Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

APOE deficiency triggers anti-tumour activity of macrophages in liver cancer

Cancer Gene Therapy volume 32, pages 949–962 (2025)Cite this article

Subjects

Abstract

Macrophage infiltration correlates with poor prognosis in patients with liver cancer and resistance to immunotherapy. However, it is difficult to target tumour-associated macrophages (TAMs) because of their inherent heterogeneity. Specific TAM subsets may exhibit distinct functions in tumorigenesis. Herein, we identify a TAM subset characterised by elevated APOE expression, which is correlated with poor overall survival of patients with HCC. The APOE+ TAM intensity is highly elevated in ICB non-responder tumours and negatively correlated with CD8+ T cell infiltration. Pathway analysis and cell interaction reveal that APOE+ TAMs suppress CD8+ T cells through signal integration and cholesterol efflux. Furthermore, APOE deficiency in macrophages delays tumour growth and promotes the infiltration of CD8+ T cells. Using an immunotherapy-resistant mouse model, we showed that APOE blockade synergises with anti-PD-1 therapy and inhibits tumour growth. Our results elucidate the crucial role of APOE+ TAMs in the formation of immunosuppressive microenvironments and offer a potential therapeutic target for ICB combined therapy.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: APOE is upregulated in TAMs in liver cancer.
Fig. 2: APOE+ TAMs are engaged in cholesterol efflux.
Fig. 3: APOE+ TAMs inhibit HCC tumour growth through the immunomodulation of CD8+ T cells.
Fig. 4: APOE+ TAMs are enriched in ICB non-responder tumours.
Fig. 5: APOE+ TAMs cause ICB treatment nonresponse by mediating CD8+ T cell dysfunction.
Fig. 6: APOE inhibitor enhances the ICB efficacy of HCC.

Similar content being viewed by others

Data availability

The single-cell RNA sequence datasets used in this study are publicly available in the GEO under accession numbers GSE140228, GSE138709, and GSE206325, and in the China National GeneBank Database (CNGBdb) under accession number CNP0000650. The bulk RNA sequencing is available in GEO under accession number GSE215011.

References

  1. Bray F, Laversanne M, Sung H, Me JF, Siegel RL, Soerjomataram I, et al. Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2022. https://doi.org/10.3322/caac.21834.

  2. Ribas A, Wolchok JD. Cancer immunotherapy using checkpoint blockade. Science. 2018;359:1350–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Sangro B, Gomez-Martin C, De La Mata M, Iñarrairaegui M, Garralda E, Barrera P, et al. A clinical trial of CTLA-4 blockade with tremelimumab in patients with hepatocellular carcinoma and chronic hepatitis C. J Hepatol. 2013;59:81–88.

    Article  CAS  PubMed  Google Scholar 

  4. Kambhampati S, Bauer KE, Bracci PM, Keenan BP, Behr SC, Gordan JD, et al. Nivolumab in patients with advanced hepatocellular carcinoma and Child–Pugh class B cirrhosis: safety and clinical outcomes in a retrospective case series. Cancer. 2019;125:3234–41.

    Article  CAS  Google Scholar 

  5. 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. J Immunother Cancer. 2017;5:44.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Ringelhan M, Pfister D, O’Connor T, Pikarsky E, Heikenwalder M. The immunology of hepatocellular carcinoma. Nat Immunol. 2018;19:222–32.

    Article  CAS  PubMed  Google Scholar 

  7. Zhu G-Q, Tang Z, Huang R, Qu W-F, Fang Y, Yang R, et al. CD36+ cancer-associated fibroblasts provide immunosuppressive microenvironment for hepatocellular carcinoma via secretion of macrophage migration inhibitory factor. Cell Discov. 2023;9:25.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Wang L, Zhu L, Liang C, Huang X, Liu Z, Huo J, et al. Targeting N6-methyladenosine reader YTHDF1 with siRNA boosts antitumor immunity in NASH-HCC by inhibiting EZH2-IL-6 axis. J Hepatol. 2023;79:1185–1200.

