The Mitochondrial Protease, Neurolysin (NLN), Regulates Respiratory Chain Supercomplex Formation and Represents a New Therapeutic Target for AML

Our group and others have shown that acute myeloid leukemia (AML) cells have unique mitochondrial characteristics with an increased reliance on oxidative phosphorylation. Through an shRNA screen for new biological vulnerabilities in the mitochondria of AML cells, we identified the mitochondrial protease, neurolysin (NLN). NLN is a zinc metalloprotease whose mitochondrial function is not well understood and whose role in AML growth and viability has not been previously reported.

We analyzed the expression of NLN in AML cells and normal hematopoietic cells. By immunoblotting, NLN was overexpressed in 80% of primary AML patient samples compared to normal hematopoietic cells. Likewise, in an analysis of gene expression databases, NLN mRNA was increased in a subset of AML patient samples, compared to normal hematopoietic cells.

Next, we assessed the effects of knocking down NLN in AML cell lines (OCI-AML2, NB4, and MV4-11) using three independent shRNAs in lentiviral vectors. Target knockdown was confirmed by immunoblotting. NLN knockdown reduced growth in all three tested cell lines by 50-70%. NLN knockdown also targeted the leukemia initiating cells in vitro and in vivo as NLN knockdown reduced the clonogenic growth of AML cells (40-75%) and the engraftment of TEX cells into immune deficient mice by 85%. Taken together, these data suggest that NLN is necessary for the growth of AML cells.

The role of NLN in the mitochondria is not well understood. To gain insight into NLN's mitochondrial function, we investigated NLN's protein interactors using proximity-dependent biotin labeling (BioID). The top hits in the protein-protein interaction screen were mitochondrial matrix proteins and respiratory chain subunits were particularly enriched. Therefore, we measured the effects of NLN knockdown on mitochondrial structure and function. Knockdown of NLN in AML cells reduced basal oxygen consumption without altering reactive oxygen species generation, mitochondrial membrane potential, or mitochondrial mass. No changes were seen in the total levels of respiratory chain complex subunits as measured by immunoblotting on denaturing gels. Respiratory chain complexes assemble into higher order supercomplex structures that maintain the integrity of the mitochondria and promote efficient oxidative metabolism. Therefore, we tested whether NLN is required for the formation of respiratory chain supercomplexes. As measured by blue native polyacrylamide gel electrophoresis, knockdown of NLN impaired the formation of respiratory chain supercomplexes.

Through our BioID analysis, we also identified the mitochondrial Ca^2+/H+ antiporter, LETM1 (leucine zipper-EF-hand containing transmembrane protein 1) as a top interactor with NLN. LETM1 is a known regulator of respiratory chain supercomplex formation. We showed that knockdown of NLN impaired LETM1 assembly, potentially explaining how NLN regulates supercomplex formation.

Finally, we tested if hypoxia influences respiratory chain supercomplex formation and sensitivity to NLN inhibition. OCI-AML2 cells cultured for 72 hours under hypoxic conditions (0.2% O₂) showed impaired assembly of respiratory chain supercomplexes, decreased levels of LETM1 protein, and resistance to NLN knockdown.

Thus, we discovered that the mitochondrial protease NLN regulates oxidative metabolism by controlling the assembly of respiratory chain supercomplexes. Moreover, we highlight NLN as a potential new therapeutic target for AML.