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Clinical Studies

APOBEC3B stratifies ovarian clear cell carcinoma with distinct immunophenotype and prognosis

Abstract

Background

Ovarian clear cell carcinoma (OCCC) is a challenging disease due to its intrinsic chemoresistance. Immunotherapy is an emerging treatment option but currently impeded by insufficient understanding of OCCC immunophenotypes and their molecular determinants.

Methods

Whole-genome sequencing on 23 pathologically confirmed patients was employed to depict the genomic profile of primary OCCCs. APOBEC3B expression and digital pathology-based Immunoscore were assessed by performing immunohistochemistry and correlated with clinical outcomes.

Results

An APOBEC-positive (APOBEC+) subtype was identified based on the characteristic mutational signature and prevalent kataegis events. APOBEC + OCCC displayed favourable prognosis across one internal and two external patient cohorts. The improved outcome was ascribable to increased lymphocytic infiltration. Similar phenomena of APOBEC3B expression and T-cell accumulation were observed in endometriotic tissues, suggesting that APOBEC-induced mutagenesis and immunogenicity could occur early during OCCC pathogenesis. Corroborating these results, a case report was presented for an APOBEC + patient demonstrating inflamed tumour microenvironment and clinical response to immune checkpoint blockade.

Conclusions

Our findings implicate APOBEC3B as a novel mechanism of OCCC stratification with prognostic value and as a potential predictive biomarker that may inform immunotherapeutic opportunities.

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Fig. 1: WGS identifies an APOBEC + OCCC subtype.
Fig. 2: APOBEC + OCCC shows superior prognosis.
Fig. 3: APOBEC + OCCC has increased lymphocytic infiltration.
Fig. 4: Immune density and localisation impact patient survival.
Fig. 5: APOBEC + OCCC may benefit from immunotherapy.

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Data availability

The sequencing data generated in this study have been deposited in NCBI SRA database under the accession number SRP157148. All the other data and materials are available within the article or upon request from the corresponding authors.

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Acknowledgements

Not applicable.

Funding

This work was supported by the National Natural Science Foundation of China (82173077 and 82211540402 to XY; 81922047 and 82172596 to GZ; 81974454 to WD; 82022078 to LC), National Key Research and Development Program of China (2021YFC2700400 to WD), Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant Support (20161313 to GZ), Shanghai Natural Science Foundation (20ZR1433100 to XY), Shanghai Shenkang Hospital Development Center (SHDC2020CR3057B to XY; SHDC2020CR6009-002 to WD), Shanghai Municipal Key Clinical Specialty, Shanghai Collaborative Innovation Center for Translational Medicine (TM202004 to XY), Beijing Kuanghua foundation for the development of Chinese and Western Medicine (BKF) (KH-2021-LLZX-018 to XY; KH-2021-LLZX-049 to HL), Shanghai Jiao Tong University School of Medicine (YG2021GD02 and TMSK-2021-207 to XY), innovative research team of high-level local universities in Shanghai (SHSMU-ZLCX20210200 to GZ), and 111project (no. B21024 to GZ).

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Contributions

XY, GZ and WD designed and supervised the study. XL, HL, JZ, ZZ, JW, XL, LC, JC, LWTC, ZS and YZ performed the experiments and analysed the data. MCC developed the bioinformatics pipeline. GZ and XL wrote the manuscript. All authors read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Wen Di, Guanglei Zhuang or Xia Yin.

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The authors declare no competing interests.

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The study protocols were reviewed and approved by the institutional ethics committee of Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine (approval number: 2018-114). Written informed consent was obtained from all the patients.

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Long, X., Lu, H., Cai, MC. et al. APOBEC3B stratifies ovarian clear cell carcinoma with distinct immunophenotype and prognosis. Br J Cancer 128, 2054–2062 (2023). https://doi.org/10.1038/s41416-023-02239-5

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