Phenotype prediction based on microRNA expression profiles: a novel diagnostic tool for inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic relapsing disorder of the alimentary tract, encompassing Crohn's disease (CD) and ulcerative colitis (UC) as its two major subtypes. The diagnosis of inflammatory bowel disease remains a clinical challenge and involves the assessment of numerous parameters. A multitude of biomarkers has been proposed to complement the diagnostic process. However, none of them can be recommended for routine clinical practice. MicroRNAs (miRNAs) represent a class of short, non-coding RNAs that act as post-transcriptional regulators of gene expression. In the scope of this work we evaluate whether systematic miRNA or miRNA variant expression profiling, in conjunction with state-of-the-art machine learning techniques, is suitable as a non-invasive tool for diagnostics of IBD. In a first study we employed microarray technology to determine expression levels of 863 miRNAs for whole blood samples drawn from a cohort comprising 314 individuals, to establish miRNA signature being informative for the highly accurate distinction of CD and UC among each other as well as from healthy and inflammatory controls. In another study we extended this approach by additionally incorporating expression profiles of miRNA variants. We employed next generation sequencing technology to examine isomiR expression profiles drawn from a cohort of 515 individuals, comprising IBD cases as well as healthy and symptomatic controls. Incorporating distinctive isomiR signatures, we generated classifiers performing with median balanced accuracies of 78.57%/78.83% (untreated/treated CD vs. UC) and 100.00%/98.28% (untreated/treated CD or UC vs. HC), respectively. Hence, we provide sampling-based evidence for our models' superiority over established biomarkers.Bei entzündlichen Darmerkrankungen (IBD) handelt es sich um eine Gruppe chronischer, rezidivierender Krankheiten des Verdauungstraktes, die die Hauptformen Morbus Crohn (CD) und Colitis ulcerosa (UC) umfasst. Nach wie vor stellt die Diagnostik von IBD eine klinische Herausforderung dar und schließt die Bewertung zahlreicher Parameter ein. Als Ergänzung des diagnostischen Prozesses wurden zahlreiche Biomarker vorgeschlagen. Für die routinemäßige klinische Praxis jedoch kann keiner dieser Biomarker empfohlen werden. Bei microRNAs (miRNAs) handelt es sich um eine Klasse kurzer, nicht-kodierender RNAs, die als post-transkriptionelle Regulatoren der Genexpression fungieren. Unter Verwendung globaler Expressionprofile sowie Methoden des maschinellen Lernens, wird im Rahmen der vorliegenden Arbeit die Eignung dieser Moleküle als nicht-invasives Werkzeug für die Diagnose von IBD evaluiert. In einer ersten Studie verwendeten wir Microarray-Technologie zur Quantifizierung blutbasierter Expressionslevel von 863 miRNAs, generiert auf Grundlage einer 314 Individuen umfassenden Kohorte. Die resultierenden Expressionsprofile bildeten die Grundlage für die Etablierung von miRNA-Signaturen, hilfreich für die Unterscheidung zwischen CD and UC, sowie deren Abgrenzung von gesunden/inflammatorischen Kontrollen. In einer weiteren Studie wurde dieser Ansatz um die Berücksichtung von miRNA-Varianten erweitert. Wir verwendeten Sequenzier-Technologie zur Bestimmung von isomiR-Expressionsprofilen, generiert auf Grundlage einer Kohorte von 515 Individuen, einschließlich IBD-Patienten sowie gesunder/symptomatischer Kontrollen. Unter Verwendung von isomiR-Signaturen generierten wir Modelle, deren Klassifikationgüte wir mit medianen balanced accuracies von 78.57%/78.83% (CD vs. UC, unbehandelt/behandelt) bzw. 100.00%/98.28% (CD oder UC vs. HC, unbehandelt/behandelt) bewerten konnten. Damit liefern wir Belege für eine Überlegenheit unserer Modelle bezüglich etablierter Biomarker

Current Developments of Clinical Sequencing and the Clinical Utility of Polygenic Risk Scores in Inflammatory Diseases

