Xiuliang Bao

The features of mucosa-associated microbiota in primary sclerosing cholangitis

Little is known about the role of the microbiome in primary sclerosing cholangitis.

Trefoil factor-3 expression in human colon cancer liver metastasis.

Deaths from colorectal cancer are often due to liver metastasis. Trefoil factor-3 (TFF3) is expressed by normal intestinal epithelial cells and its expression is maintained throughout the colon adenoma-carcinoma sequence. Our previous work demonstrated a correlation between TFF3 expression and metastatic potential in an animal model of colon cancer. The aim of this study was to determine whether TFF3 is expressed in human colon cancer liver metastasis (CCLM) and whether inhibiting TFF3 expression in colon cancer cells would alter their invasive potential in vitro. Human CCLMs were analyzed at the mRNA and protein level for TFF3 expression. Two highly metastatic rat colon cancer cell lines that either natively express TFF3 (LN cells) or were transfected with TFF3 (LPCRI-2 cells), were treated with two rat TFF3 siRNA constructs (si78 and si365), and analyzed in an in vitro invasion assay. At the mRNA and protein level, TFF3 was expressed in 17/17 (100%) CCLMs and 10/11 (91%) primary colon cancers, but not in normal liver tissue. By real time PCR, TFF3 expression was markedly inhibited by both siRNA constructs in LN and LPCRI-2 cells. The si365 and si78 constructs inhibited invasion by 44% and 53%, respectively, in LN cells, and by 74% and 50%, respectively, in LPCRI-2 cells. These results provide further evidence that TFF3 contributes to the malignant behavior of colon cancer cells. These observations may have relevance for designing new diagnostic and treatment approaches to colorectal cancer.

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

BackgroundHigh-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rRNA gene reads into biologically meaningful OTUs is challenging, in part because nucleotide variation along the 16S rRNA gene is only partially captured by short reads. The recent emergence of long-read platforms, such as single-molecule real-time (SMRT) sequencing from Pacific Biosciences, offers the potential for improved taxonomic and phylogenetic profiling. Here, we evaluate the performance of long- and short-read 16S rRNA gene sequencing using simulated and experimental data, followed by OTU inference using computational pipelines based on heuristic and complete-linkage hierarchical clustering.ResultsIn simulated data, long-read sequencing was shown to improve OTU quality and decrease variance. We then profiled 40 human gut microbiome samples using a combination of Illumina MiSeq and Blautia-specific SMRT sequencing, further supporting the notion that long reads can identify additional OTUs. We implemented a complete-linkage hierarchical clustering strategy using a flexible computational pipeline, tailored specifically for PacBio circular consensus sequencing (CCS) data that outperforms heuristic methods in most settings: https://github.com/oscar-franzen/oclust/.ConclusionOur data demonstrate that long reads can improve OTU inference; however, the choice of clustering algorithm and associated clustering thresholds has significant impact on performance.

Farnesoid X receptor expression is decreased in colonic mucosa of patients with primary sclerosing cholangitis and colitis-associated neoplasia.

Background:The expression and distribution of farnesoid X receptor (FXR) in colitis and colitis-associated neoplasia (CAN) is unknown. We investigated FXR expression in neoplastic and nonneoplastic tissue from ulcerative colitis (UC) patients, with or without primary sclerosing cholangitis (PSC), as well as the role of DNA methylation in FXR expression in colorectal cancer (CRC) cell lines. Methods:Samples from the right (RC) and left (LC) colon of patients with UC, with and without PSC, and with or without CAN, were stained by immunohistochemistry and scored semiquantitatively for nuclear FXR expression. FXR expression was analyzed by western blot and polymerase chain reaction (PCR) in nine different CRC cell lines before and after demethylation with 5-azacytidine. Results:In nondysplastic samples, FXR expression demonstrated a diminishing expression from proximal to distal colon (strong FXR expression: 39% RC samples vs. 14% LC samples; P = 0.007). With moderate-to-severe inflammation, FXR expression was almost always absent or weak in both UC and PSC-UC, regardless of location. With quiescent/mild inflammation, 56% of UC samples in the RC retained strong FXR expression versus 24% of PSC-UC samples (P= 0.017). FXR was absent in 72% of the neoplastic samples, with an inverse association with the grade of dysplasia. FXR expression was absent in all CRC cell lines, in some cases due to DNA methylation. Conclusions:FXR expression is inversely correlated with neoplastic progression and severity of inflammation in UC. Patients with PSC-UC have diminished FXR expression in the proximal colon compared to UC patients. This finding could contribute to the higher risk of proximal neoplasia in PSC patients.

