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Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.

ABSTRACT: Molecular mechanisms driving disease course and response to therapy in ulcerative colitis (UC) are not well understood. Here, we use RNAseq to define pre-treatment rectal gene expression, and fecal microbiota profiles, in 206 pediatric UC patients receiving standardised therapy. We validate our key findings in adult and paediatric UC cohorts of 408 participants. We observe a marked suppression of mitochondrial genes and function across cohorts in active UC, and that increasing disease severity is notable for enrichment of adenoma/adenocarcinoma and innate immune genes. A subset of severity genes improves prediction of corticosteroid-induced remission in the discovery cohort; this gene signature is also associated with response to anti-TNF? and anti-?4?7 integrin in adults. The severity and therapeutic response gene signatures were in turn associated with shifts in microbes previously implicated in mucosal homeostasis. Our data provide insights into UC pathogenesis, and may prioritise future therapies for nonresponders to current approaches.

SUBMITTER: Haberman Y

PROVIDER: S-EPMC6318335 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.

Haberman Yael Y Karns Rebekah R Dexheimer Phillip J PJ Schirmer Melanie M Somekh Judith J Jurickova Ingrid I Braun Tzipi T Novak Elizabeth E Bauman Laura L Collins Margaret H MH Mo Angela A Rosen Michael J MJ Bonkowski Erin E Gotman Nathan N Marquis Alison A Nistel Mason M Rufo Paul A PA Baker Susan S SS Sauer Cary G CG Markowitz James J Pfefferkorn Marian D MD Rosh Joel R JR Boyle Brendan M BM Mack David R DR Baldassano Robert N RN Shah Sapana S Leleiko Neal S NS Heyman Melvin B MB Grifiths Anne M AM Patel Ashish S AS Noe Joshua D JD Aronow Bruce J BJ Kugathasan Subra S Walters Thomas D TD Gibson Greg G Thomas Sonia Davis SD Mollen Kevin K Shen-Orr Shai S Huttenhower Curtis C Xavier Ramnik J RJ Hyams Jeffrey S JS Denson Lee A LA

Nature communications 20190103 1

Molecular mechanisms driving disease course and response to therapy in ulcerative colitis (UC) are not well understood. Here, we use RNAseq to define pre-treatment rectal gene expression, and fecal microbiota profiles, in 206 pediatric UC patients receiving standardised therapy. We validate our key findings in adult and paediatric UC cohorts of 408 participants. We observe a marked suppression of mitochondrial genes and function across cohorts in active UC, and that increasing disease severity i ...[more]

PMID: 30604764

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Project description:Ulcerative colitis (UC) is a common chronic recurrent inflammatory disease, which seriously threatens human life and health. Therefore, the present study aimed to explore the role of tripartite motif‑containing (TRIM)22 in UC and its potential mechanism. C57BL/6 mice and HT‑29 cell models of UC were constructed using 2% dextran sulphate sodium (DSS). The protein and mRNA expression levels were detected by western blotting and reverse transcription‑quantitative PCR, respectively. Cell transfection was performed to overexpress Kruppel‑like factor 2 (KLF2), or knockdown KLF2, TRIM22 and TRIM30 expression. The levels of inflammatory factors were evaluated by enzyme‑linked immunosorbent assays. Cell Counting Kit‑8 and TUNEL staining assay were employed to assess cell viability and apoptosis. Dual‑luciferase reporter assay and chromatin immunoprecipitation assay were performed to determine the binding ability of the TRIM22 promoter to KLF2. The results revealed that DSS increased the expression levels of TRIM22 in HT‑29 cells and TRIM30 in mice. Short hairpin RNA (sh)‑TRIM30 could inhibit the NF‑κB pathway, and reduce the levels of TNF‑α, IL‑6 and IFN‑γ. Furthermore, KLF2 expression was downregulated in the cell model of UC, and the luciferase assay confirmed that the 3' untranslated region of TRIM22 was a direct target of KLF2. The ChIP assay also verified the binding of KLF2 with the TRIM22 promoter. Notably, knockdown of KLF2 reversed the enhancing effects of sh‑TRIM22 on the viability of DSS‑treated HT‑29 cells. In addition, compared with in the DSS + sh‑TRIM22 group, the protein expression levels of phosphorylated (p)‑NF‑κB and p‑IκBα were increased in the DSS + sh‑TRIM22 + sh‑KLF2 group, as were the levels of TNF‑α, IL‑6 and IFN‑γ. In conclusion, TRIM22 was upregulated in DSS‑induced HT‑29 cells. TRIM22 knockdown increased DSS‑induced HT‑29 cell viability and decreased apoptosis and inflammation; this was reversed by knockdown of KLF2. These findings suggested that TRIM22 may promote disease development through the NF‑κB signaling pathway in UC and could be inhibited by KLF2 transcription.

