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Jeffrey R. Marks

Jeffrey R. Marks

Joseph W. and Dorothy W. Beard Distinguished Professor of Experimental Surgery
Surgery, Surgical Sciences
marks003@mc.duke.edu
Box 3873 Med Ctr, Durham, NC 27710
B216, LSRC, Duke University, Durham, NC 27710

Selected Publications

Spatial localization of collagen hydroxylated proline site variation as an ancestral trait in the breast cancer microenvironment.

Journal Article Matrix Biol · April 2025 Collagen stroma interactions within the extracellular microenvironment of breast tissue play a significant role in breast cancer, including risk, progression, and outcomes. Hydroxylation of proline (HYP) is a common post-translational modification directly ... Full text Link to item Cite

Evolutionary measures show that recurrence of DCIS is distinct from progression to breast cancer.

Journal Article Breast Cancer Res · March 21, 2025 BACKGROUND: Progression from pre-cancers like ductal carcinoma in situ (DCIS) to invasive disease (cancer) is driven by somatic evolution and is altered by clinical interventions. We hypothesized that genetic and/or phenotypic intra-tumor heterogeneity wou ... Full text Link to item Cite

Active Monitoring With or Without Endocrine Therapy for Low-Risk Ductal Carcinoma In Situ: The COMET Randomized Clinical Trial.

Journal Article JAMA · March 2025 ImportanceActive monitoring for low-risk ductal carcinoma in situ (DCIS) of the breast has been proposed as an alternative to guideline-concordant care, but the safety of this approach is unknown.ObjectiveTo compare rates of invasive canc ... Full text Cite

Genomic alterations are associated with response to aromatase inhibitor therapy for ER-positive postmenopausal ductal carcinoma in situ: (CALGB 40903, Alliance).

Journal Article Breast Cancer Res · February 20, 2025 PURPOSE: CALGB 40903 (Alliance) was a phase II single arm multicenter trial conducted in postmenopausal patients diagnosed with estrogen-receptor (ER) positive breast ductal carcinoma in situ (DCIS) without invasion. Patients were treated with the aromatas ... Full text Link to item Cite

Comorbid conditions and survival among Black women with ovarian cancer.

Journal Article Cancer · January 1, 2025 BACKGROUND: Black women with epithelial ovarian cancer (EOC) have worse survival and a higher burden of comorbid conditions compared with other racial groups. This study examines the association of comorbid conditions and medication use for these condition ... Full text Link to item Cite

The role of multiple mediation with contextual neighborhood measures in ovarian cancer survival.

Journal Article Ann Epidemiol · November 2024 BACKGROUND: Mediation by multiple agents can affect the relation between neighborhood deprivation and segregation indices and ovarian cancer survival. In this paper, we examine a variety of potential clinical mediators in the association between deprivatio ... Full text Link to item Cite

Diet and Survival in Black Women With Epithelial Ovarian Cancer.

Journal Article JAMA network open · October 2024 ImportanceOvarian cancer survival among Black women is the lowest across all racial and ethnic groups. Poor dietary quality also disproportionately affects Black populations, but its association with ovarian cancer survival in this population rema ... Full text Cite

Analysis of ductal carcinoma in situ by self-reported race reveals molecular differences related to outcome.

Journal Article Breast Cancer Res · September 2, 2024 BACKGROUND: Ductal carcinoma in situ (DCIS) is a non-obligate precursor to invasive breast cancer (IBC). Studies have indicated differences in DCIS outcome based on race or ethnicity, but molecular differences have not been investigated. METHODS: We examin ... Full text Link to item Cite

Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms.

Journal Article Cancer Epidemiol Biomarkers Prev · August 1, 2024 BACKGROUND: High-grade serous carcinoma (HGSC) gene expression subtypes are associated with differential survival. We characterized HGSC gene expression in Black individuals and considered whether gene expression differences by self-identified race may con ... Full text Link to item Cite

Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics.

Journal Article Int J Mol Sci · June 19, 2024 Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) ... Full text Link to item Cite

Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions.

Journal Article Am J Hum Genet · June 6, 2024 To identify credible causal risk variants (CCVs) associated with different histotypes of epithelial ovarian cancer (EOC), we performed genome-wide association analysis for 470,825 genotyped and 10,163,797 imputed SNPs in 25,981 EOC cases and 105,724 contro ... Full text Link to item Cite

Classification performance bias between training and test sets in a limited mammography dataset.

Journal Article PLoS One · 2024 OBJECTIVES: To assess the performance bias caused by sampling data into training and test sets in a mammography radiomics study. METHODS: Mammograms from 700 women were used to study upstaging of ductal carcinoma in situ. The dataset was repeatedly shuffle ... Full text Link to item Cite

The Association between Mediated Deprivation and Ovarian Cancer Survival among African American Women.

Journal Article Cancers (Basel) · October 4, 2023 BACKGROUND: Deprivation indices are often used to adjust for socio-economic disparities in health studies. Their role has been partially evaluated for certain population-level cancer outcomes, but examination of their role in ovarian cancer is limited. In ... Full text Link to item Cite

Ipsilateral Lesion Detection Refinement for Tomosynthesis.

Journal Article IEEE Trans Med Imaging · October 2023 Computer-aided detection (CAD) frameworks for breast cancer screening have been researched for several decades. Early adoption of deep-learning models in CAD frameworks has shown greatly improved detection performance compared to traditional CAD on single- ... Full text Link to item Cite

Deprivation and segregation in ovarian cancer survival among African American women: a mediation analysis.

Journal Article Ann Epidemiol · October 2023 PURPOSE: Deprivation and segregation indices are often examined as possible explanations for observed health disparities in population-based studies. In this study, we assessed the role of recognized deprivation and segregation indices specifically as they ... Full text Link to item Cite

Association of inflammation-related exposures and ovarian cancer survival in a multi-site cohort study of Black women.

Journal Article British journal of cancer · October 2023 BackgroundAn association was observed between an inflammation-related risk score (IRRS) and worse overall survival (OS) among a cohort of mostly White women with invasive epithelial ovarian cancer (EOC). Herein, we evaluated the association betwee ... Full text Cite

Archival single-cell genomics reveals persistent subclones during DCIS progression.

Journal Article Cell · August 2023 Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embed ... Full text Cite

Microcalcification crystallography as a potential marker of DCIS recurrence.

Journal Article Sci Rep · June 8, 2023 Ductal carcinoma in-situ (DCIS) accounts for 20-25% of all new breast cancer diagnoses. DCIS has an uncertain risk of progression to invasive breast cancer and a lack of predictive biomarkers may result in relatively high levels (~ 75%) of overtreatment. T ... Full text Link to item Cite

Survival of epithelial ovarian cancer in Black women: a society to cell approach in the African American cancer epidemiology study (AACES).

Journal Article Cancer Causes Control · March 2023 PURPOSE: The causes for the survival disparity among Black women with epithelial ovarian cancer (EOC) are likely multi-factorial. Here we describe the African American Cancer Epidemiology Study (AACES), the largest cohort of Black women with EOC. METHODS: ... Full text Link to item Cite

Anti-adhesive bioresorbable elastomer-coated composite hernia mesh that reduce intraperitoneal adhesions.

Journal Article Biomaterials · January 2023 Intraperitoneal adhesions (IAs) are a major complication arising from abdominal repair surgeries, including hernia repair procedures. Herein, we fabricated a composite mesh device using a macroporous monofilament polypropylene mesh and a degradable elastom ... Full text Link to item Cite

Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts.

Journal Article Cancer Cell · December 12, 2022 Ductal carcinoma in situ (DCIS) is the most common precursor of invasive breast cancer (IBC), with variable propensity for progression. We perform multiscale, integrated molecular profiling of DCIS with clinical outcomes by analyzing 774 DCIS samples from ... Full text Link to item Cite

Spatial interplay of tissue hypoxia and T-cell regulation in ductal carcinoma in situ.

Journal Article NPJ Breast Cancer · September 15, 2022 Hypoxia promotes aggressive tumor phenotypes and mediates the recruitment of suppressive T cells in invasive breast carcinomas. We investigated the role of hypoxia in relation to T-cell regulation in ductal carcinoma in situ (DCIS). We designed a deep lear ... Full text Link to item Cite

Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer.

Journal Article Nat Genet · June 2022 Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5-10%) of DCIS patients develop subsequent invasive disease. A fundamental biologic question is whether the invasive disease aris ... Full text Link to item Cite

Racial Differences in the Tumor Immune Landscape and Survival of Women with High-Grade Serous Ovarian Carcinoma.

Journal Article Cancer Epidemiol Biomarkers Prev · May 4, 2022 BACKGROUND: Tumor-infiltrating lymphocytes (TIL) confer a survival benefit among patients with ovarian cancer; however, little work has been conducted in racially diverse cohorts. METHODS: The current study investigated racial differences in the tumor immu ... Full text Link to item Cite

Anomaly Detection of Calcifications in Mammography Based on 11,000 Negative Cases.

Journal Article IEEE Trans Biomed Eng · May 2022 In mammography, calcifications are one of the most common signs of breast cancer. Detection of such lesions is an active area of research for computer-aided diagnosis and machine learning algorithms. Due to limited numbers of positive cases, many supervise ... Full text Link to item Cite

A multi-modal exploration of heterogeneous physico-chemical properties of DCIS breast microcalcifications.

Journal Article Analyst · April 11, 2022 Ductal carcinoma in situ (DCIS) is frequently associated with breast calcification. This study combines multiple analytical techniques to investigate the heterogeneity of these calcifications at the micrometre scale. X-ray diffraction, scanning electron mi ... Full text Link to item Cite

Prediction of Upstaging in Ductal Carcinoma in Situ Based on Mammographic Radiomic Features.

Journal Article Radiology · April 2022 Background Improving diagnosis of ductal carcinoma in situ (DCIS) before surgery is important in choosing optimal patient management strategies. However, patients may harbor occult invasive disease not detected until definitive surgery. Purpose To assess t ... Full text Cite

Polygenic risk modeling for prediction of epithelial ovarian cancer risk.

Journal Article European journal of human genetics : EJHG · March 2022 Polygenic risk scores (PRS) for epithelial ovarian cancer (EOC) have the potential to improve risk stratification. Joint estimation of Single Nucleotide Polymorphism (SNP) effects in models could improve predictive performance over standard approaches of P ... Full text Cite

Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma.

Journal Article Cell · January 20, 2022 Ductal carcinoma in situ (DCIS) is a pre-invasive lesion that is thought to be a precursor to invasive breast cancer (IBC). To understand the changes in the tumor microenvironment (TME) accompanying transition to IBC, we used multiplexed ion beam imaging b ... Full text Link to item Cite

Abstract PO-232: Racial differences in the tumor immune landscape and survival of high-grade serous ovarian carcinoma

Conference Cancer Epidemiology, Biomarkers & Prevention · January 1, 2022 AbstractA survival benefit has been consistently observed for tumor infiltrating lymphocytes (TILs) among ovarian cancer patients; however, prior studies consist of predominantly white women and little work ... Full text Cite

Automated Dcis Identification From Multiplex Immunohistochemistry Using Generative Adversarial Networks

Conference Proceedings - International Symposium on Biomedical Imaging · January 1, 2022 Ductal Carcinoma In Situ (DCIS) is a non-obligatory precursor of Invasive Breast Cancer. It is the most common mammographically detected breast cancer. Predicting DCIS progression to invasive ductal carcinoma is a major clinical challenge due to the lack o ... Full text Cite

DCIS AI-TIL: Ductal Carcinoma In Situ Tumour Infiltrating Lymphocyte Scoring Using Artificial Intelligence

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2022 Tumour infiltrating lymphocytes (TIL) influence the prognosis of Ductal carcinoma in situ (DCIS). Currently, manual assessment of TIL by expert pathologists is considered a gold standard. However, there are issues with a shortage of expert pathologists and ... Full text Cite

Genomic predictor can discriminate between high- and low-risk DCIS

Conference CANCER PREVENTION RESEARCH · 2022 Cite

Genomic predictor can discriminate between high- and low-risk DCIS

Conference CANCER PREVENTION RESEARCH · 2022 Cite

Unmasking the immune microecology of ductal carcinoma in situ with deep learning

Conference npj Breast Cancer · December 1, 2021 Despite increasing evidence supporting the clinical relevance of tumour infiltrating lymphocytes (TILs) in invasive breast cancer, TIL spatial variability within ductal carcinoma in situ (DCIS) samples and its association with progression are not well unde ... Full text Cite

Tumor-associated autoantibodies from mouse breast cancer models are found in serum of breast cancer patients

Journal Article npj Breast Cancer · December 1, 2021 B cell responses to tumor antigens occur early in breast tumors and may identify immunogenic drivers of tumorigenesis. Sixty-two candidate antigens were identified prior to palpable tumor development in TgMMTV-neu and C3(1)Tag transgenic mouse mammary tumo ... Full text Cite

A new method to accurately identify single nucleotide variants using small FFPE breast samples.

