Original Article
 

A Novel Prognostic Immune-related Gene Signature in Hepatocellular Carcinoma Through Bioinformatics and Experimental Approaches

Abstract

Despite therapeutic advancements, treatment failure in hepatocellular carcinoma (HCC) continues to pose a significant obstacle. Given the vital role of the tumor immune microenvironment (TIM) in HCC and the promising effectiveness of immune therapies, we aimed to elucidate potential predictive biomarkers by developing a prognostic model based on immune-related genes (IRGs).
After obtaining data, differentially expressed IRGs were identified, and prognostic models were developed using Cox regression analyses. Key contributors of the model were identified and the results were validated by experimental assays in HCC cell lines.
Our eight-IRG signature can serve as an independent prognostic factor in HCC. The low-risk group exhibited superior overall survival and lower tumor mutation burden (TMB). The high-risk group showed elevated proportions of immune cells, including regulatory T cells and resting CD4+ memory T cells. We found that the "NEAT1-C1/miR-542-5p/BIRC5" regulatory network may serve as a potential target in HCC. The experimental investigations showed that BIRC5 inhibition reduced the metabolic activity in four HCC cell lines.
The results of this study facilitate patient stratification and the development of more effective treatment strategies, particularly for high-risk HCC patients.

1. Chidambaranathan-Reghupaty S, Fisher PB, Sarkar D. Hepatocellular carcinoma (HCC): Epidemiology, etiology and molecular classification. Advances in cancer research. 2021;149:1-61.
2. Samant H, Amiri HS, Zibari GB. Addressing the worldwide hepatocellular carcinoma: Epidemiology, prevention and management. Journal of gastrointestinal oncology. 2021;12(Suppl 2):S361.
3. Pinter M, Pinato DJ, Ramadori P, Heikenwalder M. NASH and Hepatocellular Carcinoma: Immunology and Immunotherapy. Clin Cancer Res. 2023;29(3):513-20.
4. Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E, Roayaie S, et al. Hepatocellular carcinoma. Nat Rev Dis Primers. 2021;7(1):6.
5. Chen Z, Xie H, Hu M, Huang T, Hu Y, Sang N, Zhao Y. Recent progress in treatment of hepatocellular carcinoma. American journal of cancer research. 2020;10(9):2993.
6. Marin JJ, Macias RI, Monte MJ, Romero MR, Asensio M, Sanchez-Martin A, et al. Molecular bases of drug resistance in hepatocellular carcinoma. Cancers. 2020;12(6):1663.
7. Papaconstantinou D, Tsilimigras DI, Pawlik TM. Recurrent hepatocellular carcinoma: Patterns, detection, staging and treatment. Journal of Hepatocellular Carcinoma. 2022:947-57.
8. Hanahan D, Weinberg RA. Biological hallmarks of cancer. Holland‐Frei Cancer Medicine. 2016:1-10.
9. Gnjatic S, Bronte V, Brunet LR, Butler MO, Disis ML, Galon J, et al. Identifying baseline immune-related biomarkers to predict clinical outcome of immunotherapy. Journal for immunotherapy of cancer. 2017;5(1):1-18.
10. Ge P, Wang W, Li L, Zhang G, Gao Z, Tang Z, et al. Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of colorectal cancer. Biomedicine & Pharmacotherapy. 2019;118:109228.
11. Chen P, Yang Y, Zhang Y, Jiang S, Li X, Wan J. Identification of prognostic immune-related genes in the tumor microenvironment of endometrial cancer. Aging (Albany NY). 2020;12(4):3371.
12. Jiang B, Sun Q, Tong Y, Wang Y, Ma H, Xia X, et al. An immune-related gene signature predicts prognosis of gastric cancer. Medicine. 2019;98(27).
13. Bou-Dargham MJ, Sha L, Sang Q-XA, Zhang J. Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy. BMC cancer. 2020;20:1-10.
14. Fu M, Wang Q, Wang H, Dai Y, Wang J, Kang W, et al. Immune-related genes are prognostic markers for prostate cancer recurrence. Frontiers in Genetics. 2021;12:639642.
15. Liao R, Ma Q-Z, Zhou C-Y, Li J-J, Weng N-N, Yang Y, Zhu Q. Identification of biomarkers related to Tumor-Infiltrating Lymphocytes (TILs) infiltration with gene co-expression network in colorectal cancer. Bioengineered. 2021;12(1):1676-88.