    Article  CAS  PubMed  Google Scholar 

  9. Wan S, Zhao E, Kryczek I, Vatan L, Sadovskaya A, Ludema G, et al. Tumor-associated macrophages produce interleukin 6 and sSignal via STAT3 to promote expansion of human hepatocellular carcinoma stem cells. Gastroenterology. 2014;147:1393–404.

    Article  CAS  PubMed  Google Scholar 

  10. Dhanasekaran R, Venkatesh SK, Torbenson M, Roberts LR. Clinical implications of basic research in hepatocellular carcinoma. J Hepatol. 2017. https://doi.org/10.1016/j.jhep.2015.09.008.

  11. Lai Q, Vitale A, Manzia T, Foschi F, Levi Sandri G, Gambato M, et al. Platelets and hepatocellular cancer: bridging the bench to the clinics. Cancers. 2019;11:1568.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Dong S, Guo X, Han F, He Z, Wang Y. Emerging role of natural products in cancer immunotherapy. Acta Pharm Sin B. 2022;12:1163–85.

    Article  CAS  PubMed  Google Scholar 

  13. Wei C-Y, Zhu M-X, Zhang P-F, Huang X-Y, Wan J-K, Yao X-Z, et al. PKCα/ZFP64/CSF1 axis resets the tumor microenvironment and fuels anti-PD1 resistance in hepatocellular carcinoma. J Hepatol. 2022;77:163–76.

    Article  CAS  PubMed  Google Scholar 

  14. Lu J-C, Zhang P-F, Huang X-Y, Guo X-J, Gao C, Zeng H-Y, et al. Amplification of spatially isolated adenosine pathway by tumor–macrophage interaction induces anti-PD1 resistance in hepatocellular carcinoma. J Hematol Onco. 2021;14:200.

    Article  CAS  Google Scholar 

  15. Cheng K, Cai N, Zhu J, Yang X, Liang H, Zhang W. Tumor-associated macrophages in liver cancer: From mechanisms to therapy. Cancer Commun. 2022;42:1112–40.

    Article  Google Scholar 

  16. Liu Y, Xun Z, Ma K, Liang S, Li X, Zhou S, et al. Identification of a tumour immune barrier in the HCC microenvironment that determines the efficacy of immunotherapy. J Hepatol. 2023;78:770–82.

    Article  CAS  PubMed  Google Scholar 

  17. Tan J, Fan W, Liu T, Zhu B, Liu Y, Wang S, et al. TREM2+ macrophages suppress CD8+ T-cell infiltration after transarterial chemoembolisation in hepatocellular carcinoma. J Hepatol. 2023;79:126–40.

    Article  CAS  PubMed  Google Scholar 

  18. He H, Chen S, Fan Z, Dong Y, Wang Y, Li S, et al. Multi-dimensional single-cell characterization revealed suppressive immune microenvironment in AFP-positive hepatocellular carcinoma. Cell Discov. 2023;9:60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lu J-C, Wu L-L, Sun Y-N, Huang X-Y, Gao C, Guo X-J, et al. Macro CD5L+ deteriorates CD8+T cells exhaustion and impairs combination of Gemcitabine-Oxaliplatin-Lenvatinib-anti-PD1 therapy in intrahepatic cholangiocarcinoma. Nat Commun. 2024;15:621.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Li Y, Lu R, Abuduhailili X, Feng Y. Apolipoprotein E: a potential prognostic and diagnostic biomarker for hepatocellular carcinoma. J Hepatocell Carcinoma. 2025;12:301–24.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Wang Y, Zhu G-Q, Yang R, Wang C, Qu W-F, Chu T-H, et al. Deciphering intratumoral heterogeneity of hepatocellular carcinoma with microvascular invasion with radiogenomic analysis. J Transl Med. 2023;21:734.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Wan S, He Q-Y, Yang Y, Liu F, Zhang X, Guo X, et al. SPARC stabilizes ApoE to induce cholesterol-dependent invasion and sorafenib resistance in hepatocellular carcinoma. Cancer Res. 2024;84:1872–88.