Journal Article Briefings in bioinformatics · November 2021 Most tissue collections of neoplasms are composed of formalin-fixed and paraffin-embedded (FFPE) excised tumor samples used for routine diagnostics. DNA sequencing is becoming increasingly important in cancer research and clinical management; however it is ... Full text Cite

Unmasking the immune microecology of ductal carcinoma in situ with deep learning.

Journal Article NPJ Breast Cancer · March 1, 2021 Despite increasing evidence supporting the clinical relevance of tumour infiltrating lymphocytes (TILs) in invasive breast cancer, TIL spatial variability within ductal carcinoma in situ (DCIS) samples and its association with progression are not well unde ... Full text Open Access Link to item Cite

Retina-Match: Ipsilateral Mammography Lesion Matching in a Single Shot Detection Pipeline

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2021 In mammography and tomosynthesis, radiologists use the geometric relationship of the four standard screening views to detect breast abnormalities. To date, computer aided detection methods focus on formulations based only on a single view. Recent multi-vie ... Full text Cite

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Journal Article Nat Commun · November 30, 2020 Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20128-w. ... Full text Link to item Cite

Abstract 2502: Genetic and functional heterogeneity of DCIS as predictors of invasive cancer

Conference Cancer Research · August 15, 2020 AbstractGenetic diversity both between and within individual tumors constitutes a challenge to personalized cancer medicine. Intra-tumor heterogeneity provides the genetic fuel for natural selection in clona ... Full text Cite

RIPK3 upregulation confers robust proliferation and collateral cystine-dependence on breast cancer recurrence.

Journal Article Cell Death Differ · July 2020 The molecular and genetic basis of tumor recurrence is complex and poorly understood. RIPK3 is a key effector in programmed necrotic cell death and, therefore, its expression is frequently suppressed in primary tumors. In a transcriptome profiling between ... Full text Link to item Cite

Prediction of Upstaged Ductal Carcinoma In Situ Using Forced Labeling and Domain Adaptation.

Journal Article IEEE Trans Biomed Eng · June 2020 OBJECTIVE: The goal of this study is to use adjunctive classes to improve a predictive model whose performance is limited by the common problems of small numbers of primary cases, high feature dimensionality, and poor class separability. Specifically, our ... Full text Link to item Cite

Phase II Single-Arm Study of Preoperative Letrozole for Estrogen Receptor-Positive Postmenopausal Ductal Carcinoma In Situ: CALGB 40903 (Alliance).

Journal Article J Clin Oncol · April 20, 2020 PURPOSE: Primary endocrine therapy for ductal carcinoma in situ (DCIS) as a potential alternative to surgery has been understudied. This trial explored the feasibility of a short-term course of letrozole and sought to determine whether treatment results in ... Full text Link to item Cite

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Journal Article Cell · April 16, 2020 Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial mu ... Full text Open Access Link to item Cite

Minimal barriers to invasion during human colorectal tumor growth.

Journal Article Nature communications · March 2020 Intra-tumoral heterogeneity (ITH) could represent clonal evolution where subclones with greater fitness confer more malignant phenotypes and invasion constitutes an evolutionary bottleneck. Alternatively, ITH could represent branching evolution with invasi ... Full text Cite

Abstract P1-21-07: The Patient-reported Outcomes after Routine Treatment of Atypical Lesions (PORTAL) study: Pain, psychosocial wellbeing, and quality of life among women undergoing guideline concordant care for DCIS vs. active surveillance for in situ and atypical lesions

Conference Cancer Research · February 15, 2020 AbstractBackground: Guideline-concordant care (GCC) for DCIS includes surgery, radiation, and endocrine treatment. Active surveillance (AS) is a strategy under study for management of low risk DCIS. The PORT ... Full text Cite

Abstract P2-10-18: Deciphering racial disparities in breast cancer collagen reorganization by targeted extracellular matrix proteomics

Conference Cancer Research · February 15, 2020 AbstractAlthough European American women have a higher incidence of breast cancer, African American women have higher mortality rates with increased occurrence of lethal cancers at a younger age. Breast dens ... Full text Cite

Pan-cancer analysis of whole genomes.

Journal Article Nature · February 2020 Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matchin ... Full text Link to item Cite

DNA methylation markers predict recurrence-free interval in triple-negative breast cancer.

Journal Article NPJ breast cancer · January 2020 We lack tools to risk-stratify triple-negative breast cancer (TNBC). Our goal was to develop molecular tools to predict disease recurrence. Methylation array analysis was performed on 110 samples treated by locoregional therapy obtained from institutional ... Full text Cite

Microcalcification localization and cluster detection using unsupervised convolutional autoencoders and structural similarity index

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2020 Detecting microcalcification clusters in mammograms is important to the diagnosis of breast diseases. Previous studies which mainly focused on supervised methods require abundant annotated training data but these data are usually hard to acquire. In this w ... Full text Cite

A multitask deep learning method in simultaneously predicting occult invasive disease in ductal carcinoma in-situ and segmenting microcalcifications in mammography

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2020 We proposed a two-branch multitask learning convolutional neural network to solve two different but related tasks at the same time. Our main task is to predict occult invasive disease in biopsy proven Ductal Carcinoma in-situ (DCIS), with an auxiliary task ... Full text Cite

The Lineage Determining Factor GRHL2 Collaborates with FOXA1 to Establish a Targetable Pathway in Endocrine Therapy-Resistant Breast Cancer.

Journal Article Cell reports · October 2019 Notwithstanding the positive clinical impact of endocrine therapies in estrogen receptor-alpha (ERα)-positive breast cancer, de novo and acquired resistance limits the therapeutic lifespan of existing drugs. Taking the position that resistance is nearly in ... Full text Cite

The Immune Landscape of Cancer.

Journal Article Immunity · August 20, 2019 Full text Link to item Cite

Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression.

Journal Article Nat Immunol · July 2019 How tumor cells genetically lose antigenicity and evade immune checkpoints remains largely elusive. We report that tissue-specific expression of the human long noncoding RNA LINK-A in mouse mammary glands initiates metastatic mammary gland tumors, which ph ... Full text Link to item Cite

Association of distant recurrence-free survival with algorithmically extracted MRI characteristics in breast cancer.

Journal Article J Magn Reson Imaging · June 2019 BACKGROUND: While important in diagnosis of breast cancer, the scientific assessment of the role of imaging in prognosis of outcomes and treatment planning is limited. PURPOSE: To evaluate the potential of using quantitative imaging variables for stratifyi ... Full text Link to item Cite

LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition.

Journal Article Cell Res · April 2019 Despite the structural conservation of PTEN with dual-specificity phosphatases, there have been no reports regarding the regulatory mechanisms that underlie this potential dual-phosphatase activity. Here, we report that K27-linked polyubiquitination of PTE ... Full text Link to item Cite

Abstract P3-06-12: Genetic heterogeneity of DCIS is a predictor of invasive cancer

Conference Cancer Research · February 15, 2019 AbstractBackground: Heterogeneity is a hallmark of human cancers that is apparent both between and within individual tumors. Intra-tumor heterogeneity provides the genetic fuel for natural selection in clona ... Full text Cite

Multivariate machine learning models for prediction of pathologic response to neoadjuvant therapy in breast cancer using MRI features: a study using an independent validation set.

Journal Article Breast Cancer Res Treat · January 2019 PURPOSE: To determine whether a multivariate machine learning-based model using computer-extracted features of pre-treatment dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) can predict pathologic complete response (pCR) to neoadjuvant therap ... Full text Link to item Cite

Synthesis and texture manipulation of screening mammograms using conditional generative adversarial network

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2019 Annotated data availability has always been a major limiting f actor for the development of algorithms in the field of computer aided diagnosis. The purpose of this study is to investigate the feasibility of using a conditional generative adversarial netwo ... Full text Cite

Malignant microcalcification clusters detection using unsupervised deep autoencoders

Journal Article Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2019 Detection and localization of microcalcification (MC) clusters are very important in mammography diagnosis. Supervised MC detectors require learning from extracted individual MCs and MC clusters. However, they are limited by number of datasets given that M ... Full text Cite

Multiview mammographic mass detection based on a single shot detection system

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2019 Detection of suspicious breast cancer lesion in screening mammography images is an important step for the downstream diagnosis the of breast cancer. A trained radiologist can usually take advantage of multi-view correlation of suspicious lesions to locate ... Full text Cite

Mask Embedding for Realistic High-Resolution Medical Image Synthesis

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2019 Generative Adversarial Networks (GANs) have found applications in natural image synthesis and begin to show promises generating synthetic medical images. In many cases, the ability to perform controlled image synthesis using masked priors such as shape and ... Full text Cite

Intra-tumor molecular heterogeneity in breast cancer: definitions of measures and association with distant recurrence-free survival.

Journal Article Breast Cancer Res Treat · November 2018 PURPOSE: The purpose of the study was to define quantitative measures of intra-tumor heterogeneity in breast cancer based on histopathology data gathered from multiple samples on individual patients and determine their association with distant recurrence-f ... Full text Link to item Cite

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer.

Journal Article Cell Rep · October 30, 2018 Hippo signaling has been recognized as a key tumor suppressor pathway. Here, we perform a comprehensive molecular characterization of 19 Hippo core genes in 9,125 tumor samples across 33 cancer types using multidimensional "omic" data from The Cancer Genom ... Full text Link to item Cite

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily.

Journal Article Cell Syst · October 24, 2018 We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and re ... Full text Link to item Cite

LncRNA CamK-A Regulates Ca2+-Signaling-Mediated Tumor Microenvironment Remodeling.

Journal Article Mol Cell · October 4, 2018 Cancer cells entail metabolic adaptation and microenvironmental remodeling to survive and progress. Both calcium (Ca2+) flux and Ca2+-dependent signaling play a crucial role in this process, although the underlying mechanism has yet to be elucidated. Throu ... Full text Link to item Cite

CircIRAK3 sponges miR-3607 to facilitate breast cancer metastasis.

Journal Article Cancer Lett · August 28, 2018 As a class of endogenous noncoding RNAs, circular RNAs (circRNAs) have been recently identified to regulate tumourigenesis and progression in multiple malignancies. However, the expression profiles and function of circRNAs in breast cancer metastasis are l ... Full text Link to item Cite

Expression of Long Noncoding RNA YIYA Promotes Glycolysis in Breast Cancer.

Journal Article Cancer Res · August 15, 2018 Long noncoding RNA (lncRNA) is yet to be linked to cancer metabolism. Here, we report that upregulation of the lncRNA LINC00538 (YIYA) promotes glycolysis, cell proliferation, and tumor growth in breast cancer. YIYA is associated with the cytosolic cyclin- ... Full text Link to item Cite

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Journal Article Cancer Cell · August 13, 2018 Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects alternative splicing events and tumor variants by reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more alte ... Full text Link to item Cite

Abstract 5318: High-grade serous ovarian cancer DNA methylation and survival in African-American women

Conference Cancer Research · July 1, 2018 AbstractOvarian cancer is the most lethal gynecologic cancer in the United States, and African-American (AA) women have the poorest outcomes compared to other racial/ethnic groups. Although several biomarker ... Full text Cite

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas.

Journal Article Cancer cell · April 2018 We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct regardless of cancer type and c ... Full text Cite

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

Journal Article Cell reports · April 2018 Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, includ ... Full text Cite

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.

Journal Article Cell reports · April 2018 Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling th ... Full text Cite

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Journal Article Cell reports · April 2018 Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation ra ... Full text Cite

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

Journal Article Cell · April 2018 The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we pr ... Full text Cite

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

Journal Article Cell · April 2018 We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chr ... Full text Cite

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

Journal Article Cell reports · April 2018 Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA t ... Full text Cite

Pathogenic Germline Variants in 10,389 Adult Cancers.

Journal Article Cell · April 2018 We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including ... Full text Cite

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers.

Journal Article Cell reports · April 2018 Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabo ... Full text Cite

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

Journal Article Cell reports · April 2018 This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recu ... Full text Cite

The Immune Landscape of Cancer.

Journal Article Immunity · April 2018 We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyt ... Full text Cite

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types.

Journal Article Cell reports · April 2018 Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atla ... Full text Cite

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Journal Article Cell reports · April 2018 Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these "hidden responders" may reveal responsive molecular states. We describe and evaluate a machine-le ... Full text Cite

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer.

Journal Article Cancer cell · April 2018 We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to the CpG island hypermethylation phenotype in cancer, we observed a recurrent hypomethylation of 1, ... Full text Cite

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.

Journal Article Cell · April 2018 The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 892 ... Full text Cite

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

Journal Article Cell · April 2018 Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tu ... Full text Cite

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Journal Article Cell · April 2018 Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one ... Full text Cite

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.

Journal Article Cell · April 2018 For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features represe ... Full text Cite

Genomic and Functional Approaches to Understanding Cancer Aneuploidy.

Journal Article Cancer cell · April 2018 Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of pro ... Full text Cite

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.

Journal Article Cancer cell · April 2018 We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We f ... Full text Cite

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Journal Article Cell · April 2018 Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analy ... Full text Cite

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types.

