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:

Cellular and Molecular Biology

Proteomics analysis and immune profiling reveal regulators of PD-L1 in oesophageal squamous cell carcinoma

British Journal of Cancer volume 133, pages 448–463 (2025)Cite this article

Subjects

Abstract

Background

Proteomics studies have advanced our comprehension of cancer biology, accelerated targeted therapy, and improved patient outcomes.

Methods

High-resolution mass spectrometry and immune profiling based on immunohistochemistry and multiple immunohistochemistry were employed to investigate proteomic and immune landscapes in oesophageal squamous cell carcinoma (ESCC) and explore the regulators of PD-L1 in ESCC. Molecular validation was performed using qRT-PCR, western blotting, and in vitro functional assays.

Results

Proteomic profiling of 89 treatment-naive ESCC specimens identified over 9300 proteins, with 6900 proteins detected across most samples. Proteome-based stratification identified three subtypes related to diverse clinical and molecular features. Combined proteomics and immune analyses revealed core proteins associated with the immune landscape in ESCC. Further, integrated proteomics, transcriptomics, and immune profiling nominated COTL1 as a potential regulator of PD-L1 in ESCC. Overexpression of COTL1 upregulated both mRNA and protein levels of PD-L1 and promoted cell proliferation in ESCC. Patients with high COTL1 protein expression were likely to have a poor prognosis, along with increased infiltration of CD4+CD8+ and CD4+GrB+ cells.

Conclusions

Collectively, our integrative analysis enables a more comprehensive understanding of the proteomic and immune landscape of ESCC and implicates COTL1 as a potential modulator of PD-L1 and immune cell infiltration.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

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

Fig. 1: Proteomics landscape of ESCC patients.
Fig. 2: Proteomic subtyping of ESCC patients and its associations with clinical outcomes.
Fig. 3: Tumour immune microenvironment in ESCC patients.
Fig. 4: Higher expression of six potential PD-L1 regulators correlates with poor prognosis and clinical characteristics of ESCC patients.
Fig. 5: COTL1, GMFG, and TK1 upregulate the expression of PD-L1 at both protein and transcriptional levels.
Fig. 6: COTL1, GMFG, and TK1 promote cell proliferation and metastasis by upregulating PD-L1 in ESCC.
Fig. 7: COTL1 regulates the ESCC tumour immune microenvironment.

Similar content being viewed by others

Data availability

The proteomics data of 89 ESCC samples have been deposited in the ProteomeXchange Consortium (https://pdc.cancer.gov/pdc/) under the accession number PXD053809.

References

  1. Thrift AP. Global burden and epidemiology of Barrett oesophagus and oesophageal cancer. Nat Rev Gastroenterol Hepatol. 2021;18:432–43.

    Article  PubMed  Google Scholar 

  2. Yang H, Liu H, Chen Y, Zhu C, Fang W, Yu Z, et al. Neoadjuvant chemoradiotherapy followed by surgery versus surgery alone for locally advanced squamous cell carcinoma of the esophagus (NEOCRTEC5010): a phase III multicenter, randomized, open-label clinical trial. J Clin Oncol. 2018;36:2796–803.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Liu W, Xie L, He YH, Wu ZY, Liu LX, Bai XF, et al. Large-scale and high-resolution mass spectrometry-based proteomics profiling defines molecular subtypes of esophageal cancer for therapeutic targeting. Nat Commun. 2021;12:4961.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Xu JY, Zhang C, Wang X, Zhai L, Ma Y, Mao Y, et al. Integrative proteomic characterization of human lung adenocarcinoma. Cell. 2020;182:245.e17–61.e17.

    Article  Google Scholar 

  5. Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, et al. Integrated proteogenomic characterization of clear cell renal cell carcinoma. Cell. 2019;179:964.e31–83.e31.