16. Kim S, Kim JR, Lee JH, Moon S-H, In Jo S, Bae D-J, et al. Differential RNA expression of immune-related genes and tumor cell proximity from intratumoral M1 macrophages in acral lentiginous melanomas treated with PD-1 blockade. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2022;1868(11):166516.
17. Huang M, Liu L, Zhu J, Jin T, Chen Y, Xu L, et al. Identification of immune-related subtypes and characterization of tumor microenvironment infiltration in bladder cancer. Frontiers in Cell and Developmental Biology. 2021;9:723817.
18. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic acids research. 2015;43(7):e47-e.
19. Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics: a journal of integrative biology. 2012;16(5):284-7.
20. Wang H, Lengerich BJ, Aragam B, Xing EP. Precision Lasso: accounting for correlations and linear dependencies in high-dimensional genomic data. Bioinformatics. 2019;35(7):1181-7.
21. Heagerty PJ, Saha-Chaudhuri P, Saha-Chaudhuri MP. Package ‘survivalROC’. San Francisco: GitHub. 2013.
22. Mayakonda A, Lin D-C, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome research. 2018;28(11):1747-56.
23. Kolde R, Kolde MR. Package ‘pheatmap’. R package. 2015;1(7):790.
24. Villanueva RAM, Chen ZJ. ggplot2: elegant graphics for data analysis. Taylor & Francis; 2019.
25. Sun T, Mao W, Peng H, Wang Q, Jiao L. YAP promotes sorafenib resistance in hepatocellular carcinoma by upregulating survivin. Cell Oncol (Dordr). 2021;44(3):689-99.
26. Namgung Y, Kim SY, Kim I. Down-regulation of Survivin by BIX-01294 pretreatment overcomes resistance of hepatocellular carcinoma cells to TRAIL. Anticancer Research. 2019;39(7):3571-8.
27. Aravalli RN. Role of innate immunity in the development of hepatocellular carcinoma. World journal of gastroenterology: WJG. 2013;19(43):7500.
28. Llovet JM, Castet F, Heikenwalder M, Maini MK, Mazzaferro V, Pinato DJ, et al. Immunotherapies for hepatocellular carcinoma. Nature reviews Clinical oncology. 2022;19(3):151-72.
29. Shang X, Liu G, Zhang Y, Tang P, Zhang H, Jiang H, Yu Z. Downregulation of BIRC5 inhibits the migration and invasion of esophageal cancer cells by interacting with the PI3K/Akt signaling pathway. Oncology letters. 2018;16(3):3373-9.
30. Wang N, Huang X, Cheng J. BIRC5 promotes cancer progression and predicts prognosis in laryngeal squamous cell carcinoma. PeerJ. 2022;10:e12871.
31. Li Y, Zhao Z-G, Luo Y, Cui H, Wang H-Y, Jia Y-F, Gao Y-T. Dual targeting of Polo-like kinase 1 and baculoviral inhibitor of apoptosis repeat-containing 5 in TP53-mutated hepatocellular carcinoma. World Journal of Gastroenterology. 2020;26(32):4786.
32. de Moraes GN, Delbue D, Silva KL, Robaina MC, Khongkow P, Gomes AR, et al. FOXM1 targets XIAP and Survivin to modulate breast cancer survival and chemoresistance. Cellular signalling. 2015;27(12):2496-505.
33. Brittain AL, Basu R, Qian Y, Kopchick JJ. Growth hormone and the epithelial-to-mesenchymal transition. The Journal of Clinical Endocrinology & Metabolism. 2017;102(10):3662-73.
34. Basu R, Kopchick JJ. The effects of growth hormone on therapy resistance in cancer. Cancer Drug Resistance. 2019;2(3):827.
35. Kopchick JJ, Basu R, Berryman DE, Jorgensen JO, Johannsson G, Puri V. Covert actions of growth hormone: fibrosis, cardiovascular diseases and cancer. Nature Reviews Endocrinology. 2022;18(9):558-73.
36. Gebre-Medhin M, Kindblom L-G, Wennbo H, Törnell J, Meis-Kindblom JM. Growth hormone receptor is expressed in human breast cancer. The American journal of pathology. 2001;158(4):1217-22.
37. Fu Y, Liu S, Rodrigues RM, Han Y, Guo C, Zhu Z, et al. Activation of VIPR1 suppresses hepatocellular carcinoma progression by regulating arginine and pyrimidine metabolism. Int J Biol Sci. 2022;18(11):4341-56.
38. Aliyu M, Saboor-Yaraghi AA, Nejati S, Robat-Jazi B. Urinary VPAC1: A potential biomarker in prostate cancer. AIMS Allergy and Immunology. 2022;6(2):42-63.
