Charles M Perou

Summary

Affiliation: University of North Carolina
Country: USA

Publications

  1. pmc Systems biology and genomics of breast cancer
    Charles M Perou
    Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Cold Spring Harb Perspect Biol 3:. 2011
  2. pmc Luminal progenitor and fetal mammary stem cell expression features predict breast tumor response to neoadjuvant chemotherapy
    Adam D Pfefferle
    Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
    Breast Cancer Res Treat 149:425-37. 2015
  3. pmc Molecular features of the basal-like breast cancer subtype based on BRCA1 mutation status
    Aleix Prat
    Translational Genomics Group, Vall d Hebron Institute of Oncology VHIO, Pg Vall d Hebron, 119 129, 08035, Barcelona, Spain
    Breast Cancer Res Treat 147:185-91. 2014
  4. pmc Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer
    Aaron R Thorner
    Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
    PLoS ONE 5:e13073. 2010
  5. pmc Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling
    Wei Zhao
    Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill NC 27599, USA
    BMC Genomics 15:419. 2014
  6. pmc A comparison of gene expression signatures from breast tumors and breast tissue derived cell lines
    D T Ross
    Applied Genomics, Inc, Sunnyvale, CA, USA
    Dis Markers 17:99-109. 2001
  7. pmc In vitro and in vivo analysis of B-Myb in basal-like breast cancer
    A R Thorner
    Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
    Oncogene 28:742-51. 2009
  8. pmc Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen
    A Prat
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
    Ann Oncol 23:2866-73. 2012
  9. pmc PAM50 assay and the three-gene model for identifying the major and clinically relevant molecular subtypes of breast cancer
    A Prat
    Departament de Medicina, Universitat Autonoma de Barcelona, Barcelona, Spain
    Breast Cancer Res Treat 135:301-6. 2012
  10. pmc Molecular analysis reveals heterogeneity of mouse mammary tumors conditionally mutant for Brca1
    Mollie H Wright
    Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Mol Cancer 7:29. 2008

Collaborators

Detail Information

Publications97

  1. pmc Systems biology and genomics of breast cancer
    Charles M Perou
    Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Cold Spring Harb Perspect Biol 3:. 2011
    ..Here, we describe the discovery and basic biology of the intrinsic subtypes of breast cancer, and detail how this interacts with underlying genetic alternations, response to therapy, and the metastatic process...
  2. pmc Luminal progenitor and fetal mammary stem cell expression features predict breast tumor response to neoadjuvant chemotherapy
    Adam D Pfefferle
    Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
    Breast Cancer Res Treat 149:425-37. 2015
    ..This work identifies new clinically relevant gene signatures and highlights the value of a developmental biology perspective for uncovering relationships between tumor subtypes and their potential normal cellular counterparts. ..
  3. pmc Molecular features of the basal-like breast cancer subtype based on BRCA1 mutation status
    Aleix Prat
    Translational Genomics Group, Vall d Hebron Institute of Oncology VHIO, Pg Vall d Hebron, 119 129, 08035, Barcelona, Spain
    Breast Cancer Res Treat 147:185-91. 2014
    ....
  4. pmc Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer
    Aaron R Thorner
    Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
    PLoS ONE 5:e13073. 2010
    ..However, the role of c-Myb in mammopoeisis and breast tumorigenesis is poorly understood, despite its high expression in the majority of breast cancer cases (60-80%)...
  5. pmc Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling
    Wei Zhao
    Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill NC 27599, USA
    BMC Genomics 15:419. 2014
    ..Hence, a mRNA-Seq protocol will not be compatible for use with RNAs coming from Formalin-Fixed and Paraffin-Embedded (FFPE) samples...
  6. pmc A comparison of gene expression signatures from breast tumors and breast tissue derived cell lines
    D T Ross
    Applied Genomics, Inc, Sunnyvale, CA, USA
    Dis Markers 17:99-109. 2001
    ....
  7. pmc In vitro and in vivo analysis of B-Myb in basal-like breast cancer
    A R Thorner
    Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
    Oncogene 28:742-51. 2009
    ..These data provide insight into the influence of B-Myb in human breast cancer, which is of potential clinical importance for determining disease risk and for guiding treatment...
  8. pmc Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen
    A Prat
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
    Ann Oncol 23:2866-73. 2012
    ..In this study, we evaluated the ability of six clinically relevant genomic signatures to predict relapse in patients with ER+ tumors treated with adjuvant tamoxifen only...
