Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation.

Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin. We show that coordinate disruption of four CTCF motifs in the boundary fuses the adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes its robust induction. High-resolution micro-C maps reveal specific contact between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scales with FGF3 induction such that modest changes in contact frequency result in strong changes in expression, consistent with a causal relationship.

A Combination of Bio-Orthogonal Supramolecular Clicking and Proximity Chemical Tagging as a Supramolecular Tool for Discovery of Putative Proteins Associated with Laminopathic Disease.

Protein mutations alter protein-protein interactions that can lead to a number of illnesses. Mutations in lamin A (LMNA) have been reported to cause laminopathies. However, the proteins associated with the LMNA mutation have mostly remained unexplored. Herein, a new chemical tool for proximal proteomics is reported, developed by a combination of proximity chemical tagging and a bio-orthogonal supramolecular latching based on cucurbit[7]uril (CB[7])-based host-guest interactions. As this host-guest interaction acts as a noncovalent clickable motif that can be unclicked on-demand, this new chemical tool is exploited for reliable detection of the proximal proteins of LMNA and its mutant that causes laminopathic dilated cardiomyopathy (DCM). Most importantly, a comparison study reveals, for the first time, mutant-dependent alteration in LMNA proteomic environments, which allows to identify putative laminopathic DCM-linked proteins including FOXJ3 and CELF2. This study demonstrates the feasibility of this chemical tool for reliable proximal proteomics, and its immense potential as a new research platform for discovering biomarkers associated with protein mutation-linked diseases.

Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution.

Epigenetic modifications control the stability and translation of mRNA molecules. Here, we present a microscopy-based platform for quantifying modified RNA molecules and for relating the modification patterns to single-cell phenotypes. We directly capture mRNAs from cell lysates on oligo-dT-coated coverslips, then visually detect and sequence individual m6A-immunolabled transcripts without amplification. Integration of a nanoscale device enabled us to isolate single cells on the platform, and thereby relate single-cell m6A modification states to gene expression signatures and cell surface markers. Application of the platform to MUTZ3 leukemia cells revealed a marked reduction in cellular m6A levels as CD34+ leukemic progenitors differentiate to CD14+ myeloid cells. We then coupled single-molecule m6A detection with fluorescence in situ hybridization (FISH) to relate mRNA and m6A levels of individual genes to single-cell phenotypes. This single-cell multi-modal assay suite can empower investigations of RNA modifications in rare populations and single cells.

Supra-blot: an accurate and reliable assay for detecting target proteins with a synthetic host molecule-enzyme hybrid.

In accordance with the rapid increase in demand for selective and spatial chemical tagging, and accurate detection of proteins of interest, we develop a sensitive protein detection method, termed "Supra-blot" capitalizing on high-affinity host-guest interaction between cucurbit[7]uril (CB[7]) and adamantylammonium (AdA). The method can directly detect chemically tagged proteins without false-positive signals caused by endogenous biomolecules. Not only a single specific protein, but also spatially localized proteins in cells were labeled with AdA, and selectively detected by a host molecule-enzyme hybrid, CB[7]-conjugated horseradish peroxidase (CB[7]-HRP) generating amplified chemiluminescence signals. This study shows the great potential of Supra-blot for accurate and reliable detection of proteins of interest in cells.

Direct Profiling the Post-Translational Modification Codes of a Single Protein Immobilized on a Surface Using Cu-free Click Chemistry.

Combinatorial post-translational modifications (PTMs), which can serve as dynamic "molecular barcodes", have been proposed to regulate distinct protein functions. However, studies of combinatorial PTMs on single protein molecules have been hindered by a lack of suitable analytical methods. Here, we describe erasable single-molecule blotting (eSiMBlot) for combinatorial PTM profiling. This assay is performed in a highly multiplexed manner and leverages the benefits of covalent protein immobilization, cyclic probing with different antibodies, and single molecule fluorescence imaging. Especially, facile and efficient covalent immobilization on a surface using Cu-free click chemistry permits multiple rounds (>10) of antibody erasing/reprobing without loss of antigenicity. Moreover, cumulative detection of coregistered multiple data sets for immobilized single-epitope molecules, such as HA peptide, can be used to increase the antibody detection rate. Finally, eSiMBlot enables direct visualization and quantitative profiling of combinatorial PTM codes at the single-molecule level, as we demonstrate by revealing the novel phospho-codes of ligand-induced epidermal growth factor receptor. Thus, eSiMBlot provides an unprecedentedly simple, rapid, and versatile platform for analyzing the vast number of combinatorial PTMs in biological pathways.

