{
  "abstract": "Bone-marrow mesenchymal stromal cell (MSC) isolation typically couples plastic-adherence selection to planar expansion. Therefore, the recovered cells may reflect culture adaptation as much as native stromal biology. Direct isolation within a three-dimensional matrix could reduce planar selection, but its effects on cellular recovery, composition and MSC transcriptional profiles remain insufficiently resolved. We therefore developed a gelatin methacryloyl (GelMA) workflow progressing from bulk hydrogels to medium-surrounded GelMA microbeads (GMBs) and compared 3D-derived cells with conventional 2D cultures. Qualitative live/dead staining with calcein acetoxymethyl ester (CAM) and propidium iodide (PI) and 5-ethynyl-2'-deoxyuridine (EdU) imaging established cellular activity in both GelMA formats. In bulk GelMA cultures from four human donors, CD73-, CD90- and CD105-associated flow-cytometric readouts did not increase from day 7 to day 21. At day 21, the combined marker readout was numerically higher in donor-matched 2D cultures than in bulk 3D cultures, which retained heterogeneous marker-defined populations. GMBs enabled cell recovery and flow-cytometric characterization and motivated an exploratory one-donor single-cell RNA sequencing (scRNA-seq) analysis. The final dataset contained 37,784 cells across four samples and 23 annotated populations. MSC-focused re-embedding resolved 13,175 cells into two 3D and four 2D clusters. A pooled comparison identified 4,840 differentially expressed genes (DEGs, false discovery rate [FDR]<0.01, |log2FC|[≥]1), indicating a broad method-associated expression shift. The 3D C1 cluster combined progenitor-, extracellular-matrix-, adhesion-, cytokine-, hypoxia/glycolysis- and predicted-interaction-associated programmes, whereas 2D clusters showed mitochondrial, cytoskeletal/mechanoadaptive and proliferative programmes. Thus, 2D culture yielded a more strongly represented and compositionally purer MSC compartment, while 3D isolation contained rare MSC clusters with niche-associated transcriptional profiles within a heterogeneous marrow environment. These findings support a testable native-associated tendency for 3D, but donor replication, matched recovery and direct native-reference mapping are required before inferring greater in-vivo similarity or functional superiority.",
  "abstract_shown": true,
  "affiliations": [
    "Leibniz University Hannover"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 11,
  "authors": [
    {
      "name": "N. Hussein"
    },
    {
      "name": "C. Miller"
    },
    {
      "name": "Y. Roger"
    },
    {
      "name": "L. Venturini"
    },
    {
      "name": "M. Stadler"
    },
    {
      "name": "M. Haertle"
    },
    {
      "name": "A. Lavrentieva"
    },
    {
      "name": "N. Haase"
    },
    {
      "name": "S. Rudorf"
    },
    {
      "name": "A. Hoffmann"
    },
    {
      "affs": [
        0
      ],
      "name": "D. Egger"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/70bs3gftyaf9e.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.10.758039",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.10.758039v1.full",
  "id": "70bs3gftyaf9e",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.10.758039v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "cell biology"
    ],
    [
      "openalex",
      "2716|Mesenchymal stem cell research"
    ]
  ],
  "openalex": "W7221668942",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.10.758039v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-10",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/70bs3gftyaf9e.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:27:30Z",
      "native_id": "10.64898/2026.10.10.758039",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.10.758039v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:cell biology",
      "subfield": "cell-biology"
    }
  ],
  "title": "Direct 3D isolation in gelatin methacryloyl microbeads versus conventional 2D isolation and culture: a trade-off between mesenchymal stromal cell purity and niche-associated transcriptional profiles",
  "title_text": "Direct 3D isolation in gelatin methacryloyl microbeads versus conventional 2D isolation and culture: a trade-off between mesenchymal stromal cell purity and niche-associated transcriptional profiles",
  "type": "preprint",
  "updated_at": "2026-10-30T12:27:30Z",
  "url": "https://research.draconitic.com/paper/70bs3gftyaf9e",
  "venue": "bioRxiv",
  "versions": []
}