Fusion transcript discovery using RNA sequencing in formalin-fixed paraffin-embedded specimen.

Area of Science:

• Oncology
• Molecular Biology
• Bioinformatics

Background:

• Chimeric transcripts are vital biomarkers for cancer diagnosis, prognosis, and therapeutic targeting.
• Fresh tissues are the primary source for fusion transcript identification, but formalin-fixed paraffin-embedded (FFPE) tissues offer long-term histological preservation.
• RNA extracted from FFPE tissues is often of low quality and quantity, posing challenges for transcriptomic studies.

Purpose of the Study:

• To review and describe methodologies for identifying fusion transcripts in FFPE tissues.
• To address the limitations associated with RNA quality and quantity in FFPE samples for transcript discovery.
• To highlight the potential of FFPE tissues as a valuable resource for translational and clinical cancer research.

Main Methods:

• RNA sequencing (RNA-Seq) techniques are employed for comprehensive transcriptomic analysis.
• Specific protocols and bioinformatics pipelines are adapted to handle degraded RNA from FFPE samples.
• Comparative analyses of RNA integrity and fusion transcript detection rates between fresh and FFPE tissues are discussed.

Main Results:

• Various RNA sequencing approaches can successfully identify fusion transcripts from FFPE tissues, despite RNA degradation.
• Optimization of RNA extraction and library preparation methods can mitigate the challenges posed by FFPE samples.
• The review provides a framework for selecting appropriate methods based on RNA quality and research objectives.

Conclusions:

• Fusion transcript identification from FFPE tissues is feasible and crucial for advancing cancer research and clinical applications.
• Overcoming RNA quality issues in FFPE samples expands the utility of these archival tissues for biomarker discovery.
• RNA sequencing offers a powerful tool to unlock the potential of FFPE archives for identifying novel diagnostic and therapeutic targets.