    Article  CAS  PubMed  Google Scholar 

  23. Yao J, Wu D, Qiu Y. In vitro analyses of paracrine effects of murine classically activated macrophage on beige adipocyte metabolism. STAR Protoc. 2022;3:101480.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Siegert I, Schatz V, Prechtel AT, Steinkasserer A, Bogdan C, Jantsch J. Electroporation of siRNA into mouse bone marrow-derived macrophages and dendritic cells. In: Li S, Cutrera J, Heller R, Teissie J, editors. Electroporation Protocols. 2014. https://doi.org/10.1007/978-1-4614-9632-8_9.

  25. Zhang Q, He Y, Luo N, Patel SJ, Han Y, Gao R, et al. Landscape and dynamics of single immune cells in hepatocellular carcinoma. Cell. 2019;179:829–845.e20.

    Article  CAS  PubMed  Google Scholar 

  26. Tall AR, Yvan-Charvet L. Cholesterol, inflammation and innate immunity. Nat Rev Immunol. 2015;15:104–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Xiao J, Wang S, Chen L, Ding X, Dang Y, Han M, et al. 25-Hydroxycholesterol regulates lysosome AMP kinase activation and metabolic reprogramming to educate immunosuppressive macrophages. Immunity. 2024;57:1087–1104.e7.

    Article  CAS  PubMed  Google Scholar 

  28. Goossens P, Rodriguez-Vita J, Etzerodt A, Masse M, Rastoin O, Gouirand V, et al. Membrane cholesterol efflux drives tumor-associated macrophage reprogramming and tumor progression. Cell Metab. 2019;29:1376–89.e4.

    Article  CAS  PubMed  Google Scholar 

  29. Li T, Li X, Zamani A, Wang W, Lee C-N, Li M, et al. c-Rel is a myeloid checkpoint for cancer immunotherapy. Nat Cancer. 2020;1:507–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Klement JD, Redd PS, Lu C, Merting AD, Poschel DB, Yang D, et al. Tumor PD-L1 engages myeloid PD-1 to suppress type I interferon to impair cytotoxic T lymphocyte recruitment. Cancer Cell. 2023;41:620–36.e9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Chang Y, Kang P, Cui T, Guo W, Zhang W, Du P, et al. Pharmacological inhibition of demethylzeylasteral on JAK-STAT signaling ameliorates vitiligo. J Transl Med. 2023;21:434.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Sharma A, Seow JJW, Dutertre C-A, Pai R, Blériot C, Mishra A, et al. Onco-fetal reprogramming of endothelial cells drives immunosuppressive macrophages in hepatocellular carcinoma. Cell. 2020;183:377–94.e21.

    Article  CAS  PubMed  Google Scholar 

  33. Li Y, Shen Z, Chai Z, Zhan Y, Zhang Y, Liu Z, et al. Targeting MS4A4A on tumour-associated macrophages restores CD8+ T-cell-mediated antitumour immunity. Gut. 2023;72:2307–20.

    Article  CAS  PubMed  Google Scholar 

  34. Liu C, Xie J, Lin B, Tian W, Wu Y, Xin S, et al. Pan-cancer single-cell and spatial-resolved profiling reveals the immunosuppressive role of APOE+ Macrophages In Immune Checkpoint Inhibitor Therapy. Adv Sci. 2024;11:2401061.

    Article  CAS  Google Scholar 

  35. Tharp KM, Kersten K, Maller O, Timblin GA, Stashko C, Canale FP, et al. Tumor-associated macrophages restrict CD8+ T cell function through collagen deposition and metabolic reprogramming of the breast cancer microenvironment. Nat Cancer. 2024;5:1045–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Khan MN, Mao B, Hu J, Shi M, Wang S, Rehman AU, et al. Tumor-associated macrophages and CD8+ T cells: dual players in the pathogenesis of HBV-related HCC. Front Immunol. 2024;15:1472430.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Ma S, Sun B, Duan S, Han J, Barr T, Zhang J, et al. YTHDF2 orchestrates tumor-associated macrophage reprogramming and controls antitumor immunity through CD8+ T cells. Nat Immunol. 2023;24:255–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Pascual-García M, Bonfill-Teixidor E, Planas-Rigol E, Rubio-Perez C, Iurlaro R, Arias A, et al. LIF regulates CXCL9 in tumor-associated macrophages and prevents CD8+ T cell tumor-infiltration impairing anti-PD1 therapy. Nat Commun. 2019;10:2416.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Franco F, Jaccard A, Romero P, Yu Y-R, Ho P-C. Metabolic and epigenetic regulation of T-cell exhaustion. Nat Metab. 2020;2:1001–12.