    Article  Google Scholar 

  6. Chen YJ, Roumeliotis TI, Chang YH, Chen CT, Han CL, Lin MH, et al. Proteogenomics of non-smoking lung cancer in East Asia delineates molecular signatures of pathogenesis and progression. Cell. 2020;182:226.e17–44.e17.

    Article  Google Scholar 

  7. Jiang YZ, Ma D, Jin X, Xiao Y, Yu Y, Shi J, et al. Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities. Nat Cancer. 2024;5:673–90.

    Article  CAS  PubMed  Google Scholar 

  8. Jiang YZ, Ma D, Suo C, Shi J, Xue M, Hu X, et al. Genomic and transcriptomic landscape of triple-negative breast cancers: subtypes and treatment strategies. Cancer Cell. 2019;35:428.e5–40.e5.

    Article  Google Scholar 

  9. Tanaka Y, Chiwaki F, Kojima S, Kawazu M, Komatsu M, Ueno T, et al. Multi-omic profiling of peritoneal metastases in gastric cancer identifies molecular subtypes and therapeutic vulnerabilities. Nat Cancer. 2021;2:962–77.

    Article  CAS  PubMed  Google Scholar 

  10. Sun Y, Wu P, Zhang Z, Wang Z, Zhou K, Song M, et al. Integrated multi-omics profiling to dissect the spatiotemporal evolution of metastatic hepatocellular carcinoma. Cancer Cell. 2024;42:135.e17–56.e17.

    Article  Google Scholar 

  11. Gao Q, Zhu H, Dong L, Shi W, Chen R, Song Z, et al. Integrated proteogenomic characterization of HBV-related hepatocellular carcinoma. Cell. 2019;179:561.e22–77.e22.

    Article  Google Scholar 

  12. Liu Z, Zhao Y, Kong P, Liu Y, Huang J, Xu E, et al. Integrated multi-omics profiling yields a clinically relevant molecular classification for esophageal squamous cell carcinoma. Cancer Cell. 2023;41:181.e9–95.e9.

    Article  Google Scholar 

  13. Jin X, Liu L, Wu J, Jin X, Yu G, Jia L, et al. A multi-omics study delineates new molecular features and therapeutic targets for esophageal squamous cell carcinoma. Clin Transl Med. 2021;11:e538.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wen J, Fang S, Hu Y, Xi M, Weng Z, Pan C, et al. Impacts of neoadjuvant chemoradiotherapy on the immune landscape of esophageal squamous cell carcinoma. EBioMedicine. 2022;86:104371.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wen J, Yang H, Liu MZ, Luo KJ, Liu H, Hu Y, et al. Gene expression analysis of pretreatment biopsies predicts the pathological response of esophageal squamous cell carcinomas to neo-chemoradiotherapy. Ann Oncol. 2014;25:1769–74.

    Article  CAS  PubMed  Google Scholar 

  16. Shah MA, Kojima T, Hochhauser D, Enzinger P, Raimbourg J, Hollebecque A, et al. Efficacy and safety of pembrolizumab for heavily pretreated patients with advanced, metastatic adenocarcinoma or squamous cell carcinoma of the esophagus: the phase 2 KEYNOTE-180 study. JAMA Oncol. 2019;5:546–50.

    Article  PubMed  Google Scholar 

  17. Yin J, Yuan J, Li Y, Fang Y, Wang R, Jiao H, et al. Neoadjuvant adebrelimab in locally advanced resectable esophageal squamous cell carcinoma: a phase 1b trial. Nat Med. 2023;29:2068–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Zheng DD, Li YY, Yuan XY, Lu JL, Zhang MF, Fu J, et al. Immune cell patterns before and after neoadjuvant immune checkpoint blockade combined with chemoradiotherapy in locally advanced esophageal squamous cell carcinoma. BMC Cancer. 2024;24:649.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Reck M, Rodríguez-Abreu D, Robinson AG, Hui R, Csőszi T, Fülöp A, et al. Pembrolizumab versus chemotherapy for PD-L1-positive non-small-cell lung cancer. N Engl J Med. 2016;375:1823–33.

