Basic Study
Copyright ©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Stem Cells. Mar 26, 2024; 16(3): 305-323
Published online Mar 26, 2024. doi: 10.4252/wjsc.v16.i3.305
Evaluation of genetic response of mesenchymal stem cells to nanosecond pulsed electric fields by whole transcriptome sequencing
Jian-Jing Lin, Tong Ning, Shi-Cheng Jia, Ke-Jia Li, Yong-Can Huang, Qiang Liu, Jian-Hao Lin, Xin-Tao Zhang
Jian-Jing Lin, Shi-Cheng Jia, Xin-Tao Zhang, Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
Tong Ning, Institute of Medical Science, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, Shandong Province, China
Ke-Jia Li, Department of Biomedical Engineering, Institute of Future Technology, Peking University, Beijing 100871, China
Yong-Can Huang, Shenzhen Engineering Laboratory of Orthopaedic Regenerative Technologies, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
Qiang Liu, Jian-Hao Lin, Arthritis Clinical and Research Center, Peking University People’s Hospital, Beijing 100044, China
Co-first authors: Jian-Jing Lin and Tong Ning.
Co-corresponding authors: Jian-Hao Lin and Xin-Tao Zhang.
Author contributions: Lin JJ, Ning T, and Jia SC designed the project, wrote the original draft, and edited the final version of the manuscript; Ning T and Li KJ analyzed the data; Jia SC drew the tables and figures; Huang YC, Liu Q, and Lin JH revised the manuscript; Lin JH and Zhang XT provided financial support and ensured the final manuscript, and they are the co-corresponding authors of this manuscript; Lin JJ and Ning T contributed equally to the work; and all authors have read and approved the final version of the manuscript.
Supported by the National Natural Science Foundation, China, No. 82272568, 81902247, and 32201013; Natural Science Foundation of Shandong Province, China, No. ZR2021QH275; Natural Science Foundation of Jinan City, China, No. 202225070; and Guangdong Basic and Applied Basic Research Foundation, China, No. 2022A1515220056.
Institutional animal care and use committee statement: This study was approved by the Ethics Committee of Peking University (No. COE-GeZ-7).
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Data sharing statement: The datasets supporting the conclusions of this article are available in the NCBI database, with unique accession code PRJNA931816. The hyperlink to dataset(s) is https://www.ncbi.nlm.nih.gov/bioproject/PRJNA931816/. All other data are included in this article.
ARRIVE guidelines statement: The authors have read the ARRIVE guidelines, and the manuscript was prepared and revised according to the ARRIVE guidelines.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/
Corresponding author: Xin-Tao Zhang, PhD, Chief Physician, Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, No. 1120 Lianhua Road, Futian District, Shenzhen 518036, Guangdong Province, China. zhangxintao@sina.com
Received: December 13, 2023
Peer-review started: December 13, 2023
First decision: January 24, 2024
Revised: January 31, 2024
Accepted: February 28, 2024
Article in press: February 28, 2024
Published online: March 26, 2024
Processing time: 102 Days and 13 Hours
ARTICLE HIGHLIGHTS
Research background

Mesenchymal stem cells (MSCs) have been extensively applied in preclinical and clinical research in regenerative medicine. Their differentiation and function are modulated by various exogenous signals, which provide potential strategies for researchers to explore appropriate exogenous signals to regulate the functions and differentiation of stem cells. Nanosecond pulsed electric fields (nsPEFs) represent nanosecond-duration, high-strength electric fields to significantly influence cell phenotypes and regulate stem cell differentiation through multiple pathways. Thus, we used transcriptomics analysis to analyze messenger RNA (mRNA), long noncoding RNA (lncRNA), microRNA (miRNA), and circular RNA (circRNA) expression to identify changes in gene expression following treatment with nsPEFs.

Research motivation

The differentiation and function of MSCs are regulated by nsPEFs. However, the mechanism, especially changes in gene expression after nsPEFs treatment, remains unclear.

Research objectives

To reveal gene expression in MSCs pretreated with nsPEFs and explore the potential gene regulatory mechanism.

Research methods

We used whole transcriptome sequencing to investigate the effects of nsPEFs on MSC transcriptome. Five pulses of nsPEFs (100 ns at 10 kV/cm, 1 Hz) were applied to pretreat MSCs. Total RNA was isolated after pretreatment of MSCs; each transcript was normalized by fragments per kilobase per million. Fold change and difference significance were used to screen the differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were conducted to identify gene function, and the results were verified by quantitative polymerase chain reaction.

Research results

The top 20 differentially expressed lncRNAs and mRNAs were revealed. Two hundred and sixty-three DEGs were identified in the PRJNA931816 dataset, of which 92 were upregulated and 171 were significantly downregulated, respectively. DEGs were mainly enriched in epithelial cell proliferation, osteoblast differentiation, mesenchymal cell differentiation, nuclear division, and wound healing. As for cellular components, DEGs were mainly involved in condensed chromosome, chromosomal region, actin cytoskeleton, and the kinetochore. With regard to molecular functions, DEGs are mainly involved in glycosaminoglycan binding, integrin binding, nuclear steroid receptor activity, cytoskeletal motor activity, and steroid binding. Quantitative real-time polymerase chain reaction was used to verify the seven upregulated mRNAs, Aldh3a1, Cenpf, Kif20b, Ereg, Nek2, Nr3c2, and Scin, and six downregulated mRNAs, Actg2, Asic3, Crybat4, Nog, Stxbp5 L, and Tubb2b.

Research conclusions

Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs, 2 miRNAs, and 65 lncRNAs. We showed that nsPEFs may affect stem cells via several signaling pathways and involve vesicular transport, calcium ion transport, the cytoskeleton, and cell differentiation.

Research perspectives

This study is the first to investigate the expression profile of the whole transcriptome in nsPEFs-treated stem cells. The findings provide a certain basis for the application of nsPEFs in stem cell differentiation and tissue regeneration.