Regulation: New Approaches to Inflammatory Bowel Disease Therapies

Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models

Background

Ulcerative colitis (UC) is a chronic inflammatory disease of the colonic mucosa with increasing incidence worldwide. Growing evidence highlights the pivotal role of nicotinamide adenine dinucleotide (NAD+) metabolism in UC pathogenesis, prompting our investigation into the subtype-specific molecular underpinnings and diagnostic potential of NAD+ metabolism-related genes (NMRGs).

Methods

Transcriptome data from UC patients and healthy controls were downloaded from the GEO database, specifically GSE75214 and GSE87466. We performed unsupervised clustering based on differentially expressed NAD+ metabolism-related genes (DE-NMRGs) to classify UC cases into distinct subtypes. GSEA and GSVA identified potential biological pathways active within these subtypes, while the CIBERSORT algorithm assessed differential immune cell infiltration. Weighted gene co-expression network analysis (WGCNA) combined with differential gene expression analysis was used to pinpoint specific NMRGs in UC. Robust gene features for subtyping and diagnosis were selected using two machine learning algorithms. Nomograms were constructed and their effectiveness was evaluated using receiver operating characteristic (ROC) curves. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted to verify gene expression in cell lines.

Results

In our study, UC patients were classified into two subtypes based on DE-NMRGs expression levels, with Cluster A exhibiting enhanced self-repair capabilities during inflammatory responses and Cluster B showing greater inflammation and tissue damage. Through comprehensive bioinformatics analyses, we identified four key biomarkers (AOX1, NAMPT, NNMT, PTGS2) for UC subtyping, and two (NNMT, PARP9) for its diagnosis. These biomarkers are closely linked to various immune cells within the UC microenvironment, particularly NAMPT and PTGS2, which were strongly associated with neutrophil infiltration. Nomograms developed for subtyping and diagnosis demonstrated high predictive accuracy, achieving area under curve (AUC) values up to 0.989 and 0.997 in the training set and up to 0.998 and 0.988 in validation sets. RT-qPCR validation showed a significant upregulation of NNMT and PARP9 in inflamed versus normal colonic epithelia, underscoring their diagnostic relevance.

Conclusion

Our study reveals two NAD+ subtypes in UC, identifying four biomarkers for subtyping and two for diagnosis. These findings could suggest potential therapeutic targets and contribute to advancing personalized treatment strategies for UC, potentially improving patient outcomes.

Nicotinamide Mononucleotide Restores NAD+ Levels to Alleviate LPS-Induced Inflammation via the TLR4/NF-κB/MAPK Signaling Pathway in Mice Granulosa Cells

Inflammation disrupts the normal function of granulosa cells (GCs), which leads to ovarian dysfunction and fertility decline. Inflammatory conditions such as polycystic ovary syndrome (PCOS), primary ovarian insufficiency (POI), endometriosis, and age-related ovarian decline are often associated with chronic low-grade inflammation. Nicotinamide mononucleotide (NMN) is an important precursor of NAD+ and has gained attention for its potential to modulate cellular metabolism, redox homeostasis, and mitigate inflammation. This study investigated the protective roles of NMN against lipopolysaccharide LPS-mediated inflammation in GCs. The results of this experiment demonstrated that LPS had negative effects on GCs in term of reduced viability and proliferation rates and upregulated the production of pro-inflammatory cytokines, including interleukin-1 beta (IL-1β), interleukin-6 (IL-6), cyclooxygenase-2 (Cox-2), and tumor necrosis factor-alpha (TNF-α). Notably, the levels of NAD+ and NAD+/NADH ratio in GCs were reduced in response to inflammation. On the other hand, NMN supplementation restored the NAD+ levels and the NAD+/NADH ratio in GCs and significantly reduced the expression of pro-inflammatory markers at both mRNA and protein levels. It also enhanced cell viability and proliferation rates of GCs. Furthermore, NMN also reduced apoptosis rates in GCs by downregulating pro-apoptotic markers, including Caspase-3, Caspase-9, and Bax while upregulating anti-apoptotic marker Bcl-2. NMN supplementation significantly reduced reactive oxygen species ROS and improved steroidogenesis activity by restoring the estradiol (E2) and progesterone (P4) levels in LPS-treated GCs. Mechanistically, this study found that NMN suppressed the activation of the TLR4/NF-κB/MAPK signaling pathways in GCs, which regulates inflammatory processes. In conclusion, the findings of this study revealed that NMN has the potential to reduce LPS-mediated inflammatory changes in GCs by modulating NAD+ metabolism and inflammatory signaling pathways. NMN supplementation can be used as a potential therapeutic agent for ovarian inflammation and related fertility disorders.

