Prognostic Value of Endoplasmic Reticulum Stress-Related Gene Signature in Thyroid Cancer

Abstract

Objective

To investigate the contribution of endoplasmic reticulum (ER) stress to the progression of thyroid cancer (TC) and to construct a prognostic gene signature.

Methods

Differential expression analysis was performed on 572 samples from The Cancer Genome Atlas (TCGA). ER stress-related genes (ERSGs) were obtained from the GeneCards database. Overlap analysis revealed 178 differentially expressed ERSGs. Least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression were used to construct a prognostic risk model. The model was validated in a test set (n = 172) and an independent clinical cohort (n = 90) by RT-qPCR. Immune infiltration, immune checkpoint expression, and drug sensitivity were compared between the high- and low-risk groups using the CIBERSORT algorithm and the Genomics of Drug Sensitivity in Cancer (GDSC) database.

Results

A total of 5,253 differentially expressed genes and 518 ERSGs were identified, yielding 178 overlapping genes. An 11-gene prognostic model (CDKN1A, HTR2A, ATF3, MTTP, BRSK2, EGF, CASP12, HSPA5, IL1A, FOXRED2, CASQ2) was constructed. Patients in the high-risk group had significantly worse overall survival than those in the low-risk group did (log-rank P < 0.001; hazard ratio [HR] = 2.34; 95% CI: 1.58–3.47). The model showed good predictive performance, with AUC values of 0.74, 0.72, and 0.71 for 1-, 3-, and 5-year overall survival, respectively. Significant differences in tumor immune cell infiltration (e.g., Tregs, P < 0.01; M2 macrophages, P < 0.05) and drug sensitivity (e.g., gefitinib, P < 0.05) were detected between the two groups. In 90 clinical samples, the expression patterns of the 11 genes were validated by RT-qPCR (all P < 0.05), which was consistent with the bioinformatics findings.

Conclusion

The 11-gene ER stress-related signature independently predicted prognosis in patients with TC across both the TCGA cohort and an independent cohort. This study provides new insight into the role of ER stress in TC and may facilitate the identification of prognostic biomarkers and support clinical decision-making.

Keywords

Endoplasmic reticulum stress / Thyroid cancer / Prognosis / Gene signature / Unfolded protein response / Risk model / Biomarker / Survival prediction

References

[1] Chen YX, Hong HZ, Gao ZH, et al. . Global trend and disparity in the burden of thyroid cancer attributable to high body-mass index from 1990 to 2021 and projection to 2049: a systematic analysis based on the Global Burden of Disease Study 2021. BMC Public Health., 2025, 25(1): 1051

[2] Prete A, Borges de Souza P, Censi S, et al. Update on fundamental mechanisms of thyroid cancer. Front Endocrinol. 2020;11:102.

[3] Carneiro RM, Carneiro BA, Agulnik M, et al. . Targeted therapies in advanced differentiated thyroid cancer. Cancer Treat Rev., 2015, 41(8): 690-698

[4] Durante C, Haddy N, Baudin E, et al. . Long-term outcome of 444 patients with distant metastases from papillary and follicular thyroid carcinoma: benefits and limits of radioiodine therapy. J Clin Endocrinol Metab., 2006, 91(8): 2892-2899

[5] Urra H, Dufey E, Avril T, et al. . Endoplasmic reticulum stress and the hallmarks of cancer. Trends Cancer., 2016, 2(5): 252-262

[6] Nie Z, Chen M, Wen X, et al. . Endoplasmic reticulum stress and tumor microenvironment in bladder cancer: the missing link. Front Cell Dev Biol., 2021, 9: 683940

[7] Chen X, Cubillos-Ruiz JR. Endoplasmic reticulum stress signals in the tumour and its microenvironment. Nat Rev Cancer., 2021, 21(2): 71-88

[8] Urra H, Dufey E, Lisbona F, et al. . When ER stress reaches a dead end. Biochim Biophys Acta., 2013, 1833(12): 3507-3517

[9] Lam M, Marsters SA, Ashkenazi A, et al. . Misfolded proteins bind and activate death receptor 5 to trigger apoptosis during unresolved endoplasmic reticulum stress. Elife., 2020, 9: e52291

[10] Upton JP, Wang L, Han D, et al. . IRE1α cleaves select microRNAs during ER stress to derepress translation of proapoptotic Caspase-2. Science., 2012, 338(6108): 818-822

[11] Dadey DY, Kapoor V, Khudanyan A, et al. . The ATF6 pathway of the ER stress response contributes to enhanced viability in glioblastoma. Oncotarget., 2016, 7(2): 2080-2092

[12] Ritchie ME, Phipson B, Wu D, et al. . Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 2015, 43(7): e47

[13] Szklarczyk D, Gable AL, Nastou KC, et al. . The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res., 2021, 49(D1): D605-D612

[14] Shannon P, Markiel A, Ozier O, et al. . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 2003, 13(11): 2498-2504

[15] Tay JK, Narasimhan B, Hastie T. Elastic net regularization paths for all generalized linear models. J Stat Softw., 2023, 106: 1

[16] Yoshihara K, Shahmoradgoli M, Martínez E, et al. . Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun., 2013, 4: 2612

[17] Newman AM, Liu CL, Green MR, et al. . Robust enumeration of cell subsets from tissue expression profiles. Nat Methods., 2015, 12(5): 453-457

[18] Geeleher P, Cox N, Huang RS. pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. PLoS One., 2014, 9(9): e107468

[19] Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics., 2010, 26(12): 1572-1573

[20] Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics., 2013, 14: 7

[21] Kolde R. pheatmap: Pretty Heatmaps [software]. R package version 1.0.12. Vienna, Austria: R Foundation for Statistical Computing; 2019.

