Project description:We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome.
Project description:We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome.
Project description:Native MS analysis of single mutant and double mutant cycle experiments. See: https://www.biorxiv.org/content/10.1101/2023.09.19.558516v1
Project description:Mutations in RNA splicing factors are prevalent across cancers and generate recurrently mis-spliced mRNA isoforms. Here we identified a series of bona fide neoantigens translated from highly stereotyped splicing alterations promoted by neomorphic, leukemia-associated somatic mutations in the splicing machinery. We utilized feature-barcoded peptide-MHC dextramers to isolate neoantigen-specific T cell receptors (TCR) from both healthy donors and patients with leukemia. While circulating neoantigen-specific CD8+ T cells were identified in patients with active disease, they were dysfunctional with reduced inflammatory response gene signatures. In contrast, donor CD8+ T cells with tumor-reactive TCRs were present following curative allogeneic hematopoietic cell transplant. T cells engineered with TCRs recognizing an SRSF2 mutant-induced neoantigen in CLK3 resulted in specific recognition and cytotoxicity of SRSF2 mutant leukemia. These data identify RNA mis-splicing derived neoantigens and neoantigen-specific TCRs across patients and provide proof-of-concept to genetically redirect T cells to public mis-splicing derived neoantigens in myeloid leukemias.
Project description:Genome compartmentalization mediated by the cohesin complex plays an essential role in the maintenance of genome integrity and transcriptional regulation. Recurrent somatic mutations in multiple members of the cohesin complex are frequent genetic drivers in several types of cancer, including acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), but the cellular consequences of cohesin mutations have not been determined and no therapies have been identified with selective efficacy in cohesin-mutant cancers. Using quantitative proteomics and genome-wide genetic screens in genetically engineered models of STAG2-mutant AML, we identify changes in cohesin complex composition and dependency on STAG1, DNA damage repair, master transcription factors, and RNA splicing machinery. Consistent with these findings, loss of STAG2 leads to DNA replication fork stalling and is associated with increased levels of dsDNA breaks and activation of DNA damage checkpoints, as well as aberrant splicing. Genetic or pharmacologic perturbation of DNA damage repair or splicing creates a synthetic vulnerability for cohesin-mutant cells in vitro and in vivo. Finally, STAG2 loss leads to a global reduction in cohesin binding to chromatin and expansion of super-enhancers, and mutant cohesin complexes spatially co-localize with super-enhancer enriched factors, DNA damage and splicing machinery. Our findings inform the biology of cohesins in cancer cells, and highlight novel therapeutic possibilities for cohesin-mutant malignancies.
Project description:Manuscript Title: Pyochelin biotransformation shapes bacterial competition LC-MS/MS analysis of P. aeruginosa interaction with S. aureus wildtype, fhuG mutant and fhuD1/D2 double mutant.
Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in idm2 single mutant and idm1idm2 double mutant MethylC-Seq: 2 mutants examined, idm2 single mutant (two biological replicates) and idm1idm2 double mutant
Project description:To identify the effect of additional deletion of rel and mprA in the aa3 mutant strain lacking the aa3 cytochrome c oxidase of the respiratory electron transport chain of Mycobacterium smegmatis MC2 155, we constructed the aa3 rel double mutant and aa3 mprA double mutant and profiled the transcriptomes of the aa3 mutant, aa3 mprA double mutant and aa3 rel double mutant strains. Our comparative RNA sequencing analysis revealed that expression of most ribosomal proteins was induced in the aa3 rel double mutant and aa3 mprA double mutant relative to the aa3 mutant.
Project description:We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome. RNA-seq experiments (polyA+ RNA) in triplicates for each condition WT and nsrab mutants.
