In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures.

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Material properties are sensitive to atomistic structure defects such as vacancies or impurities, and it is therefore important to determine not only the local atomic configuration but also their chemical bonding state. Annular dark-field scanning transmission electron microscopy (STEM) combined with electron energy-loss spectroscopy has been utilized to investigate the local electronic structures of such defects down to the level of single atoms. However, it is still challenging to two-dimensionally map the local bonding states, because the electronic fine-structure signal from a single atom is extremely weak. Here, we show that atomic-resolution differential phase-contrast STEM imaging can directly visualize the anisotropy of single Si atomic electric fields in monolayer graphene. We also visualize the atomic electric fields of Stone–Wales defects and nanopores in graphene. Our results open the way to directly examine the local chemistry of the defective structures in materials at atomistic dimensions.

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Werner's syndrome is a potential model of accelerated human aging. The gene responsible for Werner's syndrome encodes a protein that has a helicase domain homologous to Escherichia coli RecQ. To identify binding partners that regulate the function in concert with Wrn, we screened for proteins using the yeast two-hybrid system with mouse Wrn as bait and found three. One was a novel protein, and the other two were mouse Ubc9 and SUMO-1. Ubc9 also interacted with the mouse homologue of the Bloom's syndrome gene product, another eukaryotic RecQ-type helicase, but not mouse DNA helicase Q1/RecQL (RecQL1). Deletion experiments indicated that both proteins interacted with the N-terminal segment of Wrn (amino acid 272-514). The interaction between Wrn and SUMO-1 was weaker than that between Wrn and Ubc9. Positive interaction was observed in the heterogeneous combination of Wrn and yeast Ubc9 (yUbc9), as well as yUbc9 and SUMO-1, in the two-hybrid system. The interaction between yUbc9 and SUMO-1 was abolished by deleting the C-terminal Gly residue of SUMO-1, which is reportedly required for the formation of Ubc9-SUMO-1 thioester linkage. The interaction of Wrn and SUMO-1 was also abolished by deleting the Gly residue, indicating that the interaction of Wrn and SUMO-1 is mediated by yUbc9 in the two-hybrid system. Finally, we confirmed by immunoblotting with an anti-SUMO-1 antibody that Wrn was covalently attached with SUMO-1.

Bloom's syndrome (BS) is an autosomal disorder characterized by predisposition to a wide variety of cancers. The gene product whose mutation leads to BS is the RecQ family helicase BLM, which forms a complex with DNA topoisomerase III␣ (Top3␣). However, the physiological relevance of the interaction between BLM and Top3␣ within the cell remains unclear. We show here that Top3␣ depletion causes accumulation of cells in G 2 phase, enlargement of nuclei, and chromosome gaps and breaks that occur at the same position in sister chromatids. The transition from metaphase to anaphase is also inhibited. All of these phenomena except cell lethality are suppressed by BLM gene disruption. Taken together with the biochemical properties of BLM and Top3␣, these data indicate that BLM and Top3␣ execute the dissolution of sister chromatids.Eukaryotic TOP3 was first identified in Saccharomyces cerevisiae as a gene that is required to suppress recombination between repeated sequences (28). Deletion of TOP3 results in a slow-growth phenotype that is suppressed by the disruption of SGS1, the gene encoding the sole RecQ helicase in S. cerevisiae (5). Further analyses revealed that the function of Sgs1 is closely associated with that of DNA topoisomerase III (Top3) (2,13,19,27). The close relationship between RecQ helicases and Top3 seems to be maintained in higher eukaryotes. Higher eukaryotic cells have two Top3s, Top3␣ and Top3␤ (8,22,23). Knocking out the Top3␣ gene in mice results in embryonic lethality (17), while knocking out Top3␤ does not affect development but reduces the life span (15). Various Top3 and RecQ helicase molecules have been reported to interact physically, including Top3␣ and BLM (35), one of the RecQ family helicases in higher eukaryotic cells (3). BLM is a causative gene for Bloom's syndrome (3), which is an autosomal disorder characterized by predisposition to a wide variety of cancers (6). Biochemical analyses have suggested that BLM and Top3␣ together affect the in vitro resolution of a recombination intermediate containing a double Holliday junction (HJ) via a double-junction dissolution mechanism (34). However, the phenotypes of cells that lack Top3␣ have not been characterized precisely, since TOP3␣ knockout is lethal. Furthermore, the phenotypes of Top3␣-depleted cells before they die have not been examined. Moreover, the physiological relevance of the interaction between BLM and Top3␣ within the cell remains unclear. Therefore, elucidating higher eukaryotic Top3␣ function may enhance our understanding of the physiological roles of BLM.In this study, to assess the function of Top3␣ and its interactions with BLM, we constructed cells whose expression of Top3␣ can be switched off by doxycycline hydrochloride (Dox) treatment. To our knowledge, we present the first evidence to support the hypothesis that vertebrate Top3␣ together with the BLM helicase executes the dissolution of sister chromatids during DNA replication. MATERIALS AND METHODSPlasmid construction. Fragments of chicken TOP3␣ and TOP3␤ cDNAs ...

