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Inhibition of the deubiquitinating enzyme USP1 can induce synthetic lethality in tumors characterized by homologous recombination deficiency (HRD) and represents a novel therapeutic strategy for the treatment of BRCA1/2 mutant cancers, potentially including patients whose tumors have primary or acquired resistance to PARP inhibitors (PARPi). Here, we present a comprehensive characterization of TNG348, an allosteric, selective, and reversible inhibitor of USP1 (USP1i). TNG348 induces dose-dependent accumulation of ubiquitinated protein substrates both in vitro and in vivo. CRISPR screens show that TNG348 exerts its anti-tumor effect by disrupting the translesion synthesis pathway of DNA damage tolerance through RAD18-dependent ub-PCNA induction. Though TNG348 and PARPi share the ability to selectively kill HRD tumor cells, CRISPR screens reveal that TNG348 and PARPi do so through discrete mechanisms. Particularly, knocking out PARP1 causes resistance to PARPi but sensitizes cells to TNG348 treatment. Consistent with these findings, combination of TNG348 with PARPi leads to synergistic anti-tumor effects in HRD tumors, resulting in tumor growth inhibition and regression in multiple mouse xenograft tumor models. Importantly, our data in human cancer models further show that the addition of TNG348 to PARPi treatment can overcome acquired PARPi resistance in vivo. While the clinical development of TNG348 has been discontinued due to unexpected liver toxicity in patients (NCT06065059), the present data provides preclinical and mechanistic support for the continued exploration of USP1 as a drug target for the treatment of patients with BRCA1/2 mutant or HRD cancers.

Synthetic lethality approaches in BRCA1/2-mutated cancers have focused on poly(ADP-ribose) polymerase (PARP) inhibitors, which are subject to high rates of innate or acquired resistance in patients. Here, we used CRISPR/Cas9-based screening to identify DNA Ligase I (LIG1) as a novel target for synthetic lethality in BRCA1-mutated cancers. Publicly available data supported LIG1 hyperdependence of BRCA1-mutant cells across a variety of breast and ovarian cancer cell lines. We used CRISPRn, CRISPRi, RNAi, and protein degradation to confirm the lethal effect of LIG1 inactivation at the DNA, RNA, and protein level in BRCA1-mutant cells in vitro. LIG1 inactivation resulted in viability loss across multiple BRCA1-mutated cell lines, whereas no effect was observed in BRCA1/2 wild-type cell lines, demonstrating target selectivity for the BRCA1-mutant context. On-target nature of the phenotype was demonstrated through rescue of viability with exogenous wild-type LIG1 cDNA. Next, we demonstrated a concentration-dependent relationship of LIG1 protein expression and BRCA1 mutant cell viability using a titratable, degradable LIG1 fusion protein. BRCA1 mutant viability required LIG1 catalytic activity, as catalytically dead mutant LIG1K568A failed to rescue viability loss caused by endogenous LIG1 depletion. LIG1 perturbation produced proportional increases in PAR staining in BRCA1 mutant cells, indicating a mechanism consistent with the function of LIG1 in sealing ssDNA nicks. Finally, we confirmed LIG1 hyperdependence in vivo using a xenograft model in which LIG1 loss resulted in tumor stasis in all mice. Our cumulative findings demonstrate that LIG1 is a promising synthetic lethal target for development in patients with BRCA1 mutant cancers.

CRISPR Cas9-based screening is a powerful approach for identifying and characterizing novel drug targets. Here, we elucidate the synthetic lethal mechanism of deubiquitinating enzyme USP1 in cancers with underlying DNA damage vulnerabilities, specifically BRCA1/2 mutant tumors and a subset of BRCA1/2 wild-type (WT) tumors. In sensitive cells, pharmacologic inhibition of USP1 leads to decreased DNA synthesis concomitant with S-phase-specific DNA damage. Genome-wide CRISPR-Cas9 screens identify RAD18 and UBE2K, which promote PCNA mono- and polyubiquitination respectively, as mediators of USP1 dependency. The accumulation of mono- and polyubiquitinated PCNA following USP1 inhibition is associated with reduced PCNA protein levels. Ectopic expression of WT or ubiquitin-dead K164R PCNA reverses USP1 inhibitor sensitivity. Our results show, for the first time, that USP1 dependency hinges on the aberrant processing of mono- and polyubiquitinated PCNA. Moreover, this mechanism of USP1 dependency extends beyond BRCA1/2 mutant tumors to selected BRCA1/2 WT cancer cell lines enriched in ovarian and lung lineages. We further show PARP and USP1 inhibition are strongly synergistic in BRCA1/2 mutant tumors. We postulate USP1 dependency unveils a previously uncharacterized vulnerability linked to posttranslational modifications of PCNA. Taken together, USP1 inhibition may represent a novel therapeutic strategy for BRCA1/2 mutant tumors and a subset of BRCA1/2 WT tumors., (©2022 The Authors; Published by the American Association for Cancer Research.)