In this mini-review, we highlight selected research by the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence "Precision Medicine in Chronic Inflammation" focusing on clinical sequencing and the clinical utility of polygenic risk scores as well as its implication on precision medicine in the field of the inflammatory diseases inflammatory bowel disease, atopic dermatitis and coronary artery disease. Additionally, we highlight current developments and discuss challenges to be faced in the future. Exemplary, we point to residual challenges in detecting disease-relevant variants resulting from difficulties in the interpretation of candidate variants and their potential interactions. While polygenic risk scores represent promising tools for the stratification of patient groups, currently, polygenic risk scores are not accurate enough for clinical setting. Precision medicine, incorporating additional data from genomics, transcriptomics and proteomics experiments, may enable the identification of distinct disease pathogeneses. In the future, data-intensive biomedical innovation will hopefully lead to improved patient stratification for personalized medicine

PSA and PSA Kinetics Thresholds for the Presence of 68Ga-PSMA-11 PET/CT-Detectable Lesions in Patients with Biochemical Recurrent Prostate Cancer

68Ga-PSMA-11 positron-emission tomography/computed tomography (PET/CT) is commonly used for restaging recurrent prostate cancer (PC) in European clinical practice. The goal of this study is to determine the optimum time for performing these PET/CT scans in a large cohort of patients by identifying the prostate-specific-antigen (PSA) and PSA kinetics thresholds for detecting and localizing recurrent PC. This retrospective analysis includes 581 patients with biochemical recurrence (BC) by definition. The performance of 68Ga-PSMA-11 PET/CT in relation to the PSA value at the scan time as well as PSA kinetics was assessed by the receiver-operating-characteristic-curve (ROC) generated by plotting sensitivity versus 1-specificity. Malignant prostatic lesions were identified in 77%. For patients that were treated with radical prostatectomy (RP) a PSA value of 1.24 ng/mL was found to be the optimal cutoff level for predicting positive and negative scans, while for patients previously treated with radiotherapy (RT) it was 5.75 ng/mL. In RP-patients with PSA value <1.24 ng/mL, 52% scans were positive, whereas patients with PSA ≥1.24 ng/mL had positive scan results in 87%. RT-patients with PSA <5.75 ng/mL had positive scans in 86% and for those with PSA ≥5.75 ng/mL 94% had positive scans. This study identifies the PSA and PSA kinetics threshold levels for the presence of 68Ga-PSMA-11 PET/CT-detectable PC-lesions in BC patients

Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study

Background Human well-being has been linked to the composition and functional capacity of the intestinal microbiota. As regular exercise is known to improve human health, it is not surprising that exercise was previously described to positively modulate the gut microbiota, too. However, most previous studies mainly focused on either elite athletes or animal models. Thus, we conducted a randomised intervention study that focused on the effects of different types of training (endurance and strength) in previously physically inactive, healthy adults in comparison to controls that did not perform regular exercise. Overall study duration was ten weeks including six weeks of intervention period. In addition to 16S rRNA gene amplicon sequencing of longitudinally sampled faecal material of participants (six time points), detailed body composition measurements and analysis of blood samples (at baseline and after the intervention) were performed to obtain overall physiological changes within the intervention period. Activity tracker devices (wrist-band wearables) provided activity status and sleeping patterns of participants as well as exercise intensity and heart measurements. Conclusions We could show that different types of exercise have distinct but moderate effects on the overall physiology of humans and very distinct microbial changes in the gut. The observed overall changes during the intervention highlight the importance of physical activity on well-being. Future studies should investigate the effect of exercise on a longer timescale, investigate different training intensities and consider high-resolution shotgun metagenomics technology. Trial registration DRKS, DRKS00015873 . Registered 12 December 2018; Retrospectively registered

Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders.

