{
  "abstract": "Distinct in vitro B-cell stimulation strategies, defined by stimulation condition and incubation duration, have been described in diverse studies. Often, these approaches are considered interchangeable due to comparable flow-cytometric outputs concerning fluorescence intensities and B-cell subset distributions. However, whether these phenotypic similarities also reflect comparable underlying transcriptional states have not been systematically evaluated yet. In this study, we provide an unbiased comparison of B-cell activation strategies on healthy individuals, resulting in a single-cell transcriptomic atlas (4 donors; ~2,029 cells per sample; 81,160 cells in total with 56.3% annotated as B cells). Two T-cell independent stimulators targeting toll-like receptors (ODN2006 and IFN-{gamma}/R-848), were assessed next to two T-cell dependent stimulators (anti-CD40 and anti-CD3/CD28 antibodies), all incubated for eight and 30 hours. Observed overlap for differential abundance, differential gene expression and cell-cell interactions could directly be linked to T-cell (in)dependent working mechanism. Strategy-specific results uncovered time-point specific transcriptional changes, revealed the largest set of differentially expressed genes for IFN-{gamma}/R-848 and ODN2006, and showed that IFN-{gamma}/R-848 and anti-CD3/CD28 induced the majority of the cell-cell interactions. Ultimately, our reference atlas emphasizes the importance and facilitates the rational selection of optimal B-cell stimulation strategies, particularly for studies aiming to interrogate B-cell dysregulation in immune-mediated diseases.",
  "abstract_shown": true,
  "affiliations": [
    "VIB - Ghent University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "name": "T. D'hamers"
    },
    {
      "name": "J. Neirinck"
    },
    {
      "name": "M. Buysse"
    },
    {
      "name": "C. De Vriendt"
    },
    {
      "name": "T. Kerre"
    },
    {
      "name": "F. Haerynck"
    },
    {
      "name": "M. Hofmans"
    },
    {
      "name": "C. Bonroy"
    },
    {
      "affs": [
        0
      ],
      "name": "C. Everaert"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/da4j5y9734z2c.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.22.760934",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.22.760934v1.full",
  "id": "da4j5y9734z2c",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.22.760934v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "immunology"
    ],
    [
      "openalex",
      "2403|T-cell and B-cell Immunology"
    ]
  ],
  "openalex": "W7223817407",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.22.760934v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-22",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/da4j5y9734z2c.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:53Z",
      "native_id": "10.64898/2026.10.22.760934",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.22.760934v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:immunology",
      "subfield": "immunology"
    }
  ],
  "title": "Stimulation strategy matters: A B-cell focused single-cell transcriptomic study on in vitro stimulated immune cells",
  "title_text": "Stimulation strategy matters: A B-cell focused single-cell transcriptomic study on in vitro stimulated immune cells",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:53Z",
  "url": "https://research.draconitic.com/paper/da4j5y9734z2c",
  "venue": "bioRxiv",
  "versions": []
}