CHAF1B promotes the progression of lung squamous-cell carcinoma by inhibiting SETD7 expression

Abstract

The p60 subunit of the chromatin assembly factor-1 complex, that is, chromatin assembly factor-1 subunit B (CHAF1B), is a histone H3/H4 chaperone crucial for the transcriptional regulation of cell differentiation and self-renewal. CHAF1B is overexpressed in several cancers and may represent a potential target for cancer therapy. However, its expression and clinical significance in lung squamous-cell carcinoma (LUSC) remain unclear. In this study, we performed weighted gene correlation network analysis to analyze the Gene Expression Omnibus GSE68793 LUSC dataset and identified CHAF1B as one of the most important driver gene candidates. Immunohistochemical analysis of 126 LUSC tumor samples and 80 adjacent normal lung tissues showed the marked upregulation of CHAF1B in tumor tissues and the negative association of its expression level with patient survival outcomes. Silencing of CHAF1B suppressed LUSC proliferation in vitro and LUSC tumor growth in vivo. Furthermore, bulk RNA sequencing of CHAF1B knockdown cells indicated SET domain containing 7 (SETD7) as a significant CHAF1B target gene. In addition, CHAF1B competitively binds to the SETD7 promoter region and represses its transcription. Altogether, these results imply that CHAF1B plays a vital role in LUSC tumorigenesis and may represent a potential molecular target for this deadly disease.

Keywords

CHAF1B / cell cycle / lung squamous cell carcinoma / SETD7 / WGCNA

References

[1] Bray F, Laversanne M, Sung H, Ferlay J, Siegel RL, Soerjomataram I, Jemal A. Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2024; 74(3): 229–263

[2] Zheng RS, Chen R, Han BF, Wang SM, Li L, Sun KX, Zeng HM, Wei WW, He J. Cancer incidence and mortality in China, 2022. Chinese Journal of Oncology (Zhonghua Zhongliu Zazhi) 2024; 46(3): 221–231

[3] Thai AA, Solomon BJ, Sequist LV, Gainor JF, Heist RS. Lung cancer. Lancet 2021; 398(10299): 535–554

[4] Pan Y, Han H, Labbe KE, Zhang H, Wong KK. Recent advances in preclinical models for lung squamous cell carcinoma. Oncogene 2021; 40(16): 2817–2829

[5] Zhong J, Bai H, Wang Z, Duan J, Zhuang W, Wang D, Wan R, Xu J, Fei K, Ma Z, Zhang X, Wang J. Treatment of advanced non-small cell lung cancer with driver mutations: current applications and future directions. Front Med 2023; 17(1): 18–42

[6] Garon EB, Rizvi NA, Hui R, Leighl N, Balmanoukian AS, Eder JP, Patnaik A, Aggarwal C, Gubens M, Horn L, Carcereny E, Ahn MJ, Felip E, Lee JS, Hellmann MD, Hamid O, Goldman JW, Soria JC, Dolled-Filhart M, Rutledge RZ, Zhang J, Lunceford JK, Rangwala R, Lubiniecki GM, Roach C, Emancipator K, Gandhi L. Pembrolizumab for the treatment of non-small-cell lung cancer. N Engl J Med 2015; 372(21): 2018–2028

[7] Horn L, Spigel DR, Vokes EE, Holgado E, Ready N, Steins M, Poddubskaya E, Borghaei H, Felip E, Paz-Ares L, Pluzanski A, Reckamp KL, Burgio MA, Kohlhäeufl M, Waterhouse D, Barlesi F, Antonia S, Arrieta O, Fayette J, Crinò L, Rizvi N, Reck M, Hellmann MD, Geese WJ, Li A, Blackwood-Chirchir A, Healey D, Brahmer J, Eberhardt WEE. Nivolumab versus docetaxel in previously treated patients with advanced non-small-cell lung cancer: two-year outcomes from two randomized, open-label, phase III trials (CheckMate 017 and CheckMate 057). J Clin Oncol 2017; 35(35): 3924–3933

[8] Novello S, Kowalski DM, Luft A, Gümüş M, Vicente D, Mazières J, Rodríguez-Cid J, Tafreshi A, Cheng Y, Lee KH, Golf A, Sugawara S, Robinson AG, Halmos B, Jensen E, Schwarzenberger P, Pietanza MC, Paz-Ares L. Pembrolizumab plus chemotherapy in squamous non-small-cell lung cancer: 5-year update of the phase III KEYNOTE-407 study. J Clin Oncol 2023; 41(11): 1999–2006

[9] Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2021; 71(3): 209–249

[10] Duma N, Santana-Davila R, Molina JR. Non-small cell lung cancer: epidemiology, screening, diagnosis, and treatment. Mayo Clin Proc 2019; 94(8): 1623–1640

[11] Volk A, Liang K, Suraneni P, Li X, Zhao J, Bulic M, Marshall S, Pulakanti K, Malinge S, Taub J, Ge Y, Rao S, Bartom E, Shilatifard A, Crispino JD. A CHAF1B-dependent molecular switch in hematopoiesis and leukemia pathogenesis. Cancer Cell 2018; 34(5): 707–723.e7

