bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPROUTY2 INHIBITS EXPRESSION OF THE HOST DEFENSE PEPTIDE RELMβ IN THE COLONIC EPITHELIUM
Authors: Schumacher Michael , Liu Cambrian , Hsieh Jonathan , Purnell Benjamin , Frey Mark 
Published: January 2021

Abstract

Background
Sprouty2 (Spry2) is an inflammation-responsive regulator of intracellular signaling that is suppressed in colitis. Loss of Spry2 levels leads to increased colonic tuft and goblet cell numbers; cell types protective against injury and infection. In particular, goblet cells produce host defense peptides (HDPs) which can enhance barrier effectiveness and limit pathogen colonization. While the activity of these cells is regulated and responsive to environmental cues, the precise mechanisms driving functional changes in goblet cells are largely unknown. Here, we tested the role of Spry2 in mediating colonic goblet cell function and HDP production.

Hypothesis
Spry2 regulates HDP production in colonic goblet cells and bacterial levels.

Methods
Distal colons from mice with an intestinal epithelial-specific Spry2 deletion (Spry2flox/flox;Villin-Cre, Spry2KOIE) and littermate controls were collected at 8 w of age, and analyzed by bulk and single-cell RNA sequencing. Fecal pellets from the distal colon were 16S sequenced to assess changes in microbial populations. Changes in HDP expression were assessed at the bulk tissue level and within individual cellular populations.

Results
Expression of the host defense peptide RELMβ, but not RELMα, RELMγ, or Resistin, was increased 15-fold (p&lt;0.05) in Spry2KOIE mice in bulk RNA sequencing analysis. Single cell RNA sequencing showed RELMβ was highly enriched in Reg4+/Spink4+ putative crypt base goblet cells of both control and Spry2KOIE mice. Quantification of these cells by single-cell RNA sequencing revealed no significant difference in Reg4+/Spink4+ cell numbers in Spry2KOIE mice versus wild-type, suggesting increased RELMβ is due to goblet cell activation and not goblet cell population shifts. Taxonomic analysis of feces from 2 litters of mice showed a decreased abundance of Eggerthella spp. (reduced 61%, p&lt;0.05) and Streptococcus spp. (reduced 50%, p&lt;0.05), genera that have been identified in patients with inflammatory bowel disease.

Conclusion
Loss of epithelial Spry2 drives HDP production in the colon and alterations in the colonic microbiota. Impairment of this mechanism may impact colitis severity.
TRANSFER RNA QUEUOSINE MODIFICATION ENZYME MANIPULATES TIGHT JUNCTION PROTEINS IN INFLAMMATORY BOWEL DISEASE
Authors: Zhang Jilei , Zhang Yong-guo , Xia Yinglin , Sun Jun 
Published: January 2021

Abstract

Background
Transfer RNA (tRNA) queuosine (Q)-modification occur at the wobble anticodon position of four special cellular tRNAs. In eukaryotes, tRNA-Q modification relies on the intestinal microbial product queuine and eukaryotic tRNA-guanine transglycosylase complex contains of Q tRNA ribosyltransferase catalytic subunit 1 (QTRT1). Q-tRNA modification is critical for the fidelity and accuracy to translate RNA to protein. It is known that dysfunction of Q-tRNA associates with cancer proliferation and malignancy. However, mechanisms of how Q and Q-tRNA modifications influence intestinal epithelial biology and chronic inflammation are unknown.

Methods
We explored the expression of QTRT1 in patients with IBD by investigating human biopsy tissues and re-analyzing gene expression datasets (with both UC and CD patients). To further investigate the QTRT1 role in IBD, the dextran sodium sulfate (DSS) induced colitis mouse model and IL10-deficient mouse model were used to evaluate the molecular mechanism. We further investigated the impact of QTRT1 reduction on intestinal cells by generating QTRT1 knockdown HCT116 and Caco-2 BBE cells using a Double Nickase Plasmid.

Results
We found that the QTRT1 expression in IHC staining was significantly downregulated in the colon of both Ulcerative Colitis (UC) and Crohn’s Disease (CD) patients compared with normal controls. After extracting and analyzing the datasets, we found the gene expression of QTRT1 was significantly suppressed in colonic mucosa of UC and intestinal mucosa of CD, compared with controls. Moreover, the four tRNA-Q-related tRNA synthetase (asparaginyl-tRNA synthetase, aspartyl-tRNA synthetase, histidyl-tRNA synthetase and tyrosyl-tRNA synthetase) were also decreased in IBD patients. The decreased QTRT1-expression was further confirmed in both DSS-induced colitis mice and IL10-defecient mice. Meanwhile, the significantly downregulated beta-catenin and Claudin-5, and upregulated Caludin-2 were identified in these two colitis models. All these molecular alterations, which are important in cell adhesion and tight junction formation, were further verified in protein expression and mRNA level using QTRT1 reduction HCT116 and Caco-2 BBE cells in vitro.

