Project description:Retinoblastoma (RB) is an intraocular childhood tumor which, if left untreated, leads to blindness and mortality. Nucleolin (NCL) protein which is differentially expressed on the tumor cell surface, binds ligands and regulates carcinogenesis and angiogenesis. We found that NCL is over expressed in RB tumor tissues and cell lines compared to normal retina. We studied the effect of nucleolin-aptamer (NCL-APT) to reduce proliferation in RB tumor cells. Aptamer treatment on the RB cell lines (Y79 and WERI-Rb1) led to significant inhibition of cell proliferation. Locked nucleic acid (LNA) modified NCL-APT administered subcutaneously (s.c.) near tumor or intraperitoneally (i.p.) in Y79 xenografted nude mice resulted in 26 and 65% of tumor growth inhibition, respectively. Downregulation of inhibitor of apoptosis proteins, tumor miRNA-18a, altered serum cytokines, and serum miRNA-18a levels were observed upon NCL-APT treatment. Desorption electrospray ionization mass spectrometry (DESI MS)-based imaging of cell lines and tumor tissues revealed changes in phosphatidylcholines levels upon treatment. Thus, our study provides proof of concept illustrating NCL-APT-based targeted therapeutic strategy and use of DESI MS-based lipid imaging in monitoring therapeutic responses in RB.
Project description:Methanococcus maripaludis is a methanogenic archaeon. Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). The S40 and S2 strains were grown in 14N and 15N media with acetate separately. A biological replicate was made by switching the media. Mass spectrometry based quantitative proteomics were done on the mixtures to investigate the differences in expression patterns between S40 and S2. Keywords: isotope labeling mass spectrometry, quantitative proteomics
Project description:Endotoxin-induced uveitis (EIU) in rodents is a good animal model to study uveitis and associated acute retinal inflammation. To understand the pathogenic mechanism of uveitis and screen the potential targets for treatment, we analyzed the retinal proteomic profiles of EIU and normal C57BL/6J mice using a data-independent acquisition-based mass spectrometry (SWATH-MS).
Project description:In this project, two NSCLC cohorts were analyzed by Data Independent Acquisition (DIA-MS). A cohort of early stage NSCLC samples (141) as well as an additional cohort of late stage NSCLC samples (84) with the aim to demonstrate utility of MS for subtyping and treatment prediction in a clinical setting. Further, six identified NSCLC proteome subtypes were investigated in relation to cancer driver pathways and immune phenotypes based on the generated MS-data.
Project description:Challenges in the precision diagnosis and treatment of nasopharyngeal carcinoma (NPC) persist, primarily due to the lack of a multi-omics-based molecular typing system and effective targeted therapeutic strategies. In this study, we integrated proteomic and phosphoproteomic analyses of NPC tissues and normal nasopharyngeal tissues to systematically identify key dysregulated protein networks, which are enriched in genes associated with cell cycle, cilium function, immune response, metabolism, mTOR signaling, and responses to virus infection. Based on these proteomic characteristics, we classified NPC into two molecular subtypes, subtype 1 and 2, which exhibit significant clinical heterogeneity. Moreover, we identify protein signatures for both normal and cancerous tissues, as well as for the two molecular subtypes, and developed diagnostic and prognostic models. Through computational drug repurposing and experimental validation, we identified the pan-histone deacetylase inhibitor Panobinostat as a potent anti-tumor agent for NPC in both in vitro and in vivo models. Our findings revealed that Panobinostat inhibits MYC signaling, thereby disrupting the transcriptional activation of the ATR-CHK1 axis. This reduction in ATR-CHK1 activity leads to impaired homologous recombination repair efficiency, ultimately leading to DNA damage accumulation. Notably, we demonstrated a synergistic therapeutic effect when Panobinostat was combined with radiotherapy, resulting in enhanced cytotoxicity against NPC cells. In summary, we established a multi-omics molecular typing system for NPC, developed diagnostic and prognostic marker panels, and highlighted the therapeutic potential of Panobinostat in combination with radiotherapy. These findings lay a solid foundation for precision diagnosis, prognostic stratification, and personalized treatment strategies in NPC.
Project description:LC-MS/MS-based identification of HLA-peptides is poised to provide a deep understanding of the rules underlying antigen presentation. However, a key obstacle limiting the utility of MS data is the ambiguity arising from the co-expression of multiple HLA alleles. Here, we introduce a strategy for profiling the HLA ligandome one allele at a time. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing a novel spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of novel binding motifs, and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on datasets of peptides with measured affinities. We thus demonstrate a scalable strategy for systematically learning the rules of endogenous antigen presentation.
Project description:This dataset contains mass spectrometry-based proteomic data generated from pleural tissuesamples.Proteins were extracted, digested, and labeled using TMT isobaric labeling for quantitative analysis. Samples were analyzed using LC–MS/MS to profile the global proteome.The dataset includes raw mass spectrometry files, processed search results, and experimentalmetadata. Multiple biological and technical replicates were included for each condition toensure reproducibility. This dataset supports quantitative protein profiling and can be used for downstream analyses of pleural tissue proteomes.