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Durham, NC, United States

Dahlman K.B.,Sloan Kettering Cancer Center | Parker J.S.,Expression Analysis Inc. | Shamu T.,Sloan Kettering Cancer Center | Hieronymus H.,Sloan Kettering Cancer Center | And 7 more authors.
PLoS ONE | Year: 2012

There is significant need to identify novel prostate cancer drug targets because current hormone therapies eventually fail, leading to a drug-resistant and fatal disease termed castration-resistant prostate cancer. To functionally identify genes that, when silenced, decrease prostate cancer cell proliferation or induce cell death in combination with antiandrogens, we employed an RNA interference-based short hairpin RNA barcode screen in LNCaP human prostate cancer cells. We identified and validated four candidate genes (AKT1, PSMC1, STRADA, and TTK) that impaired growth when silenced in androgen receptor positive prostate cancer cells and enhanced the antiproliferative effects of antiandrogens. Inhibition of AKT with a pharmacologic inhibitor also induced apoptosis when combined with antiandrogens, consistent with recent evidence for PI3K and AR pathway crosstalk in prostate cancer cells. Recovery of hairpins targeting a known prostate cancer pathway validates the utility of shRNA library screening in prostate cancer as a broad strategy to identify new candidate drug targets. © 2012 Dahlman et al. Source

Fannin R.D.,U.S. National Institutes of Health | Russo M.,Carolinas Medical Center Liver Transplant Unit | O'Connell T.M.,North Park University | O'Connell T.M.,University of North Carolina at Chapel Hill | And 11 more authors.
Hepatology | Year: 2010

The diagnosis and management of drug-induced liver injury (DILI) is hindered by the limited utility of traditional clinical chemistries. It has recently been shown that hepatotoxicants can produce compound-specific changes in the peripheral blood (PB) transcriptome in rodents, suggesting that the blood transcriptome might provide new biomarkers of DILI. To investigate in humans, we used DNA microarrays as well as serum metabolomic methods to characterize changes in the transcriptome and metabolome in serial PB samples obtained from six healthy adults treated with a 4-g bolus dose of acetaminophen (APAP) and from three receiving placebo. Treatment did not cause liver injury as assessed by traditional liver chemistries. However, 48 hours after exposure, treated subjects showed marked downregulation of genes involved in oxidative phosphorylation/mitochondrial function that was not observed in the placebos (P < 1.66E-19). The magnitude of down-regulation was positively correlated with the percent of APAP converted to the reactive metabolite N-acetyl-p- benzoquinone-imide (NAPQI) (r = 0.739; P = 0.058). In addition, unbiased analysis of the serum metabolome revealed an increase in serum lactate from 24 to 72 hours postdosing in the treated subjects alone (P < 0.005). Similar PB transcriptome changes were observed in human overdose patients and rats receiving toxic doses. Conclusion: The single 4-g APAP dose produced a transcriptome signature in PB cells characterized by down-regulation of oxidative phosphorylation genes accompanied by increased serum lactate. Similar gene expression changes were observed in rats and several patients after consuming hepatotoxic doses of APAP. The timing of the changes and the correlation with NAPQI production are consistent with mechanisms known to underlie APAP hepatoxicity. These studies support the further exploration of the blood transcriptome for biomarkers of DILI. Copyright © 2009 by the American Association for the Study of Liver Diseases. Source

Mavrakis K.J.,Sloan Kettering Cancer Center | Wolfe A.L.,Sloan Kettering Cancer Center | Wolfe A.L.,The New School | Oricchio E.,Sloan Kettering Cancer Center | And 15 more authors.
Nature Cell Biology | Year: 2010

MicroRNAs (miRNAs) have emerged as novel cancer genes. In particular, the miR-17-92 cluster, containing six individual miRNAs, is highly expressed in haematopoietic cancers and promotes lymphomagenesis in vivo. Clinical use of these findings hinges on isolating the oncogenic activity within the 17-92 cluster and defining its relevant target genes. Here we show that miR-19 is sufficient to promote leukaemogenesis in Notch1-induced T-cell acute lymphoblastic leukaemia (T-ALL) in vivo. In concord with the pathogenic importance of this interaction in T-ALL, we report a novel translocation that targets the 17-92 cluster and coincides with a second rearrangement that activates Notch1. To identify the miR-19 targets responsible for its oncogenic action, we conducted a large-scale short hairpin RNA screen for genes whose knockdown can phenocopy miR-19. Strikingly, the results of this screen were enriched for miR-19 target genes, and include Bim (Bcl2L11), AMP-activated kinase (Prkaa1) and the phosphatases Pten and PP2A (Ppp2r5e). Hence, an unbiased, functional genomics approach reveals a coordinate clampdown on several regulators of phosphatidylinositol-3-OH kinase-related survival signals by the leukaemogenic miR-19. © 2010 Macmillan Publishers Limited. All rights reserved. Source

Sandhu R.,University of North Carolina at Chapel Hill | Parker J.S.,University of North Carolina at Chapel Hill | Jones W.D.,Expression Analysis Inc. | Livasy C.A.,University of North Carolina at Chapel Hill | Coleman W.B.,University of North Carolina at Chapel Hill
Laboratory Medicine | Year: 2010

Basal-like breast cancers represent approximately 15%-20% of all breast carcinomas, are aggressive, have variable responses to chemotherapy, and associated with poor clinical outcome. The molecular mechanisms governing the biological behavior of basal-like breast cancers are not well understood. Hence, it is difficult to predict which chemotherapeutics are most likely to be effective and to determine appropriate management strategies for individual patients. Transcriptomic analysis may allow further stratification of basal-like breast cancers enabling prediction of 1) cancer recurrence after surgery; 2) likelihood of metastatic spread; 3) probable tissue sites for metastatic spread; and 4) responses to specific therapies and treatment modalities. Furthermore, careful examination of microarray-based gene expression profiles may identify new molecular targets (or pathways) for the development of targeted therapeutics. Targeted therapies may prove to be more efficacious in basal-like breast cancer treatment than the cytotoxic chemotherapeutics currently employed. Source

Haugen A.C.,National Health Research Institute | Di Prospero N.A.,U.S. National Institutes of Health | Parker J.S.,Expression Analysis Inc. | Fannin R.D.,National Health Research Institute | And 7 more authors.
PLoS Genetics | Year: 2010

The neurodegenerative disease Friedreich's ataxia (FRDA) is the most common autosomal-recessively inherited ataxia and is caused by a GAA triplet repeat expansion in the first intron of the frataxin gene. In this disease, transcription of frataxin, a mitochondrial protein involved in iron homeostasis, is impaired, resulting in a significant reduction in mRNA and protein levels. Global gene expression analysis was performed in peripheral blood samples from FRDA patients as compared to controls, which suggested altered expression patterns pertaining to genotoxic stress. We then confirmed the presence of genotoxic DNA damage by using a gene-specific quantitative PCR assay and discovered an increase in both mitochondrial and nuclear DNA damage in the blood of these patients (p<0.0001, respectively). Additionally, frataxin mRNA levels correlated with age of onset of disease and displayed unique sets of gene alterations involved in immune response, oxidative phosphorylation, and protein synthesis. Many of the key pathways observed by transcription profiling were downregulated, and we believe these data suggest that patients with prolonged frataxin deficiency undergo a systemic survival response to chronic genotoxic stress and consequent DNA damage detectable in blood. In conclusion, our results yield insight into the nature and progression of FRDA, as well as possible therapeutic approaches. Furthermore, the identification of potential biomarkers, including the DNA damage found in peripheral blood, may have predictive value in future clinical trials. Source

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