386 results on '"Susan K Murphy"'
Search Results
2. Correction: Distinct Epigenetic Effects of Tobacco Smoking in Whole Blood and among Leukocyte Subtypes.
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Dan Su, Xuting Wang, Michelle R Campbell, Devin K Porter, Gary S Pittman, Brian D Bennett, Ma Wan, Neal A Englert, Christopher L Crowl, Ryan C Gimple, Kelly N Adamski, Zhiqing Huang, Susan K Murphy, and Douglas A Bell
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Medicine ,Science - Abstract
[This corrects the article DOI: 10.1371/journal.pone.0166486.].
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- 2017
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3. Maternal adverse childhood experiences (ACEs) and offspring imprinted gene DMR methylation at birth
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Adriana C. Vidal, David W. Sosnowski, Joddy Marchesoni, Carole Grenier, John Thorp, Susan K. Murphy, Sara B. Johnson, William Schlief, and Cathrine Hoyo
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ACEs ,pregnancy ,methylation ,imprinted genes ,race ,Genetics ,QH426-470 - Abstract
Adverse childhood experiences (ACEs) contribute to numerous negative health outcomes across the life course and across generations. Here, we extend prior work by examining the association of maternal ACEs, and their interaction with financial stress and discrimination, with methylation status within eight differentially methylated regions (DMRs) in imprinted domains in newborns. ACEs, financial stress during pregnancy, and experience of discrimination were self-reported among 232 pregnant women. DNA methylation was assessed at PEG10/SGCE, NNAT, IGF2, H19, PLAGL1, PEG3, MEG3-IG, and DLK1/MEG3 regulatory sequences using pyrosequencing. Using multivariable linear regression models, we found evidence to suggest that financial stress was associated with hypermethylation of MEG3-IG in non-Hispanic White newborns; discrimination was associated with hypermethylation of IGF2 and NNAT in Hispanic newborns, and with hypomethylation of PEG3 in non-Hispanic Black newborns. We also found evidence that maternal ACEs interacted with discrimination to predict offspring PLAGL1 altered DMR methylation, in addition to interactions between maternal ACEs score and discrimination predicting H19 and SGCE/PEG10 altered methylation in non-Hispanic White newborns. However, these interactions were not statistically significant after multiple testing corrections. Findings from this study suggest that maternal ACEs, discrimination, and financial stress are associated with newborn aberrant methylation in imprinted gene regions.
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- 2024
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4. Distinct Epigenetic Effects of Tobacco Smoking in Whole Blood and among Leukocyte Subtypes.
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Dan Su, Xuting Wang, Michelle R Campbell, Devin K Porter, Gary S Pittman, Brian D Bennett, Ma Wan, Neal A Englert, Christopher L Crowl, Ryan N Gimple, Kelly N Adamski, Zhiqing Huang, Susan K Murphy, and Douglas A Bell
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Medicine ,Science - Abstract
Tobacco smoke exposure dramatically alters DNA methylation in blood cells and may mediate smoking-associated complex diseases through effects on immune cell function. However, knowledge of smoking effects in specific leukocyte subtypes is limited. To better characterize smoking-associated methylation changes in whole blood and leukocyte subtypes, we used Illumina 450K arrays and Reduced Representation Bisulfite Sequencing (RRBS) to assess genome-wide DNA methylation. Differential methylation analysis in whole blood DNA from 172 smokers and 81 nonsmokers revealed 738 CpGs, including 616 previously unreported CpGs, genome-wide significantly associated with current smoking (p 22 cigarettes/day, n = 86) which might relate to long-term heavy-smoking pathology. In purified leukocyte subtypes from an independent group of 20 smokers and 14 nonsmokers we further examined methylation and gene expression for selected genes among CD14+ monocytes, CD15+ granulocytes, CD19+ B cells, and CD2+ T cells. In 10 smokers and 10 nonsmokers we used RRBS to fine map differential methylation in CD4+ T cells, CD8+ T cells, CD14+, CD15+, CD19+, and CD56+ natural killer cells. Distinct cell-type differences in smoking-associated methylation and gene expression were identified. AHRR (cg05575921), ALPPL2 (cg21566642), GFI1 (cg09935388), IER3 (cg06126421) and F2RL3 (cg03636183) showed a distinct pattern of significant smoking-associated methylation differences across cell types: granulocytes> monocytes>> B cells. In contrast GPR15 (cg19859270) was highly significant in T and B cells and ITGAL (cg09099830) significant only in T cells. Numerous other CpGs displayed distinctive cell-type responses to tobacco smoke exposure that were not apparent in whole blood DNA. Assessing the overlap between these CpG sites and differential methylated regions (DMRs) with RRBS in 6 cell types, we confirmed cell-type specificity in the context of DMRs. We identified new CpGs associated with current smoking, pack-years, duration, and revealed unique profiles of smoking-associated DNA methylation and gene expression among immune cell types, providing potential clues to hematopoietic lineage-specific effects in disease etiology.
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- 2016
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5. ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate.
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Melissa M Keenan, Beiyu Liu, Xiaohu Tang, Jianli Wu, Derek Cyr, Robert D Stevens, Olga Ilkayeva, Zhiqing Huang, Laura A Tollini, Susan K Murphy, Joseph Lucas, Deborah M Muoio, So Young Kim, and Jen-Tsan Chi
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Genetics ,QH426-470 - Abstract
In order to propagate a solid tumor, cancer cells must adapt to and survive under various tumor microenvironment (TME) stresses, such as hypoxia or lactic acidosis. To systematically identify genes that modulate cancer cell survival under stresses, we performed genome-wide shRNA screens under hypoxia or lactic acidosis. We discovered that genetic depletion of acetyl-CoA carboxylase (ACACA or ACC1) or ATP citrate lyase (ACLY) protected cancer cells from hypoxia-induced apoptosis. Additionally, the loss of ACLY or ACC1 reduced levels and activities of the oncogenic transcription factor ETV4. Silencing ETV4 also protected cells from hypoxia-induced apoptosis and led to remarkably similar transcriptional responses as with silenced ACLY or ACC1, including an anti-apoptotic program. Metabolomic analysis found that while α-ketoglutarate levels decrease under hypoxia in control cells, α-ketoglutarate is paradoxically increased under hypoxia when ACC1 or ACLY are depleted. Supplementation with α-ketoglutarate rescued the hypoxia-induced apoptosis and recapitulated the decreased expression and activity of ETV4, likely via an epigenetic mechanism. Therefore, ACC1 and ACLY regulate the levels of ETV4 under hypoxia via increased α-ketoglutarate. These results reveal that the ACC1/ACLY-α-ketoglutarate-ETV4 axis is a novel means by which metabolic states regulate transcriptional output for life vs. death decisions under hypoxia. Since many lipogenic inhibitors are under investigation as cancer therapeutics, our findings suggest that the use of these inhibitors will need to be carefully considered with respect to oncogenic drivers, tumor hypoxia, progression and dormancy. More broadly, our screen provides a framework for studying additional tumor cell stress-adaption mechanisms in the future.
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- 2015
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6. Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis.
