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Research Paper

DNA hypomethylation mediates immune response in pan-cancer

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Article: 2192894 | Received 23 Aug 2022, Accepted 08 Mar 2023, Published online: 22 Mar 2023

References

  • Hori S, Nomura T, Sakaguchi S. Control of regulatory T cell development by the transcription factor Foxp3. Science. 2003;299(5609):1057–18.
  • Sakaguchi S, Yamaguchi T, Nomura T, et al. Regulatory T cells and immune tolerance. Cell. 2008;133(5):775–787.
  • Bates GJ, Fox SB, Han C, et al. Quantification of regulatory T cells enables the identification of high-risk breast cancer patients and those at risk of late relapse. J Clin Oncol. 2006;24(34):5373–5380.
  • Curiel TJ, Coukos G, Zou L, et al. Specific recruitment of regulatory T cells in ovarian carcinoma fosters immune privilege and predicts reduced survival. Nat Med. 2004;10(9):942–949. DOI:10.1038/nm1093
  • Gao Q, Qiu SJ, Fan J, et al. Intratumoral balance of regulatory and cytotoxic T cells is associated with prognosis of hepatocellular carcinoma after resection. J Clin Oncol. 2007;25(18):2586–2593.
  • Petersen RP, Campa MJ, Sperlazza J, et al. Tumor infiltrating Foxp3+ regulatory T-cells are associated with recurrence in pathologic stage I NSCLC patients. Cancer. 2006;107(12):2866–2872.
  • Shah W, Yan X, Jing L, et al. A reversed CD4/CD8 ratio of tumor-infiltrating lymphocytes and a high percentage of CD4(+)FOXP3(+) regulatory T cells are significantly associated with clinical outcome in squamous cell carcinoma of the cervix. Cell Mol Immunol. 2011;8(1):59–66.
  • Haslam A, Prasad V. Estimation of the percentage of US patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA Netw Open. 2019;2(5):e192535.
  • Sharma P, Hu-Lieskovan S, Wargo JA, et al. Primary, adaptive, and acquired resistance to cancer immunotherapy. Cell. 2017;168(4):707–723.
  • Cavalli G, Heard E. Advances in epigenetics link genetics to the environment and disease. Nature. 2019;571(7766):489–499.
  • Zhang C, Zhao H, Li J, et al. The identification of specific methylation patterns across different cancers. PLoS ONE. 2015;10(3):e0120361.
  • Li Y, Qiao G, Wang K, et al. Drug–target interaction predication via multi-channel graph neural networks. Brief Bioinform. 2022;23(1). DOI:10.1093/bib/bbab346
  • Dawson MA, Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell. 2012;150(1):12–27.
  • Feinberg AP, Tycko B. The history of cancer epigenetics. Nat Rev Cancer. 2004;4(2):143–153.
  • Shen H, Laird PW. Interplay between the cancer genome and epigenome. Cell. 2013;153(1):38–55.
  • Counts JL, Goodman JI. Alterations in DNA methylation may play a variety of roles in carcinogenesis. Cell. 1995;83(1):13–15.
  • Argos M. Arsenic exposure and epigenetic alterations: recent findings based on the illumina 450K DNA methylation array. Curr Environ Health Rep. 2015;2(2):137–144.
  • McEwen LM, Jones MJ, Lin DTS, et al. Systematic evaluation of DNA methylation age estimation with common preprocessing methods and the Infinium MethylationEPIC BeadChip array. Clin Epigenetics. 2018;10(1):123. DOI:10.1186/s13148-018-0556-2
  • Gkountela S, Zhang KX, Shafiq TA, et al. DNA demethylation dynamics in the human prenatal germline. Cell. 2015;161(6):1425–1436.
  • Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet. 2002;3(6):415–428.
  • Agarwal S, Rao A. Long-range transcriptional regulation of cytokine gene expression. Curr Opin Immunol. 1998;10(3):345–352.
  • Fitzpatrick DR, Shirley KM, McDonald LE, et al. Distinct methylation of the interferon γ (IFN-γ) and interleukin 3 (IL-3) genes in newly activated primary CD8+ T lymphocytes: regional IFN-γ promoter demethylation and mRNA expression are heritable in CD44highCD8+ T cells. J Exp Med. 1998;188(1):103–117.
  • Gett AV, Hodgkin PD. Cell division regulates the T cell cytokine repertoire, revealing a mechanism underlying immune class regulation. Proc Natl Acad Sci U S A. 1998;95(16):9488–9493.
  • Bestor TH, Ingram VM. Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA. Proc Natl Acad Sci U S A. 1983;80(18):5559–5563.