[12] Volk A, Crispino JD. The role of the chromatin assembly complex (CAF-1) and its p60 subunit (CHAF1b) in homeostasis and disease. Biochim Biophys Acta 2015; 1849(8): 979–86

[13] Shrestha RL, Balachandra V, Kim JH, Rossi A, Vadlamani P, Sethi SC, Ozbun L, Lin S, Cheng KCC, Chari R, Karpova TS, Pegoraro G, Foltz DR, Caplen NJ, Basrai MA. The histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability. J Cell Sci 2023; 136(10): jcs260944

[14] Polo SE, Theocharis SE, Grandin L, Gambotti L, Antoni G, Savignoni A, Asselain B, Patsouris E, Almouzni G. Clinical significance and prognostic value of chromatin assembly factor-1 overexpression in human solid tumours. Histopathology 2010; 57(5): 716–724

[15] Staibano S, Mascolo M, Mancini FP, Kisslinger A, Salvatore G, Di Benedetto M, Chieffi P, Altieri V, Prezioso D, Ilardi G, De Rosa G, Tramontano D. Overexpression of chromatin assembly factor-1 (CAF-1) p60 is predictive of adverse behaviour of prostatic cancer. Histopathology 2009; 54(5): 580–589

[16] Peng X, Fu H, Yin J, Zhao Q. CHAF1B knockdown blocks migration in a hepatocellular carcinoma model. Oncol Rep 2018; 40(1): 405–413

[17] Di M, Wang M, Miao J, Chen B, Huang H, Lin C, Jian Y, Li Y, Ouyang Y, Chen X, Wang L, Zhao C. CHAF1B induces radioresistance by promoting DNA damage repair in nasopharyngeal carcinoma. Biomed Pharmacother 2020; 123: 109748

[18] Saleiro D, Kosciuczuk EM, Fischietti M, Perez RE, Yang GS, Eckerdt F, Beauchamp EM, Hou Y, Wang Q, Weinberg RS, Fish EN, Yue F, Hoffman R, Platanias LC. Targeting CHAF1B enhances IFN activity against myeloproliferative neoplasm cells. Cancer Res Commun 2023; 3(5): 943–51

[19] Li Q, Zhang X, Zhang Z. CHAF1B overexpression: a brake for the differentiation of leukemia cells. Cancer cell 2018; 34(5): 693–4

[20] Dean ST, Ishikawa C, Zhu X, Walulik S, Nixon T, Jordan JK, Henderson S, Wyder M, Salomonis N, Wunderlich M, Greis KD, Starczynowski DT, Volk AG. Repression of TRIM13 by chromatin assembly factor CHAF1B is critical for AML development. Blood Adv 2023; 7(17): 4822–37

[21] Ge L, Tan W, Li G, Gong N, Zhou L. Circ_0026134 promotes NSCLC progression by the miR-3619–5p/CHAF1B axis. Thorac Cancer 2022; 13(4): 582–92

[22] Gong L, Hu Y, He D, Zhu Y, Xiang L, Xiao M, Bao Y, Liu X, Zeng Q, Liu J, Zhou M, Zhou Y, Cheng Y, Zhang Y, Deng L, Zhu R, Lan H, Cao K. Ubiquitin ligase CHAF1B induces cisplatin resistance in lung adenocarcinoma by promoting NCOR2 degradation. Cancer Cell Int 2020; 20: 194

[23] Duan Y, Liu T, Li S, Huang M, Li X, Zhao H, Li J. CHAF1B promotes proliferation and reduces apoptosis in 95-D lung cancer cells and predicts a poor prognosis in non-small cell lung cancer. Oncol Rep 2019; 41(4): 2518–2528

[24] Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008; 9: 559

[25] Langfelder P, Horvath S. Fast R functions for robust correlations and hierarchical clustering. J Stat Softw 2012; 46(11): i11

[26] Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003; 13(11): 2498–504

[27] Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC bioinformatics 2003; 4: 2

[28] Ben-Porath I, Thomson MW, Carey VJ, Ge R, Bell GW, Regev A, Weinberg RA. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet 2008; 40(5): 499–507

[29] Huang J, Li Y, Lu Z, Che Y, Sun S, Mao S, Lei Y, Zang R, Li N, Zheng S, Liu C, Wang X, Sun N, He J. Analysis of functional hub genes identifies CDC45 as an oncogene in non-small cell lung cancer-a short report. Cell Oncol (Dordr) 2019; 42(4): 571–578

[30] Chen X, Yu C, Gao J, Zhu H, Cui B, Zhang T, Zhou Y, Liu Q, He H, Xiao R, Huang R, Xie H, Gao D, Zhou H. A novel USP9X substrate TTK contributes to tumorigenesis in non-small-cell lung cancer. Theranostics 2018; 8(9): 2348–60

