Abstract
As the use of immune checkpoint inhibitors for the treatment of cancer has expanded, convincing data have emerged correlating active WNT signaling with resistance to immunotherapies. To identify mechanisms through which WNT signaling limits anti-tumor immunity, we examined the response to WNT inhibition in a variety of human cancer cell lines that harbor distinct WNT pathway mutations. Our data show that inhibition of WNT signaling leads to activation of the TBK1/IRF3 dsRNA-sensing pathway and expression of interferon-stimulated genes (ISGs), independently of IFN/JAK/STAT signaling. Mechanistically, we show that WNT inhibition leads to increased chromatin accessibility at genomic loci harboring endogenous retroviruses (ERVs), resulting in ERV re-expression and activation of the dsRNA response. Increased ISG expression following WNT inhibition does not involve decreased MAP kinase signaling and therefore differs from reports documenting ISG induction in response to inhibition of other oncogenic pathways. Given the variety of tumor cell lines and WNT pathway mutations examined, these data suggest a mechanism by which WNT may drive immune evasion and several therapeutic avenues to reverse it, including tumor-targeted type 1 interferon stimulation and/or epigenetic therapies.
Data availability
RNAseq data are available in supplemental file. TheATACseq datasets generated and analyzed during he current study are available inthe Gene Expression Omnibus (GEO), ascension number GSE309663. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE309663__;!!ODpDvJZr5w!He6iXSFys_nyT_OfWHZ40qoi0faUaRfZ1E5XGMJsk6pVod7aGAQ3nhrBUSQXrGsXTaTPA6swt8dRwd1St1KH1jmttmg$Enter token yjgzcgwqvxobhmj.
References
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. 2, e192535. https://doi.org/10.1001/jamanetworkopen.2019.2535 (2019).
Grasso, C. S. et al. Genetic mechanisms of immune evasion in colorectal cancer. Cancer Discov. 8, 730–749. https://doi.org/10.1158/2159-8290.CD-17-1327 (2018).
Harding, J. J. et al. Prospective genotyping of hepatocellular carcinoma: Clinical implications of next-generation sequencing for matching patients to targeted and immune therapies. Clin. Cancer Res. 25, 2116–2126. https://doi.org/10.1158/1078-0432.CCR-18-2293 (2019).
Luke, J. J., Bao, R., Sweis, R. F., Spranger, S. & Gajewski, T. F. <article-title update=“modified” original="WNT/beta-catenin Pathway Activation Correlates with Immune Exclusion across Human Cancers">WNT/β-catenin pathway activation correlates with immune exclusion across human cancers. Clin. Cancer Res. 25, 3074–3083. https://doi.org/10.1158/1078-0432.CCR-18-1942 (2019).
Sia, D. et al. Identification of an immune-specific class of hepatocellular carcinoma, based on molecular features. Gastroenterology 153, 812–826. https://doi.org/10.1053/j.gastro.2017.06.007 (2017).
Xue, J. et al. Intrinsic beta-catenin signaling suppresses CD8(+) T-cell infiltration in colorectal cancer. Biomed. Pharmacother. 115, 108921. https://doi.org/10.1016/j.biopha.2019.108921 (2019).
Casey, S. C. et al. MYC regulates the antitumor immune response through CD47 and PD-L1. Science 352, 227–231. https://doi.org/10.1126/science.aac9935 (2016).
Spranger, S., Bao, R. & Gajewski, T. F. Melanoma-intrinsic beta-catenin signalling prevents anti-tumour immunity. Nature 523, 231–235. https://doi.org/10.1038/nature14404 (2015).
Pilard, C. et al. Cancer immunotherapy: It’s time to better predict patients’ response. Br. J. Cancer 125, 927–938. https://doi.org/10.1038/s41416-021-01413-x (2021).
Loh, K. M., van Amerongen, R. & Nusse, R. Generating cellular diversity and spatial form: Wnt signaling and the evolution of multicellular animals. Dev. Cell 38, 643–655. https://doi.org/10.1016/j.devcel.2016.08.011 (2016).
Yu, R., Zhu, B. & Chen, D. Type I interferon-mediated tumor immunity and its role in immunotherapy. Cell. Mol. Life Sci. 79, 191. https://doi.org/10.1007/s00018-022-04219-z (2022).
Marron, T. U. et al. Neoadjuvant cemiplimab for resectable hepatocellular carcinoma: A single-arm, open-label, phase 2 trial. Lancet Gastroenterol. Hepatol. 7, 219–229. https://doi.org/10.1016/S2468-1253(21)00385-X (2022).
