Main description:

This extensive book brings together leading melanoma researchers from across the world and highlights many of the cutting-edge protocols and experimental systems currently being used to investigate questions surrounding this disease. The volume opens with sections on 2D and 3D cell culture-based approaches for studying melanoma biology, and continues with collections of chapters examining various approaches for detecting, isolating, and characterizing circulating melanoma cells, circulating tumor DNA, and exosomes, as well as experimental procedures for studying and detecting melanoma metastasis in both pre-clinical and clinical settings, bioinformatics-based approaches, protocols for quantifying and characterizing immune cell infiltrates in both melanoma tumors and tertiary lymphoid structures, and development and evaluation of therapeutic strategies for melanoma treatment. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and comprehensive, Melanoma: Methods and Protocols aims to serve basic research scientists and clinicians who bring questions from the clinic into the lab in order to translate observations in the laboratory into improved patient care for this highly malignant form of cancer.

Chapter 14 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Contents:

1. Model Systems for the Study of Malignant Melanoma

Randal K. Gregg

Part I: 2D Cell Culture-Based Approaches for Studying Melanoma Biology

2. Generation of Functional Gene Knockout Melanoma Cell Lines by CRISPR-Cas9 Gene Editing

Kristian M. Hargadon, David Z. Bushhouse, Coleman E. Johnson, and Corey J. Willams

3. A Fluorescent Gelatin Degradation Assay to Study Melanoma Breakdown of Extracellular Matrix

Ewa Mazurkiewicz, Ewa Mrowczynska, Aleksandra Simiczyjew, Dorota Nowak, and Antonina J. Mazur

4. Wound Healing Assay for Melanoma Cell Migration

Juliano T. Freitas, Ivan Jozic, and Barbara Bedogni

5. A Fluorescence-Based Assay for Measuring Glucose Uptake in Living Melanoma Cells

Jelena Grahovac, Marijana Pavlovic, and Marija Vidosavljevic

6. Analyzing Melanoma Cell Oxygen Consumption and Extracellular Acidification Rates Using Seahorse Technology

Ashley V. Menk and Greg M. Delgoffe

7. Analysis of Melanoma Cell Glutamine Metabolism by Stable Isotope Tracing and Gas Chromatography-Mass Spectrometry

David A. Scott

8. Determination of Cytotoxic Activities Against Melanoma Cells Using Flow Cytometry

Guilan Shi and Richard Heller

9. In Vitro Differentiation of Tumor-Associated Macrophages from Monocyte Precursors with Modified Melanoma-Conditioned Medium

Tao Wang and Russel E. Kaufman

10. A Flow Cytometric Assay for Investigating Melanoma Cell Adhesion to Lymphatic Endothelial Cells

Kristian M. Hargadon and Coleman E. Johnson

Part II: 3D Cell Culture Systems for Studying Melanoma

11. An Approach to Study Melanoma Invasion and Crosstalk with Lymphatic Endothelial Cell Spheroids in 3D Using Immunofluorescence

Sanni Alve, Silvia Gramolelli, and Paivi M. Ojala

12. Evaluating Melanoma Viability and Proliferation in 3D Microenvironments

Vasanth Siruvallur Murali, Murat Can Cobanoglu, and Erik S. Welf

13. Preparation, Drug Treatment, and Immunohistological Analysis of Tri-Culture Spheroid 3D Melanoma-Like Models

Maximilian E.A. Schafer, Julia Klicks, Mathias Hafner, and Rudiger Rudolf

14. Enrichment of Melanoma Cancer Stem Cells via Sphere Assays

Nabanita Mukherjee, Karoline A. Lambert, David A. Norris, and Yiqun G. Shellman

Part III: Techniques for Isolating and Studying Circulating Melanoma Cells

15. Capture and Isolation of Circulating Melanoma Cells Using Photoacoustic Flowmetry

Robert H. Edgar, Justin Cook, Madeline Douglas, Anie-Pier Samson, and John A. Viator

