Targeted Gene Panel Sequencing for Early-onset Inflammatory Bowel Disease and Chronic Diarrhea

Background: In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients. Methods: We selected 28 genes of interest associated with monogenic IBD and performed targeted panel sequencing in 71 patients diagnosed with eoIBD or early-onset chronic diarrhea to detect causative variants. We compared these results to whole-exome sequencing (WES) data available for 25 of these patients. Results: Target coverage was significantly higher in the targeted gene panel approach compared with WES, whereas the cost of the panel was considerably lower (approximately 25% of WES). Disease-causing variants affecting protein function were identified in 5 patients (7%), located in genes of the IL10 signaling pathway (3), WAS (1), and DKC1 (1). The functional effects of 8 candidate variants in 5 additional patients (7%) are under further investigation. WES did not identify additional causative mutations in 25 patients. Conclusions: Targeted gene panel sequencing is a fast and effective screening method for monogenic causes of eoIBD that should be routinely established in national referral centers.info:eu-repo/semantics/publishedVersio

Towards Improving Transparency of Count Data Regression Models for Health Impacts of Air Pollution

In studies on the health impacts of air pollution, regression analysis continues to advance far beyond classical linear regression, which many scientists may have become familiar with in an introductory statistics course. With each new level of complexity, regression analysis may become less transparent, even to the analyst working with the data. This may be especially true in count data regression models, where the response variable (typically given the symbol y) is count data (i.e., takes on values of 0, 1, 2, …). In such models, the normal distribution (the familiar bell-shaped curve) for the residuals (i.e., the differences between the observed values and the values predicted by the regression model) no longer applies. Unless care is taken to correctly specify just how those residuals are distributed, the tendency to accept untrue hypotheses may be greatly increased. The aim of this paper is to present a simple histogram of predicted and observed count values (POCH), which, while rarely found in the environmental literature but presented in authoritative statistical texts, can dramatically reduce the risk of accepting untrue hypotheses. POCH can also increase the transparency of count data regression models to analysts themselves and to the scientific community in general

H&E staining of biceps tendons—Group-1 (Patient numbers—PT3, PT6, PT8 and PT10) and Group-2 (Patient numbers–PT2, PT4, PT13 and PT9).

<p>The green arrows show tendon cells; black arrows point inflammation; red arrows indicate angiogenesis; blue arrows show ECM disorganization; violet arrows point fatty infiltration; and yellow arrows indicate normal ECM with dense collagen deposition. The inflammation and fatty infiltration were not evident in Group-2 while ECM disorganization was less prominent compared to Group-1. The figures are shown in 400x magnification.</p

Mean fluorescence intensity for the evaluation of gene expression analysis by immunofluorescence using ImageJ software.

<p>The expression levels of CD68, TREM-1, HMGB1 and RAGE were significantly higher in the tissues of Group-1 when compared to Group-2. TREM-2 expression was enhanced in Group-1 but was not significant. The expression of TM and SLX between both the groups was mostly similar and not significant. <i>Group-1 (n = 4)</i>, <i>Group-1 (n = 11) * p<0</i>.<i>05; NS–Not significant</i>.</p

Flow cytometry analysis of TREM-1 and TREM-2 expression on CD16⁺ and CD14⁺ cells.

<p>(A) Representative images for the gating of the cells in Group-1 and Group-2 patients. (B) Comparison between Group-1 and Group-2 patients showing increased TREM-1 expression in the cells of Group-1 revealing the severity of inflammation. <i>n = 8 for both the groups</i>, <i>* p<0</i>.<i>05; NS–Not significant</i></p

The mRNA expression of TREM-1 and TREM-2 genes in tendon tissue.

<p>The expression level of TREM-1 was significantly higher in Group-1 when compared to Group-2 as the control. There was no significant difference in TREM-2 expression between the Group 1 and Group 2. <i>Group-1 (n = 4)</i>, <i>Group-1 (n = 8) * p<0</i>.<i>05; NS–Not significant</i>.</p

Primers and their sequences used for RT-PCR analysis.

<p>Primers and their sequences used for RT-PCR analysis.</p

MicroRNAs Associated with Shoulder Tendon Matrisome Disorganization in Glenohumeral Arthritis

<div><p>The extracellular matrix (ECM) provides core support which is essential for the cell and tissue architectural development. The role of ECM in many pathological conditions has been well established and ECM-related abnormalities leading to serious consequences have been identified. Though much has been explored in regards to the role of ECM in soft tissue associated pathologies, very little is known about its role in inflammatory disorders in tendon. In this study, we performed microRNA (miRNA) expression analysis in the long head of the human shoulder biceps tendon to identify key genes whose expression was altered during inflammation in patients with glenohumeral arthritis. We identified differential regulation of matrix metalloproteinases (MMPs) that could be critical in collagen type replacement during tendinopathy. The miRNA profiling showed consistent results between the groups and revealed significant changes in the expression of seven different miRNAs in the inflamed tendons. Interestingly, all of these seven miRNAs were previously reported to have either a direct or indirect role in regulating the ECM organization in other pathological disorders. In addition, these miRNAs were also found to alter the expression levels of MMPs, which are the key matrix degrading enzymes associated with ECM-related abnormalities and pathologies. To our knowledge, this is the first report which identifies specific miRNAs associated with inflammation and the matrix reorganization in the tendons. Furthermore, the findings also support the potential role of these miRNAs in altering the collagen type ratio in the tendons during inflammation which is accompanied with differential expression of MMPs.</p></div