Integrating Clinical Cancer and PTM Proteomics Data Identifies a Mechanism of ACK1 Kinase Activation

Beyond the most common oncogenes activated by mutation (mut-drivers), there likely exists a variety of low-frequency mut-drivers, each of which is a possible frontier for targeted therapy. To identify new and understudied mut-drivers, we developed a machine learning (ML) model that integrates curated clinical cancer data and posttranslational modification (PTM) proteomics databases. We applied the approach to 62,746 patient cancers spanning 84 cancer types and predicted 3,964 oncogenic mutations across 1,148 genes, many of which disrupt PTMs of known and unknown function. The list of putative mut-drivers includes established drivers and others with poorly understood roles in cancer. This ML model is available as a web application. As a case study, we focused the approach on nonreceptor tyrosine kinases (NRTK) and found a recurrent mutation in activated CDC42 kinase-1 (ACK1) that disrupts the Mig6 homology region (MHR) and ubiquitin-association (UBA) domains on the ACK1 C-terminus. By studying these domains in cultured cells, we found that disruption of the MHR domain helps activate the kinase while disruption of the UBA increases kinase stability by blocking its lysosomal degradation. This ACK1 mutation is analogous to lymphoma-associated mutations in its sister kinase, TNK1, which also disrupt a C-terminal inhibitory motif and UBA domain. This study establishes a mut-driver discovery tool for the research community and identifies a mechanism of ACK1 hyperactivation shared among ACK family kinases.

IMPLICATIONS

This research identifies a potentially targetable activating mutation in ACK1 and other possible oncogenic mutations, including PTM-disrupting mutations, for further study.

Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain

Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1 ubiquitin-associated (UBA) domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. No experimentally determined molecular structure of this unusual UBA domain is available. We fused the UBA domain to the 1TEL variant of the translocation ETS leukemia protein sterile alpha motif (TELSAM) crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and crystallize at protein concentrations as low as 0.2 mg/mL. Our studies support a mechanism of 1TEL fusion crystallization and show that 1TEL fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.

The formation of ubiquitin rich condensates triggers recruitment of the ATG9A lipid transfer complex to initiate basal autophagy

Autophagy is an essential cellular recycling process that maintains protein and organelle homeostasis. ATG9A vesicle recruitment is a critical early step in autophagy to initiate autophagosome biogenesis. The mechanisms of ATG9A vesicle recruitment are best understood in the context of starvation-induced non-selective autophagy, whereas less is known about the signals driving ATG9A vesicle recruitment to autophagy initiation sites in the absence of nutrient stress. Here we demonstrate that loss of ATG9A or the lipid transfer protein ATG2 leads to the accumulation of phosphorylated p62 aggregates in the context of basal autophagy. Furthermore, we show that p62 degradation requires the lipid scramblase activity of ATG9A. Lastly, we present evidence that poly-ubiquitin is an essential signal that recruits ATG9A and mediates autophagy foci assembly in nutrient replete cells. Together, our data support a ubiquitin-driven model of ATG9A recruitment and autophagosome formation during basal autophagy.

Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics

We combined efficient sample preparation and ultra-low-flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in rapid label-free analyses. WWA employs large isolation windows to intentionally co-isolate and co-fragment adjacent precursors along with the selected precursor. Optimized WWA increased the number of MS2-identified proteins by ≈40 % relative to standard data-dependent acquisition. For a 40-min LC gradient operated at ≈15 nL/min, we identified an average of 3,524 proteins per single-cell-sized aliquot of protein digest. Reducing the active gradient to 20 min resulted in a modest 10 % decrease in proteome coverage. Using this platform, we compared protein expression between single HeLa cells having an essential autophagy gene, atg9a, knocked out, with their isogenic WT parental line. Similar proteome coverage was observed, and 268 proteins were significantly up- or downregulated. Protein upregulation primarily related to innate immunity, vesicle trafficking and protein degradation.

Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain

Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1-UBA domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. Sequence analysis suggests an unusual architecture for the TNK1 UBA domain, but an experimentally-validated molecular structure is undetermined. To gain insight into TNK1 regulation, we fused the UBA domain to the 1TEL crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. A 1TEL search model enabled solution of the X-ray phases. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and to crystallize at protein concentrations as low as 0.1 mg/mL. Our studies support a mechanism of TELSAM fusion crystallization and show that TELSAM fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.

Abstract 4469: Disruption of ATG9A-dependent basal autophagy sensitizes cancer cells to innate inflammatory signaling

Pathogen-derived nucleic acids are recognized by pattern recognition receptors (PRRs), including cGAS and RIG-I, which trigger the innate immune response by activating IRF3-mediated interferon gene expression. In tumors, high levels of chromosomal instability can also lead to DNA fragments leaking into the cytosol to trigger PRR-mediated interferon response, resulting in pro-inflammatory cytokine secretion from the tumor. This could potentially expose tumor cells to immune attack. However, through mechanisms that are not completely understood, tumor cells dampen the interferon response to escape immune recognition. Previous work demonstrated that loss of ATG9A, but not ATG5, increased inflammatory signaling through the STING-IRF3 cascade, suggesting that perhaps an autophagy-independent function of ATG9A regulates inflammation. Here we found that loss of ATG9A or other upstream regulators of basal autophagy (e.g., ATG101), but not core LC3 lipidation machinery (ATG5 or ATG7), sensitizes cells to dsDNA-induced IRF3 activation and interferon gene expression. We also found that loss of ATG9A or ATG101, but not ATG5 or ATG7, increases the basal activity of the ubiquitin-sensing, IRF3-targeted kinase TBK1, which increases further upon dsDNA treatment. In these ATG9A and ATG101 deficient cells, TBK1 is clustered around large p62-positive condensates that previously been shown to contain large accumulations of LC3. Our preliminary data suggest a model in which ATG9A deletion causes the accumulation of LC3-positive membrane at p62 condensates, which may act as a platform for inflammatory signaling. Our current work focuses on identifying the upstream pathways and core mechanism that regulates IRF3 activation in ATG9A-deficient cells and exploiting this mechanism to improve anti-tumor immunity.

Citation Format: Dasun N. Jayatunge, Tsz-Ming Tsang, Colten M. McEwan, Joshua L. Andersen. Disruption of ATG9A-dependent basal autophagy sensitizes cancer cells to innate inflammatory signaling. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4469.

The Integration of Proteome-Wide PTM Data with Protein Structural and Sequence Features Identifies Phosphorylations that Mediate 14-3-3 Interactions

14-3-3s are abundant proteins that regulate essentially all aspects of cell biology, including cell cycle, motility, metabolism, and cell death. 14-3-3s work by docking to phosphorylated Ser/Thr residues on a large network of client proteins and modulating client protein function in a variety of ways. In recent years, aided by improvements in proteomics, the discovery of 14-3-3 client proteins has far outpaced our ability to understand the biological impact of individual 14-3-3 interactions. The rate-limiting step in this process is often the identification of the individual phospho-serines/threonines that mediate 14-3-3 binding, which are difficult to distinguish from other phospho-sites by sequence alone. Furthermore, trial-and-error molecular approaches to identify these phosphorylations are costly and can take months or years to identify even a single 14-3-3 docking site phosphorylation. To help overcome this challenge, we used machine learning to analyze predictive features of 14-3-3 binding sites. We found that accounting for intrinsic protein disorder and the unbiased mass spectrometry identification rate of a given phosphorylation significantly improves the identification of 14-3-3 docking site phosphorylations across the proteome. We incorporated these features, coupled with consensus sequence prediction, into a publicly available web app, called "14-3-3 site-finder". We demonstrate the strength of this approach through its ability to identify 14-3-3 binding sites that do not conform to the loose consensus sequence of 14-3-3 docking phosphorylations, which we validate with 14-3-3 client proteins, including TNK1, CHEK1, MAPK7, and others. In addition, by using this approach, we identify a phosphorylation on A-kinase anchor protein-13 (AKAP13) at Ser2467 that dominantly controls its interaction with 14-3-3.