Synthetic lethality is a genetic interaction that results in cell death when two genetic deficiencies co-occur but not when either deficiency occurs alone, which can be co-opted for cancer therapeutics. Pairs of paralog genes are among the most straightforward potential synthetic-lethal interactions by virtue of their redundant functions. Here, we demonstrate a paralog-based synthetic lethality by targeting vaccinia-related kinase 1 (VRK1) in glioblastoma (GBM) deficient of VRK2, which is silenced by promoter methylation in approximately two thirds of GBM. Genetic knockdown of VRK1 in VRK2-null or VRK2-methylated cells resulted in decreased activity of the downstream substrate barrier to autointegration factor (BAF), a regulator of post-mitotic nuclear envelope formation. Reduced BAF activity following VRK1 knockdown caused nuclear lobulation, blebbing, and micronucleation, which subsequently resulted in G2-M arrest and DNA damage. The VRK1-VRK2 synthetic-lethal interaction was dependent on VRK1 kinase activity and was rescued by ectopic expression of VRK2. In VRK2-methylated GBM cell line-derived xenograft and patient-derived xenograft models, knockdown of VRK1 led to robust tumor growth inhibition. These results indicate that inhibiting VRK1 kinase activity could be a viable therapeutic strategy in VRK2-methylated GBM., Significance: A paralog synthetic-lethal interaction between VRK1 and VRK2 sensitizes VRK2-methylated glioblastoma to perturbation of VRK1 kinase activity, supporting VRK1 as a drug discovery target in this disease., (©2022 The Authors; Published by the American Association for Cancer Research.)

Room temperature oxygen hydrogenation below graphene flakes supported by Ir(111) is investigated through a combination of X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations using an evolutionary search algorithm. We demonstrate how the graphene cover and its doping level can be used to trap and characterize dense mixed O-OH-H 2 O phases that otherwise would not exist. Our study of these graphene-stabilized phases and their response to oxygen or hydrogen exposure reveals that additional oxygen can be dissolved into them at room temperature creating mixed O-OH-H 2 O phases with an increased areal coverage underneath graphene. In contrast, additional hydrogen exposure converts the mixed O-OH-H 2 O phases back to pure OH-H 2 O with a reduced areal coverage underneath graphene., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Prodrugs engineered for preferential activation in diseased versus normal tissues offer immense potential to improve the therapeutic indexes (TIs) of preclinical and clinical-stage active pharmaceutical ingredients that either cannot be developed otherwise or whose efficacy or tolerability it is highly desirable to improve. Such approaches, however, often suffer from trial-and-error design, precluding predictive synthesis and optimization. Here, using bromodomain and extra-terminal (BET) protein inhibitors (BETi)-a class of epigenetic regulators with proven anticancer potential but clinical development hindered in large part by narrow TIs-we introduce a macromolecular prodrug platform that overcomes these challenges. Through tuning of traceless linkers appended to a "bottlebrush prodrug" scaffold, we demonstrate correlation of in vitro prodrug activation kinetics with in vivo tumor pharmacokinetics, enabling the predictive design of novel BETi prodrugs with enhanced antitumor efficacies and devoid of dose-limiting toxicities in a syngeneic triple-negative breast cancer murine model. This work may have immediate clinical implications, introducing a platform for predictive prodrug design and potentially overcoming hurdles in drug development.

