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The heterogeneity of tumour immune microenvironment revealing the CRABP2/CD69 signature discriminates distinct clinical outcomes in breast cancer

British Journal of Cancer volume 129, pages 1645–1657 (2023)Cite this article

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Abstract

Background

It has been acknowledged that the tumour immune microenvironment (TIME) plays a critical role in determining therapeutic responses and clinical outcomes in breast cancer (BrCa). Thus, the identification of the TIME features is essential for guiding therapy and prognostic assessment for BrCa.

Methods

The heterogeneous cellular composition of the TIME in BrCa by single-cell RNA sequencing (scRNA-seq). Two subtype-special genes upregulated in the tumour-rich subtype and the immune-infiltrating subtype were extracted, respectively. The CRABP2/CD69 signature was established based on CRABP2 and CD69 expression, and its predictive values for the clinical outcome and the neoadjuvant chemotherapy (NAT) responses were validated in multiple cohorts. Moreover, the oncogenic role of CRABP2 was explored in BrCa cells.

Results

Based on the heterogeneous cellular composition of the TIME in BrCa, the BrCa samples could be divided into the tumour-rich subtype and the immune-infiltrating subtype, which exhibited distinct prognosis and chemotherapeutic responses. Next, we extracted CRABP2 as the biomarker for the tumour-rich subtype and CD69 as the biomarker for the immune-infiltrating subtype. Based on the CRABP2/CD69 signature, BrCa samples were re-divided into three subtypes, and the CRABP2highCD69low subtype exhibited the worst prognosis and the lowest chemotherapeutic response, while the CRABP2lowCD69high subtype showed the opposite results. Furthermore, CARBP2 functioned as a novel oncogene in BrCa, which promoted tumour cell proliferation, migration, and invasion, and CRABP2 inhibition triggered the activation of cytotoxic T lymphocytes (CTLs).

Conclusion

The CRABP2/CD69 signature is significantly associated with the TIME features and could effectively predict the clinical outcome. Also, CRABP2 is determined to be a novel oncogene, which could be a therapeutic target in BrCa.

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Fig. 1: Integrated scRNA-seq analysis of tumour samples from BrCa patients.
Fig. 2: Recognition of molecular subtypes of BrCa patients at the single-cell levels.
Fig. 3: Recognition of molecular subtypes of BrCa patients in the RNA-seq datasets.
Fig. 4: Establishment of the CRABP2/CD69 signature.
Fig. 5: Validation of the CRABP2/CD69 signature.
Fig. 6: The cellular role of CRABP2 in BrCa.

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Data availability

Available of public BrCa datasets are described in “Methods”. Data can be provided upon reasonable request to the corresponding author.

Materials availability

Materials can be provided upon reasonable request to the corresponding author.

Code availability

The bioinformatics analysis used in this work was conducted using R 4.0.4, and the R packages that were utilised were thoroughly described in the materials and methods section. The authors are willing to provide any codes upon reasonable request.

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Funding

This study was supported by the Precision Medicine Project of Wuxi Municipal Health Commission (J202106), the Maternal and Child Health Research Project of Jiangsu Province (F202034), the Major project of Wuxi Science and Technology Bureau (N20201006), the 333 Project of Province (BRA2020380), the Wujieping Project (320.6750.2022-19-38).

Author information

Author notes

  1. These authors contributed equally: Jie Mei, Yun Cai, Lingyan Chen, Youqing Wu.

Authors and Affiliations

  1. Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, 214023, Wuxi, China

    Jie Mei, Yun Cai, Lingyan Chen, Zhiwen Qian & Yan Zhang

  2. The First Clinical Medical College, Nanjing Medical University, 211166, Nanjing, China

    Jie Mei

  3. School of Artificial Intelligence and Computer Science, Jiangnan University, 214122, Wuxi, China

    Youqing Wu & Xiang Pan

  4. Department of Oncology, The Women’s Hospital of Jiangnan University, 214023, Wuxi, China

    Jiayu Liu, Ying Jiang & Yan Zhang

  5. Department of Breast Surgery, The Women’s Hospital of Jiangnan University, 214023, Wuxi, China

    Ping Zhang

  6. Jiangsu Breast Disease Center, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, China

    Tiansong Xia

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Contributions

YZ, XP and TX designed and performed the experiments. JM, YC, LC, YW and JL conducted the data analysis of single-cell sequencing. JM, ZQ, YJ and PZ performed the statistics and analysis of clinical data. JL and YJ helped the research methods. YC handled the processing of single-cell RNA sequencing. JM, YC, LC and YW organised the data and wrote the manuscript. YZ, XP and TX supervised the study. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Tiansong Xia, Xiang Pan or Yan Zhang.

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The authors declare no competing interests.

Ethics approval and consent to participate

The collection of the cohort 1 and the cohort 6 was approved by the institutional review board at Wuxi Maternal and Child Health Hospital (2021-01-0927-28), and the collection of the cohort 8 was approved by the Clinical Research Ethics Committee in Outdo Biotech (YB-M-05-02). The cohort 2, the cohort 3, the cohort 4, the cohort 5, and the cohort 7 were public cohorts and no ethical approval was needed. All experiments were performed in accordance with the Declaration of Helsinki, and informed consent was obtained from all subjects.

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Mei, J., Cai, Y., Chen, L. et al. The heterogeneity of tumour immune microenvironment revealing the CRABP2/CD69 signature discriminates distinct clinical outcomes in breast cancer. Br J Cancer 129, 1645–1657 (2023). https://doi.org/10.1038/s41416-023-02432-6

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