Mapping the proximity interactome of ATG9A reveals unexpected dynamics of ULK1 complex proteins

ATG9A is essential for macroautophagy/autophagy and considered to be one of the earliest ATG (autophagy related) proteins recruited to sites of autophagosome biogenesis. Recent data suggest ATG9A vesicles may even form the lipid seed of the autophagosome. However, ATG9A regulation is still poorly understood, which is likely at least partly due to challenges inherent to studying an intracellular transmembrane protein with no apparent enzymatic activity. To help overcome these challenges, we used BioID and quantitative LC-MS/MS to map the proximity interactome of ATG9A, which included entire protein complexes involved in protein trafficking, and proteins implicated in autophagy but previously lacking any physical link to core autophagy machinery. We also unexpectedly found an ATG9A interaction with an ULK1-independent ATG13-ATG101 dimer that promotes autophagy in fed cells.

Abstract 1469: 14-3-3 binding during G1 stabilizes and sequesters PTOV1 to the cytoplasm

Cells must respond to changing environments by modulating signaling and gene expression patterns to maintain homeostasis, health, and viability. Inappropriate responses lead to disease processes, such as cancer. Despite improvements in targeted treatment options, cancer remains the second leading cause of death in the United States, illustrating the need to develop new highly effective targeted therapies. 14-3-3 interacts with a network of proteins to support signaling pathways promoting oncogenesis, metastasis, growth, cellular survival, and chemoresistance in a variety of cancers, including lung, prostate, and breast. We recently identified prostate tumor overexpressed 1 (PTOV1) as a novel 14-3-3 interacting protein promoting tumorigenic gene expression patterns. We showed that 14-3-3 binding sequesters PTOV1 in the cytoplasm and protects PTOV1 from proteasomal degradation. Using double thymidine block synchronization, we now demonstrate that both PTOV1 phosphorylation and total PTOV1 levels peak in G1, prior to PTOV1 translocating into the nucleus during S phase. These data support our model that 14-3-3-PTOV1 binding maintains PTOV1 in the cytoplasm during G1, where it is stabilized to carry out translational regulation. As the cell enters S phase, loss of phosphorylation and the accompanying loss of 14-3-3 binding allows PTOV1 to translocate into the nucleus, carry out relevant nuclear functions, and then be degraded via the proteasome.

Citation Format: Katie L. Pennington, Colten M. McEwan, James Woods, Colin M. Muir, A G Pramoda Sahankumari, Riley Eastmond, Eranga R. Balasooriya, Christina M. Egbert, Katherine K. McCormack, Joshua L. Andersen. 14-3-3 binding during G1 stabilizes and sequesters PTOV1 to the cytoplasm [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1469.

Mechanistic discoveries and simulation-guided assay optimization of portable hormone biosensors with cell-free protein synthesis

Nuclear receptors (NRs) influence nearly every system of the body and our lives depend on correct NR signaling. Thus, a key environmental and pharmaceutical quest is to identify and detect chemicals which interact with nuclear hormone receptors, including endocrine disrupting chemicals (EDCs), therapeutic receptor modulators, and natural hormones. Previously reported biosensors of nuclear hormone receptor ligands facilitated rapid detection of NR ligands using cell-free protein synthesis (CFPS). In this work, the advantages of CFPS are further leveraged and combined with kinetic analysis, autoradiography, and western blot to elucidate the molecular mechanism of this biosensor. Additionally, mathematical simulations of enzyme kinetics are used to optimize the biosensor assay, ultimately lengthening its readable window by five-fold and improving sensor signal strength by two-fold. This approach enabled the creation of an on-demand thyroid hormone biosensor with an observable color-change readout. This mathematical and experimental approach provides insight for engineering rapid and field-deployable CFPS biosensors and promises to improve methods for detecting natural hormones, therapeutic receptor modulators, and EDCs.

SGK2, 14-3-3, and HUWE1 Cooperate to Control the Localization, Stability, and Function of the Oncoprotein PTOV1

PTOV1 is an oncogenic protein, initially identified in prostate cancer, that promotes proliferation, cell motility, and invasiveness. However, the mechanisms that regulate PTOV1 remain unclear. Here, we identify 14-3-3 as a PTOV1 interactor and show that high levels of 14-3-3 expression, like PTOV1, correlate with prostate cancer progression. We discover an SGK2-mediated phosphorylation of PTOV1 at S36, which is required for 14-3-3 binding. Disruption of the PTOV1-14-3-3 interaction results in an accumulation of PTOV1 in the nucleus and a proteasome-dependent reduction in PTOV1 protein levels. We find that loss of 14-3-3 binding leads to an increase in PTOV1 binding to the E3 ubiquitin ligase HUWE1, which promotes proteasomal degradation of PTOV1. Conversely, our data suggest that 14-3-3 stabilizes PTOV1 protein by sequestering PTOV1 in the cytosol and inhibiting its interaction with HUWE1. Finally, our data suggest that stabilization of the 14-3-3-bound form of PTOV1 promotes PTOV1-mediated expression of cJun, which drives cell-cycle progression in cancer. Together, these data provide a mechanism to understand the regulation of the oncoprotein PTOV1. IMPLICATIONS: These findings identify a potentially targetable mechanism that regulates the oncoprotein PTOV1.

BioID reveals an ATG9A interaction with ATG13-ATG101 in the degradation of p62/SQSTM1-ubiquitin clusters

ATG9A, the only multi-pass transmembrane protein among core ATG proteins, is an essential regulator of autophagy, yet its regulatory mechanisms and network of interactions are poorly understood. Through quantitative BioID proteomics, we identify a network of ATG9A interactions that includes members of the ULK1 complex and regulators of membrane fusion and vesicle trafficking, including the TRAPP, EARP, GARP, exocyst, AP-1, and AP-4 complexes. These interactions mark pathways of ATG9A trafficking through ER, Golgi, and endosomal systems. In exploring these data, we find that ATG9A interacts with components of the ULK1 complex, particularly ATG13 and ATG101. Using knockout/reconstitution and split-mVenus approaches to capture the ATG13-ATG101 dimer, we find that ATG9A interacts with ATG13-ATG101 independently of ULK1. Deletion of ATG13 or ATG101 causes a shift in ATG9A distribution, resulting in an aberrant accumulation of ATG9A at stalled clusters of p62/SQSTM1 and ubiquitin, which can be rescued by an ULK1 binding-deficient mutant of ATG13. Together, these data reveal ATG9A interactions in vesicle-trafficking and autophagy pathways, including a role for an ULK1-independent ATG13 complex in regulating ATG9A.

Abstract 2295: SGK2, 14-3-3, and HUWE1 coordinately regulate the localization and stability of PTOV1

PTOV1 is an oncogenic protein, initially identified in prostate cancer, that promotes proliferation, cell motility, and invasiveness. However, the mechanism of PTOV1 regulation is poorly understood. To understand these mechanisms, we identify 14-3-3 as a PTOV1 interactor and show that high levels of 14-3-3 expression, like PTOV1, correlate with prostate cancer progression. Further, we found that SGK2-mediated phosphorylation of PTOV1 is required for 14-3-3 binding. This phosphorylation occurs in a cell cycle-dependent manner and peaks in the G1 phase. Disruption of the PTOV1-14-3-3 interaction results in an accumulation of PTOV1 in the nucleus and a proteasome-dependent reduction in PTOV1 protein levels. To understand the effect of 14-3-3 on PTOV1 stability, we found that loss of 14-3-3 binding leads to an increase in PTOV1 binding to the E3 ubiquitin ligase HUWE1, which promotes proteasomal degradation of PTOV1. Conversely, our data suggest that 14-3-3 stabilizes PTOV1 protein by sequestering PTOV1 in the cytosol and inhibiting its interaction with HUWE1. Finally, our data suggest that stabilization of the 14-3-3-bound form of PTOV1 promotes PTOV1-mediated expression of cJun. Together, these data provide a first mechanism to understand the regulation of PTOV1 stability, localization, and function within the cell.