Conclusion
Our results demonstrate that the QTRT1 plays a novel role in human IBD by altering intestinal cell adhesion and junctions. Microbiome-dependent Q supply can be altered during disease development or when a limited variety of food-types are ingested. Investigations on the gut microbiome-derived tRNA modification in IBD will uncover novel molecular mechanisms for potential prevention and therapy.
DUSP16 IS A NOVEL IBD GENE IMPLICATED IN THE REGULATION OF DIFFERENTIATION AND HOMEOSTASIS OF INTESTINAL EPITHELIAL CELLS
Authors: Ntunzwenimana Jessy , Alikashani Azadeh , Beauchamp Claudine , Paquette Jean , Boucher Gabrielle , Goyette Philippe , Rioux John 
Published: January 2021

Abstract
Inflammatory bowel disease (IBD) are chronic inflammatory diseases including Crohn’s disease (CD) and ulcerative colitis (UC). More than 200 genomic regions have been identified and validated (association values〈 5x10-8) to be associated with CD, UC or IBD. These regions may contain multiple genes and the current challenge lies in identifying the causal gene in each of these. To address this problem, we performed a functional genomic screen of 145 genes from validated IBD loci, in a relevant intestinal epithelial cell model (HT-29). The results of this transcriptome-based screening revealed that the candidate IBD gene DUSP16 (a dual specificity phosphatase targeting MAP kinases (MAPKs) phosphorylation) as well as the known IBD gene KSR1 (a scaffold protein regulating the spatiotemporal activation of the ERK) regulate the expression of genes involved in intestinal differentiation and homeostasis. They induce, among others, the expression of the PIGR gene that encodes the polymeric immunoglobulin receptor. PIGR plays a role in transporting dimeric IgA molecules from the basolateral membrane of epithelial cells to the intestinal lumen, via transcytosis, where they play an essential role in protecting the epithelium against intestinal pathogens. Our hypothesis is that DUSP16 and KSR1 modulate the activity of MAPKs in intestinal epithelial cells to induce PIGR expression, thus participating in the maintenance of homeostasis of the intestinal barrier.
To better understand how DUSP16 modulates the expression of PIGR, we used an approach of over- expression (cDNA) and knockdown (shRNA) of DUSP16 in HT-29 cells. Our results confirmed that DUSP16 induction increases the expression of PIGR, whereas a knockdown of DUSP16 reduces the basal level of PIGR. Next we confirmed by Western Blot that the induction of DUSP16 was accompanied by a decrease in MAPK phosphorylation. The involvement of MAPKs was also confirmed through the use of chemical inhibitors specific for each MAPK, with inhibition of ERK and p38 showing the strongest induction of PIGR expression. We are currently analyzing known functional mutants of DUSP16 and KSR1 to determine their impact on MAPK activity and on PIGR expression. This work supports a role for PIGR in disease pathogenesis, adding to two recent studies that documented that patients suffering from UC accumulated somatic mutations in a group of genes regulating the expression of PIGR by Interleukin 17. The mutated genes, including PIGR, were positively selected in inflamed tissues, indicating the importance of the biological function occupied by this gene in the maintenance of homeostasis.
In conclusion, our study successfully identified functional links between two genes from independent IBD loci, and suggests that these DUSP16 and KSR1 play a role in the process of epithelial transcytosis and the development of IBD.
GENETIC POLYMOPRHISMS MAY DIFFERENTIATE BETWEEN COMPLICATED PEDIATRIC SMALL BOWEL VERSUS COLONIC CROHN’S DISEASE
Authors: Patel Halee , Harris R Alan , Qian Justin , Britto Savini , Opekun Antone , Kellermayer Richard 
Published: January 2021

Abstract

Objectives
About 9% of pediatric Crohn’s disease (CD) patients experience complications within 3 years from diagnosis in spite of anti-Tumor Necrosis Factor-alpha (anti-TNF) biologic treatment. Within 5 years, such complications may require surgical interventions in up to 20% of cases. Due to the relatively rare nature of these complicated pediatric CD cases within large CD cohorts, traditional genome wide association studies (GWAS) rarely capture this patient population. Our aim was to identify critical genetic associations of anti-TNF refractory complicated pediatric CD subtypes.

