Research Topics
Genomes and Genes | Srinivasan YegnasubramanianSummaryAffiliation: Johns Hopkins University Country: USA Publications
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Publications
Aiming for the outliers: cancer precision medicine through targeting kinases with extreme expressionSrinivasan Yegnasubramanian
Sidney Kimmel Comprehensive Cancer Center, The Sol Golman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland 21231, USA
Cancer Discov 3:252-4. 2013....
DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneitySrinivasan Yegnasubramanian
Sidney Kimmel Comprehensive Cancer Center, School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
Cancer Res 68:8954-67. 2008....- Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequencesSrinivasan Yegnasubramanian
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
BMC Genomics 12:313. 2011..This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells... - Global levels of H3K27me3 track with differentiation in vivo and are deregulated by MYC in prostate cancerLaxmi G Pellakuru
Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
Am J Pathol 181:560-9. 2012..These findings suggest that increased levels of decondensed chromatin in both normal progenitor cells and cancer cells are associated with global loss of H3K27me3, which is linked to MYC overexpression... - CpG island hypermethylation profile in the serum of men with clinically localized and hormone refractory metastatic prostate cancerPatrick J Bastian
James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
J Urol 179:529-34; discussion 534-5. 2008..In this study we investigated the hypermethylation profile of several genes in the serum of men with localized and hormone refractory prostate cancer... 
Prognostic value of preoperative serum cell-free circulating DNA in men with prostate cancer undergoing radical prostatectomyPatrick J Bastian
The James Buchanan Brady Urological Institute, Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
Clin Cancer Res 13:5361-7. 2007..We evaluated the association of preoperative serum cell-free circulating DNA concentration in men with clinically localized prostate cancer who underwent radical prostatectomy with prostate-specific antigen (PSA) recurrence...- Myc enforces overexpression of EZH2 in early prostatic neoplasia via transcriptional and post-transcriptional mechanismsCheryl M Koh
Departments of Pathology, The Johns Hopkins University, School of Medicine, Baltimore, MD, USA
Oncotarget 2:669-83. 2011..Further, the results implicate EZH2-driven mechanisms by which Myc may stimulate prostate tumor initiation and disease progression... - Alterations in nucleolar structure and gene expression programs in prostatic neoplasia are driven by the MYC oncogeneCheryl M Koh
Department of Pathology, The Johns Hopkins University, School of Medicine, Baltimore, MD 21231, USA
Am J Pathol 178:1824-34. 2011.... - Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylationSrinivasan Yegnasubramanian
Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA
Nucleic Acids Res 34:e19. 2006..This novel technology could significantly improve our ability to detect CGI hypermethylation... - Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancersMichael C Haffner
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
Oncotarget 2:627-37. 2011..Our findings suggest a distinct role for 5 hmC in tissue differentiation, and provide evidence for its large-scale loss in cancers... - Abnormal DNA methylation, epigenetics, and prostate cancerWilliam G Nelson
Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Brady Urological Institute, Baltimore, MD 21231, USA
Front Biosci 12:4254-66. 2007..If sufficiently safe strategies for chromatin modulation can be discovered and developed, epigenetic alterations may become rational targets for both prostate cancer prevention and prostate cancer treatment... - Preoperative serum DNA GSTP1 CpG island hypermethylation and the risk of early prostate-specific antigen recurrence following radical prostatectomyPatrick J Bastian
The James Buchanan Brady Urological Institute and Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231-1000, USA
Clin Cancer Res 11:4037-43. 2005..4; 95% confidence interval, 2.2, 8.8; P < 0.001). CONCLUSION: Our study suggests that GSTP1 CpG island hypermethylation may be an important DNA-based prognostic serum biomarker for prostate cancer... - Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangementsMichael C Haffner
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
Nat Genet 42:668-75. 2010..These findings implicate androgen-induced TOP2B-mediated DSBs in generating TMPRSS2-ERG rearrangements... - A DNA hypermethylation module for the stem/progenitor cell signature of cancerHariharan Easwaran
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins and the Johns Hopkins Medical Institutions, Baltimore, MD 21117, USA
Genome Res 22:837-49. 2012..Additionally, the capacity for global methylation profiling to cluster tumors by phenotype may have important implications for further refining tumor behavior patterns that may ultimately aid therapeutic interventions... - Molecular alterations in prostate cancer as diagnostic, prognostic, and therapeutic targetsBora Gurel
