Project description:Pluripotent stem cells have the potential to differentiate in vitro in many, if not all, functional cell types. Induced pluripotent stem cells (iPS) have recently emerged as a reproducible model of pluripotent stem cells that can be generated from post-natal tissues. To understand this process at the transcriptome level, we generated iPS cell lines, partially reprogrammed cell lines and compared their transcriptome with that of the partental human foreskin fibroblasts and human embryonic stem cell lines.
Project description:Pluripotent stem cells have the potential to differentiate in vitro in many, if not all, functional cell types. Induced pluripotent stem cells (iPS) have recently emerged as a reproducible model of pluripotent stem cells that can be generated from post-natal tissues. To understand this process at the transcriptome level, we generated iPS cell lines, partially reprogrammed cell lines and compared their transcriptome with that of the partental human foreskin fibroblasts and human embryonic stem cell lines. Four categories of samples, comprising human foreskin fibroblasts, fully reprogrammed iPS cell lines, partially reprogrammed iPS cell lines and human embryonic stem cell lines were compared using Significance Analysis of Microarrays (SAM). These data were also compared to a compendium of differentiated human samples and a pluripotency classifier was computed.
Project description:The molecular mechanisms in the development of laryngeal and hypopharyngeal squamous cell carcinoma (LHSCC) remain poorly understood. Previous studies suggest molecular overlap between head and neck SCC (HNSCC) and lung SCC. In this study, we investigated whether lung cancer-associated genes are enriched among differentially expressed genes during stepwise LHSCC development. Spatial transcriptomic profiling using the Xenium platform (10x Genomics) was performed on formalin-fixed paraffin embedded tissue of normal mucosa, low-grade dysplasia (LG-Dys), high-grade dysplasia/carcinoma in situ (HG-Dys/CIS) and invasive carcinoma from eleven patients. Over 40 differentially expressed genes were identified, grouped into key biological processes, including transport, immune modulation, epithelial integrity, signaling and metabolism. Gene expression patterns segregated lesions into two molecular groups, whereby LG-Dys resembled normal mucosa, while HG-Dys aligned with CIS. Six genes (CCDC39, DNAAF1, GDF15, GKN2, RGS16 and TSPAN19) were consistently altered between HG-Dys/CIS and invasive carcinoma, highlighting them as potential biomarkers of malignant transformation. Additionally, EPCAM and SERPINB3 showed altered expression in LHSCC development, consistent with previous studies in other epithelial malignancies. These findings further support similar genetic pathways involved in lung cancer and LHSCC development. Furthermore, our results revealed novel molecular events underlying LHSCC development and identified candidate biomarkers of early invasiveness.
Project description:Space radiations and microgravity both could cause DNA damage in cells, but the effects of microgravity on DNA damage response to space radiations are still controversial. A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured spaceflight environment and space radiations environment during 16.5-day Shenzhou-8 space mission were performed. The analyzation this study are further described in Gao, Y., Xu, D., Zhao, L., Zhang, M. and Sun, Y. (2015) Effects of microgravity on DNA damage response in Caenorhabditis elegans during Shenzhou-8 spaceflight. International journal of radiation biology, 91, 531-539.