Citation Format: Katie L. Pennington, James Woods, Colin Muir, Colten M. McEwan, Pramoda S. Aththota Gamage, Riley J. Eastmond, Crissy M. Egbert, Tyler Heaton, Stephen R. Piccolo, Joshua L. Andersen. SGK2, 14-3-3, and HUWE1 coordinately regulate the localization and stability of PTOV1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2295.

Abstract 2304: Regulation of the oncogenic tyrosine kinase ACK1 through ubiquitin-dependent mechanism

ACK1 is an oncogene in the ACK family of non-receptor tyrosine kinases (NRTK). In humans, ACK1 is located on chromosome 3q29, a region that is frequently amplified in a variety of cancers including prostate, lung and breast. The ACK kinase family has a unique domain arrangement with, most notably, a putative ubiquitin association (UBA) domain at their C-termini. In the present study, we focus on understanding the ubiquitin-binding nature of the ACK1 UBA and its role in kinase regulation. Structural modeling and sequence analysis suggest that the ACK1 UBA diverges from many other UBAs but shares similarities with the ACK family kinase, TNK1. We found that the ACK family UBA has a remarkably high affinity for diverse poly-ubiquitin linkages with dissociation constants in the low nanomolar range. Our preliminary data suggest that a non-covalent interaction between the UBA and ubiquitin is necessary for ACK kinase activation in cell culture systems. Furthermore, our preliminary data suggest this interaction is sufficient to induce ACK1 activation in vitro. In support of the idea that the UBA is important for ACK1 activation, we identified a variety of cancer patient mutations that disrupt the ACK1 UBA, which we are currently testing for oncogenic activity. Lastly, we have identified small molecule inhibitors of ACK with low nanomolar IC50 values in ACK1-driven cells. Altogether, our data suggest a model of ACK1 activation that involves direct, non-covalent interaction with ubiquitin and potential therapeutic approaches to inhibit ACK1 in cancer.

Citation Format: Eranga Roshan Balasooriya Loku Balasooriyage, Jacob Owen, Jack Gashler, Colin Muir, Katie Pennington, James Moody, Joshua L. Andersen. Regulation of the oncogenic tyrosine kinase ACK1 through ubiquitin-dependent mechanism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2304.

Abstract LB109: A critical role for SIRT5 in acute myeloid leukemia metabolism

Standard of care for AML includes chemotherapy and stem cell transplant, with 5-year survival rates <30%. We sought to identify genes critical to AML cells, irrespective of mutational status, and performed an shRNA screen targeting 1,287 genes on 12 AML patient samples. This screen identified Sirtuin 5 (SIRT5) as a top candidate. SIRT5 is the only known enzyme with desuccinylase, demalonylase, and/or deglutarylase activity and we are the first to report the dependence of AML cells on SIRT5. Next, we stably transduced a panel of AML cell lines with doxycycline (dox)-inducible shSIRT5 (dox-shSIRT5). SIRT5 knockdown (KD) strongly inhibited cell growth, colony formation and increased apoptosis in 15/22 lines (SIRT5-dependent), while 7/22 lines were SIRT5-independent. SIRT5 dependence did not correlate with AML-related mutations nor basal SIRT5 expression. SIRT5 KD in primary AML samples (N=25) revealed a therapeutic window (~50% reduction), with no effect in CB samples (N=5). We examined the requirement of SIRT5 in vivo using three mouse models of leukemia. In a xenograft model with AML cell lines, SIRT5 KD indefinitely prolonged survival of mice injected with SIRT5-dependent cells with no sign of leukemia. Bone marrow transplant with transduced (MLL-AF9 or BCR-ABL1) SIRT5 null cells showed reduced leukemia cell burden and splenomegaly, and significantly prolonged survival. FLT3-ITD-driven disease was also blunted by the absence of SIRT5 in a genetic knockout mouse model. Mechanically, SIRT5 KD profoundly reduced oxidative phosphorylation (OXPHOS) and glycolysis. Additionally, SIRT5 KD increased mitochondrial superoxide selectively in annexin V-negative, SIRT5-dependent cells. Concomitant, ectopic expression of SOD2 abrogated the increase in superoxide, rescued cells from apoptosis, and rescued the colony formation deficit. Untargeted metabolomics revealed RNA charging and alanine and serine metabolism as top metabolic pathways regulated by SIRT5, with glutaminase (GLS) and α-ketoglutarate identified as potential upstream regulators. Metabolic tracing experiments with [13C5,15N2]-glutamine confirmed disrupted glutamine metabolism in SIRT5-dependent cells. Together, these results indicate that SIRT5 is required to regulate glutamine flux to sustain redox homeostasis and/or anabolism. NRD167, a novel SIRT5 inhibitor, was used to target SIRT5 in AML. NRD167 reduced cell proliferation, induced apoptosis, and reduced OXPHOS in SIRT5-dependent but not SIRT5-independent cells. NRD167 inhibited colony formation from AML patient samples, but not in CB samples. An AML patient-derived xenograft model trended toward prolonged survival following ex vivo treatment with NRD167. Our data suggest that the majority of AML samples are dependent on SIRT5 and that inhibition preferentially targets AML cells, implicating SIRT5 as a therapy target in AML.

Citation Format: Dongqing Yan, Anca Franzini, Anthony D. Pomicter, Brayden J. Halverson, Orlando Antelope, Clinton C. Mason, Jonathan M. Ahmann, Anna V. Senina, Courtney L. L. Jones, Matthew S. Zabriskie, Hein Than, Michael J. Xiao, Alexandria van Scoyk, Ami B. Patel, William L. L. Heaton, Shawn C. Owen, Joshua L. Andersen, Christina M. Egbert, Julie A. Reisz, Angelo D'Alessandro, James E. Cox, Kevin C. Gantz, Hannah M. Redwine, Siddharth M. Iyer, Jamshid S. Khorashad, Nima Rajabi, Christian A. Olsen, Thomas O'Hare, Michael W. Deininger. A critical role for SIRT5 in acute myeloid leukemia metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB109.

Abstract 2306: The ubiquitin-binding non-receptor tyrosine kinase TNK1 is regulated by a MARK-mediated interaction with 14-3-3

Tyrosine non-receptor kinase 1 (TNK1) is a poorly characterized member of the ACK family of non-receptor tyrosine kinases. We identified TNK1 as a mediator of cell survival in subsets of primary hematological malignancies. Previous studies have indicated a role for TNK1 in driving oncogenic potential; however, the function, regulation, and substrates of TNK1 still remain unknown. We identified an interaction between TNK1 and 14-3-3 that is promoted by a MARK-mediated phosphorylation at S502 on TNK1. 14-3-3 binding sequesters TNK1 to the cytosol. Upon the release of 14-3-3 binding, TNK1 moves to perinuclear puncta and is in a highly active state. This highly active form of TNK1 is able to drive growth factor independent proliferation of lymphoid cells in culture and in mice more potently than TNK1 WT. A unique feature of TNK1 is its C-terminal ubiquitin association domain (UBA) domain. In vitro ubiquitin pulldowns indicate a high affinity between the TNK1 UBA and polyubiquitin of varying linkages, with dissociation constants in the low nanomolar range. Mutation of residues within ubiquitin-binding interfaces of the UBA and ubiquitin leads to a reduction of ubiquitin association and a marked shift of TNK1 from perinuclear puncta to a diffuse cytosolic localization. Importantly, we show that loss of ubiquitin binding reduces TNK1 activity and oncogenic signaling. Taken together, our data uncovers a 14-3-3 and UBA-mediated mechanism of TNK1 regulation.

Citation Format: Christina Marie Egbert, Tsz Yin Chan, Logan Larsen, Eranga Roshan Balasooriya, Kristina Kohler, Jeremy Tsang, Madison Frey, Julia Maxson, David Huang, Kenneth A. Christensen, James Moody, Jeffrey W. Tyner, Joshua L. Andersen. The ubiquitin-binding non-receptor tyrosine kinase TNK1 is regulated by a MARK-mediated interaction with 14-3-3 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2306.

