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    50537 results match your criteria Cancer research[Journal]

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    The Biology of Cancer Exosomes: Insights and New Perspectives.
    Cancer Res 2017 Nov 21. Epub 2017 Nov 21.
    Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
    Exosomes are a subclass of extracellular vesicles involved in intercellular communication that are released by all cell types, including cancer cells. Cancer exosomes carry malignant information in the form of proteins, lipids, and nucleic acids that can reprogram recipient cells. Exosomes have emerged as putative biological mediators in cancer contributing to major steps of disease progression. Read More

    Precision Oncology: Between Vaguely Right and Precisely Wrong.
    Cancer Res 2017 Nov 21. Epub 2017 Nov 21.
    Institute for Systems Biology, Seattle, Washington.
    Precision Oncology seeks to identify and target the mutation that drives a tumor. Despite its straightforward rationale, concerns about its effectiveness are mounting. What is the biological explanation for the "imprecision?" First, Precision Oncology relies on indiscriminate sequencing of genomes in biopsies that barely represent the heterogeneous mix of tumor cells. Read More

    Interferon-γ signaling in melanocytes and melanoma cells regulates expression of CTLA-4.
    Cancer Res 2017 Nov 17. Epub 2017 Nov 17.
    Fels Institute for Cancer Research & Molecular Biology, Temple University School of Medicine
    CTLA-4 is a cell surface receptor on T cells that functions as an immune checkpoint molecule to enforce tolerance to cognate antigens. Anti-CTLA-4 immunotherapy is highly effective at reactivating T cell responses against melanoma, which is postulated to be due to targeting CTLA-4 on T cells. Here we report that CTLA-4 is also highly expressed by most human melanoma cell lines, as well as in normal human melanocytes. Read More

    Type II Diabetes and Incidence of Estrogen Receptor Negative Breast Cancer in African American Women.
    Cancer Res 2017 Nov;77(22):6462-6469
    Department of Medicine, Boston University School of Medicine, Boston, Massachusetts.
    White women with type II diabetes (T2D) have an estimated 20% increased risk of developing breast cancer. Little is known about associations by breast cancer subtype or among African American (AA) women, who are disproportionately affected by T2D and estrogen receptor negative (ER-) breast cancer. We assessed the relation of T2D to incidence of ER- and ER+ breast cancer in data from the Black Women's Health Study, a prospective cohort of AA women enrolled in 1995 and followed biennially. Read More

    Atypical G protein β5 promotes cardiac oxidative stress, apoptosis, and fibrotic remodeling in response to multiple cancer chemotherapeutics.
    Cancer Res 2017 Nov 15. Epub 2017 Nov 15.
    Biomedical Sciences, Charles E. Schmidt College of Medicine.
    The clinical use of multiple classes of cancer chemotherapeutics is limited by irreversible, dose-dependent, and sometimes life-threatening cardiotoxicity. We report here that, though distinct in their mechanisms of action, doxorubicin, paclitaxel, and 5-FU all induce rapid and robust upregulation of atypical G protein Gβ5 in the myocardium, correlating with oxidative stress, myocyte apoptosis, and the accumulation of pro-inflammatory and pro-fibrotic cytokines. In ventricular cardiac myocytes (VCM), Gβ5 deficiency provided substantial protection against the cytotoxic actions of chemotherapeutics, including reductions in oxidative stress and simultaneous attenuation of ROS-dependent activation of the ATM and CaMKII pro-apoptotic signaling cascades. Read More

    Retention of Interstitial Genes between TMPRSS2 and ERG Is Associated with Low-Risk Prostate Cancer.
    Cancer Res 2017 Nov 10;77(22):6157-6167. Epub 2017 Nov 10.
    Biomarker Discovery Program, Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota.
    TMPRSS2-ERG gene fusions occur in over 50% of prostate cancers, but their impact on clinical outcomes is not well understood. Retention of interstitial genes between TMPRSS2 and ERG has been reported to influence tumor progression in an animal model. In this study, we analyzed the status of TMPRSS2-ERG fusion genes and interstitial genes in tumors from a large cohort of men treated surgically for prostate cancer, associating alterations with biochemical progression. Read More