39. Chang T-Y, Lan K-C, Chiu C-Y, Sheu M-L, Liu S-H. ANGPTL1 attenuates cancer migration, invasion, and stemness through regulating FOXO3a-mediated SOX2 expression in colorectal cancer. Clinical Science. 2022;136(9):657-73.
40. Sun R, Yang L, Hu Y, Wang Y, Zhang Q, Zhang Y, et al. ANGPTL1 is a potential biomarker for differentiated thyroid cancer diagnosis and recurrence. Oncology Letters. 2020;20(5):1-.
41. Chen HA, Kuo TC, Tseng CF, Ma JT, Yang ST, Yen CJ, et al. Angiopoietin‐like protein 1 antagonizes MET receptor activity to repress sorafenib resistance and cancer stemness in hepatocellular carcinoma. Hepatology. 2016;64(5):1637-51.
42. Wu H, Bi J, Peng Y, Huo L, Yu X, Yang Z, et al. Nuclear receptor NR4A1 is a tumor suppressor down-regulated in triple-negative breast cancer. Oncotarget. 2017;8(33):54364.
43. Deutsch AJ, Rinner B, Wenzl K, Pichler M, Troppan K, Steinbauer E, et al. NR4A1-mediated apoptosis suppresses lymphomagenesis and is associated with a favorable cancer-specific survival in patients with aggressive B-cell lymphomas. Blood, The Journal of the American Society of Hematology. 2014;123(15):2367-77.
44. Yu W, He J, Wang F, He Q, Shi Y, Tao X, Sun B. NR4A1 mediates NK‐cell dysfunction in hepatocellular carcinoma via the IFN‐γ/p‐STAT1/IRF1 pathway. Immunology. 2023;169(1):69-82.
45. Huang Q, Xu J, Ge Y, Shi Y, Wang F, Zhu M. NR4A1 inhibits the epithelial–mesenchymal transition of hepatic stellate cells: Involvement of TGF-β–Smad2/3/4–ZEB signaling. Open Life Sciences. 2022;17(1):447-54.
46. WANG H, LIU Y, LI D, SHEN G. Expression of interleukin-33 in hepatocellular carcinoma patients and its role in regulating CD8. Journal of Clinical Hepatology. 2022:117-23.
47. Yangngam S, Thongchot S, Pongpaibul A, Vaeteewoottacharn K, Pinlaor S, Thuwajit P, et al. High level of interleukin-33 in cancer cells and cancer-associated fibroblasts correlates with good prognosis and suppressed migration in cholangiocarcinoma. Journal of Cancer. 2020;11(22):6571.
48. Kienzl M, Hasenoehrl C, Valadez-Cosmes P, Maitz K, Sarsembayeva A, Sturm E, et al. IL-33 reduces tumor growth in models of colorectal cancer with the help of eosinophils. Oncoimmunology. 2020;9(1):1776059.
49. Zhou Y, Ran X, Han M. Identification of a immune-related gene signature as a novel prognostic biomarker of cholangiocarcinoma. 2023.
50. Chu T-H, Ko C-Y, Tai P-H, Chang Y-C, Huang C-C, Wu T-Y, et al. Leukocyte cell-derived chemotaxin 2 regulates epithelial-mesenchymal transition and cancer stemness in hepatocellular carcinoma. Journal of Biological Chemistry. 2022;298(10).
51. Zhang B, Wu H. Decreased expression of COLEC10 predicts poor overall survival in patients with hepatocellular carcinoma. Cancer management and research. 2018:2369-75.
52. Cai M-N, Chen D-M, Xiao L-X, Li S-S, Liao C-H, Li J, et al. COLEC10 Induces Endoplasmic Reticulum Stress by Occupying GRP78 and Inhibits Hepatocellular Carcinoma. Laboratory Investigation. 2023;103(7):100130.
53. Kang Z, Chen B, Ma X, Yan F, Wang Z. Immune-related gene-based model predicts the survival of colorectal carcinoma and reflected various biological statuses. Front Mol Biosci. 2023;10:1277933.
54. Chen R, Zhao M, An Y, Liu D, Tang Q, Teng G. A Prognostic Gene Signature for Hepatocellular Carcinoma. Front Oncol. 2022;12:841530.
55. Zhang J, Han H, Wang L, Wang W, Yang M, Qin Y. Overcoming the therapeutic resistance of hepatomas by targeting the tumor microenvironment. Front Oncol. 2022;12:988956.
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SectionOriginal Article(s)
Keywords
Bioinformatics BIRC5 Hepatocellular carcinoma Immune-related signature Prognostic model Survivin

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1.
Pourbagheri-Sigaroodi A, Momeny M, Rezaei N, Fallah F, Bashash D. A Novel Prognostic Immune-related Gene Signature in Hepatocellular Carcinoma Through Bioinformatics and Experimental Approaches. Iran J Allergy Asthma Immunol. 2024;:1-28.