IGSF8 is an innate immune checkpoint and cancer immunotherapy target.

Antigen presentation defects in tumors are prevalent mechanisms of adaptive immune evasion and resistance to cancer immunotherapy, whereas how tumors evade innate immunity is less clear. Using CRISPR screens, we discovered that IGSF8 expressed on tumors suppresses NK cell function by interacting with human KIR3DL2 and mouse Klra9 receptors on NK cells. IGSF8 is normally expressed in neuronal tissues and is not required for cell survival in vitro or in vivo. It is overexpressed and associated with low antigen presentation, low immune infiltration, and worse clinical outcomes in many tumors. An antibody that blocks IGSF8-NK receptor interaction enhances NK cell killing of malignant cells in vitro and upregulates antigen presentation, NK cell-mediated cytotoxicity, and T cell signaling in vivo. In syngeneic tumor models, anti-IGSF8 alone, or in combination with anti-PD1, inhibits tumor growth. Our results indicate that IGSF8 is an innate immune checkpoint that could be exploited as a therapeutic target.

Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate Vγ9Vδ2 T cells.

In both cancer and infections, diseased cells are presented to human Vγ9Vδ2 T cells through an 'inside out' signalling process whereby structurally diverse phosphoantigen (pAg) molecules are sensed by the intracellular domain of butyrophilin BTN3A11-4. Here we show how-in both humans and alpaca-multiple pAgs function as 'molecular glues' to promote heteromeric association between the intracellular domains of BTN3A1 and the structurally similar butyrophilin BTN2A1. X-ray crystallography studies visualized that engagement of BTN3A1 with pAgs forms a composite interface for direct binding to BTN2A1, with various pAg molecules each positioned at the centre of the interface and gluing the butyrophilins with distinct affinities. Our structural insights guided mutagenesis experiments that led to disruption of the intracellular BTN3A1-BTN2A1 association, abolishing pAg-mediated Vγ9Vδ2 T cell activation. Analyses using structure-based molecular-dynamics simulations, 19F-NMR investigations, chimeric receptor engineering and direct measurement of intercellular binding force revealed how pAg-mediated BTN2A1 association drives BTN3A1 intracellular fluctuations outwards in a thermodynamically favourable manner, thereby enabling BTN3A1 to push off from the BTN2A1 ectodomain to initiate T cell receptor-mediated γδ T cell activation. Practically, we harnessed the molecular-glue model for immunotherapeutics design, demonstrating chemical principles for developing both small-molecule activators and inhibitors of human γδ T cell function.

VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models.

SUMMARY: Although many quantitative structure-activity relationship (QSAR) models are trained and evaluated for their predictive merits, understanding what models have been learning is of critical importance. However, the interpretation and visualization of QSAR model results remain challenging, especially for 'black box' models such as deep neural network (DNN). Here, we take a step forward to interpret the learned chemical features from DNN QSAR models, and present VISAR, an interactive tool for visualizing the structure-activity relationship. VISAR first provides functions to construct and train DNN models. Then VISAR builds the activity landscapes based on a series of compounds using the trained model, showing the correlation between the chemical feature space and the experimental activity space after model training, and allowing for knowledge mining from a global perspective. VISAR also maps the gradients of the chemical features to the corresponding compounds as contribution weights for each atom, and visualizes the positive and negative contributor substructures suggested by the models from a local perspective. Using the web application of VISAR, users could interactively explore the activity landscape and the color-coded atom contributions. We propose that VISAR could serve as a helpful tool for training and interactive analysis of the DNN QSAR model, providing insights for drug design, and an additional level of model validation. AVAILABILITY AND IMPLEMENTATION: The source code and usage instructions for VISAR are available on github https://github.com/qid12/visar. CONTACT: shaoli@mail.tsinghua.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Broadband short-wave near-infrared-emitting phosphor MgNb2O6:Cr3+ for pc-LED applications.

Broadband short-wave near-infrared (NIR) phosphor-converted light-emitting diodes (pc-LEDs) have been attracting keen interest for miniature NIR spectroscopy, while still lacking sufficient novel broadband NIR-emitting phosphors. Herein, we report a novel MgNb2O6:Cr3+ polycrystalline phosphor with a broad NIR emission band centered at 970 nm and a large full-width at half-maximum of approximately 155 nm under excitation of bluish-green light at around 515 nm. The optimized phosphor MgNb2O6:1%Cr3+ features a high internal quantum efficiency (IQE) of ∼85.5% and a moderate external QE of 25.2%. The fluorescence properties determined by two distorted hexa-coordination octahedral sites (i.e. [MgO6] and [NbO6]), low crystal field strength (Dq/B ∼ 1.65), and Cr3+-doping concentration were systematically investigated for comprehensive understanding of photophysical mechanisms. Besides, this broadband NIR phosphor MgNb2O6:Cr3+ exhibits a moderate thermal quenching of 21.4%@373 K for pc-LED application. An NIR pc-LED self-built by combining the optimal phosphor with a commercial cyan of ∼515 nm exhibits an NIR output power increase from 3.19 to 11.38 mW as the drive current is varied from 40 to 220 mA. With the help of this prototype pc-LED device, multiple applications were successfully performed to clearly recognize blood vessel distributions in the human finger, penetrate a plastic cap, and distinguish multi-color text. Undoubtedly, further development of such broadband short-wave NIR-emitting phosphors will make novel pc-LED devices for significant applications in biomedical imaging, nondestructive safety detection, intelligent identification, etc.

An upstream promoter element blocks the reverse transcription of the mouse insulin-degrading enzyme gene.

