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Single-cell transcriptome provides novel insights into antler stem cells, a cell type capable of mammalian organ regeneration

  • Hengxing Ba
  • Datao Wang
  • Weiyao Wu
  • Hongmei Sun
  • Chunyi LiEmail author
Original Article

Abstract

Antler regeneration, a stem cell–based epimorphic process, has a potential as a valuable model for regenerative medicine. A pool of antler stem cells (ASCs) for antler development is located in the antlerogenic periosteum (AP). However, whether this ASC pool is homogenous or heterogeneous has not been fully evaluated. In this study, we produced a comprehensive transcriptome dataset at the single-cell level for the ASCs based on the 10× Genomics platform (scRNA-seq). A total of 4565 ASCs were sequenced and classified into a large cell cluster, indicating that the ASC resident in the AP are likely to be a homogeneous population. The scRNA-seq data revealed that tumor-related genes were highly expressed in these homogeneous ASCs, i.e., TIMP1, TMSB10, LGALS1, FTH1, VIM, LOC110126017, and S100A4. Results of screening for stem cell markers suggest that the ASCs may be considered as a special type of stem cell between embryonic (CD9) and adult (CD29, CD90, NPM1, and VIM) stem cells. Our results provide the first comprehensive transcriptome analysis at the single-cell level for the ASCs and identified only one major cell type resident in the AP and some key stem cell genes, which may hold the key to why antlers, the unique mammalian organ, can fully regenerate once lost.

Keywords

Antler Stem cell Antlerogenic periosteum Single cell Transcriptome scRNA-seq 

Notes

Acknowledgements

We wish to thank Drs. Peter Fennessy and Eric Lord for reading through the paper and giving valuable comments.

Author contributions

H.B., D.W., and C.L. conceived the experiment. D.W. collected the samples and performed molecular- and cell-related experiments. H.S. cultured the cell lines. W.W. extracted the RNA samples and prepared them for single-cell 3′ library construction and sequencing. H.B. performed QC and data analysis. H.B., W.W., and C.L. wrote the manuscript. All authors read and approved the final manuscript.

Funding information

This work was funded by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16010403), Natural Science Foundation of Jilin Province (No. 20170101003JC) and Central Public-Interest Scientific Institution Basal Research Fund (No. 1610342019026).

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.

Supplementary material

10142_2019_659_MOESM1_ESM.jpg (1.6 mb)
Figure S1. Detection of variable genes across the ASCs. A total of 2415 variable genes were selected by using FindVariableGenes function (x.low.cutoff = 0.01, x.high.cutoff = 4, y.cutoff=0.3) in Seurat R package. The parameters identify ~2943 variable genes. (JPG 1611 kb)
10142_2019_659_MOESM2_ESM.jpg (413 kb)
Figure S2. Standard deviation of principal components. To assess the true dimensionality of our dataset, the first 30 principal components were deemed as a cutoff, as there is a clear elbow in the graph. (JPG 413 kb)
10142_2019_659_MOESM3_ESM.docx (19 kb)
Table S1. List of Antibodies (DOCX 19 kb)
10142_2019_659_MOESM4_ESM.docx (23 kb)
Table S2. Summary of scRNA-seq data quality (DOCX 22 kb)
10142_2019_659_MOESM5_ESM.docx (15 kb)
Table S3. Summary of single cell sequencing data (DOCX 14 kb)
10142_2019_659_MOESM6_ESM.xlsx (13 kb)
Table S4. Summary of top 35 highly expressed genes in the scRNA-seq data. (XLSX 13 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Hengxing Ba
    • 1
  • Datao Wang
    • 1
  • Weiyao Wu
    • 2
  • Hongmei Sun
    • 1
  • Chunyi Li
    • 1
    • 3
    Email author
  1. 1.State Key Laboratory for Molecular Biology of Special Wild Economic Animals, Institute of Special Wild Economic Animals and PlantsChinese Academy of Agricultural SciencesChangchunChina
  2. 2.BGI GenomicsBGI-ShenzhenShenzhenChina
  3. 3.Changchun Sci-Tech UniversityChangchunChina

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