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Chen Y, Yin J, Zhao L, Zhou G, Dong S, Zhang Y, Niu P, Ren H, Zheng T, Yan J, Li W, Ma P, Zhang C, Wei C, Church G, Li G, Zhao D. Reconstruction of the gastric cancer microenvironment after neoadjuvant chemotherapy by longitudinal single-cell sequencing. J Transl Med 2022; 20:563. [PMID: 36474268 PMCID: PMC9724296 DOI: 10.1186/s12967-022-03792-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Little is known on the tumor microenvironment (TME) response after neoadjuvant chemotherapy (NACT) in gastric cancer on the molecular level. METHODS Here, we profiled 33,589 cell transcriptomes in 14 samples from 11 gastric cancer patients (4 pre-treatment samples, 4 post-treatment samples and 3 pre-post pairs) using single-cell RNA sequencing (scRNA-seq) to generate the cell atlas. The ligand-receptor-based intercellular communication networks of the single cells were also characterized before and after NACT. RESULTS Compered to pre-treatment samples, CD4+ T cells (P = 0.018) and CD8+ T cells (P = 0.010) of post-treatment samples were significantly decreased, while endothelial cells and fibroblasts were increased (P = 0.034 and P = 0.005, respectively). No significant difference observed with respect to CD4+ Tregs cells, cycling T cells, B cells, plasma cells, macrophages, monocytes, dendritic cells, and mast cells (P > 0.05). In the unsupervised nonnegative matrix factorization (NMF) analysis, we revealed that there were three transcriptional programs (NMF1, NMF2 and NMF3) shared among these samples. Compared to pre-treatment samples, signature score of NMF1 was significantly downregulated after treatment (P = 0.009), while the NMF2 signature was significantly upregulated after treatment (P = 0.013). The downregulated NMF1 and upregulated NMF2 signatures were both associated with improved overall survival outcomes based on The Cancer Genome Atlas (TCGA) database. Additionally, proangiogenic pathways were activated in tumor and endothelial cells after treatment, indicating that NACT triggers vascular remodeling by cancer cells together with stromal cells. CONCLUSIONS In conclusion, our study provided transcriptional profiles of TME between pre-treatment and post-treatment for in-depth understanding on the mechanisms of NACT in gastric cancer and empowering the development of potential optimized therapy procedures and novel drugs.
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Affiliation(s)
- Yingtai Chen
- grid.506261.60000 0001 0706 7839National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Beijing, 100021 China
| | - Jianhua Yin
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 Guangdong China ,grid.207374.50000 0001 2189 3846BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China ,BGI-Henan, Xinxiang, 453000 Henan China
| | - Lulu Zhao
- grid.506261.60000 0001 0706 7839National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Beijing, 100021 China
| | - Guangyu Zhou
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Shichen Dong
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 Guangdong China ,grid.207374.50000 0001 2189 3846BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China ,BGI-Henan, Xinxiang, 453000 Henan China
| | - Yueming Zhang
- grid.506261.60000 0001 0706 7839National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Beijing, 100021 China
| | - Penghui Niu
- grid.506261.60000 0001 0706 7839National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Beijing, 100021 China
| | - Hu Ren
- grid.506261.60000 0001 0706 7839National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Beijing, 100021 China
| | - Tianjiao Zheng
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 Guangdong China ,grid.207374.50000 0001 2189 3846BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China ,BGI-Henan, Xinxiang, 453000 Henan China
| | - Juan Yan
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 Guangdong China ,grid.207374.50000 0001 2189 3846BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China ,BGI-Henan, Xinxiang, 453000 Henan China
| | - Wenbin Li
- grid.506261.60000 0001 0706 7839National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Beijing, 100021 China
| | - Peiqin Ma
- grid.506261.60000 0001 0706 7839National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Beijing, 100021 China
| | - Cuijuan Zhang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 Guangdong China ,grid.207374.50000 0001 2189 3846BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China ,BGI-Henan, Xinxiang, 453000 Henan China
| | - Chen Wei
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 Guangdong China ,grid.207374.50000 0001 2189 3846BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China ,BGI-Henan, Xinxiang, 453000 Henan China ,grid.410726.60000 0004 1797 8419BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 China
| | - George Church
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA ,grid.38142.3c000000041936754XWyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 USA
| | - Guibo Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 Guangdong China ,grid.207374.50000 0001 2189 3846BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China ,BGI-Henan, Xinxiang, 453000 Henan China ,grid.21155.320000 0001 2034 1839Shenzhen Key Laboratory of Single-Cell Omics, BGI Shenzhen, Shenzhen, 518120 Guangdong China
| | - Dongbing Zhao
- grid.506261.60000 0001 0706 7839National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 Panjiayuan Nanli, Beijing, 100021 China
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