G-protein coupled receptor 35 (GPR35) regulates the colonic epithelial cell response to enterotoxigenic Bacteroides fragilis

G protein-coupled receptor (GPR)35 is highly expressed in the gastro-intestinal tract, predominantly in colon epithelial cells (CEC), and has been associated with inflammatory bowel diseases (IBD), suggesting a role in gastrointestinal inflammation. The enterotoxigenic Bacteroides fragilis (ETBF) toxin (BFT) is an important virulence factor causing gut inflammation in humans and animal models. We identified that BFT signals through GPR35. Blocking GPR35 function in CECs using the GPR35 antagonist ML145, in conjunction with shRNA knock-down and CRISPRcas-mediated knock-out, resulted in reduced CEC-response to BFT as measured by E-cadherin cleavage, beta-arrestin recruitment and IL-8 secretion. Importantly, GPR35 is required for the rapid onset of ETBF-induced colitis in mouse models. GPR35-deficient mice showed reduced death and disease severity compared to wild-type C57Bl6 mice. Our data support a role for GPR35 in the CEC and mucosal response to BFT and underscore the importance of this molecule for sensing ETBF in the colon

DESIGN AND CHARACTERIZATION OF SSDNA APTAMER CANDIDATES TO BIND BACTEROIDES FRAGILIS TOXIN SUBTYPES BFT-1 AND BFT-2

Enterotoxigenic Bacteroides fragilis (ETBF) is a diarrheal pathogen that secretes a twenty kilo-dalton protein toxin, Bacteroides fragilis toxin (BFT) which binds to an uncharacterized receptor on the surface of epithelial resulting in junctional cleavage causing chronic colitis. ETBF has also associated in colorectal cancer and irritable bowel disease patients. Magnetic bead based SELEX was used to generate aptamer pools with enriched binding specificity to BFT subtypes BFT-1 and BFT-2. A SYBR Green based Real-Time PCR assay was developed to monitor the enrichment of aptamer pools against BFT. Publicly available GUI based analyzed Illumina MiSeq sequencing aptamer pools. Secondary structure prediction algorithms and phylogeny trees of aptamer pool multiple sequence alignment data characterized eleven BFT binding aptamer candidates for future studies. These experiments demonstrate a simplified and easily adaptable set of methods for generating candidate ssDNA aptamers against bacterial protein toxins

Machine learning approaches in the prediction of positive axillary lymph nodes post neoadjuvant chemotherapy using MRI, CT, or ultrasound: A systematic review

Background and objective: Neoadjuvant chemotherapy is a standard treatment approach for locally advanced breast cancer. Conventional imaging modalities, such as magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound, have been used for axillary lymph node evaluation which is crucial for treatment planning and prognostication. This systematic review aims to comprehensively examine the current research on applying machine learning algorithms for predicting positive axillary lymph nodes following neoadjuvant chemotherapy utilizing imaging modalities, including MRI, CT, and ultrasound. Methods: A systematic search was conducted across databases, including PubMed, Scopus, and Web of Science, to identify relevant studies published up to December 2023. Articles employing machine learning algorithms to predict positive axillary lymph nodes using MRI, CT, or ultrasound data after neoadjuvant chemotherapy were included. The review follows the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, encompassing data extraction and quality assessment. Results: Seven studies were included, comprising 1502 patients. Four studies used MRI, two used CT, and one applied ultrasound. Two studies developed deep-learning models, while five used classic machine-learning models mainly based on multiple regression. Across the studies, the models showed high predictive accuracy, with the best-performing models combining radiomics and clinical data. Conclusion: This systematic review demonstrated the potential of utilizing advanced data analysis techniques, such as deep learning radiomics, in improving the prediction of positive axillary lymph nodes in breast cancer patients following neoadjuvant chemotherapy

Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria

Contains fulltext : 183987pub.pdf (publisher's version ) (Closed access

High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia.

Colorectal cancer (CRC) remains the third most common cancer worldwide, with a growing incidence among young adults. Multiple studies have presented associations between the gut microbiome and CRC, suggesting a link with cancer risk. Although CRC microbiome studies continue to profile larger patient cohorts with increasingly economical and rapid DNA sequencing platforms, few common associations with CRC have been identified, in part due to limitations in taxonomic resolution and differences in analysis methodologies. Complementing these taxonomic studies is the newly recognized phenomenon that bacterial organization into biofilm structures in the mucus layer of the gut is a consistent feature of right-sided (proximal), but not left-sided (distal) colorectal cancer. In the present study, we performed 16S rRNA gene amplicon sequencing and biofilm quantification in a new cohort of patients from Malaysia, followed by a meta-analysis of eleven additional publicly available data sets on stool and tissue-based CRC microbiota using Resphera Insight, a high-resolution analytical tool for species-level characterization. Results from the Malaysian cohort and the expanded meta-analysis confirm that CRC tissues are enriched for invasive biofilms (particularly on right-sided tumors), a symbiont with capacity for tumorigenesis (Bacteroides fragilis), and oral pathogens including Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus stomatis. Considered in aggregate, species from the Human Oral Microbiome Database are highly enriched in CRC. Although no detected microbial feature was universally present, their substantial overlap and combined prevalence supports a role for the gut microbiota in a significant percentage (>80%) of CRC cases

Erratum: Author Correction: High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia.

[This corrects the article DOI: 10.1038/s41522-017-0040-3.]

Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria.

Individuals with sporadic colorectal cancer (CRC) frequently harbor abnormalities in the composition of the gut microbiome; however, the microbiota associated with precancerous lesions in hereditary CRC remains largely unknown. We studied colonic mucosa of patients with familial adenomatous polyposis (FAP), who develop benign precursor lesions (polyps) early in life. We identified patchy bacterial biofilms composed predominately of Escherichia coli and Bacteroides fragilis Genes for colibactin (clbB) and Bacteroides fragilis toxin (bft), encoding secreted oncotoxins, were highly enriched in FAP patients colonic mucosa compared to healthy individuals. Tumor-prone mice cocolonized with E. coli (expressing colibactin), and enterotoxigenic B. fragilis showed increased interleukin-17 in the colon and DNA damage in colonic epithelium with faster tumor onset and greater mortality, compared to mice with either bacterial strain alone. These data suggest an unexpected link between early neoplasia of the colon and tumorigenic bacteria

High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia

Bowel cancer: Spotlight of suspicion on bacteria Many studies have found a link between gut microbes and bowel cancer, the third most common cancer worldwide. The details of the association, however, have remained elusive. Researchers in the USA and Malaysia, led by Dr. Cynthia Sears at John Hopkins School of Medicine in Maryland, examined mucosal biofilm status by fluorescence microscopy and performed a meta-analysis of bacterial genetic associations in stool and colon tissues to clarify the connection. They found that bowel cancers were enriched in invasive bacterial biofilms as well as several specific gut and oral species, including one - Fusobacterium nucleatum - known to promote tumorigenesis in mouse models. Analyzing gut microbial populations might help assess bowel cancer risk. Further research is needed, however, to determine if these  bacteria directly contribute to disease causality