    Article  CAS  PubMed  Google Scholar 

  20. Adams S, Loi S, Toppmeyer D, Cescon DW, De Laurentiis M, Nanda R, et al. Pembrolizumab monotherapy for previously untreated, PD-L1-positive, metastatic triple-negative breast cancer: cohort B of the phase II KEYNOTE-086 study. Ann Oncol. 2019;30:405–11.

    Article  CAS  PubMed  Google Scholar 

  21. Kim ST, Cristescu R, Bass AJ, Kim KM, Odegaard JI, Kim K, et al. Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer. Nat Med. 2018;24:1449–58.

    Article  CAS  PubMed  Google Scholar 

  22. Cha JH, Chan LC, Li CW, Hsu JL, Hung MC. Mechanisms controlling PD-L1 expression in cancer. Mol Cell. 2019;76:359–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Li H, Kuang X, Liang L, Ye Y, Zhang Y, Li J, et al. The beneficial role of sunitinib in tumor immune surveillance by regulating tumor PD-L1. Adv Sci. 2021;8:2001596.

    Article  CAS  Google Scholar 

  24. Shi ZD, Han XX, Song ZJ, Dong Y, Pang K, Wang XL, et al. Integrative multi-omics analysis depicts the methylome and hydroxymethylome in recurrent bladder cancers and identifies biomarkers for predicting PD-L1 expression. Biomark Res. 2023;11:47.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Noh JY, Lee IP, Han NR, Kim M, Min YK, Lee SY, et al. Additive effect of CD73 inhibitor in colorectal cancer treatment with CDK4/6 inhibitor through regulation of PD-L1. Cell Mol Gastroenterol Hepatol. 2022;14:769–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Casey SC, Tong L, Li Y, Do R, Walz S, Fitzgerald KN, et al. MYC regulates the antitumor immune response through CD47 and PD-L1. Science. 2016;352:227–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Maeda T, Hiraki M, Jin C, Rajabi H, Tagde A, Alam M, et al. MUC1-C induces PD-L1 and immune evasion in triple-negative breast cancer. Cancer Res. 2018;78:205–15.

    Article  CAS  PubMed  Google Scholar 

  28. Barsoum IB, Smallwood CA, Siemens DR, Graham CH. A mechanism of hypoxia-mediated escape from adaptive immunity in cancer cells. Cancer Res. 2014;74:665–74.

    Article  CAS  PubMed  Google Scholar 

  29. Atefi M, Avramis E, Lassen A, Wong DJ, Robert L, Foulad D, et al. Effects of MAPK and PI3K pathways on PD-L1 expression in melanoma. Clin Cancer Res. 2014;20:3446–57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Jiang X, Zhou J, Giobbie-Hurder A, Wargo J, Hodi FS. The activation of MAPK in melanoma cells resistant to BRAF inhibition promotes PD-L1 expression that is reversible by MEK and PI3K inhibition. Clin Cancer Res. 2013;19:598–609.

    Article  CAS  PubMed  Google Scholar 

  31. Yang H, Zhang Q, Xu M, Wang L, Chen X, Feng Y, et al. CCL2-CCR2 axis recruits tumor associated macrophages to induce immune evasion through PD-1 signaling in esophageal carcinogenesis. Mol Cancer. 2020;19:41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Wang S, Lin Y, Xiong X, Wang L, Guo Y, Chen Y, et al. Low-dose metformin reprograms the tumor immune microenvironment in human esophageal cancer: results of a phase II clinical trial. Clin Cancer Res. 2020;26:4921–32.

    Article  CAS  PubMed  Google Scholar 

  33. Park S, Joung JG, Min YW, Nam JY, Ryu D, Oh D, et al. Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma. J Immunother Cancer. 2019;7:128.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Matulonis UA, Shapira-Frommer R, Santin AD, Lisyanskaya AS, Pignata S, Vergote I, et al. Antitumor activity and safety of pembrolizumab in patients with advanced recurrent ovarian cancer: results from the phase II KEYNOTE-100 study. Ann Oncol. 2019;30:1080–7.

