Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution

Area of Science:

• Oncology
• Genetics
• Molecular Biology

Background:

• Intra-tumor heterogeneity (ITH) is a key factor in cancer therapy resistance and recurrence.
• Existing genetic analysis methods for ITH lack spatial context and may miss rare subclones.

Purpose of the Study:

• To develop and validate BaseScope, a novel mutation-specific RNA in situ hybridization assay.
• To precisely map the spatial and morphological context of mutant subclones in colorectal cancer.

Main Methods:

• Development and validation of the BaseScope assay.
• Targeting common point mutations (BRAF, KRAS, PIK3CA) in archival colorectal cancer samples.
• Utilizing computational modeling to analyze subclone formation and spatial distribution.

Main Results:

• BaseScope enables precise in situ detection of mutation-specific subclones.
• Spatial mapping revealed insights into subclone evolution, including early-arising or high-fitness subclones.
• Identified putative treatment-resistant cells within localized topographical areas.

Conclusions:

• BaseScope is a significant advancement for in situ mutation detection.
• The assay provides novel insights into tumor evolution and ITH.
• Findings may impact patient selection for cancer therapies.