NSD2 Overexpression in Myeloma Enhances Dependency on Mitochondrial High Energy Phosphate Transport Facilitated by Adenylate Kinase 2.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE245150 | GEO | 2024/10/07
REPOSITORIES: GEO
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Project description:Chromosomal translocation t(4;14), a driver of NSD2 overexpression, remains a negative prognostic factor in multiple myeloma (MM). A genome-wide CRISPR screen in MM cells identified adenylate kinase 2 (AK2) as an NSD2-driven vulnerability. AK2 depletion in t(4;14) MM cells inhibited cell growth in vitro and in vivo, impaired protein folding in the ER and increased sensitivity to proteasome inhibition, consistent with a defect in shuttling ATP from the mitochondria. Moreover, AK2 suppression decreased intracellular NADP(H) critical for thioredoxin reduction, which is key for deoxyribonucleotides (dNTP) synthesis, leading to DNA replication stress and apoptosis. The increased dependence on AK2 was attributed to insufficient creatine production due to NSD2-mediated diversion of one-carbon metabolism to the epigenome and away from S-adenosylmethionine dependent creatine synthesis. Correspondingly, supplementation with creatine restored NADP(H) levels and rescued AK2-deficient cells from apoptosis. These findings revealed a novel metabolic susceptibility and promising therapeutic strategy for targeting t(4;14) MM.
2024-10-07 | GSE245149 | GEO
Project description:Chromosomal translocation t(4;14), a driver of NSD2 overexpression, remains a negative prognostic factor in multiple myeloma (MM). A genome-wide CRISPR screen in MM cells identified adenylate kinase 2 (AK2) as an NSD2-driven vulnerability. AK2 depletion in t(4;14) MM cells inhibited cell growth in vitro and in vivo, impaired protein folding in the ER and increased sensitivity to proteasome inhibition, consistent with a defect in shuttling ATP from the mitochondria. Moreover, AK2 suppression decreased intracellular NADP(H) critical for thioredoxin reduction, which is key for deoxyribonucleotides (dNTP) synthesis, leading to DNA replication stress and apoptosis. The increased dependence on AK2 was attributed to insufficient creatine production due to NSD2-mediated diversion of one-carbon metabolism to the epigenome and away from S-adenosylmethionine dependent creatine synthesis. Correspondingly, supplementation with creatine restored NADP(H) levels and rescued AK2-deficient cells from apoptosis. These findings revealed a novel metabolic susceptibility and promising therapeutic strategy for targeting t(4;14) MM.
2024-10-07 | GSE245148 | GEO
Project description:NSD2 Overexpression in Myeloma Enhances Dependency on Mitochondrial High Energy Phosphate Transport Facilitated by Adenylate Kinase 2.
| PRJNA1027238 | ENA
Project description:NSD2 Overexpression in Myeloma Enhances Dependency on Mitochondrial High Energy Phosphate Transport Facilitated by Adenylate Kinase 2 [AS_RS]
| PRJNA1027251 | ENA
Project description:NSD2 Overexpression in Myeloma Enhances Dependency on Mitochondrial High Energy Phosphate Transport Facilitated by Adenylate Kinase 2 [AS_CR]
| PRJNA1027240 | ENA
Project description:Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg(2+) cofactor activates two distinct molecular events: phosphoryl transfer (>10(5)-fold) and lid opening (10(3)-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10(3)-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.
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Project description:Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme.
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Project description:The elastic network interpolation (ENI) (Kim et al., Biophys J 2002;83:1620-1630) is a computationally efficient and physically realistic method to generate conformational transition intermediates between two forms of a given protein. However it can be asked whether these calculated conformations provide good representatives for these intermediates. In this study, we use ENI to generate conformational transition intermediates between the open form and the closed form of adenylate kinase (AK). Based on C(alpha)-only intermediates, we construct atomic intermediates by grafting all the atoms of known AK structures onto the C(alpha) atoms and then perform CHARMM energy minimization to remove steric conflicts and optimize these intermediate structures. We compare the energy profiles for all intermediates from both the CHARMM force-field and from knowledge-based energy functions. We find that the CHARMM energies can successfully capture the two energy minima representing the open AK and closed AK forms, while the energies computed from the knowledge-based energy functions can detect the local energy minimum representing the closed AK form and show some general features of the transition pathway with a somewhat similar energy profile as the CHARMM energies. The combinatorial extension structural alignment (Shindyalov et al., 1998;11:739-747) and the k-means clustering algorithm are then used to show that known PDB structures closely resemble computed intermediates along the transition pathway.
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Project description:While fast folding of small proteins has been relatively well characterized by experiments and theories, much less is known for slow folding of larger proteins, for which recent experiments suggested quite complex and rich folding behaviors. Here, we address how the energy landscape theory can be applied to these slow folding reactions. Combining the perfect-funnel approximation with a multiscale method, we first extended our previous atomic-interaction based coarse grained (AICG) model to take into account local flexibility of protein molecules. Using this model, we then investigated the energy landscapes and folding routes of two proteins with complex topologies: a multidomain protein adenylate kinase (AKE) and a knotted protein 2ouf-knot. In the AKE folding, consistent with experimental results, the kinetic free energy surface showed several substates between the fully unfolded and native states. We characterized the structural features of these substates and transitions among them, finding temperature-dependent multiroute folding. For protein 2ouf-knot, we found that the improved atomic-interaction based coarse-grained model can spontaneously tie a knot and fold the protein with a probability up to 96%. The computed folding rate of the knotted protein was much slower than that of its unknotted counterpart, in agreement with experimental findings. Similar to the AKE case, the 2ouf-knot folding exhibited several substates and transitions among them. Interestingly, we found a dead-end substate that lacks the knot, thus suggesting backtracking mechanisms.
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Project description:Oceanic eddy-induced meridional heat transport (EHT) is an important process in the Southern Ocean heat budget, the variability of which significantly modulates global meridional overturning circulation (MOC) and Antarctic sea-ice extent. Although it is recognized that mesoscale eddies with scales of ~40-300 km greatly contribute to the EHT, the role of submesoscale eddies with scales of ~1-40 km remains unclear. Here, using two state-of-the-art high-resolution simulations (resolutions of 1/48° and 1/24°), we find that submesoscale eddies significantly enhance the total poleward EHT in the Southern Ocean with an enhancement percentage reaching 19-48% in the Antarctic Circumpolar Current band. By comparing the eddy energy budgets between the two simulations, we detect that the primary role of submesoscale eddies is to strengthen mesoscale eddies (and thus their heat transport capability) through inverse energy cascade rather than directly through submesoscale heat fluxes. Due to the submesoscale-mediated enhancement of mesoscale eddies in the 1/48° simulation, the clockwise upper cell and anti-clockwise lower cell of the residual-mean MOC in the Southern Ocean are weakened and strengthened, respectively. This finding identifies a potential route to improve the mesoscale parameterization in climate models for more accurate simulations of the MOC and sea ice variability in the Southern Ocean.
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