At present there are no drugs for the treatment of chronic liver fibrosis that have been approved by the Food and Drug administration of the United States. Telmisartan, a small-molecule antihypertensive drug, displays antifibrotic activity, but its clinical use is limited because it causes systemic hypotension. Here, we report the scalable and convergent synthesis of macromolecular telmisartan prodrugs optimized for preferential release in diseased liver tissue. We optimized the release of active telmisartan in fibrotic liver to be depot-like (that is, a constant therapeutic concentration) through the molecular design of telmisartan brush-arm star polymers, and show that these lead to improved efficacy and to the avoidance of dose-limiting hypotension in both metabolically and chemically induced mouse models of hepatic fibrosis, as determined by histopathology, enzyme levels in the liver, intact-tissue protein markers, hepatocyte necrosis protection, and gene-expression analyses. In rats and dogs, the prodrugs are retained long-term in liver tissue and have a well-tolerated safety profile. Our findings support the further development of telmisartan prodrugs that enable infrequent dosing in the treatment of liver fibrosis., Competing Interests: Competing interests J.L., J.N.A, M.V.S, S.J.H, B.V., K.D.E, A.M.N., J.C.A., J.B., S.P., S.W.B., E.J.H., J.K.S-S., P.W.K., D.E.C., and P.B.-J. are former employees and shareholders of XTuit Pharmaceuticals. P.B.-J. is President and Founder of Acrivon Therapeutics. J.A.J. is a Co-Founder of Acrivon Therapeutics.

Proteins with domains that recognize and bind post-translational modifications (PTMs) of histones are collectively termed epigenetic readers. Numerous interactions between specific reader protein domains and histone PTMs and their regulatory outcomes have been reported, but little is known about how reader proteins may in turn be modulated by these interactions. Tripartite motif-containing protein 24 (TRIM24) is a histone reader aberrantly expressed in multiple cancers. Here, our investigation revealed functional cross-talk between histone acetylation and TRIM24 SUMOylation. Binding of TRIM24 to chromatin via its tandem PHD-bromodomain, which recognizes unmethylated lysine 4 and acetylated lysine 23 of histone H3 (H3K4me0/K23ac), led to TRIM24 SUMOylation at lysine residues 723 and 741. Inactivation of the bromodomain, either by mutation or with a small-molecule inhibitor, IACS-9571, abolished TRIM24 SUMOylation. Conversely, inhibition of histone deacetylation markedly increased TRIM24's interaction with chromatin and its SUMOylation. Of note, gene expression profiling of MCF7 cells expressing WT versus SUMO-deficient TRIM24 identified cell adhesion as the major pathway regulated by the cross-talk between chromatin acetylation and TRIM24 SUMOylation. In conclusion, our findings establish a new link between histone H3 acetylation and SUMOylation of the reader protein TRIM24, a functional connection that may bear on TRIM24's oncogenic function and may inform future studies of PTM cross-talk between histones and epigenetic regulators., (© 2018 Appikonda et al.)

In this study we report on the adsorbate structures on an Ir(1 1 1) surface during the phase transition from the inactive to the active state during CO oxidation. The CO oxidation over Pt(1 1 1) is used as a reference case. Where Pt(1 1 1) either is inactive and CO covered or active and O covered, Ir(1 1 1) exhibits a transition state with co-existing chemisorbed O and CO. The observed structural differences are explained in terms of DFT-calculated adsorption energies. For Pt(1 1 1) the repulsive CO-O interaction makes co-existing chemisorbed CO and O unfavourable, while for Ir(1 1 1) the stronger O and CO adsorption allows for overcoming the repulsive interaction. At the onset of CO oxidation over Ir(1 1 1), a CO structure containing defects forms, which enables O 2 to dissociatively adsorb on the Ir(1 1 1) surface, thus enabling the CO oxidation reaction. At the mass transfer limit, the Ir(1 1 1) surface is covered by a chemisorbed O structure with defects; hence, the active surface is predominately chemisorbed O covered at a total pressure of 0.5 mbar and no oxide formation is observed.

We have studied the reaction of phenylacetylene (PA) with chloro-, bromo-, and iodobenzene on the Au(1 1 1) surface as a model system for the gold-catalysed Sonogashira cross-coupling. Both ultrahigh vacuum-based and ambient pressure x-ray photoelectron spectroscopy show that iodo- and chlorobenzene (IB and CB) undergo the cross-coupling reaction towards diphenylacetylene. Bromobenzene (BB), in contrast, does not react in the UHV experiments. Further, at ambient pressure signs are found for poisoning of the Au(1 1 1) surface by a carbon species formed in the reaction. The understanding obtained in the reaction experiments are based on a thorough investigation of the adsorption of PA, IB, CB, and BB on the Au(1 1 1) surface by soft x-ray absorption spectroscopy and temperature-dependent x-ray photoelectron spectroscopy. In particular, the experiments provide the orientation of the intact adsorbates with respect to the surfaces at liquid nitrogen temperature. Dissociation in the temperature regime between  -80 and  -15 °C is observed for iodo- and chlorobenzene, but not for BB, in agreement with that only IB and CB, but not BB, react with PA to form diphenylacetylene. The difference is tentatively attributed to a difference in surface orientation of the different halobenzenes.

