Project description:Targeted inhibition of cancer-selective tyrosine kinases (TKI) has become a successful strategy in the treatment of multiple different cancer types. A sever side effect can be the induction of cardiomyopathy. We analyzed, if we could identify transcriptomic signatures induced by different tyrosine kinase inhibitiors in human IPSC-derived cardiomyocytes from healthy donors that might be associated with a cardiotoxic resonse. To investigate, if the predicted transcriptomic signatures are modified by other cell types of the human heart, we here stimulated two cardiomyocyte cell lines either in isolation or in coculture with human coronary arterial endothelial cells (HCAECs) with the TKIs pazopanib or dabrafenib.
Project description:Hepatocellular carcinoma (HCC) is frequently diagnosed in patients with late-stage disease who are ineligible for curative surgical therapies. Furthermore, the majority of patients become resistant to sorafenib. Recently, computational methods for drug repurposing have shown great promise to accelerate the discovery of new uses for existing drugs. In order to identify novel drugs for use against sorafenib resistant (SR)-HCC, we employed a transcriptomics-based drug repurposing method termed connectivity mapping. We conducted a comprehensive analysis of available in vitro and in vivo gene signatures of (SR)-HCC, and generated our own in vitro model using the Huh7 HCC cell line. We compared coverage of SR-HCC gene signatures across seven patient-derived HCC gene expression datasets, and observed that patients harboring the Huh7 SR-HCC gene signature had significantly reduced survival. Utilizing the Huh7 SR-HCC gene signature, we applied connectivity mapping to drug-induced gene expression profiles (n= 3,740 drugs) in the HepG2 HCC cell line from the LINCS database in order to find drugs that could oppose sorafenib resistance. We validated the use of two non-receptor tyrosine kinase inhibitors, dasatinib and fostamatinib, to reduce viability of sorafenib-resistant HCC cells and confirmed up-regulated activity of Src family kinases, the targets of dasatinib, in our SR-HCC models. We prospectively validated predicted gene expression changes in fostamatinib treated Huh7-SR via RNA-seq analysis.
Project description:Gene silencing in bacteria is mediated by chromatin proteins, of which Escherichia coli H-NS is a paradigmatic example. H-NS forms nucleoprotein filaments with either one or two DNA duplexes. However, the overall structures, arrangements of DNA-binding domains (DBDs), positions of DBD–DNA contacts, and determinants of genomic distribution for these linear and bridged filaments are uncertain. To connect H-NS structures that silence genes in vivo with features elucidated in vitro, we developed a multimodal multiscale analysis that combines a new method for chromatin reconstitution and mapping (Nitro-seq), ChIP-seq, tethered-nuclease mapping of DBD–DNA contacts (TEN-map), ·OH footprinting, molecular dynamics, and bioinformatics. We find that DNA sequence principally governs H-NS-filament location with indistinguishable sequence specificity in bridged or linear forms with or without the H-NS modifiers StpA and Hha and that DBD–DNA contacts vary in orientation and position with ~10-bp average spacing. Our results support a hemi-sequestration model of linear-to-bridged filament switching.
Project description:Mycotoxin citrinin (CTN) is widely found in multiple types of grains in foods and feeds globally. CTN also contaminates Monascus-derived health supplements such as red yeast rice and red yeast extracts during the fermentation process, which are originally used for preventing cardiovascular diseases. A previous study has reported that CTN is cardiotoxic to zebrafish embryos during their development by interfering some cardiogenic genes and pathways, showing a potential risk of consuming CTN-contaminated foods and products. However, the cardiotoxic effects and the underlying mechanisms of CTN on mammalian cardiomyocytes remain unclear and need to be ellucidated. In this study, we performed RNA-seq experiments in order to investigate the transcriptomic alterations induced by CTN-exposed rat H9c2 cardiomyocytes. The transcriptome profiling we obtained may reveal some evidence regarding the toxic effects of CTN on cardiac phenotypes, chromosome segregation, tubulin arrangement, mitochondrial functioning, and stress responses, etc.
Project description:Genomic information is encoded on a wide range of distance scales, ranging from tens of base pairs to megabases. We developed a multiscale framework to analyze and visualize the information content of genomic signals. Different types of signals, such as GC content or DNA methylation, are characterized by distinct patterns of signal enrichment or depletion across scales spanning several orders of magnitude. These patterns are associated with a variety of genomic annotations, including genes, nuclear lamina associated domains, and repeat elements. By integrating the information across all scales, as compared to using any single scale, we demonstrate improved prediction of gene expression from Polymerase II ChIP-seq measurements and we observed that gene expression differences in colorectal cancer are not most strongly related to gene body methylation, but rather to methylation patterns that extend beyond the single-gene scale. ChIP-seq data of six proteins in primary murine bone marrow macrophage cells (BMMs) under unstimulated and lipopolysaccharide (LPS) stimulated conditions. The BMMs were cultured from female C57BL/6 mice (age 8-12 weeks). Amongst these six proteins were three transcription factors (TFs), ATF340, NFκB/p50 and NFκB/p65, all of which are involved in regulating macrophage activation by microbial molecular components such as LPS. The other three ChIP-seq targets were RNA polymerase II (Pol II), and two chromatin modification marks: acetylation of histone H4 (H4ac) and tri-methylation of histone H3 lysine 27 (H3K27me3).