Supramolecular latching system based on ultrastable synthetic binding pairs as versatile tools for protein imaging.

Here we report ultrastable synthetic binding pairs between cucurbit[7]uril (CB[7]) and adamantyl- (AdA) or ferrocenyl-ammonium (FcA) as a supramolecular latching system for protein imaging, overcoming the limitations of protein-based binding pairs. Cyanine 3-conjugated CB[7] (Cy3-CB[7]) can visualize AdA- or FcA-labeled proteins to provide clear fluorescence images for accurate and precise analysis of proteins. Furthermore, controllability of the system is demonstrated by treating with a stronger competitor guest. At low temperature, this allows us to selectively detach Cy3-CB[7] from guest-labeled proteins on the cell surface, while leaving Cy3-CB[7] latched to the cytosolic proteins for spatially conditional visualization of target proteins. This work represents a non-protein-based bioimaging tool which has inherent advantages over the widely used protein-based techniques, thereby demonstrating the great potential of this synthetic system.

Autophagy Caught in the Act: A Supramolecular FRET Pair Based on an Ultrastable Synthetic Host-Guest Complex Visualizes Autophagosome-Lysosome Fusion.

A supramolecular FRET pair based on the ultrahigh binding affinity between cyanine 3 conjugated cucurbit[7]uril (CB[7]-Cy3) and cyanine 5 conjugated adamantylamine (AdA-Cy5) was exploited as a new synthetic tool for imaging cellular processes in live cells. Confocal laser scanning microscopy revealed that CB[7]-Cy3 and AdA-Cy5 were intracellularly translocated and accumulated in lysosomes and mitochondria, respectively. CB[7]-Cy3 and AdA-Cy5 then formed a host-guest complex, reported by a FRET signal, as a result of the fusion of lysosomes and mitochondria. This observation not only indicated that CB[7] forms a stable complex with AdA in a live cell, but also suggested that this FRET pair can visualize dynamic organelle fusion processes, such as those involved in the degradation of mitochondria through autophagy (mitophagy), by virtue of its small size, chemical stability, and ease of use.

Iodide-Selective Synthetic Ion Channels Based on Shape-Persistent Organic Cages.

We report here a synthetic ion channel developed from a shape-persistent porphyrin-based covalent organic cage. The cage was synthesized by employing a synthetically economical dynamic covalent chemistry (DCC) approach. The organic cage selectively transports biologically relevant iodide ions over other inorganic anions by a dehydration-driven, channel mechanism as evidenced by vesicle-based fluorescence assays and planar lipid bilayer-based single channel recordings. Furthermore, the organic cage appears to facilitate iodide transport across the membrane of a living cell, suggesting that the cage could be useful as a biological tool that may replace defective iodide channels in living systems.

Pairwise detection of site-specific receptor phosphorylations using single-molecule blotting.

Post-translational modifications (PTMs) of receptor tyrosine kinases (RTKs) at the plasma membrane (PM) determine the signal transduction efficacy alone and in combination. However, current approaches to identify PTMs provide ensemble results, inherently overlooking combinatorial PTMs in a single polypeptide molecule. Here, we describe a single-molecule blotting (SiMBlot) assay that combines biotinylation of cell surface receptors with single-molecule fluorescence microscopy. This method enables quantitative measurement of the phosphorylation status of individual membrane receptor molecules and colocalization analysis of multiple immunofluorescence signals to directly visualize pairwise site-specific phosphorylation patterns at the single-molecule level. Strikingly, application of SiMBlot to study ligand-dependent epidermal growth factor receptor (EGFR) phosphorylation, which is widely thought to be multi-phosphorylated, reveals that EGFR on cell membranes is hardly multi-phosphorylated, unlike in vitro autophosphorylated EGFR. Therefore, we expect SiMBlot to aid understanding of vast combinatorial PTM patterns, which are concealed in ensemble methods, and to broaden knowledge of RTK signaling.

