FFPE-CUTAC: A Single Assay, Multiple Layers

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.

The 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.

FFPE-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.

A 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.