{
  "id": 7337200,
  "title": "ImmuneLens: linking transcriptional states and TCR clonotypes through disentangled multimodal learning",
  "url": "https://urgent.news/2026/09/14/immunelens-linking-transcriptional-states-and-tcr-clonotypes-through",
  "topic": "science",
  "section": "Science",
  "published": "2026-09-14T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.09.08.749998v1?rss=1"
  },
  "original_language": "en",
  "account": "Single-cell multi-omics technologies enable the simultaneous capture of the transcriptome and TCR sequence of T cells, offering a chance to investigate the connection between transcriptional states and clonal architectures. Nevertheless, jointly modeling the relationships between transcriptional states and TCR sequences while preserving modality-specific information proves to be a challenge. In this research, ImmuneLens, an interpretable multimodal representation learning framework, is introduced for paired single-cell transcriptome and TCR sequence data. ImmuneLens facilitates the creation of a transferable multi-cohort immune reference atlas and allows for unsupervised mapping of external query data. The integration of GEX and TCR information enhances the stability of antigen-specificity prediction. In neoadjuvant immunotherapy cohorts, ImmuneLens uncovers response-associated T cell heterogeneity and uncovers links between clonal expansion and CD8 T cell functional states. In summary, ImmuneLens offers a comprehensive solution for linking transcriptional states and TCR clonotypes through disentangled multimodal learning.",
  "summary": "Single-cell multi-omics technologies simultaneously capture the transcriptome and TCR sequence of T cells, providing an opportunity to study the relationship between transcriptional states and clonal architectures. However, jointly modeling the relationships between transcriptional states and TCR sequences while preserving modality-specific information remains challenging. Here, we present…",
  "key_points": [],
  "editors_take": null,
  "illustration": null,
  "coverage": {
    "outlets": 1,
    "also_reported_by": []
  },
  "ai_generated": true,
  "disclaimer": "Summaries, key points and the editor’s take are written by software from other outlets’ reporting and may contain errors — always check the linked original."
}