Methylation of the epigenetic regulator KMT2D by SMYD2 contributes to therapeutic response in hormone-dependent breast cancer [KMT2D_ChIP_seq]

Activating mutations in PIK3CA, the gene encoding PI3Ka, are frequently found in estrogen receptor (ER+) breast cancer and the combination of the PI3K inhibitor alpelisib with the anti-ER agent fulvestrant is approved for therapy. We have uncovered a key role for the chromatin modifier KMT2D in regulating the ER-PI3K crosstalk. PI3Ka effectors, AKT and SGK, negatively regulate KMT2D through S1331 phosphorylation. When PI3K is inhibited, this regulatory event is lost, leading to increased chromatin recruitment of KMT2D and an upregulation of ER-dependent transcription. Here we discovered a previously undescribed methylation site on KMT2D, at K1330 directly adjacent to S1331, catalyzed by the lysine methyltransferase SMYD2. SMYD2 loss attenuates alpelisib-induced KMT2D chromatin binding. Accordingly, loss of SMYD2 abrogates alpelisib-induced changes in gene expression, including ER-dependent transcription. Knockdown or pharmacological inhibition of SMYD2 sensitizes breast cancer cells, patient-derived organoids, and tumors to PI3K/AKT inhibition and endocrine therapy in part through KMT2D K1330 methylation. Methyl dead knock-in clones of KMT2D phenocopy many of the effects of SMYD2 inhibition on cell and tumor growth, drug response, and transcriptional output. Together, our findings uncover a regulatory cross-talk between posttranslational modifications that plays an important role in fine-tuning the functions of KMT2D at the chromatin. This provides a rationale for epigenetic therapy using SMYD2 inhibitors in combination with PI3Ka/AKT inhibitors for the treatment of ER+/PIK3CA mutant breast cancer. Overall design: ChIP-seq for KMT2D was performed in MCF7 cells with doxycycline-inducible knockdown of SMYD2 to determine the effect of SMYD2 on KMT2D chromatin binding FLAG-SMYD2 CUT & RUN was performed in MCF7 breast cancer cells with overexpression of FLAG-SMYD2 or empty vector in order to assess SMYD2 chromatin binding genome-wide.