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
Adv Anat Pathol 15:319-31. 2008..In addition, recent studies in which new molecular diagnostic approaches have been applied in the clinic will be discussed... - Hypermethylation of CpG islands in primary and metastatic human prostate cancerSrinivasan Yegnasubramanian
Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, 1650 Orleans Street, Baltimore, MD 21231-1000, USA
Cancer Res 64:1975-86. 2004..Furthermore, CpG island hypermethylation patterns in prostate cancer metastases were very similar to the primary prostate cancers and tended to show greater differences between cases than between anatomical sites of metastasis... - Accurate genome-scale percentage DNA methylation estimates from microarray dataMartin J Aryee
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231, USA
Biostatistics 12:197-210. 2011..We illustrate the method on data generated to detect methylation differences between tissues and between normal and tumor colon samples... - Disulfiram is a DNA demethylating agent and inhibits prostate cancer cell growthJianqing Lin
Chemical Therapeutics Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
Prostate 71:333-43. 2011..Because DNMT catalysis features attack of cytosine bases by an enzyme thiol group, we tested whether disulfiram (DSF), a thiol-reactive compound with known clinical safety, demonstrated DNMT inhibitory activity... - MYC overexpression induces prostatic intraepithelial neoplasia and loss of Nkx3.1 in mouse luminal epithelial cellsTsuyoshi Iwata
Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
PLoS ONE 5:e9427. 2010..We also identified a novel histopathologically identifiable intermediate step prior to invasion that should facilitate studies of molecular pathway alterations occurring during early progression of prostatic adenocarcinomas... - Molecular biomarker in prostate cancer: the role of CpG island hypermethylationPatrick J Bastian
The James Buchanan Brady Urological Institute, Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231 1000, USA
Eur Urol 46:698-708. 2004..CpG island hypermethylation may serve as a useful molecular biomarker for the detection and diagnosis of patients with prostate cancer... - Epigenetic alterations in human prostate cancersWilliam G Nelson
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231 1000, USA
Endocrinology 150:3991-4002. 2009..Finally, a growing portfolio of epigenetic drugs, capable of reversing the phenotypic consequences of somatic epigenetic defects, has entered clinical trials for prostate cancer in the search for a new rational therapy for the disease... - Procainamide is a specific inhibitor of DNA methyltransferase 1Byron H Lee
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
J Biol Chem 280:40749-56. 2005..Because many reports have strongly linked DNMT1 with epigenetic alterations in carcinogenesis, procainamide may be a useful drug in the prevention of cancer... - DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastasesMartin J Aryee
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA
Sci Transl Med 5:169ra10. 2013.... - A novel two-stage, transdisciplinary study identifies digoxin as a possible drug for prostate cancer treatmentElizabeth A Platz
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
Cancer Discov 1:68-77. 2011..By coupling laboratory and epidemiologic methods and thinking, we reduced the probability of identifying false-positive candidate drugs for the next steps in testing... - MDR1 promoter hypermethylation in MCF-7 human breast cancer cells: changes in chromatin structure induced by treatment with 5-Aza-cytidineGloria L David
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21231-1000, USA
Cancer Biol Ther 3:540-8. 2004..In this state, MDR1 expression was markedly sensitive to treatment with the histone deacetylase inhibitor trichostatin A... - Loss of Kelch-like ECH-associated protein 1 function in prostate cancer cells causes chemoresistance and radioresistance and promotes tumor growthPing Zhang
Division of Toxicology, Bloomberg School of Public Health, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
Mol Cancer Ther 9:336-46. 2010..Thus, targeting the Nrf2 pathway in prostate cancer cells may provide a novel strategy to enhance chemotherapy and radiotherapy responsiveness and ameliorate the growth and tumorigenicity, leading to improved clinical outcomes... - Global DNA hypomethylation in intratubular germ cell neoplasia and seminoma, but not in nonseminomatous male germ cell tumorsGeorges J Netto
Department of Pathology, Division of Genitourinary Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231 1000, USA
Mod Pathol 21:1337-44. 2008..That is, IGCNU cells and seminoma cells remain unmethylated, whereas all other histological types appear to arise after de novo methylation... - Decreased 5-hydroxymethylcytosine is associated with neural progenitor phenotype in normal brain and shorter survival in malignant gliomaBrent A Orr
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