  9. pmc PAM50 assay and the three-gene model for identifying the major and clinically relevant molecular subtypes of breast cancer
    A Prat
    Departament de Medicina, Universitat Autonoma de Barcelona, Barcelona, Spain
    Breast Cancer Res Treat 135:301-6. 2012
    ..Our results show that classification of the major and clinically relevant molecular subtypes of breast cancer are best captured using larger gene panels...
  10. pmc Molecular analysis reveals heterogeneity of mouse mammary tumors conditionally mutant for Brca1
    Mollie H Wright
    Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Mol Cancer 7:29. 2008
    ..We examined the expression profiles of original and serially transplanted mammary tumors from Brca1 deficient mice, and tumor derived cell lines to validate their use for preclinical testing and studies of tumor biology...
  11. pmc Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
    Jason I Herschkowitz
    Lineberger Comprehensive Cancer Center
    Genome Biol 8:R76. 2007
    ..To address this need, we characterized mammary tumor gene expression profiles from 13 different murine models using DNA microarrays and compared the resulting data to those from human breast tumors...
  12. pmc An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer
    Andrea H Bild
    Department of Pharmacology and Toxicology, University of Utah, 112 Skaggs Hall, Salt Lake City, UT 84112, USA
    Breast Cancer Res 11:R55. 2009
    ..Additional work has also used signatures of oncogenic pathway deregulation to dissect breast cancer heterogeneity as well as to suggest therapeutic opportunities linked to pathway activation...
  13. pmc Somatic sequence alterations in twenty-one genes selected by expression profile analysis of breast carcinomas
    Stephen J Chanock
    Section of Genomic Variation, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 4605, USA
    Breast Cancer Res 9:R5. 2007
    ....
  14. pmc Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay
    Laurent Perreard
    The ARUP Institute for Clinical and Experimental Pathology, SLC, Utah, USA
    Breast Cancer Res 8:R23. 2006
    ..In the current article, we use microarray analysis and a real-time quantitative reverse-transcription (qRT)-PCR assay to risk-stratify breast cancers based on biological 'intrinsic' subtypes and proliferation...
  15. pmc Gene expression profiles of breast biopsies from healthy women identify a group with claudin-low features
    Vilde D Haakensen
    Dept of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway
    BMC Med Genomics 4:77. 2011
    ..Increased understanding of the variability in normal breast biology will enable us to identify mechanisms of breast cancer initiation and the origin of different subtypes, and to better predict breast cancer risk...
  16. pmc Universal Reference RNA as a standard for microarray experiments
    Natalia Novoradovskaya
    Stratagene, 11011 N, Torrey Pines Road, La Jolla, CA 92037, USA
    BMC Genomics 5:20. 2004
    ..Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment...
  17. pmc Gene expression patterns associated with p53 status in breast cancer
    Melissa A Troester
    Division of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA, USA
    BMC Cancer 6:276. 2006
    ..The relation between p53 status and subtype can be better studied by combining data from primary tumors with data from isogenic cell line pairs (with and without p53 function)...
  18. doi request reprint Molecular stratification of triple-negative breast cancers
    Charles M Perou
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Oncologist 15:39-48. 2010
    ..This article will focus on the molecular stratification of triple-negative breast cancers and the therapeutic implications of these classifications...
  19. doi request reprint Molecular stratification of triple-negative breast cancers
    Charles M Perou
    Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Oncologist 16:61-70. 2011
    ..This article will focus on the molecular stratification of triple-negative breast cancers and the therapeutic implications of these classifications...
  20. pmc Characterization of cell lines derived from breast cancers and normal mammary tissues for the study of the intrinsic molecular subtypes
    Aleix Prat
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB7295, Chapel Hill, NC, 27599, USA
    Breast Cancer Res Treat 142:237-55. 2013
    ..The results presented here help to improve our understanding of the wide range of breast cancer cell line models through the appropriate pairing of cell lines with relevant in vivo tumor and normal cell counterparts. ..
  21. pmc Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse
    J Chuck Harrell
    Lineberger Comprehensive Cancer Center, University of North Carolina, 450 West Drive, CB7295, Chapel Hill, NC 27599, USA
    Breast Cancer Res Treat 132:523-35. 2012
    ..In total, these data identify that depending upon the organ of relapse, a combination of gene expression signatures most accurately predicts metastatic behavior...
