{
  "abstract": "Systemic amyloidoses are initiated by distinct amyloidogenic precursor proteins but frequently contain recurrent extracellular, complement, lipid-transport and matrix-remodelling components. Whether these recurrent proteins form a conserved systems-level environment across amyloid diseases, and how strongly that environment depends on precursor and tissue context, remains unresolved. We developed FibrilNet, a network framework that integrates experimentally defined amyloid proteomes with a human protein protein interaction graph and Gene Ontology derived semantic information. FibrilNet compares topology-only random walk with restart (RWR) with ontology aware semantic RWR in frozen leave-one-out module reconstruction and precursor-seeded prioritization tasks. The human graph contains 17,997 proteins and 925,977 physical interactions, with a 9-dimensional semantic representation of interaction context. In expanded cardiac transthyretin amyloidosis (ATTR), semantic-RWR increased mean reciprocal rank (MRR) from 0.00167 to 0.05015 and Recall@100 from 0.0199 to 0.3377, improving 132 of 151 held-out targets. Significant semantic gains were also observed in renal serum amyloid A amyloidosis (AA) and leukocyte chemotactic factor 2 amyloidosis (ALECT2). Across compact ATTR, light-chain amyloidosis (AL), AA and ALECT2 modules, APCS, VTN and TIMP3 formed a direct four-disease recurrent core, while APOE occurred in three of four modules. A tissue-aware ATTR analysis showed limited overlap between cardiac and neurologic modules (19 shared proteins; Jaccard 0.0569). In the hTTR-A97S peripheral-nerve model, semantic-RWR significantly improved reconstruction of the 202-protein mapped neurologic module, with the strongest evidence concentrated in the downregulated proteomic program. TTR-seeded propagation improved with semantic information but remained weak in absolute terms, separating precursor identity from the distributed downstream molecular environment. These results support a multilayer model in which a restricted conserved amyloid environment coexists with precursor-, tissue- and disease-specific organization",
  "abstract_shown": true,
  "affiliations": [
    "University of Catanzaro"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "P. H. Guzzi"
    },
    {
      "name": "L. H. Ugo"
    },
    {
      "name": "V. Carbonari"
    },
    {
      "name": "P. Lio'"
    },
    {
      "name": "P. Veltri"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fq9w0cx6rn9hq.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.29.747993",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.29.747993v1.full",
  "id": "fq9w0cx6rn9hq",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.29.747993v1",
  "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",
      "bioinformatics"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.29.747993v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-29",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/fq9w0cx6rn9hq.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:07Z",
      "native_id": "10.64898/2026.08.29.747993",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.29.747993v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "FibrilNet maps conserved and tissue-specific molecular environments across systemic amyloidoses",
  "title_text": "FibrilNet maps conserved and tissue-specific molecular environments across systemic amyloidoses",
  "type": "preprint",
  "updated_at": "2026-10-30T12:19:07Z",
  "url": "https://research.draconitic.com/paper/fq9w0cx6rn9hq",
  "venue": "bioRxiv",
  "versions": []
}