The expression of Tripartite motif-containing protein 28 (TRIM28)/Krüppel-associated box (KRAB)-associated protein 1 (KAP1), is elevated in at least 14 tumor types, including solid and hematopoietic tumors. High level of TRIM28 is associated with triple-negative subtype of breast cancer (TNBC), which shows higher aggressiveness and lower survival rates. Interestingly, TRIM28 is essential for maintaining the pluripotent phenotype in embryonic stem cells. Following on that finding, we evaluated the role of TRIM28 protein in the regulation of breast cancer stem cells (CSC) populations and tumorigenesis in vitro and in vivo. Downregulation of TRIM28 expression in xenografts led to deceased expression of pluripotency and mesenchymal markers, as well as inhibition of signaling pathways involved in the complex mechanism of CSC maintenance. Moreover, TRIM28 depletion reduced the ability of cancer cells to induce tumor growth when subcutaneously injected in limiting dilutions. Our data demonstrate that the downregulation of TRIM28 gene expression reduced the ability of CSCs to self-renew that resulted in significant reduction of tumor growth. Loss of function of TRIM28 leads to dysregulation of cell cycle, cellular response to stress, cancer cell metabolism, and inhibition of oxidative phosphorylation. All these mechanisms directly regulate maintenance of CSC population. Our original results revealed the role of the TRIM28 in regulating the CSC population in breast cancer. These findings may pave the way to novel and more effective therapies targeting cancer stem cells in breast tumors.

SPECIES is an undulator-based soft X-ray beamline that replaced the old I511 beamline at the MAX II storage ring. SPECIES is aimed at high-resolution ambient-pressure X-ray photoelectron spectroscopy (APXPS), near-edge X-ray absorption fine-structure (NEXAFS), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS) experiments. The beamline has two branches that use a common elliptically polarizing undulator and monochromator. The beam is switched between the two branches by changing the focusing optics after the monochromator. Both branches have separate exit slits, refocusing optics and dedicated permanent endstations. This allows very fast switching between two types of experiments and offers a unique combination of the surface-sensitive XPS and bulk-sensitive RIXS techniques both in UHV and at elevated ambient-pressure conditions on a single beamline. Another unique property of the beamline is that it reaches energies down to approximately 27 eV, which is not obtainable on other current APXPS beamlines. This allows, for instance, valence band studies under ambient-pressure conditions. In this article the main properties and performance of the beamline are presented, together with selected showcase experiments performed on the new setup.

The RAS-MAPK pathway controls many cellular programs, including cell proliferation, differentiation, and apoptosis. In colorectal cancers, recurrent mutations in this pathway often lead to increased cell signaling that may contribute to the development of neoplasms, thereby making this pathway attractive for therapeutic intervention. To this end, we developed a 26-member gene signature of RAS-MAPK pathway activity utilizing the Affymetrix QuantiGene Plex 2.0 reagent system and performed both primary and confirmatory gene expression-based high-throughput screens (GE-HTSs) using KRAS mutant colon cancer cells (SW837) and leveraging a highly annotated chemical library. The screen achieved a hit rate of 1.4% and was able to enrich for hit compounds that target RAS-MAPK pathway members such as MEK and EGFR. Sensitivity and selectivity performance measurements were 0.84 and 1.00, respectively, indicating high true-positive and true-negative rates. Active compounds from the primary screen were confirmed in a dose-response GE-HTS assay, a GE-HTS assay using 14 additional cancer cell lines, and an in vitro colony formation assay. Altogether, our data suggest that this GE-HTS assay will be useful for larger unbiased chemical screens to identify novel compounds and mechanisms that may modulate the RAS-MAPK pathway., (© 2016 Society for Laboratory Automation and Screening.)

