Mutant KMT2D Rewrites Chromatin and Immune Signals to Drive Follicular Lymphoma

A new study published in Experimental Hematology & Oncology now maps a detailed mechanistic pathway, showing that a specific truncating KMT2D mutation sets off a cascade that begins with altered chromatin marks, passes through a stemness program centered on the enzyme ALDH1A1, and ends with a rewired tumor immune microenvironment mediated by the copper transporter ATP7A.

The research team, led by investigators working with patient samples collected between 2022 and 2025, began with targeted sequencing of 48 follicular lymphoma patients and 31 diffuse large B-cell lymphoma patients. They screened a panel of chromatin-modifying genes, including EZH2, KMT2D, CREBBP, EP300, ARID1A and BCL7A. KMT2D emerged as the most frequently altered gene in follicular lymphoma, with mutations detected in approximately 63 percent of the patients analyzed. The mutation spectrum was dominated by nonsense and frameshift variants, changes that typically truncate the protein and abolish its function. In the TCGA diffuse large B-cell lymphoma dataset, by contrast, KMT2D mutations appeared in about 35 percent of cases, underscoring the particular prominence of this gene in the follicular lymphoma setting.

To probe function, the researchers focused on a specific truncating mutation, KMT2D R1252*, which they had identified in ten paired early-progression samples from their department. Using lentiviral delivery, they generated follicular lymphoma cell lines, RL and SU-DHL-4, that stably expressed either the mutant or the wild-type form of the protein. The results were striking. Cells carrying the mutant KMT2D proliferated significantly faster than controls in CCK-8 assays, and flow cytometry using 7-AAD and Annexin V staining showed a marked reduction in early apoptotic cells. Notably, wild-type KMT2D expression produced no such effects, indicating that the growth advantage was specific to the truncating mutation rather than a consequence of KMT2D overexpression.

RNA sequencing of the engineered RL cells revealed 1,785 differentially expressed genes, including 1,010 upregulated and 775 downregulated genes. Among the most strongly affected were PDK1, upregulated with a fold change of 2.34, and SGK1, upregulated with a fold change of 3.14, while the cell cycle inhibitor p21Cip1, encoded by CDKN1A, was significantly downregulated. Quantitative PCR and western blotting confirmed these changes at the transcript and protein levels, and additional immunoblots showed decreased Bax and cleaved caspase-3 alongside increased Bcl-2 in mutant-expressing cells. KEGG pathway analysis pointed to enrichment in cell death and apoptosis-related signaling, and gene set enrichment analysis highlighted the reactive oxygen species pathway and the G2/M checkpoint.

A central and unexpected finding concerned the epigenetic mark H3K9me3, a trimethylation of histone H3 associated with compact heterochromatin and cellular senescence. Although KMT2D is canonically an H3K4 methyltransferase with no recognized direct role in H3K9 modification, the mutant cells showed markedly reduced H3K9me3 levels by immunofluorescence and immunoblotting. ATAC-seq and ChIP-seq profiling revealed increased chromatin accessibility at distal regulatory regions and at the loci of stemness markers including ALDH1A1, PROM1 and POU5F1, along with reduced H3K9me3 occupancy at the transcription start site of the ALDH1A1 promoter. The authors suggest that the PI3K/PDK1/SGK1 axis, which the literature links to H3K9me3 regulation, may provide a plausible mechanistic bridge, though they acknowledge that the precise mechanism remains to be fully elucidated.

The upregulation of ALDH1A1 proved functionally consequential. KMT2D-mutant cells showed enhanced sphere-forming capacity, a readout of self-renewal, and motif analysis pointed to altered binding of transcription factors such as GATA3, PU.1, IRF and ETS1. When the researchers depleted ALDH1A1 using shRNA in the mutant background, expression of the senescence executors p21Cip1 and p16INK4A rose significantly, senescence-associated secretory phenotype components including IL-8, IL-1β and IFNβ were upregulated, and mitochondrial DNA translocated into the cytoplasm, a change associated with activation of the cGAS-STING innate immune pathway. These results tie the ALDH1A1-driven stemness program to a senescence and immunogenic signaling network that the mutant KMT2D otherwise suppresses.

