Jing Wang

We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.

A novel sequence discovered in a computational screen appears distantly related to the p35 subunit of IL-12. This factor, which we term p19, shows no biological activity by itself; instead, it combines with the p40 subunit of IL-12 to form a novel, biologically active, composite cytokine, which we term IL-23. Activated dendritic cells secrete detectable levels of this complex. IL-23 binds to IL-12R beta 1 but fails to engage IL-12R beta 2; nonetheless, IL-23 activates Stat4 in PHA blast T cells. IL-23 induces strong proliferation of mouse memory (CD4(+)CD45Rb(low)) T cells, a unique activity of IL-23 as IL-12 has no effect on this cell population. Similar to IL-12, human IL-23 stimulates IFN-gamma production and proliferation in PHA blast T cells, as well as in CD45RO (memory) T cells.

We report acute antibody responses to SARS-CoV-2 in 285 patients with COVID-19. Within 19 days after symptom onset, 100% of patients tested positive for antiviral immunoglobulin-G (IgG). Seroconversion for IgG and IgM occurred simultaneously or sequentially. Both IgG and IgM titers plateaued within 6 days after seroconversion. Serological testing may be helpful for the diagnosis of suspected patients with negative RT–PCR results and for the identification of asymptomatic infections. A cross-sectional study of hospitalized patients with COVID-19 and a longitudinal follow-up study of patients with COVID-19 suggest that SARS-CoV2-specific IgG or IgM seroconversion occurs within 20 days post symptom onset.

<h2>Summary</h2> For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.

Transforming growth factor-β (TGF-β) is a potent inhibitor of epithelial cell growth. Human colon cancer cell lines with high rates of microsatellite instability were found to harbor mutations in the type II TGF-β receptor (RII) gene. Eight such examples, due to three different mutations, were identified. The mutations were clustered within small repeated sequences in the RII gene, were accompanied by the absence of cell surface RII receptors, and were usually associated with small amounts of RII transcript. RII mutation, by inducing the escape of cells from TGF-β-mediated growth control, links DNA repair defects with a specific pathway of tumor progression.

Abstract WebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers and 155 175 functional categories, as well as user-uploaded functional databases. To address the growing and unique need for phosphoproteomics data interpretation, we have implemented phosphosite set analysis to identify important kinases from phosphoproteomics data. We have completely redesigned result visualizations and user interfaces to improve user-friendliness and to provide multiple types of interactive and publication-ready figures. To facilitate comprehension of the enrichment results, we have implemented two methods to reduce redundancy between enriched gene sets. We introduced a web API for other applications to get data programmatically from the WebGestalt server or pass data to WebGestalt for analysis. We also wrapped the core computation into an R package called WebGestaltR for users to perform analysis locally or in third party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org.

In a single-group, phase 1b trial, avelumab plus axitinib resulted in objective responses in patients with advanced renal-cell carcinoma. This phase 3 trial involving previously untreated patients with advanced renal-cell carcinoma compared avelumab plus axitinib with the standard-of-care sunitinib.We randomly assigned patients in a 1:1 ratio to receive avelumab (10 mg per kilogram of body weight) intravenously every 2 weeks plus axitinib (5 mg) orally twice daily or sunitinib (50 mg) orally once daily for 4 weeks (6-week cycle). The two independent primary end points were progression-free survival and overall survival among patients with programmed death ligand 1 (PD-L1)-positive tumors. A key secondary end point was progression-free survival in the overall population; other end points included objective response and safety.A total of 886 patients were assigned to receive avelumab plus axitinib (442 patients) or sunitinib (444 patients). Among the 560 patients with PD-L1-positive tumors (63.2%), the median progression-free survival was 13.8 months with avelumab plus axitinib, as compared with 7.2 months with sunitinib (hazard ratio for disease progression or death, 0.61; 95% confidence interval [CI], 0.47 to 0.79; P<0.001); in the overall population, the median progression-free survival was 13.8 months, as compared with 8.4 months (hazard ratio, 0.69; 95% CI, 0.56 to 0.84; P<0.001). Among the patients with PD-L1-positive tumors, the objective response rate was 55.2% with avelumab plus axitinib and 25.5% with sunitinib; at a median follow-up for overall survival of 11.6 months and 10.7 months in the two groups, 37 patients and 44 patients had died, respectively. Adverse events during treatment occurred in 99.5% of patients in the avelumab-plus-axitinib group and in 99.3% of patients in the sunitinib group; these events were grade 3 or higher in 71.2% and 71.5% of the patients in the respective groups.Progression-free survival was significantly longer with avelumab plus axitinib than with sunitinib among patients who received these agents as first-line treatment for advanced renal-cell carcinoma. (Funded by Pfizer and Merck [Darmstadt, Germany]; JAVELIN Renal 101 ClinicalTrials.gov number, NCT02684006.).

