Identification the Cellular Senescence Associated lncRNA LINC01579 in Gastric Cancer

Abstract

Cellular senescence is a key promoter of tumorigenesis and malignant progression. This study aimed to develop a predictive model for assessing cellular senescence in gastric cancer (GC) outcomes. We identified senescence-related genes and lncRNAs from 375 stomach adenocarcinoma (STAD) patients and established a prognostic senescence score using multivariate Cox regression, validated in testing, TCGA-STAD and the combined TCGA-COAD and READ cohorts. The model's predictive efficacy was evaluated across clinical subgroups, tumour microenvironments and immune cell infiltration. A total of 116 senescence-related lncRNAs were filtered, and patients were clustered into two senescent subtypes. The lncRNA signature identified LINC01579 as an independent prognostic factor for GC. Low-risk groups showed prolonged overall survival, increased immune cell infiltration and reduced mutation load. Downregulation of LINC01579 using antisense oligonucleotides (ASOs) on normal human fibroblasts decreased cellular proliferation and migration in GC. Collectively, this study established and validated a promising prognostic model connecting senescence-related lncRNAs and clinical outcome in GC and provided potential senescence-related biomarkers for GC prognosis prediction.

Keywords: cellular senescence; fibroblast; gastric cancer; prognosis; tumour microenvironment.

FIGURE 1

Workflow of this study.

FIGURE 2

Identification of DEGs and development of cellular senescence‐related lncRNAs signature (A) Volcano plot showed the 22 DEGs identified from 375 STAD patients. (B) Venn plot exhibited the cross genes between DEGs in STAD and genes in CellAge. (C) Sankey diagram demonstrated the relationship between senescence‐related lncRNAs and mRNA of DEGs with different expression levels. (D) Unsupervised hierarchical clustering analysis clustered into two distinct groups: Senescence relevant group and control group, based on expression of senescence‐related lncRNAs. (E) GO functional enrichment analysis. (F) KEGG pathway analysis showed the main related signalling pathways of lncRNAs. (G) Coefficient spectrum of senescence‐related lncRNAs. (H) LASSO correlation coefficients of 16 senescence‐related lncRNAs.

FIGURE 3

Estimation and validation of senescence‐related lncRNAs signature (A–C) The risk score distribution, Survival status scatter plots and the expression profile of independent prognostic factor of STAD patients in training cohort (A), testing cohort (B) and external cohort (C). (D–F) Kaplan–Meier survival curves of overall survival of high‐risk and low‐risk groups in the training cohort (D), testing cohort (E) and external cohort (F). (G, H) 1‐, 2‐, 3‐year ROC curve of risk scores between high‐risk group and low‐risk group in training cohort (G), testing cohort (H). (I) 1‐, 3‐, 5‐year ROC curve of risk scores between high‐risk group and low‐risk group in external cohort.

FIGURE 4

OS analysis of senescence related lncRNAs signature in diverse clinical subgroups Kaplan–Meier estimates of OS based on the senescence‐related lncRNAs signature in clinical subgroups stratified ground on age (A, B), stage (C, D), T (E, F), N (G, H) in the TCGA‐STAD cohort.

FIGURE 5

Assessment of the tumour microenvironment and immune cell infiltration (A) Summary plot of mutation information showed the mutation landscape of STAD, including mutative classification, types and classes. (B) Waterfall chart exhibited the top mutative genes of high‐risk and low‐risk group in STAD. (C) Immune infiltration differences between high‐ and low‐risk groups in STAD. (D) Comparison of stromal score and immune score between high‐ and low‐risk groups. *: p < 0.05, **: p < 0.01, ***: p < 0.001.

FIGURE 6

The knockdown of LINC01579 inhibits cellular senescence of NFs in vitro (A) Overall survival of high‐ and low‐expression of LINC01579 group of TCGA‐STAD cohort in GEPIA. (B) Disease free survival of high‐ and low‐ expression of LINC01579 group of TCGA‐STAD cohort in GEPIA. (C) qPCR analysis of LINC01579 in GC and adjacent normal tissues (n = 22, normalised to GAPDH). (D) ISH showed the spatial localization of LINC01579 within the organisation. (E) Schematic of the origin of NFs and its image under microscope. (F) Immunofluorescence analysis verified the fibroblastic phenotype of cell line NFs. (G) Verification of knock down of LINC01579 in NFs using qRT‐PCR. (H) SA‐β‐gal staining exhibited the different senescent phenotype of NFs with or without LINC01579 downregulation. (I) qRT‐PCR showing the difference of SASP expression in NFs with or without LINC01579 downregulation. *: p < 0.05, **: p < 0.01, ***: p < 0.001.

FIGURE 7

The knockdown of LINC01579 in NFs promotes the proliferation and migration of GC cells (A) Schematic of CCK‐8 assay. (B) CCK‐8 assay determining the proliferation of GC cell lines cultured with medium from NFs with or without LINC01579 downregulation. (C, E) Schematic of transwell migration assay and wound‐healing assay. (D, F) Transwell migration assay (D) and wound‐healing assay (F) exhibiting the migratory difference of GC cells co‐cultured with NFs with or without LINC01579 downregulation. *: p < 0.05, **: p < 0.01, ***: p < 0.001.