(OA-39) Targeting PHF19 Inhibits Myeloma progression and Increases IMiDs Sensitivity by Epigenetically Regulating MYC and IRF4 Pathway

Immunomodulatory drugs (IMiDs) basesd immunotherapy has greatly improved the prognosis of multiple myeloma (MM) patients. However, drug resistance remains a significant challenge, and MM is currently incurable. Epigenetic aberration is an important feature of MM, associated with disease progression and drug resistance, and urgently needed to be explored to lay the foundation for improving patient survival.

Methods:

We performed RNA-seq on primary CD138⁺ bone marrow mononuclear cells (BMMCs) from MM patients with differential responses to IMiD-based combination immunotherapy. PHF19 knockdown (KD) MM cell lines were generated. Cell proliferation, apoptosis and cell cycle upon PHF19 KD were measured using CCK-8 assay and flow cytometry. IMiDs sensitivity was evaluated in PHF19 KD cells. RNA-seq and ATAC-seq were conducted in PHF19 KD cells to further explore mechanisms.

Results:

RNA-seq analysis of myeloma patients’ samples revealed that MYC pathway was activated in non-responders (n=8) to immunotherapy compared to responders (n=8). Through integrative analysis of upregulated genes in non-responders and survival-associated genes from the MMRF-CoMMpass dataset, we identified epigenetic regulator PHF19 as the top correlated gene with both therapy resistance and poor patient survival outcomes. PHF19 KD impaired cell proliferation and induced cell apoptosis in MM. Mechanistically, RNA-seq revealed significant downregulation of MYC target and Shaffer IRF4 pathways in PHF19-KD cells, partly mirroring the dysregulated signaling observed in non-responders' myeloma cells. Meanwhile, RT-qPCR and Western blot confirmed reductions of MYC and IRF4 at both mRNA and protein levels upon PHF19 depletion. Since PHF19 is an epigenetic regulator, we performed ATAC-seq in PHF19 KD cells and found widespread reduction in genomic accessibility at multiple gene loci. An integrated analysis of RNA-seq and ATAC-seq identified 391 overlapping genes, which enriched in cell cycle pathway. Notably, MYC and IRF4 were involved in those overlapping genes, indicating that PHF19 could maintain the expression of MYC and IRF4 directly through its epigenetic regulatory function. Downregulation of MYC and IRF4 are crucial for IMiDs-mediated cell cytotoxicity. Strikingly, we found that IMiDs sensitivity increased in PHF19 KD cells, in which IMiDs induced more pronounced suppression of MYC and IRF4.

Conclusions:

PHF19 expression was elevated in non-responders to combination immunotherapy. PHF19 directly regulated MYC and IRF4 by modulating gene accessibility. Targeting PHF19/MYC /IRF4 axis enhanced myeloma cell sensitivity to IMiDs, suggesting PHF19 as a promising epigenetic target to suppress myeloma progression and overcome drug resistance.