    Article  CAS  PubMed  Google Scholar 

  40. Yang R, Sun L, Li C-F, Wang Y-H, Yao J, Li H, et al. Galectin-9 interacts with PD-1 and TIM-3 to regulate T cell death and is a target for cancer immunotherapy. Nat Commun. 2021;12:832.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Di Pilato M, Kfuri-Rubens R, Pruessmann JN, Ozga AJ, Messemaker M, Cadilha BL, et al. CXCR6 positions cytotoxic T cells to receive critical survival signals in the tumor microenvironment. Cell. 2021;184:4512–30.e22.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Feig C, Jones JO, Kraman M, Wells RJB, Deonarine A, Chan DS, et al. Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti–PD-L1 immunotherapy in pancreatic cancer. Proc Natl Acad Sci. 2013;110:20212–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Seo YD, Jiang X, Sullivan KM, Jalikis FG, Smythe KS, Abbasi A, et al. Mobilization of CD8+ T cells via CXCR4 blockade facilitates PD-1 checkpoint therapy in human pancreatic cancer. Clin Cancer Res. 2019;25:3934–45.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Gao Y, Shi H, Zhao H, Yao M, He Y, Jiang M, et al. Single-cell transcriptomics identify TNFRSF1B as a novel T-cell exhaustion marker for ovarian cancer. Clin Transl Med. 2023;13:e1416.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Qu Y, Wang X, Bai S, Niu L, Zhao G, Yao Y, et al. The effects of TNF-α/TNFR2 in regulatory T cells on the microenvironment and progression of gastric cancer. Int J Cancer. 2022;15:1373–91.

    Article  Google Scholar 

  46. Rannikko JH, Hollmén M. Clinical landscape of macrophage-reprogramming cancer immunotherapies. Br J Cancer. 2024;131:627–40.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Xiang X, Wang J, Lu D, Xu X. Targeting tumor-associated macrophages to synergize tumor immunotherapy. Signal Transduct Target Ther. 2021;6:75.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Ling GS, Crawford G, Buang N, Bartok I, Tian K, Thielens NM, et al. C1q restrains autoimmunity and viral infection by regulating CD8 + T cell metabolism. Science. 2018;360:558–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Revel M, Sautès-Fridman C, Fridman W-H, Roumenina LT. C1q+ macrophages: passengers or drivers of cancer progression. Trends Cancer. 2022;8:517–26.

    Article  CAS  PubMed  Google Scholar 

  50. Ma R-Y, Black A, Qian B-Z. Macrophage diversity in cancer revisited in the era of single-cell omics. Trends Immunol. 2022;43:546–63.

    Article  CAS  PubMed  Google Scholar 

  51. Huggins DN, LaRue RS, Wang Y, Knutson TP, Xu Y, Williams JW, et al. Characterizing macrophage diversity in metastasis-bearing lungs reveals a lipid-associated macrophage subset. Cancer Res. 2021;81:5284–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Timperi E, Gueguen P, Molgora M, Magagna I, Kieffer Y, Lopez-Lastra S, et al. Lipid-associated macrophages are induced by cancer-associated fibroblasts and mediate immune suppression in breast cancer. Cancer Res. 2022;82:3291–306.

    Article  CAS  PubMed  Google Scholar 

  53. Liu Z, Gao Z, Li B, Li J, Ou Y, Yu X, et al. Lipid-associated macrophages in the tumor-adipose microenvironment facilitate breast cancer progression. OncoImmunology. 2022;11:2085432.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Endo-Umeda K, Makishima M. Liver X receptors regulate cholesterol metabolism and immunity in hepatic nonparenchymal cells. Int J Mol Sci. 2019;20:5045.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. King RJ, Singh PK, Mehla K. The cholesterol pathway: impact on immunity and cancer. Trends Immunol. 2022;43:78–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Ma X, Bi E, Huang C, Lu Y, Xue G, Guo X, et al. Cholesterol negatively regulates IL-9-producing CD8+ T cell differentiation and antitumor activity. J Exp Med. 2018;215:1555–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Ma X. Cholesterol Induces CD8+ T cell exhaustion in the tumor microenvironment. Cell Metab. 2019;30:143–56.e5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Tingbo Liang (The First Affiliated Hospital of Zhejiang University) for providing the Hepa 1–6 cell line.