Bai, M. et al. The crosstalk between beta-catenin signaling and type I, type II and type III interferons in lung cancer cells. Am J Transl Res 9, 2788–2797 (2017).
Baril, M. et al. Genome-wide RNAi screen reveals a new role of a WNT/CTNNB1 signaling pathway as negative regulator of virus-induced innate immune responses. PLoS Pathog. 9, e1003416. https://doi.org/10.1371/journal.ppat.1003416 (2013).
Zimmerli, D. et al. MYC promotes immune-suppression in triple-negative breast cancer via inhibition of interferon signaling. Nat. Commun. 13, 6579. https://doi.org/10.1038/s41467-022-34000-6 (2022).
Krenz, B. et al. MYC- and MIZ1-dependent vesicular transport of double-strand RNA controls immune evasion in pancreatic ductal adenocarcinoma. Cancer Res. 81, 4242–4256. https://doi.org/10.1158/0008-5472.CAN-21-1677 (2021).
Muthalagu, N. et al. Repression of the type I interferon pathway underlies MYC- and KRAS-dependent evasion of NK and B cells in pancreatic ductal adenocarcinoma. Cancer Discov. 10, 872–887. https://doi.org/10.1158/2159-8290.CD-19-0620 (2020).
Alberts, R. et al. Genetic association analysis identifies variants associated with disease progression in primary sclerosing cholangitis. Gut 67, 1517–1524. https://doi.org/10.1136/gutjnl-2016-313598 (2018).
Huang, W. et al. Dual inhibitors of DNMT and HDAC induce viral mimicry to induce antitumour immunity in breast cancer. Cell Death Discov. 10, 143. https://doi.org/10.1038/s41420-024-01895-7 (2024).
Kim, S. J., Kiser, P. K., Asfaha, S., DeKoter, R. P. & Dick, F. A. EZH2 inhibition stimulates repetitive element expression and viral mimicry in resting splenic B cells. EMBO J. 42, e114462. https://doi.org/10.15252/embj.2023114462 (2023).
Sheng, W. et al. LSD1 ablation stimulates anti-tumor immunity and enables checkpoint blockade. Cell 174, 549-563 e519. https://doi.org/10.1016/j.cell.2018.05.052 (2018).
Schlesinger, S. & Meshorer, E. Open chromatin, epigenetic plasticity, and nuclear organization in pluripotency. Dev. Cell 48, 135–150. https://doi.org/10.1016/j.devcel.2019.01.003 (2019).
May, D. et al. Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo. Elife https://doi.org/10.7554/eLife.83444 (2023).
You, F. et al. ELF4 is critical for induction of type I interferon and the host antiviral response. Nat. Immunol. 14, 1237–1246. https://doi.org/10.1038/ni.2756 (2013).
Suico, M. A., Shuto, T. & Kai, H. Roles and regulations of the ETS transcription factor ELF4/MEF. J. Mol. Cell Biol. 9, 168–177. https://doi.org/10.1093/jmcb/mjw051 (2017).
Li, D. et al. IRF6 is directly regulated by ZEB1 and ELF3, and predicts a favorable prognosis in gastric cancer. Front. Oncol. 9, 220. https://doi.org/10.3389/fonc.2019.00220 (2019).
Fung, K. Y. et al. Expression of interferon epsilon in mucosal epithelium is regulated by Elf3. Mol. Cell Biol. 44, 334–343. https://doi.org/10.1080/10985549.2024.2366207 (2024).
Cortesi, A. et al. Activation of endogenous retroviruses and induction of viral mimicry by MEK1/2 inhibition in pancreatic cancer. Sci. Adv. 10, eadk5386. https://doi.org/10.1126/sciadv.adk5386 (2024).
Elewaut, A. et al. Cancer cells impair monocyte-mediated T cell stimulation to evade immunity. Nature 637, 716–725. https://doi.org/10.1038/s41586-024-08257-4 (2025).
Gong, K. et al. EGFR inhibition triggers an adaptive response by co-opting antiviral signaling pathways in lung cancer. Nat. Cancer 1, 394–409. https://doi.org/10.1038/s43018-020-0048-0 (2020).
Gurule, N. J. et al. A tyrosine kinase inhibitor-induced interferon response positively associates with clinical response in EGFR-mutant lung cancer. NPJ Precis. Oncol. 5, 41. https://doi.org/10.1038/s41698-021-00181-4 (2021).
Boumelha, J. et al. An immunogenic model of KRAS-mutant lung cancer enables evaluation of targeted therapy and immunotherapy combinations. Cancer Res. 82, 3435–3448. https://doi.org/10.1158/0008-5472.CAN-22-0325 (2022).