Journal Article Cell reports · April 2018 Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome ... Full text Cite

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Journal Article Cell reports · April 2018 For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creat ... Full text Cite

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.

Journal Article Cell reports · April 2018 DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heter ... Full text Cite

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas.

Journal Article Cell Syst · March 28, 2018 Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers is lacking. Using computational ... Full text Link to item Cite

Prediction of Occult Invasive Disease in Ductal Carcinoma in Situ Using Deep Learning Features.

Journal Article J Am Coll Radiol · March 2018 PURPOSE: The aim of this study was to determine whether deep features extracted from digital mammograms using a pretrained deep convolutional neural network are prognostic of occult invasive disease for patients with ductal carcinoma in situ (DCIS) on core ... Full text Link to item Cite

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.

Journal Article Cell systems · March 2018 The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Can ... Full text Cite

Learning better deep features for the prediction of occult invasive disease in ductal carcinoma in situ through transfer learning

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2018 Purpose: To determine whether domain transfer learning can improve the performance of deep features extracted from digital mammograms using a pre-trained deep convolutional neural network (CNN) in the prediction of occult invasive disease for patients with ... Full text Cite

Improving classification with forced labeling of other related classes: Application to prediction of upstaged ductal carcinoma in situ using mammographic features

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2018 Predicting whether ductal carcinoma in situ (DCIS) identified at core biopsy contains occult invasive disease is an import task since these "upstaged" cases will affect further treatment planning. Therefore, a prediction model that better classifies pure D ... Full text Cite

JAK2-binding long noncoding RNA promotes breast cancer brain metastasis.

Journal Article J Clin Invest · December 1, 2017 Conventional therapies for breast cancer brain metastases (BCBMs) have been largely ineffective because of chemoresistance and impermeability of the blood-brain barrier. A comprehensive understanding of the underlying mechanism that allows breast cancer ce ... Full text Link to item Cite

LncRNA wires up Hippo and Hedgehog signaling to reprogramme glucose metabolism.

Journal Article EMBO J · November 15, 2017 The Hippo pathway plays essential roles in organ size control and cancer prevention via restricting its downstream effector, Yes-associated protein (YAP). Previous studies have revealed an oncogenic function of YAP in reprogramming glucose metabolism, whil ... Full text Link to item Cite

Can algorithmically assessed MRI features predict which patients with a preoperative diagnosis of ductal carcinoma in situ are upstaged to invasive breast cancer?

Journal Article J Magn Reson Imaging · November 2017 PURPOSE: To assess the ability of algorithmically assessed magnetic resonance imaging (MRI) features to predict the likelihood of upstaging to invasive cancer in newly diagnosed ductal carcinoma in situ (DCIS). MATERIALS AND METHODS: We identified 131 pati ... Full text Link to item Cite

Can Occult Invasive Disease in Ductal Carcinoma In Situ Be Predicted Using Computer-extracted Mammographic Features?

Journal Article Acad Radiol · September 2017 RATIONALE AND OBJECTIVES: This study aimed to determine whether mammographic features assessed by radiologists and using computer algorithms are prognostic of occult invasive disease for patients showing ductal carcinoma in situ (DCIS) only in core biopsy. ... Full text Link to item Cite

Glycosylation of KEAP1 links nutrient sensing to redox stress signaling.

Journal Article EMBO J · August 1, 2017 O-GlcNAcylation is an essential, nutrient-sensitive post-translational modification, but its biochemical and phenotypic effects remain incompletely understood. To address this question, we investigated the global transcriptional response to perturbations i ... Full text Open Access Link to item Cite

The LINK-A lncRNA interacts with PtdIns(3,4,5)P3 to hyperactivate AKT and confer resistance to AKT inhibitors.

Journal Article Nat Cell Biol · March 2017 Phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P3 or PIP3) mediates signalling pathways as a second messenger in response to extracellular signals. Although primordial functions of phospholipids and RNAs have been hypothesized in the 'RNA world', p ... Full text Link to item Cite

Abstract P1-06-06: Evidence for tumor heterogeneity and clonal evolution during invasive progression of breast cancer

Conference Cancer Research · February 15, 2017 AbstractPurpose: Intratumoral heterogeneity is well recognized to be an important driver of treatment resistance and metastasis. We undertook this N of one study to measure the degree of heterogeneity in a s ... Full text Cite

Abstract P1-05-30: Genomic and microenvironmental intra-tumor heterogeneity in DCIS

Conference Cancer Research · February 15, 2017 AbstractIntra-tumor heterogeneity drives neoplastic progression by supplying the fuel for natural selection among neoplastic cells. It also complicates screening and treatment of neoplasms. We hypothesize th ... Full text Cite

Can BI-RADS features on mammography be used as a surrogate for expensive genomic testing in breast cancer patients?

Conference Proceedings of SPIE - The International Society for Optical Engineering · February 3, 2017 Cite

Algorithms for prediction of the Oncotype DX recurrence score using clinicopathologic data: a review and comparison using an independent dataset.

Journal Article Breast Cancer Res Treat · February 2017 PURPOSE: Given the potential savings in cost and resource utilization, several algorithms have been proposed to predict Oncotype DX recurrence score (ODX RS) using commonly acquired histopathologic variables. Although it is promising, additional independen ... Full text Link to item Cite

Prediction of occult invasive disease in ductal carcinoma in situ using computer-extracted mammographic features

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2017 Predicting the risk of occult invasive disease in ductal carcinoma in situ (DCIS) is an important task to help address the overdiagnosis and overtreatment problems associated with breast cancer. In this work, we investigated the feasibility of using comput ... Full text Cite

Can upstaging of ductal carcinoma in situ be predicted at biopsy by histologic and mammographic features?

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2017 Reducing the overdiagnosis and overtreatment associated with ductal carcinoma in situ (DCIS) requires accurate prediction of the invasive potential at cancer screening. In this work, we investigated the utility of pre-operative histologic and mammographic ... Full text Cite

Can BI-RADS features on mammography be used as a surrogate for expensive genomic testing in breast cancer patients?

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2017 Medical oncologists increasingly rely on expensive genomic analysis to stratify patients for different treatment. The genomic markers are able to divide patients into groups that behave differently in terms of tumor presentation, likelihood of metastatic s ... Full text Cite

PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS.

Journal Article J Med Genet · December 2016 BACKGROUND: The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk ... Full text Link to item Cite

Abstract 3407: Gene expression subtypes of high grade serous ovarian cancer in African American women

Conference Cancer Research · July 15, 2016 AbstractOvarian cancer accounts for 5% of cancer deaths and is the fifth leading cause of cancer death in women in the United States. While incidence is higher in European American (EA) than African American ... Full text Cite

Circulating Cancer-Associated Macrophage-Like Cells Differentiate Malignant Breast Cancer and Benign Breast Conditions.

Journal Article Cancer Epidemiol Biomarkers Prev · July 2016 BACKGROUND: Blood-based testing can be used as a noninvasive method to recover and analyze circulating tumor-derived cells for clinical use. Circulating cancer-associated macrophage-like cells (CAML) are specialized myeloid cells found in peripheral blood ... Full text Link to item Cite

Outcomes of Active Surveillance for Ductal Carcinoma in Situ: A Computational Risk Analysis.

Journal Article J Natl Cancer Inst · May 2016 BACKGROUND: Ductal carcinoma in situ (DCIS) is a noninvasive breast lesion with uncertain risk for invasive progression. Usual care (UC) for DCIS consists of treatment upon diagnosis, thus potentially overtreating patients with low propensity for progressi ... Full text Link to item Cite

Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

Journal Article Mol Syst Biol · March 10, 2016 The signaling events that drive familial breast cancer (FBC) risk remain poorly understood. While the majority of genomic studies have focused on genetic risk variants, known risk variants account for at most 30% of FBC cases. Considering that multiple gen ... Full text Link to item Cite

Abstract P4-09-16: A monoclonal antibody with exceptional specificity across major breast cancer subtypes

Conference Cancer Research · February 15, 2016 AbstractBackground: Breast cancer (BC) remains the second leading cause of cancer-related deaths for women in the United States and is recognized to be a heterogeneous disease. Advances in technologies such ... Full text Cite

Abstract P6-05-03: Genomic diversity of ductal carcinoma in situ (DCIS) as a driver of invasion and metastasis

Conference Cancer Research · February 15, 2016 AbstractBackground: Recent evidence indicates that breast cancers may have high levels of heterogeneity. Based on principles of tumor evolution, we are investigating whether DCIS with higher levels of intra- ... Full text Cite

The LINK-A lncRNA activates normoxic HIF1α signalling in triple-negative breast cancer.

Journal Article Nature cell biology · February 2016 Although long non-coding RNAs (lncRNAs) predominately reside in the nucleus and exert their functions in many biological processes, their potential involvement in cytoplasmic signal transduction remains unexplored. Here, we identify a cytoplasmic lncRNA, L ... Full text Cite

Common variants at the CHEK2 gene locus and risk of epithelial ovarian cancer.

Journal Article Carcinogenesis · November 2015 Genome-wide association studies have identified 20 genomic regions associated with risk of epithelial ovarian cancer (EOC), but many additional risk variants may exist. Here, we evaluated associations between common genetic variants [single nucleotide poly ... Full text Link to item Cite

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer.

Journal Article Cell · October 8, 2015 Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive breast cancer. Here, we comprehensively profiled 817 breast tumors, including 127 ILC, 490 ductal (IDC), and 88 mixed IDC/ILC. Besides E-cadherin loss, the best kn ... Full text Link to item Cite

Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion.

Journal Article Breast Cancer Res · September 17, 2015 INTRODUCTION: There are an estimated 60,000 new cases of ductal carcinoma in situ (DCIS) each year. A lack of understanding in DCIS pathobiology has led to overtreatment of more than half of patients. We profiled the temporal molecular changes during DCIS ... Full text Link to item Cite

Early detection of breast cancer using a unique tumor specific antibody

Conference JOURNAL OF CLINICAL ONCOLOGY · May 20, 2015 Link to item Cite

Construction and analysis of the NCI-EDRN breast cancer reference set for circulating markers of disease.

Journal Article Cancer Epidemiol Biomarkers Prev · February 2015 BACKGROUND: Many circulating biomarkers have been reported for the diagnosis of breast cancer, but few, if any, have undergone rigorous credentialing using prospective cohorts and blinded evaluation. METHODS: The NCI Early Detection Research Network (EDRN) ... Full text Link to item Cite

A joint analysis of metabolomics and genetics of breast cancer.

Journal Article Breast Cancer Res · August 5, 2014 INTRODUCTION: Remodeling of cellular metabolism appears to be a consequence and possibly a cause of oncogenic transformation in human cancers. Specific aspects of altered tumor metabolism may be amenable to therapeutic intervention and could be coordinated ... Full text Link to item Cite

Refining the role of BRCA1 in combating oxidative stress.

Journal Article Breast Cancer Res · December 5, 2013 The BRCA1 hereditary susceptibility gene has been studied in great depth, befitting its clear role in promoting basal type breast cancer and serous type ovarian (fallopian tube) cancer in women carrying germline mutations. The BRCA1 protein has long been i ... Full text Link to item Cite

Molecular signatures of epithelial ovarian cancer: analysis of associations with tumor characteristics and epidemiologic risk factors.

Journal Article Cancer Epidemiol Biomarkers Prev · October 2013 BACKGROUND: Six gene expression subtypes of invasive epithelial ovarian cancer were recently defined using microarrays by Tothill and colleagues. The Cancer Genome Atlas (TCGA) project subsequently replicated these subtypes and identified a signature predi ... Full text Link to item Cite

Vitamin D receptor (VDR) polymorphisms and risk of ovarian cancer in Caucasian and African American women.

Journal Article Gynecol Oncol · April 2013 OBJECTIVE: Polymorphisms in the vitamin D receptor (VDR) gene have been shown in some studies to be associated with the risk of epithelial ovarian cancer (EOC) in Caucasian women. There are no published reports among African Americans. METHODS: Case-contro ... Full text Link to item Cite

Oxidatively modified proteins as plasma biomarkers in breast cancer.

Journal Article Cancer Biomark · 2013 BACKGROUND: Post-translational protein modifications (PTMs) are increased in breast tumors. OBJECTIVE: We explored whether PTMs on proteins secreted by the breast could be detected in plasma and potentially used for the early detection of breast cancer. ME ... Full text Link to item Cite

Comprehensive molecular portraits of human breast tumours.

Journal Article Nature · October 4, 2012 We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights ... Full text Link to item Cite

Loss of ARID1A-associated protein expression is a frequent event in clear cell and endometrioid ovarian cancers.

Journal Article Int J Gynecol Cancer · January 2012 BACKGROUND: Inactivating somatic mutations in the ARID1A gene are described in a significant fraction of clear cell and endometrioid ovarian cancers leading to loss of the corresponding protein (BAF250a). Expression of BAF250a was examined in clear cell an ... Full text Link to item Cite

Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence.

