Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

Area of Science:

• Molecular Biology
• Epigenetics
• Genomics

Background:

• Formalin-fixed paraffin-embedded (FFPE) is a standard for preserving biological samples.
• FFPE processing can damage chromatin, hindering epigenomic analysis.
• Previous methods like CUT&Tag have limitations with FFPE samples.

Purpose of the Study:

• To adapt the CUTAC protocol for epigenomic profiling of FFPE samples.
• To generate high-resolution chromatin accessibility maps from FFPE tissues.
• To assess the utility of FFPE-CUTAC for biomarker identification and clinical applications.

Main Methods:

• Modified Cleavage Under Targeted Accessible Chromatin (CUTAC) protocol for FFPE samples.
• Application of the protocol in single tubes and directly on slides.
• Analysis of paused RNA Polymerase II at regulatory elements.

Main Results:

• High-resolution epigenomic maps were generated from FFPE samples.
• FFPE-CUTAC successfully distinguished between mouse brain tumors based on regulatory elements.
• Identified and mapped regulatory element markers, including microRNAs, with high precision.
• Demonstrated feasibility of epigenomic profiling on archived FFPE specimens.

Conclusions:

• Modified CUTAC protocols (FFPE-CUTAC) enable robust epigenomic profiling of FFPE samples.
• This method overcomes chromatin damage issues associated with FFPE preparation.
• FFPE-CUTAC facilitates biomarker discovery and retrospective clinical studies using archived tissues.