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

• Published in: Nature Communications
• Main Authors: Kwon, Sunghoon, Lee, Amos, Lee, Yongju, Choi, Ahyoun, Han-Byoel, Lee, Shin, Kyoungseob, Lee, Hyunho, Ji Young Kim, Ryu, Han Suk, Kim, Hoe Suk, Ryu, Seung Yeon, Lee, Sangeun, Jong-Ho Cheun, 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, Seo Woo Song, Choi, Yeongjae, Chung, Junho, Byung Gee Kim, Han, Wonshik
• Format: Web Resource
• Language: English
• Published: Durham Research Square 23.03.2022
• DOI: 10.21203/rs.3.rs-1465331/v1

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 were able to analyse the cancer stem cell-like microniches in relation to the tumour microenvironment of triple-negative breast cancer (TNBC) patients. We identified alternative splice variants, performed complementarity-determining region analysis of infiltrating T cells and B cells, and assessed adenosine-to-inosine (A-to-I) base editing in tumour tissue sections. Especially, in TNBC microniches, A-to-I editome specific to different microniche groups was identified.