The gut microbiota, bile acids and their correlation in primary sclerosing cholangitis associated with inflammatory bowel disease:

Background Patients with primary sclerosing cholangitis associated with inflammatory bowel disease (PSC-IBD) have a very high risk of developing colorectal neoplasia. Alterations in the gut microbiota and/or gut bile acids could account for the increase in this risk. However, no studies have yet investigated the net result of cholestasis and a potentially altered bile acid pool interacting with a dysbiotic gut flora in the inflamed colon of PSC-IBD. Aim The aim of this study was to compare the gut microbiota and stool bile acid profiles, as well as and their correlation in patients with PSC-IBD and inflammatory bowel disease alone. Methods Thirty patients with extensive colitis (15 with concomitant primary sclerosing cholangitis) were prospectively recruited and fresh stool samples were collected. The microbiota composition in stool was profiled using bacterial 16S rRNA sequencing. Stool bile acids were assessed by high-performance liquid chromatography tandem mass spectrometry. Results The total stool bile acid pool was significantly reduced in PSC-IBD. Although no major differences were observed in the individual bile acid species in stool, their overall combination allowed a good separation between PSC-IBD and inflammatory bowel disease. Compared with inflammatory bowel disease alone, PSC-IBD patients demonstrated a different gut microbiota composition with enrichment in Ruminococcus and Fusobacterium genus compared with inflammatory bowel disease. At the operational taxonomic unit level major shifts were observed within the Firmicutes (73%) and Bacteroidetes phyla (17%). Specific microbiota-bile acid correlations were observed in PSC-IBD, where 12% of the operational taxonomic units strongly correlated with stool bile acids, compared with only 0.4% in non-PSC-IBD. Conclusions Patients with PSC-IBD had distinct microbiota and microbiota-stool bile acid correlations as compared with inflammatory bowel disease. Whether these changes are associated with, or may predispose to, an increased risk of colorectal neoplasia needs to be further clarified.

Infants Born to Mothers with Inflammatory Bowel Disease Exhibit Distinct Microbiome Features that Persist Up to 3 Months of Life

analysis. Pregnant women with IBD present an enrichment in bacteria from the Gammaproteobacteria class, and a decrease in bacteria from the Bacteroidetes phylum, as compared to women without IBD. (B) Beta-diversity of placenta samples (p=0.001, Permanova, unweighted Unifrac distances). Women with and without IBD exhibit distinct placental microbiota composition. · Studies have demonstrated dynamic changes in the microbiome during pregnancy coinciding with changes in immune status, and maternal health status has been shown to influence the newborn’s microbiome development. Women with Inflammatory Bowel Disease (IBD) exhibit immunological and gut microbiota alterations. · No data exist on the effect of IBD on the microbiome during pregnancy, and its role on the infant gut microbiota composition. · The “Exploring MEChanisms Of disease traNsmission In Utero through the Microbiome” (MECONIUM) Study is a prospective study that recruits pregnant women with and without IBD and their offspring. The overall goal of the MECONIUM study is to explore the role that IBD plays in the composition of the maternal and infant microbiome. Infants Born to Mothers with Inflammatory Bowel Disease Exhibit Distinct Microbiome Features That Persist up to 3 Months of Life Caroline Eisele1, Jianzhong Hu1, Joana Torres1,2, Nilendra Nair1, Hinaben Panchal1, Xiuliang Bao1, Xiaohong Niu1, Justin Côté-Daigneault2, Bindia Jharap2, Elana Maser2, Asher Kornbluth2, Peter Legnani2, James George2, Marla Dubinsky3, Joanne Stone4, Ching-Lynn Chen4, José Clemente1, Jean-Frédéric Colombel2, Inga Peter1 1Department of Genetics and Genomic Sciences; 2-Division of Gastroenterology, Department of Medicine; 3-Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics; 4-Department of Obstetrics, Gynecology and Reproductive Sciences

Location-Specific Oral Microbiome Possesses Features Associated With CKD

Introduction Chronic kidney disease (CKD), a progressive loss of renal function, can lead to serious complications if underdiagnosed. Many studies suggest that the oral microbiota plays important role in the health of the host; however, little is known about the association between the oral microbiota and CKD pathogenesis. Methods In this study, we surveyed the oral microbiota in saliva, the left and right molars, and the anterior mandibular lingual area from 77 participants (18 with and 59 without CKD), and tested their association with CKD to identify microbial features that may be predictive of CKD status. Results The overall oral microbiota composition significantly differed by oral locations and was associated with CKD status in saliva and anterior mandibular lingual samples. In CKD patients, we observed a significant enrichment of Neisseria and depletion of Veillonella in both sample types and a lower prevalence of Streptococcus in saliva after adjustment for other comorbidities. Furthermore, we detected a negative association of Neisseria and Streptococcus genera with the kidney function as measured by estimated glomerular filtration rate. Neisseria abundance also correlated with plasma interleukin-18 levels. Conclusion We demonstrate the association of the oral microbiome with CKD and inflammatory kidney biomarkers, highlighting a potential role of the commensal bacteria in CKD pathogenesis. A better understanding of the interplay between the oral microbiota and CKD may help in the development of new strategies to identify at-risk individuals or to serve as a novel target for therapeutic intervention.