Early clinical trials using murine double minute 2 (MDM2) inhibitors demonstrated proof-of-concept of p53-induced apoptosis by MDM2 inhibition in cancer cells; however, not all wild-type tumors are sensitive to MDM2 inhibition. Therefore, more potent inhibitors and biomarkers predictive of tumor sensitivity are needed. The novel MDM2 inhibitor DS-3032b is 10-fold more potent than the first-generation inhibitor nutlin-3a. mutations were predictive of resistance to DS-3032b, and allele frequencies of mutations were negatively correlated with sensitivity to DS-3032b. However, sensitivity to DS-3032b of wild-type tumors varied greatly. We thus used two methods to create predictive gene signatures. First, by comparing sensitivity to MDM2 inhibition with basal mRNA expression profiles in 240 cancer cell lines, a 175-gene signature was defined and validated in patient-derived tumor xenograft models and human acute myeloid leukemia (AML) cells. Second, an AML-specific 1,532-gene signature was defined by performing random forest analysis with cross-validation using gene expression profiles of 41 primary AML samples. The combination of mutation status with the two gene signatures provided the best positive predictive values (81% and 82%, compared with 62% for mutation status alone). In addition, the top-ranked 50 genes selected from the AML-specific 1,532-gene signature conserved high predictive performance, suggesting that a more feasible size of gene signature can be generated through this method for clinical implementation. Our model is being tested in ongoing clinical trials of MDM2 inhibitors. This study demonstrates that gene expression profiling combined with mutational status predicts antitumor effects of MDM2 inhibitors and .

Chondrosarcoma is the second most common malignant bone tumor. It is characterized by low vascularity and an abundant extracellular matrix, which confer these tumors resistance to chemotherapy and radiotherapy. There are currently no effective treatment options for relapsed or dedifferentiated chondrosarcoma, and new targeted therapies need to be identified. Isocitrate dehydrogenase (IDH) mutations, which are detected in~50% of chondrosarcoma patients, contribute to malignant transformation by catalyzing the production of 2-hydroxyglutarate (2-HG), a competitive inhibitor of α-ketoglutaratedependent dioxygenases. Mutant IDH inhibitors are therefore potential novel anticancer drugs in IDH mutant tumors. Here, we examined the efficacy of the inhibition of mutant IDH1 as an antitumor approach in chondrosarcoma cells in vitro and in vivo, and investigated the association between the IDH mutation and chondrosarcoma cells. DS-1001b, a novel, orally bioavailable, selective mutant IDH1 inhibitor, impaired the proliferation of chondrosarcoma cells with IDH1 mutations in vitro and in vivo, and decreased 2-HG levels. RNA-seq analysis showed that inhibition of mutant IDH1 promoted chondrocyte differentiation in the conventional chondrosarcoma L835 cell line and caused cell cycle arrest in the dedifferentiated JJ012 cell line. Mutant IDH1-mediated modulation of SOX9 and CDKN1C expression regulated chondrosarcoma tumor progression, and DS-1001b upregulated the expression of these genes via a common mechanism involving the demethylation of H3K9me3. DS-1001b treatment reversed the epigenetic changes caused by aberrant histone modifications. The present data strongly suggest that inhibition of mutant IDH1 is a promising therapeutic approach in chondrosarcoma, particularly for the treatment of relapsed or dedifferentiated chondrosarcoma.