Time-dependent cell-state selection identifies transiently expressed genes regulating ILC2 activation

• Published in: Communications biology Vol. 6; no. 1; pp. 915 - 11
• Main Authors: Tanaka, Yumiko, Yamagishi, Mai, Motomura, Yasutaka, Kamatani, Takashi, Oguchi, Yusuke, Suzuki, Nobutake, Kiniwa, Tsuyoshi, Kabata, Hiroki, Irie, Misato, Tsunoda, Tatsuhiko, Miya, Fuyuki, Goda, Keisuke, Ohara, Osamu, Funatsu, Takashi, Fukunaga, Koichi, Moro, Kazuyo, Uemura, Sotaro, Shirasaki, Yoshitaka
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.09.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 13/21; 13/62; 14/1; 14/63; 38/91; 631/1647/245/2186; 631/1647/664/1364; 631/1647/664/2172; Biology; Biomedical and Life Sciences; Cell activation; Cells; Cytokines; Gene expression; Life Sciences; Lymphoid cells; Medicine; Science; Transcription activation; Transcriptomes
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-023-05297-w

The decision of whether cells are activated or not is controlled through dynamic intracellular molecular networks. However, the low population of cells during the transition state of activation renders the analysis of the transcriptome of this state technically challenging. To address this issue, we have developed the Time-Dependent Cell-State Selection (TDCSS) technique, which employs live-cell imaging of secretion activity to detect an index of the transition state, followed by the simultaneous recovery of indexed cells for subsequent transcriptome analysis. In this study, we used the TDCSS technique to investigate the transition state of group 2 innate lymphoid cells (ILC2s) activation, which is indexed by the onset of interleukin (IL)-13 secretion. The TDCSS approach allowed us to identify time-dependent genes, including transiently induced genes (TIGs). Our findings of IL4 and MIR155HG as TIGs have shown a regulatory function in ILC2s activation. Time-Dependent Cell-State Selection combines live cell imaging and single-cell RNA sequencing to characterize and analyse ILC2s during their activation, revealing a set of genes that are transitionally upregulated (TIGs) in ILC2s during this phase.