The pathway extended to copper biology. ChIP-seq data showed that mutant KMT2D altered H3K9me3 occupancy on transposable elements, with abundant LINE1 retrotransposons and ATP7A binding motif variations detected, and the mutant cells overexpressed ATP7A together with the ferroptosis-resistance transporter SLC7A11. When the team silenced ATP7A, SLC7A11 levels fell, intracellular copper retention increased, and mitochondrial ultrastructure changed, with reduced matrix swelling and cristae disruption visible by transmission electron microscopy. Cell death inhibitor experiments suggested that erastin, a ferroptosis inducer, notably impeded the growth of mutant cells, and the mutant cells accumulated reduced glutathione and showed reduced lipid ROS, consistent with an antioxidant, ferroptosis-protected state maintained through the ATP7A-SLC7A11 axis.

The immune consequences were examined in co-culture and in vivo. When peripheral blood mononuclear cells were co-cultured with mutant KMT2D-expressing RL cells, regulatory T cells and M2 macrophages emerged as the most prominently altered populations, and CIBERSORT deconvolution of transcriptomic data showed elevated enrichment scores for CD8 T cells, Tregs and M2 macrophages in mutant samples. Mutant cells also secreted higher levels of the immunosuppressive cytokines IL-10 and IL-4 while reducing proinflammatory cytokine expression. In a conditional Kmt2d knockout mouse model driven by Cd19-Cre, the knockout animals developed modest splenomegaly by week 10 that did not reach statistical significance, but their spleens showed a pronounced increase in Treg recruitment and follicular hyperplasia of B220-positive B lymphocytes. Multiplex immunohistochemistry on patient lymph node specimens confirmed high PD-L1 expression, colocalization of PD-L1 with FoxP3, and elevated ATP7A with H3K9me3-ALDH1A1 colocalization in KMT2D-mutant cases.

The authors frame the work as delineating a central molecular network through which mutant KMT2D operates in follicular lymphoma: relief of H3K9me3-mediated repression, activation of PDK1/SGK1 signaling and an ALDH1A1-driven stemness program, and ATP7A upregulation that rewires copper homeostasis and redox balance while reshaping the immune microenvironment. They propose that combining ATP7A-mediated cuproptosis agonists with immune checkpoint inhibitors may hold clinical promise, building on evidence that immunogenic cell death can enhance anti-PD-1 efficacy. However, they are explicit about the limits of the current evidence: canonical hallmarks of immunogenic cell death remain to be fully examined, and validation in more physiologically relevant settings is still needed before ALDH1A1 inhibition can be considered an actionable therapeutic vulnerability. The paradoxical coexistence of enriched CD8 T cells with an immunosuppressive milieu in mutant tumors also invites further study of how inhibitory cytokines and contact-dependent mechanisms blunt cytotoxicity in this disease.

For now, the study offers a mechanistic rationale for therapeutic targeting of the KMT2D pathway and positions ALDH1A1 as a candidate epigenetic therapeutic target in KMT2D-mutant follicular lymphoma. The RNA sequencing data generated in the study have been deposited in the Gene Expression Omnibus under accession number GSE335304, allowing independent verification of the transcriptomic findings. As with any preclinical work built on engineered cell lines, small patient cohorts and early mouse phenotypes, the translational distance remains substantial, but the mapped circuitry from a single recurrent mutation to chromatin state, stemness and immune evasion gives researchers a concrete set of intervention points to test.

Subject of Research: How KMT2D mutations reprogram chromatin, stemness and the immune microenvironment in follicular lymphoma

Article Title: Dysregulated KMT2D mutant targeting immunogenic rewiring to overcome epigenetic entropy promotes follicular lymphomagenesis

Article References: Zhu, Y., Yao, J., Jiang, Y., Lai, Q., Chen, Q., Zhang, J., Deng, M., Lin, Z., Luo, Y., Li, Z., Liu, L., Zheng, Z., Zha, J., & Xu, B. (2026). Dysregulated KMT2D mutant targeting immunogenic rewiring to overcome epigenetic entropy promotes follicular lymphomagenesis. Experimental Hematology & Oncology, 15(1), Article 95. https://doi.org/10.1186/s40164-026-00829-6

Image Credits: AI Generated

DOI: 10.1186/s40164-026-00829-6

Keywords: follicular lymphoma, KMT2D, H3K9me3, ALDH1A1, ATP7A, epigenetics, chromatin, tumor microenvironment, copper homeostasis, B-cell lymphoma, SGK1, SLC7A11