Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors.

The human HDAC (histone deacetylase) family, a well-validated anticancer target, plays a key role in the control of gene expression through regulation of transcription. While HDACs can be subdivided into three main classes, the class I, class II and class III HDACs (sirtuins), it is presently unclear whether inhibiting multiple HDACs using pan-HDAC inhibitors, or targeting specific isoforms that show aberrant levels in tumours, will prove more effective as an anticancer strategy in the clinic. To address the above issues, we have tested a number of clinically relevant HDACis (HDAC inhibitors) against a panel of rhHDAC (recombinant human HDAC) isoforms. Eight rhHDACs were expressed using a baculoviral system, and a Fluor de Lystrade mark (Biomol International) HDAC assay was optimized for each purified isoform. The potency and selectivity of ten HDACs on class I isoforms (rhHDAC1, rhHDAC2, rhHDAC3 and rhHDAC8) and class II HDAC isoforms (rhHDAC4, rhHDAC6, rhHDAC7 and rhHDAC9) was determined. MS-275 was HDAC1-selective, MGCD0103 was HDAC1- and HDAC2-selective, apicidin was HDAC2- and HDAC3-selective and valproic acid was a specific inhibitor of class I HDACs. The hydroxamic acid-derived compounds (trichostatin A, NVP-LAQ824, panobinostat, ITF2357, vorinostat and belinostat) were potent pan-HDAC inhibitors. The growth-inhibitory effect of the HDACis on HeLa cells showed that both pan-HDAC and class-I-specific inhibitors inhibited cell growth. The results also showed that both pan-HDAC and class-I-specific inhibitor treatment resulted in increased acetylation of histones, but only pan-HDAC inhibitor treatment resulted in increased tubulin acetylation, which is in agreement with their activity towards the HDAC6 isoform.

Activity of the histone deacetylase inhibitor belinostat (PXD101) in preclinical models of prostate cancer.

Histone deacetylase inhibitors (HDACi) represent a promising new class of anticancer agents. In the current investigation, we examined the activity of the HDACi belinostat in preclinical models of prostate cancer. In vitro proliferation assays demonstrated that belinostat potently inhibited the growth of prostate cancer cell lines (IC(50) < 1.0 microM) and was cytotoxic to these cells. Washout experiments indicated that exposure to belinostat for relatively short periods of time (<12 hr) induced suboptimal growth-inhibition and that cells exposed to 1.0 microM belinostat for 48 hr retained the capacity for regrowth following drug withdrawal, while cells exposed to 4.0 microM belinostat were irreversibly growth-inhibited. Cell cycle analyses demonstrated that belinostat induced G2/M arrest and increased the percentage of cells with subG1 DNA content, thus confirming the growth-inhibitory and cytotoxic effects of this compound. Normal prostate epithelial cells were generally less susceptible to the effects of belinostat than were prostate cancer cells. In an orthotopic prostate cancer tumor model, belinostat inhibited tumor growth by up to 43%. Moreover, metastatic lung lesions were present in 47% of vehicle-treated animals but in none of the animals administered belinostat. Consistent with its observed antimetastatic activity, belinostat inhibited the migration of prostate tumor cells and increased the production of tissue inhibitor of metalloproteinase-1 (TIMP-1) by these cells, the latter effect being replicated by siRNA knockdown of HDAC3. Belinostat also increased the expression of p21 and decreased the expression of potentially oncogenic proteins (mutant p53 and ERG). These results support the clinical evaluation of belinostat for the treatment of prostate cancer.

The striatal-enriched protein tyrosine phosphatase gates long-term potentiation and fear memory in the lateral amygdala.

