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NMRK2 leads to the depletion of CD8+T cells by mediating the enhancement of NAD+-SIRT1-CD38 axis in PRCC-TFE3 rRCC

Abstract

PRCC-TFE3 rearrangement renal cell carcinoma (rRCC) is an independent subtype of rRCC caused by chromosomal translocation and rearrangement. Previous studies have revealed that nicotinamide riboside kinase 2 (NMRK2), which is transcriptionally upregulated by PRCC-TFE3 fusion protein, as a pivotal molecule in the energy metabolism remodeling of PRCC-TFE3 rRCC. However, the molecular mechanism by which NMRK2-mediated enhancement of nicotinamide adenine dinucleotide (NAD+) synthesis contributes to tumor progression in PRCC-TFE3 rRCC remains unclear. In this study, utilizing immune system-humanized mice model and in vitro cell models, we demonstrated that elevated expression of NMRK2 impaired the cytotoxic functions of CD8+T cells, leading to the emergence of immune-ignorant phenotypes in PRCC-TFE3 rRCC. Furthermore, it was shown that the increased NAD+ metabolism driven by NMRK2 enhanced the stability of CD38 protein through SIRT1-mediated deacetylation, which underlines impairment of CD8+T cells and the development of an immunosuppressive state in PRCC-TFE3 rRCC. Our findings not only elucidated a mechanism underlying immunological ignorance in PRCC-TFE3 rRCC but also propose potential therapeutic targets.

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Fig. 1: PRCC-TFE3 fusion protein reduced the CD8+T cells infiltration in PRCC-TFE3 rRCC independent of any deficiencies in the recruitment and proliferation of CD8+T cells.
Fig. 2: PRCC-TFE3 fusion impaired the killing function of CD8+T cells in PRCC-TFE3 rRCC.
Fig. 3: NMRK2 impaired the killing activity of CD8+T cells in PRCC-TFE3 rRCC.
Fig. 4: NMRK2 was the vital kinase that catalyzed the synthesis of NAD+ in PRCC-TFE3 rRCC.
Fig. 5: NMRK2 acted in NAD+-SIRT1-CD38 pathway and enhanced the expression level of CD38 protein.
Fig. 6: NMRK2 enhanced CD38 protein stability through SIRT1-mediated deacetylation.
Fig. 7: Deacetylated modification of CD38 protein promoted its stability by reducing the recruitment of ubiquitin molecules.
Fig. 8: Pathological and survival information of patients with PRCC-TFE3 rRCC.
Fig. 9: CD38 inhibitor enhanced the cytotoxic effect of CD8+T cells on PRCC-TFE3 rRCC cells.

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Data availability

The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

We are grateful to Prof. Xiaodong Han for providing necessary reagents and suggestions about experiments. UOK cell lines derived from patients were from Dr. Marston Linehan’s lab, Urologic Oncology Branch, Tumor Cell Line Repository, NCI. We would like to sincerely thank Dr. W. Marston Linehan from the National Cancer Institute in America for giving us the UOK109 and UOK120 cell lines. We thank The Translational Medicine Core Facilities, Medical School, Nanjing University, Nanjing, China, for providing the experimental equipment. We thank Dr. Dazhi Yang from AcroGenic biotechnologies for providing us with AccuraMatrix and giving us guidance in establishing 3D cell culture. We would like to thank Home for Research editorial team (www.home-for-researchers.com).

Funding

This work was supported by the National Natural Science Foundation of China (No. 82503947), the Medical Research Project of Jiangsu Province Health Commission (No. ZD2022013), the National Natural Science Foundation of China (No. 82303942), Natural Science Foundation of Jiangsu Province (No. BK20221444), and Beijing Ronghe Medical Development Foundation.

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YC and XWTL conceived the study, designed the experiments, and wrote the original draft. YC (same first author) also curated the data and prepared all figures. MMW verified the analytical methods, cleaned the raw data, and co-wrote the Results. XD assembled the datasets, performed the statistical analyses, and helped write the Methods section. WLM compiled the literature review and co-wrote the Introduction and Discussion. FF edited the manuscript for scientific content and revised the statistical reporting. YBD and PD polished the language and ensured compliance with journal's style. WDD checked the references and managed the response-to-reviewers documents. LQZ proofread the final text and coordinated submission logistics. DML provided the clinical samples and laboratory reagents. WDG supervised the data-collection protocol and obtained ethical approvals. NL acquired the funding, administered the project, and critically reviewed all versions of the paper. All authors read and approved the final manuscript.

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Correspondence to Ning Liu, Weidong Gan or Dongmei Li.

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Chen, Y., Liu, X., Wu, M. et al. NMRK2 leads to the depletion of CD8+T cells by mediating the enhancement of NAD+-SIRT1-CD38 axis in PRCC-TFE3 rRCC. Oncogene (2025). https://doi.org/10.1038/s41388-025-03577-9

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