Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets

BACKGROUND: Genome-wide microarrays have been useful for predicting chemical-genetic interactions at the gene level. However, interpreting genome-wide microarray results can be overwhelming due to the vast output of gene expression data combined with off-target transcriptional responses many times induced by a drug treatment. This study demonstrates how experimental and computational methods can interact with each other, to arrive at more accurate predictions of drug-induced perturbations. We present a two-stage strategy that links microarray experimental testing and network training conditions to predict gene perturbations for a drug with a known mechanism of action in a well-studied organism. RESULTS: S. cerevisiae cells were treated with the antifungal, fluconazole, and expression profiling was conducted under different biological conditions using Affymetrix genome-wide microarrays. Transcripts were filtered with a formal network-based method, sparse simultaneous equation models and Lasso regression (SSEM-Lasso), under different network training conditions. Gene expression results were evaluated using both gene set and single gene target analyses, and the drug’s transcriptional effects were narrowed first by pathway and then by individual genes. Variables included: (i) Testing conditions – exposure time and concentration and (ii) Network training conditions – training compendium modifications. Two analyses of SSEM-Lasso output – gene set and single gene – were conducted to gain a better understanding of how SSEM-Lasso predicts perturbation targets. CONCLUSIONS: This study demonstrates that genome-wide microarrays can be optimized using a two-stage strategy for a more in-depth understanding of how a cell manifests biological reactions to a drug treatment at the transcription level. Additionally, a more detailed understanding of how the statistical model, SSEM-Lasso, propagates perturbations through a network of gene regulatory interactions is achieved.Published versio

Small molecule inhibitors of Late SV40 Factor (LSF) abrogate hepatocellular carcinoma (HCC): evaluation using an endogenous HCC model

Hepatocellular carcinoma (HCC) is a lethal malignancy with high mortality and poor prognosis. Oncogenic transcription factor Late SV40 Factor (LSF) plays an important role in promoting HCC. A small molecule inhibitor of LSF, Factor Quinolinone Inhibitor 1 (FQI1), significantly inhibited human HCC xenografts in nude mice without harming normal cells. Here we evaluated the efficacy of FQI1 and another inhibitor, FQI2, in inhibiting endogenous hepatocarcinogenesis. HCC was induced in a transgenic mouse with hepatocyte-specific overexpression of c-myc (Alb/c-myc) by injecting N-nitrosodiethylamine (DEN) followed by FQI1 or FQI2 treatment after tumor development. LSF inhibitors markedly decreased tumor burden in Alb/c-myc mice with a corresponding decrease in proliferation and angiogenesis. Interestingly, in vitro treatment of human HCC cells with LSF inhibitors resulted in mitotic arrest with an accompanying increase in CyclinB1. Inhibition of CyclinB1 induction by Cycloheximide or CDK1 activity by Roscovitine significantly prevented FQI-induced mitotic arrest. A significant induction of apoptosis was also observed upon treatment with FQI. These effects of LSF inhibition, mitotic arrest and induction of apoptosis by FQI1s provide multiple avenues by which these inhibitors eliminate HCC cells. LSF inhibitors might be highly potent and effective therapeutics for HCC either alone or in combination with currently existing therapies.The present study was supported in part by grants from The James S. McDonnell Foundation, National Cancer Institute Grant R01 CA138540-01A1 (DS), National Institutes of Health Grant R01 CA134721 (PBF), the Samuel Waxman Cancer Research Foundation (SWCRF) (DS and PBF), National Institutes of Health Grants R01 GM078240 and P50 GM67041 (SES), the Johnson and Johnson Clinical Innovation Award (UH), and the Boston University Ignition Award (UH). JLSW was supported by Alnylam Pharmaceuticals, Inc. DS is the Harrison Endowed Scholar in Cancer Research and Blick scholar. PBF holds the Thelma Newmeyer Corman Chair in Cancer Research. The authors acknowledge Dr. Lauren E. Brown (Dept. Chemistry, Boston University) for the synthesis of FQI1 and FQI2, and Lucy Flynn (Dept. Biology, Boston University) for initially identifying G2/M effects caused by FQI1. (James S. McDonnell Foundation; R01 CA138540-01A1 - National Cancer Institute; R01 CA134721 - National Institutes of Health; R01 GM078240 - National Institutes of Health; P50 GM67041 - National Institutes of Health; Samuel Waxman Cancer Research Foundation (SWCRF); Johnson and Johnson Clinical Innovation Award; Boston University Ignition Award; Alnylam Pharmaceuticals, Inc.)Published versio

Discovery of a small molecule dihydroquinolinone inhibitor with potent antiproliferative and antitumor activity results in catastrophic cell division

Thesis (Ph.D.)--Boston University PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at [email protected]. Thank you.A family of dihydroquinolinones that inhibited the proliferation of a number of cancer cell lines and targeted the oncogenic activities of the late simian virus 40 factor (LSF) was discovered. The lead quinolinone inhibitors, 8-(2-propoxyphenyl)-7,8-dihydro-[1,3]dioxolo[4,5-g]quinolin-6(5H)-one, FQI1, and 8-(2-propoxyphenyl)-[1,3]dioxolo[4,5-g]quinolin-6(5H)-one, FQI2, were determined by a comprehensive SAR study. The lead compounds had low micromolar to nanomolar Gi50S and IC50S (concentrations that induced 50% inhibition) in cell growth and LSF-directed luciferase reporter assays, respectively. A distinct correlation between the GI50 and IC50 values indicated antiproliferative effects resulted from inhibition of LSF activity. FQI1 had no growth effects on immortalized human hepatocytes or primary mouse hepatocytes. Overall, FQI1 proved a good drug candidate for hepatocellular carcinoma (HCC). It possessed a low molecular weight and moderate solubility, which was improved by substitution of the amide with a triazole bioisostere. FQI1 showed excellent microsomal stability, high in vivo volume of distribution and half-life in rodents, and was a potent inhibitor of HCC tumorigenesis in immunocompromised mice. FQI1 induced mitotic catastrophe in the HCC cell line, QGY-7703, the cervical carcinoma cell line, HeLa, and the NIH-3T3 fibroblasts, as evidenced by widespread multinucleated cell morphologies. Excessive micronucleation in NIH-3T3 cells treated with higher FQI1 concentrations further supported severe chromosome segregation defects. Mitotic slippage into interphase and subsequent endoreduplication was also induced by FQI1 in NIH-3T3 cells. These phenotypes have been seen with chemicals such as the microtubulin poisons and Aurora B kinase inhibitors. Together these results suggested that FQI1-induced evasion or adaptation of the spindle assembly checkpoint and abnormal chromosome segregation resulted in mitotic catastrophe, and in the case of NIH-3T3 cells, polyploid cell progeny. Expression profiling in QGY-7703 cells with FQI1 cells revealed an upregulation of multiple genes along the TGF-β/SMAD signaling cascade compared to the untreated cell population. This supported a model where the induction of p21Cip1 activity as a result of mitotic slippage activated the G1/S checkpoint in response to aberrant exit out of mitosis in QGY-7703 cells. These results together elucidated FQI1's mechanism of action in mitosis and also strongly suggested that LSF regulated genes required for the proper execution of mitosis