ICBcomb: a comprehensive expression database for immune checkpoint blockade combination therapy.

The success of immune checkpoint blockade (ICB) promotes the immunotherapy to be a new pillar in cancer treatment. However, the low response rate of the ICB therapy limits its application. To increase the response rate and enhance efficacy, the ICB combination therapy has emerged and its clinical trials are increasing. Nevertheless, the gene expression profile and its pattern of ICB combination were not comprehensively studied, which limits the understanding of the ICB combination therapy and the identification of new drugs. Here, we constructed ICBcomb (http://bioinfo.life.hust.edu.cn/ICBcomb/), a comprehensive database, by analyzing the human and mouse expression data of the ICB combination therapy and comparing them between groups treated with ICB, other drugs or their combinations. ICBcomb contains 1399 samples across 29 cancer types involving 52 drugs. It provides a user-friendly web interface for demonstrating the results of the available comparisons in the ICB combination therapy datasets with five functional modules: [1, 2] the 'Dataset/Disease' modules for browsing the expression, enrichment and comparison results in each dataset or disease; [3] the 'Gene' module for inputting a gene symbol and displaying its expression and comparison results across datasets/diseases; [4] the 'Gene Set' module for GSVA/GSEA enrichment analysis on the built-in gene sets and the user-input gene sets in different comparisons; [5] the 'Immune Cell' module for immune cell infiltration comparison between different groups by immune cell abundance analysis. The ICBcomb database provides the first resource for gene expression profile and comparison in ICB combination therapy, which may provide clues for discovering the mechanism of effective combination strategies and new combinatory drugs.

Spatially Dependent in-Gap States Induced by Andreev Tunneling through a Single Electronic State.

By using low-temperature scanning tunneling microscopy and spectroscopy (STM/STS), we observe in-gap states induced by Andreev tunneling through a single impurity state in a low carrier density superconductor (NaAlSi). The energy-symmetric in-gap states appear when the impurity state is located within the superconducting gap. In-gap states can cross the Fermi level, and they show X-shaped spatial variation. We interpret the in-gap states as a consequence of the Andreev tunneling through the impurity state, which involves the formation or breakup of a Cooper pair. Due to the low carrier density in NaAlSi, the in-gap state is tunable by controlling the STM tip-sample distance. Under strong external magnetic fields, the impurity state shows Zeeman splitting when it is located near the Fermi level. Our findings not only demonstrate the Andreev tunneling involving single electronic state but also provide new insights for understanding the spatially dependent in-gap states in low carrier density superconductors.

Probing Hidden Mott Gap and Incommensurate Charge Modulation on the Polar Surfaces of PdCrO_{2}.

Here we report a combined study of low-temperature scanning tunneling microscopy and dynamical mean-field theory on PdCrO_{2}, a delafossite metal with an antiferromagnetic order below ∼37.5 K. First, on the CrO_{2}-terminated polar surface we detect a gaplike feature both below and above the Néel temperature. The dynamical mean-field theory calculations indicate that this gap is opened due to the strong correlations of Cr-3d electrons, suggesting the hidden Mott nature of the gap. Then, we observe two kinds of Pd-terminated polar surfaces. One is a well-ordered Pd surface with the Fermi-surface-nesting-induced incommensurate charge modulation, while the other one is a reconstructed Pd surface with the individual nanoscale nonperiodic domain structures. On the well-ordered Pd surface, the interference between the incommensurate charge modulation and the atomic lattice forms the periodic moiré pattern. Our results provide important microscopic information for fully understanding the correlated electronic properties of this class of materials.

Fully Two-Dimensional Incommensurate Charge Modulation on the Pd-Terminated Polar Surface of PdCoO2.

Here, we use low-temperature scanning tunneling microscopy and spectroscopy to study the polar surfaces of PdCoO2. On the CoO2-terminated polar surface, we detect the quasiparticle interference pattern originating from the Rashba-like spin-split surface states. On the well-ordered Pd-terminated polar surface, we observe a regular lattice that has a larger lattice constant than the atomic lattice of PdCoO2. In comparison with the shape of the hexagonal Fermi surface on the Pd-terminated surface, we identify this regular lattice as a fully two-dimensional incommensurate charge modulation that is driven by the Fermi surface nesting. More interestingly, we also find the moiré pattern induced by the interference between the two-dimensional incommensurate charge modulation in the Pd layer and its atomic lattice. Our results not only show a new charge modulation on the Pd surface of PdCoO2 but also pave the way for fully understanding the novel electronic properties of this material.

Repurposing old drugs as novel inhibitors of human MIF from structural and functional analysis.

