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

Amos C. Lee, Yongju Lee, Ahyoun Choi, Han-Byoel Lee, Kyoungseob Shin, Hyunho Lee, Ji Young Kim, Han Suk Ryu, Hoe Suk Kim, Seung Yeon Ryu, Sangeun Lee, Jong-Ho Cheun, Duck Kyun Yoo, Sumin Lee, Hansol Choi, Taehoon Ryu, Huiran Yeom, Namphil Kim, Jinsung Noh, Yonghee Lee, Inyoung Kim, Sangwook Bae, Jinhyun Kim, Wooseok Lee, Okju Kim, Yushin Jung, Changhoe Kim, Seo Woo Song, Yeongjae Choi, Junho Chung, Byung Gee Kim, Wonshik Han () and Sunghoon Kwon ()
Additional contact information
Amos C. Lee: Seoul National University
Yongju Lee: Seoul National University
Ahyoun Choi: Seoul National University
Han-Byoel Lee: Seoul National University College of Medicine
Kyoungseob Shin: Seoul National University
Hyunho Lee: Seoul National University
Ji Young Kim: Seoul National University Hospital
Han Suk Ryu: Seoul National University
Hoe Suk Kim: Seoul National University Hospital
Seung Yeon Ryu: Seoul National University Hospital
Sangeun Lee: Seoul National University Hospital
Jong-Ho Cheun: Seoul National University College of Medicine
Duck Kyun Yoo: Seoul National University College of Medicine
Sumin Lee: Seoul National University
Hansol Choi: Seoul National University
Taehoon Ryu: ATG LIfetech Inc
Huiran Yeom: Seoul National University
Namphil Kim: Seoul National University
Jinsung Noh: Seoul National University
Yonghee Lee: Seoul National University
Inyoung Kim: Seoul National University
Sangwook Bae: Seoul National University
Jinhyun Kim: Seoul National University
Wooseok Lee: Seoul National University
Okju Kim: ATG LIfetech Inc
Yushin Jung: ATG LIfetech Inc
Changhoe Kim: Celemics, Inc
Seo Woo Song: Seoul National University
Yeongjae Choi: Gwangju Institute of Science and Technology (GIST)
Junho Chung: Seoul National University
Byung Gee Kim: Seoul National University
Wonshik Han: Seoul National University College of Medicine
Sunghoon Kwon: Seoul National University

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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.

Date: 2022
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30299-3

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DOI: 10.1038/s41467-022-30299-3

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