Novel immune cross-talk between inflammatory bowel disease and IgA nephropathy

The mechanisms underlying the complex correlation between immunoglobulin A nephropathy (IgAN) and inflammatory bowel disease (IBD) remain unclear. This study aimed to identify the optimal cross-talk genes, potential pathways, and mutual immune-infiltrating microenvironments between IBD and IgAN to elucidate the linkage between patients with IBD and IgAN. The IgAN and IBD datasets were obtained from the Gene Expression Omnibus (GEO). Three algorithms, CIBERSORTx, ssGSEA, and xCell, were used to evaluate the similarities in the infiltrating microenvironment between the two diseases. Weighted gene co-expression network analysis (WGCNA) was implemented in the IBD dataset to identify the major immune infiltration modules, and the Boruta algorithm, RFE algorithm, and LASSO regression were applied to filter the cross-talk genes. Next, multiple machine learning models were applied to confirm the optimal cross-talk genes. Finally, the relevant findings were validated using histology and immunohistochemistry analysis of IBD mice. Immune infiltration analysis showed no significant differences between IBD and IgAN samples in most immune cells. The three algorithms identified 10 diagnostic genes, MAPK3, NFKB1, FDX1, EPHX2, SYNPO, KDF1, METTL7A, RIDA, HSDL2, and RIPK2; FDX1 and NFKB1 were enhanced in the kidney of IBD mice. Kyoto Encyclopedia of Genes and Genomes analysis showed 15 mutual pathways between the two diseases, with lipid metabolism playing a vital role in the cross-talk. Our findings offer insights into the shared immune mechanisms of IgAN and IBD. These common pathways, diagnostic cross-talk genes, and cell-mediated abnormal immunity may inform further experimental studies.

Protein-bound AGEs derived from methylglyoxal induce pro-inflammatory response and barrier integrity damage in epithelial cells by disrupting the retinol metabolism

Advanced glycation end-products (AGEs) are complex and heterogeneous compounds widely present in processed foods. Previous studies evidenced the adverse effects of AGEs on gut homeostasis, but the precise pathological mechanisms and molecular pathways responsible for the disruption of intestinal barrier integrity by AGEs remain incompletely elucidated. In this study, protein-bound AGEs (BSA-MGO), the most common type of dietary AGE, were prepared by methylglyoxal-mediated glycation, and an in vitro human epithelial colorectal adenocarcinoma (Caco-2) cell model was employed to evaluate the impact of protein-bound AGEs on gut epithelial function. Results showed that exposure to BSA-MGO significantly increased the permeability of Caco-2 cell monolayers as evidenced by the decreased transepithelial electrical resistance value, increased paracellular transport of FITC-dextran, and down-regulated tight-junction proteins. In parallel, BSA-MGO induced pro-inflammatory responses and oxidative stress in the monolayers. Transcriptomic profiling further revealed that BSA-MGO disrupted the retinol metabolism, thereby contributing to the barrier integrity damage in epithelial cells. Overall, these results provide valuable insights into the disrupting effects of dietary AGEs on intestinal barrier function, and the perturbed pathways present potential targets for further exploration of the molecular mechanisms underlying the detrimental effect of processed foods on gut health.

