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

Cited 13 time in Web of Science Cited 16 time in Scopus

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; Kim, Inyoung; Bae, Sangwook; Kim, Jinhyun; Lee, Wooseok; Kim, Okju; Jung, Yushin; Kim, Changhoe; Song, Seo Woo; Choi, Yeongjae; Chung, Junho; Kim, Byung Gee; Han, Wonshik; Kwon, Sunghoon

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Nature Publishing Group
Nature Communications, Vol.13 No.1, p. 2540
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.
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