Objective: To investigate associations between motor skills, exercise capacity and cognitive functions, and evaluate how they correlate to academic performance in mathematics and reading comprehension using standardised, objective tests., Methods: This cross-sectional study included 423 Danish children (age: 9.29±0.35 years, 209 girls). Fine and gross motor skills were evaluated in a visuomotor accuracy-tracking task, and a whole-body coordination task, respectively. Exercise capacity was estimated from the Yo-Yo intermittent recovery level 1 children's test (YYIR1C). Selected tests from the Cambridge Neuropsychological Test Automated Battery (CANTAB) were used to assess different domains of cognitive functions, including sustained attention, spatial working memory, episodic and semantic memory, and processing speed. Linear mixed-effects models were used to investigate associations between these measures and the relationship with standard tests of academic performance in mathematics and reading comprehension., Results: Both fine and gross motor skills were associated with better performance in all five tested cognitive domains (all P<0.001), whereas exercise capacity was only associated with better sustained attention (P<0.046) and spatial working memory (P<0.038). Fine and gross motor skills (all P<0.001), exercise capacity and cognitive functions such as working memory, episodic memory, sustained attention and processing speed were all associated with better performance in mathematics and reading comprehension., Conclusions: The data demonstrate that fine and gross motor skills are positively correlated with several aspects of cognitive functions and with academic performance in both mathematics and reading comprehension. Moreover, exercise capacity was associated with academic performance and performance in some cognitive domains. Future interventions should investigate associations between changes in motor skills, exercise capacity, cognitive functions, and academic performance to elucidate the causality of these associations., Competing Interests: The research grants received from the FIFA Medical Assessment and Research Centre (F-MARC) and the Danish Football Association (DBU) does not alter our adherence to PLOS ONE policies on sharing data and materials.

The bromodomain containing proteins TRIM24 (tripartite motif containing protein 24) and BRPF1 (bromodomain and PHD finger containing protein 1) are involved in the epigenetic regulation of gene expression and have been implicated in human cancer. Overexpression of TRIM24 correlates with poor patient prognosis, and BRPF1 is a scaffolding protein required for the assembly of histone acetyltransferase complexes, where the gene of MOZ (monocytic leukemia zinc finger protein) was first identified as a recurrent fusion partner in leukemia patients (8p11 chromosomal rearrangements). Here, we present the structure guided development of a series of N,N-dimethylbenzimidazolone bromodomain inhibitors through the iterative use of X-ray cocrystal structures. A unique binding mode enabled the design of a potent and selective inhibitor 8i (IACS-9571) with low nanomolar affinities for TRIM24 and BRPF1 (ITC Kd = 31 nM and ITC Kd = 14 nM, respectively). With its excellent cellular potency (EC50 = 50 nM) and favorable pharmacokinetic properties (F = 29%), 8i is a high-quality chemical probe for the evaluation of TRIM24 and/or BRPF1 bromodomain function in vitro and in vivo.

Background: Proteins that 'read' the histone code are central elements in epigenetic control and bromodomains, which bind acetyl-lysine motifs, are increasingly recognized as potential mediators of disease states. Notably, the first BET bromodomain-based therapies have entered clinical trials and there is a broad interest in dissecting the therapeutic relevance of other bromodomain-containing proteins in human disease. Typically, drug development is facilitated and expedited by high-throughput screening, where assays need to be sensitive, robust, cost-effective and scalable. However, for bromodomains, which lack catalytic activity that otherwise can be monitored (using classical enzymology), the development of cell-based, drug-target engagement assays has been challenging. Consequently, cell biochemical assays have lagged behind compared to other protein families (e.g., histone deacetylases and methyltransferases)., Results: Here, we present a suite of novel chromatin and histone-binding assays using AlphaLISA, in situ cell extraction and fluorescence-based, high-content imaging. First, using TRIM24 as an example, the homogenous, bead-based AlphaScreen technology was modified from a biochemical peptide-competition assay to measure binding of the TRIM24 bromodomain to endogenous histone H3 in cells (AlphaLISA). Second, a target agnostic, high-throughput imaging platform was developed to quantify the ability of chemical probes to dissociate endogenous proteins from chromatin/nuclear structures. While overall nuclear morphology is maintained, the procedure extracts soluble, non-chromatin-bound proteins from cells with drug-target displacement visualized by immunofluorescence (IF) or microscopy of fluorescent proteins. Pharmacological evaluation of these assays cross-validated their utility, sensitivity and robustness. Finally, using genetic and pharmacological approaches, we dissect domain contribution of TRIM24, BRD4, ATAD2 and SMARCA2 to chromatin binding illustrating the versatility/utility of the in situ cell extraction platform., Conclusions: In summary, we have developed two novel complementary and cell-based drug-target engagement assays, expanding the repertoire of pharmacodynamic assays for bromodomain tool compound development. These assays have been validated through a successful TRIM24 bromodomain inhibitor program, where a micromolar lead molecule (IACS-6558) was optimized using cell-based assays to yield the first single-digit nanomolar TRIM24 inhibitor (IACS-9571). Altogether, the assay platforms described herein are poised to accelerate the discovery and development of novel chemical probes to deliver on the promise of epigenetic-based therapies.

