Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts

Overview

Journal Front Genet

Date 2020 Aug 28

PMID 32849838

Citations 13

Authors

Wei Chen

Xuefei Wang

Gang Wei

Yin Huang

Yufang Shi

Dan Li

Shengnu Qiu

Bin Zhou

Junhong Cao

Meng Chen

Pengfei Qin

Wenfei Jin

Ting Ni

Affiliations

Soon will be listed here.

Abstract

Replicative senescence is a hallmark of aging, which also contributes to individual aging. Mouse embryonic fibroblasts (MEFs) provide a convenient replicative senescence model. However, the heterogeneity of single MEFs during cellular senescence has remained unclear. Here, we conducted single-cell RNA sequencing on senescent MEFs. Principal component analysis showed obvious heterogeneity among these MEFs such that they could be divided into six subpopulations. Three types of gene expression analysis revealed distinct expression features of these six subpopulations. Trajectory analysis revealed three distinct lineages during MEF senescence. In the main lineage, some senescence-associated secretory phenotypes were upregulated in a subset of cells from senescent clusters, which could not be distinguished in a previous bulk study. In the other two lineages, a possibility of escape from cell cycle arrest and coupling between translation-related genes and ATP synthesis-related genes were also discovered. Additionally, we found co-expression of transcription factor HOXD8 coding gene and its potential target genes in the main lineage. Overexpression of led to senescence-associated phenotypes, suggesting HOXD8 is a new regulator of MEF senescence. Together, our single-cell sequencing on senescent MEFs largely expanded the knowledge of a basic cell model for aging research.

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References

Ruscetti M, Leibold J, Bott M, Fennell M, Kulick A, Salgado N . NK cell-mediated cytotoxicity contributes to tumor control by a cytostatic drug combination. Science. 2018; 362(6421):1416-1422. PMC: 6711172. DOI: 10.1126/science.aas9090. View

Olovnikov A . Telomeres, telomerase, and aging: origin of the theory. Exp Gerontol. 1996; 31(4):443-8. DOI: 10.1016/0531-5565(96)00005-8. View

Elkon R, Ugalde A, Agami R . Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet. 2013; 14(7):496-506. DOI: 10.1038/nrg3482. View

Tice R, Schneider E, Kram D, Thorne P . Cytokinetic analysis of the impaired proliferative response of peripheral lymphocytes from aged humans to phytohemagglutinin. J Exp Med. 1979; 149(5):1029-41. PMC: 2184873. DOI: 10.1084/jem.149.5.1029. View

Kim Y, Byun H, Jee B, Cho H, Seo Y, Kim Y . Implications of time-series gene expression profiles of replicative senescence. Aging Cell. 2013; 12(4):622-34. DOI: 10.1111/acel.12087. View

Schworer S, Becker F, Feller C, Baig A, Kober U, Henze H . Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals. Nature. 2016; 540(7633):428-432. PMC: 5415306. DOI: 10.1038/nature20603. View

Kowalczyk M, Tirosh I, Heckl D, Rao T, Dixit A, Haas B . Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Genome Res. 2015; 25(12):1860-72. PMC: 4665007. DOI: 10.1101/gr.192237.115. View

Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi A, Tanaseichuk O . Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019; 10(1):1523. PMC: 6447622. DOI: 10.1038/s41467-019-09234-6. View

Deng Q, Ramskold D, Reinius B, Sandberg R . Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science. 2014; 343(6167):193-6. DOI: 10.1126/science.1245316. View

10.

Carlos Acosta J, Banito A, Wuestefeld T, Georgilis A, Janich P, Morton J . A complex secretory program orchestrated by the inflammasome controls paracrine senescence. Nat Cell Biol. 2013; 15(8):978-90. PMC: 3732483. DOI: 10.1038/ncb2784. View

11.

Lyu G, Guan Y, Zhang C, Zong L, Sun L, Huang X . TGF-β signaling alters H4K20me3 status via miR-29 and contributes to cellular senescence and cardiac aging. Nat Commun. 2018; 9(1):2560. PMC: 6028646. DOI: 10.1038/s41467-018-04994-z. View

12.

Street K, Risso D, Fletcher R, Das D, Ngai J, Yosef N . Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics. 2018; 19(1):477. PMC: 6007078. DOI: 10.1186/s12864-018-4772-0. View

13.

Liu Y, Miao L, Ni R, Zhang H, Li L, Wang X . microRNA-520a-3p inhibits proliferation and cancer stem cell phenotype by targeting HOXD8 in non-small cell lung cancer. Oncol Rep. 2016; 36(6):3529-3535. DOI: 10.3892/or.2016.5149. View

14.

Xu S, Wu W, Huang H, Huang R, Xie L, Su A . The p53/miRNAs/Ccna2 pathway serves as a novel regulator of cellular senescence: Complement of the canonical p53/p21 pathway. Aging Cell. 2019; 18(3):e12918. PMC: 6516184. DOI: 10.1111/acel.12918. View

15.

Herbig U, Jobling W, Chen B, Chen D, Sedivy J . Telomere shortening triggers senescence of human cells through a pathway involving ATM, p53, and p21(CIP1), but not p16(INK4a). Mol Cell. 2004; 14(4):501-13. DOI: 10.1016/s1097-2765(04)00256-4. View

16.

Parrinello S, Samper E, Krtolica A, Goldstein J, Melov S, Campisi J . Oxygen sensitivity severely limits the replicative lifespan of murine fibroblasts. Nat Cell Biol. 2003; 5(8):741-7. PMC: 4940195. DOI: 10.1038/ncb1024. View

17.

Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X . Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell. 2010; 6(5):468-78. PMC: 2954317. DOI: 10.1016/j.stem.2010.03.015. View

18.

Di Leonardo A, Linke S, Clarkin K, Wahl G . DNA damage triggers a prolonged p53-dependent G1 arrest and long-term induction of Cip1 in normal human fibroblasts. Genes Dev. 1994; 8(21):2540-51. DOI: 10.1101/gad.8.21.2540. View

19.

Liao Y, Smyth G, Shi W . featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30(7):923-30. DOI: 10.1093/bioinformatics/btt656. View

20.

Todaro G, Green H . Quantitative studies of the growth of mouse embryo cells in culture and their development into established lines. J Cell Biol. 1963; 17:299-313. PMC: 2106200. DOI: 10.1083/jcb.17.2.299. View