PLoS ONE 7:e41036. 2012..These findings suggest that 5hmC regulation in malignant glioma may represent an important determinant of tumor differentiation and aggressive behavior, as well as a potential therapeutic target... - Identification of replication competent murine gammaretroviruses in commonly used prostate cancer cell linesKaren Sandell Sfanos
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
PLoS ONE 6:e20874. 2011..Importantly, our results suggest a need for regular screening of cancer cell lines for retroviral "contamination", much like routine mycoplasma testing... - Transcription-induced DNA double strand breaks: both oncogenic force and potential therapeutic target?Michael C Haffner
Authors Affiliation Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
Clin Cancer Res 17:3858-64. 2011..Such strategies may find particular utility in cancers, like prostate cancer, which show low proliferation rates, in which other chemotherapeutic strategies that target rapidly proliferating cells have had limited success... - Molecular profiling and classification of sporadic renal cell carcinoma by quantitative methylation analysisMark L Gonzalgo
The James Buchanan Brady Urological Institute, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
Clin Cancer Res 10:7276-83. 2004..We determine the utility of molecular profiling based on quantitative methylation analysis for characterization of sporadic renal cell carcinoma... - USP2a activation of MYC in prostate cancerWilliam G Nelson
Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
Cancer Discov 2:206-7. 2012..Ubiquitin-specific protease 2a, a deubiquitinating enzyme, elevates MYC levels in prostate cancer cells via its stabilization of MDM2, undermining p53 regulation of microRNAs that target MYC mRNA... - A novel source for miR-21 expression through the alternative polyadenylation of VMP1 gene transcriptsJudit Ribas
The James Buchannan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
Nucleic Acids Res 40:6821-33. 2012..Collectively, these results indicate that miR-21 is a unique miRNA capable of being regulated by alternative polyadenylation and two independent gene promoters... - Humanizing π-class glutathione S-transferase regulation in a mouse model alters liver toxicity in response to acetaminophen overdoseMatthew P Vaughn
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, United States of America
PLoS ONE 6:e25707. 2011..class GSTs are known to be critical determinants of liver responses to drugs and toxins: when treated with high doses of acetaminophen, mGstp1/2+/+ mice suffer marked liver damage, while mGstp1/2-/- mice escape liver injury... - Increased protein stability causes DNA methyltransferase 1 dysregulation in breast cancerAgoston T Agoston
Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University, School of Medicine, Baltimore, Maryland 21231 1000, USA
J Biol Chem 280:18302-10. 2005..The regulation of DNMT1 destruction via this domain may be dysfunctional in cancer cells leading to subsequent cytosine hypermethylation in the genome... - miR-21: an androgen receptor-regulated microRNA that promotes hormone-dependent and hormone-independent prostate cancer growthJudit Ribas
The James Buchanan Brady Urological Institute, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
Cancer Res 69:7165-9. 2009..Moreover, quantitative reverse transcription-PCR analysis revealed elevated miR-21 expression in CaP when compared with adjacent normal tissue. These results suggest that miR-21 may contribute to CaP pathogenesis... - Prostate cancer: New answers prompt new questions regarding cell of originAngelo M De Marzo
The Brady Urological Research Institute and The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
Nat Rev Urol 7:650-2. 2010..However, these results are not mutually exclusive: there are potential solutions, and alternative views on the initiating cell derivation of prostate tumors also exist... - GSTP1 CpG island hypermethylation as a molecular biomarker for prostate cancerMasashi Nakayama
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
J Cell Biochem 91:540-52. 2004..GSTP1 CpG island hypermethylation, a somatic epigenetic alteration, appears poised to serve as a molecular biomarker useful for prostate cancer screening, detection, and diagnosis... - Distinct transcriptional programs mediated by the ligand-dependent full-length androgen receptor and its splice variants in castration-resistant prostate cancerRong Hu
Department of Urology, Johns Hopkins University, Baltimore, Maryland, USA
Cancer Res 72:3457-62. 2012..Together, our findings support an adaptive shift toward AR-V-mediated signaling in a subset of CRPC tumors as the AR-LBD is rendered inactive, suggesting an important mechanism contributing to drug resistance to CRPC therapy... - Beefing up prostate cancer therapy with performance-enhancing (anti-) steroidsWilliam G Nelson
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231 1000, USA
Cancer Cell 20:7-9. 2011..report that the inhibition of androgen synthesis by abiraterone acetate prolonged the survival of men with prostate cancer previously treated by androgen suppression...