Dataset Information

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.

ABSTRACT: Although genetic approaches are the standard in microbiome analysis, proteome-level information is largely absent. This discrepancy warrants a better understanding of the relationship between gene copy number and protein abundance, as this is crucial information for inferring protein-level changes from metagenomic data. As it remains unknown how metaproteomic systems evolve during dynamic disease states, we leveraged a 4.5-year fecal time series using samples from a single patient with colonic Crohn's disease. Utilizing multiplexed quantitative proteomics and shotgun metagenomic sequencing of eight time points in technical triplicate, we quantified over 29,000 protein groups and 110,000 genes and compared them to five protein biomarkers of disease activity. Broad-scale observations were consistent between data types, including overall clustering by principal-coordinate analysis and fluctuations in Gene Ontology terms related to Crohn's disease. Through linear regression, we determined genes and proteins fluctuating in conjunction with inflammatory metrics. We discovered conserved taxonomic differences relevant to Crohn's disease, including a negative association of Faecalibacterium and a positive association of Escherichia with calprotectin. Despite concordant associations of genera, the specific genes correlated with these metrics were drastically different between metagenomic and metaproteomic data sets. This resulted in the generation of unique functional interpretations dependent on the data type, with metaproteome evidence for previously investigated mechanisms of dysbiosis. An example of one such mechanism was a connection between urease enzymes, amino acid metabolism, and the local inflammation state within the patient. This proof-of-concept approach prompts further investigation of the metaproteome and its relationship with the metagenome in biologically complex systems such as the microbiome. IMPORTANCE A majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a patient with colonic Crohn's disease. Our results indicate that despite a low level of correlation, taxonomic associations were consistent in the two data types. While there was overlap of the data types, several associations were uniquely discovered by analyzing the metaproteome component. This case study provides unique and important insights into the fundamental relationship between the genes and proteins of a single individual's fecal microbiome associated with clinical consequences.

SUBMITTER: Mills RH

PROVIDER: S-EPMC6372841 | biostudies-literature | 2019 Jan-Feb

REPOSITORIES: biostudies-literature

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Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.

Mills Robert H RH Vázquez-Baeza Yoshiki Y Zhu Qiyun Q Jiang Lingjing L Gaffney James J Humphrey Greg G Smarr Larry L Knight Rob R Gonzalez David J DJ

mSystems 20190101 1

Although genetic approaches are the standard in microbiome analysis, proteome-level information is largely absent. This discrepancy warrants a better understanding of the relationship between gene copy number and protein abundance, as this is crucial information for inferring protein-level changes from metagenomic data. As it remains unknown how metaproteomic systems evolve during dynamic disease states, we leveraged a 4.5-year fecal time series using samples from a single patient with colonic C ...[more]

PMID: 30801026

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Project description:BackgroundThis study aims to characterize, the gut and oral microbiome in Asian subjects with Crohn's disease (CD) using whole genome shotgun sequencing, thereby allowing for strain-level comparison.MethodsA case-control study with age, sex and ethnicity matched healthy controls was conducted. CD subjects were limited to well-controlled patients without oral manifestations. Fecal and saliva samples were collected for characterization of gut and oral microbiome respectively. Microbial DNA were extracted, libraries prepared and sequenced reads profiled. Taxonomic diversity, taxonomic association, strain typing and microbial gene pathway analyses were conducted.ResultsThe study recruited 25 subjects with CD and 25 healthy controls. The oral microbe Streptococcus salivarius was found to be enriched and of concordant strains in the gut and oral microbiome of Crohn's disease subjects. This was more likely in CD subjects with higher Crohn's Disease Activity Index (184.3?±?2.9 vs 67.1?±?82.5, p?=?0.012) and active disease status (Diarrhoea/abdominal pain/blood-in-stool/fever and fatigue) (p?=?0.016). Gut species found to be significantly depleted in CD compared to control (Relative abundance: Median[Range]) include: Faecalibacterium prausnitzii (0.03[0.00-4.56] vs 13.69[5.32-18.71], p?=?0.010), Roseburia inulinivorans (0.00[0.00-0.03] vs 0.21[0.01-0.53], p?=?0.010) and Alistipes senegalensis (0.00[0.00-0.00] vs 0.00[0.00-0.02], p?=?0.029). While Clostridium nexile (0.00[0.00-0.12] vs 0.00[0.00-0.00], p?=?0.038) and Ruminococcus gnavus (0.43[0.02-0.33] vs 0.00[0.00-0.13], p?=?0.043) were found to be enriched. C. nexile enrichment was not found in CD subjects of European descent. Microbial arginine (Linear-discriminant-analysis: 3.162, p?=?0.001) and isoprene (Linear-discriminant-analysis: 3.058, p?<?0.001) pathways were found at a higher relative abundance level in gut microbiome of Crohn's disease.ConclusionsThere was evidence of ectopic gut colonization by oral bacteria, especially during the active phase of CD. Previously studied gut microbial differences were detected, in addition to novel associations which could have resulted from geographical/ethnic differences to subjects of European descent. Differences in microbial pathways provide possible targets for microbiome modification.