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Xiaohu Tang, Melissa M Keenan, Jianli Wu, Chih-An Lin, Laura Dubois, J Will Thompson, Stephen J Freedland, Susan K Murphy, and Jen-Tsan Chi
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Genetics ,QH426-470 - Abstract
Besides being building blocks for protein synthesis, amino acids serve a wide variety of cellular functions, including acting as metabolic intermediates for ATP generation and for redox homeostasis. Upon amino acid deprivation, free uncharged tRNAs trigger GCN2-ATF4 to mediate the well-characterized transcriptional amino acid response (AAR). However, it is not clear whether the deprivation of different individual amino acids triggers identical or distinct AARs. Here, we characterized the global transcriptional response upon deprivation of one amino acid at a time. With the exception of glycine, which was not required for the proliferation of MCF7 cells, we found that the deprivation of most amino acids triggered a shared transcriptional response that included the activation of ATF4, p53 and TXNIP. However, there was also significant heterogeneity among different individual AARs. The most dramatic transcriptional response was triggered by methionine deprivation, which activated an extensive and unique response in different cell types. We uncovered that the specific methionine-deprived transcriptional response required creatine biosynthesis. This dependency on creatine biosynthesis was caused by the consumption of S-Adenosyl-L-methionine (SAM) during creatine biosynthesis that helps to deplete SAM under methionine deprivation and reduces histone methylations. As such, the simultaneous deprivation of methionine and sources of creatine biosynthesis (either arginine or glycine) abolished the reduction of histone methylation and the methionine-specific transcriptional response. Arginine-derived ornithine was also required for the complete induction of the methionine-deprived specific gene response. Collectively, our data identify a previously unknown set of heterogeneous amino acid responses and reveal a distinct methionine-deprived transcriptional response that results from the crosstalk of arginine, glycine and methionine metabolism via arginine/glycine-dependent creatine biosynthesis.
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- 2015
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7. Ascites Increases Expression/Function of Multidrug Resistance Proteins in Ovarian Cancer Cells.
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Lihong Mo, Vendula Pospichalova, Zhiqing Huang, Susan K Murphy, Sturgis Payne, Fang Wang, Margaret Kennedy, George J Cianciolo, Vitezslav Bryja, Salvatore V Pizzo, and Robin E Bachelder
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Medicine ,Science - Abstract
Chemotherapy resistance is the major reason for the failure of ovarian cancer treatment. One mechanism behind chemo-resistance involves the upregulation of multidrug resistance (MDR) genes (ABC transporters) that effectively transport (efflux) drugs out of the tumor cells. As a common symptom in stage III/IV ovarian cancer patients, ascites is associated with cancer progression. However, whether ascites drives multidrug resistance in ovarian cancer cells awaits elucidation. Here, we demonstrate that when cultured with ascites derived from ovarian cancer-bearing mice, a murine ovarian cancer cell line became less sensitive to paclitaxel, a first line chemotherapeutic agent for ovarian cancer patients. Moreover, incubation of murine ovarian cancer cells in vitro with ascites drives efflux function in these cells. Functional studies show ascites-driven efflux is suppressible by specific inhibitors of either of two ABC transporters [Multidrug Related Protein (MRP1); Breast Cancer Related Protein (BCRP)]. To demonstrate relevance of our findings to ovarian cancer patients, we studied relative efflux in human ovarian cancer cells obtained from either patient ascites or from primary tumor. Immortalized cell lines developed from human ascites show increased susceptibility to efflux inhibitors (MRP1, BCRP) compared to a cell line derived from a primary ovarian cancer, suggesting an association between ascites and efflux function in human ovarian cancer. Efflux in ascites-derived human ovarian cancer cells is associated with increased expression of ABC transporters compared to that in primary tumor-derived human ovarian cancer cells. Collectively, our findings identify a novel activity for ascites in promoting ovarian cancer multidrug resistance.
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- 2015
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8. Lack of detectable sex differences in the mitochondrial function of Caenorhabditis elegans
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Dillon E. King, A. Clare Sparling, Abigail S. Joyce, Ian T. Ryde, Beverly DeSouza, P. Lee Ferguson, Susan K. Murphy, and Joel N. Meyer
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C. elegans ,Sex differences ,Mitochondria ,Mitochondrial toxicity ,Ecology ,QH540-549.5 ,Evolution ,QH359-425 - Abstract
Abstract Background Sex differences in mitochondrial function have been reported in multiple tissue and cell types. Additionally, sex-variable responses to stressors including environmental pollutants and drugs that cause mitochondrial toxicity have been observed. The mechanisms that establish these differences are thought to include hormonal modulation, epigenetic regulation, double dosing of X-linked genes, and the maternal inheritance of mtDNA. Understanding the drivers of sex differences in mitochondrial function and being able to model them in vitro is important for identifying toxic compounds with sex-variable effects. Additionally, understanding how sex differences in mitochondrial function compare across species may permit insight into the drivers of these differences, which is important for basic biology research. This study explored whether Caenorhabditis elegans, a model organism commonly used to study stress biology and toxicology, exhibits sex differences in mitochondrial function and toxicant susceptibility. To assess sex differences in mitochondrial function, we utilized four male enriched populations (N2 wild-type male enriched, fog-2(q71), him-5(e1490), and him-8(e1498)). We performed whole worm respirometry and determined whole worm ATP levels and mtDNA copy number. To probe whether sex differences manifest only after stress and inform the growing use of C. elegans as a mitochondrial health and toxicologic model, we also assessed susceptibility to a classic mitochondrial toxicant, rotenone. Results We detected few to no large differences in mitochondrial function between C. elegans sexes. Though we saw no sex differences in vulnerability to rotenone, we did observe sex differences in the uptake of this lipophilic compound, which may be of interest to those utilizing C. elegans as a model organism for toxicologic studies. Additionally, we observed altered non-mitochondrial respiration in two him strains, which may be of interest to other researchers utilizing these strains. Conclusions Basal mitochondrial parameters in male and hermaphrodite C. elegans are similar, at least at the whole-organism level, as is toxicity associated with a mitochondrial Complex I inhibitor, rotenone. Our data highlights the limitation of using C. elegans as a model to study sex-variable mitochondrial function and toxicological responses.
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- 2024
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9. TP53 status is associated with thrombospondin1 expression in vitro
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Angeles eAlvarez Secord, Marcus Q Bernardini, Gloria eBroadwater, Lisa A Grace, Zhiqing eHuang, Tsukasa eBaba, Eiji eKondo, Gregory eSfakianos, Laura J Havrilesky, and Susan K Murphy
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Angiogenesis Inhibitors ,Methylation ,Thrombospondins ,ovarian cancer ,TP53 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Objectives: To elucidate the association between thrombospondin1 (THBS1) expression and TP53 status and THBS1 promoter methylation in epithelial ovarian cancer (EOC). Methods: EOC cell lines with known TP53 status were analyzed for THBS1 gene expression using Affymetrix U133 microarrays and promoter methylation by pyrosequencing. THBS1 mRNA expression was obtained pre- and post-exposure to radiation and hypoxia treatment in A2780 parent wild-type (wt) and mutant (m)TP53 cells. THBS1 expression was compared to tumor growth properties. Results: THBS1 gene expression was higher in cells containing a wtTP53 gene or null TP53 mutation (p = 0.005) and low or absent TP53 protein expression (p = 0.008) compared to those harboring a missense TP53 gene mutation and exhibiting high TP53 protein expression. Following exposure to radiation, there was a 3.4 fold increase in THBS1 mRNA levels in the mTP53 versus wtTP53 A2780 cells. After exposure to hypoxia, THBS1 mRNA levels increased approximately 4-fold in both wtTP53 and mTP53 A2780 cells. Promoter methylation levels were low (median=8.6%; range=3.5-88.8%). There was a non-significant inverse correlation between THBS1 methylation and transcript levels. There was no association between THBS1 expression and population doubling time, invasive capacity, or anchorage-independent growth. Conclusion: THBS1 expression may be regulated via the TP53 pathway, and induced by hypoxic tumor microenvironment conditions. Overall low levels of THBS1 promoter methylation imply that methylation is not the primary driver of THBS1 expression in EOC.