The SWI/SNF multisubunit complex modulates chromatin structure through the activity of two mutually exclusive catalytic subunits, SMARCA2 and SMARCA4, which both contain a bromodomain and an ATPase domain. Using RNAi, cancer-specific vulnerabilities have been identified in SWI/SNF-mutant tumors, including SMARCA4-deficient lung cancer; however, the contribution of conserved, druggable protein domains to this anticancer phenotype is unknown. Here, we functionally deconstruct the SMARCA2/4 paralog dependence of cancer cells using bioinformatics, genetic, and pharmacologic tools. We evaluate a selective SMARCA2/4 bromodomain inhibitor (PFI-3) and characterize its activity in chromatin-binding and cell-functional assays focusing on cells with altered SWI/SNF complex (e.g., lung, synovial sarcoma, leukemia, and rhabdoid tumors). We demonstrate that PFI-3 is a potent, cell-permeable probe capable of displacing ectopically expressed, GFP-tagged SMARCA2-bromodomain from chromatin, yet contrary to target knockdown, the inhibitor fails to display an antiproliferative phenotype. Mechanistically, the lack of pharmacologic efficacy is reconciled by the failure of bromodomain inhibition to displace endogenous, full-length SMARCA2 from chromatin as determined by in situ cell extraction, chromatin immunoprecipitation, and target gene expression studies. Furthermore, using inducible RNAi and cDNA complementation (bromodomain- and ATPase-dead constructs), we unequivocally identify the ATPase domain, and not the bromodomain of SMARCA2, as the relevant therapeutic target with the catalytic activity suppressing defined transcriptional programs. Taken together, our complementary genetic and pharmacologic studies exemplify a general strategy for multidomain protein drug-target validation and in case of SMARCA2/4 highlight the potential for drugging the more challenging helicase/ATPase domain to deliver on the promise of synthetic-lethality therapy., (©2015 American Association for Cancer Research.)

Using in situ surface-sensitive electron microscopy performed in real time, we show that the dynamics of micron-sized Ga droplets on GaP(111) can be manipulated locally using Au nanoparticles. Detailed measurements of structure and dynamics of the surface from microns to atomic scale are done using both surface electron and scanning probe microscopies. Imaging is done simultaneously on areas with and without Au particles and on samples spanning an order of magnitude in particle coverages. Based on this, we establish the equations of motion that can generally describe the Ga droplet dynamics, taking into account three general features: the affinity of Ga droplets to cover steps and rough structures on the surface, the evaporation-driven transition of the surface nanoscale morphology from rough to flat, and the enhanced evaporation due to Ga droplets and Au nanoparticles. Separately, these features can induce either self-propelled random motion or directional motion, but in combination, the self-propelled motion acts to increase the directional motion even if the directional force is 100 times weaker than the random force. We then find that the Au particles initiate a faster native oxide desorption and speed up the rough to flat surface transition in their vicinity. This changes the balance of forces on the Ga droplets near the Au particles, effectively deflecting the droplets from these areas. The model is experimentally verified for the present materials system, but due to its very general assumptions, it could also be relevant for the many other materials systems that display self-propelled random motion.

Preventing histone recognition by bromodomains emerges as an attractive therapeutic approach in cancer. Overexpression of ATAD2 (ATPase family AAA domain-containing 2 isoform A) in cancer cells is associated with poor prognosis making the bromodomain of ATAD2 a promising epigenetic therapeutic target. In the development of an in vitro assay and identification of small molecule ligands, we conducted structure-guided studies which revealed a conformationally flexible ATAD2 bromodomain. Structural studies on apo-, peptide-and small molecule-ATAD2 complexes (by co-crystallization) revealed that the bromodomain adopts a 'closed', histone-compatible conformation and a more 'open' ligand-compatible conformation of the binding site respectively. An unexpected conformational change of the conserved asparagine residue plays an important role in driving the peptide-binding conformation remodelling. We also identified dimethylisoxazole-containing ligands as ATAD2 binders which aided in the validation of the in vitro screen and in the analysis of these conformational studies.

