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- Title
Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches.
- Authors
Lee, Amos C.; Lee, Yongju; Choi, Ahyoun; Lee, Han-Byoel; Shin, Kyoungseob; Lee, Hyunho; Kim, Ji Young; Ryu, Han Suk; Kim, Hoe Suk; Ryu, Seung Yeon; Lee, Sangeun; Cheun, Jong-Ho; Yoo, Duck Kyun; Lee, Sumin; Choi, Hansol; Ryu, Taehoon; Yeom, Huiran; Kim, Namphil; Noh, Jinsung; Lee, Yonghee
- Abstract
Epitranscriptomic features, such as single-base RNA editing, are sources of transcript diversity in cancer, but little is understood in terms of their spatial context in the tumour microenvironment. Here, we introduce spatial-histopathological examination-linked epitranscriptomics converged to transcriptomics with sequencing (Select-seq), which isolates regions of interest from immunofluorescence-stained tissue and obtains transcriptomic and epitranscriptomic data. With Select-seq, we analyse the cancer stem cell-like microniches in relation to the tumour microenvironment of triple-negative breast cancer patients. We identify alternative splice variants, perform complementarity-determining region analysis of infiltrating T cells and B cells, and assess adenosine-to-inosine base editing in tumour tissue sections. Especially, in triple-negative breast cancer microniches, adenosine-to-inosine editome specific to different microniche groups is identified. The spatial context of epitranscriptomic features in the tumour microenvironment remains poorly understood. Here, a method for transcriptomic and epitranscriptomic analysis of immunofluorescence-stained tissue, Select-seq, is applied to stem cell-like microniches in triple negative breast cancer.
- Subjects
TRIPLE-negative breast cancer; ALTERNATIVE RNA splicing; TUMOR microenvironment; CANCER stem cells; B cells; RNA editing; T cells
- Publication
Nature Communications, 2022, Vol 13, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-022-30299-3