Journal Article Cancer Res · October 1, 2011 To better understand the biology of hormone receptor-positive and-negative breast cancer and to identify methylated gene markers of disease progression, we carried out a genome-wide methylation array analysis on 103 primary invasive breast cancers and 21 n ... Full text Link to item Cite

Glutamine synthetase is a genetic determinant of cell type-specific glutamine independence in breast epithelia.

Journal Article PLoS Genet · August 2011 Although significant variations in the metabolic profiles exist among different cells, little is understood in terms of genetic regulations of such cell type-specific metabolic phenotypes and nutrient requirements. While many cancer cells depend on exogeno ... Full text Link to item Cite

The turnover of estrogen receptor α by the selective estrogen receptor degrader (SERD) fulvestrant is a saturable process that is not required for antagonist efficacy.

Journal Article Biochem Pharmacol · July 15, 2011 It has become apparent of late that even in tamoxifen and/or aromatase resistant breast cancers, ERα remains a bona fide therapeutic target. Not surprisingly, therefore, there has been considerable interest in developing Selective ER Degraders (SERDs), com ... Full text Link to item Cite

Plasma biomarker profiles differ depending on breast cancer subtype but RANTES is consistently increased.

Journal Article Cancer Epidemiol Biomarkers Prev · July 2011 BACKGROUND: Current biomarkers for breast cancer have little potential for detection. We determined whether breast cancer subtypes influence circulating protein biomarkers. METHODS: A sandwich ELISA microarray platform was used to evaluate 23 candidate bio ... Full text Link to item Cite

Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal features in HER2-related breast tumor subtypes.

Journal Article Breast Cancer Res · June 7, 2011 INTRODUCTION: Breast cancer heterogeneity occurs as a consequence of the dysregulation of numerous oncogenic pathways as well as many non-genetic factors, including tumor microenvironmental stresses such as hypoxia, lactic acidosis, and glucose deprivation ... Full text Link to item Cite

Regulator of G protein signaling 5 is highly expressed in parathyroid tumors and inhibits signaling by the calcium-sensing receptor.

Journal Article Mol Endocrinol · May 2011 The molecular mechanisms responsible for aberrant calcium signaling in parathyroid disease are poorly understood. The loss of appropriate calcium-responsive modulation of PTH secretion observed in parathyroid disease is commonly attributed to decreased exp ... Full text Link to item Cite

Abstract 3182: PTM ELISA microarray for breast cancer biomarker discovery

Conference Cancer Research · April 15, 2011 AbstractPost-translational modifications (PTMs) of proteins are known to be altered during breast cancer development. These PTMs are potentially useful biomarkers for breast cancer. In order to study the pot ... Full text Cite

Development of an ovarian cancer screening decision model that incorporates disease heterogeneity: implications for potential mortality reduction.

Journal Article Cancer · February 1, 2011 BACKGROUND: Pathologic and genetic data suggest that epithelial ovarian cancer may consist of indolent and aggressive phenotypes. The objective of the current study was to estimate the impact of a 2-phenotype paradigm of epithelial ovarian cancer on the mo ... Full text Link to item Cite

Methylation patterns in cell-free plasma DNA reflect removal of the primary tumor and drug treatment of breast cancer patients.

Journal Article Int J Cancer · January 15, 2011 Abnormal DNA methylation is a feature of most types of cancer, which is reflected in cell-free circulating DNA in plasma. It is, however, unknown whether surgical removal of the tumor and subsequent therapy induces changes in plasma DNA methylation, which ... Full text Link to item Cite

Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer.

Journal Article J Proteome Res · January 7, 2011 Cancer patients spontaneously generate autoantibodies (AAb) to tumor-derived proteins. To detect AAb, we have probed novel high-density custom protein microarrays (NAPPA) expressing 4988 candidate tumor antigens with sera from patients with early stage bre ... Full text Link to item Cite

Individual responses to chemotherapy-induced oxidative stress.

Journal Article Breast Cancer Res Treat · January 2011 Differences in redox homeostatic control between cancer patients may underlie predisposition to drug resistance and toxicities. To evaluate interindividual differences in redox response among newly diagnosed breast cancer patients undergoing standard chemo ... Full text Link to item Cite

Evaluation of established breast cancer risk factors as modifiers of BRCA1 or BRCA2: a multi-center case-only analysis.

Journal Article Breast Cancer Res Treat · November 2010 The incomplete penetrance of mutations in BRCA1 and BRCA2 suggests that some combination of environmental and genetic factors modifies the risk of breast cancer in mutation carriers. This study sought to identify possible interactions between established b ... Full text Link to item Cite

Severe obesity is associated with symptomatic presentation, higher parathyroid hormone levels, and increased gland weight in primary hyperparathyroidism.

Journal Article J Clin Endocrinol Metab · November 2010 CONTEXT: A relationship between primary hyperparathyroidism (PHPT) and obesity has been observed but is incompletely understood. Furthermore, obesity has been associated with vitamin D deficiency, suggesting that the three conditions may be linked. OBJECTI ... Full text Link to item Cite

Urinary biomarkers of oxidative status in a clinical model of oxidative assault.

Journal Article Cancer Epidemiol Biomarkers Prev · June 2010 BACKGROUND: We used doxorubicin-based chemotherapy as a clinical model of oxidative assault in humans. METHODS: The study recruited newly diagnosed breast cancer patients (n = 23). Urine samples were collected immediately before (T0) and at 1 hour (T1) and ... Full text Link to item Cite

Expression signatures of TP53 mutations in serous ovarian cancers.

Journal Article BMC Cancer · May 26, 2010 BACKGROUND: Mutations in the TP53 gene are extremely common and occur very early in the progression of serous ovarian cancers. Gene expression patterns that relate to mutational status may provide insight into the etiology and biology of the disease. METHO ... Full text Open Access Link to item Cite

Intratumor heterogeneity and precision of microarray-based predictors of breast cancer biology and clinical outcome.

Journal Article J Clin Oncol · May 1, 2010 PURPOSE: Identifying sources of variation in expression microarray data and the effect of variance in gene expression measurements on complex predictive and diagnostic models is essential when translating microarray-based experimental approaches into clini ... Full text Link to item Cite

Development of a multimarker assay for early detection of ovarian cancer.

Journal Article J Clin Oncol · May 1, 2010 PURPOSE: Early detection of ovarian cancer has great promise to improve clinical outcome. PATIENTS AND METHODS: Ninety-six serum biomarkers were analyzed in sera from healthy women and from patients with ovarian cancer, benign pelvic tumors, and breast, co ... Full text Link to item Cite

Improved staging in node-positive breast cancer patients using lymph node ratio: results in 1,788 patients with long-term follow-up.

Journal Article J Am Coll Surg · May 2010 BACKGROUND: Axillary lymph node status remains the most important prognostic factor in breast cancer. Established staging systems emphasize the absolute number of positive nodes, without regard for the total number of lymph nodes examined. We sought to con ... Full text Link to item Cite

Association between DNA damage response and repair genes and risk of invasive serous ovarian cancer.

Journal Article PLoS One · April 8, 2010 BACKGROUND: We analyzed the association between 53 genes related to DNA repair and p53-mediated damage response and serous ovarian cancer risk using case-control data from the North Carolina Ovarian Cancer Study (NCOCS), a population-based, case-control st ... Full text Open Access Link to item Cite

Ovarian cancer tumor infiltrating T-regulatory (T(reg)) cells are associated with a metastatic phenotype.

Journal Article Gynecol Oncol · March 2010 OBJECTIVE: The objective of this study was to examine the clinicopathologic correlates of T-regulatory (T(reg)) cell infiltration in serous ovarian cancers and to define gene signatures associated with high T(reg)s. METHODS: Tumor infiltrating T(reg) and c ... Full text Link to item Cite

An adenoviral vaccine encoding full-length inactivated human Her2 exhibits potent immunogenicty and enhanced therapeutic efficacy without oncogenicity.

Journal Article Clin Cancer Res · March 1, 2010 PURPOSE: Overexpression of the breast cancer oncogene HER2 correlates with poor survival. Current HER2-directed therapies confer limited clinical benefits and most patients experience progressive disease. Because refractory tumors remain strongly HER2+, va ... Full text Link to item Cite

Polymorphism in the GALNT1 gene and epithelial ovarian cancer in non-Hispanic white women: the Ovarian Cancer Association Consortium.

Journal Article Cancer Epidemiol Biomarkers Prev · February 2010 Aberrant glycosylation is a well-described hallmark of cancer. In a previous ovarian cancer case control study that examined polymorphisms in 26 glycosylation-associated genes, we found strong statistical evidence (P = 0.00017) that women who inherited two ... Full text Link to item Cite

Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care.

Journal Article Breast Cancer Res Treat · December 2009 Feasibility and reproducibility of microarray biomarkers in clinical settings are doubted because of reliance on fresh frozen tissue. We sought to develop and validate a paradigm of frozen tissue collection from early breast tumors to enable use of microar ... Full text Link to item Cite

IGF2R polymorphisms and risk of esophageal and gastric adenocarcinomas.

Journal Article Int J Cancer · December 1, 2009 The mannose-6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2R) encodes a protein that plays a critical role in tumor suppression, in part by modulating bioavailability of a potent mitogen, insulin-like growth factor-2 (IGF2). We tested the hypot ... Full text Link to item Cite

Markers of oxidative status in a clinical model of oxidative assault: a pilot study in human blood following doxorubicin administration.

Journal Article Biomarkers · August 2009 We used doxorubicin-based chemotherapy as a clinical model for oxidative assault. Study recruited 23 breast cancer patients and collected blood samples before (T0), at 1 (T1) and 24 hours (T24) after treatment administration. Measurements included protein ... Full text Link to item Cite

Predictors of variation in serum IGF1 and IGFBP3 levels in healthy African American and white men.

Journal Article J Natl Med Assoc · July 2009 BACKGROUND: Individual variation in circulating insulinlike growth factor-1 (IGF1) and its major binding protein, insulinlike growth factor binding protein-3 (IGFBP3), have been etiologically linked to several chronic diseases, including some cancers. Fact ... Full text Link to item Cite

Comparative genome-wide screening identifies a conserved doxorubicin repair network that is diploid specific in Saccharomyces cerevisiae.

Journal Article PLoS One · June 8, 2009 The chemotherapeutic doxorubicin (DOX) induces DNA double-strand break (DSB) damage. In order to identify conserved genes that mediate DOX resistance, we screened the Saccharomyces cerevisiae diploid deletion collection and identified 376 deletion strains ... Full text Link to item Cite

Do serum biomarkers really measure breast cancer?

Journal Article BMC Cancer · May 28, 2009 BACKGROUND: Because screening mammography for breast cancer is less effective for premenopausal women, we investigated the feasibility of a diagnostic blood test using serum proteins. METHODS: This study used a set of 98 serum proteins and chose diagnostic ... Full text Link to item Cite

Role of eotaxin-1 signaling in ovarian cancer.

Journal Article Clin Cancer Res · April 15, 2009 PURPOSE: Tumor cell growth and migration can be directly regulated by chemokines. In the present study, the association of CCL11 with ovarian cancer has been investigated. EXPERIMENTAL DESIGN AND RESULTS: Circulating levels of CCL11 in sera of patients wit ... Full text Link to item Cite

Microarray analysis of early stage serous ovarian cancers shows profiles predictive of favorable outcome.

Journal Article Clin Cancer Res · April 1, 2009 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 advan ... Full text Link to item Cite

Single nucleotide polymorphisms in the TP53 region and susceptibility to invasive epithelial ovarian cancer.

Journal Article Cancer Res · March 15, 2009 The p53 protein is critical for multiple cellular functions including cell growth and DNA repair. We assessed whether polymorphisms in the region encoding TP53 were associated with risk of invasive ovarian cancer. The study population includes a total of 5 ... Full text Link to item Cite

Inactivation of the MAL gene in breast cancer is a common event that predicts benefit from adjuvant chemotherapy.

Journal Article Mol Cancer Res · February 2009 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 ... Full text Link to item Cite

Epigenetic regulation of CD133 and tumorigenicity of CD133+ ovarian cancer cells.

Journal Article Oncogene · January 15, 2009 The cancer stem cell hypothesis posits that malignant growth arises from a rare population of progenitor cells within a tumor that provide it with unlimited regenerative capacity. Such cells also possess increased resistance to chemotherapeutic agents. Res ... Full text Link to item Cite

Her2/neu signaling blockade improves tumor oxygenation in a multifactorial fashion in Her2/neu+ tumors.

Journal Article Cancer Chemother Pharmacol · January 2009 PURPOSE: Tumor hypoxia reduces the efficacy of radiation and chemotherapy as well as altering gene expression that promotes cell survival and metastasis. The growth factor receptor, Her2/neu, is overexpressed in 25-30% of breast tumors. Tumors that are Her ... Full text Link to item Cite

Young age at diagnosis correlates with worse prognosis and defines a subset of breast cancers with shared patterns of gene expression.

Journal Article J Clin Oncol · July 10, 2008 PURPOSE: Breast cancer arising in young women is correlated with inferior survival and higher incidence of negative clinicopathologic features. The biology driving this aggressive disease has yet to be defined. PATIENTS AND METHODS: Clinically annotated, m ... Full text Link to item Cite

ISG15 as a novel tumor biomarker for drug sensitivity.

