Project description:Introducing a clinical-practical, alternative splicing activity-based proteogenomic method that identifies, in their oncogenically active states, biomarker genes bearing patient-specific GE or copy-number alterations of prognostic significance. This integrated multi-omics method uses intronic splicing enhancers (ISEs) probes to sort in situ ISE-interacting trans-acting protein factors (trans-interactome) directly from a heterogeneous tumor for subsequent mass spectrometry (MS) characterization.
Project description:The telomeric amplicon at 8p12 is common in ER+ breast cancers. Array-CGH and expression analyses of 1172 tumors revealed ZNF703/Zeppo1 was the single gene within the minimal amplicon and was amplified predominantly in the Luminal B subtype. Amplification was shown to correlate with increased gene and protein expression and was associated with a distinct expression signature and poor outcome. In the luminal MCF-7 cell line manipulation of ZNF703 expression altered transcription of genes also present within the primary tumor signature, including TGFBR2 (whose promoter was bound by ZNF703). Overexpression of ZNF703 rendered MCF-7 cells insensitive to TGFβ-induced suppression of mammosphere formation. Forced overexpression of ZNF703 in normal human breast epithelial cells enhanced the frequency of in vitro colony-forming cells from luminal progenitors. Together these data strongly point to ZNF703/Zeppo1 as a novel oncogene in Luminal B breast cancer. MCF-7 breast cancer cell line was infected with ZNF703 overexpression (ZNF703) or control (HIV) virus and following GFP sorting of infected cells, were transfected with control siRNA (siC) or siRNA against endogenous ZNF703 (siZNF), resulting in four different conditions: siC_HIV, siC_ZNF, siZNF_HIV and siZNF-ZNF. RNA for each condition was harvested from triplicate plates.
Project description:We report for the first time movement of Correia Repeat Enclosed Elements, through inversion of the element at its chromosomal location. Analysis of Ion Torrent generated genome sequence data from Neisseria gonorrhoeae strain NCCP11945 passaged for 8 weeks in the laboratory under standard conditions and stress conditions revealed a total of 37 inversions: 24 were exclusively seen in the stressed sample; 7 in the control sample; and the remaining 3 were seen in both samples. These inversions have the capability to alter gene expression in N. gonorrhoeae through the previously determined activities of the sequence features of these elements. In addition, the locations of predicted non-coding RNAs were investigated to identify potential associations with CREE. Associations varied between strains, as did the number of each element identified. The analysis indicates a role for CREE in disrupting ancestral regulatory networks, including non-coding RNAs. RNA-Seq was used to examine expression changes related to Correia repeats in the strain
Project description:The MCF7 cell line represents a typical epithelial cell line and corresponds to luminal A breast cancer (estrogen-responsive). Overexpression of HAX1 was demonstrated in MCF7 cell line as well as in breast cancer samples, suggesting a role of HAX1 in breast cancer progression. HAX1 is a 32-kDa protein of unknown structure, involved in the regulation of apoptosis, cell migration and calcium homeostasis. It was also shown to bind mRNA. Scarcity of structural elements and the presence of a disordered region, inferred from HAX1 sequence, suggests that HAX1 is intrinsically disordered, and may have many protein-protein interactions. So far about 40 different proteins were characterized as HAX1 protein partners. In the present work, applying immunoaffinity chromatography coupled with mass spectrometry, we identified new candidates for HAX1 binding partners in breast cancer cells. Newly identified proteins may be divided into three, partially overlapping groups: cytoskeleton-associated proteins, GTP-ase associated proteins and RNA-binding proteins. These results imply that HAX1 has more protein partners than hitherto described. Subsequent analysis of these interactions may shed some light into molecular mechanisms of HAX1 functions.
Project description:The PI3Kalpha-specific inhibitor Alpelisib (BYL719) has been approved for the treatment of metastatic ER+/HER2- breast cancer patients in combination with Fulvestrant. After initial response, patients develop drug resistance and disease relapses. In order to identify signalling pathways contributing to the acquired resistance to BYL719 in breast cancer, we generated BYL719-resistant T47D cells and used them together with the parental cells to perform label-free quantitative phosphoproteomics.