Cu/Zn Superoxide Dismutase (Sod1) regulates the canonical Wnt signaling pathway

Cu/Zn Superoxide Dismutase (Sod1) catalyzes the disproportionation of cytotoxic superoxide radicals (O2•-) into oxygen (O2) and hydrogen peroxide (H2O2), a key signaling molecule. In Saccharomyces cerevisiae, we previously discovered that Sod1 participates in an H2O2-mediated redox signaling circuit that links nutrient availability to the control of energy metabolism. In response to glucose and O2, Sod1-derived H2O2 stabilizes a pair of conserved plasma membrane kinases - yeast casein kinase 1 and 2 (Yck1/2) - that signal glycolytic growth and the repression of respiration. The Yck1/2 homolog in humans, casein kinase 1-γ (CK1γ), is an integral component of the Wingless and Int-1 (Wnt) signaling pathway, which is essential for regulating cell fate and proliferation in early development and adult tissue and is dysregulated in many cancers. Herein, we establish the conservation of the SOD1/YCK1 redox signaling axis in humans by finding that SOD1 regulates CK1γ expression in human embryonic kidney 293 (HEK293) cells and is required for canonical Wnt signaling and Wnt-dependent cell proliferation.

SIRT5 IS A DRUGGABLE METABOLIC VULNERABILITY IN ACUTE MYELOID LEUKEMIA

We discovered that the survival and growth of many primary acute myeloid leukemia (AML) samples and cell lines, but not normal CD34+ cells, are dependent on SIRT5, a lysine deacylase implicated in regulating multiple metabolic pathways. Dependence on SIRT5 is genotype-agnostic and extends to RAS- and p53-mutated AML. Results were comparable between SIRT5 knockdown and SIRT5 inhibition using NRD167, a potent and selective SIRT5 inhibitor. Apoptosis induced by SIRT5 disruption is preceded by reductions in oxidative phosphorylation and glutamine utilization, and an increase in mitochondrial superoxide that is attenuated by ectopic superoxide dismutase 2. These data indicate that SIRT5 controls and coordinates several key metabolic pathways in AML and implicate SIRT5 as a vulnerability in AML.

Mechanisms of SOD1 regulation by post-translational modifications

SOD1 is commonly known for its ROS scavenging activity, but recent work has uncovered additional roles in modulating metabolism, maintaining redox balance, and regulating transcription. This new paradigm of expanded SOD1 function raises questions regarding the regulation of SOD1 and the cellular partitioning of its biological roles. Despite decades of research on SOD1, much of which focuses on its pathogenic role in amyotrophic lateral sclerosis, relatively little is known about its regulation by post-translational modifications (PTMs). However, over the last decade, advancements in mass spectrometry have led to a boom in PTM discovery across the proteome, which has also revealed new mechanisms of SOD1 regulation by PTMs and an array of SOD1 PTMs with high likelihood of biological function. In this review, we address emerging mechanisms of SOD1 regulation by post-translational modifications, many of which begin to shed light on how the various functions of SOD1 are regulated within the cell.

Proteomic Analysis of Resistance of Gram-Negative Bacteria to Chlorhexidine and Impacts on Susceptibility to Colistin, Antimicrobial Peptides, and Ceragenins

Use of chlorhexidine in clinical settings has led to concerns that repeated exposure of bacteria to sub-lethal doses of chlorhexidine might result in chlorhexidine resistance and cross resistance with other cationic antimicrobials including colistin, endogenous antimicrobial peptides (AMPs) and their mimics, ceragenins. We have previously shown that colistin-resistant Gram-negative bacteria remain susceptible to AMPs and ceragenins. Here, we investigated the potential for cross resistance between chlorhexidine, colistin, AMPs and ceragenins by serial exposure of standard strains of Gram-negative bacteria to chlorhexidine to generate resistant populations of organisms. Furthermore, we performed a proteomics study on the chlorhexidine-resistant strains and compared them to the wild-type strains to find the pathways by which bacteria develop resistance to chlorhexidine. Serial exposure of Gram-negative bacteria to chlorhexidine resulted in four- to eight-fold increases in minimum inhibitory concentrations (MICs). Chlorhexidine-resistant organisms showed decreased susceptibility to colistin (8- to 32-fold increases in MICs) despite not being exposed to colistin. In contrast, chlorhexidine-resistant organisms had the same MICs as the original strains when tested with representative AMPs (LL-37 and magainin I) and ceragenins (CSA-44 and CSA-131). These results imply that there may be a connection between the emergence of highly colistin-resistant Gram-negative pathogens and the prevalence of chlorhexidine usage. Yet, use of chlorhexidine may not impact innate immune defenses (e.g., AMPs) and their mimics (e.g., ceragenins). Here, we also show that chlorhexidine resistance is associated with upregulation of proteins involved in the assembly of LPS for outer membrane biogenesis and virulence factors in Pseudomonas aeruginosa. Additionally, resistance to chlorhexidine resulted in elevated expression levels of proteins associated with chaperones, efflux pumps, flagella and cell metabolism. This study provides a comprehensive overview of the evolutionary proteomic changes in P. aeruginosa following exposure to chlorhexidine and colistin. These results have important clinical implications considering the continuous application of chlorhexidine in hospitals that could influence the emergence of colistin-resistant strains.

The nuclear variant of bone morphogenetic protein 2 (nBMP2) is expressed in macrophages and alters calcium response

We previously identified a nuclear variant of bone morphogenetic protein 2 (BMP2), named nBMP2, that is translated from an alternative start codon. Decreased nuclear localization of nBMP2 in the nBmp2NLS^tm mouse model leads to muscular, neurological, and immune phenotypes—all of which are consistent with aberrant intracellular calcium (Ca²⁺) response. Ca²⁺ response in these mice, however, has yet to be measured directly. Because a prior study suggested impairment of macrophage function in nBmp2NLS^tm mutant mice, bone marrow derived (BMD) macrophages and splenic macrophages were isolated from wild type and nBmp2NLS^tm mutant mice. Immunocytochemistry revealed that nuclei of both BMD and splenic macrophages from wild type mice contain nBMP2, while the protein is decreased in nuclei of nBmp2NLS^tm mutant macrophages. Live-cell Ca²⁺ imaging and engulfment assays revealed that Ca²⁺ response and phagocytosis in response to bacterial supernatant are similar in BMD macrophages isolated from naïve (uninfected) nBmp2NLS^tm mutant mice and wild type mice, but are deficient in splenic macrophages isolated from mutant mice after secondary systemic infection with Staphylococcus aureus, suggesting progressive impairment as macrophages respond to infection. This direct evidence of impaired Ca²⁺ handling in nBMP2 mutant macrophages supports the hypothesis that nBMP2 plays a role in Ca²⁺ response.

Imbalanced sphingolipid signaling is maintained as a core proponent of a cancerous phenotype in spite of metabolic pressure and epigenetic drift

Tumor heterogeneity may arise through genetic drift and environmentally driven clonal selection for metabolic fitness. This would promote subpopulations derived from single cancer cells that exhibit distinct phenotypes while conserving vital pro-survival pathways. We aimed to identify significant drivers of cell fitness in pancreatic adenocarcinoma (PDAC) creating subclones in different nutrient formulations to encourage differential metabolic reprogramming. The genetic and phenotypic expression profiles of each subclone were analyzed relative to a healthy control cell line (hTert-HPNE). The subclones exhibited distinct variations in protein expression and lipid metabolism. Relative to hTert-HPNE, PSN-1 subclones uniformly maintained modified sphingolipid signaling and specifically retained elevated sphingosine-1-phosphate (S1P) relative to C16 ceramide (C16 Cer) ratios. Each clone utilized a different perturbation to this pathway, but maintained this modified signaling to preserve cancerous phenotypes, such as rapid proliferation and defense against mitochondria-mediated apoptosis. Although the subclones were unique in their sensitivity, inhibition of S1P synthesis significantly reduced the ratio of S1P/C16 Cer, slowed cell proliferation, and enhanced sensitivity to apoptotic signals. This reliance on S1P signaling identifies this pathway as a promising drug-sensitizing target that may be used to eliminate cancerous cells consistently across uniquely reprogrammed PDAC clones.

Correction to: Cardiovascular, muscular, and skeletal adaptations to recreational team handball training: a randomized controlled trial with young adult untrained men

The author would like to correct the errors in the publication of the original article. The corrected details are given below for your reading.

