Targeting m⁶A reader YTHDF1 augments antitumour immunity and boosts anti-PD-1 efficacy in colorectal cancer

Abstract

ObjectiveThe role of N6-methyladenosine (m6A) in tumour immune microenvironment (TIME) remains understudied. Here, we elucidate function and mechanism of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) in colorectal cancer (CRC) TIME.DesignClinical significance of YTHDF1 was assessed in tissue microarrays (N=408) and TCGA (N=526) cohorts.YTHDF1function was determined in syngeneic tumours, intestine-specificYthdf1knockin mice, and humanised mice. Single-cell RNA-seq (scRNA-seq) was employed to profile TIME. Methylated RNA immunoprecipitation sequencing (MeRIP-seq), RNA sequencing (RNA-seq) and ribosome sequencing (Ribo-seq) were used to identify YTHDF1 direct targets. Vesicle-like nanoparticles (VNPs)-encapsulatedYTHDF1-siRNA was used forYTHDF1silencing in vivo.ResultsYTHDF1expression negatively correlated with interferon-γ gene signature in TCGA-CRC. Concordantly, YTHDF1 protein negatively correlated with CD8+T-cell infiltration in independent tissue microarrays cohorts, implying its role in TIME. Genetic depletion ofYthdf1augmented antitumour immunity in CT26 (MSS-CRC) and MC38 (MSI-H-CRC) syngeneic tumours, whileYthdf1knockin promoted an immunosuppressive TIME facilitating CRC in azoxymethane-dextran sulphate-sodium orApcMin/+models. scRNA-seq identified reduction of myeloid-derived suppressor cells (MDSCs), concomitant with increased cytotoxic T cells inYthdf1knockout tumours. Integrated MeRIP-seq, RNA-seq and Ribo-seq revealed p65/Rela as a YTHDF1 target. YTHDF1 promoted p65 translation to upregulate CXCL1, which increased MDSC migration via CXCL1-CXCR2 axis. Increased MSDCs in turn antagonised functional CD8+T cells in TIME. Importantly, targeting YTHDF1 by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) or VNPs-siYTHDF1boosted anti-PD1 efficacy in MSI-H CRC, and overcame anti-PD1 resistance in MSS CRC.ConclusionYTHDF1 impairs antitumour immunity via an m6A-p65-CXCL1/CXCR2 axis to promote CRC and serves as a therapeutic target in immune checkpoint blockade therapy.

Discovery of Novel PD-L1 Small-Molecular Inhibitors with Potent In Vivo Anti-tumor Immune Activity

“…CT26 tumor model was characterized as "cold tumors" owing to their immunosuppressive microenvironment, resulting in a diminished sensitivity to tumor immunotherapy interventions. 28 The inherent challenge in tumor immunotherapy lies in the low reactivity of "cold tumors", impeding effective responses to immunotherapeutic interventions. To explore the in vivo therapeutic efficacy of Flow cytometric analysis of tumor-infiltrating immune cells provided insights into the impact of X22 on the tumor immune microenvironment, particularly focusing on key immunosuppressive Treg and MDSC cells, and CD8 + T cells, which are essential for tumor-killing.…”

Aberrant RNA m6A modification in gastrointestinal malignancies: versatile regulators of cancer hallmarks and novel therapeutic opportunities

“…In a recent report, intestine-specific YTHDF1 knock-in promotes MDSC migration, antagonizing functional CD8 + T cells in the TIME enhancing CRC growth. In this case, YTHDF1 activates the CXCL1-CXCR2 axis to promote m 6 A-p65 translation [143].…”

Breast cancer intrinsic YTHDF1 forms “cold” tumor and inhibits CD8+ T cells infiltration and function

“…Recent studies have shown that epigenetic regulation, speci cally N 6 -methyl adenosine (m 6 A) modi cation, holds substantial importance in the immune microenvironment of tumors. The presence of m 6 A in uences the activation, invasion, proliferation, and effector function of immune cells that in ltrate the tumor [5,6] . Furthermore, research indicates that targeting m 6 A can impact the response rate of immunotherapy, highlighting its potential as a target for sensitizing immunotherapy [7,8] .…”

“…Furthermore, research indicates that targeting m 6 A can impact the response rate of immunotherapy, highlighting its potential as a target for sensitizing immunotherapy [7,8] . Three protein factors, namely methyltransferase as the writers (METTL3, METTL14, etc), binding protein as the readers (YTHDF1, YTHDF2, YTHDC1, etc), and demethylase as the erasers (FTO, ALKBH5, etc), participate in and regulate the modi cation of m 6 A [5,9,10] .The core methyltransferase complex METTL3-METTL14-WTAP m 6 A catalyzes the procedure, while two key erasers, FTO and ALKBH5, remove the modi cation [11][12][13] .…”