{
  "abstract": "Three-dimensional (3D) spheroid models have become essential in cancer biology, drug screening, and tissue engineering. However, their small size, fragile structure, and tendency to disintegrate during routine histoprocessing present persistent technical challenges. Conventional paraffin embedding often results in tissue fragmentation, loss of spatial orientation, and poor section quality, whereas cryosectioning often compromises cellular morphology. Here, we present a robust, cost-effective protocol for preserving and sectioning fragile 3D spheroids, resulting in high-quality histological sections with intact architecture and excellent cellular detail. The method involves optimized handling and embedding procedures that stabilize spheroids during standard formalin fixation, paraffin infiltration, and microtomy, eliminating mechanical distortion and preserving spherical integrity for consistent sectioning. We demonstrate the successful application of this protocol across different tumor spheroids derived from distinct tissue types, including MDA-MB-231 (breast carcinoma), Caco-2 (colorectal adenocarcinoma), and A549 (lung carcinoma) cell lines, with subsequent compatibility with hematoxylin and eosin (H&E) staining protocols. This protocol is compatible with immunohistochemistry (IHC) and immunofluorescence (IF). In our qualitative comparison with conventional methods, we found that our approach effectively limits sample loss, promotes consistent inter-section reproducibility, and preserves fine structural features, such as necrotic cores, proliferative zones, and extracellular matrix components. This protocol provides a reliable, accessible solution for routine histological analysis of fragile 3D spheroids, facilitating more accurate morphological assessment in translational research settings.\n\nKey features\n\n• Cost-effective agarose-coated plates for reproducible spheroid formation.\n\n• Complete in-tube processing to minimize sample loss and damage.\n\n• Floating tube system for reliable paraffin infiltration without specialized equipment.\n\n• Produces high-quality sections compatible with H&E.\n\nGraphical overview",
  "abstract_shown": true,
  "affiliations": [
    "Centro Multidisciplinario de Estudios en Biotecnología (CMEB), Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México",
    "Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México",
    "Secretaría de Ciencia, Humanidades, Tecnología e Innovación, Ciudad de México, México",
    "Instituto de Investigaciones Sobre los Recursos Naturales. Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México"
  ],
  "article_type": "methods article",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Ramón Cervantes-Rivera"
    },
    {
      "affs": [
        0
      ],
      "name": "Sandra Jetsamari Figueroa Ortiz"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Atalia Ziret Romero Rosas"
    },
    {
      "affs": [
        1
      ],
      "name": "Adrián Sánchez Orozco"
    },
    {
      "affs": [
        3
      ],
      "name": "Ma. Antonia Herrera-Vargas"
    },
    {
      "affs": [
        3
      ],
      "name": "Esperanza Meléndez-Herrera"
    },
    {
      "affs": [
        1
      ],
      "name": "Manuel López Rodríguez"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Alejandra Ochoa-Zarzosa"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Joel E. López-Meza"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/843r9f58bvkvd.bib",
  "cited_by": 0,
  "doi": "10.21769/bioprotoc.5850",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13710297/",
  "id": "843r9f58bvkvd",
  "issns": [
    "2331-8325"
  ],
  "landing_url": "https://doi.org/10.21769/bioprotoc.5850",
  "language": "en",
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Biology"
    ],
    [
      "heading",
      "Clinical Protocols"
    ],
    [
      "heading",
      "Methods Article"
    ],
    [
      "openalex",
      "2204|3D Printing in Biomedical Research"
    ]
  ],
  "openalex": "W7221310662",
  "pdf_url": null,
  "pmcid": "PMC13710297",
  "pmid": "42947815",
  "published": "2026-10-20",
  "publisher": "Bio-protocol, LLC",
  "ris": "https://research.draconitic.com/paper/843r9f58bvkvd.ris",
  "sources": [
    {
      "first_seen": "2026-10-31T12:21:17Z",
      "native_id": "PMC13710297",
      "source": "pmc",
      "url": "https://doi.org/10.21769/bioprotoc.5850"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "journal-openalex:1312|Molecular Biology Techniques and Applications",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Microtube-Assisted Paraffin Embedding and Sectioning of Fragile 3D Tumor Spheroids for High-Quality Histology",
  "title_text": "Microtube-Assisted Paraffin Embedding and Sectioning of Fragile 3D Tumor Spheroids for High-Quality Histology",
  "type": "peer-reviewed",
  "updated_at": "2026-10-31T12:21:17Z",
  "url": "https://research.draconitic.com/paper/843r9f58bvkvd",
  "venue": "Bio-protocol",
  "versions": []
}