Project description:Isolation and enrichment of cancer stem cells in colorectal carcinoma to study role of epithelial-mesenchymal transition regilators in tumor malignancy. Experiment Overall Design: Genome-wide comparision in sphere cells and parental control cells revealed potential regulators involved tumor malignancy . Experiment Overall Design: Overexpression of these key regulators drafted cellular context toward therapy resistance
Project description:miRNAs exert various biological functions by targeting different cellular targets. Studying miR-146a functions in colon cancer cells helps to understand colorectal cancer (CRC) malignancy and progression. HT29 miR-146a-expressing cells and empty control cells were established for mining the gene expression profiles upon miR-146a expression.
Project description:In order to explore the status of DNA methylation in hypoxia response, we show that TET1, a DNA dioxygenase converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), regulates hypoxia-responsive gene expression. Hypoxia/HIF-2α regulates the expression of TET1. Knockdown of TET1 mitigated hypoxia-induced EMT. RNA sequencing and 5hmC sequencing identified the set of TET1-regulated genes. Four samples (Four samples, Hypoxia (scrambled control), Hypoxia (TET1-si), Normoxia (scrambled control) and Normoxia (TET1-si), are performed by RNA-Seq and hMeDIP-Seq RNA-Seq and hMeDIP-Seq
Project description:Colorectal carcinoma (CRC) is one of the most common cancers worldwide. Re-evaluating our current knowledge on CRC and developing novel therapeutic strategies is still crucial. Accumulating evidence suggests that cancer cells possess characters reminiscent of those of normal stem cells. Unveiling small RNAs responsible for cell stemness and chemoradioresistance should eventually lead to the development of novel therapeutic approaches. Expression profiles of parental CRC cells and cancer spheres expanded under stem cell medium cultivation were generated for identifying key regulators.
Project description:Twist1 induces cancer metastasis. Identification of Twist1 downstream targets should help to delineate the mechanisms of Twist1-induced cancer metastasis. Expression profiles of H1299 control cells vs. H1299 with knockdown of Twist1 were compared to identify Twist1 downstream targets.
Project description:In order to explore the status of DNA methylation in hypoxia response, we show that TET1, a DNA dioxygenase converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), regulates hypoxia-responsive gene expression. Hypoxia/HIF-2α regulates the expression of TET1. Knockdown of TET1 mitigated hypoxia-induced EMT. RNA sequencing and 5hmC sequencing identified the set of TET1-regulated genes. Four samples (Four samples, Hypoxia (scrambled control), Hypoxia (TET1-si), Normoxia (scrambled control) and Normoxia (TET1-si), are performed by RNA-Seq and hMeDIP-Seq
Project description:In recent times, high throughput screening analyses have broadly defined the RNA cellular targets of TDP-43, a nuclear factor involved in neurodegeneration. A common outcome of all these studies is that changing the expression levels of this protein can alter the expression of several hundred RNAs within cells. What still remains to be clarified is which changes represent direct cellular targets of TDP-43 or just secondary variations due to the general role played by this protein in RNA metabolism. Using a HTS-based splicing junction analysis we have now identified 162 splicing events that are consistent with being directly controlled by TDP-43. Validation of the data, both in neuronal and non-neuronal cell lines demonstrated that TDP-43 substantially alters the levels of isoform expression in four genes potentially important for neuropathology: MADD/IG20, STAG2, FNIP1, and BRD8. Most importantly, for MADD/IG20 and STAG2 these changes could also be confirmed at the protein level. These alterations were also observed in a cellular model that successfully mimics TDP-43 loss of function effects following its aggregation. These novel splicing events may represent potential biomarkers to predict disease onset, progression, and to test the efficacy of novel therapeutic agents to recover TDP-43 functional properties. We have performed an HTS-based splicing junction analysis of a series of stable cell lines that lack TDP-43, overexpress this factor, or express an RNA-binding mutant, in order to find splicing events, potentially associated with neurodegenerativce diseases, regulated by this splicing factor. Samples were analyzed in triplicate from: The following samples were analyzed in triplicate: wild-type HEK-293 cells, siTDP43-treated HEK-293 cells, siTDP43-treated HEK-293 cells overexpressing a flagged-wildtype TDP-43, siTDP43-treated HEK-293 cells overexpressing a RNA-binding deficient mutant.
Project description:Omega-3 polyunsaturated fatty acids are normal constituents of the diet and have an essential role in maintaining important cellular functions. Docosahexaenoic acid (DHA) have demonstrated anticancer activities in several in vitro and in vivo studies, and in some clinical studies. The mechanism by which n-3 PUFAs reduce tumor growth probably involves the inhibition of cell proliferation, induction of cell death, or a combination of both. There are differences in sensitivity towards DHA treatment among colorectal cell lines, although the reason why is unclear. 10 human colorectal cell lines, representing 5 different subtypes of colorectal cancer, were included in gene expression analysis. (Pleae refer to Sadanandam A, Lyssiotis CA, Homicsko K, Collisson EA, Gibb WJ, Wullschleger S, Ostos LC, Lannon WA, Grotzinger C, Del Rio M, et al. “A colorectal cancer classification system that associates cellular phenotype and responses to therapy”. Nat Med. 2013;19:619-625. doi:10.1038/nm.3175 for details on cancer subtype classifications.) Our aim is to identify different levels of genes and pathways correlating with differences in sensitivity towards DHA between the colorectal cell lines for future classification of patients that could benefit from omega-3 PUFA treatment in addition to conventional treatment.