University of Texas MD Anderson Cancer Center

10 ARTICLES PUBLISHED IN JoVE

Medicine

Working with Human Tissues for Translational Cancer Research

Alexandre Reuben^*1, Vancheswaran Gopalakrishnan^*1, Heidi E. Wagner³, Christine N. Spencer², Jacob Austin-Breneman¹, Hong Jiang¹, Zachary A. Cooper¹, Jennifer A. Wargo¹

¹Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, ²Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, ³Department of Pathology and Institutional Tissue Bank, University of Texas MD Anderson Cancer Center

Translational cancer research is dependent on extraction of human tissues. Much work has gone into optimizing extraction methods for ex vivo analysis. Here, we describe tissue processing methods allowing for maximal data output from limited samples.

Developmental Biology

Technique to Target Microinjection to the Developing Xenopus Kidney

Bridget D. DeLay¹, Vanja Krneta-Stankic^1,2, Rachel K. Miller^1,2,3,4

¹Department of Pediatrics, Pediatric Research Center, University of Texas McGovern Medical School, ²Program in Genes & Development, University of Texas Graduate School of Biomedical Sciences, ³Program in Cell & Regulatory Biology, University of Texas Graduate School of Biomedical Sciences, ⁴Department of Genetics, University of Texas MD Anderson Cancer Center

Here, we present a protocol to use fate maps and lineage tracers to target injections into individual blastomeres that give rise to the kidney of Xenopus laevis embryos.

Biology

En Face Preparation of Mouse Blood Vessels

Kyung Ae Ko¹, Keigi Fujiwara¹, Sunil Krishnan², Jun-ichi Abe¹

¹Department of Cardiology, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, ²Department of Radiation Oncology, University of Texas MD Anderson Cancer Center

A procedure for making en face preparations of the mouse carotid artery and aorta is described. Such preparations, when immunofluorescently stained with specific antibodies, enable us to study localization of proteins and identification of cell types within the entire vascular wall by confocal microscopy.

Immunology and Infection

In Vivo Assay for Detection of Antigen-specific T-cell Cytolytic Function Using a Vaccination Model

Cara L. Haymaker^*1, Yared Hailemichael^*1, Yi Yang^2,3, Roza Nurieva²

¹Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, ²Department of Immunology, University of Texas MD Anderson Cancer Center, ³Department of Radiation Oncology, The Second Hospital of Jilin University

The goal of this protocol is to allow for detection of in vivo antigen-specific killing of a target cell in a murine model.

Cancer Research

Preparation of Primary Acute Lymphoblastic Leukemia Cells in Different Cell Cycle Phases by Centrifugal Elutriation

Magdalena Delgado^*1, Anisha Kothari^*1, Walter N. Hittelman², Timothy C. Chambers¹

¹Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, ²Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center

This protocol describes the use of centrifugal elutriation to separate primary acute lymphoblastic leukemia cells into different cell cycle phases.

Cancer Research

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Christopher Terranova¹, Ming Tang¹, Elias Orouji¹, Mayinuer Maitituoheti¹, Ayush Raman¹, Samirkumar Amin², Zhiyi Liu¹, Kunal Rai¹

¹Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, ²The Jackson Laboratory for Genomic Medicine

Here, we describe an optimized high-throughput ChIP-sequencing protocol and computational analyses pipeline for the determination of genome-wide chromatin state patterns from frozen tumor tissues and cell lines.

Medicine

Radiation Planning Assistant - A Streamlined, Fully Automated Radiotherapy Treatment Planning System

Laurence E. Court¹, Kelly Kisling¹, Rachel McCarroll¹, Lifei Zhang¹, Jinzhong Yang¹, Hannah Simonds², Monique du Toit², Chris Trauernicht², Hester Burger³, Jeannette Parkes³, Mike Mejia⁴, Maureen Bojador⁴, Peter Balter¹, Daniela Branco¹, Angela Steinmann¹, Garrett Baltz¹, Skylar Gay¹, Brian Anderson¹, Carlos Cardenas¹, Anuja Jhingran⁵, Simona Shaitelman⁵, Oliver Bogler⁶, Kathleen Schmeller⁷, David Followill¹, Rebecca Howell¹, Christopher Nelson¹, Christine Peterson⁸, Beth Beadle^5,9

¹Department of Radiation Physics, University of Texas MD Anderson Cancer Center, ²Department of Radiation Oncology, Stellenbosch University and Tygerberg Hospital, ³Departments of Radiation Oncology and Medical Physics, Groote Schuur Hospital and University of Cape Town, ⁴Department of Radiation Oncology, University of Santo Tomas Hospital, Benavides Cancer Institute, ⁵Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, ⁶Academic Affairs, University of Texas MD Anderson Cancer Center, ⁷Department of Gynecological Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, ⁸Department of Biostatistics, University of Texas MD Anderson Cancer Center, ⁹Department of Radiation Oncology, Stanford University

Radiation therapy is a highly complex cancer treatment that requires multiple specialists to create a treatment plan and provide quality assurance (QA) prior to delivery to a patient. This protocol describes the use of a fully automated system, the Radiation Planning Assistant (RPA), to create high-quality radiation treatment plans.

Cancer Research

Generation and Expansion of Primary, Malignant Pleural Mesothelioma Tumor Lines

Tamara M. Griffiths¹, Carlos Ramos¹, Cara L. Haymaker¹

¹Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center

The goal of this method paper is to demonstrate a robust and reproducible methodology for the enrichment, generation, and expansion of primary tumor cell lines from surgically resected pleural mesothelioma.

Neuroscience

Mechanical Conflict-Avoidance Assay to Measure Pain Behavior in Mice

Caitlyn M. Gaffney¹, Gabriella Muwanga², Huaishuang Shen², Vivianne L. Tawfik², Andrew J. Shepherd²

¹Laboratories of Neuroimmunology, Department of Symptom Research, and the MD Anderson Pain Research Consortium, University of Texas MD Anderson Cancer Center, ²Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine

The mechanical conflict-avoidance assay is used as a non-reflexive readout of pain sensitivity in mice which can be used to better understand affective-motivational responses in a variety of mouse pain models.

Genetics

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Junwoo Lee¹, Biji Chatterjee^1,2, Nakyung Oh¹, Dhurjhoti Saha¹, Yue Lu¹, Blaine Bartholomew¹, Charles A. Ishak^1,3

¹Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, ²Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, ³Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center

This protocol guides bioinformatics beginners through an introductory CUT&RUN analysis pipeline that enables users to complete an initial analysis and validation of CUT&RUN sequencing data. Completing the analysis steps described here, combined with downstream peak annotation, will allow users to draw mechanistic insights into chromatin regulation.