The University of Texas MD Anderson Cancer Center 8 articles published in JoVE Medicine Radiation Planning Assistant - A Web-based Tool to Support High-quality Radiotherapy in Clinics with Limited Resources Laurence Edward Court1, Ajay Aggarwal2, Hester Burger3, Carlos Cardenas4, Christine Chung1, Raphael Douglas1, Monique du Toit5, Anuja Jhingran1, Raymond Mumme1, Sikudhani Muya6, Komeela Naidoo5, Jerry Ndumbalo6, Tucker Netherton1, Callistus Nguyen1, Adenike Olanrewaju1, Jeannette Parkes3, Willie Shaw7, Christoph Trauernicht5, Melody Xu8, Jinzhong Yang1, Lifei Zhang1, Hannah Simonds9, Beth M. Beadle10 1The University of Texas MD Anderson Cancer Center, 2Guy’s and St. Thomas’ Hospital, 3Groote Schuur Hospital and University of Cape Town, 4University of Alabama at Birmingham, 5Tygerberg Hospital and Stellenbosch University, 6Ocean Road Cancer Institute, 7University of the Free State, 8University of California-San Francisco, 9University Hospitals Plymouth NHS Trust, 10Stanford University This protocol describes a series of automated tools designed for high-quality radiotherapy autocontouring and autoplanning that are being packaged into a web-based service to maximize robustness and scalability while minimizing operational costs. Cancer Research Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples Saxon Rodriguez*1, Baohua Sun*1, Salome McAllen1, Mei Jiang1, Edwin Roger Parra1 1Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center Multiplexed barcoding image analysis has recently improved the characterization of the tumor microenvironment, permitting comprehensive studies of cell composition, functional state, and cell-cell interactions. Herein, we describe a staining and imaging protocol using the barcoding of oligonucleotide-conjugated antibodies and cycle imaging, which allows for the use of a high-dimensional image analysis technique. Cancer Research Expanding the Comprehension of the Tumor Microenvironment using Mass Spectrometry Imaging of Formalin-Fixed and Paraffin-Embedded Tissue Samples Leticia Campos Clemente1, Ou Shi1, Frank Rojas1, Edwin Roger Parra1 1Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center In the era of cancer immunotherapy, interest in elucidating tumor microenvironment dynamics has increased strikingly. This protocol details a mass spectrometry imaging technique with respect to its staining and imaging steps, which allow for highly multiplexed spatial analysis. Cancer Research Modeling Brain Metastasis Via Tail-Vein Injection of Inflammatory Breast Cancer Cells Xiaoding Hu*1,2, Emilly S. Villodre*1,2, Wendy A. Woodward2,3, Bisrat G. Debeb1,2 1Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 2Morgan Welch Inflammatory Breast Cancer Clinic and Research Program, The University of Texas MD Anderson Cancer Center, 3Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center We describe a xenograft mouse model of breast cancer brain metastasis generated via tail-vein injection of an endogenously HER2-amplified inflammatory breast cancer cell line. Cancer Research Enhanced Viability for Ex vivo 3D Hydrogel Cultures of Patient-Derived Xenografts in a Perfused Microfluidic Platform Lindsey K. Sablatura1, Kristin M. Bircsak2, Peter Shepherd3, Karla Queiroz4, Mary C. Farach-Carson1,5,6, Pamela E. Constantinou1,7, Anthony Saleh2, Nora Navone3, Daniel A. Harrington1,5,6 1Department of BioSciences, Rice University, 2Mimetas US Inc, 3Department of Genitourinary Medical Oncology Research, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, 4Mimetas B.V., 5Department of Bioengineering, Rice University, 6Department of Diagnostic and Biomedical Sciences, The University of Texas Health Science Center, 7Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center This protocol demonstrates methods to enable extended in vitro culture of patient-derived xenografts (PDX). One step enhances overall viability of multicellular cluster cultures in 3D hydrogels, through straightforward removal of non-viable single cells. A secondary step demonstrates best practices for PDX culture in a perfused microfluidic platform. Immunology and Infection Cigarette Smoke Exposure in Mice using a Whole-Body Inhalation System Daniel E. Morales-Mantilla1,2, Xinyan Huang3,7, Philip Erice1,3, Paul Porter4, Yun Zhang1,5, Mary Figueroa6, Joya Chandra6, Katherine Y. King2, Farrah Kheradmand4,8, Antony Rodríguez3,8 1Program in Immunology, Baylor College of Medicine, 2Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine, 3Department of Medicine - Immunology Allergy and Rheumatology, Baylor College of Medicine, 4Department of Medicine, Pulmonary, Critical Care, Sleep Medicine, Baylor College of Medicine, 5Department of Pathology and Immunology, Baylor College of Medicine, 6Department of Pediatrics, Research and Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 7Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, 8Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center This protocol demonstrates the study of the pathophysiologic effects of cigarette smoke (CS) with a whole-body inhalation (WBI) exposure system (WBIS) built in-house. This system can expose animals to CS under controlled repeatable conditions for research of CS-mediated effects on lung emphysema and hematopoiesis. Bioengineering Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome Uri Rozovski1, Inbal Hazan-Halevy2, George Calin3, David Harris4, Ping Li4, Zhiming Liu4, Michael J. Keating4, Zeev Estrov4 1Division of Hematology, Davidoff Cancer Center, Rabin Medical Center, 2The Center of Nanoscience and Nanotechnology, Tel Aviv University, 3Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 4Department of Leukemia, The University of Texas MD Anderson Cancer Center Herein we propose a strategy to study the effect of a transcription factor of interest on the microRNA transcriptome using publically available data, computational resources and high throughput data from microRNA arrays after transfecting cells with small hairpin (sh)RNA targeting a transcription factor of interest. Immunology and Infection Assessing the Development of Murine Plasmacytoid Dendritic Cells in Peyer's Patches Using Adoptive Transfer of Hematopoietic Progenitors Haiyan S. Li1, Stephanie S. Watowich1,2 1Department of Immunology, The University of Texas MD Anderson Cancer Center, 2The University of Texas Graduate School of Biomedical Sciences This protocol describes experimental procedures to assess the differentiation of plasmacytoid dendritic cells in Peyer’s patch from common dendritic cell progenitors, using techniques involving FACS-mediated cell isolation, hydrodynamic gene transfer, and flow analysis of immune subsets in Peyer’s patch.