    Deficiency in protein tyrosine phosphatase PTP1B shortens lifespan and leads to development of acute leukemia.
    Cancer Res 2017 Nov 9. Epub 2017 Nov 9.
    Metabolic and Cardiovascular Health, Institute of Medical Sciences
    Protein tyrosine phosphatase PTP1B is a critical regulator of signaling pathways controlling metabolic homeostasis, cell proliferation and immunity. In this study, we report that global or myeloid-specific deficiency of PTP1B in mice decreases lifespan. We demonstrate that myeloid-specific deficiency of PTP1B is sufficient to promote the development of acute myeloid leukemia (AML). Read More

    Complement activation via a C3a receptor pathway alters CD4+ T lymphocytes and mediates lung cancer progression.
    Cancer Res 2017 Nov 8. Epub 2017 Nov 8.
    Medicine, University of Colorado Anschutz Medical Campus
    The complement cascade is a part of the innate immune system which acts primarily to remove pathogens and injured cells. However, complement activation is also peculiarly associated with tumor progression. Here we report mechanistic insights into this association in multiple immunocompetent orthotopic models of lung cancer. Read More

    Oncolytic virotherapy blockade by microglia and macrophages requires STAT1/3.
    Cancer Res 2017 Nov 8. Epub 2017 Nov 8.
    Surgery, University of British Columbia
    The first oncolytic virotherapy employing HSV-1 (oHSV-1) was approved recently by the FDA to treat cancer, but further improvements in efficacy are needed to eradicate challenging refractory tumors such as glioblastomas (GBM). Microglia/macrophages comprising ~40% of a GBM tumor may limit virotherapeutic efficacy. Here we show these cells suppress oHSV-1 growth in gliomas by internalizing the virus through phagocytosis. Read More

    IDO Immune Status after Chemoradiation May Predict Survival in Lung Cancer Patients.
    Cancer Res 2017 Nov 8. Epub 2017 Nov 8.
    Radiation Oncology, Indiana University School of Medicine
    Host immunity influences the impact of radiotherapy (RT) in cancer but mechanistic connections remain obscure. In this study, we investigated the relationship of indoleamine 2,3-dioxygenase (IDO) systemic activity on clinical outcomes in RT-treated non-small cell lung cancer (NSCLC). IDO-mediated production of kynurenine and the kynurenine:tryptophan ratio in patient blood serum were determined for stage III NSCLC patients at times before, during and after RT administration and then correlated to overall survival (OS), progression-free survival and disease progression rate in patients. Read More

    Localized Synchrotron Irradiation of Mouse Skin Induces Persistent Systemic Genotoxic and Immune Responses.
    Cancer Res 2017 Nov 7;77(22):6389-6399. Epub 2017 Nov 7.
    Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
    The importance of nontargeted (systemic) effects of ionizing radiation is attracting increasing attention. Exploiting synchrotron radiation generated by the Imaging and Medical Beamline at the Australian Synchrotron, we studied radiation-induced nontargeted effects in C57BL/6 mice. Mice were locally irradiated with a synchrotron X-ray broad beam and a multiplanar microbeam radiotherapy beam. Read More

    Understanding Mitochondrial Polymorphisms in Cancer.
    Cancer Res 2017 Nov 2;77(22):6051-6059. Epub 2017 Nov 2.
    Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, Pennsylvania.
    Alterations in mitochondrial DNA (mtDNA) were once thought to be predominantly innocuous to cell growth. Recent evidence suggests that mtDNA undergo naturally occurring alterations, including mutations and polymorphisms, which profoundly affect the cells in which they appear and contribute to a variety of diseases, including cardiovascular disease, diabetes, and cancer. Furthermore, interplay between mtDNA and nuclear DNA has been found in cancer cells, necessitating consideration of these complex interactions for future studies of cancer mutations and polymorphisms. Read More

    Recent Advances of Cell-Cycle Inhibitor Therapies for Pediatric Cancer.
    Cancer Res 2017 Nov 2. Epub 2017 Nov 2.
    Nemours Center for Cancer and Blood Disorders, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware.
    This review describes the pivotal roles of cell-cycle and checkpoint regulators and discusses development of specific cell-cycle inhibitors for therapeutic use for pediatric cancer. The mechanism of action as well as the safety and tolerability of drugs in pediatric patients, including compounds that target CDK4/CDK6 (palbociclib, ribociclib, and abemaciclib), aurora kinases (AT9283 and MLN8237), Wee1 kinase (MK-1775), KSP (ispinesib), and tubulin (taxanes, vinca alkaloids), are presented. The design of mechanism-based combinations that exploit the cross-talk of signals activated by cell-cycle arrest, as well as pediatric-focused drug development, are critical for the advancement of drugs for rare childhood diseases. Read More

