The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness

Mitochondrial metabolites regulate leukaemic and normal stem cells by affecting epigenetic marks. How mitochondrial enzymes localize to the nucleus to control stem cell function is less understood. We discovered that the mitochondrial metabolic enzyme hexokinase 2 (HK2) localizes to the nucleus in leukaemic and normal haematopoietic stem cells. Overexpression of nuclear HK2 increases leukaemic stem cell properties and decreases differentiation, whereas selective nuclear HK2 knockdown promotes differentiation and decreases stem cell function. Nuclear HK2 localization is phosphorylation-dependent, requires active import and export, and regulates differentiation independently of its enzymatic activity. HK2 interacts with nuclear proteins regulating chromatin openness, increasing chromatin accessibilities at leukaemic stem cell-positive signature and DNA-repair sites. Nuclear HK2 overexpression decreases double-strand breaks and confers chemoresistance, which may contribute to the mechanism by which leukaemic stem cells resist DNA-damaging agents. Thus, we describe a non-canonical mechanism by which mitochondrial enzymes influence stem cell function independently of their metabolic function.

Thomas, Egan et al. report that hexokinase 2 localizes to the nucleus of leukaemic and normal haematopoietic cells to maintain stemness by interacting with nuclear proteins and modulating chromatin accessibility independently of its kinase activity.

IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells

AML cells are arranged in a hierarchy with stem/progenitor cells giving rise to more differentiated bulk cells. Despite the importance of stem/progenitors in the pathogenesis of AML, the determinants of the AML stem/progenitor state are not fully understood. Through a comparison of genes that are significant for growth and viability of AML cells by way of a CRISPR screen, with genes that are differentially expressed in leukemia stem cells (LSC), we identified importin 11 (IPO11) as a novel target in AML. Importin 11 (IPO11) is a member of the importin β family of proteins that mediate transport of proteins across the nuclear membrane. In AML, knockdown of IPO11 decreased growth, reduced engraftment potential of LSC, and induced differentiation. Mechanistically, we identified the transcription factors BZW1 and BZW2 as novel cargo of IPO11. We further show that BZW1/2 mediate a transcriptional signature that promotes stemness and survival of LSC. Thus, we demonstrate for the first time how specific cytoplasmic-nuclear regulation supports stem-like transcriptional signature in relapsed AML.

The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplex formation and is necessary for AML viability

Neurolysin (NLN) is a zinc metallopeptidase whose mitochondrial function is unclear. We found that NLN was overexpressed in almost half of patients with acute myeloid leukemia (AML), and inhibition of NLN was selectively cytotoxic to AML cells and stem cells while sparing normal hematopoietic cells. Mechanistically, NLN interacted with the mitochondrial respiratory chain. Genetic and chemical inhibition of NLN impaired oxidative metabolism and disrupted the formation of respiratory chain supercomplexes (RCS). Furthermore, NLN interacted with the known RCS regulator, LETM1, and inhibition of NLN disrupted LETM1 complex formation. RCS were increased in patients with AML and positively correlated with NLN expression. These findings demonstrate that inhibiting RCS formation selectively targets AML cells and stem cells and highlights the therapeutic potential of pharmacologically targeting NLN in AML.

Abstract 3784: The metabolic enzyme Hexokinase 2 localizes to the nucleus and regulates stemness in AML through a kinase independent mechanism

Leukemia stem cells are responsible for the initiation and recurrence of AML. Cell differentiation requires the coordination of metabolic state and gene expression programs. It is known that metabolic intermediates can serve as cofactors in epigenetic modifications in the nucleus. Whether metabolic enzymes can directly localize to the nucleus, influence gene expression and regulate stemness in AML is unknown. To identify mitochondrial metabolic enzymes that localize to the nucleus of stem cells we analyzed stem and bulk fractions of 8227 leukemia cells, which are arranged in a hierarchy with functionally defined stem cells in the CD34+CD38- fraction. Hexokinase 2 (HK2) was detected in the nuclear fraction of 8227 cells and nuclear HK2 was increased in 8227 stem cells compared to bulk cells. Conversely, the metabolic enzymes aconitase, citrate synthesase, enolase, fumarase, GAPDH, glucose-6-phosphate isomerase, phosphofructokinase, pyruvate kinase and succinate dehydrogenase A were not detectable in the nuclear fraction of either stem or bulk cells. We confirmed that HK2 was present in the nuclear fraction of OCI-AML2, NB4, HL60 and TEX AML cell lines and 7/9 primary patient samples. To determine whether nuclear HK2 was functionally important for AML stem cells, we overexpressed HK2 tagged with a nuclear localizing sequence (PAAKRVKLD). Over-expression of nuclear localized HK2 enhanced clonogenic growth and engraftment into immune deficient mice. Likewise, over-expression of nuclear localized HK2 blocked differentiation after treatment with all-trans retinoic acid (ATRA). Next, we investigated whether the kinase activity of HK2 was necessary for its nuclear effects on AML stemness and differentiation. We generated a kinase dead mutant of HK2 (D209A, D657A) tagged with a nuclear localizing signal (PAAKRVKLD). Over-expression of nuclear-localized kinase dead HK2 exerted a similar phenotype to overexpressed nuclear HK2 without manipulation of the kinase domain as it enhanced clonogenic growth and blocked cell differentiation after ATRA treatment. To understand the mechanism by which nuclear HK2 influenced AML stemness, we identified proteins that interacted with nuclear HK2 using proximity-dependent biotin labeling (BioID) and mass spectrometry. Proteins involved in DNA damage repair and chromatin remodeling were identified, including exonuclease 3′-5′ domain-containing 2 (EXD2), sirtuin 1 (SIRT1), E3 ubiquitin-protein ligase (URB5) and tyrosyl-DNA phosphodiesterase 2 (TDP2). Thus, our data suggest that nuclear HK2 influences DNA repair, which has been linked to stemness and differentiation. In support of this hypothesis, we identified a PAR binding motif in HK2 and over-expression of nuclear HK2 conferred resistance to the PARP inhibitor, olaparib. In summary, HK2 localizes to the nucleus in AML stem cells and maintains stemness. These effects are independent of its kinase activity. Rather, HK2 may regulate DNA damage repair through a PAR dependent mechanism. Thus, we have identified a new role for metabolic enzymes in the regulation of stemness and differentiation.