Endothelial deletion of phospholipase D2 reduces hypoxic response and pathological angiogenesis.

OBJECTIVE: Aberrant regulation of the proliferation, survival, and migration of endothelial cells (ECs) is closely related to the abnormal angiogenesis that occurs in hypoxia-induced pathological situations, such as cancer and vascular retinopathy. Hypoxic conditions and the subsequent upregulation of hypoxia-inducible factor-1α and target genes are important for the angiogenic functions of ECs. Phospholipase D2 (PLD2) is a crucial signaling mediator that stimulates the production of the second messenger phosphatidic acid. PLD2 is involved in various cellular functions; however, its specific roles in ECs under hypoxia and in vivo angiogenesis remain unclear. In the present study, we investigated the potential roles of PLD2 in ECs under hypoxia and in hypoxia-induced pathological angiogenesis in vivo. APPROACH AND RESULTS: Pld2 knockout ECs exhibited decreased hypoxia-induced cellular responses in survival, migration, and thus vessel sprouting. Analysis of hypoxia-induced gene expression revealed that PLD2 deficiency disrupted the upregulation of hypoxia-inducible factor-1α target genes, including VEGF, PFKFB3, HMOX-1, and NTRK2. Consistent with this, PLD2 contributed to hypoxia-induced hypoxia-inducible factor-1α expression at the translational level. The roles of PLD2 in hypoxia-induced in vivo pathological angiogenesis were assessed using oxygen-induced retinopathy and tumor implantation models in endothelial-specific Pld2 knockout mice. Pld2 endothelial-specific knockout retinae showed decreased neovascular tuft formation, despite a larger avascular region. Tumor growth and tumor blood vessel formation were also reduced in Pld2 endothelial-specific knockout mice. CONCLUSIONS: Our findings demonstrate a novel role for endothelial PLD2 in the survival and migration of ECs under hypoxia via the expression of hypoxia-inducible factor-1α and in pathological retinal angiogenesis and tumor angiogenesis in vivo.

Proteomic analysis of hypoxia-induced U373MG glioma secretome reveals novel hypoxia-dependent migration factors.

High-grade gliomas are one of the most common brain tumors and notorious for poor prognosis due to their malignant nature. Gliomas have an extensive area of hypoxia, which is critical for glioma progression by inducing aggressiveness and activating the angiogenesis process in the tumor microenvironment. To resolve the factors responsible for the highly malignant nature of gliomas, we comprehensively profiled the U373MG glioma cell secretome-exosome and soluble fraction under hypoxic and normoxic conditions. A total of 239 proteins were identified from the exosome and soluble fractions. Vascular endothelial growth factor, stanniocalcin 1 (STC1) and stanniocalcin 2, and insulin-like growth factor binding protein 3 and 6, enriched in the soluble fraction, and lysyl oxidase homolog 2 enriched in the exosomal fraction were identified as upregulated proteins by hypoxia based on a label-free quantitative analysis. STCs and insulin-like growth factor binding proteins, which were identified as secretory proteins under hypoxic conditions, were highly correlated with glioma grade in human patients by microarray analysis. An in vitro scratch wound assay revealed that STC1 and 2 have important functions in the induction of cell migration in a hypoxia-dependent manner, suggesting that they are hypoxia-dependent migration factors.

Computational design of binding proteins to EGFR domain II.