Methods
The study was approved by BCM IRB. Included patients had developed CD between the ages of 6 and 18. The Paris classification was used to place patients in the following categories:
1. Anti-TNF refractory small bowel CD (RSB-CD): L4b; L4b/B2; or L4b/B2B3 who had or were imminent to have small bowel resection.
2.. Anti-TNF refractory colonic CD (RC-CD): L2 requiring ileal diversion; or L2/B2; or L2/B2B3 who had or were considered to receive colectomy or partial colonic resection.
Whole-exome sequencing (WES) was performed from peripheral blood derived DNA. PLINK (https://www.cog-genomics.org/plink2/) was used to identify enriched single nucleotide polymorphisms (SNPs). The level of significance for exome wide differentiation was relaxed to p&lt;0.01. The potential deleteriousness of single nucleotide variants was determined by CADD (https://cadd.gs.washington.edu/). Gene Ontology enRIchment anaLysis and visuaLizAtion tool (GORILLA) was used to compare gene lists associated with colonic enriched SNPs versus ileal enriched SNPs (http://geneontology.org/).

Results
In eight RSB-CD and 11 RC-CD cases, age at presentation, gender, ethnicity, and need for surgery (75% and 55%, respectively) did not significantly differ between the groups. There were 269 genes associated with 277 SNPs that had significantly (p&lt;0.01) different allele variation between colonic vs ileal CD. Of these, 170 genes associated with 116 distinct SNPs had a CADD score of &gt;10. Out of the top five SNP candidate associated genes, four (4/5 = 80%: EFNA3, STEAP1B, DSG1, and CYP4F2) have been already linked with Crohn’s disease and/or colitis. GORILLA based investigation indicated that colonic CD associated genes were enriched (p&lt;0.001) in biologic function relevant for lipid metabolic process (GO:0006629), small molecule metabolic process (GO:0044281), and organic substance metabolic process (GO:0071704) compared to ileal CD associated genes.

Conclusions
We have uncovered candidate genetic risk loci, which may differentially influence pediatric CD towards developing primarily small intestinal or colonic complications. The discovered loci hold significant potential as novel genetic modifiers, which may set the basis for risk assessment, prevention and personalized treatment against complicated pediatric CD.
UTILIZATION OF WHOLE EXOME SEQUENCING DATA TO IDENTIFY CLINICALLY RELEVANT PHARMACOGENOMIC VARIANTS IN INFLAMMATORY BOWEL DISEASE
Authors: Mulder Daniel , Khalouei Sam , Warner Neil , Gonzaga-Jauregui Claudia , Church Peter , Walters Tom , Ramani Arun , Griffiths Anne , Cohn Iris , Muise Aleixo 
Published: January 2021

Abstract

Objectives
We hypothesized that variants within clinically relevant pharmacogenes could be identified using a whole exome sequencing (WES) dataset derived from a cohort of over 1000 IBD patients.

Methods
Pediatric patients diagnosed with IBD underwent WES. We selected 18 genes with supporting literature where specific exonic variants would influence clinical care.

Results
We identified actionable pharmacogenes variants in 63% of patients. Importantly, 5% of IBD patients were at risk for serious adverse effects from anaesthesia and 3% were at increased risk for thrombosis.

Conclusions
We identified exonic variants in the majority of our IBD patients that directly impact clinical care.

Flowchart of our pharmacogenomic analysis pipeline. After enrolment (n=2309), each patient underwent whole exome sequencing and sequence alignment. Available family members were also sequenced. Analyzed samples were limited to patients and family members with IBD (n=1097). Pharmacogenes relevant to patients with IBD were identified by literature review and evaluation of pharmGKB (total of 18 genes). Variant filtering was performed using Stargazer and GEMINI frameworks. In our cohort, there were 8 relevant pharmacogenes with variants that would alter clinical care based on current guidelines and standard of care. 63% of the patients had at least one variant that could impact care.
BMC322- A RATIONALLY-DESIGNED LIVE BACTERIAL CONSORTIUM BASED ON MICROBIOME FUNCTIONAL GENOMIC ANALYSIS FOR TREATMENT OF IBD
Authors: Polonsky Omri , Meshner Shiri , Eshar Shiri , Ben-Shabat Sheerli Kruger , Tirosh Osnat , Haber Elran , Ringel Yehuda 
Published: January 2021

