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A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation
Th17 cells are essential for protection against extracellular pathogens, but their aberrant activity can cause autoimmunity. Molecular mechanisms that dictate Th17 cell-differentiation have been extensively studied using ...
Differential ATAC-seq and ChIP-seq peak detection using ROTS
<p> Changes in cellular chromatin states fine-tune transcriptional output and ultimately lead to phenotypic changes. Here we propose a novel application of our reproducibility-optimized test statistics (ROTS) to detect ...
Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data
<div><h3>Background</h3><p>Detection
of copy number variations (CNVs) from high-throughput next-generation
whole-genome sequencing (WGS) data has become a widely used research
method during the recent years. However, ...
Umbilical cord blood DNA methylation in children who later develop type 1 diabetes
<p><strong>Aims/hypothesis:</strong> Distinct DNA methylation patterns have recently been observed to precede type 1 diabetes in whole blood collected from young children. Our aim was to determine whether perinatal DNA ...
Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease
<p>Background <br></p><p>Alzheimer's disease results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease ...
Early DNA methylation changes in children developing beta cell autoimmunity at a young age
<p><br></p><p>Aims/hypothesis <br></p><p>Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically ...
Exon-level estimates improve the detection of differentially expressed genes in RNA-seq studies
Detection of differentially expressed genes (DEGs) between different biological conditions is a key data analysis step of most RNA-sequencing studies. Conventionally, computational tools have used gene-level read counts ...
MYO10-filopodia support basement membranes at pre-invasive tumor boundaries
<p>Ductal carcinoma in situ (DCIS) is a pre-invasive stage of breast cancer. During invasion, the encapsulating DCIS basement membrane (BM) is compromised, and tumor cells invade the surrounding stroma. The mech-anisms that regulate functional epithelial BMs in vivo are poorly understood. Myosin-X (MYO10) is a filopodia-inducing protein associated with metastasis and poor clinical outcome in invasive breast cancer (IBC). We identify elevated MYO10 expression in human DCIS and IBC, and this suggests links with disease progres-sion. MYO10 promotes filopodia formation and cell invasion in vitro and cancer-cell dissemination from pro-gressively invasive human DCIS xenografts. However, MYO10-depleted xenografts are more invasive. These lesions exhibit compromised BMs, poorly defined borders, and increased cancer-cell dispersal and EMT -marker-positive cells. In addition, cancer spheroids are dependent on MYO10-filopodia to generate a near-continuous extracellular matrix boundary. Thus, MYO10 is protective in early-stage breast cancer, correlating with tumor-limiting BMs, and pro-invasive at later stages, facilitating cancer-cell dissemination.</p>...