{
  "abstract": "NF{kappa}B signaling drives inflammatory responses by rapidly assembling membrane-proximal multiprotein supercomplexes, yet how these assemblies are organized in space and time within the 3D interior of a single cell has remained uncharacterized. We addressed this by profiling endogenous NF{kappa}B protein-protein interactions with an intelligent sequential proximity ligation assay (iseqPLA), read out by spinning disk confocal microscopy and 3D reconstruction. Each detected protein-protein proximity event is represented by a rolling-circle amplification product, and we treat clusters of co-localized puncta as a measure of supercomplex spatial organization. Across NIH-3T3 mouse fibroblasts, cystic fibrosis (CF) patient-derived macrophage co-cultures with IMR-90 human fibroblasts, and an independent set of healthy- and CF-donor monocyte-fibroblast co-cultures profiled by 3D iseqPLA, we tracked supercomplex dissociation, p65 nuclear translocation, and negative-feedback engagement across cytokine time courses. Three findings emerge: 3D volumetric quantification reduces the variance in nuclear-to-cytoplasmic ratio measurements relative to 2D projections, the choice of extracellular matrix coating shapes the fraction of NF{kappa}B-responsive cells, and CF airway-conditioned macrophages amplify paracrine NF{kappa}B signaling in neighboring fibroblasts in a CF model. A single-cell Generative Pretrained Transformer (scGPT) foundation model, fine-tuned on curated transcriptomic datasets, further places our NF{kappa}B gene panel within an inflammation-relevant feature space. Together, these results establish a 3D spatial interactomics workflow for dissecting supercomplex dynamics in health and disease.",
  "abstract_shown": true,
  "affiliations": [
    "Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA; Interdisciplinary Bioengineerin"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "name": "N. Zhang"
    },
    {
      "name": "C. Leese-Thompson"
    },
    {
      "name": "H. Ozuna"
    },
    {
      "name": "B. Peng"
    },
    {
      "name": "S. Sirigireddy"
    },
    {
      "name": "D. Nambiar"
    },
    {
      "name": "L. Ramanan"
    },
    {
      "name": "R. Tirouvanziam"
    },
    {
      "name": "B. Kopp"
    },
    {
      "affs": [
        0
      ],
      "name": "A. F. Coskun"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9st1pnh9fyazk.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.14.751198",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751198v1.full",
  "id": "9st1pnh9fyazk",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751198v1",
  "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",
      "bioengineering"
    ],
    [
      "openalex",
      "1306|NF-κB Signaling Pathways"
    ]
  ],
  "openalex": "W7213500588",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751198v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-14",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9st1pnh9fyazk.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:22:55Z",
      "native_id": "10.64898/2026.09.14.751198",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751198v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioengineering",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "3D Spatial Interactomics Maps the Dynamics of NF-κB Multiprotein Signalosomes in Single Cells",
  "title_text": "3D Spatial Interactomics Maps the Dynamics of NF-κB Multiprotein Signalosomes in Single Cells",
  "type": "preprint",
  "updated_at": "2026-10-30T12:22:55Z",
  "url": "https://research.draconitic.com/paper/9st1pnh9fyazk",
  "venue": "bioRxiv",
  "versions": []
}