Journal Article Mol Cancer Ther · June 2008 Tumor cells are known to exhibit highly varied sensitivity to camptothecins (CPT; e.g., irinotecan and topotecan). However, the factors that determine CPT sensitivity/resistance are largely unknown. Recent studies have shown that the ubiquitin-like protein ... Full text Link to item Cite

Cyclin E overexpression in epithelial ovarian cancer characterizes an etiologic subgroup.

Journal Article Cancer Epidemiol Biomarkers Prev · March 2008 BACKGROUND: The objective of this study was to determine whether cyclin E overexpression defines an etiologically distinct subgroup of ovarian cancer. METHODS: We analyzed data from 538 epithelial ovarian cancer cases and 629 controls enrolled in a populat ... Full text Link to item Cite

Yeast screens identify the RNA polymerase II CTD and SPT5 as relevant targets of BRCA1 interaction.

Journal Article PLoS One · January 16, 2008 BRCA1 has been implicated in numerous DNA repair pathways that maintain genome integrity, however the function responsible for its tumor suppressor activity in breast cancer remains obscure. To identify the most highly conserved of the many BRCA1 functions ... Full text Open Access Link to item Cite

Age-specific differences in oncogenic pathway deregulation seen in human breast tumors.

Journal Article PLoS One · January 2, 2008 PURPOSE: To define the biology driving the aggressive nature of breast cancer arising in young women. EXPERIMENTAL DESIGN: Among 784 patients with early stage breast cancer, using prospectively-defined, age-specific cohorts (young or=6 ... Full text Open Access Link to item Cite

Serum biomarker profiles and response to neoadjuvant chemotherapy for locally advanced breast cancer.

Journal Article Breast Cancer Res · 2008 INTRODUCTION: Neoadjuvant chemotherapy has become the standard of care for the diverse population of women diagnosed with locally advanced breast cancer. Serum biomarker levels are increasingly being investigated for their ability to predict therapy respon ... Full text Link to item Cite

A clinicogenomic model to predict lymph node metastasis in breast cancer

Conference JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS · 2008 Full text Cite

Decision fusion of circulating markers for breast cancer detection in premenopausal women

Chapter · December 1, 2007 Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and co ... Full text Cite

Grade-specific prostate cancer associations of IGF1 (CA)19 repeats and IGFBP3-202A/C in blacks and whites.

Journal Article J Natl Med Assoc · July 2007 Carrying the cytosine-adenosine (CA)19 repeat polymorphism in insulin-like growth factor-1 (IGF1) is associated with lower serum proteins and decreased prostate cancer risk. Carrying the -202A/C genotype in insulin-like growth factor binding protein-3 (IGF ... Link to item Cite

Regulation of the metastasis suppressor gene MKK4 in ovarian cancer.

Journal Article Gynecol Oncol · May 2007 OBJECTIVES: MKK4 is a metastasis suppressor that is downregulated in some ovarian cancers. We sought to investigate whether promoter methylation, loss of heterozygosity, or changes in phosphorylation are involved in MKK4 dysregulation during ovarian carcin ... Full text Link to item Cite

Tagging single nucleotide polymorphisms in cell cycle control genes and susceptibility to invasive epithelial ovarian cancer.

Journal Article Cancer Res · April 1, 2007 High-risk susceptibility genes explain <40% of the excess risk of familial ovarian cancer. Therefore, other ovarian cancer susceptibility genes are likely to exist. We have used a single nucleotide polymorphism (SNP)-tagging approach to evaluate common var ... Full text Link to item Cite

Isogenic normal basal and luminal mammary epithelial isolated by a novel method show a differential response to ionizing radiation.

Journal Article Cancer Res · April 1, 2007 Epithelial cells within the normal breast duct seem to be the primary target for neoplastic transformation events that eventually produce breast cancer. Normal epithelial cells are easily isolated and propagated using standard techniques. However, these te ... Full text Link to item Cite

Trinucleotide repeat polymorphisms in the androgen receptor gene and risk of ovarian cancer.

Journal Article Cancer Epidemiol Biomarkers Prev · March 2007 INTRODUCTION: Androgens may play a role in the development of ovarian cancers. Two trinucleotide repeat polymorphisms have been described in exon 1 of the androgen receptor (AR) gene that may affect its function. Previous studies of ovarian cancer and AR r ... Full text Link to item Cite

An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer.

Other J Clin Oncol · February 10, 2007 PURPOSE: The purpose of this study was to develop an integrated genomic-based approach to personalized treatment of patients with advanced-stage ovarian cancer. We have used gene expression profiles to identify patients likely to be resistant to primary pl ... Full text Link to item Cite

Pooling of case specimens to create standard serum sets for screening cancer biomarkers.

Journal Article Cancer Epidemiol Biomarkers Prev · February 2007 BACKGROUND: Multiple identical sets of sera from cancer cases and controls would facilitate standardized testing of biomarkers. We describe the creation and use of standard serum sets developed from healthy donors and pooled sera from ovarian, breast, and ... Full text Link to item Cite

The type III TGF-beta receptor suppresses breast cancer progression.

Journal Article J Clin Invest · January 2007 The TGF-beta signaling pathway has a complex role in regulating mammary carcinogenesis. Here we demonstrate that the type III TGF-beta receptor (TbetaRIII, or betaglycan), a ubiquitously expressed TGF-beta coreceptor, regulated breast cancer progression an ... Full text Link to item Cite

Genomic signatures to guide the use of chemotherapeutics.

Other Nat Med · November 2006 Using in vitro drug sensitivity data coupled with Affymetrix microarray data, we developed gene expression signatures that predict sensitivity to individual chemotherapeutic drugs. Each signature was validated with response data from an independent set of ... Full text Link to item Cite

Maspin expression in epithelial ovarian cancer and associations with poor prognosis: a Gynecologic Oncology Group study.

Journal Article Gynecol Oncol · June 2006 OBJECTIVE: This study examined MASPIN expression in human ovarian cancer, and explored the association between MASPIN and prognosis in patients with advanced stage disease treated with first-line cisplatin, carboplatin and/or paclitaxel. METHODS: Frozen pr ... Full text Link to item Cite

Evaluation of expression based markers for the detection of breast cancer cells.

Journal Article Breast Cancer Res Treat · May 2006 INTRODUCTION: Genes that are expressed in a highly tissue- or disease-specific manner provide possible targets for therapeutics, early detection of cancer, and monitoring of disease burden during and after treatment. Further, genes of this type that code f ... Full text Link to item Cite

Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression.

Journal Article Cancer Res · April 15, 2006 To identify genetic changes involved in the progression of breast carcinoma, we did cDNA array comparative genomic hybridization (CGH) on a panel of breast tumors, including 10 ductal carcinoma in situ (DCIS), 18 invasive breast carcinomas, and two lymph n ... Full text Link to item Cite

Frequent IGF2/H19 domain epigenetic alterations and elevated IGF2 expression in epithelial ovarian cancer.

Journal Article Mol Cancer Res · April 2006 Overexpression of the imprinted insulin-like growth factor-II (IGF2) is a prominent characteristic of gynecologic malignancies. The purpose of this study was to determine whether IGF2 loss of imprinting (LOI), aberrant H19 expression, and/or epigenetic der ... Full text Link to item Cite

Enhanced sensitivity to cytochrome c-induced apoptosis mediated by PHAPI in breast cancer cells.

Journal Article Cancer Res · February 15, 2006 Apoptotic signaling defects both promote tumorigenesis and confound chemotherapy. Typically, chemotherapeutics stimulate cytochrome c release to the cytoplasm, thereby activating the apoptosome. Although cancer cells can be refractory to cytochrome c relea ... Full text Link to item Cite

Gene expression profiles of multiple breast cancer phenotypes and response to neoadjuvant chemotherapy.

Journal Article Clin Cancer Res · February 1, 2006 PURPOSE: Breast cancer is a heterogeneous disease, and markers for disease subtypes and therapy response remain poorly defined. For that reason, we employed a prospective neoadjuvant study in locally advanced breast cancer to identify molecular signatures ... Full text Link to item Cite

Oncogenic pathway signatures in human cancers as a guide to targeted therapies.

Journal Article Nature · January 19, 2006 The development of an oncogenic state is a complex process involving the accumulation of multiple independent mutations that lead to deregulation of cell signalling pathways central to the control of cell growth and cell fate. The ability to define cancer ... Full text Link to item Cite

High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer.

Journal Article Nucleic Acids Res · 2006 Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, wi ... Full text Link to item Cite

Analgesic drug use and risk of ovarian cancer.

Journal Article Epidemiology · January 2006 BACKGROUND: Previous epidemiologic research suggests that analgesic use may reduce the risk of ovarian cancer, although results are not consistent. METHODS: In a population-based, case-control study, we analyzed data from 586 ovarian cancer cases and 627 m ... Full text Link to item Cite

High expression of insulin-like growth factor binding protein-2 messenger RNA in epithelial ovarian cancers produces elevated preoperative serum levels.

Journal Article Int J Gynecol Cancer · 2006 The molecular etiology of epithelial ovarian cancer remains unclear. Using microarray expression analysis, we recently reported that expression of the insulin-like growth factor binding protein-2 (IGFBP-2) gene is elevated in advanced epithelial ovarian ca ... Full text Link to item Cite

Identification of genes associated with ovarian cancer metastasis using microarray expression analysis.

Journal Article Int J Gynecol Cancer · 2006 Although the transition from early- to advanced-stage ovarian cancer is a critical determinant of survival, little is known about the molecular underpinnings of ovarian metastasis. We hypothesize that microarray analysis of global gene expression patterns ... Full text Link to item Cite

Associations between drug metabolism genotype, chemotherapy pharmacokinetics, and overall survival in patients with breast cancer.

Journal Article J Clin Oncol · September 1, 2005 PURPOSE: To evaluate associations between patient survival, pharmacokinetics, and drug metabolism-related genetic polymorphisms in patients receiving a combination chemotherapy regimen for breast cancer. PATIENTS AND METHODS: A genotype association study w ... Full text Link to item Cite

Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers.

Journal Article Clin Cancer Res · May 15, 2005 PURPOSE: A better understanding of the underlying biology of invasive serous ovarian cancer is critical for the development of early detection strategies and new therapeutics. The objective of this study was to define gene expression patterns associated wi ... Full text Link to item Cite

Transforming growth factor beta receptor I polyalanine repeat polymorphism does not increase ovarian cancer risk.

Journal Article Gynecol Oncol · May 2005 OBJECTIVES: It has been suggested that the 6A allele of the type I TGFbeta receptor (TGFbetaR1) polyalanine repeat tract polymorphism may increase susceptibility to various types of cancer including ovarian cancer. METHODS: The TGFbetaR1 polyalanine polymo ... Full text Link to item Cite

Analysis of methylation-sensitive transcriptome identifies GADD45a as a frequently methylated gene in breast cancer.

Journal Article Oncogene · April 14, 2005 Treatment of the breast cancer cell line, MDAMB468 with the DNA methylation inhibitor, 5-azacytidine (5-AzaC) results in growth arrest, whereas the growth of the normal breast epithelial line DU99 (telomerase immortalized) is relatively unaffected. Compari ... Full text Link to item Cite

High insulin-like growth factor-2 (IGF-2) gene expression is an independent predictor of poor survival for patients with advanced stage serous epithelial ovarian cancer.

Journal Article Gynecol Oncol · February 2005 OBJECTIVE: Epithelial ovarian cancer is the deadliest gynecologic malignancy, yet its molecular etiology remains poorly understood. Evidence is accumulating to support a role for the insulin-like growth factor family in human carcinogenesis, and recently u ... Full text Link to item Cite

IGF1 (CA)19 repeat and IGFBP3 -202 A/C genotypes and the risk of prostate cancer in Black and White men.

Journal Article Cancer Epidemiol Biomarkers Prev · February 2005 We investigated the relationship between the insulin-like growth factor-1 (IGF1) cytosine-adenine repeat (CA)(19) polymorphism located upstream of the gene's transcription start site, the insulin-like growth factor binding protein-3 (IGFBP3) -202 A/C promo ... Full text Link to item Cite

Progesterone receptor promoter +331A polymorphism is associated with a reduced risk of endometrioid and clear cell ovarian cancers.

Journal Article Cancer Epidemiol Biomarkers Prev · December 2004 OBJECTIVE: The progestagenic milieu of pregnancy and oral contraceptive use is protective against epithelial ovarian cancer. A functional single nucleotide polymorphism in the promoter of the progesterone receptor (+331A) alters the relative abundance of t ... Link to item Cite

Gene expression signature characterizing cyclin E protein overexpression in primary breast tumors

Conference JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS · September 1, 2004 Link to item Cite

TAFII70 isoform-specific growth suppression correlates with its ability to complex with the GADD45a protein.