We developed a process to produce novel interactions between two previously unrelated proteins. This process selects protein scaffolds and designs protein interfaces that bind to a surface patch of interest on a target protein. Scaffolds with shapes complementary to the target surface patch were screened using an exhaustive computational search of the human proteome and optimized by directed evolution using phage display. This method was applied to successfully design scaffolds that bind to epidermal growth factor receptor (EGFR) domain II, the interface of EGFR dimerization, with high reactivity toward the target surface patch of EGFR domain II. One potential application of these tailor-made protein interactions is the development of therapeutic agents against specific protein targets.

Effect of organic vapors on Au, Ag, and Au-Ag alloy nanoparticle films with adsorbed 2,6-dimethylphenyl isocyanide.

The physicochemical properties of metallic substrates are affected by the environment in different ways. It is generally difficult to determine these effects because the molecules in the environment interact weakly with metallic substrates. In this work, we demonstrate that even the effect of volatile organic compounds (VOCs) can be identified by utilizing the surface-enhanced Raman scattering of isocyanide molecules. The NC stretching band of 2,6-dimethylphenyl isocyanide (2,6-DMPI) adsorbed on Au, for instance, is blueshifted by 6 cm(-1) under an acetone flow and is redshifted by 20 cm(-1) under an ammonia flow. The same band of 2,6-DMPI adsorbed on Ag and Au0.5Ag0.5 alloy films is, however, redshifted equally by 8 and 13 cm(-1) under acetone and ammonia flows, respectively. This indicates that although the surface plasmons of Au0.5Ag0.5 alloy nanoparticles are clearly distinct from those of Ag (as well as Au) nanoparticles, both Au0.5Ag0.5 and Ag nanoparticles show a similar response to VOCs. These observations led us to conclude that the outermost parts of Au-Ag alloy nanoparticles are enriched with Ag atoms and that only the surfaces of metal nanoparticles, and not the bulk material, are affected by VOCs.

Raman spectral characteristics of 4-aminobenzenethiol adsorbed on ZnO nanorod arrays.

Interest in the surface-enhanced Raman scattering (SERS) of 4-aminobenzenethiol (4-ABT) has surged recently. The SERS spectral features are highly dependent on the measurement conditions; a notable example is the appearance of b2-type bands that are not evident in the normal Raman (NR) spectrum. In an effort to discover new information and make any necessary corrections, we measured the Raman spectrum of 4-ABT adsorbed on a semiconducting material that would only enable the chemical enhancement mechanism; accordingly, the Raman spectrum of 4-ABT adsorbed on ZnO nanorods grown on an indium tin oxide substrate was measured for the first time. In the NR spectrum of the zinc salt of 4-ABT, which was taken as a reference, only the a1-type bands of 4-ABT were identified. However, in the surface Raman spectrum of 4-ABT on ZnO, the b2-type bands were also clearly evident, suggesting that the b2-type bands arose owing to its adsorption onto ZnO. The b2-type bands were also observed for 4-ABT analogs adsorbed on ZnO; this confirms that the b2-type bands were not a result of a surface-catalyzed photoreaction. Based on electric-potential and excitation-wavelength dependence studies, the a1- and b2-type bands were attributed to a charge-transfer (CT) transition from the surface defect levels of ZnO to the unoccupied La and Lb states (in Platt's notation) of 4-ABT, respectively; the bands gained intensity via the Herzberg-Teller coupling terms. The enhancement factor associated with the CT transition was estimated to be around 22, suggesting that it is, at best, a moderately effective process.

Photoreduction of 4,4'-dimercaptoazobenzene on ag revealed by Raman scattering spectroscopy.