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- 2013
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10. Increased intragenic IGF2 methylation is associated with repression of insulator activity and elevated expression in serous ovarian carcinoma
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Zhiqing eHuang and Susan K Murphy
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Chromatin Immunoprecipitation ,DNA Methylation ,Spermatozoa ,CTCF ,epithelial ovarian cancer ,Insulin-like Growth Factor 2 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Overexpression of insulin-like growth factor-II (IGF2) is a prominent characteristic of many epithelial ovarian malignancies. IGF2 imprinting and transcription are regulated in part through DNA methylation, which in turn regulates binding of the insulator protein, CTCF, within the IGF2/H19 imprint center. We have shown that IGF2 overexpression in ovarian cancer is associated with hypermethylation of CTCF binding sites within the IGF2/H19 imprint center. The aim of this study was to investigate the methylation and binding capacity of a novel putative CTCF binding motif located intragenic to IGF2 and determine how this relates to IGF2 expression. In 35 primary serous epithelial ovarian cancer specimens, methylation of two CpGs, including one within the core binding motif and another adjacent to this motif, was higher in the 18 cancers with elevated IGF2 expression versus 10 with low expression (avg. 68.2% vs. 38.5%; p92%; avg. 93.2%; N=16). We confirmed binding of CTCF to this region in ovarian cancer cells, as well as the paralog of CTCF, BORIS, which is frequently overexpressed in cancers. The unmethylated CTCF binding motif has insulator activity in cells that express CTCF or BORIS, but not in cells that express both CTCF and BORIS. These intragenic CpG dinucleotides comprise a novel paternal germline imprint mark and are located in a binding motif for the insulator protein CTCF. Methylation of the CpG dinucleotides is positively correlated with IGF2 transcription, supporting that increased methylation represses insulator function. These combined results suggest that methylation and CTCF binding at this region play important roles in regulating the level of IGF2 transcription. Our data have revealed a novel epigenetic regulatory element within the IGF2/H19 imprinted domain that is highly relevant to aberrant IGF2 expression in ovarian malignancies.
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- 2013
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11. Associations between methylation of paternally expressed gene 3 (PEG3), cervical intraepithelial neoplasia and invasive cervical cancer.
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Monica D Nye, Cathrine Hoyo, Zhiqing Huang, Adriana C Vidal, Frances Wang, Francine Overcash, Jennifer S Smith, Brandi Vasquez, Brenda Hernandez, Britta Swai, Olola Oneko, Pendo Mlay, Joseph Obure, Marilie D Gammon, John A Bartlett, and Susan K Murphy
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Medicine ,Science - Abstract
Cytology-based screening for invasive cervical cancer (ICC) lacks sensitivity and specificity to discriminate between cervical intraepithelial neoplasia (CIN) likely to persist or progress from cases likely to resolve. Genome-wide approaches have been used to identify DNA methylation marks associated with CIN persistence or progression. However, associations between DNA methylation marks and CIN or ICC remain weak and inconsistent. Between 2008-2009, we conducted a hospital-based, case-control study among 213 Tanzania women with CIN 1/2/3 or ICC. We collected questionnaire data, biopsies, peripheral blood, cervical scrapes, Human papillomavirus (HPV) and HIV-1 infection status. We assessed PEG3 methylation status by bisulfite pyrosequencing. Multinomial logistic regression was used to estimate odds ratios (OR) and confidence intervals (CI 95%) for associations between PEG3 methylation status and CIN or ICC. After adjusting for age, gravidity, hormonal contraceptive use and HPV infection, a 5% increase in PEG3 DNA methylation was associated with increased risk for ICC (OR = 1.6; 95% CI 1.2-2.1). HPV infection was associated with a higher risk of CIN1-3 (OR = 15.7; 95% CI 5.7-48.6) and ICC (OR = 29.5, 95% CI 6.3-38.4). Infection with high risk HPV was correlated with mean PEG3 differentially methylated regions (DMRs) methylation (r = 0.34 p
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- 2013
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12. Differentially methylated regions of imprinted genes in prenatal, perinatal and postnatal human tissues.
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Susan K Murphy, Zhiqing Huang, and Cathrine Hoyo
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Medicine ,Science - Abstract
Epigenetic plasticity in relation to in utero exposures may mechanistically explain observed differences in the likelihood of developing common complex diseases including hypertension, diabetes and cardiovascular disease through the cumulative effects of subtle alterations in gene expression. Imprinted genes are essential mediators of growth and development and are characterized by differentially methylated regulatory regions (DMRs) that carry parental allele-specific methylation profiles. This theoretical 50% level of methylation provides a baseline from which endogenously- or exogenously-induced deviations in methylation can be detected. We quantified DNA methylation at imprinted gene DMRs in a large panel of human conceptal tissues, in matched buccal cell specimens collected at birth and at one year of age, and in the major cell fractions of umbilical cord blood to assess the stability of methylation at these regions. DNA methylation was measured using validated pyrosequencing assays at seven DMRs regulating the IGF2/H19, DLK1/MEG3, MEST, NNAT and SGCE/PEG10 imprinted domains. DMR methylation did not significantly differ for the H19, MEST and SGCE/PEG10 DMRs across all conceptal tissues analyzed (ANOVA p>0.10). Methylation differences at several DMRs were observed in tissues from brain (IGF2 and MEG3-IG DMRs), liver (IGF2 and MEG3 DMRs) and placenta (both DLK1/MEG3 DMRs and NNAT DMR). In most infants, methylation profiles in buccal cells at birth and at one year of age were comparable, as was methylation in the major cell fractions of umbilical cord blood. Several infants showed temporal deviations in methylation at multiple DMRs. Similarity of inter-individual and intra-individual methylation at some, but not all of the DMRs analyzed supports the possibility that methylation of these regions can serve as useful biosensors of exposure.