Abstract
The mechanisms by which the intestinal microbiome affects intestinal inflammation and disease activity in IBD is not clear. Most of the current data on the association between the intestinal microbiome and IBD is focusing on the intestinal microbial taxa and very little is known about the functionality of the microbiome in this condition.
Aim: To construct a live bacterial consortium for reduction of intestinal inflammation in IBD based on a high-resolution functional microbial analysis, and its association with anti-inflammatory processes.
Methods: Fecal metagenomics samples (n=581) and corresponding fecal calprotectin (FCP) levels from patients with Crohn’s disease and Ulcerative Colitis were downloaded from the NCBI (SRA SRP057027, http://hmpdacc.org, SRA SRP002163 and SRP056641 (BioProject PRJNA275349)).
Computational analysis was performed using PRISM (Biomica Ltd, Rehovot Israel), a proprietary metagenomics analysis platform integrating assembly-based and reference-based analyses for functional genomics profiling and utilizing BioCOGS, Biomica’s internal comprehensive catalogue of microbial gene-orthology groups. We compared microbial functions between subjects based on severity of inflammation (FCP&lt;70 vs FCP &gt;250 and FCP &gt;250 vs FCP &lt;250) and identified microbial functions associated with low inflammation (FDR 0.1).
Validation of the anti-inflammatory activity of BMC322 was performed using a DSS-induced colitis mouse model.
Results: Out of the dozens of identified functions, 32 were related to host anti-inflammatory processes, intestinal barrier integrity and colonocyte function. Our functional microbiome investigation has pointed to novel metabolic mechanisms by which specific strains may attenuate mucosal inflammation. Using functional annotations, we infer the biological processes governing microbe-host interactions contributing to reduced inflammation, and identify 16 bacteria of which 4 strains comprise the full array of the identified microbial functions associated with lower disease severity. These strains comprise BMC322- a novel live-bacterial consortium for inflammation reduction in IBD.
The anti-inflammatory activity of these strains was validated in in-vitro studies and demonstrated efficacy in preliminary a mouse model of DSS-induced colitis; including shortening period of recovery, disease activity index and fecal lipocalin 2.
Conclusion: High-resolution functional genomics profiling of the gut microbiome enables identification of microbial-derived functions relevant to inflammatory disease activity, and microbial strains bearing specific inflammation-reduction activity. These strains have provided the basis for the construction of a 4-strain consortium for intervention in IBD. Preliminary work has validated the anti-inflammatory activity of these strains and their potential as novel therapeutic modality for IBD.
DIETARY FIBER DEPRIVATION QUELLS COLONIC INFLAMMATION BY TARGETING GUT PATHOBIONTS IN A NEW MODEL OF CROHN’S DISEASE
Authors: Caruso Roberta , Kuffa Peter , Inohara Naohiro , Nunez Gabriel 
Published: January 2021

Abstract
Crohn’s disease (CD) is a chronic intestinal inflammatory disorder that results from a dysregulated mucosal immune response to symbiotic bacteria in genetically susceptible individuals. While genetic predispositions to CD have been well documented, the overall contribution of genetic factors to disease development remains unclear. Indeed, abnormal interactions between microbes and the immune system have been identified as the core defect leading to chronic intestinal inflammation. We used a “multi-hit” genetic approach to study the complex interplay between host immunity and microbes in the context of CD. We have found that the combined deficiency of NOD2 and phagocyte NADPH oxidase (i.e. CYBB), two CD susceptibility genes, triggers microbiota-dependent and spontaneous TH1-type colitis in mice that is accompanied by the pathological hallmarks seen in CD patients. Disease was induced by Mucispirillum schaedleri, a gram-negative mucus-dwelling anaerobe. The absence of the two anti-microbial genes (i.e. NOD2 and CYBB) resulted in a marked accumulation of M. schaedleri in the gut lumen, the colonic mucus layer and ultimately a focal penetration of the intestinal wall. Accumulation of M. schaedleri was associated with impaired recruitment of neutrophils in the intestine and subsequently inefficient elimination of the bacterium. Among the environmental factors associated with CD, diet shapes the composition of the gut microbiota and can be used to manage disease symptoms. Our experiments have shown that consumption of a fiber-free diet leads to a depletion of the colonic mucus layer and increased proximity between microbes and the gut epithelium. Interestingly, these experimental conditions are effective at inhibiting intestinal inflammation observed in our model of CD-like colitis when used both as a preventive and as a therapeutic approach. In addition to shaping the overall gut microbiota composition, this dietary intervention specifically alters the abundance and/or localization of the disease-causing M. schaedleri in the double mutant mice. Our results provide direct evidence that a specific intestinal microbe can, in conjunction with impaired bacterial clearance, trigger CD-like disease. Our results also indicate that dietary approaches can be successfully used to target microbial-driven intestinal pathology.
EXPLORING CO-INFECTIONS IN THE GASTROINTESTINAL TRACT: DISSECTING THE INTERACTION BETWEEN FUSOBACTERIUM NUCLEATUM AND CLOSTRIDIODES DIFFICILE
Authors: Engevik Melinda , Danhof Heather , Auchtung Jennifer , Nicholson Maribeth , Wu Qinglong , Savidge Tor , Britton Robert , Versalovic James 
Published: January 2021

