Project description:MAPK pathway alterations are the most common oncogenic drivers. Among the approved therapies targeting this pathway are MEK and RAF inhibitors. However, therapeutic resistance and toxicities have limited their clinical success. To overcome these liabilities, we developed IK595, a potent MEK-RAF molecular glue. IK-595 traps MEK in an inactive complex with all RAF isoforms. In addition, IK-595 precludes CRAF-mediated MEK reactivation and ARAF heterodimerization allowing for prolonged target engagement and durable MAPK pathway inhibition. This project aimed to explore gene expression modulation by IK-595 in AsPC-1 cell line-derived xenograft mice at different time points following last dose. Tumor RNA-seq was performed in AsPC-1 tumor-bearing mice treated with three doses of vehicle or IK-595 (at 6 mg/kg QOD). Tumors from the drug-treated mice were collected and profiled at the following time points after the last dose: 2 hours, 4 hours, 8 hours, 24 hours, and 48 hours (four animals per time point group) - to understand longitudinal gene expression changes after dosing. A significant reduction in most ERK1/2 target genes was observed as early as 2 hours after the last dose, with maximal inhibition observed at 8 hours. Partial recovery of ERK1/2 target gene expression occurred at 24 hours, with most genes returning to baseline levels by 48 hours. While elevated pathway activation following chronic treatment of MAPK pathway inhibitors is known to be associated with resistance in the literature, the expression of ERK1/2 target genes in our study never rebounded above baseline levels upon IK-595 treatment.
Project description:Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.
Project description:The barcode probe is a convenient and efficient tool for molecular cytogenetics. Tripidium arundinaceum, as a polyploid wild allied genus of Saccharum, is a useful genetic resource that confers biotic and abiotic stress resistance for sugarcane breeding. Unfortunately, the basic cytogenetic information is still unclear due to the complex genome. We constructed the Cot-20 library for screening moderately and highly repetitive sequences from T. arundinaceum, and the chromosomal distribution of these repetitive sequences was explored. We used the barcode of repetitive sequence probes to distinguish the ten chromosome types of T. arundinaceum by fluorescence in situ hybridization (FISH) with Ea-0907, Ea-0098, and 45S rDNA. Furthermore, the distinction among homology chromosomes based on repetitive sequences was constructed in T. arundinaceum by the repeated FISH using the barcode probes including Ea-0663, Ea-0267, EaCent, 5S rDNA, Ea-0265, Ea-0070, and 45S rDNA. We combined these probes to distinguish 37 different chromosome types, suggesting that the repetitive sequences may have different distributions on homologous chromosomes of T. arundinaceum. In summary, this method provide a basis for the development of similar applications for cytogenetic analysis in other species.
Project description:Tripidium arundinaceum isolate:BC5 progeny of a cross between Saccharum spp. and Erianthus arundinaceus | cultivar:1679-33 Genome sequencing