Journal Article Mol Cancer Res · August 2004 TAFII70, a member of the basal transcription complex implicated in p53-mediated transcription, is synthesized as several alternately spliced variants. The predominant forms found in normal and neoplastic breast epithelial cells are shown to be 72 kDa (TAFI ... Link to item Cite

Treatment of intracerebral neoplasia and neoplastic meningitis with regional delivery of oncolytic recombinant poliovirus.

Journal Article Clin Cancer Res · July 15, 2004 PURPOSE: Spread to the central nervous system (CNS) and the leptomeninges is a frequent complication of systemic cancers that is associated with serious morbidity and high mortality. We have evaluated a novel therapeutic approach against CNS complications ... Full text Link to item Cite

Acquired expression of periostin by human breast cancers promotes tumor angiogenesis through up-regulation of vascular endothelial growth factor receptor 2 expression.

Journal Article Mol Cell Biol · May 2004 The late stages of human breast cancer development are poorly understood complex processes associated with the expression of genes by cancers that promote specific tumorigenic activities, such as angiogenesis. Here, we describe the identification of perios ... Full text Link to item Cite

Estrogen receptor alpha (ESR1) mutant A908G is not a common feature in benign and malignant proliferations of the breast.

Journal Article Genes Chromosomes Cancer · May 2004 Alterations in estrogen responsive pathways are thought to contribute to benign and malignant breast disease. It has been reported previously that more than a third of typical epithelial hyperplasia lesions harbor the missense mutation A908G in the estroge ... Full text Link to item Cite

Cell cycle progression in G1 and S phases is CCR4 dependent following ionizing radiation or replication stress in Saccharomyces cerevisiae.

Journal Article Eukaryot Cell · April 2004 To identify new nonessential genes that affect genome integrity, we completed a screening for diploid mutant Saccharomyces cerevisiae strains that are sensitive to ionizing radiation (IR) and found 62 new genes that confer resistance. Along with those prev ... Full text Link to item Cite

Prediction of optimal versus suboptimal cytoreduction of advanced-stage serous ovarian cancer with the use of microarrays.

Journal Article Am J Obstet Gynecol · April 2004 OBJECTIVE: The purpose of this study was to define gene expression patterns that are associated with the optimal versus suboptimal debulking of advanced-stage serous ovarian cancers. STUDY DESIGN: RNA from 44 advanced serous ovarian cancers (19 optimal, 25 ... Full text Link to item Cite

Gene expression patterns that characterize advanced stage serous ovarian cancers.

Journal Article J Soc Gynecol Investig · January 2004 OBJECTIVE: To identify gene expression patterns that characterize advanced stage serous ovarian cancers by using microarray expression analysis. METHODS: Using genome-wide expression analysis, we compared a series of 31 advanced stage (III or IV) serous ov ... Full text Link to item Cite

Polymorphisms in BRCA1 and BRCA2 and risk of epithelial ovarian cancer.

Journal Article Clin Cancer Res · October 1, 2003 PURPOSE: Because inherited BRCA1 or BRCA2 mutations strikingly increase ovarian cancer risk, polymorphisms in these genes could represent low penetrance susceptibility alleles. Previous studies of the BRCA2 N372H polymorphism suggested that HH homozygotes ... Link to item Cite

A neural survival factor is a candidate oncogene in breast cancer.

Journal Article Proc Natl Acad Sci U S A · September 16, 2003 Using serial analysis of gene expression (SAGE), we identified a SAGE tag that was present only in invasive breast carcinomas and their lymph node metastases. The transcript corresponding to this SAGE tag, dermcidin (DCD), encodes a secreted protein normal ... Full text Link to item Cite

Matrix metalloproteinase-1 gene promoter polymorphism and risk of ovarian cancer.

Journal Article J Soc Gynecol Investig · September 2003 OBJECTIVE: It has been suggested that the 2G allele of a guanine insertion-deletion promoter polymorphism in the promoter of the matrix metalloproteinase-1 (MMP1) gene may increase susceptibility to ovarian cancer. The 2G allele also has been associated wi ... Full text Link to item Cite

Neoadjuvant comparisons of aromatase inhibitors and tamoxifen: pretreatment determinants of response and on-treatment effect.

Journal Article J Steroid Biochem Mol Biol · September 2003 Adjuvant endocrine therapy reduces the risk of relapse and death from early stage hormone receptor positive breast cancer. However, tamoxifen is only partially effective because of the development of tumor resistance. Aromatase inhibitors (letrozole, anast ... Full text Link to item Cite

Dhh1 regulates the G1/S-checkpoint following DNA damage or BRCA1 expression in yeast.

Journal Article J Surg Res · July 2003 BACKGROUND: Heterologous expression of the tumor suppressor BRCA1 in the yeast Saccharomyces cerevisiae is lethal. To identify potential new BRCA1-interacting gene targets, we characterized highly conserved ionizing radiation (IR) sensitive gene deletions ... Full text Link to item Cite

Genomic amplification and oncogenic properties of the KCNK9 potassium channel gene.

Journal Article Cancer Cell · March 2003 Representational difference analysis (RDA) of human breast cancer was used to discover a novel amplicon located at chromosomal region 8q24.3. We examined a series of breast cancer samples harboring amplification of this region and determined that KCNK9 is ... Full text Link to item Cite

Molecular markers in ductal carcinoma in situ of the breast.

Journal Article Mol Cancer Res · March 2003 Gene expression patterns in ductal carcinoma in situ (DCIS), and in invasive, and metastatic breast tumors were determined using serial analysis of gene expression (SAGE). We used mRNA in situ hybridization to examine gene expression at the cellular level ... Link to item Cite

High expression of tumor necrosis factor-related apoptosis-inducing ligand is associated with favorable ovarian cancer survival.

Journal Article Clin Cancer Res · February 2003 PURPOSE: The molecular determinants of survival in ovarian cancer are poorly understood. Using expression microarrays, we recently found that high expression of the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) gene is associated with pro ... Link to item Cite

BRCA2 monoclonal antibodies react with differentiating epithelium.

Journal Article Hybrid Hybridomics · August 2002 The BRCA2 gene has previously been suggested to play a role in proliferation and DNA repair. Germline mutations in the BRCA2 gene predispose individuals to early onset, hereditary breast cancer. To better understand the expression pattern and function of t ... Full text Link to item Cite

Oncogenic properties of PPM1D located within a breast cancer amplification epicenter at 17q23.

Journal Article Nat Genet · June 2002 Featured Publication We found that PPM1D, encoding a serine/threonine protein phosphatase, lies within an epicenter of the region at 17q23 that is amplified in breast cancer. We show that overexpression of this gene confers two oncogenic phenotypes on cells in culture: attenua ... Full text Link to item Cite

Prediction and uncertainty in the analysis of gene expression profiles.

Journal Article In Silico Biol · 2002 We have developed a complete statistical model for the analysis of tumor specific gene expression profiles. The approach provides investigators with a global overview on large scale gene expression data, indicating aspects of the data that relate to tumor ... Link to item Cite

Loss of expression of the p16 tumor suppressor gene is more frequent in advanced ovarian cancers lacking p53 mutations.

Journal Article Gynecol Oncol · December 2001 OBJECTIVE: The aim of this study was to test the hypothesis that p53 mutations are less frequent in ovarian cancers with alterations in other genes that regulate G1 progression. METHODS: Expression of G1 stimulatory (cyclins D1 and E, cdk4, Ki67) and inhib ... Full text Link to item Cite

Predicting the clinical status of human breast cancer by using gene expression profiles.

Journal Article Proc Natl Acad Sci U S A · September 25, 2001 Featured Publication Prognostic and predictive factors are indispensable tools in the treatment of patients with neoplastic disease. For the most part, such factors rely on a few specific cell surface, histological, or gross pathologic features. Gene expression assays have the ... Full text Link to item Cite

HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells.

Journal Article Proc Natl Acad Sci U S A · August 14, 2001 To identify molecular alterations implicated in the initiating steps of breast tumorogenesis, we compared the gene expression profiles of normal and ductal carcinoma in situ (DCIS) mammary epithelial cells by using serial analysis of gene expression (SAGE) ... Full text Link to item Cite

A SAGE (serial analysis of gene expression) view of breast tumor progression.

Journal Article Cancer Res · August 1, 2001 To identify molecular alterations involved in the initiation and progression of breast carcinomas, we analyzed the global gene expression profiles of normal mammary epithelial cells and in situ, invasive, and metastatic breast carcinomas using serial analy ... Link to item Cite

Prognostic significance of the number of lymph nodes examined in patients with lymph node-negative breast carcinoma.

Journal Article Cancer · June 15, 2001 BACKGROUND: A recent report suggested that the number of lymph nodes examined was a strong predictor of survival in patients with lymph node-negative breast carcinoma. Among women who had >or= 20 lymph nodes examined, the risk of dying from breast carcinom ... Link to item Cite

Hypermethylation of 14-3-3 sigma (stratifin) is an early event in breast cancer.

Journal Article Oncogene · June 7, 2001 We have identified 14-3-3 sigma (sigma) as a gene whose expression is lost in breast carcinomas, primarily by methylation-mediated silencing. In this report, we investigated the timing of loss of sigma gene expression during breast tumorigenesis in vivo. W ... Full text Link to item Cite

Loss of cyclin D2 expression in the majority of breast cancers is associated with promoter hypermethylation.

Journal Article Cancer Res · March 15, 2001 Cyclin D2 is a member of the D-type cyclins, implicated in cell cycle regulation, differentiation, and malignant transformation. It was noted previously that cyclin D2 is not expressed in the majority of breast cancer cell lines, whereas abundant expressio ... Link to item Cite

Relationship between expression of coactivators and corepressors of hormone receptors and resistance of ovarian cancers to growth regulation by steroid hormones.

Journal Article J Soc Gynecol Investig · 2001 OBJECTIVE: To determine whether aberrant expression of hormone receptor corepressors or coactivators or defects in estrogen receptor-mediated transcription might underlie resistance of ovarian cancers to hormonal therapy. METHODS: Northern analysis, Wester ... Link to item Cite

Phenol sulfotransferases: hormonal regulation, polymorphism, and age of onset of breast cancer.

Journal Article Cancer Res · December 15, 2000 In recent years, significant effort has been made to identify genes that influence breast cancer risk. Because the high-penetrance breast cancer susceptibility genes BRCA1 and 2 play a role only in a small fraction of breast cancer cases, understanding the ... Link to item Cite

Estrogen-induced mitogenesis of MCF-7 cells does not require the induction of mitogen-activated protein kinase activity.

Journal Article J Steroid Biochem Mol Biol · December 1, 2000 Featured Publication Estrogen mediates the transcription of responsive genes via its interaction with the estrogen receptor (ER). This ligand-dependent transcriptional activity has been the mechanistic basis for understanding estrogen-induced proliferation. However, recent rep ... Full text Link to item Cite

Compromised HOXA5 function can limit p53 expression in human breast tumours.

Journal Article Nature · June 22, 2000 Expression of the p53 gene protects cells against malignant transformation. Whereas control of p53 degradation has been a subject of intense scrutiny, little is known about the factors that regulate p53 synthesis. Here we show that p53 messenger RNA levels ... Full text Link to item Cite

High frequency of hypermethylation at the 14-3-3 sigma locus leads to gene silencing in breast cancer.

Journal Article Proc Natl Acad Sci U S A · May 23, 2000 Expression of 14-3-3 final sigma (final sigma) is induced in response to DNA damage, and causes cells to arrest in G(2). By SAGE (serial analysis of gene expression) analysis, we identified final sigma as a gene whose expression is 7-fold lower in breast c ... Full text Link to item Cite

Inhibition of mitogen-activated protein kinase and phosphatidylinositol 3-kinase activity in MCF-7 cells prevents estrogen-induced mitogenesis.

Journal Article Cell Growth Differ · February 2000 Featured Publication Estrogen acts to promote DNA synthesis in the MCF-7 human breast cancer cell line via its interaction with high levels of estrogen receptor. The primary mode of estrogen action has been considered to be through transcriptional activation of genes containin ... Link to item Cite

Relationship between alterations in the p53 gene and chemosensitivity of ovarian cancers

Other CME Journal of Gynecologic Oncology · December 1, 1999 It is thought that the cytotoxic effect of chemotherapy drugs is largely due to their ability to initiate programmed cell death (apoptosis). Although the molecular pathways involved in regulation of apoptosis have not been completely elucidated, it has bee ... Cite

Isolation and initial characterization of the BRCA2 promoter.

Journal Article Oncogene · October 28, 1999 Featured Publication The hereditary breast cancer susceptibility gene, BRCA2, is considered to be a tumor suppressor gene that may be involved in the cellular response to DNA damage. The transcript for this gene is cell cycle regulated with mRNA levels reaching a peak just bef ... Full text Link to item Cite

Telomerase activity and prognosis in primary breast cancers.

Journal Article J Clin Oncol · October 1999 PURPOSE: Recent studies associate telomerase activity with prognostic factors and survival. We compared quantitative telomerase activity in primary tumors with traditional prognostic factors and outcome in a group of invasive but nonmetastatic breast cance ... Full text Link to item Cite

Bcl10 is not a target for frequent mutation in human carcinomas.