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- 2012
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13. Periostin facilitates ovarian cancer recurrence by enhancing cancer stemness
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Zhiqing Huang, Olivia Byrd, Sarah Tan, Katrina Hu, Bailey Knight, Gaomong Lo, Lila Taylor, Yuan Wu, Andrew Berchuck, and Susan K. Murphy
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Medicine ,Science - Abstract
Abstract The lethality of epithelial ovarian cancer (OC) is largely due to a high rate of recurrence and development of chemoresistance, which requires synergy between cancer cells and the tumor microenvironment (TME) and is thought to involve cancer stem cells. Our analysis of gene expression microarray data from paired primary and recurrent OC tissues revealed significantly elevated expression of the gene encoding periostin (POSTN) in recurrent OC compared to matched primary tumors (p = 0.015). Secreted POSTN plays a role in the extracellular matrix, facilitating epithelial cell migration and tissue regeneration. We therefore examined how elevated extracellular POSTN, as we found is present in recurrent OC, impacts OC cell functions and phenotypes, including stemness. OC cells cultured with conditioned media with high levels of periostin (CM POSTNhigh ) exhibited faster migration (p = 0.0044), enhanced invasiveness (p = 0.006), increased chemoresistance (p
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- 2023
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14. Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude
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Latha Kadalayil, Md. Zahangir Alam, Cory Haley White, Akram Ghantous, Esther Walton, Olena Gruzieva, Simon Kebede Merid, Ashish Kumar, Ritu P. Roy, Olivia Solomon, Karen Huen, Brenda Eskenazi, Peter Rzehak, Veit Grote, Jean-Paul Langhendries, Elvira Verduci, Natalia Ferre, Darek Gruszfeld, Lu Gao, Weihua Guan, Xuehuo Zeng, Enrique F. Schisterman, John F. Dou, Kelly M. Bakulski, Jason I. Feinberg, Munawar Hussain Soomro, Giancarlo Pesce, Nour Baiz, Elena Isaevska, Michelle Plusquin, Marina Vafeiadi, Theano Roumeliotaki, Sabine A. S. Langie, Arnout Standaert, Catherine Allard, Patrice Perron, Luigi Bouchard, Evelien R. van Meel, Janine F. Felix, Vincent W. V. Jaddoe, Paul D. Yousefi, Cecilia H. Ramlau-Hansen, Caroline L. Relton, Elmar W. Tobi, Anne P. Starling, Ivana V. Yang, Maria Llambrich, Gillian Santorelli, Johanna Lepeule, Lucas A. Salas, Mariona Bustamante, Susan L. Ewart, Hongmei Zhang, Wilfried Karmaus, Stefan Röder, Ana Claudia Zenclussen, Jianping Jin, Wenche Nystad, Christian M. Page, Maria Magnus, Dereje D. Jima, Cathrine Hoyo, Rachel L. Maguire, Tuomas Kvist, Darina Czamara, Katri Räikkönen, Tong Gong, Vilhelmina Ullemar, Sheryl L. Rifas-Shiman, Emily Oken, Catarina Almqvist, Robert Karlsson, Jari Lahti, Susan K. Murphy, Siri E. Håberg, Stephanie London, Gunda Herberth, Hasan Arshad, Jordi Sunyer, Regina Grazuleviciene, Dana Dabelea, Régine P. M. Steegers-Theunissen, Ellen A. Nohr, Thorkild I. A. Sørensen, Liesbeth Duijts, Marie-France Hivert, Vera Nelen, Maja Popovic, Manolis Kogevinas, Tim S. Nawrot, Zdenko Herceg, Isabella Annesi-Maesano, M. Daniele Fallin, Edwina Yeung, Carrie V. Breton, Berthold Koletzko, Nina Holland, Joseph L. Wiemels, Erik Melén, Gemma C. Sharp, Matt J. Silver, Faisal I. Rezwan, and John W. Holloway
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PACE ,Meta-analysis ,Birth season ,DNA methylation ,Differentially methylated regions (DMR) ,Latitude ,Medicine ,Genetics ,QH426-470 - Abstract
Abstract Background Seasonal variations in environmental exposures at birth or during gestation are associated with numerous adult traits and health outcomes later in life. Whether DNA methylation (DNAm) plays a role in the molecular mechanisms underlying the associations between birth season and lifelong phenotypes remains unclear. Methods We carried out epigenome-wide meta-analyses within the Pregnancy And Childhood Epigenetic Consortium to identify associations of DNAm with birth season, both at differentially methylated probes (DMPs) and regions (DMRs). Associations were examined at two time points: at birth (21 cohorts, N = 9358) and in children aged 1–11 years (12 cohorts, N = 3610). We conducted meta-analyses to assess the impact of latitude on birth season-specific associations at both time points. Results We identified associations between birth season and DNAm (False Discovery Rate-adjusted p values
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- 2023
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15. The use of race terms in epigenetics research: considerations moving forward
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Dillon E. King, Pooja D. Lalwani, Gilberto Padilla Mercado, Emma L. Dolan, Johnna M. Frierson, Joel N. Meyer, and Susan K. Murphy
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race ,epigenetic mechanisms ,health inequities ,structural determinants of health ,data transparency ,Genetics ,QH426-470 - Abstract
The field of environmental epigenetics is uniquely suited to investigate biologic mechanisms that have the potential to link stressors to health disparities. However, it is common practice in basic epigenetic research to treat race as a covariable in large data analyses in a way that can perpetuate harmful biases without providing any biologic insight. In this article, we i) propose that epigenetic researchers open a dialogue about how and why race is employed in study designs and think critically about how this might perpetuate harmful biases; ii) call for interdisciplinary conversation and collaboration between epigeneticists and social scientists to promote the collection of more detailed social metrics, particularly institutional and structural metrics such as levels of discrimination that could improve our understanding of individual health outcomes; iii) encourage the development of standards and practices that promote full transparency about data collection methods, particularly with regard to race; and iv) encourage the field of epigenetics to continue to investigate how social structures contribute to biological health disparities, with a particular focus on the influence that structural racism may have in driving these health disparities.
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- 2024
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16. Maternal exposure to perfluorobutane sulfonate (PFBS) during pregnancy: evidence of adverse maternal and fetoplacental effects in New Zealand White (NZW) rabbits
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Christine E Crute, Chelsea D Landon, Angela Garner, Samantha M Hall, Jeffery I Everitt, Sharon Zhang, Bevin Blake, Didrik Olofsson, Henry Chen, Heather M Stapleton, Susan K Murphy, and Liping Feng
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Toxicology - Abstract
Perfluorobutanesulfonic acid (PFBS) is a replacement for perfluorooctanesulfonic acid (PFOS) that is increasingly detected in drinking water and human serum. Higher PFBS exposure is associated with risk for preeclampsia, the leading cause of maternal and infant morbidity and mortality in the United States. This study investigated relevant maternal and fetal health outcomes after gestational exposure to PFBS in a New Zealand White rabbit model. Nulliparous female rabbits were supplied drinking water containing 0 mg/l (control), 10 mg/l (low), or 100 mg/l (high) PFBS. Maternal blood pressure, body weights, liver and kidney weights histopathology, clinical chemistry panels, and thyroid hormone levels were evaluated. Fetal endpoints evaluated at necropsy included viability, body weights, crown-rump length, and liver and kidney histopathology, whereas placenta endpoints included weight, morphology, histopathology, and full transcriptome RNA sequencing. PFBS-high dose dams exhibited significant changes in blood pressure markers, seen through increased pulse pressure and renal resistive index measures, as well as kidney histopathological changes. Fetuses from these dams showed decreased crown-rump length. Statistical analysis of placental weight via a mixed model statistical approach identified a significant interaction term between PFBS high dose and fetal sex, suggesting a sex-specific effect on placental weight. RNA sequencing identified the dysregulation of angiotensin (AGT) in PFBS high-dose placentas. These results suggest that PFBS exposure during gestation leads to adverse maternal outcomes, such as renal injury and hypertension, and fetal outcomes, including decreased growth parameters and adverse placenta function. These outcomes raise concerns about pregnant women’s exposure to PFBS and pregnancy outcomes.