Insights into Alkaline Phosphatase Anti-Inflammatory Mechanisms

BACKGROUND

The endogenous ecto-enzyme and exogenously administered alkaline phosphatase (ALP) have been evidenced to significantly attenuate inflammatory conditions, including Toll-like receptor 4 (TLR4)-related signaling and cytokine overexpression, barrier tissue dysfunction and oxidative stress, and metabolic syndrome and insulin resistance, in experimental models of colitis, liver failure, and renal and cardiac ischemia-reperfusion injury. This suggests multiple mechanisms of ALP anti-inflammatory action that remain to be fully elucidated.

METHODS

Recent studies have contributed to a deeper comprehension of the role played by ALP in immune metabolism. This review outlines the established effects of ALP on lipopolysaccharide (LPS)-induced inflammation, including the neutralization of LPS and the modulation of purinergic signaling.

RESULTS

The additional mechanisms of anti-inflammatory activity of ALP observed in different pathologies are proposed.

CONCLUSIONS

The anti-inflammatory pathways of ALP may include a scavenger receptor (CD36)-mediated activation of β-oxidation and oxidative phosphorylation, caveolin-dependent endocytosis, and selective autophagy-dependent degradation.

Effects of baicalin and chlorogenic acid on growth performance, slaughter performance, antioxidant capacity, immune function and intestinal health of broilers

This study aimed to investigate the effects of baicalin and chlorogenic acid (BC) on growth performance, intestinal barrier function, antioxidant capacity, intestinal microbiota, and mucosal metabolism in broilers. A total of 720 twenty-one-day-old broilers were randomly allocated into 3 groups, with 6 replicates per group and 40 chickens per replicate. They were fed a basal diet (Con group) or a basal diet supplemented with 250 or 400 mg/kg BC (BC250 and BC400 groups) for 40 consecutive days. The results revealed that 250 mg/kg BC significantly increased 60-d body weight and average daily gain during 39 to 60 d (P < 0.05). Furthermore, Supplementation with 250 mg/kg BC improved the antioxidant capacity and immunity of broilers, as evidenced by increased (P < 0.05) superoxide dismutase and decreased (P < 0.05) malondialdehyde levels in serum and ileum, as well as increased (P < 0.05) immunoglobulin G levels. Supplementation with 250 mg/kg BC enhanced intestinal development by improving intestinal morphology and promoting the proliferation of intestinal crypts. Moreover, Supplementation with 250 mg/kg BC improved (P < 0.05) intestinal permeability, up-regulated (P < 0.05) the expression of tight junction-related genes (Occludin and ZO-1), and down-regulated (P < 0.05) the expression of pro-inflammatory genes (IL-2, IL-8, and IFN-γ). 16S rRNA sequencing revealed significant enrichment of Microbacteriaceae, Micromonosporaceae, Anaerovoracaceae, and Coriobacteriaceae in the BC250 group. Metabolomics showed that 250 mg/kg BC up-regulated the lysosome, foxo signaling pathway, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, and oxidative phosphorylation pathways, while down-regulating the biosynthesis of cofactors pathway. In conclusion, supplementing diets with 250 mg/kg BC is recommended to modulate intestinal microbiota, mucosal metabolism, and antioxidant capacity, thereby improving broiler growth performance and intestinal health.

Nicotinamide Alleviates Synergistic Impairment of Intestinal Barrier Caused by MC-LR and NaNO2 Coexposure

Microcystin-LR (MC-LR) and nitrites from the environment and daily life can be ingested and absorbed by humans via the digestive tract. However, their combined effects on intestinal health remain unclear. Here, the combined impact of MC-LR and sodium nitrite (NaNO2) on the intestines of mice was investigated under actual human exposure conditions. After mice were exposed to MC-LR (10, 100 μg/L) and NaNO2 (30, 300 mg/L) individual and in combination for 6 months, it was found that MC-LR and NaNO2 synergistically decreased intestinal permeability and disrupted intestinal physical, chemical, immune, and microbial barriers. In the coexposure groups, the synergistic impairment to the intestinal barrier was noted with increasing concentrations of MC-LR or NaNO2, but this adverse effect was alleviated by nicotinamide supplementation. This study underscores the potential risks of simultaneous ingestion of MC-LR and nitrite on intestinal health. The protective role of nicotinamide suggests avenues for therapeutic intervention against environmental toxin-induced intestinal impairment.