    Uncoupling the Oncogenic Engine.
    Cancer Res 2017 Nov 2;77(22):6060-6064. Epub 2017 Nov 2.
    Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.
    Inhibition of oncogenic signaling and correction of aberrant metabolic processes may be key paradigms to eliminate cancer cells. The high incidence of activating RAS mutations and hyperactivated ERK1/2 signaling observed in many human tumors and the lack of effective targeted therapies to elicit long-term inhibition of the RAS-ERK1/2 signaling pathway add to the importance of discovering novel strategies to treat malignancies characterized by elevated RAS-ERK1/2 signaling. In this review, we describe connections between oncogenic signaling and cancer cell metabolism and how these links may be exploited for novel modern molecular medicine approaches. Read More

    Adaptive evolution of the GDH2 allosteric domain promotes gliomagenesis by resolving IDH1(R132H) induced metabolic liabilities.
    Cancer Res 2017 Nov 2. Epub 2017 Nov 2.
    Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center at Duke
    Hot-spot mutations in the isocitrate dehydrogenase 1 (IDH1) gene occur in a number of human cancers and confer a neomorphic enzyme activity that catalyzes the conversion of α-ketoglutarate (αKG) to the oncometabolite D-(2)-hydroxyglutarate (D2HG). In malignant gliomas, IDH1(R132H) expression induces widespread metabolic reprogramming, possibly requiring compensatory mechanisms to sustain the normal biosynthetic requirements of actively proliferating tumor cells. We used genetically engineered mouse models of glioma and quantitative metabolomics to investigate IDH1(R132H)-dependent metabolic reprogramming and its potential to induce biosynthetic liabilities that can be exploited for glioma therapy. Read More

    Deletion of neuropilin 1 from microglia or bone marrow-derived macrophages slows glioma progression.
    Cancer Res 2017 Nov 2. Epub 2017 Nov 2.
    Pharmacological Sciences, Stony Brook University
    Glioma-associated microglia and macrophages (GAM) which infiltrate high-grade gilomas represent constitute a major cellular component of these lesions. GAM behavior is influenced by tumor-derived cytokines that suppress initial anti-tumorigenic properties, causing them to support tumor growth and to convert and suppress adaptive immune responses to the tumor. Mice which lack the transmembrane receptor neuropilin-1 (Nrp1) which modulates GAM immune polarization exhibit a decrease in glioma volumes and neoangiogenesis and an increase in anti-tumorigenic GAM infiltrate. Read More

    Interleukin-27 Exerts Its Antitumor Effects by Promoting Differentiation of Hematopoietic Stem Cells to M1 Macrophages.
    Cancer Res 2017 Nov 1. Epub 2017 Nov 1.
    Department of Immunoregulation, Institute of Medical Science, Tokyo Medical University
    The interleukin (IL)-27 promotes expansion and differentiation of hematopoietic stem cells into myeloid progenitor cells. Many tumor-infiltrating myeloid cells exert immunosuppressive effects but we hypothesized that the myeloid cells induced by IL-27 would have antitumor activity. In this study we corroborated this hypothesis as investigated in two distinct mouse transplantable tumor models. Read More

    MicroRNA-519d promotes melanoma progression by downregulating EphA4.
    Cancer Res 2017 Nov 1. Epub 2017 Nov 1.
    Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine
    Increasing evidence suggests that there is a unique cell subpopulation in melanoma that can form nonadherent melanospheres in serum-free stem cell medium, mimicking aggressive malignancy. Using melanospheres as a model to investigate progression mechanisms, we found that miR-519d overexpression was sufficient to promote cell proliferation, migration, invasion and adhesion in vitro and lung metastatic capability in vivo. The cell adhesion receptor EphA4 was determined to be a direct target of miR-519d. Read More

