Leslie Cope

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. doi request reprint High level of chromosomal aberration in ovarian cancer genome correlates with poor clinical outcome
    Leslie Cope
    The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Gynecol Oncol 128:500-5. 2013
  2. pmc Identifying differential correlation in gene/pathway combinations
    Rosemary Braun
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Bioinformatics 9:488. 2008
  3. pmc Aberrant silencing of cancer-related genes by CpG hypermethylation occurs independently of their spatial organization in the nucleus
    Hariharan P Easwaran
    The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
    Cancer Res 70:8015-24. 2010
  4. pmc Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells
    Kelly M McGarvey
    Divisions of Cancer Biology, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland 21231, USA
    Cancer Res 68:5753-9. 2008
  5. pmc HMGA1: a master regulator of tumor progression in triple-negative breast cancer cells
    Sandeep N Shah
    Hematology Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 8:e63419. 2013
  6. pmc Methylation of the claudin 1 promoter is associated with loss of expression in estrogen receptor positive breast cancer
    Francescopaolo Di Cello
    The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 8:e68630. 2013
  7. pmc Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells
    Joyce E Ohm
    Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
    Cancer Res 70:7662-73. 2010
  8. pmc HMGA1 reprograms somatic cells into pluripotent stem cells by inducing stem cell transcriptional networks
    Sandeep N Shah
    Hematology Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    PLoS ONE 7:e48533. 2012
  9. pmc HMGA1 correlates with advanced tumor grade and decreased survival in pancreatic ductal adenocarcinoma
    Alexandra C Hristov
    Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mod Pathol 23:98-104. 2010
  10. pmc The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations
    Xue Lin
    Department of Applied Mathematics and Statistics, The Johns Hopkins University, Baltimore, Maryland, USA
    BMC Bioinformatics 10:256. 2009

