{
  "id": 9213934,
  "title": "FFPE-CUTAC: A Single Assay, Multiple Layers",
  "url": "https://urgent.news/2026/09/22/ffpe-cutac-a-single-assay-multiple-layers",
  "topic": "science",
  "section": "Science",
  "published": "2026-09-22T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753320v1?rss=1"
  },
  "original_language": "en",
  "account": "FFPE-CUTAC, a novel RNA polymerase II-targeted DNA assay, is designed to profile regulatory activity in formalin-fixed paraffin-embedded (FFPE) tissue specimens. These biobanks often contain vast collections of archived specimens, yet their limited scalability for genomic and transcriptomic profiling poses challenges. FFPE-CUTAC addresses these limitations by offering a robust solution for analyzing archival FFPE tissues.\n\nThe assay was evaluated in meningioma and breast cancer cohorts, where it was compared against matched fresh-frozen RNA-seq, FFPE RNA-seq, and FFPE whole-genome sequencing data. Over a period of up to 25 years, FFPE-CUTAC demonstrated no systematic decline in library yield or signal-quality metrics. In contrast, FFPE RNA-seq was more susceptible to degradation and specimen age-related impairments, affecting read composition, gene-body coverage, and gene detection.\n\nFFPE-CUTAC operates differently by measuring RNA polymerase II occupancy on chromatin rather than relying on mature RNA abundance. This approach is less constrained by transcript half-life, polyadenylation, or the need for specific transcript-capture designs. The assay extends its capabilities beyond gene regions to include non-coding regulatory elements, which complement its integration with existing RNA-seq cohorts for large-scale, long-term clinical association studies.\n\nA notable advantage of FFPE-CUTAC is its ability to retain DNA dosage information, enabling the recovery of chromosome-arm gain, loss, and intact states with a remarkable 96% concordance to matched whole-genome sequencing. By transforming routinely preserved pathology sections into integrated regulatory and copy-number profiles, FFPE-CUTAC offers a practical foundation for constructing clinically annotated disease maps. This foundation supports molecular stratification, prognostic modeling, and treatment-association studies, ultimately enhancing our understanding of disease mechanisms and improving patient outcomes.",
  "summary": "Background: Archival biobanks of formalin-fixed paraffin-embedded (FFPE) specimens represent a vast and underused resource for retrospective molecular studies linked to clinical follow-up. However, fixation-induced chemical modification and nucleic acid fragmentation limit scalable genomic and transcriptomic profiling. FFPE-CUTAC (Cleavage Under Targeted Accessible Chromatin) is an RNA polymerase…",
  "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."
}