Irritable bowel syndrome (IBS) results from disordered brain-gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. We designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. We conducted a genome-wide association study with 53,400 cases and 433,201 controls and replicated significant associations in a 23andMe panel (205,252 cases and 1,384,055 controls). Our study identified and confirmed six genetic susceptibility loci for IBS. Implicated genes included NCAM1, CADM2, PHF2/FAM120A, DOCK9, CKAP2/TPTE2P3 and BAG6. The first four are associated with mood and anxiety disorders, expressed in the nervous system, or both. Mirroring this, we also found strong genome-wide correlation between the risk of IBS and anxiety, neuroticism and depression (rg > 0.5). Additional analyses suggested this arises due to shared pathogenic pathways rather than, for example, anxiety causing abdominal symptoms. Implicated mechanisms require further exploration to help understand the altered brain-gut interactions underlying IBS

A novel unconventional T cell population enriched in Crohn's disease

Objective One of the current hypotheses to explain the proinflammatory immune response in IBD is a dysregulated T cell reaction to yet unknown intestinal antigens. As such, it may be possible to identify disease-associated T cell clonotypes by analysing the peripheral and intestinal T-cell receptor (TCR) repertoire of patients with IBD and controls. Design We performed bulk TCR repertoire profiling of both the TCR alpha and beta chains using high-throughput sequencing in peripheral blood samples of a total of 244 patients with IBD and healthy controls as well as from matched blood and intestinal tissue of 59 patients with IBD and disease controls. We further characterised specific T cell clonotypes via single-cell RNAseq. Results We identified a group of clonotypes, characterised by semi-invariant TCR alpha chains, to be significantly enriched in the blood of patients with Crohn's disease (CD) and particularly expanded in the CD8+ T cell population. Single-cell RNAseq data showed an innate-like phenotype of these cells, with a comparable gene expression to unconventional T cells such as mucosal associated invariant T and natural killer T (NKT) cells, but with distinct TCRs. Conclusions We identified and characterised a subpopulation of unconventional Crohn-associated invariant T (CAIT) cells. Multiple evidence suggests these cells to be part of the NKT type II population. The potential implications of this population for CD or a subset thereof remain to be elucidated, and the immunophenotype and antigen reactivity of CAIT cells need further investigations in future studies

Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders

Funder: Kennedy Trust Rheumatology Research Prize StudentshipFunder: DFG Cluster of Excellence “Precision Medicine in Chronic In-flammation” (PMI; ID: EXC2167)Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: “Ideas” Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)); doi: https://doi.org/10.13039/100011199; Grant(s): 715772Funder: NWO-VIDI grant 016.178.056, the Netherlands Heart Foundation CVON grant 2018-27, and NWO Gravitation grant ExposomeNLFunder: Li Ka Shing Foundation (Li Ka Shing Foundation Limited); doi: https://doi.org/10.13039/100007421Abstract: Irritable bowel syndrome (IBS) results from disordered brain–gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. We designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. We conducted a genome-wide association study with 53,400 cases and 433,201 controls and replicated significant associations in a 23andMe panel (205,252 cases and 1,384,055 controls). Our study identified and confirmed six genetic susceptibility loci for IBS. Implicated genes included NCAM1, CADM2, PHF2/FAM120A, DOCK9, CKAP2/TPTE2P3 and BAG6. The first four are associated with mood and anxiety disorders, expressed in the nervous system, or both. Mirroring this, we also found strong genome-wide correlation between the risk of IBS and anxiety, neuroticism and depression (rg > 0.5). Additional analyses suggested this arises due to shared pathogenic pathways rather than, for example, anxiety causing abdominal symptoms. Implicated mechanisms require further exploration to help understand the altered brain–gut interactions underlying IBS

miRNA expression profiles of the perilesional skin of atopic dermatitis and psoriasis patients are highly similar

Abstract Atopic dermatitis (AD) and psoriasis vulgaris (PV) are chronic inflammatory skin diseases with heterogeneous molecular backgrounds. MicroRNAs (miRNAs) contribute to either development or regulation of many immune system related diseases. Only few miRNA profiling studies are available for AD and no comparisons between AD and PV skin miRNA profiles have been performed recently. We conducted a miRNA profiling analysis of skin, as well as serum, from adult AD and PV patients and control individuals. 130 miRNAs were differentially expressed in AD skin, of which 77 were common differentially expressed in AD and PV. No differentially expressed miRNAs were detected in serum. Pathway analyses revealed differentially expressed miRNAs to potentially target immune-system related pathways, including TNF-α, IL-2/STAT4 and IL-6/JAK/STAT3. Additional genetic analysis of published AD GWAS dataset detected association of several target genes of differentially expressed miRNAs in skin. Moreover, miR-28-5p, miR-31-5p, miR-378a-3p and miR-203a were validated as upregulated in the skin of AD and PV patients. All validated miRNAs were reliable predictive markers for AD or PV. In conclusion, miRNA expression pattern in the skin of adult AD patients is highly similar to that of PV with multiple differentially expressed miRNAs potentially involved in the regulation of immune responses in AD and PV

