Epitranscriptomic silencing of the ZC3H13/m6A axis orchestrates immunosuppressive microenvironment remodeling in renal cell carcinoma via CSF2-mediated MDSCs recruitment.

Abstract

Background: The immunosuppressive tumor microenvironment (TME) is a cardinal driver of immune escape and resistance to immunotherapy in renal cell carcinoma (RCC). The N6-methyladenosine (m⁶A), the most prevalent RNA modification, critically governs tumor aggressiveness and TME reprogramming. We aimed to exploit whether and how tumor-intrinsic m⁶A modification driven by ZC3H13 (zinc finger CCCH-type containing 13) can dictate the immune landscape of RCC.

Methods: Loss- and gain-of-function studies were performed in vitro and in allograft tumor model. Tumor-infiltrating immune cells were profiled with flow cytometry and immunostaining. The pivotal cytokine mediated by ZC3H13 depletion was identified through an integrated analysis of RNA-seq and PCR array. The molecular target of ZC3H13 was elucidated through integrated m⁶A sequencing and RNA sequencing.

Results: Low ZC3H13 expression was an independent predictor of poor prognosis in RCC. Functionally, ZC3H13 silencing enhanced the malignant behaviors of RCC cells and drove an immunosuppressive microenvironment characterized by aberrant recruitment of myeloid-derived suppressor cells (MDSCs). Mechanistically, ZC3H13 promoted m⁶A methylation on UNC5CL (UNC-5 Family C-Terminal Like) mRNA, facilitating YTHDC1-mediated stabilization of UNC5CL transcripts, which subsequently suppressed the NF-κB-CSF2 signaling axis, ultimately inhibiting MDSCs accumulation. Furthermore, therapeutic targeting CSF2 in combination with anti-PD1 exerts stronger antitumor effects in RCC by synergistically reversing the MDSCs mediated immunosuppressive microenvironment.

Conclusion: We identified that ZC3H13 loss unleashes the NF-κB-CSF2 signaling cascade via m⁶A-dependent silencing of UNC5CL, converting the RCC milieu into an MDSCs-dominated immunosuppressive niche. Targeting CSF2 combined with anti-PD1 may represent a novel therapeutic strategy to achieve better efficacy in RCC.