Project description:ObjectiveThe pathogenesis of UC relates to gut microbiota dysbiosis. We postulate that alterations in the viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to characterise the mucosal virome and their functions in health and UC.DesignDeep metagenomics sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on the rectal mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76). Virome and bacteriome alterations in UC mucosa were assessed and correlated with patient metadata. We applied partition around medoids clustering algorithm and classified mucosa viral communities into two clusters, referred to as mucosal virome metacommunities 1 and 2.ResultsIn UC, there was an expansion of mucosa viruses, particularly Caudovirales bacteriophages, and a decrease in mucosa Caudovirales diversity, richness and evenness compared with healthy controls. Altered mucosal virome correlated with intestinal inflammation. Interindividual dissimilarity between mucosal viromes was higher in UC than controls. Escherichia phage and Enterobacteria phage were more abundant in the mucosa of UC than controls. Compared with metacommunity 1, metacommunity 2 was predominated by UC subjects and displayed a significant loss of various viral species. Patients with UC showed substantial abrogation of diverse viral functions, whereas multiple viral functions, particularly functions of bacteriophages associated with host bacteria fitness and pathogenicity, were markedly enriched in UC mucosa. Intensive transkingdom correlations between mucosa viruses and bacteria were significantly depleted in UC.ConclusionWe demonstrated for the first time that UC is characterised by substantial alterations of the mucosa virobiota with functional distortion. Enrichment of Caudovirales bacteriophages, increased phage/bacteria virulence functions and loss of viral-bacterial correlations in the UC mucosa highlight that mucosal virome may play an important role in UC pathogenesis.

Project description:BackgroundVariability in endoscopic assessment necessitates rigorous investigation of descriptors for scoring severity of ulcerative colitis (UC).ObjectiveTo evaluate variation in the overall endoscopic assessment of severity, the intra- and interindividual variation of descriptive terms and to create an Ulcerative Colitis Endoscopic Index of Severity which could be validated.DesignA two-phase study used a library of 670 video sigmoidoscopies from patients with Mayo Clinic scores 0-11, supplemented by 10 videos from five people without UC and five hospitalised patients with acute severe UC. In phase 1, each of 10 investigators viewed 16/24 videos to assess agreement on the Baron score with a central reader and agreed definitions of 10 endoscopic descriptors. In phase 2, each of 30 different investigators rated 25/60 different videos for the descriptors and assessed overall severity on a 0-100 visual analogue scale. κ Statistics tested inter- and intraobserver variability for each descriptor. A general linear mixed regression model based on logit link and β distribution of variance was used to predict overall endoscopic severity from descriptors.ResultsThere was 76% agreement for 'severe', but 27% agreement for 'normal' appearances between phase I investigators and the central reader. In phase 2, weighted κ values ranged from 0.34 to 0.65 and 0.30 to 0.45 within and between observers for the 10 descriptors. The final model incorporated vascular pattern, (normal/patchy/complete obliteration) bleeding (none/mucosal/luminal mild/luminal moderate or severe), erosions and ulcers (none/erosions/superficial/deep), each with precise definitions, which explained 90% of the variance (pR(2), Akaike Information Criterion) in the overall assessment of endoscopic severity, predictions varying from 4 to 93 on a 100-point scale (from normal to worst endoscopic severity).ConclusionThe Ulcerative Colitis Endoscopic Index of Severity accurately predicts overall assessment of endoscopic severity of UC. Validity and responsiveness need further testing before it can be applied as an outcome measure in clinical trials or clinical practice.

Dataset Information

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.

Publications

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.

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