Materials research has driven the development of modern nano-electronic devices. In particular, research in magnetic thin films has revolutionized the development of spintronic devices1,2 because identifying new magnetic materials is key to better device performance and design. Van der Waals crystals retain their chemical stability and structural integrity down to the monolayer and, being atomically thin, are readily tuned by various kinds of gate modulation3,4. Recent experiments have demonstrated that it is possible to obtain two-dimensional ferromagnetic order in insulating Cr2Ge2Te6 (ref. 5) and CrI3 (ref. 6) at low temperatures. Here we develop a device fabrication technique and isolate monolayers from the layered metallic magnet Fe3GeTe2 to study magnetotransport. We find that the itinerant ferromagnetism persists in Fe3GeTe2 down to the monolayer with an out-of-plane magnetocrystalline anisotropy. The ferromagnetic transition temperature, Tc, is suppressed relative to the bulk Tc of 205 kelvin in pristine Fe3GeTe2 thin flakes. An ionic gate, however, raises Tc to room temperature, much higher than the bulk Tc. The gate-tunable room-temperature ferromagnetism in two-dimensional Fe3GeTe2 opens up opportunities for potential voltage-controlled magnetoelectronics7–11 based on atomically thin van der Waals crystals. Monolayers of Fe3GeTe2 exhibit itinerant ferromagnetism with an out-of-plane magnetocrystalline anisotropy; ionic gating raises the ferromagnetic transition temperature of few-layer Fe3GeTe2 to room temperature.

We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development.

Four forms of school bullying behaviors among US adolescents and their association with sociodemographic characteristics, parental support, and friends were examined.Data were obtained from the Health Behavior in School-Aged Children (HBSC) 2005 Survey, a nationally representative sample of grades 6-10 (N = 7,182). The revised Olweus Bully/Victim Questionnaire was used to measure physical, verbal, and relational forms of bullying. Two items were added using the same format to measure cyber bullying. For each form, four categories were created: bully, victim, bully-victim, and not involved. Multinomial logistic regressions were applied, with sociodemographic variables, parental support, and number of friends as predictors.Prevalence rates of having bullied others or having been bullied at school for at least once in the last 2 months were 20.8% physically, 53.6% verbally, 51.4% socially, or 13.6% electronically. Boys were more involved in physical or verbal bullying, whereas girls were more involved in relational bullying. Boys were more likely to be cyber bullies, whereas girls were more likely to be cyber victims. African-American adolescents were involved in more bullying (physical, verbal, or cyber) but less victimization (verbal or relational). Higher parental support was associated with less involvement across all forms and classifications of bullying. Having more friends was associated with more bullying and less victimization for physical, verbal, and relational forms but was not associated with cyber bullying.Parental support may protect adolescents from all four forms of bullying. Friends associate differentially with traditional and cyber bullying. Results indicate that cyber bullying is a distinct nature from that of traditional bullying.

