Single-cell RNA sequencing deconvolutes the <i>in vivo</i> heterogeneity of human bone marrow-derived mesenchymal stem cells

Wang, Zun; Li, Xiaohua; Yang, Junxiao; Gong, Yun; Zhang, Huixi; Qiu, Xiang; Liu, Ying; Zhou, Cui; Chen, Yu; Greenbaum, Jonathan; Cheng, Liang; Hu, Yihe; Xie, Jie; Yang, Xucheng; Li, Yusheng; Schiller, Martin R.; Chen, Yiping; Tan, Lijun; Tang, Si-Yuan; Shen, Hui; Xiao, Hong-Mei; Deng, Hong-Wen

doi:10.7150/ijbs.61950

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Int J Biol Sci 2021; 17(15):4192-4206. doi:10.7150/ijbs.61950 This issue Cite

Research Paper

Single-cell RNA sequencing deconvolutes the in vivo heterogeneity of human bone marrow-derived mesenchymal stem cells

Zun Wang^1,2#, Xiaohua Li^1#, Junxiao Yang⁶, Yun Gong², Huixi Zhang³, Xiang Qiu⁴, Ying Liu³, Cui Zhou³, Yu Chen³, Jonathan Greenbaum², Liang Cheng⁷, Yihe Hu⁶, Jie Xie⁶, Xucheng Yang⁶, Yusheng Li⁶, Martin R. Schiller⁹, Yiping Chen¹⁰, Lijun Tan³, Si-Yuan Tang^1,8, Hui Shen², Hong-Mei Xiao^4,5✉, Hong-Wen Deng^2,4✉

1. Xiangya School of Nursing, Central South University, Changsha, 410013, China; Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Human Normal University, Changsha, 410081, China.
2. Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, 70112, USA.
3. Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Human Normal University, Changsha, 410081, China.
4. School of Basic Medical Science, Central South University, Changsha, 410008, China.
5. Center of Reproductive Health, System Biology and Data Information, Institute of Reproductive & Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, China.
6. Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, China.
7. Department of Orthopedics and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
8. Hunan Women's Research Association, Changsha, 410011, China.
9. Nevada Institute of Personalized Medicine and School of Life Science, 4505 S. Maryland Pkwy, Las Vegas, NV 89154-4004, USA.
10. Department of Cell and Molecular Biology, School of Science and Engineering, Tulane University, New Orleans, LA 70112, USA.
#These authors contributed equally to this work.

✉ Corresponding authors: Hong-Wen Deng, Ph.D. Professor, Chief, Section of Biomedical Informatics and Genomics, Director, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, 1440 More

Citation:

Wang Z, Li X, Yang J, Gong Y, Zhang H, Qiu X, Liu Y, Zhou C, Chen Y, Greenbaum J, Cheng L, Hu Y, Xie J, Yang X, Li Y, Schiller MR, Chen Y, Tan L, Tang SY, Shen H, Xiao HM, Deng HW. Single-cell RNA sequencing deconvolutes the in vivo heterogeneity of human bone marrow-derived mesenchymal stem cells. Int J Biol Sci 2021; 17(15):4192-4206. doi:10.7150/ijbs.61950. https://www.ijbs.com/v17p4192.htm

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Abstract

Bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stromal cells that have a critical role in the maintenance of skeletal tissues such as bone, cartilage, and the fat in bone marrow. In addition to providing microenvironmental support for hematopoietic processes, BM-MSCs can differentiate into various mesodermal lineages including osteoblast/osteocyte, chondrocyte, and adipocyte that are crucial for bone metabolism. While BM-MSCs have high cell-to-cell heterogeneity in gene expression, the cell subtypes that contribute to this heterogeneity in vivo in humans have not been characterized. To investigate the transcriptional diversity of BM-MSCs, we applied single-cell RNA sequencing (scRNA-seq) on freshly isolated CD271⁺ BM-derived mononuclear cells (BM-MNCs) from two human subjects. We successfully identified LEPR^hiCD45^low BM-MSCs within the CD271⁺ BM-MNC population, and further codified the BM-MSCs into distinct subpopulations corresponding to the osteogenic, chondrogenic, and adipogenic differentiation trajectories, as well as terminal-stage quiescent cells. Biological functional annotations of the transcriptomes suggest that osteoblast precursors induce angiogenesis coupled with osteogenesis, and chondrocyte precursors have the potential to differentiate into myocytes. We also discovered transcripts for several clusters of differentiation (CD) markers that were either highly expressed (e.g., CD167b, CD91, CD130 and CD118) or absent (e.g., CD74, CD217, CD148 and CD68) in BM-MSCs, representing potential novel markers for human BM-MSC purification. This study is the first systematic in vivo dissection of human BM-MSCs cell subtypes at the single-cell resolution, revealing an insight into the extent of their cellular heterogeneity and roles in maintaining bone homeostasis.

Keywords: single-cell RNA sequencing (scRNA-seq), mesenchymal stem cell (MSC), bone marrow, osteogenesis, chondrogenesis, adipogenesis

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APA

Wang, Z., Li, X., Yang, J., Gong, Y., Zhang, H., Qiu, X., Liu, Y., Zhou, C., Chen, Y., Greenbaum, J., Cheng, L., Hu, Y., Xie, J., Yang, X., Li, Y., Schiller, M.R., Chen, Y., Tan, L., Tang, S.Y., Shen, H., Xiao, H.M., Deng, H.W. (2021). Single-cell RNA sequencing deconvolutes the in vivo heterogeneity of human bone marrow-derived mesenchymal stem cells. International Journal of Biological Sciences, 17(15), 4192-4206. https://doi.org/10.7150/ijbs.61950.

ACS

Wang, Z.; Li, X.; Yang, J.; Gong, Y.; Zhang, H.; Qiu, X.; Liu, Y.; Zhou, C.; Chen, Y.; Greenbaum, J.; Cheng, L.; Hu, Y.; Xie, J.; Yang, X.; Li, Y.; Schiller, M.R.; Chen, Y.; Tan, L.; Tang, S.Y.; Shen, H.; Xiao, H.M.; Deng, H.W. Single-cell RNA sequencing deconvolutes the in vivo heterogeneity of human bone marrow-derived mesenchymal stem cells. Int. J. Biol. Sci. 2021, 17 (15), 4192-4206. DOI: 10.7150/ijbs.61950.

NLM

CSE

Wang Z, Li X, Yang J, Gong Y, Zhang H, Qiu X, Liu Y, Zhou C, Chen Y, Greenbaum J, Cheng L, Hu Y, Xie J, Yang X, Li Y, Schiller MR, Chen Y, Tan L, Tang SY, Shen H, Xiao HM, Deng HW. 2021. Single-cell RNA sequencing deconvolutes the in vivo heterogeneity of human bone marrow-derived mesenchymal stem cells. Int J Biol Sci. 17(15):4192-4206.

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