Report: Intrinsic Role of m6A Reader Protein YTHDF2 in Regulating Tumor Immune Evasion

Background Introduction

In recent years, immunotherapy has become a hotspot in the field of tumor treatment, attracting attention for its ability to break through immune suppression barriers or enhance existing anti-tumor immunity. However, despite some successes with current strategies, the phenomenon of resistance to immunotherapy due to tumor immune evasion mechanisms remains common. Tumor cells have an intrinsic ability to create an inhibitory microenvironment through various mechanisms, thereby evading immune surveillance and ultimately leading to immune evasion, which limits the effectiveness of existing immunotherapies.

Existing studies have revealed mechanisms by which tumor cells achieve immune evasion through epigenetic reprogramming. Multi-omics analysis has found that epigenetic reprogramming of RUNX3 in tumor cells promotes the infiltration of CD8+ T cells and alleviates their exhaustion. Additionally, the histone regulatory factor PRC2 (Polycomb Repressive Complex 2) has been reported to block MHC-I-mediated antigen presentation, promoting tumor evasion from T cell-mediated immunity. Inhibiting DNA methylation can induce type I interferon expression and tumor regression. These studies suggest that tumor cells evade immune surveillance at the epigenetic level through histone modifications or DNA methylation. However, whether and how RNA epigenetic modifications participate in immune evasion still needs further exploration.

In this study, we discovered the role of YTHDF2 (YTH domain family protein 2) in regulating immune evasion of tumor cells. YTHDF2 is a known N6-methyladenosine (m6A) reader protein that typically functions by destabilizing m6A-modified mRNA. We found that the loss of YTHDF2 in tumors inhibits tumor growth and extends survival in immunocompetent tumor models.

Research Source

This research was conducted by Sai Xiao, Shoubao Ma, Baofa Sun, Wenchen Pu, Songqi Duan, Jingjing Han, Yaqun Hong, Jianying Zhang, Yong Peng, Chuan He, Ping Yi, Michael A. Caligiuri, and Jianhua Yu. These authors are from City of Hope National Medical Center, Nankai University, West China Hospital, Sichuan Agricultural University, University of Chicago, and Third Affiliated Hospital of Chongqing Medical University. The paper was published on May 31, 2024, in the journal Science Immunology, article number eadl2171.

Research Details

Experimental Procedure

In the study, researchers used CRISPR-Cas9 technology to knock out the YTHDF2 gene in two mouse tumor cell lines: the MC38 colon cancer cell line and the ovalbumin (OVA)-expressing B16 (B16-OVA) melanoma cell line. Immunoblot analysis revealed a complete absence of YTHDF2 protein in both cell lines, with no effect on the expression of YTHDF1 or YTHDF3. Further experiments showed that YTHDF2 knockout had no significant impact on the in vitro proliferation or apoptosis of MC38 and B16-OVA tumor cells, but tumor growth was significantly slowed in immunocompetent C57BL/6 mice, and the survival period of the mice was notably extended.

Main Results

Immune Evasion Mechanism

YTHDF2 deficiency promoted the expression of CX3CL1, thereby enhancing the recruitment and polarization of macrophages. Compared to wild-type tumor cells, YTHDF2-deficient tumor cells exhibited significantly higher CX3CL1 expression, promoting macrophage recruitment. These macrophages were polarized to the M1 type (anti-tumor or inflammatory) in the presence of CD8+ T cell-derived IFN-γ. These anti-tumor macrophages, in turn, activated CD8+ T cells through antigen cross-presentation. Additionally, YTHDF2-deficient tumor cells showed higher sensitivity to CD8+ T cell-mediated cytotoxicity by weakening tumor glycolytic metabolism.

IFN-γ-Mediated Autophagic Degradation

IFN-γ downregulated the expression of YTHDF2 in tumors through the autophagic degradation pathway, making tumor cells more sensitive to CD8+ T cell-mediated cytotoxicity. Researchers also discovered a small molecule compound that preferentially induces YTHDF2 degradation. This compound alone had significant anti-tumor effects, but when used in combination with anti-PD-L1 or anti-PD-1 antibodies, the effect was even better.

Research Conclusions

Overall, YTHDF2 appears to be an intrinsic regulator of tumor immune evasion, representing a promising target for enhancing cancer immunotherapy.

Research Significance

This study revealed the critical role of YTHDF2 in tumor immune evasion, indicating that it not only inhibits macrophage recruitment and anti-tumor polarization but also suppresses the anti-tumor effector function of CD8+ T cells. These characteristics enable tumors to establish a tumor microenvironment that allows immune suppression, promoting tumor progression. Genetic knockout or pharmacological inhibition of YTHDF2 promotes macrophage polarization to the anti-tumor M1 phenotype and enhances their antigen cross-presentation ability in the presence of IFN-γ. CD8+ T cells and their associated IFN-γ increase the sensitivity of tumor cells to CD8+ T cell-mediated cytotoxicity by promoting the degradation of intrinsic YTHDF2 in tumors.

Research Highlights

1. Intrinsic YTHDF2 in Tumors: YTHDF2 not only inhibits macrophage recruitment and anti-tumor polarization but also suppresses the anti-tumor effector function of CD8+ T cells.
2. IFN-γ-Mediated Autophagic Degradation: IFN-γ downregulates the expression of YTHDF2 in tumors through the autophagic degradation pathway, making tumor cells more sensitive to CD8+ T cell-mediated cytotoxicity.
3. New Small Molecule Compound: The study discovered a small molecule compound that preferentially induces YTHDF2 degradation, which alone has significant anti-tumor effects and shows even better effects when combined.

Further Research

The study shows that YTHDF2-deficient tumor cells exhibit lower glucose metabolism compared to wild-type tumor cells. However, RNA immunoprecipitation sequencing and m6A sequencing data suggest that YTHDF2 may indirectly regulate glucose metabolism genes in tumors. Therefore, YTHDF2 may control these metabolic genes through other mechanisms. The detailed mechanism behind this observation requires further determination.

Conclusion

This study reveals the intrinsic and core role of m6A reader protein YTHDF2 in tumor immune evasion. Our work emphasizes that YTHDF2 is an attractive target not only within immune cells but also within tumor cells. Finally, we identified df-a7 as a safe, effective, and potentially druggable small molecule compound for targeting YTHDF2.

The results of this study not only provide new insights into the mechanisms of tumor immune evasion but also offer new potential targets for the development of cancer immunotherapy.