Translational ResearchLocation-Specific Oral Microbiome Possesses Features Associated With Chronic Kidney Disease

Introduction Chronic kidney disease (CKD), a progressive loss of renal function, can lead to serious complications if underdiagnosed. Many studies suggest that the oral microbiota plays important role in the health of the host; however, little is known about the association between the oral microbiota and CKD pathogenesis. Methods In this study, we surveyed the oral microbiota in saliva, the left and right molars, and the anterior mandibular lingual area from 77 participants (18 with and 59 without CKD), and tested their association with CKD to identify microbial features that may be predictive of CKD status. Results The overall oral microbiota composition significantly differed by oral locations and was associated with CKD status in saliva and anterior mandibular lingual samples. In CKD patients, we observed a significant enrichment of Neisseria and depletion of Veillonella in both sample types and a lower prevalence of Streptococcus in saliva after adjustment for other comorbidities. Furthermore, we detected a negative association of Neisseria and Streptococcus genera with the kidney function as measured by estimated glomerular filtration rate. Neisseria abundance also correlated with plasma interleukin-18 levels. Conclusion We demonstrate the association of the oral microbiome with CKD and inflammatory kidney biomarkers, highlighting a potential role of the commensal bacteria in CKD pathogenesis. A better understanding of the interplay between the oral microbiota and CKD may help in the development of new strategies to identify at-risk individuals or to serve as a novel target for therapeutic intervention.

Location-Specific Oral Microbiome Possesses Features Associated With Chronic Kidney Disease

Introduction Chronic kidney disease (CKD), a progressive loss of renal function, can lead to serious complications if underdiagnosed. Many studies suggest that the oral microbiota plays important role in the health of the host; however, little is known about the association between the oral microbiota and CKD pathogenesis. Methods In this study, we surveyed the oral microbiota in saliva, the left and right molars, and the anterior mandibular lingual area from 77 participants (18 with and 59 without CKD), and tested their association with CKD to identify microbial features that may be predictive of CKD status. Results The overall oral microbiota composition significantly differed by oral locations and was associated with CKD status in saliva and anterior mandibular lingual samples. In CKD patients, we observed a significant enrichment of Neisseria and depletion of Veillonella in both sample types and a lower prevalence of Streptococcus in saliva after adjustment for other comorbidities. Furthermore, we detected a negative association of Neisseria and Streptococcus genera with the kidney function as measured by estimated glomerular filtration rate. Neisseria abundance also correlated with plasma interleukin-18 levels. Conclusion We demonstrate the association of the oral microbiome with CKD and inflammatory kidney biomarkers, highlighting a potential role of the commensal bacteria in CKD pathogenesis. A better understanding of the interplay between the oral microbiota and CKD may help in the development of new strategies to identify at-risk individuals or to serve as a novel target for therapeutic intervention.

Mo1757 Evidence for a Role of Superantigens in the Pathogenesis of Ulcerative Colitis-Associated Primary Sclerosing Cholangitis

G A A b st ra ct s 0.002) and downregulation of Mmp-2 (FC=3.3, p=0.020), Mmp-9 (FC=3.1, p=0.030), Cldn1 (FC=3, p=0.040) compared to control mice. After chronic DSS administration, Xpnpep2 (FC=4.2, p=0.020) was upregulated in TIMP-1 KO mice compared to control mice. Young TIMP-1 KO mice (10-12 weeks) versus older animals (19-21 weeks) showed significantly increased expression of Reg3g (FC=16, p=0.030), Reg3b (FC=12.6, p=0.040) and Ido1 (FC= 3.5, p=0.008), whereas the expression levels of Mir200b (FC=2.2, p=0.009), Ctse (FC=1.3, p=0.030) and Wnt2b (FC=1.1, p=0.002) were decreased. Conclusion: TIMP-1 deficiency leads to upregulation of anti-bacterial and innate immunity genes, resulting in an attenuated development of acute colitis. In a chronic setting of inflammation, TIMP-1 KO mice have less remodeling and fibrosis. Unraveling the role of TIMP-1 in extracellular matrix remodeling will be necessary to understand the biology of intestinal wound healing and fibrosis in IBD.