Cardiovascular, muscular, and skeletal adaptations to recreational team handball training: a randomized controlled trial with young adult untrained men

PURPOSE

The prevalence of lifestyle diseases has escalated, and effective exercise training programmes are warranted. This study tested the hypothesis that regular participation in small-sided team handball training could provide beneficial health effects on cardiovascular, skeletal, and muscular parameters in young adult untrained men.

METHOD

Twenty-six untrained 20-30-year-old men were randomly allocated to either a team handball training group (HG; n = 14), which completed 1.9 ± 0.3 training sessions per week over 12 weeks, or an inactive control group (CG; n = 12). Physiological training adaptations were assessed pre- and post interventions by DXA scans, blood samples, muscle biopsies, and physical tests.

RESULTS

The average heart rate during training was equivalent to 84 ± 4% of maximal heart rate. Compared to CG, HG displayed significant increases in VO_2max (11 ± 6%), proximal femur bone mineral density (2 ± 1%), whole-body bone mineral content (2 ± 1%), intermittent endurance performance (32 ± 16%), incremental treadmill test performance (16 ± 7%) and muscle citrate synthase activity (22 ± 28%) as well as decreases in total fat mass (7 ± 7%) and total fat percentage (6 ± 7%) (all p < 0.05). There were no significant changes in muscle mass, blood pressure, resting heart rate, muscle hydroxyl-acyl-dehydrogenase activity, or blood lipids (all p > 0.05).

CONCLUSION

Participation in regular recreational team handball training was associated with positive cardiovascular, skeletal, and muscular adaptations, including increased maximal oxygen uptake, increased muscle enzymatic activity, and improved bone mineralization as well as lower fat percentage. These findings suggest that recreational team handball training may be an effective health-promoting activity for young adult men.

The dynamic and stress-adaptive signaling hub of 14-3-3: emerging mechanisms of regulation and context-dependent protein-protein interactions

14-3-3 proteins are a family of structurally similar phospho-binding proteins that regulate essentially every major cellular function. Decades of research on 14-3-3s have revealed a remarkable network of interacting proteins that demonstrate how 14-3-3s integrate and control multiple signaling pathways. In particular, these interactions place 14-3-3 at the center of the signaling hub that governs critical processes in cancer, including apoptosis, cell cycle progression, autophagy, glucose metabolism, and cell motility. Historically, the majority of 14-3-3 interactions have been identified and studied under nutrient-replete cell culture conditions, which has revealed important nutrient driven interactions. However, this underestimates the reach of 14-3-3s. Indeed, the loss of nutrients, growth factors, or changes in other environmental conditions (e.g., genotoxic stress) will not only lead to the loss of homeostatic 14-3-3 interactions, but also trigger new interactions, many of which are likely stress adaptive. This dynamic nature of the 14-3-3 interactome is beginning to come into focus as advancements in mass spectrometry are helping to probe deeper and identify context-dependent 14-3-3 interactions-providing a window into adaptive phosphorylation-driven cellular mechanisms that orchestrate the tumor cell's response to a variety of environmental conditions including hypoxia and chemotherapy. In this review, we discuss emerging 14-3-3 regulatory mechanisms with a focus on post-translational regulation of 14-3-3 and dynamic protein-protein interactions that illustrate 14-3-3's role as a stress-adaptive signaling hub in cancer.

Histone deacetylase 6 (HDAC6) promotes the pro-survival activity of 14-3-3ζ via deacetylation of lysines within the 14-3-3ζ binding pocket

The phospho-binding protein 14-3-3ζ acts as a signaling hub controlling a network of interacting partners and oncogenic pathways. We show here that lysines within the 14-3-3ζ binding pocket and protein-protein interface can be modified by acetylation. The positive charge on two of these lysines, Lys(49) and Lys(120), is critical for coordinating 14-3-3ζ-phosphoprotein interactions. Through screening, we identified HDAC6 as the Lys(49)/Lys(120) deacetylase. Inhibition of HDAC6 blocks 14-3-3ζ interactions with two well described interacting partners, Bad and AS160, which triggers their dephosphorylation at Ser(112) and Thr(642), respectively. Expression of an acetylation-refractory K49R/K120R mutant of 14-3-3ζ rescues both the HDAC6 inhibitor-induced loss of interaction and Ser(112)/Thr(642) phosphorylation. Furthermore, expression of the K49R/K120R mutant of 14-3-3ζ inhibits the cytotoxicity of HDAC6 inhibition. These data demonstrate a novel role for HDAC6 in controlling 14-3-3ζ binding activity.

Metabolic-stress-induced rearrangement of the 14-3-3ζ interactome promotes autophagy via a ULK1- and AMPK-regulated 14-3-3ζ interaction with phosphorylated Atg9

14-3-3ζ promotes cell survival via dynamic interactions with a vast network of binding partners, many of which are involved in stress regulation. We show here that hypoxia (low glucose and oxygen) triggers a rearrangement of the 14-3-3ζ interactome to favor an interaction with the core autophagy regulator Atg9A. Our data suggest that the localization of mammalian Atg9A to autophagosomes requires phosphorylation on the C terminus of Atg9A at S761, which creates a 14-3-3ζ docking site. Under basal conditions, this phosphorylation is maintained at a low level and is dependent on both ULK1 and AMPK. However, upon induction of hypoxic stress, activated AMPK bypasses the requirement for ULK1 and mediates S761 phosphorylation directly, resulting in an increase in 14-3-3ζ interactions, recruitment of Atg9A to LC3-positive autophagosomes, and enhanced autophagosome production. These data suggest a novel mechanism whereby the level of autophagy induction can be modulated by AMPK/ULK1-mediated phosphorylation of mammalian Atg9A.

Safety and efficacy of resistance training in germ cell cancer patients undergoing chemotherapy: a randomized controlled trial

Background:

Bleomycin–etoposid–cisplatin (BEP) chemotherapy is curative in most patients with disseminated germ cell cancer (GCC) but also associated with toxic actions and dysfunction in non-targeted tissues. We investigated changes in muscle function during BEP and the safety and efficacy of resistance training to modulate these changes.

Methods:

Thirty GCC patients were randomly assigned to resistance training (resistance training group (INT), n=15) or usual care (CON, n=15) during 9 weeks of BEP therapy. Resistance training consisted of thrice weekly sessions of four exercises, 3–4 sets/exercise of 10–15 repetitions at 12–15 repetition maximum load. The primary endpoint was muscle fibre size, assessed in muscle biopsies from musculus vastus lateralis. Secondary endpoints were fibre phenotype composition, body composition, strength, blood biochemistry and patient-reported endpoints. Healthy age-matched subjects (REF, n=19) performed the same RT-programme for comparison purposes.

Results:

Muscle fibre size decreased by −322 μm² (95% confidence interval (CI): −899 to 255; P=0.473) in the CON-group and increased by +206 μm² (95% CI: −384 to 796; P=0.257) in the INT-group (adjusted mean difference (AMD), +625 μm², 95% CI: −253 to 1503, P=0.149). Mean differences in type II fibre size (AMD, +823 μm², P=0.09) and lean mass (AMD, +1.49 kg, P=0.07) in favour of the INT-group approached significance. The REF-group improved all muscular endpoints and had significantly superior changes compared with the INT-group (P<0.05).

Conclusions:

BEP was associated with significant reduction in lean mass and strength and trends toward unfavourable changes in muscle fibre size and phenotype composition. Resistance training was safe and attenuated dysfunction in selected endpoints, but BEP blunted several positive adaptations observed in healthy controls. Thus, our study does not support the general application of resistance training in this setting but larger-scaled trials are required to confirm this finding.