Human macrophage migration inhibitory factor (MIF) is an important pro-inflammatory cytokine that plays multiple pleiotropic functions. It is considered as a promising therapeutic target for the infectious, autoimmune, and cardiovascular diseases and cancers. The development of MIF inhibitors has not been translated into clinical success despite decades of research. Given the time and cost of developing new drugs, existing drugs with clarified safety and pharmacokinetics are explored for their potential as novel MIF inhibitors. This study identified five known drugs that could inhibit MIF's tautomerase activity and MIF-mediated cell chemotaxis in RAW264.7 cells. It was found that compounds D2 (histamine), D5 (metaraminol), and D8 (nebivolol) exhibited micromolar-range inhibition potency close to the positive control ISO-1. Kinetics and the mechanism for inhibition were subsequently determined. Moreover, the detailed inhibitor-binding patterns were investigated by X-ray crystallography, computational molecular docking, and structure-based analysis. Therefore, this study elucidates the molecular mechanism of repurposed drugs acting on MIF and provides a structural foundation for lead optimization to promote the clinical development of MIF-targeted drugs.

Synthesis and evaluation of glycosylated quercetin to enhance neuroprotective effects on cerebral ischemia-reperfusion.

Quercetin (Que), a polyphenolic flavonoid compound with antioxidant properties has been explicated to have neuroprotective effects on neuronal injury/neurodegenerative diseases. However, low water-solubility, instability and inability to cross the blood-brain barrier (BBB) imped its application. To enhance the neuroprotective effects and improve the potential application of quercetins as a nutraceutical or medicine, we designed and synthesized two types of glycosylated quercetins--Glu-Que and 2Glu-Que through click reaction. Glu-Que and 2Glu-Que improved the water solubility and stability of quercetin, as well as alleviating H2O2-induced neurotoxicity by increasing the cell viability of PC12 cells and reducing the ROS generation. What's more, glycosylated quercetins enhanced neuroprotective effects on cerebral ischemia-reperfusion (I/R). Among the two types of glycosylated quercetin, 2Glu-Que displayed higher neuroprotective potential than Glu-Que. In conclusion, the glycosylated quercetin 2Glu-Que, with better water solubility, bioavailability and brain-targeting ability, significantly enhanced the neuroprotective effects of quercetin, making it a promising nutraceutical or candidate drug in neuroprotection.

Charge reactions on crystalline/amorphous lanthanum nickel oxide cocatalyst modified hematite photoanode.

Understanding the charge reactions at the semiconductor/cocatalyst interface is of great interest for boosting photoelectrochemical water splitting since the charge transfer to water molecules is the sluggish one. Besides the dopants, porosity, or ion-penetration of the cocatalyst, the crystallinity of the cocatalyst may also influence the charge reactions at the interface. Herein, we prepared amorphous LaNiOx and crystalline La-doped NiO (c-LaNiOx) cocatalysts through photochemical decomposition and ion-exchange of Ni(OH)2 precipitation, respectively. Both lanthanum nickel oxides (LaNiOx) showed considerable improvement of hematite photoanodes. By using electrochemical impedance measurements, we confirmed that the catalyst could store photogenerated charges with reduced transfer resistance and passivate the surface state, resulting in the overall charge transfer rate enhancement. This study may lead to a chance to uncover the kinetic bottleneck with an efficient cocatalyst in well-controlled crystallinity in the future.

Structural basis of molecular recognition between ESCRT-III-like protein Vps60 and AAA-ATPase regulator Vta1 in the multivesicular body pathway.

The AAA-ATPase Vps4 is critical for function of the multivesicular body sorting pathway, which impacts cellular phenomena ranging from receptor down-regulation to viral budding to cytokinesis. Vps4 activity is stimulated by the interaction between Vta1 and Vps60, but the structural basis for this interaction is unclear. The fragment Vps60(128-186) was reported to display the full activity of Vps60. Vta1 interacts with Vps60 using its N-terminal domain (Vta1NTD). In this work, the structure of Vps60(128-186) in complex with Vta1NTD was determined using NMR techniques, demonstrating a novel recognition mode of the microtubule-interacting and transport (MIT) domain in which Vps60(128-186) interacts with Vta1NTD through helices α4' and α5', extending over Vta1NTD MIT2 domain helices 1-3. The Vps60 binding does not result in Vta1 conformational changes, further revealing the fact that Vps4 ATPase is enhanced by the interaction between Vta1 and Vps60 in an unanticipated manner.

DNA strand displacement and TdT-Mediated DNA extension for swift, convenient, and quantitative evaluation of sperm DNA integrity and its clinical implications.