    Rapid Intraoperative Diagnosis of Pediatric Brain Tumors Using Stimulated Raman Histology.
    Cancer Res 2017 Nov 1. Epub 2017 Nov 1.
    Neurosurgery, University of Michigan
    Accurate histopathologic diagnosis is essential for providing optimal surgical management of pediatric brain tumors. Current methods for intraoperative histology are time- and labor-intensive and often introduce artifacts that limit interpretation. Stimulated Raman histology (SRH) is a novel label-free imaging technique that provides intraoperative histologic images of fresh, unprocessed surgical specimens. Read More

    Dendritic cells enhance polyfunctionality of adoptively transferred T cells which target cytomegalovirus in glioblastoma.
    Cancer Res 2017 Nov 1. Epub 2017 Nov 1.
    Neurosurgery, Duke University Medical Center
    Median survival for glioblastoma (GBM) remains <15 months. Human Cytomegalovirus (CMV) antigens have been identified in GBM but not normal brain, providing an unparalleled opportunity to subvert CMV antigens as tumor-specific immunotherapy targets. A recent trial in recurrent GBM patients demonstrated the potential clinical benefit of adoptive T cell therapy (ATCT) of CMV phosphoprotein 65 (pp65)-specific T cells. Read More

    "Personalized Cancer Therapy": A Publicly Available Precision Oncology Resource.
    Cancer Res 2017 Nov;77(21):e123-e126
    Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas.
    High-throughput genomic and molecular profiling of tumors is emerging as an important clinical approach. Molecular profiling is increasingly being used to guide cancer patient care, especially in advanced and incurable cancers. However, navigating the scientific literature to make evidence-based clinical decisions based on molecular profiling results is overwhelming for many oncology clinicians and researchers. Read More

    LesionTracker: Extensible Open-Source Zero-Footprint Web Viewer for Cancer Imaging Research and Clinical Trials.
    Cancer Res 2017 Nov;77(21):e119-e122
    Open Health Imaging Foundation, Chicago, Illinois.
    Oncology clinical trials have become increasingly dependent upon image-based surrogate endpoints for determining patient eligibility and treatment efficacy. As therapeutics have evolved and multiplied in number, the tumor metrics criteria used to characterize therapeutic response have become progressively more varied and complex. The growing intricacies of image-based response evaluation, together with rising expectations for rapid and consistent results reporting, make it difficult for site radiologists to adequately address local and multicenter imaging demands. Read More

    DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records.
    Cancer Res 2017 Nov;77(21):e115-e118
    Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania.
    Precise phenotype information is needed to understand the effects of genetic and epigenetic changes on tumor behavior and responsiveness. Extraction and representation of cancer phenotypes is currently mostly performed manually, making it difficult to correlate phenotypic data to genomic data. In addition, genomic data are being produced at an increasingly faster pace, exacerbating the problem. Read More

    TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.
    Cancer Res 2017 Nov;77(21):e111-e114
    Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, California.
    Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex "omics" data in an interactive and easily interpretable way. Read More

    TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells.
    Cancer Res 2017 Nov;77(21):e108-e110
    Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.
    Recent clinical successes of cancer immunotherapy necessitate the investigation of the interaction between malignant cells and the host immune system. However, elucidation of complex tumor-immune interactions presents major computational and experimental challenges. Here, we present Tumor Immune Estimation Resource (TIMER; cistrome. Read More

    Computational Radiomics System to Decode the Radiographic Phenotype.
    Cancer Res 2017 Nov;77(21):e104-e107
    Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
    Radiomics aims to quantify phenotypic characteristics on medical imaging through the use of automated algorithms. Radiomic artificial intelligence (AI) technology, either based on engineered hard-coded algorithms or deep learning methods, can be used to develop noninvasive imaging-based biomarkers. However, lack of standardized algorithm definitions and image processing severely hampers reproducibility and comparability of results. Read More

    SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research.
    Cancer Res 2017 Nov;77(21):e101-e103
    Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts.
    Diffusion MRI (dMRI) is the only noninvasive method for mapping white matter connections in the brain. We describe SlicerDMRI, a software suite that enables visualization and analysis of dMRI for neuroscientific studies and patient-specific anatomic assessment. SlicerDMRI has been successfully applied in multiple studies of the human brain in health and disease, and here, we especially focus on its cancer research applications. Read More

