Project description:The KRAS oncogene triggers complex phosphorylation cascades, including canonical pathways such as RAF/MEK/ERK, PI3K/AKT, and RALGDS/RAL, and their engagement varies depending on the cancer context. Integration of transcriptomic, proteomic, and phosphoproteomic analysis of KRAS mutant cancers has been used to assess new therapeutic combinations, highlighting KRAS mutant cancer heterogeneity. To dissect the complexity of KRAS dependency in PDAC, we employed unbiased proteome and phosphoproteome analysis to inform on the engagement of phosphorylation cascades and define a proteomic profile of orthotopic mouse tumors with a KrasG12D mutation treated with panKRASi (BI-2493). Treatment-specific changes at phospo/proteomic level (7,134 significantly dysregulated proteins and 6,173 dysregulated phosphosites). Specifically, cell cycle regulatory CDKs are the most significantly suppressed kinases following panKRASi treatment, with a strong downregulation of cell cycle regulatory CDKs and ERK1/2. We also identified enrichment in oxidative phosphorylation and metabolic pathways and suppression of G2M checkpoint and E2F targets, coupled with a decline in DNA replication and cell cycle pathways, suggesting impairment in cell cycle progression. Together, these studies revealed robust suppression of Kras activity and cell cycle progression consistent with tumor growth inhibition and Ki67 staining under panKRASi treatment.
Project description:Ataxia telangiectasia mutated (ATM) is a protein that belongs to the family of phosphatidylinositol 3-kinase (PI3K)-like serine/threonine kinases. Initially identified as a nuclear protein essential for the DNA damage response (DDR) in mitotic cells, it serves as repair coordinator for DNA double-strand breaks (DSBs). Dysfunction of the ATM protein underlies ataxia telangiectasia (A-T), a rare autosomal recessive disorder characterized by immunodeficiency and progressive cerebellar degeneration leading to ataxia. The cause of cerebellar neurodegeneration cannot be explained at present, given that in postmitotic neurons ATM has a cytoplasmic localization. The non-nuclear functions of ATM and their mechanistic link to cerebellar degeneration in A-T remain elusive. In this study we established both phosphoproteomic and proteomic profiles of ATM deficiency in neuroblastoma cells and mouse cerebellum tissue to identify the underlying molecular mechanism and relevant signaling networks.
Project description:Sample multiplexing using isobaric tagging is a powerful strategy for proteome-wide protein quantification. One major caveat of isobaric tagging is ratio compression that results from the isolation, fragmentation, and quantification of co-eluting, near-isobaric peptides, a phenomenon typically referred to as “ion interference.” A robust platform to ensure quality control, optimize parameters, and enable comparisons across samples is essential as new instrumentation and analytical methods evolve. Here, we introduce TKO-iQC, an integrated platform consisting of the Triple Knock-Out (TKO) yeast digest standard and an automated web-based database search and protein profile visualization application. We highlight two new TKO standards based on the TMTpro reagent (TKOpro9 and TKOpro16), as well as an updated TKO Viewing Tool, TVT2.0. TKO-iQC greatly facilitates the comparison of instrument performance with a straightforward and streamlined workflow.
Project description:Serine/threonine kinase 40 (Stk40) was previously identified as a direct target gene of pluripotency-associated transcription factor Oct4 and its overexpression could facilitate differentiation of mouse embryonic stem cells (mESCs) towards the extraembryonic endoderm. Stk40-/- mice are lethal at the perinatal stage, displaying multiple organ failures. However, the molecular mechanisms underlying the physiological functions of Stk40 remain elusive. Here, we report that Stk40 ablation compromises the mesoderm differentiation from mESCs in vitro and in embryos. Mechanistically, Stk40 interacts with both mammalian constitutive photomorphogenic protein 1 (Cop1) and c-Jun, promoting degradation of c-Jun. Consequently, Stk40 knockout leads to c-Jun protein accumulation, which, in turn, might suppress the Wnt signaling activity and impair the mesoderm differentiation process. Overall, this study reveals that Stk40, together with Cop1, represent a novel axis for modulating c-Jun protein levels within an appropriate range during mesoderm differentiation from mESCs. Our finding provides new insight into the molecular mechanism regulating c-Jun protein stability and may have potential for managing related cellular disorders.
Project description:Anthelmintic resistance is a major problem in the global fight against parasitic nematodes., Most previous studies have focused on the analysis of potential candidate genes that may have a role in resistance. Here we take a novel approach in the important parasite, Haemonchus contortus, by investigating changes in microRNA expression between resistant and susceptible parasites. The resistant worms included two geographically distinct strains and two lines generated by multiple rounds of backcrossing between susceptible and resistant parents, with ivermectin selection. All four resistant strains showed increased abundance of a single miRNA, hco-miR-9551, compared to the susceptible strain. hco-miR-9551 is enriched in female worms, is likely to be located on the X chromosome and is found only in clade V parasitic nematodes. Approximately 5-10% of the genomes of the resistant parental strains are introgressed into the respective backcrosses, suggesting that hco-miR-9551, or genes regulated by the miRNA, may be genetically linked to a locus that determines resistance. Genes containing predicted binding sites for hco-miR-9551 were identified computationally and refined based on differential expression in a transcriptomic dataset. These findings advance our conceptual understanding of the molecular mechanisms of anthelmintic resistance in H. contortus and indicate that altered miRNA expression may be linked with drug resistance. All samples were carried out using three biological replicates
Project description:Gene expression profiling was carried out HeyA8 and SKOV3-ip1 ovarian cancer cell lines, treated either with vehicle control or 10 uM norepinephrine. The primary research question is whether ovarian cancer cell gene expression differs as a function of norepinephrine exposure. Gene expression profiling was carried out HeyA8 and SKOV3-ip1 ovarian cancer cell lines, treated either with vehicle control or 10 uM norepinephrine.
Project description:A mild olfactory dysfunction has been observed in frontotemporal dementias (FTD). However, the underlying molecular mechanisms associated to this deficit are poorly understood. Here, we applied mass spectrometry-based quantitative proteomics to analyse pathological effects on the olfactory bulb (OB) from progressive supranuclear palsy (PSP) and frontotemporal lobar degeneration TDP43 proteinopathy (FTLD-TDP) subjects
Project description:Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from 4 mo old rhesus macaques subject to maternal rearing, peer rearing, or surrogate peer rearing. The primary research question is whether gene expression differs as a function of early rearing conditions. Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from 4 mo old rhesus macaques subject to maternal rearing, peer rearing, or surrogate peer rearing. The primary research question is whether gene expression differs as a function of early rearing conditions.
Project description:Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from renal cell carcinoma patients. The primary research question is whether gene expression differs as a function of patient's level of depression as measured by CESD score > 16. Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from renal cell carcinoma patients. The primary research question is whether gene expression differs as a function of patient's level of depression as measured by CESD score > 16.