The surface-enhanced Raman scattering (SERS) of 4,4'-dimercaptoazobenzene (4,4'-DMAB) has recently seen a surge of interest, since it might be possible to form 4,4'-DMAB from 4-aminobenzenethiol (4-ABT) via a surface-induced photoreaction. We found in this study, however, that the reverse conversion of 4,4'-DMAB to 4-ABT on Ag is a more feasible process upon irradiation with a 514.5 nm (not 632.8 nm) laser under ambient conditions. First of all, the SERS spectral pattern of 4,4'-DMAB on Ag varied as a function of laser irradiation time, finally becoming the same as that of 4-ABT on Ag. Second, the coupling reaction with 4-cyanobenzoic acid to form amide bonds proceeded readily like 4-ABT once 4,4'-DMAB on Ag was exposed to 514.5 nm radiation. Third, the growth of a calcite crystal occurred on 4,4'-DMAB on Ag, also likely on 4-ABT, when it was exposed to 514.5 nm radiation beforehand. All of these results led us to conclude that the appearance of the so-called b(2)-type bands in the SERS of 4-ABT must be due to the involvement of the chemical enhancement mechanism, not due to the formation of 4,4'-DMAB.

Selective detection of aqueous nitrite ions by surface-enhanced Raman scattering of 4-aminobenzenethiol on Au.

In this work, we have devised a selective nitrite-ion detection method based on the surface-enhanced Raman scattering (SERS) of 4-aminobenzenethiol (4-ABT) on Au. This is possible because, firstly, SERS is a very surface-sensitive technique with monolayer detection capability, and secondly, the amine group of 4-ABT reacts readily with nitrites in acidic media, forming a diazonium group, which can subsequently form an azo bond by reacting with a variety of benzene derivatives. From the peak intensity of the diazonium group, the presence of nitrite ions above 20 µM can be identified readily. From the peak intensity of the azo moiety alone, it is even possible to detect nitrite ions at concentrations as low as 5 µM, without interference from other anions. This work clearly illustrates the usefulness of SERS in environmental science research.

PDZ domain-containing 1 (PDZK1) protein regulates phospholipase C-ß3 (PLC-ß3)-specific activation of somatostatin by forming a ternary complex with PLC-ß3 and somatostatin receptors.

Phospholipase C-ß (PLC-ß) is a key molecule in G protein-coupled receptor (GPCR)-mediated signaling. Many studies have shown that the four PLC-ß subtypes have different physiological functions despite their similar structures. Because the PLC-ß subtypes possess different PDZ-binding motifs, they have the potential to interact with different PDZ proteins. In this study, we identified PDZ domain-containing 1 (PDZK1) as a PDZ protein that specifically interacts with PLC-ß3. To elucidate the functional roles of PDZK1, we next screened for potential interacting proteins of PDZK1 and identified the somatostatin receptors (SSTRs) as another protein that interacts with PDZK1. Through these interactions, PDZK1 assembles as a ternary complex with PLC-ß3 and SSTRs. Interestingly, the expression of PDZK1 and PLC-ß3, but not PLC-ß1, markedly potentiated SST-induced PLC activation. However, disruption of the ternary complex inhibited SST-induced PLC activation, which suggests that PDZK1-mediated complex formation is required for the specific activation of PLC-ß3 by SST. Consistent with this observation, the knockdown of PDZK1 or PLC-ß3, but not that of PLC-ß1, significantly inhibited SST-induced intracellular Ca(2+) mobilization, which further attenuated subsequent ERK1/2 phosphorylation. Taken together, our results strongly suggest that the formation of a complex between SSTRs, PDZK1, and PLC-ß3 is essential for the specific activation of PLC-ß3 and the subsequent physiologic responses by SST.

Surface-enhanced Raman scattering of 4,4'-dimercaptoazobenzene trapped in Au nanogaps.