Abstract

Background
Clostridioides difficile is a common healthcare associated pathogen in U.S. hospitals, incurring billions of dollars in treatment costs each year. Microbiome analysis of C. difficile infected (CDI) patients have revealed alterations of the gut microbiota. It has been speculated that select members of this altered microbiota may influence C. difficile pathogenesis. C. difficile is known to reside in the intestinal mucus layer, but at present the interactions between C. difficile and other mucus-associated bacteria are poorly defined. To address these gaps in knowledge, we have focused on an entirely human-centered approach, employing human-derived MUC2, fecal bioreactors and patient samples. We hypothesized that select mucus-associated bacteria would promote C. difficile colonization and biofilm formation.

Methods & Results
To create a model of the human intestinal mucus layer and gut microbiota, we developed a bioreactor system with human MUC2-coated coverslips. Bioreactors were inoculated with healthy human feces, treated with clindamycin and infected with C. difficile to mimic CDI. C. difficile was found to colonize and form biofilms on MUC2-coated coverslips and 16S rRNA sequencing revealed a unique biofilm profile with substantial co-colonization with Fusobacterium. Consistent with our bioreactor data, publicly available datasets and patient stool samples revealed that a subset of patients with C. difficile infection harbored high levels of F. nucleatum OTUs. We also isolated microbes from adult patients and pediatric IBD patient stool who were positive for C. difficile and F. nucleatum and identified co-localization between these strains. RNAseq data revealed significant changes in C. difficile chemotaxis and surface adhesion genes following exposure to F. nucleatum metabolites. C. difficile was found to co-aggregate with F. nucleatum; an effect that was inhibited by blocking the Fusobacterial adhesin RadD and C. difficile flagella. Moreover, a ΔradD mutant of F. nucleatum lost the ability to aggregate with C. difficile. Conversely, removal of flagella from C. difficile significantly reduced the interaction between WT F. nucleatum and C. difficile. Addition of F. nucleatum also enhanced C. difficile biofilm formation, increasing the levels extracellular polysaccharide.

Conclusions
Collectively, these data demonstrate the unique role of mucus-associated bacteria such as F. nucleatum in facilitating colonization of the mucus layer by pathogenic C. difficile.
DIAGNOSIS CHANGES IN PEDIATRIC IBD: DATA FROM THE IMPROVECARENOW REGISTRY
Authors: Sandberg Kelly , Duarte Harold , Stolfi Adrienne , Saeed Shehzad 
Published: January 2021

Abstract

Background
The change in subclassification of inflammatory bowel diseases (IBD) among patients with Crohn’s (CD), ulcerative colitis (UC), and IBD-unclassified (IBD-u) has previously been described in subpopulations of adult and pediatric patients. To date, no large, multinational registries have described characteristics of pediatric patients who change diagnosis.

Methods
We used the largest (27,628 individual patients for this study) prospective registry in the world for pediatric patients with IBD, ImproveCareNowR (ICN) to characterize those who change diagnosis. Diagnosis in the ICN registry is based on the Paris classification.

Results
7.52% of pediatric patients had any change in diagnosis; 5.19% of patients experienced a change in diagnosis after the initial 3 visits (Table 1). Those who start with a diagnosis of Crohn’s are more likely to change, as compared with starting diagnoses of ulcerative colitis or IBD-u (p &lt; 0.05). A majority of changes involve a diagnosis of IBD-u (75.8%, Figure 1). Among those who change diagnoses, those with initial diagnoses of Crohn’s or IBD-u are more likely to have a BMI Z-score of less than -2, as compared to those with initial diagnosis of UC (p &lt; 0.05). Patients with initial diagnosis of Crohn’s who changed after 3 visits were less likely to have ileocolonic extent, penetrating or stricturing phenotype, or perianal disease documented (p &lt; 0.05). Signs of initial miscoding occurred in less than 0.3% of patients.

Discussion
This is the first reported use of a large prospective pediatric registry to investigate diagnosis changes within IBD. Registration diagnosis of Crohn’s appears to have more clinically impactful findings than those with UC or IBD-u. A majority of all changes involved a diagnosis of IBD-unclassified. Further investigation of diagnosis changes across time and modeling will supplement our understanding of clinical factors predictive of change.