Detecting patient subgroups using reduced set of disease-related markers with iterative pruning Principal Component Analysis (ipPCA)

Genetic markers such as Single Nucleotide Polymorphisms (SNPs) can be used to find subgroups of populations or patients with carefully selected clustering algorithms. The iterative pruning principal component analysis (ipPCA) has been shown to be a powerful tool to identify fine substructures within general populations based on SNP profiles. Usually, SNPs contributing to such profiles have passed rigorous quality control procedures, similar to the ones used for GWAs. Alternatively, attention is restricted to a smaller subset such as PCA-correlated SNPs. Here, we applied ipPCA on real-life data consisting of the 163 known inflammatory-bowel disease (IBD) associated loci in 13,400 healthy individuals and 29,500 IBD (16,902 Crohn’s disease (CD), and 12,598 ulcerative colitis (UC)) patients from the IIBDGC. Prior to clustering by ipPCA, in each group separately, we regressed out the first five Principal Components (PCs) that were computed from a filtered panel of genome-wide SNPs, to account for general population strata. Next, we applied ipPCA on the healthy group, to learn about the presence of a population-specific partitioning in controls. Then we performed three subphenotype analyses: CD only, UC only and the combined group of CD and UC patients (IBD). For each patient subgroup analysis and for the ipPCA analysis on controls, we highlighted and compared the key SNP drivers. CD patients could be molecularly reclassified in two groups, and similar for UC patients. The combined patient group could be subdivided in four groups. Finally, we compared demographic and clinical features among the different groups and looked for meaningful characterizations of adjusted patient clusters by performing pathway analysis on driver genes.Foresting in Integromics Inferenc

Sparse Modeling Reveals miRNA Signatures for Diagnostics of Inflammatory Bowel Disease

<div><p>The diagnosis of inflammatory bowel disease (IBD) still remains a clinical challenge and the most accurate diagnostic procedure is a combination of clinical tests including invasive endoscopy. In this study we evaluated whether systematic miRNA expression profiling, in conjunction with machine learning techniques, is suitable as a non-invasive test for the major IBD phenotypes (Crohn's disease (CD) and ulcerative colitis (UC)). Based on microarray technology, expression levels of 863 miRNAs were determined for whole blood samples from 40 CD and 36 UC patients and compared to data from 38 healthy controls (HC). To further discriminate between disease-specific and general inflammation we included miRNA expression data from other inflammatory diseases (inflammation controls (IC): 24 chronic obstructive pulmonary disease (COPD), 23 multiple sclerosis, 38 pancreatitis and 45 sarcoidosis cases) as well as 70 healthy controls from previous studies. Classification problems considering 2, 3 or 4 groups were solved using different types of penalized support vector machines (SVMs). The resulting models were assessed regarding sparsity and performance and a subset was selected for further investigation. Measured by the area under the ROC curve (AUC) the corresponding median holdout-validated accuracy was estimated as ranging from 0.75 to 1.00 (including IC) and 0.89 to 0.98 (excluding IC), respectively. In combination, the corresponding models provide tools for the distinction of CD and UC as well as CD, UC and HC with expected classification error rates of 3.1 and 3.3%, respectively. These results were obtained by incorporating not more than 16 distinct miRNAs. Validated target genes of these miRNAs have been previously described as being related to IBD. For others we observed significant enrichment for IBD susceptibility loci identified in earlier GWAS. These results suggest that the proposed miRNA signature is of relevance for the etiology of IBD. Its diagnostic value, however, should be further evaluated in large, independent, clinically well characterized cohorts.</p></div