16. Multi-Marker Immunomagnetic Enrichment of Circulating Melanoma Cells

Aaron B. Beasley, Emmanuel Acheampong, Weitao Lin, and Elin S. Gray

17. PD-L1 Detection on Circulating Melanoma Cells

Joseph W. Po, Yafeng Ma, Bavanthi Balakrishnar, Daniel Brungs, Farhad Azimi, Adam Cooper, Erin Saricilar, Vinay Murthy, Paul de Souza, and Therese M. Becker

18. Transcript-Based Detection of Circulating Melanoma Cells

Michael Morici, Weitao Lin, and Elin S. Gray

19. Isolation and Quantification of Plasma Circulating Tumor DNA from Melanoma Patients

Gabriela Marsavela, Anna Reid, Elin S. Gray, and Leslie Calapre

20. Simultaneous BRAFV600E Protein and DNA Aberration Detection in Circulating Melanoma Cells Using an Integrated Multi-Molecular Sensor

Alain Wuethrich, Shuvashis Dey, Kevin M. Koo, Abu A.I. Sina, and Matt Trau

21. Single Cell Analysis of BRAFV600E and NRASQ61R Mutation Status in Melanoma Cell Lines as Method Generation for Circulating Melanoma Cells

Joseph W. Po, Yafeng Ma, Alison W.S. Luk, David Lynch, Bavanthi Balakrishnar, Daniel Brungs, Farhad Azimi, Adam Cooper, Erin Saricilar, Vinay Murthy, Paul de Souza, and Therese M. Becker

Part IV: Methods to Study Melanoma-Derived and Melanoma-Associated Exosomes

22. A Rapid Exosome Isolation Using Size Exclusion Chromatography (REIUS) Method for Exosome Isolation from Melanoma Cell Lines

Shin La Shu, Cheryl L. Allen, Shawna Benjamin-Davalos, Marina Koroleva, Don MacFarland, Hans Minderman, and Marc S. Ernstoff

23. Immunoaffinity-Based Isolation of Melanoma Cell-Derived and T Cell-Derived Exosomes from Plasma of Melanoma Patients

Sujan Kumar Mondal and Theresa L. Whiteside

24. An Immunocapture-Based Assay for Detecting Multiple Antigens in Melanoma-Derived Extracellular Vesicles

Carmen Campos-Silva, Yaiza Caceres-Martell, Sheila Lopez-Cobo, Maria Josefa Rodriguez, Ricardo Jara, Maria Yanez-Mo, and Mar Vales-Gomez

25. Post-Lymphadenectomy Analysis of Exosomes from Lymphatic Exudate/Exudative Seroma of Melanoma Patients

Susana Garcia-Silva, Pilar Ximenez-Embun, Javier Munoz, and Hector Peinado

Part V: Assessing Melanoma Metastasis in Pre-Clinical and Clinical Settings

26. Fate Mapping of Cancer Cells in Metastatic Lymph Nodes Using Photoconvertible Proteins

Ethel R. Pereira, Dmitriy Kedrin, and Timothy P. Padera

27. Detection of Melanoma Cells in Lymphatic Drainage (LD) after Lymph Nodes Dissection via Nested RT-PCR Analysis of Molecular Melanocytic Markers

Aleksandra Gos, Piotr Rutkowski, and Janusz A. Siedlecki

28. A Clonogenic Assay to Quantify Melanoma Micrometastases in Pulmonary Tissue

Fabrizio Mattei, Sara Andreone, and Giovanna Schiavoni

29. PET Imaging of Melanoma Using Melanin-Targeted Probe

Xiaowei Ma and Zhen Cheng

30. Imaging and Isolation of Extravasation-Participating Endothelial and Melanoma Cells During Angiopellosis

Tyler A. Allen and Ke Cheng

Part VI: Strategies for Diagnostic and Prognostic Biomarker Identification for Melanoma and Computational/Bioinformatic Approaches to OMICS Analysis of Melanoma

