What question did this study set out to answer?

This research aims to enhance molecular characterization of peripheral T-cell lymphomas (PTCL) using FFPE samples by mapping transcriptional activation.

June 26, 2026

Abstract A039: FFPE-CUT&Tag transcriptional activation mapping in FFPE patient biopsies reveals novel druggable pathways in lymphoma

Key Points

This research aims to enhance molecular characterization of peripheral T-cell lymphomas (PTCL) using FFPE samples by mapping transcriptional activation.
Developed FFPE-CUT&Tag to map RNA Polymerase II occupancy in FFPE samples.
Utilized optimized antibody selection and workflows for genome-wide profiling.
Conducted comparative analysis against FFPE-ATAC and conventional ATAC methodologies.
FFPE-CUT&Tag provided high-quality transcriptional profiles with strong enrichment at regulatory elements.
Identified transcriptional activation at AP-1 loci, including BATF3, linked to oncogenic pathways such as IL-2/STAT5, PI3K–AKT, and TP53.
Demonstrated improved resolution and signal-to-noise ratios compared to existing methods.

Abstract

Abstract Peripheral T-cell lymphomas (PTCL) are aggressive malignancies where clinical assessment relies on formalin-fixed paraffin-embedded (FFPE) biopsies, yet molecular characterization of these samples remains limited by RNA degradation and poor performance of existing genomic assays. This constraint has hindered the ability to define active regulatory programs directly in patient tissue. To address this challenge, we developed FFPE-CUT all authors reviewed and approved the final content. Citation Format: Andrea L. Johnstone, Eva Brill, Vishnu U. Sunitha Kumary, Makoto Iwasaki, Eric Minwei Liu, Morgan Oatley, Alysha E. Simmons, Eva Oswald, Georg Kuales, Julia B. Schueler, Keith Maier, Martis W. Cowles, Bryan J. Venters, Salvia Jain, Michael-Christopher Keogh. FFPE-CUT 2026 Jun 24-27; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2026;7 (3Suppl): Abstract nr A039.

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