  22. pmc Combined PI3K/mTOR and MEK inhibition provides broad antitumor activity in faithful murine cancer models
    Patrick J Roberts
    Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
    Clin Cancer Res 18:5290-303. 2012
    ..Anticancer drug development is inefficient, but genetically engineered murine models (GEMM) and orthotopic, syngeneic transplants (OST) of cancer may offer advantages to in vitro and xenograft systems...
  23. pmc Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts
    Shunqiang Li
    Section of Breast Oncology, Division of Oncology, Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA Siteman Cancer Center Breast Cancer Program, Washington University in St Louis, St Louis, MO 63110, USA
    Cell Rep 4:1116-30. 2013
    ..The originating tumor genome provides a benchmark for assessing genetic drift and clonal representation after transplantation. ..
  24. pmc Predicting drug responsiveness in human cancers using genetically engineered mice
    Jerry Usary
    Lineberger Comprehensive Cancer Center, Department of Genetics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Clin Cancer Res 19:4889-99. 2013
    ..These mouse models offer advantages including precise genetics and an intact microenvironment/immune system...
  25. pmc Prediction of toxicant-specific gene expression signatures after chemotherapeutic treatment of breast cell lines
    Melissa A Troester
    Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Environ Health Perspect 112:1607-13. 2004
    ..These analyses also showed that toxicant-specific gene expression patterns, similar to general stress responses, vary according to cell type...
  26. pmc EGFR associated expression profiles vary with breast tumor subtype
    Katherine A Hoadley
    Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
    BMC Genomics 8:258. 2007
    ..An EGFR-associated gene expression signature was identified in the basal-like SUM102 cell line and was used to classify a diverse set of sporadic breast tumors...
  27. pmc Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures
    Cheng Fan
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, USA
    BMC Med Genomics 4:3. 2011
    ..We evaluated whether combining the prognostic powers of standard breast cancer clinical variables with a large set of gene expression signatures could improve on our ability to predict patient outcomes...
  28. pmc The molecular portraits of breast tumors are conserved across microarray platforms
    Zhiyuan Hu
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
    BMC Genomics 7:96. 2006
    ..To overcome this problem we used publicly available breast cancer gene expression data sets and a novel approach to data fusion, in order to validate a new breast tumor intrinsic list...
  29. pmc Activation of host wound responses in breast cancer microenvironment
    Melissa A Troester
    Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Clin Cancer Res 15:7020-8. 2009
    ..Despite the widespread acknowledgment of commonalities between host responses to wounds and host responses to cancer, the gene expression responses of normal tissue adjacent to cancers have not been well characterized...
  30. pmc Prediction of lung cancer histological types by RT-qPCR gene expression in FFPE specimens
    Matthew D Wilkerson
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    J Mol Diagn 15:485-97. 2013
    ..The HEP also exhibited good performance in specimens with low tumor cellularity. Therefore, RT-qPCR gene expression from FFPE specimens can be effectively used to predict lung cancer histology. ..
  31. pmc Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer
    Aleix Prat
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599, USA
    Breast Cancer Res 12:R68. 2010
    ..Here, we comprehensively characterize the recently identified claudin-low tumor subtype...
  32. ncbi request reprint Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study
    Lisa A Carey
    Division of Hematology Oncology, School of Public Health, Department of Epidemiology, University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599 7305, USA
    JAMA 295:2492-502. 2006
    ..Gene expression analysis has identified several breast cancer subtypes, including basal-like, human epidermal growth factor receptor-2 positive/estrogen receptor negative (HER2+/ER-), luminal A, and luminal B...
  33. ncbi request reprint Estrogen-regulated genes predict survival in hormone receptor-positive breast cancers
    Daniel S Oh
    Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
    J Clin Oncol 24:1656-64. 2006
    ..Therefore, we developed a gene expression-based outcome predictor for ER+ and/or PR+ (ie, luminal) breast cancer patients using biologic differences among these tumors...
  34. pmc Role of HGF in obesity-associated tumorigenesis: C3(1)-TAg mice as a model for human basal-like breast cancer
    Sneha Sundaram
    Department of Nutrition, Gillings School of Global Public Health and School of Medicine, University of North Carolina at Chapel Hill, CB 7461, 2203 McGavran Greenberg Hall, Chapel Hill, NC, 27599 7461, USA
    Breast Cancer Res Treat 142:489-503. 2013
    ..Understanding the effects of obesity on risk and progression is important given that epidemiologic studies imply a portion of BBC could be eliminated by reducing obesity...