    Article  CAS  PubMed  Google Scholar 

  35. Burr ML, Sparbier CE, Chan YC, Williamson JC, Woods K, Beavis PA, et al. CMTM6 maintains the expression of PD-L1 and regulates anti-tumour immunity. Nature. 2017;549:101–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Zhang J, Bu X, Wang H, Zhu Y, Geng Y, Nihira NT, et al. Cyclin D-CDK4 kinase destabilizes PD-L1 via cullin 3-SPOP to control cancer immune surveillance. Nature. 2018;553:91–5.

    Article  CAS  PubMed  Google Scholar 

  37. Green MR, Rodig S, Juszczynski P, Ouyang J, Sinha P, O’Donnell E, et al. Constitutive AP-1 activity and EBV infection induce PD-L1 in Hodgkin lymphomas and posttransplant lymphoproliferative disorders: implications for targeted therapy. Clin Cancer Res. 2012;18:1611–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Zerdes I, Matikas A, Bergh J, Rassidakis GZ, Foukakis T. Genetic, transcriptional and post-translational regulation of the programmed death protein ligand 1 in cancer: biology and clinical correlations. Oncogene. 2018;37:4639–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Garcia-Diaz A, Shin DS, Moreno BH, Saco J, Escuin-Ordinas H, Rodriguez GA, et al. Interferon receptor signaling pathways regulating PD-L1 and PD-L2 expression. Cell Rep. 2017;19:1189–201.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Pulko V, Liu X, Krco CJ, Harris KJ, Frigola X, Kwon ED, et al. TLR3-stimulated dendritic cells up-regulate B7-H1 expression and influence the magnitude of CD8 T cell responses to tumor vaccination. J Immunol. 2009;183:3634–41.

    Article  CAS  PubMed  Google Scholar 

  41. Wang X, Ni S, Chen Q, Ma L, Jiao Z, Wang C, et al. Bladder cancer cells induce immunosuppression of T cells by supporting PD-L1 expression in tumour macrophages partially through interleukin 10. Cell Biol Int. 2017;41:177–86.

    Article  CAS  PubMed  Google Scholar 

  42. Zhu X, Shi C, Peng Y, Yin L, Tu M, Chen Q, et al. Thymidine kinase 1 silencing retards proliferative activity of pancreatic cancer cell via E2F1-TK1-P21 axis. Cell Prolif. 2018;51:e12428.

    Article  PubMed  Google Scholar 

  43. Yogev O, Almeida GS, Barker KT, George SL, Kwok C, Campbell J, et al. In vivo modeling of chemoresistant neuroblastoma provides new insights into chemorefractory disease and metastasis. Cancer Res. 2019;79:5382–93.

    Article  CAS  PubMed  Google Scholar 

  44. Li Q, Zhang L, Yang Q, Li M, Pan X, Xu J, et al. Thymidine kinase 1 drives hepatocellular carcinoma in enzyme-dependent and -independent manners. Cell Metab. 2023;35:912.e7–27.e7.

    Article  Google Scholar 

  45. Ikeda K, Kundu RK, Ikeda S, Kobara M, Matsubara H, Quertermous T. Glia maturation factor-gamma is preferentially expressed in microvascular endothelial and inflammatory cells and modulates actin cytoskeleton reorganization. Circ Res. 2006;99:424–33.

    Article  CAS  PubMed  Google Scholar 

  46. Lippert DN, Wilkins JA. Glia maturation factor gamma regulates the migration and adherence of human T lymphocytes. BMC Immunol. 2012;13:21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Zuo P, Ma Y, Huang Y, Ye F, Wang P, Wang X, et al. High GMFG expression correlates with poor prognosis and promotes cell migration and invasion in epithelial ovarian cancer. Gynecol Oncol. 2014;132:745–51.