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- 2022
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17. Maternal diet disrupts the placenta–brain axis in a sex-specific manner
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Alexis M. Ceasrine, Benjamin A. Devlin, Jessica L. Bolton, Lauren A. Green, Young Chan Jo, Carolyn Huynh, Bailey Patrick, Kamryn Washington, Cristina L. Sanchez, Faith Joo, A. Brayan Campos-Salazar, Elana R. Lockshin, Cynthia Kuhn, Susan K. Murphy, Leigh Ann Simmons, and Staci D. Bilbo
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Physiology (medical) ,Endocrinology, Diabetes and Metabolism ,Internal Medicine ,Cell Biology - Published
- 2022
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18. Urinary 1-hydroxypyrene in pregnant women in a Northeastern U.S. city: socioeconomic disparity and contributions from air pollution sources
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Yan Lin, Emily Craig, Xiaodong Liu, Yihui Ge, Jessica Brunner, Xiangtian Wang, Zhenchun Yang, Philip K. Hopke, Richard K. Miller, Emily S. Barrett, Sally W. Thurston, Susan K. Murphy, Thomas G. O’Connor, David Q. Rich, and Junfeng Zhang
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Epidemiology ,Public Health, Environmental and Occupational Health ,Toxicology ,Pollution - Published
- 2023
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19. Correction: Financial stress as a mediator of the association between maternal childhood adversity and infant birth weight, gestational age, and NICU admission
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David W. Sosnowski, Alejandra Ellison-Barnes, Joan Kaufman, Cathrine Hoyo, Susan K. Murphy, Raquel G. Hernandez, Joddy Marchesoni, Lauren M. Klein, and Sara B. Johnson
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Public Health, Environmental and Occupational Health - Published
- 2023
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20. Tobacco Retail Outlets, Neighborhood Deprivation and the Risk of Prenatal Smoke Exposure
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David C Wheeler, Joseph Boyle, D Jeremy Barsell, Rachel L Maguire, Junfeng (Jim) Zhang, Jason A Oliver, Shaun Jones, Bassam Dahman, Susan K Murphy, Cathrine Hoyo, Chris D Baggett, Joseph McClernon, and Bernard F Fuemmeler
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Pregnancy ,Tobacco ,Public Health, Environmental and Occupational Health ,Humans ,Female ,Tobacco Smoke Pollution ,Bayes Theorem ,Pregnant Women ,Cotinine - Abstract
Introduction Smoking and smoke exposure among pregnant women remain persistent public health issues. Recent estimates suggest that approximately one out of four nonsmokers have measurable levels of cotinine, a marker indicating regular exposure to secondhand smoke. Epidemiological research has attempted to pinpoint individual-level and neighborhood-level factors for smoking during pregnancy. However, most of these studies have relied upon self-reported measures of smoking. Aims and Methods To more accurately assess smoke exposure resulting from both smoking and secondhand exposure in mothers during pregnancy, we used Bayesian regression models to estimate the association of cotinine levels with tobacco retail outlet (TRO) exposure and a neighborhood deprivation index (NDI) in six counties in North Carolina centered on Durham County. Results Results showed a significant positive association between TRO exposure (β = 0.008, 95% credible interval (CI) = [0.003, 0.013]) and log cotinine after adjusting for individual covariates (eg, age, race/ethnicity, education, marital status). TRO exposure was not significant after including the NDI, which was significantly associated with log cotinine (β = 0.143, 95% CI = [0.030, 0.267]). However, in a low cotinine stratum (indicating secondhand smoke exposure), TRO exposure was significantly associated with log cotinine (β = 0.005, 95% CI = [0.001, 0.009]), while in a high cotinine stratum (indicating active smoking), the NDI was significantly associated with log cotinine (β = 0.176, 95% CI = [0.005, 0.372]). Conclusions In summary, our findings add to the evidence that contextual factors are important for active smoking during pregnancy. Implications In this study, we found several significant associations that suggest a more nuanced understanding of the potential influence of environmental- and individual-level factors for levels of prenatal smoke exposure. Results suggested a significant positive association between TRO exposure and cotinine levels, after adjusting for the individual factors such as race, education, and marital status. Individually, NDI was similarly positively associated with cotinine levels as well. However, when combining TRO exposure alongside NDI in the same model, TROs were no longer significantly associated with overall cotinine levels.
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21. Informing women about the risks of exposing babies to tobacco smoke: outreach and education efforts using Facebook 'boost posts'
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Carrie A Miller, Sunny Jung Kim, Rochelle D Schwartz-Bloom, Paul N Bloom, Susan K Murphy, and Bernard F Fuemmeler
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Behavioral Neuroscience ,Pregnancy ,Tobacco ,Humans ,Female ,Smoking Cessation ,Smoking Prevention ,Tobacco Smoke Pollution ,Substance Use ,Child ,Social Media ,Applied Psychology - Abstract
Maternal smoking is associated with a host of negative health outcomes, including an increased risk of children developing attention-deficit/hyperactivity disorder (ADHD). This study evaluated the efficacy of health messages disseminated through Facebook Ads focused on reducing tobacco smoke exposure during pregnancy. Two message versions were promoted via post advertisements on Facebook—a static infographic and a video containing an animated version of the infographic. The reach of and engagement with each message version was evaluated. Comments made to the posts were assessed using content analysis. The infographic reached approximately 60,000 people and the video reached about 16,000 people. The average costs were $10.00 and $40.00 per 1,000 people reached for the infographic- and video-based posts, respectively. While there was no engagement with the video, the infographic was liked (n = 157), given alternative likes (n = 59), shared (n = 171 to 341), and commented on (n = 221). About one-quarter of comments contained a personal narrative and mentions of health history related to ADHD and/or smoking. Comments were more often negative (than positive) (16.6% vs 3.9%) and expressed skepticism more often than message acceptance (21.5% vs 12.2%). Facebook users were more responsive to the infographic (compared to the video) and static posts were a preferred channel (i.e., higher engagement at a lower cost) to disseminate messages when using the boost post feature on Facebook for health education. Our review of the comments provided insights into message acceptance and guidance for future social media-based health message campaigns. However, it is not known whether and if so, how, these findings on message exposure would correlate with behavioral intentions or changes in behavior, such as intentions to quit smoking or smoking cessation.
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- 2022
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22. Toward understanding the roles of matrix metallopeptidase 1 in ovarian cancer
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Cassie, Hobbs, primary, Isabella, Coogan, additional, Jun Hee, Shin, additional, Derek Y, Yao, additional, Olivia, Neely, additional, Parmida, Jamshidi, additional, Andrew, Berchuck, additional, Susan K, Murphy, additional, and Zhiqing, Huang, additional
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- 2023
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23. Developmental nicotine exposure and masculinization of the rat preoptic area
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Rashmi Joglekar, Marty Cauley, Taylor Lipsich, David L. Corcoran, Heather B. Patisaul, Edward D. Levin, Joel N. Meyer, Margaret M. McCarthy, and Susan K. Murphy
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Male ,Nicotine ,Sex Characteristics ,Sex Differentiation ,General Neuroscience ,Animals ,Female ,Testosterone ,Electronic Nicotine Delivery Systems ,Toxicology ,Preoptic Area ,Article ,Rats - Abstract
Nicotine is a neuroteratogenic component of tobacco smoke, e-cigarettes, and other products and can exert sex-specific effects in the developing brain, likely mediated through sex hormones. Estradiol modulates expression of nicotinic acetylcholine receptors in rats, and plays critical roles in neurodevelopmental processes, including sexual differentiation of the brain. Here, we examined the effects of developmental nicotine exposure on the sexual differentiation of the preoptic area (POA), a brain region that normally displays robust structural sexual dimorphisms and controls adult mating behavior in rodents. Using a rat model of gestational exposure, developing pups were exposed to nicotine (2 mg/kg/day) via maternal osmotic minipump (subcutaneously, sc) throughout the critical window for brain sexual differentiation. At postnatal day (PND) 4, a subset of offspring was analyzed for epigenetic effects in the POA. At PND40, all offspring were gonadectomized, implanted with a testosterone-releasing capsule (sc), and assessed for male sexual behavior at PND60. Following sexual behavior assessment, the area of the sexually dimorphic nucleus of the POA (SDN-POA) was measured using immunofluorescent staining techniques. In adults, normal sex differences in male sexual behavior and in the SDN-POA area were eliminated in nicotine-treated animals. Using novel analytical approaches to evaluate overall masculinization of the adult POA, we identified significant masculinization of the nicotine-treated female POA. In neonates (PND4), nicotine exposure induced trending alterations in methylation-dependent masculinizing gene expression and DNA methylation levels at sexually-dimorphic differentially methylated regions, suggesting that developmental nicotine exposure is capable of triggering masculinization of the rat POA via epigenetic mechanisms.