  35. pmc A compact VEGF signature associated with distant metastases and poor outcomes
    Zhiyuan Hu
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    BMC Med 7:9. 2009
    ..Tumor metastases pose the greatest threat to a patient's survival, and thus, understanding the biology of disseminated cancer cells is critical for developing effective therapies...
  36. pmc Micro-scale genomic DNA copy number aberrations as another means of mutagenesis in breast cancer
    Hann Hsiang Chao
    Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
    PLoS ONE 7:e51719. 2012
    ..There is evidence that this genomic instability extends to smaller scale genomic aberrations, as shown by a previously described micro-deletion event in the PTEN gene in the Basal-like SUM149 breast cancer cell line...
  37. pmc SWI/SNF chromatin-remodeling factor Smarcd3/Baf60c controls epithelial-mesenchymal transition by inducing Wnt5a signaling
    Nicole Vincent Jordan
    Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
    Mol Cell Biol 33:3011-25. 2013
    ..Inhibition of Wnt5a by either RNAi knockdown or blocking antibody reversed Smarcd3/Baf60c-induced EMT. Thus, Smarcd3/Baf60c epigenetically regulates EMT by activating WNT signaling pathways...
  38. pmc Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation
    Matthew D Wilkerson
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS ONE 7:e36530. 2012
    ..Patients may have incurred different mutations and alterations that led to the different subtypes. We hypothesized that the LAD molecular subtypes co-occur with distinct mutations and alterations in patient tumors...
  39. pmc Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer
    James S Duncan
    Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
    Cell 149:307-21. 2012
    ..This approach defines mechanisms of drug resistance, allowing rational design of combination therapies for cancer...
  40. pmc Intrinsic breast tumor subtypes, race, and long-term survival in the Carolina Breast Cancer Study
    Katie M O'Brien
    Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Clin Cancer Res 16:6100-10. 2010
    ....
  41. ncbi request reprint Phenotypic evaluation of the basal-like subtype of invasive breast carcinoma
    Chad A Livasy
    Department of Pathology and Lab Medicine, University of North Carolina, Chapel Hill, NC 27599 7525, USA
    Mod Pathol 19:264-71. 2006
    ..These findings should further assist in the identification of basal-like carcinomas in clinical specimens, facilitating treatment and epidemiologic studies of this tumor subtype...
  42. ncbi request reprint The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes
    Lisa A Carey
    Division of Hematology Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 7305, USA
    Clin Cancer Res 13:2329-34. 2007
    ..Gene expression analysis identifies several breast cancer subtypes. We examined the relationship of neoadjuvant chemotherapy response to outcome among these breast cancer subtypes...
  43. pmc Endothelial-like properties of claudin-low breast cancer cells promote tumor vascular permeability and metastasis
    J Chuck Harrell
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Campus Box 7295, 450 West Drive, Chapel Hill, NC, 27599, USA
    Clin Exp Metastasis 31:33-45. 2014
    ..We hypothesize that the genetic signatures we have identified highlight patients that should respond most favorably to anti-vascular agents. ..
  44. pmc Pharmacokinetics and efficacy of PEGylated liposomal doxorubicin in an intracranial model of breast cancer
    Carey K Anders
    Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS ONE 8:e61359. 2013
    ..We compared pharmacokinetics (PK) and efficacy of PEGylated liposomal doxorubicin (PLD) with non-liposomal doxorubicin (NonL-doxo) in an intracranial model of BC...
  45. pmc Genetic variation in Transaldolase 1 and risk of squamous cell carcinoma of the head and neck
    Patricia V Basta
    Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7435, USA
    Cancer Detect Prev 32:200-8. 2008
    ..Here we present data examining the association of genetic variation in one of the key enzymes of the PPP, Transaldolase 1 (TALDO1) with squamous cell carcinoma of the head and neck (SCCHN)...
  46. pmc Molecular characterization of human breast tumor vascular cells
    Rajendra Bhati
    Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    Am J Pathol 172:1381-90. 2008
    ..Therefore, these genetic markers may serve as potential targets for the development of angiogenesis inhibitors...
  47. pmc A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma
    Jeran K Stratford
    Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS Med 7:e1000307. 2010
    ....
  48. pmc SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples
    Patrick K Kimes
    Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Nucleic Acids Res 42:e113. 2014
    ..By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor. ..