  • Broske AM, Vockentanz L, Kharazi S, et al. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet. 2009;41(11):1207–1215. DOI:10.1038/ng.463
  • Filipski K, Scherer M, Zeiner KN, et al. DNA methylation-based prediction of response to immune checkpoint inhibition in metastatic melanoma. J Immunother Cancer. 2021;9(7):e002226. DOI:10.1136/jitc-2020-002226
  • Goltz D, Gevensleben H, Grunen S, et al. PD-L1 (CD274) promoter methylation predicts survival in patients with acute myeloid leukemia. Leukemia. 2017;31(3):738–743.
  • Sasidharan Nair V, Toor SM, Taha RZ, et al. DNA methylation and repressive histones in the promoters of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, PD-L1, and galectin-9 genes in human colorectal cancer. Clin Epigenetics. 2018;10(1):104.
  • Sasidharan Nair V, El Salhat H, Taha RZ, et al. DNA methylation and repressive H3K9 and H3K27 trimethylation in the promoter regions of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, and PD-L1 genes in human primary breast cancer. Clin Epigenetics. 2018;10(1):78.
  • Jones PA, Issa JP, Baylin S. Targeting the cancer epigenome for therapy. Nat Rev Genet. 2016;17(10):630–641.
  • Loo Yau H, Ettayebi I, De Carvalho DD. The cancer epigenome: exploiting its vulnerabilities for immunotherapy. Trends Cell Biol. 2019;29(1):31–43.
  • Jones PA, Ohtani H, Chakravarthy A, et al. Epigenetic therapy in immune-oncology. Nat Rev Cancer. 2019;19(3):151–161.
  • Aryee MJ, Jaffe AE, Corrada-Bravo H, et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30(10):1363–1369.
  • Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621–628.
  • Killian JK, Kim SY, Miettinen M, et al. Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discov. 2013;3(6):648–657. DOI:10.1158/2159-8290.CD-13-0092
  • Lipponen A, El-Osta A, Kaspi A, et al. Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury. Acta Neuropathol Commun. 2018;6(1):17.
  • Ren X, Kuan PF. methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics. 2019;35(11):1958–1959.
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550. DOI:10.1073/pnas.0506580102
  • He S, Wu Z. Gene-based Higher Criticism methods for large-scale exonic single-nucleotide polymorphism data. BMC Proc. 2011;5(Suppl 9):S65.
  • Liu C, Li Z, Xu L, et al. GALNT6 promotes breast cancer metastasis by increasing mucin-type O-glycosylation of α2M. Aging (Albany NY). 2020;12(12):11794–11811. DOI:10.18632/aging.103349
  • Li Y, Jiang T, Zhou W, et al. Pan-cancer characterization of immune-related lncRnas identifies potential oncogenic biomarkers. Nat Commun. 2020;11(1):1000. DOI:10.1038/s41467-020-14802-2
  • Rooney MS, Shukla SA, Wu CJ, et al. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160(1–2):48–61.
  • Narayanan S, Kawaguchi T, Yan L, et al. Cytolytic activity score to assess anticancer immunity in colorectal cancer. Ann Surg Oncol. 2018;25(8):2323–2331.
  • Basu R, Whitlock BM, Husson J, et al. Cytotoxic T cells use mechanical force to potentiate target cell killing. Cell. 2016;165(1):100–110. DOI:10.1016/j.cell.2016.01.021
  • Zhang C, Zhao N, Zhang X, et al. SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis. Brief Bioinform. 2021;22(3). DOI:10.1093/bib/bbaa162
  • Bastian PJ, Yegnasubramanian S, Palapattu GS, et al. Molecular biomarker in prostate cancer: the role of CpG island hypermethylation. Eur Urol. 2004;46(6):698–708.
  • Vesely MD, Kershaw MH, Schreiber RD, et al. Natural innate and adaptive immunity to cancer. Annu Rev Immunol. 2011;29(1):235–271.
  • Alspach E, Dm L, Rd S. Interferon γ and its important roles in promoting and inhibiting spontaneous and therapeutic cancer immunity. Cold Spring Harb Perspect Biol. 2019;11(3):11.
  • Sm C, Fr B. Inflammation and cancer: advances and new agents. Nat Rev Clin Oncol. 2015;12(10):584–596.
  • Liu P, Lu Z, Liu L, et al. NOD-like receptor signaling in inflammation-associated cancers: from functions to targeted therapies. Phytomedicine. 2019;64:152925.
