Fig 1.
Identification of circRNAs in senescent fibroblast subjected to different stimuli.
(A) Schematic representation of the workflow in this study. (B) Comparison between circRNAs detected in distinct types of senescent WI38 cells. RS: Replicative senescence; DOX: Doxorubicin-induced senescence; OIS: oncogene-induced senescence; IR: ionizing radiation-induced senescence.
Fig 2.
Expression changes of circRNAs in WI38 cells undergoing different types of senescence.
Volcano plots depict circRNAs that are upregulated and downregulated during the aging process in replicative senescence (A), oncogene-induced senescence (B), doxycycline (dox)-induced senescence (C), and ionizing radiation-induced senescence (D). Red dots represent up-regulated circRNAs, and blue dots represent down-regulated circRNAs. A p-value threshold of < 0.05 was set a priori to determine statistical significance. (E) general signature of senescent WI38 cells regardless of the stimulus. Combined analysis with three methods was performed for detecting general senescence-associated circRNAs across stimuli (see Methods for details).
Fig 3.
Functional analysis of stimulus-specific circRNAs (SS-circRNAs).
(A) Construction of circRNA-gene (mRNA) co-expression networks in three senescence types (RS, OIS and DOX). Genes exhibiting strong co-expression with circRNAs were identified using a Benjamini-Hochberg (BH)-adjusted p-value threshold of < 0.05. Red triangles and green dots represent circRNAs and genes, respectively. (B-D) Functional enrichment of SS-circRNAs-correlated genes in three co-expression networks. The top five significantly enriched Gene Ontology (GO) terms from each category (Biological Process [BP], Cellular Component [CC], and Molecular Function [MF]) are presented. (B) RS. (C) OIS. (D) DOX. (E) Comparison of enriched GO terms in different senescence types. Metascape was employed for multi-gene list enrichment analysis, with significant pathways defined by p < 0.01, minimum 3 genes, and enrichment factor > 1.5.
Fig 4.
Essential circRNAs linked to senescence across multiple cell types and stimuli.
(A) Comparative analysis of senescence-associated circRNAs across diverse stimuli and cell types. (B) Heatmap plot present the expression changes of key eight senescence-associated circRNAs in different cell types and stimuli. Heatmap visualization of the core senescence-associated circRNAs expression changes during cellular senescence. Each cell in the heatmap is color-coded to represent the log2 fold change (log2FC) value. Red indicates upregulation in senescent conditions, while blue indicates downregulation. The intensity of the color corresponds to the magnitude of the fold change, with darker shades reflecting greater differences. WI38_DOX_study_1 and _2 are two batches from GSE130727 treated with 2 µg/mL doxorubicin for 24 h. WI38_OIS/RS_study_1 are from GSE130727 (OIS: HRASG12V lentivirus, MOI = 10, with puromycin), whereas WI38_OIS/RS_study_2 are from GSE130306 (OIS: 20 nM 4-hydroxy-tamoxifen for 10 days). *: p-value < 0.05; **: p-value < 0.01; ***: p-value < 0.001. (C) The genomic information of the core senescence-associated circRNAs. Graphical representation of circRNA structure (right) sourced from CSCD database (http://gb.whu.edu.cn/CSCD/) with exon-specific color mapping.