    Integrative Analysis of Histopathological Images and Genomic Data Predicts Clear Cell Renal Cell Carcinoma Prognosis.
    Cancer Res 2017 Nov;77(21):e91-e100
    Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio.
    In cancer, both histopathologic images and genomic signatures are used for diagnosis, prognosis, and subtyping. However, combining histopathologic images with genomic data for predicting prognosis, as well as the relationships between them, has rarely been explored. In this study, we present an integrative genomics framework for constructing a prognostic model for clear cell renal cell carcinoma. Read More

    dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM.
    Cancer Res 2017 Nov;77(21):e87-e90
    Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts.
    Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology. Read More

    An Image Analysis Resource for Cancer Research: PIIP-Pathology Image Informatics Platform for Visualization, Analysis, and Management.
    Cancer Res 2017 Nov;77(21):e83-e86
    The Ohio State University, Columbus, Ohio.
    Pathology Image Informatics Platform (PIIP) is an NCI/NIH sponsored project intended for managing, annotating, sharing, and quantitatively analyzing digital pathology imaging data. It expands on an existing, freely available pathology image viewer, Sedeen. The goal of this project is to develop and embed some commonly used image analysis applications into the Sedeen viewer to create a freely available resource for the digital pathology and cancer research communities. Read More

    A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images.
    Cancer Res 2017 Nov;77(21):e79-e82
    Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York.
    Well-curated sets of pathology image features will be critical to clinical studies that aim to evaluate and predict treatment responses. Researchers require information synthesized across multiple biological scales, from the patient to the molecular scale, to more effectively study cancer. This article describes a suite of services and web applications that allow users to select regions of interest in whole slide tissue images, run a segmentation pipeline on the selected regions to extract nuclei and compute shape, size, intensity, and texture features, store and index images and analysis results, and visualize and explore images and computed features. Read More

    The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research.
    Cancer Res 2017 Nov;77(21):e75-e78
    Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia.
    Tissue-based cancer studies can generate large amounts of histology data in the form of glass slides. These slides contain important diagnostic, prognostic, and biological information and can be digitized into expansive and high-resolution whole-slide images using slide-scanning devices. Effectively utilizing digital pathology data in cancer research requires the ability to manage, visualize, share, and perform quantitative analysis on these large amounts of image data, tasks that are often complex and difficult for investigators with the current state of commercial digital pathology software. Read More

    Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images.
    Cancer Res 2017 Nov;77(21):e71-e74
    Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.
    We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. Read More

    The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer.
    Cancer Res 2017 Nov;77(21):e67-e70
    The Jackson Laboratory, Bar Harbor, Maine.
    Research using laboratory mice has led to fundamental insights into the molecular genetic processes that govern cancer initiation, progression, and treatment response. Although thousands of scientific articles have been published about mouse models of human cancer, collating information and data for a specific model is hampered by the fact that many authors do not adhere to existing annotation standards when describing models. The interpretation of experimental results in mouse models can also be confounded when researchers do not factor in the effect of genetic background on tumor biology. Read More

    PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.
    Cancer Res 2017 Nov;77(21):e62-e66
    The Jackson Laboratory, Bar Harbor, Maine.
    Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, mechanisms of drug response and resistance, and tailoring chemotherapeutic approaches for individual patients. The lack of robust standards for reporting on PDX models has hampered the ability of researchers to find relevant PDX models and associated data. Here we present the PDX models minimal information standard (PDX-MI) for reporting on the generation, quality assurance, and use of PDX models. Read More

    DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.
    Cancer Res 2017 Nov;77(21):e55-e57
    Department of Computer Science, Rice University, Houston, Texas.
    Molecular docking is a standard computational approach to predict binding modes of protein-ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Read More

    Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas.
    Cancer Res 2017 Nov;77(21):e51-e54
    Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
    Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications. Read More

    P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets.
    Cancer Res 2017 Nov;77(21):e47-e50
    Pacific Northwest National Laboratory, Richland, Washington.
    P-MartCancer is an interactive web-based software environment that enables statistical analyses of peptide or protein data, quantitated from mass spectrometry-based global proteomics experiments, without requiring in-depth knowledge of statistical programming. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification, and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access and the capability to analyze multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium at the peptide, gene, and protein levels. Read More

