Biology subjects

Mosbruger, T.

Publications and source records attributed to Mosbruger, T..

3 recordsLinked to original sources

bioRxiv2026

A Rare T-Cell Factor 4 Lineage-negative Epithelial Stem Cell Supports Wound Repair and APC-deletion-induced Colon Tumorigenesis

To maintain barrier homeostasis, the colonic and intestinal epithelial lining is continually renewed by rapidly proliferating epithelial crypt base columnar (CBC) stem cells that reside at the base of crypts. Using mouse lineage tracing, immunohistochemistry, and single-cell sequencing, we have identified a rare, non-CBC, T-cell factor 4 lineage-negative (Tcf4 Lin-) stem cell population that gives rise to secretory and absorptive precursors. Following endoscopic biopsy-induced injury, Tcf4 Lin- stem cells are recruited to the wound bed and to the site of expanding crypts and function in barrier restoration and wound repair. We show that in a Tcf4-haploinsufficient background, the Tcf4 Lin-, but not the Tcf4 Lin+, cell population represents the cell of origin for colon tumors driven by deletion of Apc. Our results provide a foundation for understanding Apc-allele-specific differences during colon tumorigenesis and identify a new stem-cell population that may prove valuable in the treatment of diseases caused by intestinal barrier homeostasis defects.

cell biology↗

bioRxiv2019

AnthOligo: Automating the design of oligonucleotides for capture/enrichment technologies

SummaryA number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, Region-specific extraction (RSE) of DNA is characterized by the capture of long DNA fragments (15-20 kb) by magnetic beads, after enzymatic extension of oligonucleotides hybridized to selected genomic regions. Facilitating the selection of the most optimal capture oligos targeting a region of interest, satisfying the properties of temperature (Tm) and entropy ({Delta}G), while minimizing the formation of primer dimers in a pooled experiment is therefore necessary. Manual design and selection of oligos becomes an extremely arduous task complicated by factors such as length of the target region and number of targeted regions. Here we describe, AnthOligo, a web-based application developed to optimally automate the process of generation of oligo sequences to be used for the targeting and capturing the continuum of large and complex genomic regions. Apart from generating oligos for RSE, this program may have wider applications in the design of customizable internal oligos to be used as baits for gene panel analysis or even probes for large-scale comparative genomic hybridization (CGH) array processes. Implementation and AvailabilityThe application written in Java8 and run on Tomcat9 is a lightweight Java Spring MVC framework that provides the user with a simple interface to upload an input file in BED format and customize parameters for each task. A Redis-like MapReduce framework is implemented to run sub-tasks in parallel to optimize time and system resources alongside a task-queuing system that runs submitted jobs as a server-side background daemon. The task of probe design in AnthOligo commences when a user uploads an input file and concludes with the generation of a result-set containing an optimal set of region-specific oligos. AnthOligo is currently available as a public web application with URL: http://antholigo.chop.edu.

bioinformatics↗

bioRxiv2017

Nkx2.5-dependent alterations of the embryonic heart DNA methylome identify novel cis-regulatory elements in cardiac development

Transcription factor Nkx2.5 is frequently mutated in congenital heart disease, but the mechanisms by which Nkx2.5 regulates heart development are poorly understood. By generating comprehensive DNA methylome maps from zebrafish embryonic hearts in nxk2.5 mutants and siblings, we discovered that Nkx2.5 regulates DNA methylation patterns during cardiac morphogenesis. We identified hundreds of Nkx-dependent heart-specific Differentially Methylated Regions (nhDMRs). A majority of the nhDMRs were hypomethylated in nkx2.5-/- hearts, correlating with changes in the mutant transcriptome, suggesting Nkx2.5 functions largely as a repressor. Distinct Nkx DNA-binding motifs were significantly enriched in subclasses of nhDMRs. Furthermore, nhDMRs were significantly associated with histone H3K4me1 and H3K27ac post-translational modifications, suggesting Nkx2.5 regulates gene expression by differential methylation of cis-regulatory elements. Using transgenics, we validated several nhDMRs with enhancer activities in the heart. We propose a novel role of Nkx2.5 mediated DNA methylation is integral in activating and repressing Nkx2.5 target genes during heart development.

developmental biology↗