  49. pmc Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival
    Victor J Weigman
    Bioinformatics and Computational Biology Program, University of North Carolina, Chapel Hill, NC 27599, USA
    Breast Cancer Res Treat 133:865-80. 2012
    ..These data suggest a possible genetic cause for genomic instability in Basal-like breast cancers and a biological rationale for the use of DNA repair inhibitor related therapeutics in this breast cancer subtype...
  50. pmc Differential methylation relative to breast cancer subtype and matched normal tissue reveals distinct patterns
    Sabrina A Bardowell
    School of Nursing, The University of North Carolina at Chapel Hill, Office 5102, Carrington Hall, CB 7460, Chapel Hill, NC, 27599 7460, USA
    Breast Cancer Res Treat 142:365-80. 2013
    ..These findings highlight the need to control for subtype when interpreting DNA methylation results, and the importance of interrogating multiple CpGs across varied gene regions. ..
  51. pmc Integrated RNA and DNA sequencing improves mutation detection in low purity tumors
    Matthew D Wilkerson
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Nucleic Acids Res 42:e107. 2014
    ..g. PIK3CA, ERBB2 and FGFR2). In summary, integrating RNA-seq with DNA-WES increases mutation detection performance, especially for low purity tumors. ..
  52. pmc Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types
    Matthew D Wilkerson
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 27599, USA
    Clin Cancer Res 16:4864-75. 2010
    ..We sought to determine if SCC mRNA expression subtypes exist, are reproducible across multiple patient cohorts, and are clinically relevant...
  53. pmc BlackOPs: increasing confidence in variant detection through mappability filtering
    Christopher R Cabanski
    Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC 27599, USA, The Genome Institute at Washington University, St Louis, MO 63108, USA, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Computer Science, University of Kentucky, Lexington, KY 40506, USA, Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA and Division of Medical Oncology, Department of Internal Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
    Nucleic Acids Res 41:e178. 2013
    ..In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing. ..
  54. pmc Impact of tumor microenvironment and epithelial phenotypes on metabolism in breast cancer
    Heather Ann Brauer
    Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Clin Cancer Res 19:571-85. 2013
    ..This study conducted genomic and metabolomic analyses to elucidate how tumor and stromal genomic characteristics influence tumor metabolism...
  55. pmc LKB1/STK11 inactivation leads to expansion of a prometastatic tumor subpopulation in melanoma
    Wenjin Liu
    Department of Genetics, The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599 7295, USA
    Cancer Cell 21:751-64. 2012
    ..These results suggest that LKB1 inactivation in the context of RAS activation facilitates metastasis by inducing an SFK-dependent expansion of a prometastatic, CD24(+) tumor subpopulation...
  56. pmc SWISS MADE: Standardized WithIn Class Sum of Squares to evaluate methodologies and dataset elements
    Christopher R Cabanski
    Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, North Carolina, United States of America
    PLoS ONE 5:e9905. 2010
    ..Analysis of the MACQ data shows differential intersite reproducibility by array platform. SWISS also shows that one lane of RNA-Seq clusters data by biological phenotypes as well as a single Agilent two-color microarray...
  57. ncbi request reprint Identification of a basal-like subtype of breast ductal carcinoma in situ
    Chad A Livasy
    Department of Pathology and Lab Medicine, University of North Carolina, Chapel Hill, NC 27599 7525, USA
    Hum Pathol 38:197-204. 2007
    ..0001), p53 overexpression (P < .0001), and elevated Ki-67 index (P < .0001). These studies demonstrate the presence of a basal-like in situ carcinoma, a potential precursor lesion to invasive basal-like carcinoma...
  58. ncbi request reprint Cell-type-specific responses to chemotherapeutics in breast cancer
    Melissa A Troester
    Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 27599, USA
    Cancer Res 64:4218-26. 2004
    ..Similarities between in vivo and in vitro responses help to identify important response mechanisms to chemotherapeutics...
  59. pmc The functional loss of the retinoblastoma tumour suppressor is a common event in basal-like and luminal B breast carcinomas
    Jason I Herschkowitz
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599, USA
    Breast Cancer Res 10:R75. 2008
    ....
  60. pmc Mitochondrial Hep27 is a c-Myb target gene that inhibits Mdm2 and stabilizes p53
    Chad Deisenroth
    University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, School of Medicine, Chapel Hill, NC, USA
    Mol Cell Biol 30:3981-93. 2010
    ..Our data demonstrate a unique c-Myb-Hep27-Mdm2-p53 mitochondria-to-nucleus signaling pathway that may have functional significance for ER-positive breast cancers...