Journal Article Br J Cancer · July 1999 The recently described Bcl10 gene has been suggested to be a major target gene for inactivation in a variety of human cancers. In order to further evaluate the role of this gene in human adult malignancies, we have analysed a series of carcinomas for mutat ... Full text Link to item Cite

Telomerase activity in ductal carcinoma in situ and invasive breast cancer.

Journal Article Oncogene · June 3, 1999 The increasing number of breast carcinoma in situ detected by screening procedures makes it imperative to develop improved markers to stratify the risk of invasive cancer. Telomerase is detectable in invasive cancer, but not in normal tissues. We have micr ... Full text Link to item Cite

Co-expression of p53 by epithelial and stromal elements in carcinosarcoma of the female genital tract: an immunohistochemical study of 19 cases.

Journal Article Int J Gynecol Cancer · March 1999 Carcinosarcoma is an aggressive neoplasm of the female genital tract, which comprises 1-2% of malignancies of the uterine corpus. Because of the broad range of differentiation exhibited by these tumors, the precise nature of the relationship between epithe ... Full text Link to item Cite

Multiple DNA repair mechanisms and alkylator resistance in the human medulloblastoma cell line D-283 Med (4-HCR).

Journal Article Cancer Chemother Pharmacol · 1999 PURPOSE: We have previously reported preferential repair of DNA interstrand crosslinks in the 4-hydroperoxycyclophosphamide-resistant human medulloblastoma cell line D-283 Med (4-HCR). We now report further studies that explored the potential mechanisms un ... Full text Link to item Cite

Repression of interleukin-2 mRNA translation in primary human breast carcinoma tumor-infiltrating lymphocytes.

Journal Article Cell Immunol · December 15, 1998 Human breast carcinoma tumor-infiltrating lymphocytes (TIL) express activation antigens in situ indicative of ongoing immune response-CD28, CD45RO, CD69, CD71, and DR. However, interleukin 2 (IL-2) receptor was poorly expressed: CD25 was detected in only 1 ... Full text Link to item Cite

Frequency of germline and somatic BRCA1 mutations in ovarian cancer.

Journal Article Clin Cancer Res · October 1998 Featured Publication Germline mutations in the BRCA1 tumor suppressor gene are thought to be the most common cause of hereditary ovarian cancer. The aim of this study was to explore further the role of BRCA1 alterations in the development of ovarian cancers. We sought to deter ... Link to item Cite

Repression of IL-2 mRNA translation in primary human breast cancer tumor infiltrating lymphocytes

Conference FASEB Journal · March 20, 1998 Tumor infiltrating lymphocytes (TIL) are abundant in primary human carcinomas but display diminished proliferative response to TCR ligation in vitro. We demonstrate by immunocytochemistry analysis that breast carcinoma TII. express both early and late cell ... Cite

Predicting response to adjuvant and radiation therapy in patients with early stage breast carcinoma.

Journal Article Cancer · March 1, 1998 Featured Publication BACKGROUND: Screening and surveillance is increasing the detection of early stage breast carcinoma. The ability to predict accurately the response to adjuvant therapy (chemotherapy or tamoxifen therapy) or postlumpectomy radiation therapy in these patients ... Full text Link to item Cite

Aberrant splicing of the TSG101 tumor suppressor gene in human breast and ovarian cancers.

Journal Article J Soc Gynecol Investig · 1998 OBJECTIVE: To determine whether large deletions or other alterations in the putative tumor suppressor gene TSG101 play a role in the molecular pathogenesis of breast and ovarian cancers. METHODS: Expression of TSG101 transcripts was examined in breast and ... Full text Link to item Cite

Complex response of breast epithelial cell lines to topoisomerase inhibitors.

Journal Article Anticancer Res · 1998 The topoisomerase inhibitors, camptothecin and etoposide target the activity of topoisomerase I and II respectively. These agents, or their analogues, are undergoing clinical trials for the treatment of metastatic breast cancer. In this study, we examined ... Link to item Cite

Expression of Tie2/Tek in breast tumour vasculature provides a new marker for evaluation of tumour angiogenesis.

Journal Article Br J Cancer · 1998 Endothelial receptor tyrosine kinases may play important roles in pathological vascular growth, particularly in tumours. In this study, immunohistochemistry was used to evaluate the expression of a novel endothelial receptor tyrosine kinase, Tie2/Tek, in t ... Full text Link to item Cite

Artificial neural networks improve the accuracy of cancer survival prediction.

Journal Article Cancer · February 15, 1997 BACKGROUND: The TNM staging system originated as a response to the need for an accurate, consistent, universal cancer outcome prediction system. Since the TNM staging system was introduced in the 1950s, new prognostic factors have been identified and new m ... Full text Link to item Cite

BRCA1 expression is not directly responsive to estrogen.

Journal Article Oncogene · January 9, 1997 Featured Publication Expression of the breast cancer susceptibility gene, BRCA1, is induced by 17-beta estradiol (E2) in estrogen receptor containing breast cancer cell lines. Our previous studies have shown that BRCA1 transcription is also regulated with the cell cycle, reach ... Full text Link to item Cite

Tissue transglutaminase is associated with the neovasculature and extracellular matrix of human breast cancer

Conference FASEB Journal · December 1, 1996 Tissue transglutaminase (tTG) is a calcium-dependent enzyme that catalyzes intermolecular covalent bonds. This protein cross-linking activity of tTG stabilizes the extracellular matrix (ECM) by making it resistant proteolytic degradation. Since angiogenesi ... Cite

Inhibition of the erbB-2 tyrosine kinase receptor in breast cancer cells by phosphoromonothioate and phosphorodithioate antisense oligonucleotides.

Journal Article Nucleic Acids Res · November 15, 1996 Antisense activity against erbB-2 of a variety of sulfur-modified oligonucleotides was examined in a breast cancer cell line which overexpresses this oncogene. Using a 15 base anti-erbB-2 sequence previously shown to be effective, various backbone configur ... Full text Link to item Cite

Tissue transglutaminase expression in human breast cancer.

Journal Article Lab Invest · November 1996 Tissue transglutaminase (tTG) is postulated to play a role in apoptosis, cell adhesion, metastasis, and extracellular matrix (ECM) assembly. In this study, the distribution and expression of tissue transglutaminase was investigated in normal human mammary ... Link to item Cite

Microsomal epoxide hydrolase polymorphism as a risk factor for ovarian cancer.

Journal Article Mol Carcinog · November 1996 Microsomal epoxide hydrolase (EPHX) is one of many enzymes involved in the metabolism of endogenous and exogenous toxicants. Polymorphic forms of the human EPHX gene have been described that vary in enzymatic activity, and one, Tyr113His, has been associat ... Full text Link to item Cite

p53 overexpression in advanced-stage endometrial adenocarcinoma.

Journal Article Am J Obstet Gynecol · November 1996 OBJECTIVES: Mutation and overexpression of the p53 tumor suppressor gene in endometrial cancers are associated with advanced stage and poor survival. We sought to determine whether p53 overexpression is an independent variable predictive of poor prognosis ... Full text Link to item Cite

Cell cycle control of BRCA2.

Journal Article Cancer Res · October 15, 1996 Identifying the conditions and kinetics of the induction of BRCA2 gene expression may implicate roles for the function of the tumor suppressor gene. In this study, expression of BRCA2 mRNA is shown to be regulated by the cell cycle and associated with prol ... Link to item Cite

Dominance of wild-type p53-mediated transcriptional activation in breast epithelial cells.

Journal Article Oncogene · September 19, 1996 The p53 gene is a recessive oncogene whose loss of function can result in cell transformation. Approximately 25% of human breast cancers contain missense mutations in one p53 allele, leading to inactivation of the mutated protein. In almost all of these ca ... Link to item Cite

Relationship between p21 expression and mutation of the p53 tumor suppressor gene in normal and malignant ovarian epithelial cells.

Journal Article Clin Cancer Res · September 1996 In many cell types, p53-mediated growth inhibition is dependent on induction of p21, which is an inhibitor of cyclin-dependent kinases that are required for cell cycle progression. Failure of mutant p53 proteins to transactivate p21 may lead to uncontrolle ... Link to item Cite

BRCA1 expression is induced before DNA synthesis in both normal and tumor-derived breast cells.

Journal Article Cell Growth Differ · June 1996 Featured Publication Insight into the function of the BRCA1 tumor suppressor gene may be gained by studying its regulation. In this study, the expression of BRCA1 was examined as a function of the cell cycle in normal and tumor-derived breast epithelial cells. Cells arrested i ... Link to item Cite

BRCA2 mutations in primary breast and ovarian cancers.

Journal Article Nat Genet · June 1996 The second hereditary breast cancer gene, BRCA2, was recently isolated. Germline mutations of this gene predispose carriers to breast cancer, and, to a lesser extent, ovarian cancer. Loss of heterozygosity (LOH) at the BRCA2 locus has been observed in 30-4 ... Full text Link to item Cite

M6P/IGF2 receptor: a candidate breast tumor suppressor gene.

Journal Article Oncogene · May 2, 1996 The mannose 6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2r) functions in the activation of TGFbeta, a potent growth inhibitor for most cell types, the degradation of the mitogen, IGF2, and the intracellular trafficking of lysosomal enzymes. W ... Link to item Cite

Identification of a new subclass of Alu DNA repeats which can function as estrogen receptor-dependent transcriptional enhancers.

Journal Article J Biol Chem · September 29, 1995 We have utilized a genetic selection system in yeast to identify novel estrogen-responsive genes within the human genome and to define the sequences in the BRCA-1 gene responsible for its estrogen responsiveness. This approach led to the identification of ... Full text Link to item Cite

Antisense DNA downregulation of the ERBB2 oncogene measured by a flow cytometric assay.

Journal Article Proc Natl Acad Sci U S A · August 29, 1995 A causal role has been inferred for ERBB2 overexpression in the etiology of breast cancer and other epithelial malignancies. The development of therapeutics that inhibit this tyrosine kinase cell surface receptor remains a high priority. This report descri ... Full text Link to item Cite

Maintenance of DNA content and erbB-2 alterations in intraductal and invasive phases of mammary cancer.

Journal Article Breast Cancer Res Treat · June 1995 Ductal carcinoma in situ (intraductal carcinoma) of the breast is a commonly recognized and curable clinical entity. Patients with intraductal carcinoma are at risk to develop invasive breast cancer presumably due to a transition from the noninvasive to th ... Full text Link to item Cite

Localized adenocarcinoma of the lung: oncogene expression of erbB-2 and p53 in 150 patients.

Journal Article Clin Cancer Res · June 1995 Historical information and pathological material from 150 consecutive patients with localized adenocarcinoma of the lung was collected to evaluate oncogene expression of erbB-2 and p53, and erbB-2 gene amplification. Pathological material after resection w ... Link to item Cite

Simultaneous endometrial malignant mixed mesodermal tumor and ovarian serous adenocarcinoma.

Journal Article Arch Pathol Lab Med · January 1995 Although simultaneous endometrial and ovarian tumors are observed occasionally, rarely are the two neoplasms histologically disparate. We report a case of simultaneous endometrial malignant mixed mesodermal tumor and ovarian serous adenocarcinoma with a si ... Link to item Cite

A prognostic model of recurrence and death in stage I non-small cell lung cancer utilizing presentation, histopathology, and oncoprotein expression.

Journal Article Cancer Res · January 1, 1995 In order to construct a multivariate model for predicting early recurrence and cancer death for patients with stage I non-small cell lung cancer, 271 consecutive patients (mean age, 63 +/- 8 years) who were diagnosed, treated, and followed at one instituti ... Link to item Cite

Determination of Proliferation Index By MIB‐1 Immunostaining in Early Stage Breast Cancer Using Quantitative Image Analysis

Journal Article The Breast Journal · January 1, 1995 Abstract: Several clinicopathologic variables influence prognosis in breast cancer, including stage, histologic grade, nodal status, and tumor size. Multiple studies have shown an independent value of proliferation index as a prognostic variable for the st ... Full text Cite

Transforming growth factor beta 1 can induce CIP1/WAF1 expression independent of the p53 pathway in ovarian cancer cells.

Journal Article Cell Growth Differ · December 1994 Featured Publication Transforming growth factor beta (TGF beta) is an important regulator of cellular proliferation. In normal ovarian epithelial cells, TGF beta acts to inhibit growth. However, in ovarian cancer cell lines, this effect is usually lost. Although the regulatory ... Link to item Cite

BRCA1 mutations in primary breast and ovarian carcinomas.

Journal Article Science · October 7, 1994 Loss of heterozygosity data from familial tumors suggest that BRCA1, a gene that confers susceptibility to ovarian and early-onset breast cancer, encodes a tumor suppressor. The BRCA1 region is also subject to allelic loss in sporadic breast and ovarian ca ... Full text Link to item Cite

Localization of the VHR phosphatase gene and its analysis as a candidate for BRCA1.