Despite the prevalence of bidirectional promoters among the mammalian genomes, the majority of promoters are unidirectional. The mechanism through which unidirectional promoters are prevented from reverse transcription remains to be clarified. Here we investigate the transcriptional directionality of the mouse insulin-degrading enzyme (IDE) promoter, which contains a CpG island and has dispersed transcription initiation sites. Although IDE is unidirectionally transcribed according to its genomic context, the basic promoter region of mouse IDE has bidirectional transcriptional properties. The region between -219 and +133 of mouse IDE relative to its first transcription initiation site has bidirectional transcriptional activities, but the region between -350 and +133 can only be transcribed from the normal direction, implying that an upstream promoter element locating between -350 and -219 blocks the reverse transcription of mouse IDE. We further mapped this upstream promoter element to the region between -243 and -287. Promoter mutation analysis showed that the upstream promoter element contains two functional sub-regions. In conclusion, we identified an upstream promoter element which blocks the reverse transcription of mouse IDE. Our studies are suggestive for the transcriptional mechanism of bidirectional promoters in mammalian genomes.

Transcriptional directionality of the human insulin-degrading enzyme promoter.

Unidirectional promoters dominate among mammalian genomes. However, the mechanism through which the transcriptional directionality of promoters is accomplished remains to be clarified. Insulin-degrading enzyme (IDE) is a ubiquitously expressed zinc metalloprotease, whose promoter contains a CpG island. We previously showed that the basal promoter region of mouse IDE has bidirectional transcriptional activity, but an upstream promoter element blocks its antisense transcription. Therefore, we wonder whether the human IDE promoter contains an analogous element. Similarly, the basal promoter region of human IDE (-102 ~ +173 and -196 ~ +173 relative to the transcription start site) showed bidirectional transcriptional activity. However, the region from -348 to +173 could only be transcribed from the normal orientation, implying that an upstream promoter element between -348 and -196 blocks the antisense transcription of the human IDE promoter. Through promoter deletion and mutagenesis analysis, we mapped this element precisely and found that the upstream promoter element locates between -318 and -304. Furthermore, the transcription-blocking elements in the mouse and human IDE promoters inhibited the transcription of the SV40 promoter when put downstream of it. In conclusion, we identify an upstream promoter element which blocks the antisense transcription of the human IDE promoter. Our studies are helpful to clarify the transcriptional directionality of promoters.

Cadmium Exposure and Risk of Any Fracture: A PRISMA-Compliant Systematic Review and Meta-Analysis.

Several observational studies have investigated the relation between cadmium exposure and risk of any fracture. However, the results from epidemiological studies for the association are inconsistent.We conducted a meta-analysis to evaluate the relationship between cadmium exposure and risk of any fracture. The pertinent studies were identified by a search of PubMed and Embase databases from 1966 to June 2015.Seven articles involving 21,941 fracture cases and 504,346 participants were included. The meta-analysis showed that the pooled relative risk of any fracture for the highest versus lowest category of cadmium concentration was 1.30 (95% confidence interval = 1.13-1.49). In subgroup analyses, the significant association remained consistent when stratified by study type, geographical region, method of cadmium exposure assessment, and gender.Our meta-analysis showed that a high cadmium exposure may be a risk factor for any fracture. However, this result should be interpreted cautiously because of the heterogeneity among studies and existence of publication bias. Additional large, high-quality prospective studies are needed to evaluate the association between cadmium exposure and the risk of development of fracture.

Screening of transcription factors with transcriptional initiation activity.

A majority of mammalian promoters are associated with CpG islands. CpG island promoters frequently lack common core promoter elements, such as the TATA box, and often have dispersed transcription start sites. The mechanism through which CpG island promoters are transcriptionally initiated remains unclear. We speculate that some transcription factors can direct transcription initiation by themselves. To test this hypothesis, we screened a variety of transcription factors to see whether they could initiate transcription. Most transcription factors, including specificity protein 1 (Sp1) and nuclear factor Y (NF-Y), showed little transcriptional initiation activity. However, nuclear respiratory factor 1 (NRF-1), the basic helix-loop-helix/leucine zipper (bHLH/ZIP) family of proteins and the E-twenty six (Ets) family of proteins had strong transcriptional activity. We further demonstrated that these transcription factors initiate dispersed transcription. Our studies provide perspectives to the mechanism of transcription initiation from CpG island promoters.

Nuclear respiratory factor 1 mediates the transcription initiation of insulin-degrading enzyme in a TATA box-binding protein-independent manner.

CpG island promoters often lack canonical core promoter elements such as the TATA box, and have dispersed transcription initiation sites. Despite the prevalence of CpG islands associated with mammalian genes, the mechanism of transcription initiation from CpG island promoters remains to be clarified. Here we investigate the mechanism of transcription initiation of the CpG island-associated gene, insulin-degrading enzyme (IDE). IDE is ubiquitously expressed, and has dispersed transcription initiation sites. The IDE core promoter locates within a 32-bp region, which contains three CGGCG repeats and a nuclear respiratory factor 1 (NRF-1) binding motif. Sequential mutation analysis indicates that the NRF-1 binding motif is critical for IDE transcription initiation. The NRF-1 binding motif is functional, because NRF-1 binds to this motif in vivo and this motif is required for the regulation of IDE promoter activity by NRF-1. Furthermore, the NRF-1 binding site in the IDE promoter is conserved among different species, and dominant negative NRF-1 represses endogenous IDE expression. Finally, TATA-box binding protein (TBP) is not associated with the IDE promoter, and inactivation of TBP does not abolish IDE transcription, suggesting that TBP is not essential for IDE transcription initiation. Our studies indicate that NRF-1 mediates IDE transcription initiation in a TBP-independent manner, and provide insights into the potential mechanism of transcription initiation for other CpG island-associated genes.