  61. pmc CDK inhibitor p18(INK4c) is a downstream target of GATA3 and restrains mammary luminal progenitor cell proliferation and tumorigenesis
    Xin Hai Pei
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
    Cancer Cell 15:389-401. 2009
    ..Hence, p18(INK4C) is a downstream target of GATA3, constrains luminal progenitor cell expansion, and suppresses luminal tumorigenesis in the mammary gland...
  62. pmc Vimentin DNA methylation predicts survival in breast cancer
    Jacob Ulirsch
    The University of North Carolina at Chapel Hill School of Nursing, Lab 013, Carrington Hall, CB 7460, Chapel Hill, NC 27599 7460, USA
    Breast Cancer Res Treat 137:383-96. 2013
    ..Vimentin methylation predicted poor overall survival independent of race, subtype, stage, nodal status, or metastatic disease and holds promise as a new prognostic biomarker for breast cancer patients...
  63. pmc Supervised risk predictor of breast cancer based on intrinsic subtypes
    Joel S Parker
    Lineberger Comprehensive Cancer Center, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
    J Clin Oncol 27:1160-7. 2009
    ..Test sets from 761 patients (no systemic therapy) were evaluated for prognosis, and 133 patients were evaluated for prediction of pathologic complete response (pCR) to a taxane and anthracycline regimen...
  64. pmc TBCRC 001: randomized phase II study of cetuximab in combination with carboplatin in stage IV triple-negative breast cancer
    Lisa A Carey
    Hematology Oncology, University of North Carolina Lineberger Comprehensive Cancer Center, 170 Manning Dr, Chapel Hill, NC 27599 7305, USA
    J Clin Oncol 30:2615-23. 2012
    ..Epidermal growth factor receptor (EGFR) is a targetable receptor frequently overexpressed in basal-like breast cancer, which comprises most triple-negative breast cancers (TNBCs), the only subtype without established targeted therapy...
  65. ncbi request reprint RNA expression analysis of formalin-fixed paraffin-embedded tumors
    Shannon K Penland
    Department of Medicine, The University of North Carolina School of Medicine, Chapel Hill, NC 27599 7295, USA
    Lab Invest 87:383-91. 2007
    ..Although only a minority of FFPE blocks could be analyzed, we show that informative RNA expression analysis can be derived from selected FFPE samples...
  66. pmc Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases
    Katherine A Hoadley
    Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS Med 13:e1002174. 2016
    ....
  67. pmc ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data
    Christopher R Cabanski
    Department of Statistics and Operations Research, Chapel Hill, NC, USA
    BMC Bioinformatics 13:221. 2012
    ..However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results...
  68. pmc Interactions with fibroblasts are distinct in Basal-like and luminal breast cancers
    J Terese Camp
    Department of Epidemiology, University of North Carolina at Chapel Hill, Campus Box 7435, 135 Dauer Ln, Chapel Hill, NC 27599, USA
    Mol Cancer Res 9:3-13. 2011
    ..The phenotypes and gene expression changes invoked by cancer cell interactions with fibroblasts support the microenvironment and cell-cell interactions as intrinsic features of breast cancer subtypes...
  69. pmc Multiple roles of cyclin-dependent kinase 4/6 inhibitors in cancer therapy
    Patrick J Roberts
    Department of Genetics, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
    J Natl Cancer Inst 104:476-87. 2012
    ....
  70. pmc Practical implications of gene-expression-based assays for breast oncologists
    Aleix Prat
    Department of Genetics and Pathology, Lineberger Comprehensive Cancer Center, University of North Carolina, 450 West Drive, Chapel Hill, NC 27599, USA
    Nat Rev Clin Oncol 9:48-57. 2011
    ..In this Review, we discuss the clinical utility of gene-expression-based assays and their technical potential as clinical tools vis-a-vis the performance of breast cancer biomarkers that are the current standard of care...
  71. pmc Epidemiology of basal-like breast cancer
    Robert C Millikan
    Department of Epidemiology, CB 7435, School of Public Health, University of North Carolina, Chapel Hill, NC 27599 7435, USA
    Breast Cancer Res Treat 109:123-39. 2008
    ..Among younger African-American women, we estimate that up to 68% of basal-like breast cancer could be prevented by promoting breastfeeding and reducing abdominal adiposity...
