PubMed · 9348587
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1997. Computerized system streamlines chemotherapy order process.. https://pubmed.ncbi.nlm.nih.gov/9348587/
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Drug response differs substantially in cancer patients due to inter- and intra-tumor heterogeneity. Particularly, transcriptome context, especially tumor microenvironment, has been shown playing a significant role in shaping the actual treatment outcome. In this study, we develop a deep variational autoencoder (VAE) model to compress thousands of genes into latent vectors in a low-dimensional space. We then demonstrate that these encoded vectors could accurately impute drug response, outperform standard signature-gene based approaches, and appropriately control the overfitting problem. We apply rigorous quality assessment and validation, including assessing the impact of cell line lineage, cross-validation, cross-panel evaluation, and application in independent clinical data sets, to warrant the accuracy of the imputed drug response in both cell lines and cancer samples. Specifically, the expression-regulated component (EReX) of the observed drug response achieves high correlation across panels. Using the well-trained models, we impute drug response of The Cancer Genome Atlas data and investigate the features and signatures associated with the imputed drug response, including cell line origins, somatic mutations and tumor mutation burdens, tumor microenvironment, and confounding factors. In summary, our deep learning method and the results are useful for the study of signatures and markers of drug response.
The intracellular aryl hydrocarbon receptor (AhR) mediates signal transduction by environmental pollutants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and benzo[a]pyrene by functioning as a ligand-activated transcription factor. We have investigated AhR signaling in sublines of the human breast cancer cell line MCF-7 selected for resistance to AdriamycinR (AdrR) and benzo[a]pyrene (BP(R)). Previously we reported that AdrR cells have a loss of estrogen receptor (ER) expression and are Ah-nonresponsive. Here we show that AhR mRNA and protein are expressed at normal levels in AdrR cells, and the activated AhR complex is functionally capable of binding a xenobiotic responsive element. In MCF-7 cells AhR was depleted to 15% of normal levels after 4 hr TCDD treatment; however, 45% of AhR remained in AdrR cells during this time course. In BP(R) cells AhR mRNA levels were found to be decreased relative to wild-type cells, which led to decreased AhR protein levels and DNA-binding activity. Cellular ER content has been shown to correlate with Ah-responsiveness in human breast cancer cell lines. BP(R) cells were found to be ER-positive, although chronic (BP(R) cells) and acute (24 hr) exposure to benzo[a]pyrene led to significantly lower ER protein levels in MCF-7 cells. We conclude that loss of Ah-responsiveness occurs by different mechanisms in xenobiotic-resistant MCF-7 sublines: AhR mRNA is down-regulated in BP(R) cells, whereas AdrR cells are deficient in AhR signaling by a mechanism unrelated to AhR expression and activity.
The transcription factors of the Myc/Max/Mad network are important regulators of cell growth, differentiation, and apoptosis and are frequently involved in tumor development. Constitutive expression of v-Myc blocks phorbol ester (TPA)-induced differentiation of human U-937 monoblasts. However, costimulation with interferon-gamma (IFN-gamma) and TPA restores terminal differentiation and G1 cell-cycle arrest despite continuous expression of v-Myc. The mechanism by which TPA + IFN-gamma counteract v-Myc activity has not been unravelled. Our results show that TPA + IFN-gamma treatment led to an inhibition of v-Myc- and c-Myc-dependent transcription, and a specific reduction of v-Myc:Max complexes and associated DNA-binding activity, whereas the steady state level of the v-Myc protein was only marginally affected. In contrast, TPA + IFN-gamma costimulation neither increased the expression of Mad1 or other mad/mnt family genes nor altered heterodimerization or DNA-binding activity of Mad1. The reduced amount of v-Myc:Max heterodimers in response to treatment was accompanied by partial dephosphorylation of v-Myc and c-Myc. Phosphatase treatment of Myc:Max complexes lead to their dissociation, thus mimicking the effect of TPA + IFN-gamma. In addition to modulation of the expression of Myc/Max/Mad network proteins, posttranslational negative regulation of Myc by external signals may, therefore, be an alternative biologically important level of control with potential therapeutic relevance for hematopoietic and other tumors with deregulated Myc expression.