    Article  CAS  PubMed  Google Scholar 

  48. Wang H, Chen Z, Chang H, Mu X, Deng W, Yuan Z, et al. Expression of glia maturation factor γ is associated with colorectal cancer metastasis and its downregulation suppresses colorectal cancer cell migration and invasion in vitro. Oncol Rep. 2017;37:929–36.

    Article  CAS  PubMed  Google Scholar 

  49. Wang X, Bai Y, Wang B. Coactosin-like protein 1 (COTL1) could be an immunological and prognostic biomarker: from pan-cancer analysis to low-grade glioma validation. J Inflamm Res. 2024;17:1805–20.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Rangaraju S, Dammer EB, Raza SA, Gao T, Xiao H, Betarbet R, et al. Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimer’s disease-related proteins. Mol Neurodegener. 2018;13:34.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Wang B, Zhao L, Chen D. Coactosin-like protein in breast carcinoma: friend or foe? J Inflamm Res. 2022;15:4013–25.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Xia L, Xiao X, Liu WL, Song Y, Liu TJJ, Li YJ, et al. Coactosin-like protein CLP/Cotl1 suppresses breast cancer growth through activation of IL-24/PERP and inhibition of non-canonical TGFβ signaling. Oncogene. 2018;37:323–31.

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This work was supported by the National Key Research and Development Program of China (2022YFA1304604), the National Natural Science Foundation of China (82273032), and the Natural Science Foundation of Guangdong Province (2025A1515012674).

Author information

Author notes

  1. These authors contributed equally: Yuying Li, Xiaoyi Yuan, Xing-Feng Yin.

Authors and Affiliations

  1. MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China

    Yuying Li, Xiaoyi Yuan, Xing-Feng Yin, Dandan Zheng, Fujin Shi, Danya Liu, Liling Hu, Xinyu Shi, Qing-Yu He & Chris Zhiyi Zhang

  2. Department of Pathology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China

    Nengqiao Wen

  3. Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou City, China

    Hong Yang

Authors
  1. Yuying Li
    View author publications

    Search author on:PubMed Google Scholar

  2. Xiaoyi Yuan
    View author publications

    Search author on:PubMed Google Scholar

  3. Xing-Feng Yin
    View author publications

    Search author on:PubMed Google Scholar

  4. Dandan Zheng
    View author publications

    Search author on:PubMed Google Scholar

  5. Fujin Shi
    View author publications

    Search author on:PubMed Google Scholar

  6. Danya Liu
    View author publications

    Search author on:PubMed Google Scholar

  7. Liling Hu
    View author publications

    Search author on:PubMed Google Scholar

  8. Xinyu Shi
    View author publications

    Search author on:PubMed Google Scholar

  9. Nengqiao Wen
    View author publications

    Search author on:PubMed Google Scholar

  10. Qing-Yu He
    View author publications

    Search author on:PubMed Google Scholar

  11. Hong Yang
    View author publications

    Search author on:PubMed Google Scholar

  12. Chris Zhiyi Zhang
    View author publications

    Search author on:PubMed Google Scholar

Contributions

CZZ, YL, and XY designed the study and prepared the manuscript. YL, XY, and X-FY conducted the experiments and analysed the data. Q-YH, HY, and CZZ reviewed and edited the manuscript. LH, DZ, FS, DL, XS, and NW were involved in experimentation and data analysis.

Corresponding authors

Correspondence to Qing-Yu He, Hong Yang or Chris Zhiyi Zhang.

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

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

Li, Y., Yuan, X., Yin, XF. et al. Proteomics analysis and immune profiling reveal regulators of PD-L1 in oesophageal squamous cell carcinoma. Br J Cancer 133, 448–463 (2025). https://doi.org/10.1038/s41416-025-03068-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Version of record:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41416-025-03068-4

Search

Advanced search

Quick links