Ageing is associated with diminished muscle re-growth and myogenic precursor cell expansion early after immobility-induced atrophy in human skeletal muscle

Recovery of skeletal muscle mass from immobilisation-induced atrophy is faster in young than older individuals, yet the cellular mechanisms remain unknown. We examined the cellular and molecular regulation of muscle recovery in young and older human subjects subsequent to 2 weeks of immobility-induced muscle atrophy. Retraining consisted of 4 weeks of supervised resistive exercise in 9 older (OM: mean age) 67.3, range 61-74 yrs) and 11 young (YM: mean age 24.4, range 21-30 yrs) males. Measures of myofibre area (MFA), Pax7-positive satellite cells (SCs) associated with type I and type II muscle fibres, as well as gene expression analysis of key growth and transcription factors associated with local skeletal muscle milieu, were performed after 2 weeks immobility (Imm) and following 3 days (+3d) and 4 weeks (+4wks) of retraining. OM demonstrated no detectable gains in MFA (vastus lateralis muscle) and no increases in number of Pax7-positive SCs following 4wks retraining, whereas YM increased their MFA (P < 0.05), number of Pax7-positive cells, and had more Pax7-positive cells per type II fibre than OM at +3d and +4wks (P < 0.05). No age-related differences were observed in mRNA expression of IGF-1Ea, MGF, MyoD1 and HGF with retraining, whereas myostatin expression levels were more down-regulated in YM compared to OM at +3d (P < 0.05). In conclusion, the diminished muscle re-growth after immobilisation in elderly humans was associated with a lesser response in satellite cell proliferation in combination with an age-specific regulation of myostatin. In contrast, expression of local growth factors did not seem to explain the age-related difference in muscle mass recovery.

Abstract 851: 14-3-3z-mediated suppression of tumor cell death

For many cancer patients, cytotoxic chemotherapy is the primary treatment option. While the goal of these treatments is to induce tumor cell apoptosis, treatments too often fail as tumor cells possess the dynamic ability to subvert cell death and become chemoresistant. We are interested in determining the mechanisms by which tumors develop chemoresistance, with the goal of identifying potential therapeutic targets/pathways to increase the efficacy of chemotherapy. One context in which tumor cells are though to gain.14-3-3ζ is a small acidic protein that binds to phospho-serine proteins. 14-3-3ζ binding can have wide ranging effects, from the activation of enzyme function, to the orchestration of protein-protein interactions. 14-3-3ζ is highly expressed in many cancer types, and high levels of expression have been shown to correlate with the aggressiveness of tumors and lower rates of patient survival (1). However, the mechanisms by which 14-3-3ζ may promote tumor growth/tumor cell survival have yet to be determined. In this study we show that siRNA-mediated depletion of 14-3-3ζ potently sensitizes breast tumor cells to apoptosis induced by metabolic stress (e.g., hypoxia and glucose withdrawal_stresses commonly found within solid tumors) and chemotherapy. Moreover, gel filtration data suggest that metabolic cell stress induces a shift in 14-3-3ζ from high to lower molecular weight protein complexes. Drawing from these data, we performed a proteomics experiment to characterize 14-3-3ζ interactors under these conditions. We found that 14-3-3ζ associates with numerous pro-glycolysis- and cell growth-regulating enzymes (several of which are novel 14-3-3ζ interactors), and under conditions of metabolic stress, many of these interactions are diminished or lost. We are currently examining the functional consequences of these dynamic 14-3-3z interactions with respect to tumor cell survival. Together, our data suggest that 14-3-3ζ may play an apical role in regulating the metabolic response to stress, and provide insight into the mechanism by which 14-3-3ζ promotes tumor growth and survival.

Citation Format: Vajira K. Weerasekara, Jeffrey B. Mortenson, Joshua L. Andersen. 14-3-3z-mediated suppression of tumor cell death. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 851. doi:10.1158/1538-7445.AM2013-851

Abstract 2941: The role of lysine acetylation in the tumor cell response to stress

Solid breast tumors contain heterogenous microenvironments where tumor cells are often exposed to metabolic stress (e.g., hypoxia due to poor blood supply). Such environments select for tumor cells that can adapt metabolically to survive, while other cells fail to adapt and undergo cell death. The survival of cells through periods of hypoxia can promote chemoresistance and metastasis (1). Thus, it is critical that we develop therapeutic strategies to enhance metabolic-stress-induced tumor cell death. One promising strategy is the modulation of lysine acetylation pathways by HDAC inhibitors that potently promote cell death in response to various stimuli, including hypoxia/glucose withdrawal. Given the relatively non-specific nature of chemical HDAC inhibitors, the precise acetylation-regulating enzymes and pathways that govern cell death in these settings have yet to be fully elucidated. Our goal is to identify the cellular factors that link acetylation to cell death in response to hypoxia and other metabolic stresses, with the hope that such factors could be exploited therapeutically in cancer.

Previous studies have implicated protein lysine acetylation in the coordination of cellular metabolism to the available nutrient supply (2). In line with this idea, our preliminary data suggest that lysine acetylation pathways dictate whether breast tumor cells survive (through metabolic adaptation) or die in response to hypoxia and glucose deprivation. Moreover, we have observed that general increases in protein lysine acetylation precede the activation of pro-apoptotic caspases in response to these stresses. In addition, our proteomics efforts have shown that breast tumors that are sensitive to hypoxia/glucose withdrawal exhibit significant increases in acetylation across the proteome, whereas resistant cells show very little change. Together, our data suggest that lysine acetylation pathways play a role in metabolic adaption and survival under conditions of hypoxia/glucose withdrawal. We are currently using an RNAi approach to target all known deacetylases, acetyl-transferases, and metabolic enzymes that modulate acetylation (e.g., acetyl-CoA synthetase) in order to identify the specific acetylation-regulating factors that govern tumor cell susceptibility to metabolic stress.

Citation Format: Lisa Heppler, Joshua L. Andersen. The role of lysine acetylation in the tumor cell response to stress. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2941. doi:10.1158/1538-7445.AM2013-2941

Metabolomic profiling reveals a role for caspase-2 in lipoapoptosis

The accumulation of long-chain fatty acids (LCFAs) in non-adipose tissues results in lipid-induced cytotoxicity (or lipoapoptosis). Lipoapoptosis has been proposed to play an important role in the pathogenesis of several metabolic diseases, including non-alcoholic fatty liver disease, diabetes mellitus, and cardiovascular disease. In this report, we demonstrate a novel role for caspase-2 as an initiator of lipoapoptosis. Using a metabolomics approach, we discovered that the activation of caspase-2, the initiator of apoptosis in Xenopus egg extracts, is associated with an accumulation of LCFA metabolites. Metabolic treatments that blocked the buildup of LCFAs potently inhibited caspase-2 activation, whereas adding back an LCFA in this scenario restored caspase activation. Extending these findings to mammalian cells, we show that caspase-2 was engaged and activated in response to treatment with the saturated LCFA palmitate. Down-regulation of caspase-2 significantly impaired cell death induced by saturated LCFAs, suggesting that caspase-2 plays a pivotal role in lipid-induced cytotoxicity. Together, these findings reveal a previously unknown role for caspase-2 as an initiator caspase in lipoapoptosis and suggest that caspase-2 may be an attractive therapeutic target for inhibiting pathological lipid-induced apoptosis.

The tangled circuitry of metabolism and apoptosis

For single-cell organisms, nutrient uptake and metabolism are central to the fundamental decision of whether to grow or divide. In metazoans, cell fate decisions are more complex: organismal homeostasis must be strictly maintained by balancing cell proliferation and death. Despite this increased complexity, cell fate within multicellular organisms is also influenced by metabolism; recent studies, triggered in part by an interest in tumor metabolism, are beginning to illuminate the mechanisms through which proliferation, death, and metabolism are intertwined. In particular, work on Bcl-2 family proteins suggests that the signaling pathways governing metabolism and apoptosis are inextricably linked. Here we review the crosstalk between these pathways, emphasizing recent work that illustrates the emerging dual nature of several core apoptotic proteins in regulating both metabolism and cell death.