    An Accessible Proteogenomics Informatics Resource for Cancer Researchers.
    Cancer Res 2017 Nov;77(21):e43-e46
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota.
    Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry-based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics. Read More

    Software for the Integration of Multiomics Experiments in Bioconductor.
    Cancer Res 2017 Nov;77(21):e39-e42
    Graduate School of Public Health & Health Policy, City University of New York, New York, New York.
    Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. Read More

    CRAVAT 4: Cancer-Related Analysis of Variants Toolkit.
    Cancer Res 2017 Nov;77(21):e35-e38
    Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland.
    Cancer sequencing studies are increasingly comprehensive and well powered, returning long lists of somatic mutations that can be difficult to sort and interpret. Diligent analysis and quality control can require multiple computational tools of distinct utility and producing disparate output, creating additional challenges for the investigator. The Cancer-Related Analysis of Variants Toolkit (CRAVAT) is an evolving suite of informatics tools for mutation interpretation that includes mutation mapping and quality control, impact prediction and extensive annotation, gene- and mutation-level interpretation, including joint prioritization of all nonsilent mutation consequence types, and structural and mechanistic visualization. Read More

    Variant Review with the Integrative Genomics Viewer.
    Cancer Res 2017 Nov;77(21):e31-e34
    School of Medicine, University of California San Diego, La Jolla, California.
    Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly increase the confidence in calls, reduce the risk of false positives, and help characterize complex events. The Integrative Genomics Viewer (IGV) was one of the first tools to provide NGS data visualization, and it currently provides a rich set of tools for inspection, validation, and interpretation of NGS datasets, as well as other types of genomic data. Read More

    Integrating DNA Methylation and Hydroxymethylation Data with the Mint Pipeline.
    Cancer Res 2017 Nov;77(21):e27-e30
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.
    DNA methylation (5mC) plays important roles in mammalian development, oncogenesis, treatment response, and responses to the environment. DNA hydroxymethylation (5hmC) is also an informative epigenetic mark with distinct roles in regulation and cancer. Gold-standard, widely used technologies (bisulfite conversion, followed by deep sequencing) cannot distinguish between 5mC and 5hmC. Read More

    A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data.
    Cancer Res 2017 Nov;77(21):e23-e26
    Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
    Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in web technologies to produce interactive "next-generation" clustered heatmaps (NG-CHM) that enable extreme zooming and navigation without loss of resolution. Read More

    Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer.
    Cancer Res 2017 Nov;77(21):e19-e22
    Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China.
    Cancer results from a breakdown of normal gene expression control, so the study of gene regulation is critical to cancer research. To gain insight into the transcriptional and epigenetic factors regulating abnormal gene expression patterns in cancers, we developed the Cistrome Cancer web resource (http://cistrome.org/CistromeCancer/). Read More

    Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API.
    Cancer Res 2017 Nov;77(21):e15-e18
    Center for Data Intensive Science (CDIS), University of Chicago, Chicago, Illinois.
    The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers. Read More

    WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data.
    Cancer Res 2017 Nov;77(21):e11-e14
    Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.
    Although large, complex genomic datasets are increasingly easy to generate, and the number of publicly available datasets in cancer and other diseases is rapidly growing, the lack of intuitive, easy-to-use analysis tools has remained a barrier to the effective use of such data. WebMeV (http://mev.tm4. Read More

    The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research.
    Cancer Res 2017 Nov;77(21):e7-e10
    Institute for Systems Biology, Seattle, Washington.
    The ISB Cancer Genomics Cloud (ISB-CGC) is one of three pilot projects funded by the National Cancer Institute to explore new approaches to computing on large cancer datasets in a cloud environment. With a focus on Data as a Service, the ISB-CGC offers multiple avenues for accessing and analyzing The Cancer Genome Atlas, TARGET, and other important references such as GENCODE and COSMIC using the Google Cloud Platform. The open approach allows researchers to choose approaches best suited to the task at hand: from analyzing terabytes of data using complex workflows to developing new analysis methods in common languages such as Python, R, and SQL; to using an interactive web application to create synthetic patient cohorts and to explore the wealth of available genomic data. Read More

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