RNA-Seq reveals novel function of noncoding RNA in senescence and cancer

Research from the Cancer Institute at the Japanese Foundation for Cancer Research (JFCR) reveals that noncoding RNA derived from pericentromeric repetitive sequences provokes inflammatory gene expression in senescence and cancer.

Senescence is a state of essentially irreversible cell cycle arrest induced by several stressors, i.e., aging, obesity, radiation, and chemotherapy. Senescent cells that accumulate in vivo during aging communicate with surrounding tissues through the production of proinflammatory proteins, termed the senescence-associated secretory phenotype (SASP), which plays multiple physiological and pathological roles. In aged individuals, inflammatory SASP factors promote numerous age-related diseases, including cancer. Therefore, elucidating the regulatory mechanism of the SASP is essential for developing new preventive and therapeutic strategies against age-related cancer.

A team of JFCR researchers has hypothesized that an aberrant chromatin architecture observed in senescent cells might be associated with the SASP and have commenced the analysis of genome-wide chromatin interaction and gene expression using next-generation sequencing techniques. They revealed that the region containing pericentromeric repetitive sequences called human satellite II (hSATII), which are epigenetically silenced in normal cells, showed a notably open state in senescent cells. In addition, the expression of noncoding RNA (hSATII RNA) was markedly upregulated during cellular senescence. Further analysis revealed that hSATII RNA upregulated SASP-like inflammatory gene expression by disturbing chromatin interactions in some SASP gene regions through the functional impairment of CCCTC-binding factor (CTCF), which is important for the maintenance of genomic integrity.

Pericentromeric hSATII RNA regulates SASP factor gene expression during cellular senescence

(A–C) Screening of unique transcripts showing increased chromatin accessibility and active transcription during X-ray–induced senescence in IMR-90 cells. (A) A scheme of the screening steps. (B) Volcano plot of ATAC-seq signals showing fold change (FC) (x-axis) and FDR (y-axis) of chromatin accessibility between proliferating and X-ray–induced senescent IMR-90 cells. Red peaks show significantly increased chromatin accessibility in X-ray–induced senescent cells. Blue peaks showing significantly increased chromatin accessibility in proliferating cells. Black peaks show no significant changes. Yellow peaks containing hSATII loci show significantly increased chromatin accessibility. (C) Volcano plot of RNA-seq data (GSE130727) showing FC (x-axis) and FDR (y-axis) concerning 652 transcripts involved in an increased chromatin accessibility region between proliferating and X-ray–induced senescent IMR-90 cells from ATAC-seq analysis in B. The 47 transcripts showing FDR < 1010 are shown as red (up-regulated) or blue (down-regulated) dots. (D) Peaks of uniquely mapped reads by ATAC-seq and RNA-seq (GSE130727) in hSATII loci in proliferating or X-ray–induced senescent IMR-90 cells. Two biological replicates are shown. (E–G) RNA-seq analysis of hSATα– or hSATII-overexpressed and X-ray–induced senescent SVts8 cells. (E) Heatmap regarding SASP-related gene expression in hSATα– or hSATII-overexpressed and X-ray–induced senescent SVts8 cells. (F) Scatterplot showing FC in hSATα (x-axis) or hSATII (y-axis) RNA-overexpressed SVts8 cells compared to empty vector–expressed cells. Red dots indicate genes up-regulated (FC > 10) in vicinity of specific chromatin accessible peaks in hSATII RNA–overexpressed cells. (G) Gene set enrichment analysis of signatures associated with senescence (Upper) and inflammatory response (Lower) in hSATα– or hSATII RNA–overexpressed SVts8 cells. NES, normalized enrichment score. (H) The effect of hSATII RNA knockdown on hSATII RNA and SASP gene expression in proliferating or X-ray–induced senescent SVts8 cells by RT-qPCR. The relative expression is shown as the FC from control small-interfering RNA–treated proliferating cells. Each bar represents mean ± SD of three biological replicates. ***P < 0.001 by one-way ANOVA, followed by the Tukey’s multiple comparisons post hoc test.

“Small extracellular vesicles (EVs) secreted from cancer and stromal cells dynamically contribute to tumor incidence and progression in a non–cell-autonomous manner in the tumor microenvironment. Intriguingly, the amounts of hSATII RNA were higher in small EVs derived from senescent cells than in those derived from proliferating cells. Thus, our data suggest that hSATII RNA derived from senescent stromal cells are transferred into surrounding cells through small EVs and function as a SASP-like inflammatory factor in the tumor microenvironment.”

Further, the researchers found that hSATII RNA was highly detectable in cancer cells in surgical specimens from patients with primary colon carcinoma. Strikingly, the population of hSATII RNA-positive cells was significantly higher among cancer-associated fibroblasts than fibroblasts in normal stromal tissues.

“These findings highlight the new role of the hSATII RNA, which supports tumor development in a non–cell-autonomous manner via the secretion of SASP-like inflammatory factors and small EVs. Understanding this molecular mechanism can facilitate the development of novel preventive and therapeutic strategies against age-related pathologies in the future.”


Miyata K, Imai Y, Hori S, Nishio M, Loo TM, Okada R, Yang L, Nakadai T, Maruyama R, Fujii R, Ueda K, Jiang L, Zheng H, Toyokuni S, Sakata T, Shirahige K, Kojima R, Nakayama M, Oshima M, Nagayama S, Seimiya H, Hirota T, Saya H, Hara E, Takahashi A. (2021) Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer. PNAS 118(35):e2025647118. [article]

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