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- 2022
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24. Supplementary Information from Targeting Dormant Ovarian Cancer Cells In Vitro and in an In Vivo Mouse Model of Platinum Resistance
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Susan K. Murphy, Andrew Berchuck, Shingo Fujii, Ikuo Konishi, Regina S. Whitaker, Emma Dolan, Noriomi Matsumura, Tsukasa Baba, Zachary R. Visco, Eiji Kondoh, and Zhiqing Huang
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Figures S1, S2 and Tables S1,S2 and S7
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25. Supplemental Figure legends from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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Legends describing all supplemental figures.
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26. Inhibition of DNA methylation induces p16 de-repression from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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A. ChIP-qPCR on H3.3K27M-GFP, and H3.3WT-GFP (n=3 each) expressing murine tumor lines for DNMT1 localization to p16 promoter region. B. Pyrosequencing analysis of DNA methylation at the p16 promoter after 7days of 1uM GSK343 treatment (n=3 for both groups). C. Pyrosequencing DNA methylation analysis of p16 and p19 promoters on human DIPG lines (SF8628, DIPG IV, and DIPG 007) treated with 72hr decitabine or vehicle at 10uM (*= p< 0.05, n=3). D. Western blot analysis of human DIPG lines treated with 72hr decitabine or vehicle and blotted for p16 (n=2) E. BrdU incorporation IC50 analysis of decitabine and azacitidine DNA methyltransferase inhibitors on mouse tumor cells (top 2 panels). Decitabine IC50 on human DIPG lines (bottom 3 panels). IC50''s for human lines were as follows: SF6828 (8μM), (0.5μM), DIPG IV, and DIPG 007 (2μM).
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27. Table S6 from Targeting Dormant Ovarian Cancer Cells In Vitro and in an In Vivo Mouse Model of Platinum Resistance
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Susan K. Murphy, Andrew Berchuck, Shingo Fujii, Ikuo Konishi, Regina S. Whitaker, Emma Dolan, Noriomi Matsumura, Tsukasa Baba, Zachary R. Visco, Eiji Kondoh, and Zhiqing Huang
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Functional annotations (from DAVID) for genes with higher expression in cells with low spheroid-forming capacity relative to cells with high spheroid-forming capacity.
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28. EZH2 inhibitors are not effective against H3.3K27M tumor cells from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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A. Positive (Hoxa11) and negative (actin) promoter control loci for H3K27me3 ChIP-qPCR. B. H3K27me3 ChIP-qPCR analysis of murine tumor cells on downstream p16 exon 1α and exon 2. C. Histone extraction western blot of H3.3K27M-GFP and H3.3WT-GFP expressing murine tumor lines treated with 1μM EPZ-6438 for 7 days. D. H3K4me3 ChIP-qPCR analyzing the p16 promoter region with or without 7 day GSK343 treatment (p= 0.035 by paired t-test) E. 21 day treatment with EZH2 inhibitor GSK343 followed by qPCR for p16 expression (p=0.036) F. BrdU incorporation on H3.3K27M-GFP and H3.3WT-GFP expressing murine tumor lines with EZH2 inhibitors GSK343 (p= 0.012), EPZ-6438, and GSK126 (p= 0.002) treatments incubated for 72hrs.
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29. Mouse injection survival results from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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list of all viral infection combinations performed on mice and the median survival (days) of each model.
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30. p16 promoter DNA methylation and expression in response to decitabine treatment from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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Percent DNA methylation and p16 expression changes with or without DNA methytransferase inhibition.
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31. Data from Inactivation of the MAL Gene in Breast Cancer Is a Common Event That Predicts Benefit from Adjuvant Chemotherapy
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Jeffrey R. Marks, John A. Olson, Miguel A. Alonso, Susan K. Murphy, Paula S. Lee, and Hisani N. Horne
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Dysregulation of MAL (myelin and lymphocyte protein) has been implicated in several malignancies including esophageal, ovarian, and cervical cancers. The MAL protein functions in apical transport in polarized epithelial cells; therefore, its disruption may lead to loss of organized polarity characteristic of most solid malignancies. Bisulfite sequencing of the MAL promoter CpG island revealed hypermethylation in breast cancer cell lines and 69% of primary tumors analyzed compared with normal breast epithelial cells. Differential methylation between normal and cancer DNA was confined to the proximal promoter region. In a subset of breast cancer cell lines including T47D and MCF7 cells, promoter methylation correlated with transcriptional silencing that was reversible with the methylation inhibitor 5-aza-2′-deoxycytidine. In addition, expression of MAL reduced motility and resulted in a redistribution of lipid raft components in MCF10A cells. MAL protein expression measured by immunohistochemistry revealed no significant correlation with clinicopathologic features. However, in patients who did not receive adjuvant chemotherapy, reduced MAL expression was a significant predictive factor for disease-free survival. These data implicate MAL as a commonly altered gene in breast cancer with implications for response to chemotherapy. (Mol Cancer Res 2009;7(2):199–209)
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32. Supplementary Figures 1 - 3 from A TAZ–ANGPTL4–NOX2 Axis Regulates Ferroptotic Cell Death and Chemoresistance in Epithelial Ovarian Cancer
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Jen-Tsan Chi, Susan K. Murphy, Chien-Kuang C. Ding, Jianli Wu, Zhiqing Huang, and Wen-Hsuan Yang
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Supplementary Figures 1 - 3
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33. Supplementary Data from Yin Yang 1 Modulates Taxane Response in Epithelial Ovarian Cancer
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Susan K. Murphy, Andrew Berchuck, Shingo Fujii, Joe W. Gray, Regina S. Whitaker, Alison H. Gusberg, Wen-Lin Kuo, Jeffrey T. Chang, Seiichi Mori, Jason C. Barnett, Paula S. Lee, Tsukasa Baba, Zhiqing Huang, and Noriomi Matsumura
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Supplementary Data from Yin Yang 1 Modulates Taxane Response in Epithelial Ovarian Cancer
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- 2023
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34. Supplementary Movie 1 from GPR54 Is a Target for Suppression of Metastasis in Endometrial Cancer
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Ikuo Konishi, Susan K. Murphy, Nobutaka Fujii, Shinya Oishi, Yumiko Yoshioka, Eiji Kondoh, Budiman Kharma, Junzo Hamanishi, Noriomi Matsumura, Masaki Mandai, Tsukasa Baba, and Hyun Sook Kang
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Supplementary Movie 1 from GPR54 Is a Target for Suppression of Metastasis in Endometrial Cancer
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- 2023
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35. Supplementary Figure 2 from Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques
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J. Mark Cline, Lance D. Miller, Jeff W. Chou, Janet A. Tooze, Susan K. Murphy, Zhiqing Huang, Timothy D. Howard, Cynthia J. Lees, Thomas C. Register, Cynthia J. Willson, Charles E. Wood, and Fitriya N. Dewi
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Representative photomicrographs of ERα staining in a transitional duct from a prepubertal animal (A); ERα staining in post-pubertal, differentiated lobuloalveolar tissue (B); ERβ staining in prepubertal transitional duct (C ); and ERβ staining in mature lobuloalveolar tissue (D). Bar = 50 microns.
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36. Supplementary data from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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lists of antibodies and primer information used in the manuscript.
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37. Supplementary Table 3 from Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques
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J. Mark Cline, Lance D. Miller, Jeff W. Chou, Janet A. Tooze, Susan K. Murphy, Zhiqing Huang, Timothy D. Howard, Cynthia J. Lees, Thomas C. Register, Cynthia J. Willson, Charles E. Wood, and Fitriya N. Dewi
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Immunolocalization of Steroidogenic Enzymes in the Mammary Gland.
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38. Significantly differentially expressed genes from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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List of all significantly differentially expressed genes in empty vector vs H3.3K27M tumor RNA-Seq analysis.