DNA integrity is crucial for the clinical pregnancy outcome and offspring health, while detection methods currently used (comet assay, TUNNEL assay, SCSA, etc.) can only provide the ratio of positive sperms at the cellular level and are unable to quantitatively detect the breakpoints at the DNA molecular level. Herein, we developed a detection system based on terminal deoxynucleotidyl transferase and DNA strand displacement fluorescent probe, which could efficiently and conveniently measure the number of 3'-OH (equivalent to the number of breakpoints). We further investigated the use of this technique in assisted reproduction after completing the principle verification, system optimization, and research on analytical performance. The detection system was shown to have a good linear range from 0.01 nM to 4 nM, using single-stranded DNA with 3'-OH end as the calibrator. The system underwent thorough optimization for stability and accuracy. In comparison to the widely accepted index DFI detected by SCSA, the new system demonstrated reasonable correlation and better prediction efficiency. Its applicability was also proven through its use in assisted reproductive technology procedures.

Cysteine 397 plays important roles in the folding of the neuron-restricted silencer factor/RE1-silencing transcription factor.

The neuron-restrictive silencer factor/RE1-silencing transcription factor (NRSF/REST) is regarded as not only a key transcriptional repressor but also an activator in neuron gene expression by specifically interacting with neuron-restrictive silencer element (NRSE/RE1) dsDNA and small NRSE/RE1 dsRNA, respectively. But its exact mechanism remains unclear. One major problem is that it is hard to obtain its functional multiple zinc finger (ZnF) domains in a large quantity for further structural studies. To address this issue, in this study, we for the first time attained soluble NRSF/REST functional domains named as ZnF5-8, ZnF4-8, ZnF3-8 and ZnF2-8 containing four, five, six and seven ZnF motifs in tandem, respectively, by using Circular Dichroism (CD) spectrum and two-dimensional (2D) nucleic magnetic resonance (NMR) (1)H-(1)H NOESY spectrum to monitor the folding of each single ZnF peptide. The data indicated that the residue cysteine 397 (Cys397) plays important roles in the global folding of NRSF/REST multiple ZnFs domain.

Ultrathin Fe-NiO nanosheets as catalytic charge reservoirs for a planar Mo-doped BiVO4 photoanode.

The energy conversion efficiency of a photoelectrochemical system is intimately connected to a number of processes, including light absorption, charge excitation, separation and transfer processes. Of these processes, the charge transfer rate at the electrode|electrolyte interface is the slowest and, hence, the rate-limiting step causing charge accumulation. Such an understanding underpins efforts focused on applying highly active electrocatalysts, which may contribute to the overall performance by augmenting surface charge accumulation, prolonging charge lifetime or facilitating charge transfer. How the overall effect depends on these individual possible mechanisms has been difficult to study previously. Aiming at advancing knowledge about this important interface, we applied first-order serial reactions to elucidate the charge excitation, separation and recombination kinetics on the semiconductor|electrocatalyst interfaces in air. The study platform for the present work was prepared using a two-step Mo-doped BiVO4 film modified with an ultrathin Fe-doped NiO nanosheet, which was derived from an Fe-doped α-Ni(OH)2 nanosheet by a convenient precipitation and ion-exchange method. The simulation results of the transient surface photovoltage (TSPV) data showed that the surface charge accumulation was significantly enhanced, even at an extremely low coverage (0.12-120 ppm) using ultra-thin Fe-NiO nanosheets. Interestingly, no improvement in the charge separation rate constants or reduction of recombination rate constants was observed under our experimental conditions. Instead, the ultra-thin Fe-NiO nanosheets served as a charge storage layer to facilitate the catalytic process for enhanced performance.

Synthesis and chiral recognition of amylose derivatives bearing regioselective phenylcarbamate substituents at 2,6- and 3-positions for high-performance liquid chromatography.

Eighteen novel amylose derivatives bearing different phenylcarbamate substituents at 2,6- and 3-positions of a glucose ring were synthesized through the regioselective protection at 2- and 6-positions using a bulky trialkylsilyl chloride. Their chiral recognition abilities were then evaluated as the chiral stationary phases (CSPs) for high-performance liquid chromatography (HPLC) after coating them on the surface of macroporous silica gel. The chiral recognition abilities of these CSPs intricately depended on the nature, position and number of the substituents on the phenyl moieties. The introduction of substituents at meta-position of aromatic moieties at 2- and 6-positions of glucose unit was more attractive than other positions to improve the chiral recognition ability of these amylose derivatives. Each CSP seems to possess its own characteristic resolving power, and those based on amylose 3-(3,5-dichlorophenylcarbamate) showed comparatively better chiral recognition than others. For some racemates, the amylose derivatives with different phenylcarbamate substituents at 2,6- and 3-positions exhibited higher enantioselectivity than the amylose tris(3,5-dimethylphenylcarbamate), which is commercially available as Chiralpak AD, one of the most powerful CSPs. The structures of the obtained amylose derivatives were also investigated by circular dichroism spectroscopy.

