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  • 1
    In: Journal of Thoracic Oncology, Elsevier BV, Vol. 13, No. 8 ( 2018-08), p. 1121-1127
    Type of Medium: Online Resource
    ISSN: 1556-0864
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2018
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  • 2
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 13_Supplement ( 2018-07-01), p. 2708-2708
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 2708-2708
    Abstract: Introduction: Chemical labeling of peptides using tandem mass tags (TMT) is a “barcoding” strategy, enabling relative protein quantification across a single panel of samples (as opposed to each run separately). Each multiplex assay is, effectively, its own "batch" of samples, and thus direct comparison of intensities between TMT multiplexes is problematic. Additionally, although there is relatively little missing data within a single plex, there can be large differences in missingness across plexes, with the two types of missingness exhibiting different behavior (infrequent and biased towards low abundances within-plex; more frequent and more stochastic between-plex). We have addressed these issues by developing new pipelines for data normalization, protein-level rollup, and downstream clustering, which seek to minimize the negative impact of missingness. This method development was driven by, and applied to, a set of 116 human lung squamous (SQLC) tumors, with the aim of improving the strength of down-stream biological signal and interpretation. Experiment: TMT analysis was performed on 116 SQLC samples. Each 6-plex contained 4 tumors and 2 pool replicates. The shared pool of 116 tumors was assayed on every multiplex to allow for controlling for variability between plexes, with one pool in ch-126 and the other varying channel between plexes. IDPicker was used for spectral quantification. Spectra abundances were normalized within-plex, and ratios calculated for each channel against the ch-126 pool. Spectra-level ratios were rolled up into protein-level ratios using the geometric mean of ratios within each protein group. Geometric mean protein-level abundance rollup was performed on abundances for each ch-126 pool, normalized across pools, and the geometric mean calculated for each protein group across pools. These mean protein-level abundances were then used to scale the ratios back into final normalized abundances. Average linkage hierarchical clustering was performed on abundance z-scores using a novel distance metric, calculated as the root mean squared deviation (RMSD) of points present in both vectors, divided by a binary presence/absence similarity coefficient such as Ochiai similarity. Results: After normalization, principal component analysis showed no batch effect due to differences between plexes. Heat maps generated using the novel distance metric exhibited improved biological signal over RMSD alone. Tumors cluster into 3 major groupings: high immune + low transcriptional/translational activity, low immune + high transcriptional/translational activity, and samples with medium levels of both. Conclusion: Missingness-aware methods of shared-pool TMT normalization and clustering minimize the negative impact of missingness and yield strong biological signal. Preliminary results suggest that immune response is a major source of differences between lung squamous tumors. Citation Format: Eric A. Welsh, Paul A. Stewart, Matthew C. Chambers, Guolin Zhang, Bin Fang, Steven A. Eschrich, John M. Koomen, Eric B. Haura. Imputation-free analysis of high throughput TMT proteomics of 116 lung squamous samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2708.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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    detail.hit.zdb_id: 410466-3
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  • 3
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 5619-5619
    Abstract: Although advancements in therapeutic regimens for treating multiple myeloma (MM) have prolonged patient survival, the disease remains incurable. Several classes of drugs have contributed to these improvements, such as proteasome inhibitors, immunomodulators, deacetylase inhibitors, monoclonal antibodies, and alkylating agents including melphalan. An expanded arsenal of diverse chemotherapy targets has improved patient care significantly, yet we still lack sufficient knowledge of how cellular metabolism and drug processing can contribute to drug resistance. To address this issue, we utilize cell line models to simulate naïve and drug resistant states, which identify drug modifications, endogenous metabolites, proteins, and acute metabolic profile alterations associated with therapeutic escape. Here, we specifically focus on melphalan; an alkylating agent that forms DNA interstrand crosslinks, inhibits cell division, and leads to cell death through apoptosis (Povirk & Shuker. Mutat. Res. 1994, 318, 205). Melphalan remains a critical component of high dose therapy in the context of stem cell transplant and induction therapy in transplant ineligible patients outside the US. Ineffectiveness of alkylating agents remains a critical problem and serves as an excellent model for investigation of cellular metabolism and its contribution to drug resistance. Two parental MM cell lines (8226 & U266) were obtained from ATCC and resistant derivatives of each cell line (8226-LR5 & U266-LR6) were selected after chronic drug exposure. To assess mechanisms of melphalan resistance, we use liquid chromatography-mass spectrometry-based metabolomics and proteomics approaches, including studies of drug metabolism, untargeted metabolomics, and activity based protein profiling (ABPP). Drug metabolism monitors the intracellular and extracellular drug modifications over a 24-hour period after acute treatment. Untargeted metabolomics is used to compare the steady state endogenous intracellular metabolites of naïve and drug resistant cells. Differences in endogenous metabolites between naïve and drug resistant cell lines are also examined in the acute treatment dataset. ABPP utilizes desthiobiotinylating probes to enrich for ATP-utilizing enzymes, which are identified and quantified to enable comparison. We initially compared acute melphalan treatment in drug naive and resistant isogenic cell line pairs. Predictably, melphalan was converted into monohydroxylated and dihydroxylated metabolites more quickly in cells than in media controls. Differences in the formation of these metabolites between the naïve and resistant cell lines were not observed. The untargeted metabolomics data indicated in the 8226-LR5 model, glutathione and xanthine levels are elevated, while guanine is suppressed relative to naive cells. ABPP demonstrated changes in several enzymes related to purine and glutathione metabolism (Figure 1). Interestingly, the U266/U266-LR6 cell line models exhibit higher baseline levels of glutathione when compared with 8226/8226-LR5, indicating heterogeneous means of drug resistance. Alterations in arginine biosynthesis and nicotinate/nicotinamide metabolism are observed in the untargeted metabolomics and ABPP of U266/U266-LR6. Common pathways (e.g. purine biosynthesis) are altered in both models, although the changes involve different molecules. In examining two models of acquired melphalan resistance, we demonstrate frank differences in metabolic pathways associated with steady state and acute drug response. These data demonstrate the potential heterogeneity in drug resistance mechanisms and the need for more biomarkers to personalize treatment. Ongoing studies involve introduction of enzyme inhibitors in targeted pathways and supplementation of metabolites to validate their role in resistance. Furthermore, we will examine expression of these metabolic pathways associated with ex vivo melphalan resistance in a cohort of over 100 patient samples with paired RNA sequencing. The long term goals are to elucidate mechanisms of therapeutic response, identify biomarkers of metabolism in melphalan resistance, enhance drug efficacy, predict personalized patient treatment, and improve overall MM patient care. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
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