Collaborators

Detail Information

Publications30

  1. doi request reprint High level of chromosomal aberration in ovarian cancer genome correlates with poor clinical outcome
    Leslie Cope
    The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Gynecol Oncol 128:500-5. 2013
    ..In this study, we addressed this issue by analyzing the genomic profiles in 455 ovarian HGSCs available from The Cancer Genome Atlas (TCGA)...
  2. pmc Identifying differential correlation in gene/pathway combinations
    Rosemary Braun
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Bioinformatics 9:488. 2008
    ....
  3. pmc Aberrant silencing of cancer-related genes by CpG hypermethylation occurs independently of their spatial organization in the nucleus
    Hariharan P Easwaran
    The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
    Cancer Res 70:8015-24. 2010
    ..These findings have important implications for understanding relationships between nuclear organization and gene expression patterns in cancer...
  4. pmc Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells
    Kelly M McGarvey
    Divisions of Cancer Biology, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland 21231, USA
    Cancer Res 68:5753-9. 2008
    ..Our data have great relevance for the increasing interest in reexpression of DNA-hypermethylated genes for the treatment of cancer...
  5. pmc HMGA1: a master regulator of tumor progression in triple-negative breast cancer cells
    Sandeep N Shah
    Hematology Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 8:e63419. 2013
    ..Future studies are needed to determine how to target HMGA1 in therapy...
  6. pmc Methylation of the claudin 1 promoter is associated with loss of expression in estrogen receptor positive breast cancer
    Francescopaolo Di Cello
    The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 8:e68630. 2013
    ....
  7. pmc Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells
    Joyce E Ohm
    Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
    Cancer Res 70:7662-73. 2010
    ..Our findings suggest that by studying the process of induced reprogramming, we may gain significant insight into the origins of epigenetic gene silencing associated with human tumorigenesis, and add to means of assessing iPS for safety...
  8. pmc HMGA1 reprograms somatic cells into pluripotent stem cells by inducing stem cell transcriptional networks
    Sandeep N Shah
    Hematology Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    PLoS ONE 7:e48533. 2012
    ..The high mobility group A1 (HMGA1) gene is highly expressed in hESCs and poorly differentiated, stem-like cancers; however, its role in these settings has been unclear...
  9. pmc HMGA1 correlates with advanced tumor grade and decreased survival in pancreatic ductal adenocarcinoma
    Alexandra C Hristov
    Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mod Pathol 23:98-104. 2010
    ..These results suggest that HMGA1 promotes tumor progression in pancreatic ductal adenocarcinoma and could be a useful biomarker and rational therapeutic target in advanced disease...
  10. pmc The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations
    Xue Lin
    Department of Applied Mathematics and Statistics, The Johns Hopkins University, Baltimore, Maryland, USA
    BMC Bioinformatics 10:256. 2009
    ..Achieving biologically relevant results argues for a different strategy. A promising alternative is to base prediction entirely upon the relative expression ordering of a small number of genes...
  11. pmc HOXB13 mediates tamoxifen resistance and invasiveness in human breast cancer by suppressing ERα and inducing IL-6 expression
    Nilay Shah
    Departments of Oncology, Surgery, and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231 1000, USA
    Cancer Res 73:5449-58. 2013
    ..Taken together, our results establish a function for HOXB13 in TAM resistance through direct suppression of ERα and they identify the IL-6 pathways as mediator of disease progression and recurrence...
  12. pmc Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis
    Ie Ming Shih
    Division of Gynecologic Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
    Am J Obstet Gynecol 203:584.e1-22. 2010
    ..The purpose of this study was to analyze DNA methylation profiles among different types of ovarian serous neoplasm, which is a task that has not been performed...
  13. doi request reprint Biomarkers for detection and prognosis of breast cancer identified by a functional hypermethylome screen
    Jana Jeschke
    Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
    Epigenetics 7:701-9. 2012
    ..92) and validation cohort (HR = 2.87). Our study demonstrates an efficient method to utilize functional methylation changes in BC for the development of effective biomarkers for detection and prognosis prediction of BC...
  14. pmc Mutational analysis of BRAF and KRAS in ovarian serous borderline (atypical proliferative) tumours and associated peritoneal implants
    Laura Ardighieri
    Departments of Pathology and Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    J Pathol 232:16-22. 2014
    ....
  15. ncbi request reprint Expression of Rsf-1, a chromatin-remodeling gene, in ovarian and breast carcinoma
    Tsui Lien Mao
    Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
    Hum Pathol 37:1169-75. 2006
    ..Because Rsf-1 overexpression occurs in only a small number of breast carcinomas, it is unlikely that Rsf-1 is a critical gene in the development of breast carcinoma...
  16. doi request reprint Statistical methods for identifying differentially expressed gene combinations
    Yen Yi Ho
    Johns Hopkins University, Baltimore, MD, USA
    Methods Mol Biol 408:171-91. 2007