Citation Format: Grace Egan, Geethu E. Thomas, Parasvi S. Patel, Jordan Chin, Aaron Botham, Rose Hurren, Neil MacLean, Razq Hakem, Aaron D. Schimmer. The metabolic enzyme Hexokinase 2 localizes to the nucleus and regulates stemness in AML through a kinase independent mechanism [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3784.

Global Interactome Mapping of Mitochondrial Intermembrane Space Proteases Identifies a Novel Function for HTRA2

A number of unique proteases localize to specific sub-compartments of the mitochondria, but the functions of these enzymes are poorly defined. Here, in vivo proximity-dependent biotinylation (BioID) is used to map the interactomes of seven proteases localized to the mitochondrial intermembrane space (IMS). In total, 802 high confidence proximity interactions with 342 unique proteins are identified. While all seven proteases co-localized with the IMS markers OPA1 and CLPB, 230 of the interacting partners are unique to just one or two protease bait proteins, highlighting the ability of BioID to differentiate unique interactomes within the confined space of the IMS. Notably, high-temperature requirement peptidase 2 (HTRA2) interacts with eight of 13 components of the mitochondrial intermembrane space bridging (MIB) complex, a multiprotein assembly essential for the maintenance of mitochondrial cristae structure. Knockdown of HTRA2 disrupts cristae in HEK 293 and OCI-AML2 cells, and leads to increased intracellular levels of the MIB subunit IMMT. Using a cell-free assay it is demonstrated that HTRA2 can degrade recombinant IMMT but not two other core MIB complex subunits, SAMM50 and CHCHD3. The IMS protease interactome thus represents a rich dataset that can be mined to uncover novel IMS protease biology.

Abstract 5489: Characterization of mitochondrial STAT3 (mitostat3) function and the mitoStat3 interactome as a therapeutic strategy for multiple myeloma

The oncogenic transcription factor STAT3 is an appealing therapeutic target in cancer including multiple myeloma (MM) where its inhibition has the potential to downregulate aberrant signaling from various upstream molecules. STAT3 has been studied extensively as a transcription factor however, much less is known about its non-classical functions in the mitochondria and in turn, the role of mitochondrial STAT3 (mitoStat3) in cancer biology. Data suggests that mitoStat3 is critical for mediating Ras-induced oncogenic transformation. As activating mutations of the MAPK pathway are reported in over 50% of myeloma patients, we sought to characterize the function of mitoStat3 in MM.

We first confirmed the presence of STAT3 in the mitochondria of myeloma cell lines, AMO1 and XG6 by Western blot analysis. We next used CRISPR/CAS9 to knockdown STAT3 in XG6 and AMO1 cells, which resulted in inhibition of cell proliferation (XG6 and AMO1), apoptosis (XG6) and reduced oxygen consumption rate as measured by extracellular flux analysis (Seahorse assay). To better define the role of mitoStat3 and to identify indirect strategies to interfere with STAT3 activity, we employed a proximity-dependent Biotin Identification (BioID) method to discover mitoStat3 interacting proteins. BioID is a unique method to screen for physiologically relevant protein interactions that occur in living cells. First, wild-type STAT3 was fused to a mitochondrial localization Signal (MLS-Stat3), cloned into pcDNA5 FRT/TO [MCS]-BirAR118G-FLAG plasmid and transfected into HEK293 TRE-x Flp-In cells. BioID identified 225 high confidence mitoStat3-interacting partners in MLS-Stat3 transfected cells. The most abundant proteins in the mitoStat3 interactome included those with roles in mitochondrial translation and mitochondrial electron transport. Futhermore, mitoStat3 was found to interact with the translocase of inner membrane protein Tim44, which together with Tim23 complex facilitates translocation of proteins into the mitochondrial matrix. Genetic knockdown of Tim23 in XG6 cells resulted in decreased mitoStat3 suggesting that this complex may be involved in the import of STAT3 into the mitochondria. Additional mitoStat3 interacting proteins identified by BioID are currently being validated and will be presented.

Taken together, results support the further exploration of the role of mitoStat3 in myeloma cells. Further, identification of mitoStat3 interacting proteins including Tim44 and others may inform alternative strategies to therapeutically target oncogenic STAT3.

Citation Format: Serges P. Tsofack, Aaron Botham, Zhihua Li, Ellen Nong Wei, Danielle Croucher, Ioulia Jitkova, Neil MacLean, Aaron D. Schimmer, Brian Raught, Suzanne Trudel. Characterization of mitochondrial STAT3 (mitostat3) function and the mitoStat3 interactome as a therapeutic strategy for multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5489.