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39. Data from Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques
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J. Mark Cline, Lance D. Miller, Jeff W. Chou, Janet A. Tooze, Susan K. Murphy, Zhiqing Huang, Timothy D. Howard, Cynthia J. Lees, Thomas C. Register, Cynthia J. Willson, Charles E. Wood, and Fitriya N. Dewi
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Endogenous estrogens influence mammary gland development during puberty and breast cancer risk during adulthood. Early-life exposure to dietary or environmental estrogens may alter estrogen-mediated processes. Soy foods contain phytoestrogenic isoflavones (IF), which have mixed estrogen agonist/antagonist properties. Here, we evaluated mammary gland responses over time in pubertal female cynomolgus macaques fed diets containing either casein/lactalbumin (n = 12) or soy protein containing a human-equivalent dose of 120 mg IF/day (n = 17) for approximately 4.5 years spanning menarche. We assessed estrogen receptor (ER) expression and activity, promoter methylation of ERs and their downstream targets, and markers of estrogen metabolism. Expression of ERα and classical ERα response genes (TFF1, PGR, and GREB1) decreased with maturity, independent of diet. A significant inverse correlation was observed between TFF1 mRNA and methylation of CpG sites within the TFF1 promoter. Soy effects included lower ERβ expression before menarche and lower mRNA for ERα and GREB1 after menarche. Expression of GATA-3, an epithelial differentiation marker that regulates ERα-mediated transcription, was elevated before menarche and decreased after menarche in soy-fed animals. Soy did not significantly alter expression of other ER activity markers, estrogen-metabolizing enzymes, or promoter methylation for ERs or ER-regulated genes. Our results demonstrate greater ER expression and activity during the pubertal transition, supporting the idea that this life stage is a critical window for phenotypic modulation by estrogenic compounds. Pubertal soy exposure decreases mammary ERα expression after menarche and exerts subtle effects on receptor activity and mammary gland differentiation. Cancer Prev Res; 9(5); 385–95. ©2016 AACR.
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40. Supplementary Figure 3 from Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques
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J. Mark Cline, Lance D. Miller, Jeff W. Chou, Janet A. Tooze, Susan K. Murphy, Zhiqing Huang, Timothy D. Howard, Cynthia J. Lees, Thomas C. Register, Cynthia J. Willson, Charles E. Wood, and Fitriya N. Dewi
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Gene expression profile in the post-menarchal macaque breast by microarray. (A) Venn diagram showing number of genes that changed with time (i.e. between 7-12 months to 18-24 months after menarche) in the control (CL) and soy group (SOY), based on unadjusted P-values from a paired t-test in each diet group. (B) The list of top-10 genes that showed significant difference by dietary treatment using empirical Bayes statistics. (C) The top-10 significantly enriched KEGG pathways in CL and SOY groups across time. FC = fold-change; FDR=false discovery rate.
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41. Supplementary Table 1 from Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques
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J. Mark Cline, Lance D. Miller, Jeff W. Chou, Janet A. Tooze, Susan K. Murphy, Zhiqing Huang, Timothy D. Howard, Cynthia J. Lees, Thomas C. Register, Cynthia J. Willson, Charles E. Wood, and Fitriya N. Dewi
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1A. Cynomolgus macaque and human primer probe sets used to generate custom Taqman-based assay for qRT-PCR 1B. Applied Biosystems (ABI) Taqman gene expression assays used in qRT-PCR.
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42. Data from A TAZ–ANGPTL4–NOX2 Axis Regulates Ferroptotic Cell Death and Chemoresistance in Epithelial Ovarian Cancer
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Jen-Tsan Chi, Susan K. Murphy, Chien-Kuang C. Ding, Jianli Wu, Zhiqing Huang, and Wen-Hsuan Yang
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Ovarian cancer is the deadliest gynecologic cancer. Despite recent advances, clinical outcomes remain poor, necessitating novel therapeutic approaches. To investigate metabolic susceptibility, we performed nutrigenetic screens on a panel of clear cell and serous ovarian cancer cells and identified cystine addiction and vulnerability to ferroptosis, a novel form of regulated cell death. Our results may have therapeutic potential, but little is known about the determinants of ferroptosis susceptibility in ovarian cancer. We found that vulnerability to ferroptosis in ovarian cancer cells is enhanced by lower cell confluency. Because the Hippo pathway effectors Yes-associated protein (YAP)/transcriptional coactivator with PDZ-binding motif (TAZ) are recognized as sensors of cell density, and TAZ is the predominant effector in the tested ovarian cancer cell lines, we investigated the role of TAZ in ferroptosis of ovarian cancer. TAZ removal confers ferroptosis resistance, while TAZS89A overexpression sensitizes cells to ferroptosis. In addition, we found that lower TAZ level in chemo-resistant recurrent ovarian cancer is responsible for reduced ferroptosis susceptibility. The integrative genomic analysis identified ANGPTL4 as a direct TAZ-regulated target gene that sensitizes ferroptosis by activating NOX2. Collectively, cell density–regulated ferroptosis in ovarian cancer is mediated by TAZ through the regulation of the ANGPTL4–NOX2 axis, suggesting therapeutic potentials for ovarian cancers and other TAZ-activated tumors.Implications:This study reveals that TAZ promotes ferroptosis in ovarian cancers by regulating ANGPTL4 and NOX, offering a novel therapeutic potential for ovarian tumors with TAZ activation.
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43. H3.3K27M affects gene expression of PRC2 target genes and focally represses p16 expression from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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A. Gene set enrichment analysis of differentially upregulated genes from RNA-Seq of high grade tumor model with or without H3.3K27M-HA expression shows high association with known PRC2-regulated H3K27me3 target genes in mouse embryonic, and neuronal progenitor cells (1). B. GSEA comparing genes losing H3K27me3 (UPS) and gaining H3K27me3 (DOWN) from Chan et al to our mouse tumor RNA-Seq. C. qPCR analysis of both p16 and p19 alternate transcripts from ex-vivo infected neuronal progenitor cells isolated from neonatal Nestin-tv-a pups and infected with either H3.3K27M-HA, H3.3WT-HA, or empty vector 2 weeks prior to collection.
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44. Supplementary Table 2 from Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques
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J. Mark Cline, Lance D. Miller, Jeff W. Chou, Janet A. Tooze, Susan K. Murphy, Zhiqing Huang, Timothy D. Howard, Cynthia J. Lees, Thomas C. Register, Cynthia J. Willson, Charles E. Wood, and Fitriya N. Dewi
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Cynomolgus macaque primer sets (forward, F; reverse, R; and sequencing, S) for pyrosequencing assay.
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45. PDGF signaling cooperates with H3.3K27M to increase tumor malignancy from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
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Oren J. Becher, Rintaro Hashizume, Susan K. Murphy, Roger E. McLendon, Guo Hu, Xingyao He, Carole Grenier, Zhiqing Huang, and Francisco J. Cordero
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A. Analysis of tumor volume of PDGF driven, p53 WT models with expression of H3.3K27M (n= 6), H3.3WT (n= 6), or empty vector (n= 7) shows trend for larger tumors with mutation compared to H3.3WT (p= 0.25) or empty vector (p= 0.28) controls. B. Kaplan-Meier survival curve of murine tumors driven by co-injection of nestin tv-a; p53 floxed mice with RCAS-PDGFB; RCAS-Cre; and either RCAS-H3.3K27M-GFP (n=12) or RCAS-H3.3WT-GFP (n= 18). C. In vivo proliferation quantification of H3.3K27M or H3.3WT expressing tumors driven by PDGFB overexpression and p53 knockout using pH3 (H3.3K27M n= 5, H3.3WT n=4) or D. EdU incorporation IF quantification (n=3 each) E. Histone extraction followed by western blot using total H3 antibody comparing murine tumor cells infected with empty vector, H3.3WT, or H3.3K27M to determine the amount of H3 overexpression.