    ..Such groups are defined as being jointly differentially expressed. In this chapter several approaches for identifying jointly differentially expressed groups of genes are reviewed of compared on a set of simulations...
  17. pmc HMGA2 protein expression correlates with lymph node metastasis and increased tumor grade in pancreatic ductal adenocarcinoma
    Alexandra C Hristov
    Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mod Pathol 22:43-9. 2009
    ..Our results support a role for HMGA2 in the progression of pancreatic ductal adenocarcinoma and suggest that it could be a useful biomarker and rational therapeutic target in more advanced disease...
  18. pmc Pre-processing Agilent microarray data
    Marianna Zahurak
    Johns Hopkins University School of Medicine, Oncology Biostatistics, Baltimore, MD 21205, USA
    BMC Bioinformatics 8:142. 2007
    ..The larger goal is to define best study design and pre-processing practices for Agilent arrays, and we offer some suggestions...
  19. ncbi request reprint Sequence mutations and amplification of PIK3CA and AKT2 genes in purified ovarian serous neoplasms
    Kentaro Nakayama
    Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
    Cancer Biol Ther 5:779-85. 2006
    ....
  20. pmc Genome-wide methylation profiling and the PI3K-AKT pathway analysis associated with smoking in urothelial cell carcinoma
    Mariana Brait
    Department of Otolaryngology Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Cell Cycle 12:1058-70. 2013
    ..Therefore, our findings suggest that a tobacco signature could emerge from distinctive patterns of genetic and epigenetic alterations and can be identified using an in vitro cellular model for the development of smoking-induced cancer...
  21. ncbi request reprint Rapamycin rescues ABT-737 efficacy in small cell lung cancer
    Eric E Gardner
    Authors Affiliations Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Departments of Oncology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New YorkAuthors Affiliations Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Departments of Oncology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
    Cancer Res 74:2846-56. 2014
    ..These data have direct translational implications for SCLC clinical trials...
  22. ncbi request reprint Patterns of p53 mutations separate ovarian serous borderline tumors and low- and high-grade carcinomas and provide support for a new model of ovarian carcinogenesis: a mutational analysis with immunohistochemical correlation
    Gad Singer
    Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
    Am J Surg Pathol 29:218-24. 2005
    ....
  23. ncbi request reprint Genome-wide gene expression differences in Crohn's disease and ulcerative colitis from endoscopic pinch biopsies: insights into distinctive pathogenesis
    Feng Wu
    Department of Medicine Gastroenterology Division, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Inflamm Bowel Dis 13:807-21. 2007
    ..Ulcerative colitis (UC) and Crohn's disease (CD) are inflammatory bowel diseases (IBD) with variable, overlapping clinical features and complex pathophysiologies...
  24. pmc Comparing the DNA hypermethylome with gene mutations in human colorectal cancer
    Kornel E Schuebel
    Cancer Biology Division, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
    PLoS Genet 3:1709-23. 2007
    ....
  25. ncbi request reprint Differential regional gene expression from cardiac dyssynchrony induced by chronic right ventricular free wall pacing in the mouse
    Kenneth C Bilchick
    Division of Cardiology, Department of Medicine, School of Medicine, Baltimore, Maryland, USA
    Physiol Genomics 26:109-15. 2006
    ..Such analysis using a murine implantable pacemaker should facilitate molecular studies of cardiac dyssynchrony and help elucidate novel mechanisms by which stress/stretch stimuli due to dyssynchrony impact the normal and failing heart...
  26. pmc Therapeutic efficacy of ABT-737, a selective inhibitor of BCL-2, in small cell lung cancer
    Christine L Hann
    Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA
    Cancer Res 68:2321-8. 2008
    ..Taken together, these data have specific implications for the clinical development of Bcl-2 inhibitors for SCLC and broader implications for the testing of novel anticancer strategies in relevant preclinical models...
  27. pmc DNA copy number variations characterize benign and malignant thyroid tumors
    Yan Liu
    Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Clin Endocrinol Metab 98:E558-66. 2013
    ..Fine-needle aspiration (FNA) is the best diagnostic tool for preoperative evaluation of thyroid nodules but is often inconclusive as a guide for surgical management...
  28. pmc A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations
    Vijay K Tiwari
    Cancer Biology Division, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University Medical Institutions, Baltimore, Maryland 21231, USA
    Genome Res 18:1171-9. 2008
    ....
  29. ncbi request reprint Digital karyotyping: an update of its applications in cancer
    Ritu Salani
    Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
    Mol Diagn Ther 10:231-7. 2006
    ..This article provides an overview of digital karyotyping including the principle of the technology and its applications in identifying potential oncogenes and tumor suppressor genes...
  30. pmc Elevated microRNA miR-21 levels in pancreatic cyst fluid are predictive of mucinous precursor lesions of ductal adenocarcinoma
    Ji Kon Ryu
    Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
    Pancreatology 11:343-50. 2011
    ..Deregulated microRNA (miRNAs) expression is widespread in pancreatic cancer. We assessed whether aberrant miRNAs in pancreatic cyst fluid could be used as potential biomarkers for cystic precursor lesions of pancreatic cancer...