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Profiling Chromosome Topological Features by Super-Resolution 3D Structured Illumination Microscopy

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Cancer Cytogenetics and Cytogenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2825))

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Abstract

Three-dimensional structured illumination microscopy (3D-SIM) and fluorescence in situ hybridization on three-dimensional preserved cells (3D-FISH) have proven to be robust and efficient methodologies for analyzing nuclear architecture and profiling the genome’s topological features. These methods have allowed the simultaneous visualization and evaluation of several target structures at super-resolution. In this chapter, we focus on the application of 3D-SIM for the visualization of 3D-FISH preparations of chromosomes in interphase, known as Chromosome Territories (CTs). We provide a workflow and detailed guidelines for sample preparation, image acquisition, and image analysis to obtain quantitative measurements for profiling chromosome topological features. In parallel, we address a practical example of these protocols in the profiling of CTs 9 and 22 involved in the translocation t(9;22) in Chronic Myeloid Leukemia (CML). The profiling of chromosome topological features described in this chapter allowed us to characterize a large-scale topological disruption of CTs 9 and 22 that correlates directly with patients’ response to treatment and as a possible potential change in the inheritance systems. These findings open new insights into how the genome structure is associated with the response to cancer treatments, highlighting the importance of microscopy in analyzing the topological features of the genome.

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Author information

Authors and Affiliations

  1. Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico

    Eunice Fabian-Morales & Adriana Gudiño

  2. Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico

    Eunice Fabian-Morales, Adriana Gudiño & Luis A. Herrera

  3. Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico

    Eunice Fabian-Morales, Alfredo Rodríguez, Luis A. Herrera & Sara Frias

  4. Instituto Nacional de Pediatría (INP), Mexico City, Mexico

    Alfredo Rodríguez

  5. Escuela de Medicina y Ciencias de la Salud, Instituto Tecnológico y de Estudios Superiores de Monterrey, Mexico City, Mexico

    Luis A. Herrera

  6. Laboratorio de Citogenética, Instituto Nacional de Pediatría (INP), Mexico City, Mexico

    Sara Frias

Authors
  1. Eunice Fabian-Morales
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  2. Alfredo Rodríguez
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  3. Adriana Gudiño
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  4. Luis A. Herrera
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  5. Sara Frias
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Corresponding authors

Correspondence to Luis A. Herrera or Sara Frias .

Editor information

Editors and Affiliations

  1. Department of Lymphoma/Myeloma, UT MD Anderson Cancer Center, Houston, TX, USA

    **g Christine Ye

  2. Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA

    Henry H. Heng

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Fabian-Morales, E., Rodríguez, A., Gudiño, A., Herrera, L.A., Frias, S. (2024). Profiling Chromosome Topological Features by Super-Resolution 3D Structured Illumination Microscopy. In: Ye, J.C., Heng, H.H. (eds) Cancer Cytogenetics and Cytogenomics. Methods in Molecular Biology, vol 2825. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3946-7_12

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  • DOI: https://doi.org/10.1007/978-1-0716-3946-7_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3945-0

  • Online ISBN: 978-1-0716-3946-7

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