Mitochondrial function and gastrointestinal diseases

Mitochondria are dynamic organelles that function in cellular energy metabolism, intracellular and extracellular signalling, cellular fate and stress responses. Mitochondria of the intestinal epithelium, the cellular interface between self and enteric microbiota, have emerged as crucial in intestinal health. Mitochondrial dysfunction occurs in gastrointestinal diseases, including inflammatory bowel diseases and colorectal cancer. In this Review, we provide an overview of the current understanding of intestinal epithelial cell mitochondrial metabolism, function and signalling to affect tissue homeostasis, including gut microbiota composition. We also discuss mitochondrial-targeted therapeutics for inflammatory bowel diseases and colorectal cancer and the evolving concept of mitochondrial impairment as a consequence versus initiator of the disease.

Explainable AI-prioritized plasma and fecal metabolites in inflammatory bowel disease and their dietary associations

Fecal metabolites effectively discriminate inflammatory bowel disease (IBD) and show differential associations with diet. Metabolomics and AI-based models, including explainable AI (XAI), play crucial roles in understanding IBD. Using datasets from the UK Biobank and the Human Microbiome Project Phase II IBD Multi'omics Database (HMP2 IBDMDB), this study uses multiple machine learning (ML) classifiers and Shapley additive explanations (SHAP)-based XAI to prioritize plasma and fecal metabolites and analyze their diet correlations. Key findings include the identification of discriminative metabolites like glycoprotein acetyl and albumin in plasma, as well as nicotinic acid metabolites andurobilin in feces. Fecal metabolites provided a more robust disease predictor model (AUC [95%]: 0.93 [0.87-0.99]) compared to plasma metabolites (AUC [95%]: 0.74 [0.69-0.79]), with stronger and more group-differential diet-metabolite associations in feces. The study validates known metabolite associations and highlights the impact of IBD on the interplay between gut microbial metabolites and diet.

Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis

Ulcerative colitis (UC) is a significant inflammatory bowel disease caused by an abnormal immune response to gut microbes. However, there are still gaps in our understanding of how immune and metabolic changes specifically contribute to this disease. Our research aims to address this gap by examining mouse colons after inducing ulcerative colitis-like symptoms. Employing single-cell RNA-seq and 16 s rRNA amplicon sequencing to analyze distinct cell clusters and microbiomes in the mouse colon at different time points after induction with dextran sodium sulfate. We observe a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrate shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibit diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic conditions, suggesting the role of macrophage heterogeneity in disease severity. Increased expression of Nampt and NOX2 complex subunits in chronic UC macrophages contributes to the inflammatory processes. The chronic UC microbiome exhibits reduced taxonomic diversity compared to healthy conditions and acute UC. The study also highlights the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis.

The role of nicotinamide adenine dinucleotide salvage enzymes in cardioprotection

The increasing trend of cardiac diseases is becoming a major threat globally. Cardiac activities are based on integrated action potential through electronic flux changes within intra- and extracellular molecular activities. Nicotinamide adenine dinucleotide (NAD) is a major electron carrier present in almost all living cells and creates gated potential by electron exchange from one chemical to another in terms of oxidation (NAD+) and reduction (NADH) reactions. NAD+ plays an important role directly or indirectly in protecting against various cardiovascular diseases, including heart failure, occlusion, ischemia-reperfusion (IR) injury, arrhythmia, myocardial infarction (MI), rhythmic disorder, and a higher order of cardiovascular complexity. Nicotinamide phosphoribosyl transferase (NAMPT) is well known as a rate-limiting enzyme in this pathway except for de-novo NAD synthesis and directly involved in the cardioprotective activity. There are two more enzymes - nicotinate phosphoribosyl transferase (NAPRT) and nicotinamide riboside kinase (NRK) - which also work as rate-limiting factors in the NAD+ synthesis pathway. This study concentrated on the role of NAMPT, NAPRT, and NRK in cardioprotective activity and prospective cardiac health.

