The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD

Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn's disease, and celiac disease

Ulcerative colitis (UC), Crohn's disease (CD), and celiac disease are prevalent intestinal inflammatory disorders with nonsatisfactory therapeutic interventions. Analyzing patient data-driven cohorts can highlight disease pathways and new targets for interventions. Long noncoding RNAs (lncRNAs) are attractive candidates, since they are readily targetable by RNA therapeutics, show relative cell-specific expression, and play key cellular functions. Uniformly analyzing gut mucosal transcriptomics from 696 subjects, we have highlighted lncRNA expression along the gastrointestinal (GI) tract, demonstrating that, in control samples, lncRNAs have a more location-specific expression in comparison with protein-coding genes. We defined dysregulation of lncRNAs in treatment-naive UC, CD, and celiac diseases using independent test and validation cohorts. Using the Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) inception UC cohort, we defined and prioritized lncRNA linked with UC severity and prospective outcomes, and we highlighted lncRNAs linked with gut microbes previously implicated in mucosal homeostasis. HNF1A-AS1 lncRNA was reduced in all 3 conditions and was further reduced in more severe UC form. Similarly, the reduction of HNF1A-AS1 ortholog in mice gut epithelia showed higher sensitivity to dextran sodium sulfate-induced colitis, which was coupled with alteration in the gut microbial community. These analyses highlight prioritized dysregulated lncRNAs that can guide future preclinical studies for testing them as potential targets.This study was supported by the ERC starting grant (YH, grant No 758313), the Israel Science Foundation (YH, grant No 908/15), the I-CORE program (YH, grants No. 41/11), the Helmsley Charitable Trust, and NIDDK P30 DK078392 (Integrative Morphology and Gene Expression Cores). PROTECT was supported by the NIDDK 5U01DK095745, RISK was supported by Crohn’s & Colitis Foundation, SEEM by the Bill and Melinda Gates Foundation (OPP1144149 and OPP1138727), and SOURCE is supported by the Helmsley Charitable Trust. The funding sources did not play a role in the writing of the manuscript or the decision to submit it for publication and did not play a role in data collection, analysis, interpretation, trial design, patient recruitment, or any aspect pertaining to the study

A High Salt Diet Modulates the Gut Microbiota and Short Chain Fatty Acids Production in a Salt-Sensitive Hypertension Rat Model

Emerging data indicate a correlation between gut microbial composition and cardiovascular disease including hypertension. The host’s diet greatly affects microbial composition and metabolite production. Short chain fatty acids (SCFAs) are products of microbial fermentation, which can be utilized by the host. It has been suggested that SCFAs play a pivotal role as mediators in a microbiome host: microbial interactions occur in health and disease. The aim of this study was to evaluate the effect of a high salt diet (HSD) on microbial variation and to determine whether this effect is accompanied by an alteration in fecal SCFAs. To this end, Dahl salt-sensitive rats were divided into two groups (n = 10 each): (A) Control: fed regular chow; and (B) Fed HSD. High-throughput pyrosequencing of the 16S rRNA amplicon sequencing was used for microbiome characterizing. Chromatography-mass spectrometry was used to measure the levels of SCFAs: acetic acid, propionic acid, butyric acid, and isobutyric acid in fecal samples. Differences in microbial composition were noted between groups. Principal Coordinate Analysis (PCoA) principal coordinate 1 (PC1) primarily separated controls from the HSD. Four taxa displayed significant differences between HSD and controls. Taxa from the Erwinia genus, the Christensenellaceae and Corynebacteriaceae families, displayed an increased abundance in HSD versus control. In contrast, taxa from the Anaerostipes genus displayed a decreased abundance in HSD. We were able to identify seven unique taxa that were significantly associated with blood pressure. There was a significant difference in fecal acetic acid, as well as propionic and isobutyric acid, but not in the butyric acid composition between groups. Adding salt to a diet impacts the gut’s microbial composition, which may alter fecal SCFA production

Neutrophil FCγ Receptor 1 (CD64) Index As a Non-Invasive Biomarker for Clinical and Mucosal Disease Activity in Pediatric Inflammatory Bowel Disease

