Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches

Area of Science:

• Oncology
• Molecular Biology
• Genomics

Background:

• Epitranscriptomic modifications, including RNA editing, contribute to transcript diversity in cancer.
• The spatial context of epitranscriptomics within the tumor microenvironment remains poorly understood.
• Triple-negative breast cancer (TNBC) presents a complex microenvironment with poorly defined epitranscriptomic features.

Purpose of the Study:

• To introduce and validate a novel method, Select-seq, for spatially resolved transcriptomic and epitranscriptomic analysis.
• To investigate the epitranscriptomic landscape of cancer stem cell-like microniches in TNBC.
• To correlate epitranscriptomic features with the tumor microenvironment and cellular composition.

Main Methods:

• Development of Select-seq: spatial-histopathological examination-linked epitranscriptomics converged to transcriptomics with sequencing.
• Isolation of specific regions of interest from immunofluorescence-stained tissue sections.
• Simultaneous acquisition of transcriptomic and epitranscriptomic data, including adenosine-to-inosine base editing analysis.
• Complementarity-determining region (CDR) analysis of infiltrating immune cells (T cells and B cells).

Main Results:

• Select-seq successfully obtained spatially resolved transcriptomic and epitranscriptomic data from TNBC tissue.
• Identification of alternative splice variants within cancer stem cell-like microniches.
• Characterization of the immune cell infiltrate (T cells and B cells) via CDR analysis.
• Discovery of a distinct adenosine-to-inosine editome specific to different microniche groups within TNBC.

Conclusions:

• Select-seq is a powerful tool for dissecting the spatial epitranscriptomic heterogeneity of solid tumors.
• The study reveals novel, microniche-specific epitranscriptomic signatures in TNBC.
• These findings enhance our understanding of TNBC biology and the tumor microenvironment, potentially paving the way for targeted therapies.