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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- 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
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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