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46. Supplementary Figure 1 from Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques
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J. Mark Cline, Lance D. Miller, Jeff W. Chou, Janet A. Tooze, Susan K. Murphy, Zhiqing Huang, Timothy D. Howard, Cynthia J. Lees, Thomas C. Register, Cynthia J. Willson, Charles E. Wood, and Fitriya N. Dewi
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Serum isoflavonoid concentrations across the pubertal transition. Levels of circulating total isoflavonoids (genistein + daidzein + equol) were significantly higher in soy-fed monkeys. Values represent LSMs for n=11-17 monkeys/group (bars = SEM). Significant main effects and interactions are indicated in the panel.
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47. Data from Targeting Dormant Ovarian Cancer Cells In Vitro and in an In Vivo Mouse Model of Platinum Resistance
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Susan K. Murphy, Andrew Berchuck, Shingo Fujii, Ikuo Konishi, Regina S. Whitaker, Emma Dolan, Noriomi Matsumura, Tsukasa Baba, Zachary R. Visco, Eiji Kondoh, and Zhiqing Huang
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Spheroids exhibit drug resistance and slow proliferation, suggesting involvement in cancer recurrence. The protein kinase C inhibitor UCN-01 (7-hydroxystaurosporine) has shown higher efficacy against slow proliferating and/or quiescent ovarian cancer cells. In this study, tumorigenic potential was assessed using anchorage-independent growth assays and spheroid-forming capacity, which was determined with ovarian cancer cell lines as well as primary ovarian cancers. Of 12 cell lines with increased anchorage-independent growth, 8 formed spheroids under serum-free culture conditions. Spheroids showed reduced proliferation (P < 0.0001) and Ki-67 immunostaining (8% vs. 87%) relative to monolayer cells. Spheroid formation was associated with increased expression of mitochondrial pathway genes (P ≤ 0.001) from Affymetrix HT U133A gene expression data. UCN-01, a kinase inhibitor/mitochondrial uncoupler that has been shown to lead to Puma-induced mitochondrial apoptosis as well as ATP synthase inhibitor oligomycin, demonstrated effectiveness against spheroids, whereas spheroids were refractory to cisplatin and paclitaxel. By live in vivo imaging, ovarian cancer xenograft tumors were reduced after primary treatment with carboplatin. Continued treatment with carboplatin was accompanied by an increase in tumor signal, whereas there was little or no increase in tumor signal observed with subsequent treatment with UCN-01 or oltipraz. Taken together, our findings suggest that genes involved in mitochondrial function in spheroids may be an important therapeutic target in preventing disease recurrence.
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48. Supplementary Tables S1-S3 from Microarray Analysis of Early Stage Serous Ovarian Cancers Shows Profiles Predictive of Favorable Outcome
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Johnathan M. Lancaster, Jeffrey R. Marks, Holly K. Dressman, Susan K. Murphy, Todd Boren, Jason C. Barnett, Marcus Q. Bernardini, Angeles Alvarez Secord, Miguel A. Alonso, Jeff Boyd, Douglas A. Levine, Hisani Horne, Jennifer P. Clarke, Jingqin Luo, Edwin S. Iversen, and Andrew Berchuck
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Supplementary Tables S1-S3 from Microarray Analysis of Early Stage Serous Ovarian Cancers Shows Profiles Predictive of Favorable Outcome
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49. Data from Global Expression Analysis of Cancer/Testis Genes in Uterine Cancers Reveals a High Incidence of BORIS Expression
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J. Carl Barrett, Victor Lobanenkov, Andrew Berchuck, Susan K. Murphy, David S. Schrump, Tracy Litzi, Olga Aprelikova, Dmitri Loukinov, Svetlana Pack, Mary Custer, G. Larry Maxwell, Gadisetti V.R. Chandramouli, and John Ian Risinger
- Abstract
Purpose: Cancer/testis (CT) genes predominantly expressed in the testis (germ cells) and generally not in other normal tissues are aberrantly expressed in human cancers. This highly restricted expression provides a unique opportunity to use these CT genes for diagnostics, immunotherapeutic, or other targeted therapies. The purpose of this study was to identify those CT genes with the greatest incidence of expression in uterine cancers.Experimental Design: We queried the expression of known and putative CT gene transcripts (representing 79 gene loci) using whole genome gene expression arrays. Specifically, the global gene expressions of uterine cancers (n = 122) and normal uteri (n = 10) were determined using expression data from the Affymetrix HG-U133A and HG-U133B chips. Additionally, we also examined the brother of the regulator of imprinted sites (BORIS) transcript by reverse transcription-PCR and quantitative PCR because its transcript was not represented on the array.Results: Global microarray analysis detected many CT genes expressed in various uterine cancers; however, no individual CT gene was expressed in more than 25% of all cancers. The expression of the two most commonly expressed CT genes on the arrays, MAGEA9 (24 of 122 cancers and 0 of 10 normal tissues) and Down syndrome critical region 8 (DSCR8)/MMA1 (16 if 122 cancers and 0 of 10 normal tissues), was confirmed by reverse transcription-PCR methods, validating the array screening approach. In contrast to the relatively low incidence of expression of the other CT genes, BORIS expression was detected in 73 of 95 (77%) endometrial cancers and 24 of 31 (77%) uterine mixed mesodermal tumors.Conclusions: These data provide the first extensive survey of multiple CT genes in uterine cancers. Importantly, we detected a high frequency of BORIS expression in uterine cancers, suggesting its potential as an immunologic or diagnostic target for these cancers. Given the high incidence of BORIS expression and its possible regulatory role, an examination of BORIS function in the etiology of these cancers is warranted.
- Published
- 2023
- Full Text
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50. Data from Microarray Analysis of Early Stage Serous Ovarian Cancers Shows Profiles Predictive of Favorable Outcome
- Author
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Johnathan M. Lancaster, Jeffrey R. Marks, Holly K. Dressman, Susan K. Murphy, Todd Boren, Jason C. Barnett, Marcus Q. Bernardini, Angeles Alvarez Secord, Miguel A. Alonso, Jeff Boyd, Douglas A. Levine, Hisani Horne, Jennifer P. Clarke, Jingqin Luo, Edwin S. Iversen, and Andrew Berchuck
- Abstract
Purpose: Although few women with advanced serous ovarian cancer are cured, detection of the disease at an early stage is associated with a much higher likelihood of survival. We previously used gene expression array analysis to distinguish subsets of advanced cancers based on disease outcome. In the present study, we report on gene expression of early-stage cancers and validate our prognostic model for advanced-stage cancers.Experimental Design: Frozen specimens from 39 stage I/II, 42 stage III/IV, and 20 low malignant potential cancers were obtained from four different sites. A linear discriminant model was used to predict survival based upon array data.Results: We validated the late-stage survival model and show that three of the most differentially expressed genes continue to be predictive of outcome. Most early-stage cancers (38 of 39 invasive, 15 of 20 low malignant potential) were classified as long-term survivors (median probabilities 0.97 and 0.86). MAL, the most differentially expressed gene, was further validated at the protein level and found to be an independent predictor of poor survival in an unselected group of advanced serous cancers (P = 0.0004).Conclusions: These data suggest that serous ovarian cancers detected at an early stage generally have a favorable underlying biology similar to advanced-stage cases that are long-term survivors. Conversely, most late-stage ovarian cancers seem to have a more virulent biology. This insight suggests that if screening approaches are to succeed it will be necessary to develop approaches that are able to detect these virulent cancers at an early stage.
- Published
- 2023
- Full Text
- View/download PDF
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