Journal Article Genomics · September 1, 1994 The VH1-related human protein (VHR) gene was localized to human chromosome 17q21 in a region thought to contain the BRCA1 locus, a locus that confers susceptibility to breast and ovarian cancer. VHR encodes a phosphatase with dual specificity for tyrosine ... Full text Link to item Cite

Isolation of a diverged homeobox gene, MOX1, from the BRCA1 region on 17q21 by solution hybrid capture.

Journal Article Hum Mol Genet · August 1994 Using the technique of solution hybridization coupled with magnetic bead capture, we have isolated a novel homeobox-containing gene from the BRCA1 region of 17q21. This gene is the human homologue of the mouse Mox1 gene previously localized to a syntenic r ... Full text Link to item Cite

Loss of chromosome 8p sequences in human breast carcinoma cell lines.

Journal Article Cancer Genet Cytogenet · August 1994 Cytogenetic and molecular analyses of human breast cancer cells have identified consistent losses of specific chromosomal regions in these tumors, suggesting that such regions harbor tumor suppressor genes whose homozygous loss or inactivation directly con ... Full text Link to item Cite

Mutation analysis of the THRA1 gene in breast cancer: deletion/fusion of the gene to a novel sequence on 17q in the BT474 cell line.

Journal Article Cancer Res · April 1, 1994 We have previously described a common region of deletion and allele loss on chromosome 17q in sporadic breast cancers that is likely to contain a tumor suppressor gene. The region, mapped to 17q12-q21, was bordered by D17S250 and D17S579 on the centromeric ... Link to item Cite

Overexpression of p53 and HER-2/neu proteins as prognostic markers in early stage breast cancer.

Journal Article Ann Surg · April 1994 OBJECTIVE: Overexpression of the p53 and HER-2/neu oncogenes are the two most common genetic abnormalities associated with breast cancer. Shorter survival time has been reported in patients with tumors with p53 or HER-2/neu. This report analyzes a retrospe ... Full text Link to item Cite

Epithelial cells are an important source of tenascin in normal and malignant human breast tissue.

Journal Article Exp Cell Res · February 1994 The extracellular matrix glycoprotein tenascin is limited to the periductal matrix of normal breast tissue but is markedly increased in both malignant and fibroadenomatous proliferations. It has been hypothesized that the changes in tenascin expression in ... Full text Link to item Cite

Mutation and overexpression of the p53 tumor suppressor gene frequently occurs in uterine and ovarian sarcomas.

Journal Article Obstet Gynecol · January 1994 OBJECTIVE: To determine the frequency of mutation and overexpression of the p53 tumor suppressor gene in female genital tract sarcomas. METHODS: Immunostaining for p53 was performed in frozen sections of 46 ovarian and uterine sarcomas. Single-stranded con ... Link to item Cite

Assessment of c-erbB-2 amplification by immunohistochemistry in paraffin-embedded breast cancer.

Journal Article Mod Pathol · November 1993 The c-erbB-2 (HER-2/neu) proto-oncogenes is important in oncogenesis and for determination of prognosis in a number of human malignancies. DNA (Southern) hybridization and immunoblotting (Western) techniques are most commonly utilized for determining ampli ... Link to item Cite

Spectrum of mutation and frequency of allelic deletion of the p53 gene in ovarian cancer.

Journal Article J Natl Cancer Inst · September 15, 1993 BACKGROUND: The p53 gene encodes a nuclear phosphoprotein present in low levels in normal human cells. The wild-type form of this protein functions to restrain inappropriate cellular proliferation. Approximately one half of human epithelial ovarian cancers ... Full text Link to item Cite

Mutation of the p53 tumor-suppressor gene is not a feature of endometrial hyperplasias.

Journal Article Am J Obstet Gynecol · September 1993 OBJECTIVE: Mutation and overexpression of the p53 gene occur in approximately 20% of endometrial carcinomas. To determine whether alteration of the p53 gene is an early event in endometrial carcinogenesis, we examined the p53 gene in endometrial hyperplasi ... Full text Link to item Cite

Constitutive production of macrophage colony-stimulating factor and interleukin-6 by human ovarian surface epithelial cells.

Journal Article Exp Cell Res · August 1993 Normal and neoplastic epithelial cells produce growth factors that can affect cells from different lineages. Epithelial ovarian cancers produce M-CSF and IL-6. In the present study, production of these cytokines has been measured in the apparently normal e ... Full text Link to item Cite

Mutation and overexpression of p53 in early-stage epithelial ovarian cancer.

Journal Article Obstet Gynecol · May 1993 OBJECTIVE: To investigate whether mutation and overexpression of p53 is a feature of early-stage ovarian cancers. METHODS: Because early-stage ovarian cancers are relatively uncommon, we adapted p53 immunostaining and DNA sequencing methods for use in para ... Link to item Cite

Clonal origin of epithelial ovarian carcinoma: analysis by loss of heterozygosity, p53 mutation, and X-chromosome inactivation.

Journal Article J Natl Cancer Inst · December 2, 1992 BACKGROUND: It has been suggested that multiple sites of epithelial ovarian carcinoma on the peritoneal surface reflect polyclonal disease arising from multiple primary tumors in the peritoneal mesothelium, rather than monoclonal disease spread by metastas ... Full text Link to item Cite

The effect of interferon gamma on epidermal growth factor receptor expression in normal and malignant ovarian epithelial cells.

Journal Article Am J Obstet Gynecol · December 1992 OBJECTIVE: We examined the effect of interferon gamma on proliferation and epidermal growth factor receptor expression in ovarian cancer cell lines and normal ovarian epithelial cells. STUDY DESIGN: The tritiated thymidine incorporation assay was used to a ... Full text Link to item Cite

p53 overexpression in formalin-fixed, paraffin-embedded tissue detected by immunohistochemistry.

Journal Article J Histochem Cytochem · July 1992 Mutation and overexpression of the p53 gene have been noted in a wide range of human cancers and are thought to play a role in malignant transformation. Previously, immunohistochemical detection of p53 has been possible only in fresh-frozen tissues. We exa ... Full text Link to item Cite

Detection of frequent allelic loss on proximal chromosome 17q in sporadic breast carcinoma using microsatellite length polymorphisms.

Journal Article Cancer Res · May 1, 1992 Analyses of losses of heterozygosity and linkage studies have implicated a gene(s) on chromosome 17q in the genesis of sporadic and early-onset familial breast carcinomas, respectively. To define the critical region of 17q, we examined DNAs from a series o ... Link to item Cite

Immune response to p53 is dependent upon p53/HSP70 complexes in breast cancers.

Journal Article Proc Natl Acad Sci U S A · April 15, 1992 Featured Publication Overexpression of the p53 protein, resulting from gene mutations that increase protein stability, has been detected in greater than 25% of primary human breast cancers. In addition, approximately 10% of breast cancer patients have circulating antibodies to ... Full text Link to item Cite

Overexpression and mutation of p53 in endometrial carcinoma.

Journal Article Cancer Res · March 15, 1992 Immunohistochemical staining for the p53 protein was performed in 107 snap frozen primary endometrial adenocarcinomas and 15 benign uterine tissues using monoclonal antibody PAb1801. No staining was seen in benign samples, whereas intense nuclear staining ... Link to item Cite

Expression of p53 in human neuroblastoma- and neuroepithelioma-derived cell lines.

Journal Article Oncogene · January 1992 Overexpression of the nuclear phosphoprotein p53 has been detected in many different transformed human cell lines and primary adult tumors. Elevated steady-state levels of p53 appear to be the result of an increase in the stability of the protein and, in a ... Link to item Cite

p53 alterations in all stages of breast cancer.

Journal Article J Surg Oncol · December 1991 Overexpression of the nuclear phosphoprotein p53 is one of the most frequently detected abnormalities in human cancer and appears to be associated with mutation of the p53 gene. In this study of breast cancer, p53 overexpression was detected in two (15%) o ... Full text Link to item Cite

Proliferation index in various stages of breast cancer determined by Ki-67 immunostaining.

Journal Article J Surg Oncol · September 1991 To investigate factors involved in progression of breast cancer, we estimated the growth fraction of malignant cell populations in various stages of mammary cancer growth. Frozen sections were immunostained with the Ki-67 monoclonal antibody and the prolif ... Full text Link to item Cite

Relation between p53 overexpression and established prognostic factors in breast cancer.

Journal Article Surgery · August 1991 The nuclear phosphoprotein p53 is expressed in all normal cells and appears to function in cell cycle regulation. Abnormally high levels of the protein are found in many different types of cancer. In breast carcinoma overexpression of p53 is associated wit ... Link to item Cite

Genetic basis for p53 overexpression in human breast cancer.

Journal Article Proc Natl Acad Sci U S A · June 1, 1991 Overexpression of an activated form of the p53 protein may be involved in neoplastic transformation. We found widespread overexpression of p53 by immunohistochemical staining in 11 (22%) of 49 primary invasive human breast cancers. Northern blot analysis s ... Full text Link to item Cite

Overexpression and mutation of p53 in epithelial ovarian cancer.

Journal Article Cancer Res · June 1, 1991 We examined p53 expression in 107 epithelial ovarian cancers with immunohistochemical techniques using monoclonal antibody PAb1801. High level expression of nuclear p53 protein was detected in the malignant epithelium in 54 (50%) of these cancers. Expressi ... Link to item Cite

Maintenance of p53 alterations throughout breast cancer progression.

Journal Article Cancer Res · May 15, 1991 Overexpression of the nuclear phosphoprotein p53 is one of the most common abnormalities in primary human cancer and appears to be due to point mutation within a highly conserved region of the p53 gene which then encodes for a mutant, more stable protein. ... Link to item Cite

P53 expression in neuroblastoma

Journal Article Surgical Forum · December 1, 1990 Cite

Increased erbB-2 gene copies and expression in multiple stages of breast cancer.

Journal Article Cancer Res · October 15, 1990 In order to examine the role of the erbB-2 oncogene in human breast cancer, gene amplification and expression were examined in multiple stages of tumor progression. Gene amplification ranging from 2-fold to 32-fold was found in 30 (29%) of 130 cases analyz ... Link to item Cite

Impact of the genetic background of transgenic mice upon the formation and timing of choroid plexus papillomas.

Journal Article J Neurosci Res · September 1989 Transgenic mice harboring the SV40 large T antigen gene in a C57B1/6J genetic background (SV11) first express this gene at 1-2 weeks of age, develop papillomas of the choroid plexus by 80-90 days, and die within 125 days after birth. Transgenic mice harbor ... Full text Link to item Cite

Cellular gene expression in papillomas of the choroid plexus from transgenic mice that express the simian virus 40 large T antigen.

Journal Article J Virol · February 1989 Transgenic mice that contain the simian virus 40 (SV40) enhancer-promoter and large tumor (T) antigen gene develop papillomas of the choroid plexus. The tumors remain well differentiated on histological examination and express normal levels of tissue-speci ... Full text Link to item Cite

Replication of the murine cytomegalovirus genome: structure and role of the termini in the generation and cleavage of concatenates.

Journal Article Virology · January 1988 Following infection with murine cytomegalovirus (MCMV), the termini of the linear double-stranded DNA genome fuse to form circular or concatemeric forms which serve as replicative intermediates. To investigate the mechanisms involved in the generation and ... Full text Link to item Cite

The expression of viral and cellular genes in papillomas of the choroid plexus induced in transgenic mice.

Chapter · 1988 A line of transgenic mice that carry the SV40 gene for the large Tumor antigen express this protein during the first two weeks of life in brain tissue. By 30-40 days after birth, independently derived multiple foci of abnormal cells appear throughout the c ... Link to item Cite

Relationship between simian virus 40 large tumor antigen expression and tumor formation in transgenic mice.

Journal Article J Virol · June 1987 A line of transgenic mice containing the simian virus 40 (SV40) large tumor antigen gene under the control of the viral enhancer-promoter expressed this viral protein in the brains of these mice within the first 2 weeks after birth. Multiple foci of anapla ... Full text Link to item Cite

Fusion of the termini of the murine cytomegalovirus genome after infection.

Journal Article J Virol · October 1984 The genome of murine cytomegalovirus, extracted from extracellular virions, is a linear double-stranded DNA molecule ca. 240 kilobase pairs long. In our initial cloning of subgenomic fragments of the murine cytomegalovirus genome, we obtained a HindIII clo ... Full text Link to item Cite

Transcription in mouse embryo cells permissively infected by murine cytomegalovirus.

Journal Article Virology · November 1983 The sites of transcription and abundance of steady-state cytoplasmic viral RNA in murine cytomegalovirus (Smith strain) infected mouse embryo cells were analyzed. Cloned subgenomic DNA fragments were labeled with 32P and hybridized to filters containing po ... Full text Link to item Cite

Molecular cloning and restriction endonuclease mapping of the murine cytomegalovirus genome (Smith Strain).

Journal Article Virology · August 1983 We have cloned EcoRI and HindIII fragments of the Smith strain of murine cytomegalovirus (MCMV) in the plasmid vector pACYC184. These cloned fragments were used to establish a restriction endonuclease map of the genome with respect to the EcoRI and HindIII ... Full text Link to item Cite