31. Salivary Proteomic Analysis of Canine Oral Melanoma by MALDI-TOF Mass Spectrometry and LC-Mass Spectrometry/Mass Spectrometry

Sekkarin Ploypetch, Sittiruk Roytrakul, and Gunnaporn Suriyaphol

32. Detection of Uveal Melanoma by Multiplex Immunoassays of Serum Biomarkers

Jin Song, Zhen Zhang, and Daniel W. Chan

33. Unbiased Microbiome and Metabolomic Profiling of Fecal Samples from Patients with Melanoma

Ashley Bui, Yongbin Choi, Arthur E. Frankel, and Andrew Y. Koh

34. Assessment of Cell-Free microRNA by NGS Whole Transcriptome Analysis in Cutaneous Melanoma Patients' Blood

Kevin D. Tran, Rebecca Gross, Negin Rahimzadeh, Shanthy Chenathukattil, Dave S.B. Hoon, and Matias A. Bustos

35. High-Throughput Identification of miRNA-Target Interactions in Melanoma Using miR-CATCHv2.0

Andrea Marranci, Romina D'Aurizio, Milena Rizzo, Catherine M. Greene, and Laura Poliseno

Part VII: Characterization of Melanoma-Associated Tumor-Infiltrating Lymphocytes and Tertiary Lymphoid Structures

36. Immunotyping and Quantification of Melanoma Tumor-Infiltrating Lymphocytes

Max O. Meneveau, Zeyad T. Sahli, Kevin T. Lynch, Ileana S. Mauldin, and Craig L. Slingluff, Jr.

37. Single Cell Gene Expression, Clonality, and Feature Barcoding of Melanoma Tumor Infiltrating Lymphocytes

Angela Pizzolla, Simon Keam, Criselle D'Souza, Timothy Semple, and Paul J. Neeson

38. Using Mass Cytometry to Analyze the Tumor-Infiltrating Lymphocytes in Human Melanoma

Daniela Tantalo, Thu Nguyen, Han Xian Aw Yeang, Joe Zhu, Sean Macdonald, Minyu Wang, Harini de Silva, Criselle D'Souza, Angela Pizzolla, and Paul J. Neeson

39. Multiplex Immunohistochemistry Analysis of Melanoma Tumor Infiltrating Lymphocytes

Thu Nguyen, Nikolce Kocovski, Sean Macdonald, Han Xian Aw Yeang, Minyu Wang, and Paul J. Neeson

40. Multiplex Immunofluorescence Histology for Immune Cell Infiltrates in Melanoma-Associated Tertiary Lymphoid Structures

Ileana S. Mauldin, Adela Mahmutovic, Samuel J. Young, and Craig L. Slingluff, Jr.

Part VIII: Development and Evaluation of Therapeutic Strategies for Melanoma Treatment

41. The Use of Nanoparticles in the Delivery of Nucleic Acids for Melanoma Treatment

Mohammad A. Obeid, Alaa A.A. Aljabali, Meriem Rezigue, Haneen Amawi, Hanin Alyamani, Shatha N. Abdeljaber, and Valerie A. Ferro

42. siRNA Delivery to Melanoma Cells with Cationic Niosomes

Mohammad A. Obeid, Hanin Alyamani, Haneen Amawi, Alaa A.A. Aljabali, Meriem Rezigue, Shatha N. Abdeljaber, and Valerie A. Ferro

43. Controlled Delivery of Plasmid DNA to Melanoma Tumors by Gene Electrotransfer

Richard Heller and Guilan Shi

44. Generation of Murine Chimeric Antigen Receptor T Cells for Adoptive T Cell Therapy for Melanoma

Amorette Barber

45. Generation of Phosphopeptide-Specific T Cell Lines as Tools for Melanoma Immunotherapy

Rebecca C. Obeng and Angela L. Ambakhutwala