  • Good CR, Panjarian S, Kelly AD, et al. TET1-mediated hypomethylation activates oncogenic signaling in triple-negative breast cancer. Cancer Res. 2018;78(15):4126–4137.
  • Jung H, Kim HS, Kim JY, et al. DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load. Nat Commun. 2019;10(1):4278.
  • Bozcuk H, Uslu G, Samur M, et al. Tumour necrosis factor-alpha, interleukin-6, and fasting serum insulin correlate with clinical outcome in metastatic breast cancer patients treated with chemotherapy. Cytokine. 2004;27(2–3):58–65.
  • Michalaki V, Syrigos K, Charles P, et al. Serum levels of IL-6 and TNF-α correlate with clinicopathological features and patient survival in patients with prostate cancer. Br J Cancer. 2004;90(12):2312–2316.
  • Balkwill F. TNF-α in promotion and progression of cancer. Cancer Metastasis Rev. 2006;25(3):409–416.
  • Yoshida N, Ikemoto S, Narita K, et al. Interleukin-6, tumour necrosis factor α and interleukin-1β in patients with renal cell carcinoma. Br J Cancer. 2002;86(9):1396–1400.
  • Ricketts CJ, Morris MR, Gentle D, et al. Genome-wide CpG island methylation analysis implicates novel genes in the pathogenesis of renal cell carcinoma. Epigenetics. 2012;7(3):278–290.
  • Olk-Batz C, Poetsch AR, Nollke P, et al. Aberrant DNA methylation characterizes juvenile myelomonocytic leukemia with poor outcome. Blood. 2011;117(18):4871–4880. DOI:10.1182/blood-2010-08-298968
  • Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457.
  • Chan TA, Yarchoan M, Jaffee E, et al. Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic. Ann Oncol. 2019;30(1):44–56.
  • Rizvi H, Sanchez-Vega F, La K, et al. Molecular determinants of response to anti–programmed cell death (PD)-1 and anti–programmed death-ligand 1 (PD-L1) blockade in patients with non–small-cell lung cancer profiled with targeted next-generation sequencing. J Clin Oncol. 2018;36(7):633–641. DOI:10.1200/JCO.2017.75.3384
  • Tien FM, Lu HH, Lin SY, et al. Epigenetic remodeling of the immune landscape in cancer: therapeutic hurdles and opportunities. J Biomed Sci. 2023;30(1):3.
  • Cao J, Yan Q. Cancer epigenetics, tumor immunity, and immunotherapy. Trends Cancer. 2020;6(7):580–592.
  • Maiuri AR, O’hagan HM. Interplay between inflammation and epigenetic changes in cancer. Prog Mol Biol Transl Sci. 2016;144:69–117.
  • Marwitz S, Scheufele S, Perner S, et al. Epigenetic modifications of the immune-checkpoint genes CTLA4 and PDCD1 in non-small cell lung cancer results in increased expression. Clin Epigenetics. 2017;9(1):51.
  • Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44(W1):W90–7. DOI:10.1093/nar/gkw377
  • Comba A, Dunn PJ, Argento AE, et al. Fyn tyrosine kinase, a downstream target of receptor tyrosine kinases, modulates antiglioma immune responses. Neuro Oncol. 2020;22(6):806–818. DOI:10.1093/neuonc/noaa006
  • Cardenas MG, Oswald E, Yu W, et al. The expanding role of the BCL6 oncoprotein as a cancer therapeutic target. Clin Cancer Res. 2017;23(4):885–893.
  • Leeman-Neill RJ, Bhagat G. BCL6 as a therapeutic target for lymphoma. Expert Opin Ther Targets. 2018;22(2):143–152.
  • Crotty S. T follicular helper cell biology: a decade of discovery and diseases. Immunity. 2019;50(5):1132–1148.
  • Speiser DE, Ho PC, Verdeil G. Regulatory circuits of T cell function in cancer. Nat Rev Immunol. 2016;16(10):599–611.
  • Halama N, Zoernig I, Berthel A, et al. Tumoral immune cell exploitation in colorectal cancer metastases can be targeted effectively by anti-CCR5 therapy in cancer patients. Cancer Cell. 2016;29(4):587–601. DOI:10.1016/j.ccell.2016.03.005
  • Jiao X, Nawab O, Patel T, et al. Recent advances targeting CCR5 for cancer and its role in immuno-oncology. Cancer Res. 2019;79(19):4801–4807.
  • Hu C, Liu Y, Jiang S, et al. The variable association between expression and methylation of estrogen receptors and the survival of patients with different tumors. Clin Transl Med. 2020;10(2):e49.