Identification of methylation-sensitive human transcription factors using meSMiLE-seq.

Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding specificity of many TFs remains unknown. Here, we assayed 284 mostly poorly characterized, putative human TFs using selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq), revealing 72 new DNA binding motifs. To investigate whether some of the 158 TFs for which we did not find motifs preferably bind epigenetically modified DNA (i.

Sex-related differences in the presentation, management and response to treatment of eosinophilic esophagitis: Cross sectional analysis of EoE CONNECT registry.

Background: Eosinophilic esophagitis (EoE) predominantly affects males across all ages; however, little is known about sex differences for other aspects of EoE.

Objective: To investigate associations between sex and clinical presentation, endoscopic features, treatment choice and response in EoE patients in real-world practice.

Methods: Cross-sectional analysis of the multicenter EoE CONNECT registry.

Determinant factors for first-line treatment choice and effectiveness in pediatric eosinophilic esophagitis: an analysis of the EUREOS EoE CONNECT registry.

This study compared short-term effectiveness of proton pump inhibitors (PPI), swallowed topical corticosteroids (STC), and dietary therapies in reversing clinical and histological features in pediatric patients with eosinophilic esophagitits (EoE). Determinants for treatment choice and PPI therapy effectiveness were also assessed.  A cross-sectional study analysis of patients under 18 years old recruited onto the multicenter EoE CONNECT registry was performed.

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing.

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatments. Focusing on gene expression, the transcriptomic market exploits the benefits of next-generation sequencing (NGS), leveraging RNA sequencing (RNA-seq) as standard for measuring genome-wide gene expression in biological samples.

Differences between childhood- and adulthood-onset eosinophilic esophagitis: An analysis from the EoE connect registry.

Background: Direct comparisons of childhood- and adulthood-onset eosinophilic esophagitis (EoE) are scarce.

Aim: To compare disease characteristics, endoscopic and histological features, allergic concomitances and therapeutic choices across ages.

Methods: Cross-sectional analysis of the EoE CONNECT registry.

Live-seq enables temporal transcriptomic recording of single cells.

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity. However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy, thus allowing to couple a cell's ground-state transcriptome to its downstream molecular or phenotypic behaviour.

Accurate and timely diagnosis of Eosinophilic Esophagitis improves over time in Europe. An analysis of the EoE CONNECT Registry.

Background: Poor adherence to clinical practice guidelines for eosinophilic esophagitis (EoE) has been described and the diagnostic delay of the disease continues to be unacceptable in many settings.

Objective: To analyze the impact of improved knowledge provided by the successive international clinical practice guidelines on reducing diagnostic delay and improving the diagnostic process for European patients with EoE.

Methods: Cross-sectional analysis of the EoE CONNECT registry based on clinical practice.

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation.

Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression.

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition.

Single-cell RNA sequencing (scRNA-seq) approaches have transformed our ability to resolve cellular properties across systems, but are currently tailored toward large cell inputs (>1,000 cells). This renders them inefficient and costly when processing small, individual tissue samples, a problem that tends to be resolved by loading bulk samples, yielding confounded mosaic cell population read-outs. Here, we developed a deterministic, mRNA-capture bead and cell co-encapsulation dropleting system, DisCo, aimed at processing low-input samples (<500 cells).

Cross-validation of the high-capacity tensiometer and thermocouple psychrometer for continuous monitoring of xylem water potential in saplings.

The pressure chamber, the most popular method used to measure xylem water potential, is a discontinuous and destructive technique and is therefore not suitable for automated monitoring. Continuous non-destructive monitoring could until very recently be achieved only by use of the thermocouple psychrometer (TP). Here we present the high-capacity tensiometer (HCT) as an alternative method for continuous non-destructive monitoring.

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors.

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molecular biology to address the major limitations of standard ChIP-seq. The resulting technology, FloChIP, automates and miniaturizes ChIP in a beadless fashion while facilitating the downstream library preparation process through on-chip chromatin tagmentation.

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel.

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants affect different molecular mechanisms to determine gut immunocompetence is still limited.

Results: To address this, we perform a systems genetics analysis of the gut transcriptomes from 38 DGRP lines that were orally infected with Pseudomonas entomophila.

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer.

Krüppel-associated box zinc finger proteins (KZFPs) constitute the largest family of mammalian transcription factors, but most remain completely uncharacterized. While initially proposed to primarily repress transposable elements, recent reports have revealed that KFZPs contribute to a wide variety of other biological processes. Using murine and human in vitro and in vivo models, we demonstrate here that one poorly studied KZFP, ZFP30, promotes adipogenesis by directly targeting and activating a retrotransposon-derived Pparg2 enhancer.