Remarkable hydrogen evolution reaction (HER) or superior oxygen evolution reaction (OER) catalyst has been applied in water splitting, however, utilizing a bifunctional catalyst for simultaneously generating H2 and O2 is still a challenging issue, which is crucial for improving the overall efficiency of water electrolysis. Herein, inspired by the superiority of carbon conductivity, the propitious H atom binding energy of metallic cobalt, and better OER activity of cobalt oxide, we synthesized cobalt–cobalt oxide/N-doped carbon hybrids (CoOx@CN) composed of Co0, CoO, Co3O4 applied to HER and OER by simple one-pot thermal treatment method. CoOx@CN exhibited a small onset potential of 85 mV, low charge-transfer resistance (41 Ω), and considerable stability for HER. Electrocatalytic experiments further indicated the better performance of CoOx@CN for HER can be attributed to the high conductivity of carbon, the synergistic effect of metallic cobalt and cobalt oxide, the stability of carbon-encapsulated Co nanoparticles, and the introduction of electron-rich nitrogen. In addition, when used as catalysts of OER, the CoOx@CN hybrids required 0.26 V overpotential for a current density of 10 mA cm–2, which is comparable even superior to many other non-noble metal catalysts. More importantly, an alkaline electrolyzer that approached ∼20 mA cm–2 at a voltage of 1.55 V was fabricated by applying CoOx@CN as cathode and anode electrocatalyst, which opened new possibilities for exploring overall water splitting catalysts.

The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. Using five case studies, we demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. LinkedOmics is freely available at http://www.linkedomics.org.

Microbial modulation of diabetes Short-chain fatty acids (SCFAs) are produced by various human gut microbes. SCFAs act as an energy source to the colonic epithelium and are also sensed by host signaling pathways that modulate appetite and inflammation. Deficiency of gut SCFAs is associated with type 2 diabetes. Zhao et al. found that adopting a high-fiber diet promoted the growth of SCFA-producing organisms in diabetic humans. The high-fiber diet induced changes in the entire gut microbe community and correlated with elevated levels of glucagon-like peptide-1, a decline in acetylated hemoglobin levels, and improved blood-glucose regulation. Science , this issue p. 1151

Abstract The outbreak of the novel coronavirus disease (COVID‐19) quickly spread all over China and to more than 20 other countries. Although the virus (severe acute respiratory syndrome coronavirus [SARS‐Cov‐2]) nucleic acid real‐time polymerase chain reaction (PCR) test has become the standard method for diagnosis of SARS‐CoV‐2 infection, these real‐time PCR test kits have many limitations. In addition, high false‐negative rates were reported. There is an urgent need for an accurate and rapid test method to quickly identify a large number of infected patients and asymptomatic carriers to prevent virus transmission and assure timely treatment of patients. We have developed a rapid and simple point‐of‐care lateral flow immunoassay that can detect immunoglobulin M (IgM) and IgG antibodies simultaneously against SARS‐CoV‐2 virus in human blood within 15 minutes which can detect patients at different infection stages. With this test kit, we carried out clinical studies to validate its clinical efficacy uses. The clinical detection sensitivity and specificity of this test were measured using blood samples collected from 397 PCR confirmed COVID‐19 patients and 128 negative patients at eight different clinical sites. The overall testing sensitivity was 88.66% and specificity was 90.63%. In addition, we evaluated clinical diagnosis results obtained from different types of venous and fingerstick blood samples. The results indicated great detection consistency among samples from fingerstick blood, serum and plasma of venous blood. The IgM‐IgG combined assay has better utility and sensitivity compared with a single IgM or IgG test. It can be used for the rapid screening of SARS‐CoV‐2 carriers, symptomatic or asymptomatic, in hospitals, clinics, and test laboratories.