Tian, J. et al. Combined PD-1, BRAF and MEK inhibition in BRAF(V600E) colorectal cancer: A phase 2 trial. Nat. Med. 29, 458–466. https://doi.org/10.1038/s41591-022-02181-8 (2023).
Anastasiou, P. et al. Combining RAS(ON) G12C-selective inhibitor with SHP2 inhibition sensitises lung tumours to immune checkpoint blockade. Nat. Commun. 15, 8146. https://doi.org/10.1038/s41467-024-52324-3 (2024).
Zhao, Y. et al. IDH1 mutation inhibits differentiation of astrocytes and glioma cells with low oxoglutarate dehydrogenase expression by disturbing α-ketoglutarate-related metabolism and epigenetic modification. Life Metab. 3, loae002. https://doi.org/10.1093/lifemeta/loae002 (2024).
Bragelmann, J. et al. MAPK-pathway inhibition mediates inflammatory reprogramming and sensitizes tumors to targeted activation of innate immunity sensor RIG-I. Nat. Commun. 12, 5505. https://doi.org/10.1038/s41467-021-25728-8 (2021).
Korpela, S. P. et al. Role of epidermal growth factor receptor inhibitor-induced interferon pathway signaling in the head and neck squamous cell carcinoma therapeutic response. J. Transl. Med. 19, 43. https://doi.org/10.1186/s12967-021-02706-8 (2021).
Gureghian, V. et al. A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma. Cancer Gene Ther. 30, 1330–1345. https://doi.org/10.1038/s41417-023-00640-z (2023).
Goel, S. et al. CDK4/6 inhibition triggers anti-tumour immunity. Nature 548, 471–475. https://doi.org/10.1038/nature23465 (2017).
Adachi, Y. et al. Inhibition of FGFR reactivates IFNgamma signaling in tumor cells to enhance the combined antitumor activity of lenvatinib with anti-PD-1 antibodies. Cancer Res. 82, 292–306. https://doi.org/10.1158/0008-5472.CAN-20-2426 (2022).
Park, W. J. & Kim, M. J. A new wave of targeting “undruggable” Wnt signaling for cancer therapy: Challenges and opportunities. Cells https://doi.org/10.3390/cells12081110 (2023).
Gavine, P. R. et al. AZD4547: An orally bioavailable, potent, and selective inhibitor of the fibroblast growth factor receptor tyrosine kinase family. Cancer Res. 72, 2045–2056. https://doi.org/10.1158/0008-5472.CAN-11-3034 (2012).
Paces, J. et al. HERVd: The Human Endogenous RetroViruses Database: Update. Nucleic Acids Res. 32, D50. https://doi.org/10.1093/nar/gkh075 (2004).
Paces, J., Pavlicek, A. & Paces, V. HERVd: Database of human endogenous retroviruses. Nucleic Acids Res. 30, 205–206. https://doi.org/10.1093/nar/30.1.205 (2002).
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589. https://doi.org/10.1016/j.molcel.2010.05.004 (2010).
Nakagawa, S. & Takahashi, M. U. gEVE: A genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. Database (Oxford) https://doi.org/10.1093/database/baw087 (2016).
Tongyoo, P. et al. EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes. PLoS ONE 12, e0177119. https://doi.org/10.1371/journal.pone.0177119 (2017).
Acknowledgements
The authors wish to acknowledge the members of the Regeneron DNA Core, Tissue Culture Core, and Molecular Profiling Core.
Author information
Authors and Affiliations
Contributions
CMW conceived and designed study, performed experiments, interpreted the results, prepared the manuscript draft. JHC performed experiments wrote and edited the manuscript draft. VRD performed ATAC-seq analysis, interpreted data, wrote and edited the manuscript draft. LJL performed RNAseq analysis. SN performed experiments wrote and edited the manuscript draft. HC performed experiments. WW performed RNAseq analysis. RS and CA performed ATAC-seq. DA designed ERV primers for validation. NTG assisted with RNAseq and ATACseq study design and interpretation, gave intellectual comments. CD contributed to conception and design of this study and interpretation of results and edited the manuscript with critical intellectual input. All authors contributed to the article and approved the submission.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Williams, C.M., Calderon, J.H., DiBlasi, V.R. et al. WNT inhibition activates interferon stimulated gene expression by alleviating epigenetic repression of endogenous retroviruses. Sci Rep (2026). https://doi.org/10.1038/s41598-026-40894-9
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41598-026-40894-9