Dysregulation of CD4+ and CD8+ resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis

BACKGROUND

Colitis caused by checkpoint inhibitors (CPI) is frequent and is treated with empiric steroids, but CPI colitis mechanisms in steroid-experienced or refractory disease are unclear.

METHODS

Using colon biopsies and blood from predominantly steroid-experienced CPI colitis patients, we performed multiplexed single-cell transcriptomics and proteomics to nominate contributing populations.

RESULTS

CPI colitis biopsies showed enrichment of CD4+resident memory (RM) T cells in addition to CD8+ RM and cytotoxic CD8+ T cells. Matching T cell receptor (TCR) clonotypes suggested that both RMs are progenitors that yield cytotoxic effectors. Activated, CD38+ HLA-DR+ CD4+ RM and cytotoxic CD8+ T cells were enriched in steroid-experienced and a validation data set of steroid-naïve CPI colitis, underscoring their pathogenic potential across steroid exposure. Distinct from ulcerative colitis, CPI colitis exhibited perturbed stromal metabolism (NAD+, tryptophan) impacting epithelial survival and inflammation. Endothelial cells in CPI colitis after anti-TNF and anti-cytotoxic T-lymphocyte-associated antigen 4 (anti-CTLA-4) upregulated the integrin α4β7 ligand molecular vascular addressin cell adhesion molecule 1 (MAdCAM-1), which may preferentially respond to vedolizumab (anti-α4β7).

CONCLUSIONS

These findings nominate CD4+ RM and MAdCAM-1+ endothelial cells for targeting in specific subsets of CPI colitis patients.

Lactobacillus rhamnosus GG Stimulates Dietary Tryptophan-Dependent Production of Barrier-Protecting Methylnicotinamide

BACKGROUND & AIMS

Lacticaseibacillus rhamnosus GG (LGG) is the world's most consumed probiotic but its mechanism of action on intestinal permeability and differentiation along with its interactions with an essential source of signaling metabolites, dietary tryptophan (trp), are unclear.

METHODS

Untargeted metabolomic and transcriptomic analyses were performed in LGG monocolonized germ-free mice fed trp-free or -sufficient diets. LGG-derived metabolites were profiled in vitro under anaerobic and aerobic conditions. Multiomic correlations using a newly developed algorithm discovered novel metabolites tightly linked to tight junction and cell differentiation genes whose abundances were regulated by LGG and dietary trp. Barrier-modulation by these metabolites were functionally tested in Caco2 cells, mouse enteroids, and dextran sulfate sodium experimental colitis. The contribution of these metabolites to barrier protection is delineated at specific tight junction proteins and enterocyte-promoting factors with gain and loss of function approaches.

RESULTS

LGG, strictly with dietary trp, promotes the enterocyte program and expression of tight junction genes, particularly Ocln. Functional evaluations of fecal and serum metabolites synergistically stimulated by LGG and trp revealed a novel vitamin B3 metabolism pathway, with methylnicotinamide (MNA) unexpectedly being the most robust barrier-protective metabolite in vitro and in vivo. Reduced serum MNA is significantly associated with increased disease activity in patients with inflammatory bowel disease. Exogenous MNA enhances gut barrier in homeostasis and robustly promotes colonic healing in dextran sulfate sodium colitis. MNA is sufficient to promote intestinal epithelial Ocln and RNF43, a master inhibitor of Wnt. Blocking trp or vitamin B3 absorption abolishes barrier recovery in vivo.

CONCLUSIONS

Our study uncovers a novel LGG-regulated dietary trp-dependent production of MNA that protects the gut barrier against colitis.