Biology subjects

Chang, J.-C.

Publications and source records attributed to Chang, J.-C..

21 records · Page 2Linked to original sources

bioRxiv2019

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances reprogramming to epithelial lineages

Mesenchymal-to-epithelial transition (MET) is an important step in cell reprogramming from fibroblasts (a cell type frequently used for this purpose) to various epithelial cell types. However, the mechanism underlying MET induction in fibroblasts remains to be understood. The present study aimed to identify the transcription factors (TFs) that efficiently induce MET in dermal fibroblasts. OVOL2 was identified as a potent inducer of key epithelial genes, and OVOL2 cooperatively enhanced MET induced by HNF1A, TP63, and KLF4, which are known reprogramming TFs to epithelial lineages. In TP63/KLF4-induced keratinocyte-like cell-state reprogramming, OVOL2 greatly facilitated the activation of epithelial and keratinocyte-specific genes. This was accompanied by enhanced changes in chromatin accessibility across the genome. Mechanistically, motif enrichment analysis revealed that the target loci of KLF4 and TP63 become accessible upon induction of TFs, whereas the OVOL2 target loci become inaccessible. This indicates that KLF4 and TP63 positively regulate keratinocyte-associated genes whereas OVOL2 suppresses fibroblast-associated genes. The exogenous expression of OVOL2 therefore disrupts fibroblast lineage identity and facilitates fibroblast cell reprogramming into epithelial lineages cooperatively with tissue-specific reprogramming factors. Identification of OVOL2 as a MET inducer and an epithelial reprogramming enhancer in fibroblasts provides new insights into cellular reprogramming improvement for future applications.

cell biology↗

bioRxiv2018

Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis

BackgroundOsteoarthritis (OA) is a common joint disorder with increasing impact in an aging society; however, there is no cure or effective treatments so far due to lack of sufficient understanding of its pathogenesis. While genome-wide association studies (GWAS) and DNA methylation profiling identified many non-coding loci associated to OA, the interpretation of them remains challenging.\n\nMethodsHere, we employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients and to identify the chromatin signatures relevant to OA.\n\nResultsWe identified 109,215 accessible chromatin regions in cartilage and 71% of these regions were annotated as enhancers. We found these accessible chromatin regions are enriched for OA GWAS single nucleotide polymorphisms (SNPs) and OA differentially methylated loci, implying their relevance to OA. By linking these enhancers to their potential target genes, we have identified a list of candidate enhancers that may be relevant to OA. Through integration of ATAC-seq data with RNA-seq data, we identified genes that are altered both at epigenomic and transcriptomic levels. These genes are enriched in pathways regulating ossification and mesenchymal stem cell (MSC) differentiation. Consistently, the differentially accessible regions in OA are enriched for mesenchymal stem cell-specific enhancers and motifs of transcription factor families involved in osteoblast differentiation (e.g. bZIP and ETS).\n\nConclusionsThis study marks the first investigation of accessible chromatin landscape on clinically relevant hard tissues and demonstrates how accessible chromatin profiling can provide comprehensive epigenetic information of a disease. Our analyses provide supportive evidence towards the model of endochondral ossification-like cartilage-to-bone conversion in OA knee cartilage, which is consistent with the OA characteristic of thicker subchondral bone. The identified OA-relevant genes and their enhancers may have a translational potential for diagnosis or drug targets.

genomics↗

bioRxiv2018

Microfluidic device for on-chip mixing and encapsulation of lysates

Emulsion drops are often employed as picoliter-sized containers to perform screening assays. These assays usually entail the formation of drops encompassing discrete objects such as cells or microparticles and reagents to study interactions between the different encapsulants. Drops are also used to screen influences of reagent concentrations on the final product. However, these latter assays are less frequently performed because it is difficult to change the reagent concentration over a wide range with high precision within a single experiment. In this paper, we present a microfluidic double emulsion drop maker containing pneumatic valves that enable injection of different reagents using pulsed width modulation and subsequent mixing. This device can produce drops from reagent volumes as low as 10 l with minimal sample loss, thereby enabling experiments that would be prohibitively expensive using droplet generators that do not contain valves. We employ this device to monitor the kinetics of cell free synthesis of green fluorescent proteins inside double emulsions. To demonstrate the potential of this device, we perform DNA titration experiments in double emulsion drops to test the influence of the DNA concentration on the amount of green fluorescence proteins produced.

synthetic biology↗