[31] Rouillon C, Eckhardt BV, Kollenstart L, Gruss F, Verkennis AEE, Rondeel I, Krijger PHL, Ricci G, Biran A, van Laar T, Delvaux de Fenffe CM, Luppens G, Albanese P, Sato K, Scheltema RA, de Laat W, Knipscheer P, Dekker NH, Groth A, Mattiroli F. CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands. Nucleic Acids Res 2023; 51(8): 3770–92

[32] Li T, Fu J, Zeng Z, Cohen D, Li J, Chen Q, Li B, Liu XS. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res 2020; 48(W1): W509–W514

[33] Li T, Fan J, Wang B, Traugh N, Chen Q, Liu JS, Li B, Liu XS. TIMER: a web server for comprehensive analysis of tumor–infiltrating immune cells. Cancer Res. 2017; 77(21): e108–e10

[34] Li B, Severson E, Pignon JC, Zhao H, Li T, Novak J, Jiang P, Shen H, Aster JC, Rodig S, Signoretti S, Liu JS, Liu XS. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biol. 2016; 17(1): 174

[35] Győrffy B. Integrated analysis of public datasets for the discovery and validation of survival-associated genes in solid tumors. Innovation (Camb) 2024; 5(3): 100625

[36] Győrffy B. Transcriptome-level discovery of survival-associated biomarkers and therapy targets in non-small-cell lung cancer. Br J Pharmacol 2024; 181(3): 362–374

[37] Batista IAA, Helguero LA. Biological processes and signal transduction pathways regulated by the protein methyltransferase SETD7 and their significance in cancer. Signal Transduct Target Ther 2018; 3: 19

[38] Chiang CY, Fan S, Zheng H, Guo W, Zheng Z, Sun Y, Zhong C, Zeng J, Li S, Zhang M, Xiao T, Zheng D. Methylation of KRAS by SETD7 promotes KRAS degradation in non-small cell lung cancer. Cell Rep 2023; 42(9): 113003

[39] Smith S, Stillman B. Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro. Cell 1989; 58(1): 15–25

[40] Kaufman PD, Kobayashi R, Kessler N, Stillman B. The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication. Cell 1995; 81(7): 1105–1114

[41] Zhang Y, Yang Y, Qiao P, Wang X, Yu R, Sun H, Xing X, Zhang Y, Su J. CHAF1b, chromatin assembly factor-1 subunit b, is essential for mouse preimplantation embryos. Int J Biol Macromol 2022; 195: 547–557

[42] Chuikov S, Kurash JK, Wilson JR, Xiao B, Justin N, Ivanov GS, McKinney K, Tempst P, Prives C, Gamblin SJ, Barlev NA, Reinberg D. Regulation of p53 activity through lysine methylation. Nature 2004; 432(7015): 353–60

[43] Chiang C, Yang H, Zhu L, Chen C, Chen C, Zuo Y, Zheng D. The epigenetic regulation of nonhistone proteins by SETD7: new targets in cancer. Front Genet 2022; 13: 918509

[44] Wang Z, Petricca J, Liu M, Zhang S, Chen S, Li M, Besschetnova A, Patalano S, Venkataramani K, Siegfried KR, Macoska JA, Han D, Gao S, Vedadi M, Arrowsmith CH, He HH, Cai C. SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1. Proc Natl Acad Sci USA 2023; 120(33): e2220472120

[45] Chen Y, Yang S, Hu J, Yu C, He M, Cai Z. Increased expression of SETD7 promotes cell proliferation by regulating cell cycle and indicates poor prognosis in hepatocellular carcinoma. PloS one 2016; 11(5): e0154939

[46] Fu J, Huang Y, Xian L. LncRNA SNHG15 regulates hypoxic-ischemic brain injury via miR-153–3p/SETD7 axis. Histol Histopathol 2022; 37(11): 1113–1125

Acknowledgements

This work was supported by the National Key Research and Development Program of China (Nos. 2022YFA1103900 and 2020YFA0803300), CAMS Initiative for Innovative Medicine (Nos. 2021-1-I2M-012, 2021-I2M-1-014, 2022-I2M-2-001, 2021-I2M-1-021, and 2022-I2M-1-009), the Non-Profit Central Research Institute Fund of CAMS (Nos. 2022-RC310-05 and 2021-RC310-003), and the National Natural Science Foundation of China (Nos. 82372944, 82073092, and 82273076).

Electronic Supplementary Material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s11684-024-1122-2 and is accessible for authorized users.

Compliance with ethics guidelines

Conflicts of interest Zhuo Zheng, Yongfang Lin, Hua Guo, Zheng Liu, Xiaoliang Jie, Guizhen Wang, and Guangbiao Zhou declare that they have no conflict of interest.

The study was approved by the research ethics committee of the Cancer Hospital, Chinese Academy of Medical Sciences and performed in accordance with the ethical standards laid down in the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards. Additional informed consent was obtained from all patients, whose identifying information is included in this article.

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