NMR studies on the interactions between yeast Vta1 and Did2 during the multivesicular bodies sorting pathway.

As an AAA-ATPase, Vps4 is important for function of multivesicular bodies (MVB) sorting pathway, which involves in cellular phenomena ranging from receptor down-regulation to viral budding to cytokinesis. The activity of Vps4 is stimulated by the interactions between Vta1 N-terminus (named as Vta1NTD) and Did2 fragment (176-204 aa) (termed as Did2176-204) or Vps60 (128-186 aa) (termed as Vps60128-186). The structural basis of how Vta1NTD binds to Did2176-204 is still unclear. To address this, in this report, the structure of Did2176-204 in complex with Vta1NTD was determined by NMR techniques, demonstrating that Did2176-204 interacts with Vta1NTD through its helix α6' extending over the 2nd and the 3rd α-helices of Vta1NTD microtubule interacting and transport 1 (MIT1) domain. The residues within Did2176-204 helix α6' in the interface make up of an amino acid sequence as E192'xxL195'xxR198'L199'xxL202'R203', identical to type 1 MIT-interacting motif (MIM1) (D/E)xxLxxRLxxL(K/R) of CHMP1A180-196 observed in Vps4-CHMP1A complex structure, indicating that Did2 binds to Vta1NTD through canonical MIM1 interactions. Moreover, the Did2 binding does not result in Vta1NTD significant conformational changes, revealing that Did2, similar to Vps60, enhances Vta1 stimulation of Vps4 ATPase activity in an indirect manner.

Structural basis for cytochrome c Y67H mutant to function as a peroxidase.

The catalytic activity of cytochrome c (cyt c) to peroxidize cardiolipin to its oxidized form is required for the release of pro-apoptotic factors from mitochondria, and for execution of the subsequent apoptotic steps. However, the structural basis for this peroxidation reaction remains unclear. In this paper, we determined the three-dimensional NMR solution structure of yeast cyt c Y67H variant with high peroxidase activity, which is almost similar to that of its native form. The structure reveals that the hydrogen bond between Met80 and residue 67 is disrupted. This change destabilizes the sixth coordination bond between heme Fe(3+) ion and Met80 sulfur atom in the Y67H variant, and further makes it more easily be broken at low pH conditions. The steady-state studies indicate that the Y67H variant has the highest peroxidase activities when pH condition is between 4.0 and 5.2. Finally, a mechanism is suggested for the peroxidation of cardiolipin catalyzed by the Y67H variant, where the residue His67 acts as a distal histidine, its protonation facilitates O-O bond cleavage of H2O2 by functioning as an acidic catalyst.

¹H, ¹³C and ¹5N resonance assignments of the N-terminal domain of Vta1-Vps60 peptide complex.

Vta1 and Vps60 are two ESCRT associated proteins, their direct interaction enhances Vps4 ATPase activity. The N-terminal domain of Vta1 (residues 1-167aa, named as Vta1NTD) contains two tandem MIT domains, which specifically recognize Vps60 and Did2 but not other ESCRT-III subunits. The fragment Vps60 (128-186aa) was reported to display full activity of Vps60, which stimulates Vps4 ATPase in a Vta1-dependent manner. To study the structural basis for the interaction between Vta1 and Vps60, as a first step, here, we report the resonance assignments of the sequential backbone atoms and the side chains of the residues in the two components of Vta1NTD/Vps60(128-186) complex at pH 7.0 and 20 °C (BMRB No. 18521).

Conformational toggling of yeast iso-1-cytochrome C in the oxidized and reduced states.

To convert cyt c into a peroxidase-like metalloenzyme, the P71H mutant was designed to introduce a distal histidine. Unexpectedly, its peroxidase activity was found even lower than that of the native, and that the axial ligation of heme iron was changed to His71/His18 in the oxidized state, while to Met80/His18 in the reduced state, characterized by UV-visible, circular dichroism, and resonance Raman spectroscopy. To further probe the functional importance of Pro71 in oxidation state dependent conformational changes occurred in cyt c, the solution structures of P71H mutant in both oxidation states were determined. The structures indicate that the half molecule of cyt c (aa 50-102) presents a kind of "zigzag riveting ruler" structure, residues at certain positions of this region such as Pro71, Lys73 can move a big distance by altering the tertiary structure while maintaining the secondary structures. This finding provides a molecular insight into conformational toggling in different oxidation states of cyt c that is principle significance to its biological functions in electron transfer and apoptosis. Structural analysis also reveals that Pro71 functions as a key hydrophobic patch in the folding of the polypeptide of the region (aa 50-102), to prevent heme pocket from the solvent.