Saeed, F. | Search bioRxiv

bioRxiv2018

MaSS-Simulator: A highly configurable MS/MS simulator for generating test datasets for big data algorithms.

Mass Spectrometry (MS) based proteomics has become an essential tool in the study of proteins. The big data from MS machines has led to the development of novel serial and parallel algorithmic tools. However, the absence of data benchmarks and ground truth makes the algorithmic integrity testing and reproducibility a challenging problem. To this end, we present MaSS-Simulator, which is an easy to use simulator and can be configured to generate MS/MS datasets for a wide variety of conditions with known ground truths. MaSS-Simulator offers a large number of configuration options to simulate control datasets with desired properties thus enabling rigorous and large scale algorithmic testing. We assessed 8,031 spectra generated by MaSS-Simulator by comparing them against the experimentally generated spectra of same peptides. Our results showed that MaSS-Simulator generated spectra were very close to the real-experimental spectra and had a relative-error distribution centered around 25%. In contrast the theoretical spectra for same peptides had relative-error distribution centered around 150%. Source code, executables and a user manual can be downloaded from https://github.com/pcdslab/MaSS-Simulator

systems biology↗

bioRxiv2017

Estrogen and Soy Isoflavonoids Decrease Sensitivity of Medulloblastoma and Central Nervous System Primitive Neuroectodermal Tumor Cells to Chemotherapeutic Cytotoxicity

BackgroundOur previous studies demonstrated that growth and migration of medulloblastoma (MB), the most common malignant brain tumor in children, are stimulated by 17{beta}-estradiol. The growth stimulating effects of estrogens are mediated through ER{beta} and insulin-like growth factor 1 signaling to inhibit caspase 3 activity and reduce tumor cell apoptosis. The objective of this study was to determine whether estrogens decreased sensitivity of MB cells to cytotoxic actions of chemotherapeutic drugs.\n\nMethodsUsing in vitro cell viability and clonogenic survival assays, concentration response analysis was used to determine whether the cytoprotective effects of estradiol protected human D283 Med MB cells from the cytotoxic actions of the MB chemotherapeutic drugs cisplatin, vincristine, or lomustine. Additional experiments were done to determine whether the ER antagonist fulvestrant or the selective ER modulator tamoxifen blocked the cytoprotective actions of estradiol. ER-selective agonists and antagonists were used to define receptor specificity, and the impacts of the soy-derived phytoestrogens genistein, daidzein, and s-equol on chemosensitivity were evaluated.\n\nResultsIn D283 Med cells the presence of 10 nM estradiol increased the IC50 for cisplatin-induced inhibition of viability 2-fold from ~5 M to >10 M. In clonogenic survival assays estradiol decreased the chemosensitivity of D283 Med exposed to cisplatin, lomustine and vincristine. The ER{beta} selective agonist DPN and low physiological concentrations of the soy-derived phytoestrogens genistein, daidzein, and s-equol also decreased sensitivity of D283 Med cells to cisplatin. The protective effects of estradiol were blocked by the antiestrogens 4-hydroxytamoxifen, fulvestrant (ICI 182,780) and the ER{beta} selective antagonist PPHTP. Whereas estradiol also decreased chemosensitivity of PFSK1 cells, estradiol increased sensitivity of Daoy cell to cisplatin, suggesting that ER{beta} mediated effects may vary in different subtypes of MB.\n\nConclusionsThese findings demonstrate that E2 and environmental estrogens decrease sensitivity of MB to cytotoxic chemotherapeutics, and that ER{beta} selective and non-selective inhibition of estrogen receptor activity blocks these cytoprotective actions. These findings support the therapeutic potential of antiestrogen adjuvant therapies for MB, and findings that soy phytoestrogens also decrease sensitivity of MB cells to cytotoxic chemotherapeutics suggest that decreased exposure to environmental estrogens may benefit MB patient responses to chemotherapy.

pharmacology and toxicology↗