Regular Pt cluster arrays grown on the moiré template formed by graphene on Ir(111) were tested for their stability with respect to CO gas exposure. Cluster stability and adsorption-induced processes were analyzed as a function of cluster size, with in situ scanning tunneling microscopy and X-ray photoelectron spectroscopy. Small clusters containing fewer than 10 atoms were unstable upon CO adsorption. They sintered through Smoluchowski ripening-cluster diffusion and coalescence-rather than the frequently reported Ostwald ripening mediated by metal-adsorbate complexes. Larger clusters remained immobile upon CO adsorption but became more three-dimensional. Careful analysis of the experimental data complemented by ab initio density functional theory calculations provides insight into the origin of the CO-induced Pt cluster ripening and shape transformations.

Using X-ray photoemission spectroscopy (XPS) and scanning tunneling microscopy (STM) we resolve the temperature-, time-, and flake size-dependent intercalation phases of oxygen underneath graphene on Ir(111) formed upon exposure to molecular oxygen. Through the applied pressure of molecular oxygen the atomic oxygen created on the bare Ir terraces is driven underneath graphene flakes. The importance of substrate steps and of the unbinding of graphene flake edges from the substrate for the intercalation is identified. With the use of CO titration to selectively remove oxygen from the bare Ir terraces the energetics of intercalation is uncovered. Cluster decoration techniques are used as an efficient tool to visualize intercalation processes in real space.

Using both synchrotron-based photoemission electron microscopy/spectroscopy and scanning tunneling microscopy/spectroscopy, we obtain a complete picture of the surface composition, morphology, and electronic structure of InP nanowires. Characterization is done at all relevant length scales from micrometer to nanometer. We investigate nanowire surfaces with native oxide and molecular adsorbates resulting from exposure to ambient air. Atomic hydrogen exposure at elevated temperatures which leads to the removal of surface oxides while leaving the crystalline part of the wire intact was also studied. We show how surface chemical composition will seriously influence nanowire electronic properties. However, opposite to, for example, Ge nanowires, water or sulfur molecules adsorbed on the exterior oxidized surfaces are of less relevance. Instead, it is the final few atomic layers of the oxide which plays the most significant role by strongly negatively doping the surface. The InP nanowires in air are rather insensitive to their chemical surroundings in contrast to what is often assumed for nanowires. Our measurements allow us to draw a complete energy diagram depicting both band gap and differences in electron affinity across an axial nanowire p-n junction. Our findings thus give a robust set of quantitative values relating surface chemical composition to specific electronic properties highly relevant for simulating the performance of nanoscale devices.

The new instrument for near-ambient-pressure X-ray photoelectron spectroscopy which has been installed at the MAX II ring of the Swedish synchrotron radiation facility MAX IV Laboratory in Lund is presented. The new instrument, which is based on a SPECS PHOIBOS 150 NAP analyser, is the first to feature the use of retractable and exchangeable high-pressure cells. This implies that clean vacuum conditions are retained in the instrument's analysis chamber and that it is possible to swiftly change between near-ambient and ultrahigh-vacuum conditions. In this way the instrument implements a direct link between ultrahigh-vacuum and in situ studies, and the entire pressure range from ultrahigh-vacuum to near-ambient conditions is available to the user. Measurements at pressures up to 10(-5) mbar are carried out in the ultrahigh-vacuum analysis chamber, while measurements at higher pressures are performed in the high-pressure cell. The installation of a mass spectrometer on the exhaust line of the reaction cell offers the users the additional dimension of simultaneous reaction data monitoring. Moreover, the chosen design approach allows the use of dedicated cells for different sample environments, rendering the Swedish ambient-pressure X-ray photoelectron spectroscopy instrument a highly versatile and flexible tool.

The O adsorption on Rh(100) has been studied using high resolution core level spectroscopy, low energy electron diffraction and scanning tunnelling microscopy. In addition to the well known (2 × 2), (2 × 2)-pg and c(8 × 2) structures at coverages of 0.25, 0.5 and 1.75 ML respectively, an intermediate (3 × 1) structure with a coverage of 2/3 ML is identified.

