FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers

Area of Science:

• Epigenetics
• Molecular Biology
• Cancer Research

Background:

• Archived formalin-fixed paraffin-embedded (FFPE) tissues are crucial for cancer research and understanding gene regulation.
• Current methods for profiling histone modifications in FFPE tissues require substantial amounts of tissue, limiting detailed analysis.
• There is a need for sensitive methods that utilize minimal FFPE tissue for epigenetic profiling.

Purpose of the Study:

• To develop a highly sensitive method for profiling histone modifications in archived FFPE tissues.
• To enable genome-wide histone modification profiling using a minimal amount of FFPE tissue.
• To investigate disease-specific epigenetic alterations in cancer using FFPE samples.

Main Methods:

• Development of FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq).
• FACT-seq combines a novel fusion protein (T7-pA-Tn5) for transposition and T7 in vitro transcription.
• High-quality chromatin profiles generated from a low number of FFPE nuclei.

Main Results:

• FACT-seq successfully profiled histone modifications from a small FFPE tissue section (∼4000 nuclei).
• H3K27ac modifications were accurately decoded using FACT-seq in FFPE samples.
• Disease-specific super enhancers were identified in human colorectal and glioblastoma cancer FFPE tissues.

Conclusions:

• FACT-seq is the first highly sensitive method for efficient histone modification profiling in FFPE tissues.
• This method allows for detailed epigenetic analysis using limited clinical FFPE samples.
• FACT-seq aids in understanding epigenetic regulation in cancer and other human diseases.