Background: Neutrophil expression of the high affinity Fc γ receptor 1(CD64) is up-regulated in adult patients with active inflammatory bowel disease (IBD). Infliximab non-response has been associated with an increased mucosal CD64 mRNA expression. We assessed the clinical utility of whole blood analysis of CD64 in the pediatric IBD population as a reflection of disease activity and severity. We hypothesized that the polymorphonuclear neutrophil (PMN) CD64 index would correlate with fecal calprotectin (FC) and serve as a surrogate biomarker for mucosal activity. Methods: We enrolled children having colonoscopy for suspicion of IBD (18 Crohn\u27s disease [CD], 2 Ulcerative Colitis [UC], 10 healthy controls) and children during routine clinic visits or undergoing colonoscopy with known IBD (82 CD, 14 UC, 2 IBD-U). The polymorphonuclear neutrophil (PMN) CD64 index was determined from each subject\u27s whole blood by flow cytometry using Leuko64 (Trillium Diagnostics, LLC). RNA sequence analysis of CD64 and S100A9 (calprotectin) was performed on ileal tissue obtained at diagnosis from 32 CD patients and 18 healthy controls and provided by the PRO-KIIDS consortium. Results: Mean(SD) PMN CD64 index for new diagnosis IBD was 2.79(0.36) compared with 0.78(0.04) for healthy controls (p=0.0005). For those with known IBD (41 active, 57 quiescent), the mean(SD) PMN CD64 index for active IBD was 2.38(0.26)) compared with 1.048(0.05) for quiescent IBD (p ,0.0001). ROC curve analysis from the two groups demonstrated an AUC of 0.89 (95% CI 0.83-0.95). At a cut off of 1.2, the CD64 index was 85% sensitive and 84% specific for active IBD. In the patients with active disease, the CD64 index was elevated in 35/41 (85%) subjects compared with elevations in FC (81%), CRP (72%), and ESR (57%). The PMN CD64 index did not differ by disease location (ileum only, colon only, ileocolonic) in those with active IBD, but CD64 index was highly correlated with the pediatric CD activity index (PCDAI, Spearman r = 0.68; p , 0.0001) and the pediatric UC activity index (r = 0.88; p , 0.0001). In patients with mild disease activity (PCDAI score 10-27.5), the mean PMN CD64 index was 1.84 compared with 3.03 in those with moderate-severe disease activity (PCDAI 30-100, p=0.014). Importantly, the PMN CD64 index significantly correlated with the simplified endoscopic score-CD (SESCD) in 32 CD patients (r = 0.68, p , 0.0001), while no correlation was found with CRP or ESR and SES-CD. RNA sequencing from ileal tissue revealed Fc γR1A (CD64) correlated significantly with S100A9 (r = 0.879; p , 0.0001). The PMN CD64 index also correlated with FC (r = 0.485; p = 0.002). Conclusions: The PMN CD64 index is a useful biomarker in determining disease activity in pediatric IBD and correlates significantly with FC, disease activity indices, and the SES-CD

Neutrophil FCγ Receptor 1 (CD64) Index As a Non-Invasive Biomarker for Clinical and Mucosal Disease Activity in Pediatric Inflammatory Bowel Disease

Background: Neutrophil expression of the high affinity Fc γ receptor 1(CD64) is up-regulated in adult patients with active inflammatory bowel disease (IBD). Infliximab non-response has been associated with an increased mucosal CD64 mRNA expression. We assessed the clinical utility of whole blood analysis of CD64 in the pediatric IBD population as a reflection of disease activity and severity. We hypothesized that the polymorphonuclear neutrophil (PMN) CD64 index would correlate with fecal calprotectin (FC) and serve as a surrogate biomarker for mucosal activity. Methods: We enrolled children having colonoscopy for suspicion of IBD (18 Crohn\u27s disease [CD], 2 Ulcerative Colitis [UC], 10 healthy controls) and children during routine clinic visits or undergoing colonoscopy with known IBD (82 CD, 14 UC, 2 IBD-U). The polymorphonuclear neutrophil (PMN) CD64 index was determined from each subject\u27s whole blood by flow cytometry using Leuko64 (Trillium Diagnostics, LLC). RNA sequence analysis of CD64 and S100A9 (calprotectin) was performed on ileal tissue obtained at diagnosis from 32 CD patients and 18 healthy controls and provided by the PRO-KIIDS consortium. Results: Mean(SD) PMN CD64 index for new diagnosis IBD was 2.79(0.36) compared with 0.78(0.04) for healthy controls (p=0.0005). For those with known IBD (41 active, 57 quiescent), the mean(SD) PMN CD64 index for active IBD was 2.38(0.26)) compared with 1.048(0.05) for quiescent IBD (p ,0.0001). ROC curve analysis from the two groups demonstrated an AUC of 0.89 (95% CI 0.83-0.95). At a cut off of 1.2, the CD64 index was 85% sensitive and 84% specific for active IBD. In the patients with active disease, the CD64 index was elevated in 35/41 (85%) subjects compared with elevations in FC (81%), CRP (72%), and ESR (57%). The PMN CD64 index did not differ by disease location (ileum only, colon only, ileocolonic) in those with active IBD, but CD64 index was highly correlated with the pediatric CD activity index (PCDAI, Spearman r = 0.68; p , 0.0001) and the pediatric UC activity index (r = 0.88; p , 0.0001). In patients with mild disease activity (PCDAI score 10-27.5), the mean PMN CD64 index was 1.84 compared with 3.03 in those with moderate-severe disease activity (PCDAI 30-100, p=0.014). Importantly, the PMN CD64 index significantly correlated with the simplified endoscopic score-CD (SESCD) in 32 CD patients (r = 0.68, p , 0.0001), while no correlation was found with CRP or ESR and SES-CD. RNA sequencing from ileal tissue revealed Fc γR1A (CD64) correlated significantly with S100A9 (r = 0.879; p , 0.0001). The PMN CD64 index also correlated with FC (r = 0.485; p = 0.002). Conclusions: The PMN CD64 index is a useful biomarker in determining disease activity in pediatric IBD and correlates significantly with FC, disease activity indices, and the SES-CD