Single-cell RNA sequencing uncovers the individual alteration of intestinal mucosal immunocytes in Dusp6 knockout mice
Cherng-Shyang Chang,
Wen-Hsuan Yu,
Chang-Chao Su,
Jhen-Wei Ruan,
Chiao-Mei Lin,
Chih-Ting Huang,
Yi-Ting Tsai,
I-Jung Lin,
Chao-Yang Lai,
Tsung-Hsien Chuang,
Wen-Jye Lin,
Tse-Hua Tan,
Hsuan-Cheng Huang,
Hsueh-Fen Juan,
Cheng-Yuan Kao
Affiliations
Cherng-Shyang Chang
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan
Wen-Hsuan Yu
Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
Chang-Chao Su
Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan
Jhen-Wei Ruan
Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
Chiao-Mei Lin
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan
Chih-Ting Huang
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan
Yi-Ting Tsai
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan
I-Jung Lin
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan
Chao-Yang Lai
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan
Tsung-Hsien Chuang
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan
Wen-Jye Lin
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan
Tse-Hua Tan
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan
Hsuan-Cheng Huang
Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
Hsueh-Fen Juan
Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan; Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; Center for Systems Biology, National Taiwan University, Taipei 10617, Taiwan
Cheng-Yuan Kao
Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung 40227, Taiwan; Corresponding author
Summary: Single-cell RNA sequencing (scRNA-seq) approach can broadly and specifically evaluate the individual cells with minimum detection bias. To explore the individual compositional and transcriptional alteration of intestinal leukocytes in the Dual Specificity Phosphatase six knockout (D6KO) mice, we performed a scRNA-seq followed by the cell type annotation based on ImmGen database. Composition assessments found that D6KO-derived intestinal leukocytes tend to stay inactivate or immature status. The enrichment analysis showed that D6KO-derived intestinal leukocytes are less sensitive to microbes. The mod PhEA phenotypic analysis showed that the D6KO leukocytes may link to not only immune-associated but also diverse previously non-immune-related diseases. Integrating our dataset with the published dataset GSE124880 generated a comprehensive dataset for exploring intestinal immunity. Down-regulation of Ccl17 gene was found in the D6KO-derived dendritic cells. Our results demonstrated the advantage of applying scRNA-seq for dissecting the individual alteration of intestinal leukocytes, particularly in the D6KO mice at a naive state.