A Comprehensive Drosophila melanogaster Transcription Factor Interactome.

Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays.

Adaptive damage retention mechanism enables healthier yeast population.

During cytokinesis in budding yeast (Saccharomyces cerevisiae) damaged proteins are distributed asymmetrically between the daughter and the mother cell. Retention of damaged proteins is a crucial mechanism ensuring a healthy daughter cell with full replicative potential and an ageing mother cell. However, the protein quality control (PQC) system is tuned for optimal reproduction success which suggests optimal health and size of the population, rather than long-term survival of the mother cell.

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip.

Single-cell RNA-sequencing (scRNA-seq) has revolutionized biomedical research by enabling the in-depth analysis of cell-to-cell heterogeneity of tissues with unprecedented resolution. One of the catalyzing technologies is single cell droplet microfluidics, which has massively increased the overall cell throughput, routinely allowing the analysis of thousands of cells per experiment at a relatively low cost. Among several existing droplet-based approaches, the Drop-seq platform has emerged as one of the most widely used systems.

SMiLE-seq identifies binding motifs of single and dimeric transcription factors.

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). SMiLE-seq is neither limited by DNA bait length nor biased toward strong affinity binders; it probes the DNA-binding properties of TFs over a wide affinity range in a fast and cost-effective fashion.

Presence of commensal house dust mite allergen in human gastrointestinal tract: a potential contributor to intestinal barrier dysfunction.

Background: Abnormal gut barrier function is the basis of gut inflammatory disease. It is known that house dust mite (HDM) aero-allergens induce inflammation in respiratory mucosa. We have recently reported allergen from Dermatophagoides pteronyssinus (Der p1) to be present in rodent gut.

Osteopathy decreases the severity of IBS-like symptoms associated with Crohn's disease in patients in remission.

Background: Osteopathy may decrease the severity of irritable bowel syndrome (IBS). About 35% of patients with quiescent Crohn's disease (CD) continue to suffer from IBS-like symptoms with impaired quality of life (Qol). We aimed to evaluate the effect of osteopathy on the severity of IBS-like symptoms in quiescent CD patients.

Perception of lactose intolerance in irritable bowel syndrome patients.

Introduction: The importance of lactose malabsorption in irritable bowel syndrome (IBS) is not well defined and these patients often complain of lactose intolerance. To objectively measure lactose malabsorption, a hydrogen breath test (HBT) can be performed, but a discrepancy emerges between the results of the HBT and the symptomatic response during the HBT.

Aims: To determine in a group of IBS patients whether self-perceived lactose intolerance and the symptomatic response to lactose HBT were conditioned by other factors besides the presence of lactose malabsorption.

Functional bowel symptoms in quiescent inflammatory bowel diseases: role of epithelial barrier disruption and low-grade inflammation.

Objective: To determine the role of colonic barrier defects and low-grade inflammation in irritable bowel syndrome (IBS)-like symptoms in quiescent inflammatory bowel disease (IBD).

Design: Caecal biopsies were collected from 51 IBS, 49 quiescent IBD (31 Crohn's disease (CD) and 18 ulcerative colitis (UC)) patients and 27 controls. IBS was assessed using the Rome III criteria and the IBS severity score.

Osteopathy improves the severity of irritable bowel syndrome: a pilot randomized sham-controlled study.

Background: Effective therapies for irritable bowel syndrome (IBS) are disappointing. Therefore, IBS patients have a growing interest for alternative medicines including osteopathy.

Aim: We aimed to evaluate the effect of osteopathy on the severity of IBS in a randomized sham-controlled trial.

Role of serological markers of activated eosinophils in inflammatory bowel diseases.

Background: Activated eosinophils can infiltrate the intestinal mucosa in patients with inflammatory bowel disease (IBD), and eosinophils are also implicated in the histological damage seen in allergic diseases.

Aim: To assess, in a group of patients with IBD in remission or with a mild disease activity, whether serological markers of eosinophil activation, eosinophil cationic protein (ECP) and eosinophil protein X (EPX), are related to evidence of IgE hypersensitivity and to the eosinophilia in gut mucosa.

Methods: Sixty-one patients with IBD (21 Crohn's disease and 40 ulcerative colitis) in remission or with a mild disease activity were screened for IgE hypersensitivity and serological levels of ECP and EPX.