Identification of deacetylase substrates with the biotin switch approach

The identification of lysine-acetylated proteins and deacetylase substrates has primarily relied on protein immune-affinity techniques with antibodies that recognize acetylated lysine residues (Kac antibodies). While these antibody-based techniques are continuously improving, they can be limited by the narrow and many times unknown epitope specificity of Kac antibodies. An alternative approach is the biotin switch capture of deacetylated proteins. Similar in part to other biotin switch methodologies, this technique relies on the blocking of native lysine residues and removal of the modification of interest in vitro, after which the newly deacetylated proteins can be captured and identified by mass spectrometry (MS). In this chapter, we cover the essential steps of the procedure, highlight key points in the assay to reduce false positive protein identification, and discuss the quantitative MS methods useful for identifying the captured deacetylase substrates. We also discuss potential strategies and future improvements to overcome current limitations of the assay.

A biotin switch-based proteomics approach identifies 14-3-3ζ as a target of Sirt1 in the metabolic regulation of caspase-2

While lysine acetylation in the nucleus is well characterized, comparatively little is known about its significance in cytoplasmic signaling. Here we show that inhibition of the Sirt1 deacetylase, which is primarily cytoplasmic in cancer cell lines, sensitizes these cells to caspase-2-dependent death. To identify relevant Sirt1 substrates, we developed a proteomics strategy, enabling the identification of a range of putative substrates, including 14-3-3ζ, a known direct regulator of caspase-2. We show here that inhibition of Sirtuin activity accelerates caspase activation and overrides caspase-2 suppression by nutrient abundance. Furthermore, 14-3-3ζ is acetylated prior to caspase activation, and supplementation of Xenopus egg extract with glucose-6-phosphate, which promotes caspase-2/14-3-3ζ binding, enhances 14-3-3ζ-directed Sirtuin activity. Conversely, inhibiting Sirtuin activity promotes14-3-3ζ dissociation from caspase-2 in both egg extract and human cultured cells. These data reveal a role for Sirt1 in modulating apoptotic sensitivity, in response to metabolic changes, by antagonizing 14-3-3ζ acetylation.

Meeting the (N-terminal) end with acetylation

Cell-fate decisions are tightly linked to cellular energy status. In this issue, Yi et al. (2011) introduce a mechanism by which Bcl-xL lowers the threshold for apoptosis by suppressing acetyl-CoA production, which, in turn, suppresses the N-alpha-acetylation important for activation of the proapoptotic protease caspase-2.

Increased mitochondrial substrate sensitivity in skeletal muscle of patients with type 2 diabetes

AIMS/HYPOTHESIS

Mitochondrial respiration has been linked to insulin resistance. We studied mitochondrial respiratory capacity and substrate sensitivity in patients with type 2 diabetes (patients), and obese and lean control participants.

METHODS

Mitochondrial respiration was measured in permeabilised muscle fibres by respirometry. Protocols for respirometry included titration of substrates for complex I (glutamate), complex II (succinate) and both (octanoyl-carnitine). Myosin heavy chain (MHC) composition, antioxidant capacity (manganese superoxide dismutase [MnSOD]), citrate synthase activity and maximal oxygen uptake (VO2) were also determined. Insulin sensitivity was determined with the isoglycaemic-hyperinsulinaemic clamp technique.

RESULTS

Insulin sensitivity was different (p < 0.05) between the groups (patients<obese controls<lean controls). MnSOD was lower in patients than in lean controls. MHC I content was lowest in patients (37 ± 11% [mean ± SE] vs 53 ± 6% and 56 ± 4%) vs obese controls and lean controls, respectively. VO2 was highest in lean controls (40 ± 3 ml min(-1) kg(-1) [mean ± SE]) compared with patients (25 ± 2) and obese controls (27 ± 2). Mitochondrial content (citrate synthase) was higher (p < 0.05) in lean controls than in patients and obese controls. When normalised for mitochondrial content by citrate synthase, mitochondrial respiratory capacity was similar in all groups. However, the half maximal substrate concentration (C(50)) for complex I was significantly lower (p = 0.03) in patients (1.1 ± 0.2 mmol/l [mean ± SE]) than in obese (2.0 ± 0.3) and lean (1.8 ± 0.3) controls. Likewise, C(50) for complex II was lower (p = 0.02) in patients (3.5 ± 0.2 mmol/l [mean ± SE]) than in obese controls (4.1 ± 0.2), but did not differ from that in lean controls (3.8 ± 0.4). Substrate sensitivity for octanoyl-carnitine did not differ between groups.

CONCLUSIONS/INTERPRETATION

Increased mitochondrial substrate sensitivity is seen in skeletal muscle from type 2 diabetic patients and is confined to non-lipid substrates. Respiratory capacity per mitochondrion is not decreased with insulin resistance.

Abstract 4697: Metabolic regulation of caspase-2

Caspase-2 has been shown to act as an apical caspase, upstream of cytochrome c release, in a variety of cell death settings including chemotherapy-induced apoptosis. However, the mechanism governing caspase-2 activation in response to chemotherapeutics is poorly understood. We previously demonstrated that production of NADPH via the pentose phosphate pathway (PPP) stimulates caspase-2 suppression via a CaMKII-dependent phosphorylation on Ser135 (Nutt et al., 2005), and that as PPP activity declines, caspase-2 becomes dephosphorylated and activated to promote cell death. Our current efforts are focused on identifying the cellular factors that link metabolism to caspase-2 activation, with the hope that such factors could be exploited therapeutically in cancer.

In this study we show that inhibition of Sirt1 deacetylase overrides the anti-apoptotic effect of high PPP activity (stimulated by G6P) to cause caspase-2 activation and cell death. In an effort to more precisely understand the role of Sirt1 in caspase-2 activation, we developed a novel biotin-switch-based proteomics approach to identify Sirt1 substrates in an unbiased manner. This approach yielded a variety of high-confidence Sirt1 substrates, many of which are cytoplasmic proteins that primarily group into the areas of glycolysis/metabolism, oxidative stress, cytoskeletal dynamics, and apoptosis; all areas where Sirt1 has been implicated. We had previously shown that one of these substrates, 14-3-3ζ, binds to caspase-2 in a phosphorylation-dependent manner and protects Ser135 from dephosphorylation (Nutt et al., 2009). We show here that acetylation of 14-3-3ζ occurs in response to a drop in PPP activity and triggers 14-3-3ζ release from caspase-2, leading to caspase-2 activation. Conversely, we show that high PPP levels promote Sirt1 activity, which, in turn, promotes 14-3-3ζ binding to caspase-2 by antagonizing the acetylation of 14-3-3ζ. We have extended these results to a panel of breast tumor cell lines, in which inhibition of Sirt1 induces the rapid dissociation of caspase-2 from 14-3-3ζ, and results in a marked enhancement of the cells’ sensitivity to paclitaxel. Interestingly, we observe cytoplasmic localization of Sirt1 at high levels in these cells with very little to none in the nucleus, in contrast to a more nuclear Sirt1 distribution in normal breast tissue.

In conclusion, these data support a model in which Sirt1 promotes the pro-survival effect of high metabolic activity by directly regulating 14-3-3ζ-mediated inhibition of caspase-2, and suggest that as PPP activity declines, a consequent decrease in Sirt1 activity triggers caspase-2 activation. As Sirt1 is known to also modulate numerous transcription factors, its suppressive effect on caspase-2 may play a particularly key role under conditions in which transcription is not ongoing (e.g., paclitaxel-induced mitotic arrest) or when Sirt1 is excluded from the nucleus (breast and other tumor cell lines).

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4697. doi:10.1158/1538-7445.AM2011-4697

Improved glucose tolerance after intensive life style intervention occurs without changes in muscle ceramide or triacylglycerol in morbidly obese subjects

AIM

This study investigated the effect of a 15-week life style intervention (hypocaloric diet and regular exercise) on glucose tolerance, skeletal muscle lipids and muscle metabolic adaptations in 14 female and 9 male morbidly obese subjects (age: 32.5±2.3 years, body mass index: 46.1±1.9 kg m(-2) ).

METHOD

Before and after the life style intervention, an oral glucose tolerance test was performed and a muscle biopsy was obtained in the fasted state. Maximal oxygen uptake was measured by an indirect test.

