The mitochondrial protease YME1L regulates type 1 interferon signaling via the STING pathway in AML

Yeast mitochondrial escape 1-like 1 (YME1L) is one of four mitochondrial ATP-dependent proteases responsible for maintaining mitochondrial proteostasis and is the sole ATP-dependent protease acting on substrates in the intermembrane space. Here, we investigated the expression and functional importance of YME1L in acute myeloid leukemia (AML). YME1L protein was upregulated in 6 out of 7 AML cell lines and 17 of 23 primary AML patient samples compared to normal hematopoietic stem cells. Overexpression occurred equally across cytogenetic risk groups of AML. Moreover, high YME1L mRNA expression correlated with inferior 5-year overall survival in AML patients. To evaluate the essentiality of YME1L in AML, we knocked down the protease in AML cell lines (OCI-AML2, NB4, TEX, and THP-1) with shRNA. YME1L knockdown decreased cell proliferation and clonogenic growth in all tested cell lines. Interestingly, YME1L knockdown did not induce cell death as measured by Annexin V/PI staining. Rather, YME1L knockdown induced AML differentiation as evidenced by increased expression of CD14, a marker of monocytic differentiation. Depletion of YME1L with shRNA also reduced the engraftment of TEX cells and primary AML cells in the marrow of NSG immunodeficient mice. To investigate the functional importance of YME1L depletion, we performed RNA sequencing of AML cells after YME1L depletion. Knockdown of YME1L upregulated genes associated with type I interferon (IFN) signaling, defense response to virus, and viral mimicry. We validated the results by real-time PCR and ELISA, confirming the upregulation of IFN-beta, IFN-gamma, ISG15, IFI44, and IFIT2 following YME1L knockdown. We demonstrated that activation of IFN signaling was secondary to activation of the cGAS-STING pathway as pharmacological inhibition of STING abolished the upregulation of IFN signaling after YME1L depletion. cGAS-STING signalling can be activated by the accumulation of double-stranded DNA (dsDNA) in the cytosol. We showed that YME1L knockdown promoted the leakage of dsDNA from the mitochondria into the cytosol. We also demonstrated that dsDNA leaked into the cytosol via the mitochondrial VDAC channel as treatment of AML cells with the VDAC channel inhibitor, VBIT-4, prevented the accumulation of cytosolic dsDNA and the upregulation of IFN signaling after YME1L knockdown in AML cells. In summary, we demonstrated that YME1L is overexpressed in a subset of AML cell lines and primary patient samples and is required for AML proliferation and clonogenic growth. YME1L regulates the leakage of mtDNA into the cytoplasm, activation of the cGAS-STING-IFN axis, and controls AML differentiation. Thus, we have uncovered novel functions for the mitochondrial protease YME1L and suggest that targeting YME1L may be a novel strategy in the case of some AML patients.