BACKGROUND: Formation of long-term memories is critically dependent on extracellular-regulated kinase (ERK) signaling. Activation of the ERK pathway by the sequential recruitment of mitogen-activated protein kinases is well understood. In contrast, the proteins that inactivate this pathway are not as well characterized. METHODS: Here we tested the hypothesis that the brain-specific striatal-enriched protein tyrosine phosphatase (STEP) plays a key role in neuroplasticity and fear memory formation by its ability to regulate ERK1/2 activation. RESULTS: STEP co-localizes with the ERKs within neurons of the lateral amygdala. A substrate-trapping STEP protein binds to the ERKs and prevents their nuclear translocation after glutamate stimulation in primary cell cultures. Administration of TAT-STEP into the lateral amygdala (LA) disrupts long-term potentiation (LTP) and selectively disrupts fear memory consolidation. Fear conditioning induces a biphasic activation of ERK1/2 in the LA with an initial activation within 5 minutes of training, a return to baseline levels by 15 minutes, and an increase again at 1 hour. In addition, fear conditioning results in the de novo translation of STEP. Inhibitors of ERK1/2 activation or of protein translation block the synthesis of STEP within the LA after fear conditioning. CONCLUSIONS: Together, these data imply a role for STEP in experience-dependent plasticity and suggest that STEP modulates the activation of ERK1/2 during amygdala-dependent memory formation. The regulation of emotional memory by modulating STEP activity may represent a target for the treatment of psychiatric disorders such as posttraumatic stress disorder (PTSD), panic, and anxiety disorders.

Roles for Rho/ROCK and vinculin in parietal endoderm migration.

The first cell migration event in the mouse embryo is the movement of parietal endoderm cells from the surface of the inner cell mass facing the blastocoel cavity to line the inner surface of the trophectoderm. F9 embryoid bodies provide an in vitro model for this event. They have an inner core of undifferentiated stem cells surrounded by an outer visceral endoderm layer. When plated on a laminin coated substrate, visceral endoderm transitions to parietal endoderm and migrates onto the dish, away from the attached embryoid body. We now show that this outgrowth contains abundant focal complexes and focal adhesions, as well as lamellipodia and filopodia. Treatment with the ROCK inhibitor Y-27632 promotes a 2-fold increase in outgrowth, and a transition from focal adhesions and associated stress fibers, to focal complexes and a decrease in stress fibers. ROCK inhibition also leads to an increase in lamellipodia. Inhibition of RhoA by transfection of a vector encoding C3 transferase, direct administration of the C3 enzyme, or transfection of a vector encoding p190 Rho GTPase Activating Protein also promotes outgrowth and an apparent transition from focal adhesions to focal complexes. Parietal endoderm outgrowth generated using vinculin-deficient F9 stem cells migrates 2-fold further than wild type cultures, but this outgrowth retains the morphology of wild type parietal endoderm, including focal adhesions and stress fibers. Addition of Y-27632 to vinculin-null outgrowth cultures further stimulates migration an additional 2-fold, supporting the conclusion that Rho/ROCK and vinculin regulate parietal endoderm outgrowth by distinct pathways.

Analysis and regulation of amoeboid-like cell motility using synthetic Ca(2+)-sensitive proteins.

Several recent reports have demonstrated how engineered proteins can control cell motility, an important functional module for ultimately programming cells as therapeutics. We have reported two engineered proteins that regulate the blebbing cell morphology using chimeras of RhoA, a protein that regulates cytoskeletal tension. Here, we show that engineered switching of blebbing can be used to regulate cell motility. First, the analysis of morphology and motility characteristics showed that blebbing cells wobbled, or shifted, faster and less linearly than cells with a wild type morphology. Second, activating engineered protein switches that regulate cell morphology led to predictable changes in motility characteristics. Last, exogenous stimuli such as blue light, acetylcholine and VEGF-A were used to show that groups of proteins could cooperatively increase cell motility in vitro. This work demonstrates that control of RhoA can program the motility patterns of living cells and has implications in studying the relationship between cell morphology and motility.

Photoswitchable protein degradation: a generalizable control module for cellular function?

In this issue of Chemistry & Biology, Renicke et al. report a photosensitive degron (psd) consisting of the LOV2 domain fused to a protein degradation sequence. This design enabled light-dependent protein degradation in yeast. When psd was fused to cell-cycle-dependent proteins, it controlled cell cycle by light with spatiotemporal precision.

Simultaneous assembly of two target proteins using split inteins for live cell imaging.

Inteins are protein elements that covalently reassemble proteins from two precursor fragments in a process known as protein splicing. They are commonly used to reassemble a single target protein by protein splicing, but a second target protein can potentially reassemble by intein dimerization. Here, we use the naturally occurring split DnaE intein from Nostoc punctiforme (NpuDnaE) to demonstrate the simultaneous assembly of two target proteins in several examples studied with live cell imaging: yellow fluorescent protein (YFP) with monomeric red fluorescent protein (mRFP), dominant positive mutant of RhoA GTPase with YFP and GCaMP2 Ca(2+) indicator with mRFP. These examples showed the versatility of the strategy along with some interesting attributes: first, the two target proteins are in equal stoichiometry; second, the extent of protein splicing can be reported by a fluorescent protein. In particular, the split GCaMP2 with mRFP could find applications in tissue-specific Ca(2+) imaging in transgenic organisms, where mRFP could control for motion-related intensity changes.

