Title : Uncovering tumor-suppressive roles of histone modifiers in gastric cancer through spatial transcriptomics and epigenomics
Abstract:
Gastric adenocarcinoma (GAC) remains one of the leading causes of cancer-related mortality worldwide, largely due to its late-stage diagnosis, limited treatment options, and poorly understood molecular drivers. Recent studies have implicated epigenetic dysregulation in GAC pathogenesis, yet the functional role of specific modifiers such as the histone H3K4 methyltransferase KMT2D (also known as MLL4/MLL2) remains controversial. Here, we integrate functional genomics, spatial transcriptomics, and epigenomics to define the tumor-suppressive role of KMT2D in GAC.
Our analyses of The Cancer Genome Atlas (TCGA) revealed that KMT2D is one of the most frequently mutated epigenetic regulators in GAC (14%), with low expression or mutation correlating with poor overall survival. Immunohistochemical (IHC) analysis further showed significantly lower KMT2D protein expression in GAC tissues compared to normal gastric mucosa. Consistent with these findings, KMT2D knockdown in AGS and GA0518 GAC cell lines promoted proliferation and invasion, while in vivo deletion accelerated tumor growth in xenograft and gastric organoid models derived from Kmt2dfl/fl mice. RNA-sequencing revealed that KMT2D loss upregulated oncogenic pathways, including those related to cytokine signaling, GTPase activation, and immune response—particularly regulatory T cell (Treg) signatures. Conversely, KMT2D positively regulated tumor-suppressive genes such as NCOR2, RCOR3, TOB2, ZNF136, SIRT1, and PER2. To better characterize the tumor microenvironment (TME), spatial transcriptomic profiling of human GAC tissues revealed regional enrichment of Tregs and immunosuppressive cytokines (e.g., IL10, TGFB1) in KMT2D-low regions. Furthermore, spatial epigenomic profiling (spatial CUT&Tag for H3K4me1/2/3 marks) indicated widespread loss of active enhancer marks in immune-regulatory and tumor suppressor genes upon KMT2D depletion. Our single-cell RNA-seq data from GAC primaries, peritoneal carcinomatosis (PC), and matched normals showed that KMT2D-low tumor cells were associated with increased immune infiltration, suggesting a context- specific immunoregulatory role. Interestingly, a subset of KMT2D-high tumors exhibited higher PD-L1 expression, pointing to potential therapeutic stratification.
Together, these findings identify KMT2D as a key tumor suppressor in GAC that shapes both tumor- intrinsic transcriptional programs and the immune TME. Our data provide a rationale for further investigation of KMT2D as a prognostic biomarker and therapeutic target, particularly in the context of immunotherapy responsiveness.