Funding

This work was supported by grants from the National Natural Science Foundation of China [grant number 82303369 to Yuexiao Tang]; the Natural Science Funding of Zhejiang Province [grant number LQ23H160003 to Yuexiao Tang]; the Medical Health Science and Technology Project of Zhejiang Provincial Health Commission [grant number 2025KY048 to Xiaoxiao Zheng]; the Projects of Lishui Key Research and Development Plan in Zhejiang Province [grant number 2022ZDYF08 to Chaoyong Tu]; the Training Objects of Health Innovative Talents of Zhejiang Health to Hao Liu; the Zhejiang Province Medical Science and Technology Project [grant number 2022ZX00 to Zhiming Hu]; and the State Administration of Traditional Chinese Medicine Science and Technology Department-Zhejiang Provincial Administration of Traditional Chinese Medicine Co-construction of Key Laboratory of Research on Prevention and Treatment for depression syndrome [grant number GZY-ZJ-SY-2402 to Zhiming Hu].

Author information

Author notes

  1. These authors contributed equally: Xintong Xia, Zijun Zhou.

Authors and Affiliations

  1. College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China

    Xintong Xia, Zijun Zhou & Wei Chen

  2. Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine of Zhejiang Province, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, China

    Xiaoxiao Zheng & Hao Liu

  3. Department of Hepatobiliary and Pancreatic Surgery, Lishui Central Hospital, The Fifth Hospital Affiliated to Wenzhou Medical University, Lishui, China

    Chaoyong Tu

  4. Department of Hepatobiliary and Pancreatic Surgery, Tongde Hospital of Zhejiang Province, Hangzhou, China

    Zhiming Hu

  5. Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China

    Tao Ma

  6. Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China

    Yuexiao Tang & Wei Chen

  7. Key laboratory for accurate diagnosis and treatment of abdominal infection in Zhejiang Province, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China

    Wei Chen

Authors
  1. Xintong Xia
    View author publications

    Search author on:PubMed Google Scholar

  2. Zijun Zhou
    View author publications

    Search author on:PubMed Google Scholar

  3. Xiaoxiao Zheng
    View author publications

    Search author on:PubMed Google Scholar

  4. Chaoyong Tu
    View author publications

    Search author on:PubMed Google Scholar

  5. Hao Liu
    View author publications

    Search author on:PubMed Google Scholar

  6. Zhiming Hu
    View author publications

    Search author on:PubMed Google Scholar

  7. Tao Ma
    View author publications

    Search author on:PubMed Google Scholar

  8. Yuexiao Tang
    View author publications

    Search author on:PubMed Google Scholar

  9. Wei Chen
    View author publications

    Search author on:PubMed Google Scholar

Contributions

WC supervised the project and administered the research. YT supervised the project, administered the research, acquired funding, and conducted investigations. TM provided supervision. XX conducted investigations and wrote the original draft. ZZ conducted investigations. XXZ conducted investigations and acquired funding. CT collected human samples, and acquired funding. HL and ZH acquired funding. All authors contributed to the manuscript and approved the submitted version.

Corresponding authors

Correspondence to Tao Ma, Yuexiao Tang or Wei Chen.

Ethics declarations

Competing interests

The authors declare no competing interests.

Ethical approval

All animal experiments were performed in accordance with relevant guidelines and regulations and were approved by the Institutional Animal Care and Use Committee of The First Affiliated Hospital, Zhejiang University (Approval Number: 20241278). The research involving human participants was approved by the Ethics Committee of Lishui Central Hospital (Approval Number: 2024-212).

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Xia, X., Zhou, Z., Zheng, X. et al. APOE deficiency triggers anti-tumour activity of macrophages in liver cancer. Cancer Gene Ther 32, 949–962 (2025). https://doi.org/10.1038/s41417-025-00936-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41417-025-00936-2

Search

Advanced search

Quick links