Programming membrane fusion and subsequent apoptosis into mammalian cells.

By the delivery of specific natural or engineered proteins, mammalian cells can be programmed to perform increasingly sophisticated and useful functions. Here, we introduce a set of proteins that has potential value in cell-based therapies by programming a cell to target tumor cells. First, the delivery of VSV-G (vesicular stomatitis virus glycoprotein) allowed the cell to undergo membrane fusion with adjacent cells to form syncytia (i.e., a multinucleated cell) in conditions of low pH typically occurring at a tumor site. The formation of syncytia caused the clustering of nuclei along with an integration of the microtubule network and ER. Interestingly, the formation of syncytia between cells that are dynamically blebbing, a mode of migration preferred during tumor metastasis, resulted in the loss of these morphology changes. Lastly, the codelivery of VSV-G with L57R (an engineered photoactivated caspase-7) allowed cells to undergo low pH-dependent membrane fusion followed by blue light-dependent apoptosis. In cell-based therapies, the clearance of syncytia between tumor cells might further trigger an immune response against the tumor.

Engineering a photoactivated caspase-7 for rapid induction of apoptosis.

Apoptosis is a cell death program involved in the development of multicellular organisms, immunity, and pathologies ranging from cancer to HIV/AIDS. We present an engineered protein that causes rapid apoptosis of targeted cells in monolayer culture after stimulation with blue light. Cells transfected with the protein switch L57V, a tandem fusion of the light-sensing LOV2 domain and the apoptosis-executing domain from caspase-7, rapidly undergo apoptosis within 60 min after light stimulation. Constant illumination of under 5 min or oscillating with 1 min exposure had no effect, suggesting that cells have natural tolerance to a short duration of caspase-7 activity. Furthermore, the overexpression of Bcl-2 prevented L57V-mediated apoptosis, suggesting that although caspase-7 activation is sufficient to start apoptosis, it requires mitochondrial contribution to fully commit.

Engineered networks of synthetic and natural proteins to control cell migration.

Mammalian cells reprogrammed with engineered transgenes have the potential to be useful therapeutic platforms because they can support large genetic networks, can be taken from a host or patient, and perform useful functions such as migration and secretion. Successful engineering of mammalian cells will require the development of modules that can perform well-defined, reliable functions, such as directed cell migration toward a chemical or physical signal. One inherently modular cellular pathway is the Ca(2+) signaling pathway: protein modules that mobilize and respond to Ca(2+) are combined across cell types to create complexity. We have designed a chimera of Rac1, a GTPase that controls cell morphology and migration, and calmodulin (CaM), a Ca(2+)-responsive protein, to control cell migration. The Rac1-CaM chimera (named RACer) controlled lamellipodia growth in response to Ca(2+). RACer was combined with LOVS1K (a previously engineered light-sensitive Ca(2+)-mobilizing module) and cytokine receptors to create protein networks where blue light and growth factors regulated cell morphology and, thereby, cell migration. To show the generalizability of our design, we created a Cdc42-CaM chimera that controls filopodia growth in response to Ca(2+). The insights that have been gained into Ca(2+) signaling and cell migration will allow future work to combine engineered protein systems to enable reprogrammed cell sensing of relevant therapeutic targets in vivo.

Split-intein mediated re-assembly of genetically encoded Ca(2+) indicators.

While genetically encoded Ca(2+) indicators (GECIs) allow Ca(2+) imaging in model organisms, the gene expression is often under the control of a single promoter that may drive expression beyond, the cell types of interest. To enable more cell-type specific targeting, GECIs can be brought under the, control of the intersecting expression from two promoters. Here, we present the splitting and, reassembly of two representative GECIs (TN-XL and GCaMP2) mediated by the split intein from Nostoc, punctiforme (NpuDnaE). While the split TN-XL biosensor offered ratiometric Ca(2+) imaging, it had a, diminished Ca(2+) response relative to the native TN-XL biosensor. In contrast, the split GCaMP2, biosensor retained similar Ca(2+) response to the native GCaMP2. The split GCaMP2 biosensor was, further targeted to the pharyngeal muscles of Caenorhabditis elegans where Ca(2+) signals from feeding C. elegans, were imaged. Thus, we envision that increased cell-type targetability of GECIs is feasible with two, complementary promoters.