  72. pmc The prognostic contribution of clinical breast cancer subtype, age, and race among patients with breast cancer brain metastases
    Carey K Anders
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 7305, USA
    Cancer 117:1602-11. 2011
    ..In a single-institution cohort study, the authors attempted to determine whether the inferior outcome noted with TNBC brain metastases is more reflective of a higher risk population or the subtype itself...
  73. pmc Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial
    Maggie C U Cheang
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
    Clin Cancer Res 18:2402-12. 2012
    ..CTG MA.5, a clinical trial randomizing premenopausal women with node-positive breast cancer to adjuvant CMF (cyclophosphamide-methotrexate-fluorouracil) versus CEF (cyclophosphamide-epirubicin-fluorouracil) chemotherapy...
  74. doi request reprint Molecular subtypes in breast cancer evaluation and management: divide and conquer
    Jeffrey Peppercorn
    University of North Carolina, Chapel Hill, North Carolina, USA
    Cancer Invest 26:1-10. 2008
  75. pmc Rho GTPase Transcriptome Analysis Reveals Oncogenic Roles for Rho GTPase-Activating Proteins in Basal-like Breast Cancers
    Campbell D Lawson
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
    Cancer Res 76:3826-37. 2016
    ..We have established that, via the suppression of RhoA, ArhGAP11A and RacGAP1 are both critical drivers of BLBC growth, and propose that RhoGAPs can act as oncogenes in cancer. Cancer Res; 76(13); 3826-37. ©2016 AACR. ..
  76. pmc Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer
    Grace O Silva
    Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
    Breast Cancer Res Treat 152:347-56. 2015
    ....
  77. pmc ABRA: improved coding indel detection via assembly-based realignment
    Lisle E Mose
    Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Bioinformatics 30:2813-5. 2014
    ..Insertions and deletions (indels) in particular have been an area of great difficulty. Indels are frequent and can have substantial impact on function, which makes their detection all the more imperative...
  78. pmc Age-specific changes in intrinsic breast cancer subtypes: a focus on older women
    Emily O Jenkins
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
    Oncologist 19:1076-83. 2014
    ..Few data exist on the frequency of molecular subtypes in older women. Here, we characterize the incidence and outcomes of BC patients by molecular subtypes and age...
  79. pmc PIK3CA and PIK3CB inhibition produce synthetic lethality when combined with estrogen deprivation in estrogen receptor-positive breast cancer
    Robert J Crowder
    Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Cancer Res 69:3955-62. 2009
    ..Our results suggest that PI3K inhibitors should target both p110alpha and p110beta catalytic subunits, whether wild-type or mutant, and be combined with endocrine therapy for maximal efficacy when treating ER(+) breast cancer...
  80. pmc Genome remodelling in a basal-like breast cancer metastasis and xenograft
    Li Ding
    The Genome Center at Washington University, St Louis, Missouri 63108, USA
    Nature 464:999-1005. 2010
    ..The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour...
  81. ncbi request reprint Evaluating the comparability of gene expression in blood and brain
    Patrick F Sullivan
    Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 7264, USA
    Am J Med Genet B Neuropsychiatr Genet 141:261-8. 2006
    ..This suggests that the cautious and thoughtful use of peripheral gene expression may be a useful surrogate for gene expression in the CNS when it has been determined that the relevant gene is expressed in both...
  82. pmc The genomic landscape of breast cancer as a therapeutic roadmap
    Matthew J Ellis
    Division of Medical Oncology, Section of Breast Oncology, Siteman Cancer Center, Washington University School of Medicine, St Louis, MO 63110, USA
    Cancer Discov 3:27-34. 2013
    ..In this Prospective, we summarize some of the headline conclusions from 6 recent breast cancer "omics profiling" articles in Nature, with an emphasis on the implications for systemic therapy...
  83. pmc Integrated study of copy number states and genotype calls using high-density SNP arrays
    Wei Sun
    Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
    Nucleic Acids Res 37:5365-77. 2009
    ..We evaluated genoCN by applications to 162 HapMap individuals and a brain tumor (glioblastoma) dataset and showed that our method can successfully identify both types of copy number differences and produce high-quality genotype calls...
  84. pmc Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer
    Aleix Prat
    University of North Carolina, Chapel Hill, NC, USA
    J Clin Oncol 31:203-9. 2013
    ..In this study, we sought to improve the IHC subtyping by examining the pathologic and gene expression characteristics of genomically defined luminal A and B subtypes...