The surface-enhanced Raman scattering (SERS) of 4,4'-dimercaptoazobenzene (4,4'-DMAB), an alpha, omega-dithiol possessing also an azo moiety, has seen a surge of interest recently, since 4,4'-DMAB might be able to form from 4-aminobenzenethiol (4-ABT) via a surface-induced photoreaction. An understanding of the intrinsic SERS characteristics of 4,4'-DMAB is thus very important to evaluate the possibility of such a photoreaction. We found in this work that 4,4'-DMAB should adsorb on a flame-annealed Au substrate via one of its two thiol groups such that Au nanoparticles could adsorb further on the pendent thiol group, forming a SERS hot site. The most distinctive feature in the SERS of 4,4'-DMAB was the appearance of a(g) bands, which were quite similar to the b(2)-type bands occurring in the SERS of 4-ABT. In an electrochemical environment, the a(g) bands of 4,4'-DMAB at 1431, 1387, and 1138 cm(-1) became weakened at lower potentials, completely disappearing at -1.0 V, but the bands were restored upon increasing the electrode potential, implying that neither electro- nor photo-chemical reaction to break the azo group took place, in agreement with data from a cyclic voltammogram. The appearance and disappearance of these a(g) bands are thus concluded to be associated with the charge transfer phenomenon: 4,4'-DMAB must then be one of a unique group of compounds exhibiting chemical enhancement when subjected to a SERS environment.

Effect of volatile organic chemicals on surface-enhanced Raman scattering of 4-aminobenzenethiol on Ag: comparison with the potential dependence.

4-Aminobenzenethiol (4-ABT) is an unusual molecule in the sense that several distinct peaks whose counterparts are rarely found in the normal Raman spectrum are observed in its surface-enhanced Raman scattering (SERS) spectra. Their origin has been argued over recently as due to either a metal-to-adsorbate charge transfer or the formation of a photoreaction product such as dimercaptoazobenzene (DMAB). In an electrochemical SERS measurement, the intensities of the new peaks depended strongly not only on the excitation wavelength but also on the electrode potential. Interestingly, we observed a similar spectral variation even under ambient conditions by exposure of 4-ABT on Ag to volatile organic chemicals (VOCs) such as acetone and ammonia. Since acetone and ammonia barely react directly with 4-ABT, the effect of VOCs must be indirect, presumably associated with the movement of electrons between VOCs and the Ag substrate causing either an increase or a decrease in the surface potential of Ag. Based on the potential-dependent SERS data, the effect of acetone therefore appeared to correspond to an application of +0.15 V to the Ag substrate vs. a saturated Ag/AgCl electrode, while the effect of ammonia corresponded to the application of -0.45 V to Ag. We admit that much the same VOC effect could be observable if a photoproduct was formed immediately upon irradiation and the product was also subjected to a chemical enhancement mechanism. The Gaussian response of the peak intensities of the b(2)-type bands to applied potential, as well as to VOCs, dictated that the new peaks appearing in the SERS of 4-ABT have nothing to do with any electrochemical reaction. In addition, a separate preliminary work suggested that the b(2)-type bands are not at least due to a photoreaction product such as DMAB.

Effect of organic vapors and potential-dependent Raman scattering of 2,6-dimethylphenylisocyanide on platinum nanoaggregates.

The surface-enhanced Raman scattering characteristics of 2,6-dimethylphenylisocyanide (2,6-DMPI) on Pt nanoaggregates, in ambient and electrochemical environments and in the presence of organic vapors, were examined and compared with those on Au nanoaggregates. Due to the exclusive adsorption via the isocyanide group, the NC stretching band was very susceptible to the measurement conditions although the ring associated bands showed negligible peak shifts. In ambient conditions, the peak shift of the NC stretching vibration on Pt (29 cm(-1)) was one half of that on Au (61 cm(-1)), suggesting that the electron donation capability of the isocyanide group to Au was greater than that to Pt. In the electrochemical environment, the NC stretching peak varied linearly with slopes of ∼42 and ∼36 cm(-1) V(-1) on Pt and Au, respectively. On the other hand, the NC stretching bands of 2,6-DMPI on Pt red-shifted by as much as 15 and 41 cm(-1), in the presence of acetone and ammonia, respectively, corresponding to the lowering of the surface potential of Pt nanoaggregates from +0.2 to -0.2 and -0.8 V, respectively. On Au nanoaggregates, however, acetone appeared to increase the surface potential of Au from +0.2 to +0.3 V, although ammonia decreased the surface potential from +0.2 to -0.4 V. Acetone must then act as an electron donor when interacting with Pt while it serves as an electron acceptor when interacting with Au, in agreement with an ab initio quantum mechanical calculation.