Ca2+-mediated synthetic biosystems offer protein design versatility, signal specificity, and pathway rewiring.

Synthetic biosystems have been engineered that enable control of metazoan cell morphology, migration, and death. These systems possess signal specificity, but lack flexibility of input signal. To exploit the potential of Ca(2+) signaling, we designed RhoA chimeras for reversible, Ca(2+)-dependent control over RhoA morphology and migration. First, we inserted a calmodulin-binding peptide into a RhoA loop that activates or deactivates RhoA in response to Ca(2+) signals depending on the chosen peptide. Second, we localized the Ca(2+)-activated RhoA chimera to the plasma membrane, where it responded specifically to local Ca(2+) signals. Third, input control of RhoA morphology was rewired by coexpressing the Ca(2+)-activated RhoA chimera with Ca(2+)-transport proteins using acetylcholine, store-operated Ca(2+) entry, and blue light. Engineering synthetic biological systems with input versatility and tunable spatiotemporal responses motivates further application of Ca(2+) signaling in this field.

A synthetic photoactivated protein to generate local or global Ca(2+) signals.

Ca(2+) signals regulate diverse physiological processes through tightly regulated fluxes varying in location, time, frequency, and amplitude. Here, we developed LOVS1K, a genetically encoded and photoactivated synthetic protein to generate local or global Ca(2+) signals. With 300 ms blue light exposure, LOVS1K translocated to Orai1, a plasma membrane Ca(2+) channel, within seconds, generating a local Ca(2+) signal on the plasma membrane, and returning to the cytoplasm after tens of seconds. With repeated photoactivation, global Ca(2+) signals in the cytoplasm were generated to modulate engineered Ca(2+)-inducible proteins. Although Orai1 is typically associated with global store-operated Ca(2+) entry, we demonstrate that Orai1 can also generate local Ca(2+) influx on the plasma membrane. Our photoactivation system can be used to generate spatially and temporally precise Ca(2+) signals and to engineer synthetic proteins that respond to specific Ca(2+) signals.

Engineering Ca2+/calmodulin-mediated modulation of protein translocation by overlapping binding and signaling peptide sequences.

Protein translocation is used by cells to regulate protein activity in time and space. Synthetic systems have studied the effect of second messengers and exogenous chemicals on translocation, and have used translocation-based sensors to monitor unrelated pathways such as caspase activity. We have created a synthetic Ca2+-inducible protein using calmodulin binding peptides that selectively reveal nuclear localization and export signals in low Ca2+ (0 microM) and high Ca2+ (10 microM) environments, respectively. Experiments in live cells showed that our construct translocates between the nucleolus and plasma membrane with time constants of approximately 2 h. Further, a single amino acid mutation (Cys20Ala) in our construct prevented translocation to the plasma membrane and instead targeted it the mitochondria as predicted by bioinformatic analysis. Lastly, we studied the effect of cell line, Ca2+ concentration, chemical inhibitors, and cell morphology on translocation and found these conditions affected the rate, extent and direction of translocation. Our work demonstrates the feasibility of engineering Ca2+/calmodulin-mediated modulation of protein translocation and suggests that more natural analogs may exist.

Structure based design of a Ca2+-sensitive RhoA protein that controls cell morphology.

The Rho proteins are important regulators of cell morphology, and the prototypical protein RhoA is known to regulate contraction, blebbing and bleb retraction. We have identified and experimentally confirmed that RhoA has a binding site for calmodulin, a ubiquitous transducer of the Ca(2+) second messenger. Using structural modeling, a fusion protein was designed wherein RhoA activity was controlled by Ca(2+) via calmodulin. Living cells transfected with this synthetic protein underwent Ca(2+) sensitive and calmodulin-dependent bleb retraction within minutes. Further, the modularity of Ca(2+) signaling was exploited to induce bleb retraction in response to blue light (using channelrhodopsin-2) or exogenous chemicals (with acetylcholine receptor), showing input signal versatility. The widespread use of Ca(2+) signaling in nature suggests that fully exploring its signaling potential may allow powerful applications to other synthetic biological systems.