RESULTS

After the intervention, body weight was decreased (P<0.05) by 11±1%, maximal oxygen uptake increased (P<0.05) by 18±5% and glucose tolerance increased (P<0.05) by 12±3%. Muscle glycogen was significantly increased by 47±14%, but muscle ceramide and triacylglycerol content remained completely unchanged. No sex difference was observed for any of these parameters, but during submaximal exercise a marked decrease (P<0.05) of 15±2% in respiratory exchange ratio was seen only in females indicating an enhanced fat oxidation.

CONCLUSION

Despite a marked weight loss and an improved aerobic capacity muscle ceramide and triacylglycerol remained unchanged after intensive life style intervention, and muscle lipids hence do not seem to play a major role for the improved glucose tolerance in these morbidly obese subjects. Interestingly, only the females improved fat oxidation during submaximal exercise after the intervention implying the presence of a sex-dependent response to intensive life style adaptation.

Effects of resistance training on endurance capacity and muscle fiber composition in young top-level cyclists

Equivocal findings exist on the effect of concurrent strength (S) and endurance (E) training on endurance performance and muscle morphology. Further, the influence of concurrent SE training on muscle fiber-type composition, vascularization and endurance capacity remains unknown in top-level endurance athletes. The present study examined the effect of 16 weeks of concurrent SE training on maximal muscle strength (MVC), contractile rate of force development (RFD), muscle fiber morphology and composition, capillarization, aerobic power (VO2max), cycling economy (CE) and long/short-term endurance capacity in young elite competitive cyclists (n=14). MVC and RFD increased 12-20% with SE (P<0.01) but not E. VO2max remained unchanged. CE improved in E to reach values seen in SE. Short-term (5-min) endurance performance increased (3-4%) after SE and E (P<0.05), whereas 45-min endurance capacity increased (8%) with SE only (P<0.05). Type IIA fiber proportions increased and type IIX proportions decreased after SE training (P<0.05) with no change in E. Muscle fiber area and capillarization remained unchanged. In conclusion, concurrent strength/endurance training in young elite competitive cyclists led to an improved 45-min time-trial endurance capacity that was accompanied by an increased proportion of type IIA muscle fibers and gains in MVC and RFD, while capillarization remained unaffected.

Regional anatomic differences in skeletal muscle mitochondrial respiration in type 2 diabetes and obesity

CONTEXT

Previous studies on leg skeletal musculature have demonstrated mitochondrial dysfunction associated with type 2 diabetes mellitus (T2DM), but it is not known whether mitochondrial dysfunction is present in the upper extremities.

OBJECTIVE

The aim of the study was to compare mitochondrial respiration and markers of mitochondrial content in skeletal muscle of arm and leg in patients with T2DM and obese control subjects.

PATIENTS

Ten patients with T2DM (age, 52.3 +/- 2.7 yr; body mass index, 30.1 +/- 1.2 kg/m(2)) (mean +/- se) were studied after a 2-wk washout period of oral antihyperglycemic agents. Ten control subjects (age, 54.3 +/- 2.8 yr; body mass index, 30.4 +/- 1.2 kg/m(2)) with normal fasting and 2-h oral glucose tolerance test blood glucose levels were also included.

MAIN OUTCOME MEASURE

We measured mitochondrial respiration in saponin-treated skinned muscle fibers from biopsies of m. deltoideus and m. vastus lateralis using high-resolution respirometry.

RESULTS

In the arm, mitochondrial respiration and citrate synthase activity did not differ between groups, but mitochondrial respiration per milligram of muscle was significantly higher in the leg muscle of the control subjects compared to T2DM. Fiber type compositions in arm and leg muscles were not different between the T2DM and control group, and maximum rate of O(2) consumption did not differ between the groups.

CONCLUSION

The results demonstrate that reduced mitochondrial function in T2DM is only present in the leg musculature. This novel finding suggests that mitochondrial dysfunction is not a primary defect affecting all skeletal muscle but could be related to a decreased response to locomotor muscle use in T2DM.

A cut above the other caspases

In this issue of Molecular Cell, Bouchier-Hayes et al. (2009) develop a novel approach to visualizing caspase-2 activation in real time, enabling resolution of several controversies surrounding the position of this enzyme in apoptotic signaling cascades.

Restraint of apoptosis during mitosis through interdomain phosphorylation of caspase-2

The apoptotic initiator caspase-2 has been implicated in oocyte death, in DNA damage- and heat shock-induced death, and in mitotic catastrophe. We show here that the mitosis-promoting kinase, cdk1-cyclin B1, suppresses apoptosis upstream of mitochondrial cytochrome c release by phosphorylating caspase-2 within an evolutionarily conserved sequence at Ser 340. Phosphorylation of this residue, situated in the caspase-2 interdomain, prevents caspase-2 activation. S340 was susceptible to phosphatase 1 dephosphorylation, and an interaction between phosphatase 1 and caspase-2 detected during interphase was lost in mitosis. Expression of S340A non-phosphorylatable caspase-2 abrogated mitotic suppression of caspase-2 and apoptosis in various settings, including oocytes induced to undergo cdk1-dependent maturation. Moreover, U2OS cells treated with nocodazole were found to undergo mitotic catastrophe more readily when endogenous caspase-2 was replaced with the S340A mutant to lift mitotic inhibition. These data demonstrate that for apoptotic stimuli transduced by caspase-2, cell death is prevented during mitosis through the inhibitory phosphorylation of caspase-2 and suggest that under conditions of mitotic arrest, cdk1-cyclin B1 activity must be overcome for apoptosis to occur.

Are substrate use during exercise and mitochondrial respiratory capacity decreased in arm and leg muscle in type 2 diabetes?

AIM/HYPOTHESIS

The aim of the study was to investigate mitochondrial function, fibre type distribution and substrate oxidation in arm and leg muscle during exercise in patients with type 2 diabetes and in obese and lean controls.

METHODS

Indirect calorimetry was used to calculate fat and carbohydrate oxidation during both progressive arm-cranking and leg-cycling exercises. Muscle biopsies from arm and leg were obtained. Fibre type, as well as O(2) flux capacity of saponin-permeabilised muscle fibres were measured, the latter by high resolution respirometry, in patients with type 2 diabetes, age- and BMI-matched obese controls, and age-matched lean controls.

RESULTS

Fat oxidation was similar in the groups during either arm or leg exercise. During leg exercise at higher intensities, but not during arm exercise, carbohydrate oxidation was lower in patients with type 2 diabetes compared with the other groups. In patients with type 2 diabetes, ADP-stimulated state 3 respiration per mg muscle with parallel electron input from complex I+II was lower in m. vastus lateralis compared with obese and lean controls, whereas no differences between groups were present in m. deltoideus. A higher percentage of type IIX fibres was seen in m. vastus lateralis in patients with type 2 diabetes compared with obese and lean controls, whereas no difference was found in the deltoid muscle.

CONCLUSIONS/INTERPRETATION

This study demonstrates similar O(2) flux capacity, fibre type distribution and carbohydrate oxidation in arm muscle in the groups despite the presence of attenuated values in leg muscle in patients with type 2 diabetes compared with obese and lean controls.

Early and late rate of force development: differential adaptive responses to resistance training?

The objective of this study is to investigate the potentially opposing influence of qualitative and quantitative muscular adaptations in response to high-intensity resistance training on contractile rate of force development (RFD) in the early (<100 ms) and later phases (>200 ms) of rising muscle force. Fifteen healthy young males participated in a 14-week resistance training intervention for the lower body and 10 matched subjects participated as controls. Maximal muscle strength (MVC) and RFD were measured during maximal voluntary isometric contraction of the quadriceps femoris muscle. Muscle biopsies were obtained from the vastus lateralis. The main findings were that RFD in the late phase of rising muscle force increased in response to resistance training whereas early RFD remained unchanged and early relative RFD (i.e., RFD/MVC) decreased. Quantitatively, muscle fiber cross-sectional area and MVC increased whereas, qualitatively, the relative proportion of type IIX muscle fibers decreased. Multiple regression analysis showed that while increased MVC positively influenced both early and late RFD, decreased-type IIX negatively influenced early RFD only. In conclusion, early and late RFD responded differently to high-intensity resistance training due to differential influences of qualitative and quantitative muscular adaptations on early and later phases of rising muscle force.