The structure and chemical composition of Pd nanoparticles exposed to pure CO and mixtures of CO and O(2) at elevated temperatures have been studied in situ by a combination of X-ray Diffraction and X-ray Photoelectron Spectroscopy in pressures ranging from ultra high vacuum to 10 mbar and from room temperature to a few hundred degrees celsius. Our investigation shows that under CO exposure, above a certain temperature, carbon dissolves into the Pd particles forming a carbide phase. Upon exposure to CO and O(2) mixtures, the carbide phase forms and disappears reversibly, switching at the stoichiometric ratio for CO oxidation. This finding opens new scenarios for the understanding of catalytic oxidation of C-based molecules.

The active phase of Pd during methane oxidation is a long-standing puzzle, which, if solved, could provide routes for design of improved catalysts. Here, density functional theory and in situ surface X-ray diffraction are used to identify and characterize atomic sites yielding high methane conversion. Calculations are performed for methane dissociation over a range of Pd and PdOx surfaces and reveal facile dissociation on either under-coordinated Pd sites in PdO(101) or metallic surfaces. The experiments show unambiguously that high methane conversion requires sufficiently thick PdO(101) films or metallic Pd, in full agreement with the calculations. The established link between high activity and atomic structure enables rational design of improved catalysts.

Defining master transcription factors governing somatic and cancer stem cell identity is an important goal. Here we show that the Oct4 paralog Oct1, a transcription factor implicated in stress responses, metabolic control, and poised transcription states, regulates normal and pathologic stem cell function. Oct1(HI) cells in the colon and small intestine co-express known stem cell markers. In primary malignant tissue, high Oct1 protein but not mRNA levels strongly correlate with the frequency of CD24(LO)CD44(HI) cancer-initiating cells. Reducing Oct1 expression via RNAi reduces the proportion of ALDH(HI) and dye efflux(HI) cells, and increasing Oct1 increases the proportion of ALDH(HI) cells. Normal ALDH(HI) cells harbor elevated Oct1 protein but not mRNA levels. Functionally, we show that Oct1 promotes tumor engraftment frequency and promotes hematopoietic stem cell engraftment potential in competitive and serial transplants. In addition to previously described Oct1 transcriptional targets, we identify four Oct1 targets associated with the stem cell phenotype. Cumulatively, the data indicate that Oct1 regulates normal and cancer stem cell function., Competing Interests: The authors have declared that no competing interests exist.

Protein tyrosine phosphatase 1B (PTP1B) plays important roles in downregulation of insulin and leptin signaling and is an established therapeutic target for diabetes and obesity. PTP1B is regulated by reactive oxygen species (ROS) produced in response to various stimuli, including insulin. The reversibly oxidized form of the enzyme (PTP1B-OX) is inactive and undergoes profound conformational changes at the active site. We generated conformation-sensor antibodies, in the form of single-chain variable fragments (scFvs), that stabilize PTP1B-OX and thereby inhibit its phosphatase function. Expression of conformation-sensor scFvs as intracellular antibodies (intrabodies) enhanced insulin-induced tyrosyl phosphorylation of the β subunit of the insulin receptor and its substrate IRS-1 and increased insulin-induced phosphorylation of PKB/AKT. Our data suggest that stabilization of the oxidized, inactive form of PTP1B with appropriate therapeutic molecules may offer a paradigm for phosphatase drug development., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Using X-ray photoelectron spectroscopy we studied the coadsorption of the amino acid L-cysteine and gold on a rutile TiO(2)(110) surface under ultrahigh vacuum conditions. Irrespective of the deposition order, i.e., irrespective of whether L-cysteine or gold is deposited first, the primary interaction between L-cysteine and the gold clusters formed at the surface takes place through the deprotonated thiol group of the molecule. The deposition order, however, has a profound influence on the size of the gold clusters as well as their location on the surface. If L-cysteine is deposited first the clusters are smaller by a factor two to three compared to gold deposited onto the pristine TiO(2)(110) surface and then covered by L-cysteine. Further, in the former case the clusters cover the molecules and thus form the outermost layer of the sample. We also find that above a minimum gold cluster size the gold cluster/L-cysteine bond is stronger than the L-cysteine/surface bridging oxygen vacancy bond, which, in turn, is stronger than the gold cluster/vacancy bond., (© 2011 American Chemical Society)