Project description:Background and Aim:Interleukin-21 (IL-21) is primarily a T cell-derived cytokine; it is upregulated in patients with Crohn's Disease (CD) and could be a potential new therapeutic target in CD. Methods:In human material, IL-21 and IL-21R expression was investigated by in situ hybridization (ISH) and immunohistochemistry (IHC) in noninflammatory bowel disease (non-IBD) controls and patients with CD. The pathologic role of IL-21 was examined in murine models of T cell-dependent and T cell-independent colitis, either with a neutralizing monoclonal antibody against IL-21 or with the transfer of CD4+CD45RBhighIL-21R-/- T cells. Colonic pathology was examined by endoscopy, histopathology, IHC, ELISA, and Luminex. Results:In the human intestine, IL-21 and IL-21R mRNA and protein-expressing cells were observed in the mucosa, in lymphoid aggregates of submucosa in non-IBD controls, and in lymphoid aggregates of muscularis externa in patients with CD. IL-21 expression was most abundant in germinal centers (GCs) of the lymphoid aggregates, and IL-21R expression assessed semiquantitatively, was significantly higher in patients with CD compared to non-IBD controls. Following prophylactic and interventive anti-IL-21 mAb treatment in the adoptive transfer (AdTr) model, clinical and pathological parameters were significantly reduced. The most persistent finding was a reduction in colonic infiltrating neutrophils. As well, Rag2-/- mice receiving CD4+CD45RBhighIL-21R-/- T cells developed less severe colitis compared to Rag2-/- mice receiving CD4+CD45RBhighIL-21R+/+ T cells. No effect of reduced IL-21 signalling was observed in T cell-independent colitis. Conclusion:Our study shows that patients with CD have significant expression of IL-21 and IL-21R in the gut. As well, we show that neutralization of IL-21 in experimental T cell-driven colitis is associated with a reduction in clinical and pathological findings. This amelioration seems to be associated with a reduction in colon-infiltrating neutrophils.

Project description:Endothelial dysfunction, largely dependent on impaired nitric oxide bioavailability, has been reportedly associated with incident type 2 diabetes. Our aim was to test the hypothesis that asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide formation, might be linked to future deterioration in glucose tolerance in stable coronary artery disease (CAD).We studied 80 non-diabetic men (mean age 55 +/- 11 years) with stable angina who underwent successful elective complex coronary angioplasty and were receiving a standard medical according to practice guidelines. Plasma ADMA and its structural isomer symmetric dimethylarginine (SDMA) were measured prior to coronary angiography. An estimate of insulin resistance by homeostasis model assessment (HOMA-IR index) was calculated from fasting insulin and glucose. Deterioration in glucose tolerance was defined as development of type 2 diabetes or progression from a normal glucose tolerance to impaired fasting glucose.Over a median follow-up of 55 months 11 subjects developed type 2 diabetes and 13 progressed to impaired fasting glucose. Incident deterioration of glucose tolerance was associated with ADMA (hazard ratio [HR] per 1-SD increment 1.64 [95% CI: 1.14--2.35]; P = 0.007), log (HOMA-IR index) (HR = 1.60 [1.16--2.20]; P = 0.004) and body-mass index (HR = 1.44 [0.95--2.17]; P = 0.08) by univariate Cox regression. ADMA (HR = 1.65 [1.14--2.38]; p = 0.008) and log (HOMA-IR index) (HR = 1.55 [1.10--2.17]; P = 0.01) were multivariate predictors of a decline in glucose tolerance. ADMA and SDMA were unrelated to body-mass index, HOMA-IR index, insulin or glucose.ADMA predicts future deterioration of glucose tolerance independently of baseline insulin resistance in men with stable CAD. Whether this association reflects a contribution of endothelial dysfunction to accelerated decline of insulin sensitivity, or represents only an epiphenomenon accompanying pre-diabetes, remains to be elucidated. The observed relationship might contribute to the well-recognized ability of ADMA to predict cardiovascular outcome.

Project description:BACKGROUND:Stricturing and penetrating complications account for substantial morbidity and health-care costs in paediatric and adult onset Crohn's disease. Validated models to predict risk for complications are not available, and the effect of treatment on risk is unknown. METHODS:We did a prospective inception cohort study of paediatric patients with newly diagnosed Crohn's disease at 28 sites in the USA and Canada. Genotypes, antimicrobial serologies, ileal gene expression, and ileal, rectal, and faecal microbiota were assessed. A competing-risk model for disease complications was derived and validated in independent groups. Propensity-score matching tested the effect of anti-tumour necrosis factor ? (TNF?) therapy exposure within 90 days of diagnosis on complication risk. FINDINGS:Between Nov 1, 2008, and June 30, 2012, we enrolled 913 patients, 78 (9%) of whom experienced Crohn's disease complications. The validated competing-risk model included age, race, disease location, and antimicrobial serologies and provided a sensitivity of 66% (95% CI 51-82) and specificity of 63% (55-71), with a negative predictive value of 95% (94-97). Patients who received early anti-TNF? therapy were less likely to have penetrating complications (hazard ratio [HR] 0·30, 95% CI 0·10-0·89; p=0·0296) but not stricturing complication (1·13, 0·51-2·51; 0·76) than were those who did not receive early anti-TNF? therapy. Ruminococcus was implicated in stricturing complications and Veillonella in penetrating complications. Ileal genes controlling extracellular matrix production were upregulated at diagnosis, and this gene signature was associated with stricturing in the risk model (HR 1·70, 95% CI 1·12-2·57; p=0·0120). When this gene signature was included, the model's specificity improved to 71%. INTERPRETATION:Our findings support the usefulness of risk stratification of paediatric patients with Crohn's disease at diagnosis, and selection of anti-TNF? therapy. FUNDING:Crohn's and Colitis Foundation of America, Cincinnati Children's Hospital Research Foundation Digestive Health Center.

Dataset Information

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.

Publications

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.

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