  85. pmc Molecular characterization of basal-like and non-basal-like triple-negative breast cancer
    Aleix Prat
    Medical Oncology Department, Vall d Hebron Institute of Oncology, Barcelona, Spain
    Oncologist 18:123-33. 2013
    ....
  86. pmc Oncogenic PI3K mutations lead to NF-κB-dependent cytokine expression following growth factor deprivation
    Jessica E Hutti
    Lineberger Comprehensive Cancer Center, Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599, USA
    Cancer Res 72:3260-9. 2012
    ..These data also indicate that NF-κB plays diverse roles downstream from different oncogenic signaling pathways...
  87. pmc MAP3K4/CBP-regulated H2B acetylation controls epithelial-mesenchymal transition in trophoblast stem cells
    Amy N Abell
    Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599 7365, USA
    Cell Stem Cell 8:525-37. 2011
    ..Taken together, our data define an epigenetic switch that maintains the epithelial phenotype in TS cells and reveals previously unrecognized genes potentially contributing to breast cancer...
  88. ncbi request reprint Mutation of GATA3 in human breast tumors
    Jerry Usary
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
    Oncogene 23:7669-78. 2004
    ..These data suggest that GATA3 is involved in growth control and the maintenance of the differentiated state in epithelial cells, and that GATA3 variants may contribute to tumorigenesis in ESR1-positive breast tumors...
  89. doi request reprint Merging two gene-expression studies via cross-platform normalization
    Andrey A Shabalin
    Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, NC, USA
    Bioinformatics 24:1154-60. 2008
    ..This article considers the problem of how to merge datasets arising from different gene-expression studies of a common organism and phenotype. Of particular interest is how to merge data from different technological platforms...
  90. ncbi request reprint High reproducibility using sodium hydroxide-stripped long oligonucleotide DNA microarrays
    Zhiyuan Hu
    University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
    Biotechniques 38:121-4. 2005
    ..90-0.98, which is comparable to the ICC of two virgin arrays hybridized with the same sample. Using this method, once-stripped oligonucleotide microarrays are usable, reliable, and help to reduce costs...
  91. pmc Secreted frizzle-related protein 2 stimulates angiogenesis via a calcineurin/NFAT signaling pathway
    Andrew Courtwright
    Departments of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    Cancer Res 69:4621-8. 2009
    ..04). In conclusion, SFRP2 is a novel stimulator of angiogenesis that stimulates angiogenesis via a calcineurin/NFAT pathway and may be a favorable target for the inhibition of angiogenesis in solid tumors...
  92. doi request reprint Deconstructing the molecular portraits of breast cancer
    Aleix Prat
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Mol Oncol 5:5-23. 2011
    ....
  93. ncbi request reprint Molecular portraits and the family tree of cancer
    Christine H Chung
    Division of Hematology Oncology, University of North Carolina at Chapel Hill, CB 7305, 3009 Old Clinic Building, Chapel Hill, North Carolina 27599, USA
    Nat Genet 32:533-40. 2002
    ..The early results are painting a detailed portrait of cancer that illustrates the individuality of each tumor and allows familial relationships to be recognized through the identification of cell types sharing common expression patterns...
  94. pmc Murine microenvironment metaprofiles associate with human cancer etiology and intrinsic subtypes
    David H Nguyen
    Department of Radiation Oncology, New York University School of Medicine, New York, New York 10016, USA
    Clin Cancer Res 19:1353-62. 2013
    ..We asked whether expression metaprofiles could discern radiation-preceded human cancer or be informative in sporadic breast cancers...
  95. doi request reprint Development of an immuno tandem mass spectrometry (iMALDI) assay for EGFR diagnosis
    Jian Jiang
    Curriculum in Applied and Materials Sciences, UNC CH, Chapel Hill, NC, USA
    Proteomics Clin Appl 1:1651-9. 2007
    ..The addition of stable-labeled versions of the target peptide (synthesized from stable-isotope coded amino acids) as internal standards allows absolute quantitation of the target protein...
  96. ncbi request reprint A custom microarray platform for analysis of microRNA gene expression
    J Michael Thomson
    Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Nat Methods 1:47-53. 2004
    ..This microarray technology enables comprehensive investigation of microRNA expression, and furthers our understanding of this class of recently discovered noncoding RNAs...