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. 2024 Aug 2:18:1421342.
doi: 10.3389/fncel.2024.1421342. eCollection 2024.

Genome-wide sequencing identified extrachromosomal circular DNA as a transcription factor-binding motif of the senescence genes that govern replicative senescence in human mesenchymal stem cells

Wei Yang #  1 , Wei Ji #  2 , Boyu Liao  3   4 , Zhongbo Li  1   2 , Jian Wang  1   2 , Haishu Lin  3   4 , Jingbo Wang  3   4 , Qian He  1
Affiliations

Genome-wide sequencing identified extrachromosomal circular DNA as a transcription factor-binding motif of the senescence genes that govern replicative senescence in human mesenchymal stem cells

Wei Yang et al. Front Cell Neurosci. .

Abstract

Introduction: Mesenchymal stem cells (MSCs) have long been postulated as an important source cell in regenerative medicine. During subculture expansion, mesenchymal stem cell (MSC) senescence diminishes their multi-differentiation capabilities, leading to a loss of therapeutic potential. Up to date, the extrachromosomal circular DNAs (eccDNAs) have been demonstrated to be involved in senescence but the roles of eccDNAs during MSC.

Methods: Here we explored eccDNA profiles in human bone marrow MSCs (BM-MSCs). EccDNA and mRNA was purified and sequenced, followed by quantification and functional annotation. Moreover, we mapped our datasets with the downloading enhancer and transcription factor-regulated genes to explore the potential role of eccDNAs.

Results: Sequentially, gene annotation analysis revealed that the majority of eccDNA were mapped in the intron regions with limited BM-MSC enhancer overlaps. We discovered that these eccDNA motifs in senescent BMSCs acted as motifs for binding transcription factors (TFs) of senescence-related genes.

Discussion: These findings are highly significant for identifying biomarkers of senescence and therapeutic targets in mesenchymal stem cells (MSCs) for future clinical applications. The potential of eccDNA as a stable therapeutic target for senescence-related disorders warrants further investigation, particularly exploring chemically synthesized eccDNAs as transcription factor regulatory elements to reverse cellular senescence.

Keywords: biomarker; extrachromosomal circular DNAs; mesenchymal stem cells; senescence; transcription factors.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Identification of eccDNA in cells at different cultural stages. (A) Cells from different cultural stages were collected and lysed from Y5 and Y15; DNA fragments were purified, amplified, sequenced, and analyzed. All mappable reads were analyzed. (B) Length distribution of eccDNA identified in all samples. (C) Number distribution of eccDNA on 23 chromosomes in four samples. (D) The reads count of split reads supporting eccDNA fragments. (E) Distribution of some eccDNAs on chromosome 4. (F) Overall chromosomal distribution of eccDNAs across the genome.
Figure 2
Figure 2
Distribution of eccDNA in different genomic element regions. (A) Distribution of eccDNA reads in the genome region revealed their various genomic locations, including the gene region, LINE region, SINE_Alu region, LTR region, satellite region, simple repeat, and others. (B) The bar graph shows eccDNA fragment distribution in gene and non-gene regions. (C) The relationship between enhancer region and gene regions. Those ChIP-seq data of H3K27ac with labeled enhancers (GSM1112792, GSM1112793, GSM1112797, and GSM1112798) were downloaded, and the distribution of all enhancers was analyzed. (D) The pie chart shows the overlap between eccDNA and MSC enhancers in the Y5 and Y15 groups. (E) Genomic distribution of eccDNAs that overlapped with enhancers. (F) The distribution of enhancers and the relationship between enhancers and eccDNA location. (G–I) Chromosomal location of eccDNAs.
Figure 3
Figure 3
Functional analysis of differentially expressed genes and identification of senescence-related genes. (A) Volcano plot of significantly differentially expressed genes between the Y5 and Y15 groups. (B,C) GO and KEGG enrichment analysis results of upregulated genes in the Y5 and Y15 groups. (D) Overlap analysis between senescence-related genes from the National Aging Database and DEGs. (E) Clustered heatmap of differentially expressed senescence-related genes in Y5 and Y51 groups. Red, upregulation; blue, downregulation.
Figure 4
Figure 4
EccDNA affects TF-binding pathways. (A) Motif scan in the Y51 group and Y15 group. (B) The bar plot uncovers the expressional difference of known TF binding to the enriched motif context as above. (C) The PPI network relationship between found known TFs. (D,E) GO analysis found TFs in the Y15 and Y5 groups, respectively.
Figure 5
Figure 5
EccDNA affects the TF-binding network. (A,B) The heatmap shows the expression of DEGs regulated by TFs above in the Y15 and Y5 groups, respectively. (C–E) The comprehensive and pivotal network relationship between found TFs and corresponding DEGs in the Y15 group. (F–G) The comprehensive and pivotal network relationship between found TFs and corresponding DEGs in the Y5 group. (H) The top 1 sub-network based on MCODE and relative KEGG annotation.
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References

    1. Al-Azab M., Safi M., Idiiatullina E., al-Shaebi F., Zaky M. Y. (2022). Aging of mesenchymal stem cell: machinery, markers, and strategies of fighting. Cell. Mol. Biol. Lett. 27:69. doi: 10.1186/s11658-022-00366-0, PMID: - DOI - PMC - PubMed
    1. Ameh V. O., Chirima G. J., Quan M., Sabeta C. (2022). Public health awareness on bat rabies among bat handlers and persons residing near bat roosts in Makurdi, Nigeria. Pathogens 11:975. doi: 10.3390/pathogens11090975, PMID: - DOI - PMC - PubMed
    1. Anderson D. H., Radeke M. J., Gallo N. B., Chapin E. A., Johnson P. T., Curletti C. R., et al. . (2010). The pivotal role of the complement system in aging and age-related macular degeneration: hypothesis re-visited. Prog. Retin. Eye Res. 29, 95–112. doi: 10.1016/j.preteyeres.2009.11.003, PMID: - DOI - PMC - PubMed
    1. Bader G. D., Hogue C. W. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2. doi: 10.1186/1471-2105-4-2 - DOI - PMC - PubMed
    1. Bailey T. L., Johnson J., Grant C. E., Noble W. S. (2015). The MEME suite. Nucleic Acids Res. 43, W39–W49. doi: 10.1093/nar/gkv416, PMID: - DOI - PMC - PubMed

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This study was financially supported by the National Natural Science Foundation of China (No. 31900619), the Science and Technology Project of Shenzhen (No. 20220814224343001), the Scientific Research Startup Foundation of Shenzhen Polytechnic University (No. 6023312025K), the Youth Innovative Talents Project of Guangdong Education Department (No. 2021KQNCX082), the Natural Science Foundation of Top Talent of SZTU (GDRC202207), and the Featured Innovation Foundation of Ordinary Higher Education Institutions of Guangdong Province (2022KTSCX117).

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