[22] Yu G, Wang LG, Han Y, et al. . clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS., 2012, 16(5): 284-287

[23] Bustin SA, Ruijter JM, van den Hoff MJB, et al. MIQE 2.0: revision of the minimum information for publication of quantitative real-time PCR experiments guidelines. Clin Chem. 2025;71(6):634–651.

[24] Nakano M. Identification and validation of reference genes for quantitative real-time PCR in ficus carica. Plants., 2026, 15(1): 40

[25] Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res., 2001, 29(9): e45

[26] Zhang HH, Li C, Ren JW, et al. . OTUB1 facilitates bladder cancer progression by stabilizing ATF6 in response to endoplasmic reticulum stress. Cancer Sci., 2021, 112(6): 2199-2209

[27] Harnoss JM, Le Thomas A, Reichelt M, et al. . IRE1α disruption in triple-negative breast cancer cooperates with antiangiogenic therapy by reversing ER stress adaptation and remodeling the tumor microenvironment. Cancer Res., 2020, 80(11): 2368-2379

[28] Mujcic H, Nagelkerke A, Rouschop KM, et al. . Hypoxic activation of the PERK/eIF2α arm of the unfolded protein response promotes metastasis through induction of LAMP3. Clin Cancer Res., 2013, 19(22): 6126-6137

[29] Luo J, Wang Y, Zhao L, et al. . Anti-anaplastic thyroid cancer (ATC) effects and mechanisms of PLX3397 (pexidartinib), a multi-targeted tyrosine kinase inhibitor (TKI). Cancers., 2022, 15(1): 172

[30] Hetz C. The unfolded protein response: controlling cell fate decisions under ER stress and beyond. Nat Rev Mol Cell Biol., 2012, 13(2): 89-102

[31] Lei ST, Shen F, Chen JW, et al. . miR-639 promoted cell proliferation and cell cycle in human thyroid cancer by suppressing CDKN1A expression. Biomed Pharmacother., 2016, 84: 1834-1840

[32] Yue Y, Zhong M, An X, et al. . Serotonin (5-HT) 2A receptor involvement in melanin synthesis and transfer via activating the PKA/CREB signaling pathway. Int J Mol Sci., 2022, 23(11): 6111

[33] Kooti A, Abuei H, Jaafari A, et al. . Activating transcription factor 3 mediates apoptosis and cell cycle arrest in TP53-mutated anaplastic thyroid cancer cells. Thyroid Res., 2024, 17(1): 12

[34] Wang W, Gao Y, Liu Y, et al. . Pan-cancer analysis reveals MTTP as a prognostic and immunotherapeutic biomarker in human tumors. Front Immunol., 2025, 16: 1549965

[35] Jäger S, Handschin C, St-Pierre J, et al. . AMP-activated protein kinase (AMPK) action in skeletal muscle via direct phosphorylation of PGC-1alpha. Proc Natl Acad Sci U S A., 2007, 104(29): 12017-12022

[36] Ohno K, Shibata T, Ito KI. Epidermal growth factor receptor activation confers resistance to lenvatinib in thyroid cancer cells. Cancer Sci., 2022, 113(9): 3193-3210

[37] Yoneda T, Imaizumi K, Oono K, et al. . Activation of caspase-12, an endoplastic reticulum (ER) resident caspase, through tumor necrosis factor receptor-associated factor 2-dependent mechanism in response to the ER stress. J Biol Chem., 2001, 276(17): 13935-13940

[38] Dong W, Du D, Huang H. HSPA5 is a prognostic biomarker correlated with immune infiltrates in thyroid carcinoma. Endokrynol Pol., 2022, 73(4): 680-689

[39] Feng Y, Huang C, Liu X, et al. . A bibliometric analysis of inflammation and thyroid carcinoma: research trends and future perspectives. Front Oncol., 2025, 15: 1593006

[40] Nagy Á, Pongor LS, Szabó A, et al. . KRAS driven expression signature has prognostic power superior to mutation status in non-small cell lung cancer. Int J Cancer., 2017, 140(4): 930-937

[41] Kim JH, Lee ES, Yun J, et al. . Calsequestrin 2 overexpression in breast cancer increases tumorigenesis and metastasis by modulating the tumor microenvironment. Mol Oncol., 2022, 16(2): 466-484

[42] Wang H, Franco F, Ho PC. Metabolic regulation of tregs in cancer: opportunities for immunotherapy. Trends Cancer., 2017, 3(8): 583-592

[43] Locati M, Curtale G, Mantovani A. Diversity, mechanisms, and significance of macrophage plasticity. Annu Rev Pathol., 2020, 15: 123-147

[44] Shan F, Somasundaram A, Bruno TC, et al. . Therapeutic targeting of regulatory T cells in cancer. Trends Cancer., 2022, 8(11): 944-961

Funding

Traditional Chinese Medicine Science and Technology Project of Zhejiang Provincial Health Commission(2024ZL257)

Traditional Chinese Medicine Science and Technology Project of Zhejiang Provincial Health Commission (No.2024ZL246)

RIGHTS & PERMISSIONS

The Author(s), under exclusive licence to the Huazhong University of Science and Technology