Single-cell RNA sequencing reveals spatiotemporal heterogeneity and malignant progression in pancreatic neuroendocrine tumor

Zhou, Yu; Liu, Siyang; Liu, Chao; Yang, Jiabin; Lin, Qing; Zheng, Shangyou; Chen, Changhao; Zhou, Quanbo; Chen, Rufu

doi:10.7150/ijbs.61717

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Theranostics

International Journal of Medical Sciences

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Int J Biol Sci 2021; 17(14):3760-3775. doi:10.7150/ijbs.61717 This issue Cite

Research Paper

Single-cell RNA sequencing reveals spatiotemporal heterogeneity and malignant progression in pancreatic neuroendocrine tumor

Yu Zhou^1,#, Siyang Liu^2,#, Chao Liu^3,#, Jiabin Yang^1,4, Qing Lin¹, Shangyou Zheng¹, Changhao Chen^5,6,✉, Quanbo Zhou^5,7,✉, Rufu Chen^1,✉

1. Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
2. Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
3. Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
4. School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
5. Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, State Key Laboratory of Oncology in South China, Sun Yat-sen Memorial Hospital, Guangzhou, Guangdong, China
6. Department of Urology, Sun Yat-sen Memorial Hospital, Guangzhou, Guangdong, China
7. Department of Pancreatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
^#Yu Zhou, Siyang Liu, and Chao Liu contributed equally to this work

✉ Corresponding authors: Rufu Chen, MD, PHD, Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, No. 106, Zhongshan 2nd Road, Guangzhou, Guangdong, 510120, Chi More

Citation:

Zhou Y, Liu S, Liu C, Yang J, Lin Q, Zheng S, Chen C, Zhou Q, Chen R. Single-cell RNA sequencing reveals spatiotemporal heterogeneity and malignant progression in pancreatic neuroendocrine tumor. Int J Biol Sci 2021; 17(14):3760-3775. doi:10.7150/ijbs.61717. https://www.ijbs.com/v17p3760.htm

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Abstract

Aims: Using Single-cell RNA sequencing (scRNA-seq), we explored the spatiotemporal heterogeneity of pancreatic neuroendocrine tumors (pNETs) and the underlying mechanism for malignant progression.

Methods: scRNA-seq was conducted on three tumor tissues (two primary tissues from different sites, one liver metastatic lesion), one normal liver tissue, and peripheral blood mononuclear cells from one patient with a metastatic G2 pNET, followed by bioinformatics analysis and validation in a pNETs cohort.

Results: The transcriptome data of 24.544 cells were obtained. We identified subpopulations of functional heterogeneity within malignant cells, immune cells, and fibroblasts. There were intra- and inter-heterogeneities of cell subpopulations for malignant cells, macrophages, T cells, and fibroblasts among all tumor sites. Cell trajectory analysis revealed several hallmarks of carcinogenesis, including the hypoxia pathway, metabolism reprogramming, and aggressive proliferation, which were activated at different stages of tumor progression. Evolutionary analysis based on mitochondrial mutations defined two dominant clones with metastatic capacity. Finally, we developed a gene signature (PCSK1 and SMOC1) defining the metastatic potential of the tumor and its prognostic value was validated in a cohort of thirty G1/G2 patients underwent surgical resection.

Conclusions: Our scRNA-seq analysis revealed intra- and intertumor heterogeneities in cell populations, transcriptional states, and intercellular communications among primary and metastatic lesions of pNETs. The single-cell level characterization of the spatiotemporal dynamics of malignant cell progression provided new insights into the search for potential novel prognostic biomarkers of pNETs.

Keywords: pancreatic cancer, single-cell RNA sequencing, heterogeneity, metastatic, prognostic factors

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APA

Zhou, Y., Liu, S., Liu, C., Yang, J., Lin, Q., Zheng, S., Chen, C., Zhou, Q., Chen, R. (2021). Single-cell RNA sequencing reveals spatiotemporal heterogeneity and malignant progression in pancreatic neuroendocrine tumor. International Journal of Biological Sciences, 17(14), 3760-3775. https://doi.org/10.7150/ijbs.61717.

ACS

Zhou, Y.; Liu, S.; Liu, C.; Yang, J.; Lin, Q.; Zheng, S.; Chen, C.; Zhou, Q.; Chen, R. Single-cell RNA sequencing reveals spatiotemporal heterogeneity and malignant progression in pancreatic neuroendocrine tumor. Int. J. Biol. Sci. 2021, 17 (14), 3760-3775. DOI: 10.7150/ijbs.61717.

NLM

CSE

Zhou Y, Liu S, Liu C, Yang J, Lin Q, Zheng S, Chen C, Zhou Q, Chen R. 2021. Single-cell RNA sequencing reveals spatiotemporal heterogeneity and malignant progression in pancreatic neuroendocrine tumor. Int J Biol Sci. 17(14):3760-3775.

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