Hongkai Ji

Pharmacologic immunosuppression is essential for preventing organ rejection and controlling autoimmunity, but profoundly impairs humoral immunity, increasing the risk of vaccine failure and infection. The mechanisms by which immunosuppressive therapies disrupt human B cell responses remain poorly defined. Here, we identified dysregulated lipid metabolism as a central determinant of impaired vaccine response in solid organ transplant recipients (SOTRs). Using high-dimensional immune profiling, single-cell transcriptomics, and functional metabolic assays, we found that effective B cell responses required a homeostatic balance between lipid synthesis and fatty acid oxidation. The widely used immunosuppressive agent, mycophenolic acid (MPA) was strongly associated with vaccine non-response and induced excessive lipid synthesis, lipid accumulation, and mitochondrial stress in B cells. In contrast, CD11c ⁺ B cells retained the capacity to differentiate into plasmablasts in the presence of MPA through elevated expression of CPT1A, a mitochondrial fatty acid transporter, and enhanced fatty acid oxidation. These cells were found to be a key feature of early effective vaccine responses in healthy individuals and SOTRs. Notably, pharmacologic inhibition of cholesterol synthesis partially restored plasmablast differentiation in the presence of MPA. These findings identify B cell lipid metabolism as a critical and targetable regulator of human humoral immunity during immunosuppression.

Disruption of the epigenetic landscape is of particular interest in acute myeloid leukemia (AML) due to its relatively low mutational burden and frequent occurrence of mutations in epigenetic regulators. In this study, we applied an information-theoretic analysis of methylation potential energy landscapes, capturing changes in mean methylation level and methylation entropy, to comprehensively analyze DNA methylation stochasticity in subtypes of AML defined by mutually exclusive genetic mutations. AML subtypes with CEBPA double mutation and those with IDH mutations were identified as distinctly high-entropy subtypes, marked by methylation disruption over a convergent set of genes. The analysis revealed a core program of epigenetic landscape disruption across all AML subtypes; discordant methylation stochasticity, transcriptional dysregulation, and altered chromatin accessibility converged on functionally important leukemic signatures. Demonstration of a relationship between methylation entropy and gene expression variability connected the disruption of the epigenetic landscape to transcription in AML. Finally, the hypomethylating drug decitabine led to reduction of DNA methylation entropy specifically in IDH2-mutant AML cells. Overall, this approach identified a convergent program of epigenetic dysregulation in leukemia, clarifying the contribution of specific genetic mutations to stochastic disruption of the epigenetic and transcriptional landscapes of AML.Significance:DNA methylation stochasticity, variable gene expression, and altered chromatin accessibility converge on key leukemic regulators across AML subtypes, suggesting a genotype-independent role of stochastic disruption of the epigenetic landscape in mediating leukemogenesis.

Figure S7: Transcriptional dysregulation recapitulates leukemia signatures.

HOMER transcription factor binding motif enrichment results for CPEL DMRs.

Gene set enrichment analysis of differential expression over the MSigDB C2 gene set collection.

Gene set enrichment analysis of differential expression over MSigDB Hallmark gene set collection.

Convergent differentially expressed genes, and differentially expressed genetic drivers of AML.

CPEL DMRs with associated dMML, dNME, and UC.

Figure S10: Methylation stochasticity relates to gene expression variability within individual AML samples.

Gene expression mean-adjusted variability, variance, and mean in each AML subtype.