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METHODS article

Front. Mol. Biosci.
Sec. Genome Organization and Dynamics
Volume 11 - 2024 | doi: 10.3389/fmolb.2024.1420308
This article is part of the Research Topic Methods determining Genome Organization, Structure, and Dynamics View all 6 articles

Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single-cell transcriptome analysis

Provisionally accepted
Aura Stephenson-Gussinye Aura Stephenson-Gussinye 1Luis A. Rendón-Bautista Luis A. Rendón-Bautista 2Blanca E. Ruiz-Medina Blanca E. Ruiz-Medina 2Eduardo Blanco-Olais Eduardo Blanco-Olais 1Rosario Pérez Rosario Pérez 1Cleofas Marcial-Medina Cleofas Marcial-Medina 2Yanin Chavarri Guerra Yanin Chavarri Guerra 3Enrique Soto-Perez-de-Celis Enrique Soto-Perez-de-Celis 4,5Andrea Morales-Alfaro Andrea Morales-Alfaro 4Fernando Candanedo-González Fernando Candanedo-González 6Armando Gamboa-Domínguez Armando Gamboa-Domínguez 6Ruben Cortes-González Ruben Cortes-González 7Alejandro Alfaro-Goldaracena Alejandro Alfaro-Goldaracena 7Sara E. Vazquez-Manjarrez Sara E. Vazquez-Manjarrez 8Guido Grajales-Figueroa Guido Grajales-Figueroa 9Beatriz Astudillo-Romero Beatriz Astudillo-Romero 9Jesus Ruiz-Mariquez Jesus Ruiz-Mariquez 9Augusto César Poot-Hernández Augusto César Poot-Hernández 10Paula Licona-Limón Paula Licona-Limón 2Mayra Furlan-Magaril Mayra Furlan-Magaril 1*
  • 1 Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
  • 2 Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, México, Mexico
  • 3 Department of Hemato-Oncology. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
  • 4 Department of Geriatrics. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
  • 5 University of Colorado Cancer Center, Denver, Colorado, United States
  • 6 Department of Pathology. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
  • 7 Surgical Oncology Service, Department of Surgery. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
  • 8 Department of Radiology. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
  • 9 Department of Gastrointestinal Endoscopy. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
  • 10 Unidad de Bioinformática y Manejo de Información, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico

The final, formatted version of the article will be published soon.

    Molecular and cellular characterization of tumors is essential due to the complex and heterogeneous nature of cancer. In recent decades, many bioinformatic tools and experimental techniques have been developed to achieve personalized characterization of tumors. However, sample handling continues to be a major challenge as limitations such as prior treatments before sample acquisition, the amount of tissue obtained, transportation, or the inability to process fresh samples pose a challenge for experimental strategies that require viable cell suspensions. Here, we present an optimized protocol that allows the recovery of highly viable cell suspensions from breast cancer primary tumor biopsies. Using these cell suspensions we have successfully characterized genome architecture through Hi-C. Also, we have evaluated single-cell gene expression and the tumor cellular microenvironment through single-cell RNAseq. Both technologies are key in the detailed and personalized molecular characterization of tumor samples. The protocol described here is a cost-effective alternative to obtain viable cell suspensions from biopsies simply and efficiently.pg.

    Keywords: Structural variations (SVs), Hi-C, Single Cell RNA sequencing, 3D genome architecture, breast cancer

    Received: 19 Apr 2024; Accepted: 16 Jul 2024.

    Copyright: © 2024 Stephenson-Gussinye, Rendón-Bautista, Ruiz-Medina, Blanco-Olais, Pérez, Marcial-Medina, Chavarri Guerra, Soto-Perez-de-Celis, Morales-Alfaro, Candanedo-González, Gamboa-Domínguez, Cortes-González, Alfaro-Goldaracena, Vazquez-Manjarrez, Grajales-Figueroa, Astudillo-Romero, Ruiz-Mariquez, Poot-Hernández, Licona-Limón and Furlan-Magaril. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Mayra Furlan-Magaril, Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico

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