{
  "abstract": "RNA sequencing has advanced our understanding of molecular heterogeneity in systemic lupus erythematosus (SLE), yet most studies have focused on differential gene expression (DGE), which overlooks transcript-level complexity. Alternative splicing and polyadenylation generate multiple isoforms from a single gene, and their dysregulation may contribute to autoimmune pathogenesis, including through the production of non-canonical isoforms with potential autoantigenic properties. To explore this underexamined dimension, we analysed differential isoform usage (DIU) and major isoform switching (MIS) across SLE subgroups stratified by autoantibody profile: anti-dsDNA+, anti-ENA+ and anti-dsDNA+ENA+. Subgroup-specific DIU and MIS events were enriched in RNA-binding and transcription-related functions. In the anti-dsDNA+ subgroup, the T-cell receptor adaptor GRAP2 showed isoform switching accompanied by expansion of a non-coding retained-intron transcript. In the anti-ENA+ subgroup, IGHM switched from the membrane-bound to the secretory form, consistent with an antibody-secreting cell signature; NACA, a reported IgE autoantigen, showed isoform switching; and BRI3, linked to TNF--induced cell death, switched toward its protein-coding transcript. In the anti-dsDNA+ENA+ subgroup, TNFAIP2, a TNF--induced gene, showed isoform redistribution with loss of a uORF-containing transcript. These findings highlight isoform regulation as a distinct, subgroup-specific and functionally relevant layer of transcriptomic dysregulation in SLE.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "R. Rai"
    },
    {
      "name": "A. Das"
    },
    {
      "name": "S. K. Chauhan"
    },
    {
      "name": "V. V. Singh"
    },
    {
      "affs": [
        0
      ],
      "name": "M. Rai"
    },
    {
      "name": "D. Velayutham"
    },
    {
      "affs": [
        0
      ],
      "name": "G. Rai"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7tah2mzm6s7jd.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.11.05.764679",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.11.05.764679v1.full",
  "id": "7tah2mzm6s7jd",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.11.05.764679v1",
  "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": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.11.05.764679v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-05",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/7tah2mzm6s7jd.ris",
  "sources": [
    {
      "first_seen": "2026-11-07T00:21:22Z",
      "native_id": "10.64898/2026.11.05.764679",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.11.05.764679v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:immunology",
      "subfield": "immunology"
    }
  ],
  "title": "Preferential Isoform Usage and Isoform Switching in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Profile",
  "title_text": "Preferential Isoform Usage and Isoform Switching in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Profile",
  "type": "preprint",
  "updated_at": "2026-11-08T00:21:07Z",
  "url": "https://research.draconitic.com/paper/7tah2mzm6s7jd",
  "venue": "bioRxiv",
  "versions": []
}