Project description:To identify genes regulated by SPDEF or FOXA3 in A549 lung carcinoma cells, we analyzed the whole-transcriptomic mRNA profiles of A549 cells expressing SPDEF or FOXA3 based on RNA-seq.
Project description:ChIP-seq was performed to identify the binding regions of SPDEF and NKX2-1 in A549 lung carcinoma cells expressing NKX2-1 and SPDEF.
Project description:Background: Lung cancer is the leading cause of cancer related death worldwide. Over the past 15 years no major improvement of survival rates could be accomplished. The recently discovered histone methyltransferase KMT9 as epigenetic regulator of prostate tumor growth has now raised hopes of enabling new cancer therapies. In this study we aimed to identify the function of KMT9 in lung cancer which has remained elusive so far. Methods: We linked full transcriptome and proteome analyses of A549 lung adenocarcinoma cells using RNA-Seq and mass spectrometry with functional cell culture, real-time proliferation and flow cytometry assays. Results: KMT9 is expressed in lung cancer tissue and cell lineswith high levels of KMT9 correlating with poor patient survival. We identified 460 overlapping genes and proteins that are deregulated upon knock-down of KMT9alpha in A549 cells. These genes cluster with proliferation, cell cycle and cell death gene sets as well as with subcellular organelles in gene ontology analysis. Knock-down of KMT9alpha inhibits lung cancer cell proliferation and induces non-apoptotic cell death in A549 cells. Conclusions: The novel histone methyltransferase KMT9 is crucial for proliferation and survival of lung cancer cells harboring various mutations. Small molecule inhibitors targeting KMT9 therefore should be further examined as potential milestones in modern epigenetic lung cancer therapy.
Project description:RNA-seq was performed to identify genes affected by CRISPRi (dCas9-KRAB) with sgRNA (sgSFTPB#2) targeting the first intronic region of human SFTPB bound by NKX2-1 in an unbiased genome-wide fashion using A549 lung carcinoma cells that constitutively express dCas9-KRAB and NKX2-1.