A computational tool for Monte Carlo simulations of biomolecular reaction networks modeled on physical principles.

Deciphering and designing complex biomolecular networks in the cell are the goals of systems and synthetic biology, respectively. The effects of localization, spatial heterogeneity, and molecular fluctuations in biomolecular networks are not well understood. We present a theoretical approach based on physical principles to accurately simulate biomolecular networks using the Monte Carlo method. Incorporating this theory, a computational tool named Monte Carlo biomolecular simulator (MBS) was developed, enabling studies of biomolecular kinetics with both spatial and temporal resolutions. The accuracy of MBS was verified by comparison against the classical deterministic approaches. Furthermore, the effects of localization, spatial heterogeneity, and molecular fluctuations were studied in three simulated model systems, showing their impact on the overall reaction kinetics. This work demonstrates the unique insights that can be discovered by considering the subtle effects that can be created by the spatial and temporal kinetics of biomolecular reaction networks.

Rate and extent of protein localization is controlled by peptide-binding domain association kinetics and morphology.

Protein localization is an important regulatory mechanism in many cell signaling pathways such as cytoskeletal organization and genetic regulation. The specific mechanism of protein localization determines the kinetics and morphological constraints of protein translocation, and thus affects the rate and extent of localization. To investigate the affect of localization kinetics and morphology on protein localization, we designed a protein localization system based on Ca(2+)-calmodulin and Src homology 3 domain binding peptides that can translocate between specific localizations in response to a Ca(2+) signal. We used a stochastic biomolecular simulator to predict that such a protein localization system will exhibit slower and less complete translocations when the association kinetics of a binding domain and peptide are reduced. As well, we predicted that increasing the diffusion resistance by manipulating the morphology of the system would similarly impair translocation speed and completeness. We then constructed a network of synthetic fusion proteins and showed that these predictions could be qualitatively confirmed in vitro. This work provides a basis for explaining the different characteristics (rate and extent) of protein transport and localization in cells as a consequence of the kinetics and morphology of the transport mechanism.

Cascading signaling pathways improve the fidelity of a stochastically and deterministically simulated molecular RS latch.

BACKGROUND: While biological systems have often been compared with digital systems, they differ by the strong effect of crosstalk between signals due to diffusivity in the medium, reaction kinetics and geometry. Memory elements have allowed the creation of autonomous digital systems and although biological systems have similar properties of autonomy, equivalent memory mechanisms remain elusive. Any such equivalent memory system, however, must silence the effect of crosstalk to maintain memory fidelity. RESULTS: Here, we present a system of enzymatic reactions that behaves like an RS latch (a simple memory element in digital systems). Using both a stochastic molecular simulator and ordinary differential equation simulator, we showed that crosstalk between two latches operating in the same spatial localization disrupts the memory fidelity of both latches. Crosstalk was reduced or silenced when simple reaction loops were replaced with multiple step or cascading reactions, showing that cascading signaling pathways are less susceptible to crosstalk. CONCLUSION: Thus, the common biological theme of cascading signaling pathways is advantageous for maintaining the fidelity of a memory latch in the presence of crosstalk. The experimental implementation of such a latch system will lead to novel approaches to cell control using synthetic proteins and will contribute to our understanding of why cells behave differently even when given the same stimulus.

Pharmacologically enhanced expression of GPNMB increases the sensitivity of melanoma cells to the CR011-vcMMAE antibody-drug conjugate.

GPNMB is a melanoma-associated glycoprotein that is targeted by the CR011-vcMMAE antibody-drug conjugate (ADC). Previous studies have shown that CR011-vcMMAE induces the apoptosis of GPNMB-expressing tumor cells in vitro and tumor regression in xenograft models. This ADC is currently in clinical trials for melanoma. In the present investigation, a variety of compounds were examined for their ability to increase the expression of GPNMB by cancer cells. These experiments lead to the identification of three distinct groups of compounds that increased GPNMB, some of which were shown to enhance the sensitivity of melanoma cells to CR011-vcMMAE. These data indicate that it may be possible to increase the anticancer activity of CR011-vcMMAE through pharmacological enhancement of GPNMB expression for potential therapeutic benefit.