Hydrogen has been hailed as a clean and sustainable alternative to finite fossil fuels in many energy systems. Water splitting is an important method for hydrogen production in high purity and large quantities. To accelerate the hydrogen evolution reaction (HER) rate, it is highly necessary to develop high efficiency catalysts and to select a proper electrolyte. Herein, the performances of non‐noble metal‐based carbon composites under various pH values (acid, alkaline and neutral media) for HER in terms of catalyst synthesis, structure and molecular design are systematically discussed. A detailed analysis of the structure‐activity‐pH correlations in the HER process gives an insight on the origin of the pH‐dependence for HER, and provide guidance for future HER mechanism studies on non‐noble metal‐based carbon composites. Furthermore, this Review gives a fresh impetus to rational design of high‐performance noble‐metal‐free composites catalysts and guide researchers to employ the established electrocatalysts in proper water electrolysis technologies.

The SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires immediate investigation. Here we use high-throughput yeast display screening1,2 to determine the profiles of RBD escaping mutations for 247 human anti-RBD neutralizing antibodies and show that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A-F)-a grouping that is highly concordant with knowledge-based structural classifications3-5. Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups. Specifically, neutralizing antibodies in groups A-D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. Antibodies in group E (for example, S309)6 and group F (for example, CR3022)7, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes. In total, over 85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was greatly undermined by Omicron, whereas VIR-7831 and DXP-604 still functioned at a reduced efficacy. Together, our data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus conserved region will remain most effective. Our results inform the development of antibody-based drugs and vaccines against Omicron and future variants.

Functional enrichment analysis is an essential task for the interpretation of gene lists derived from large-scale genetic, transcriptomic and proteomic studies. WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) has become one of the popular software tools in this field since its publication in 2005. For the last 7 years, WebGestalt data holdings have grown substantially to satisfy the requirements of users from different research areas. The current version of WebGestalt supports 8 organisms and 201 gene identifiers from various databases and different technology platforms, making it directly available to the fast growing omics community. Meanwhile, by integrating functional categories derived from centrally and publicly curated databases as well as computational analyses, WebGestalt has significantly increased the coverage of functional categories in various biological contexts including Gene Ontology, pathway, network module, gene-phenotype association, gene-disease association, gene-drug association and chromosomal location, leading to a total of 78 612 functional categories. Finally, new interactive features, such as pathway map, hierarchical network visualization and phenotype ontology visualization have been added to WebGestalt to help users better understand the enrichment results. WebGestalt can be freely accessed through http://www.webgestalt.org or http://bioinfo.vanderbilt.edu/webgestalt/.

Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell. To examine the principles of the human transcriptional regulatory network, we determined the genomic binding information of 119 transcription-related factors in over 450 distinct experiments. We found the combinatorial, co-association of transcription factors to be highly context specific: distinct combinations of factors bind at specific genomic locations. In particular, there are significant differences in the binding proximal and distal to genes. We organized all the transcription factor binding into a hierarchy and integrated it with other genomic information (for example, microRNA regulation), forming a dense meta-network. Factors at different levels have different properties; for instance, top-level transcription factors more strongly influence expression and middle-level ones co-regulate targets to mitigate information-flow bottlenecks. Moreover, these co-regulations give rise to many enriched network motifs (for example, noise-buffering feed-forward loops). Finally, more connected network components are under stronger selection and exhibit a greater degree of allele-specific activity (that is, differential binding to the two parental alleles). The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease.

Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. Here we describe quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers, of which 77 provided high-quality data. Integrated analyses provided insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. Interrogation of the 5q trans-effects against the Library of Integrated Network-based Cellular Signatures, connected loss of CETN3 and SKP1 to elevated expression of epidermal growth factor receptor (EGFR), and SKP1 loss also to increased SRC tyrosine kinase. Global proteomic data confirmed a stromal-enriched group of proteins in addition to basal and luminal clusters, and pathway analysis of the phosphoproteome identified a G-protein-coupled receptor cluster that was not readily identified at the mRNA level. In addition to ERBB2, other amplicon-associated highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates the functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets.

We develop a host-guest strategy to construct an electrocatalyst with Fe-Co dual sites embedded on N-doped porous carbon and demonstrate its activity for oxygen reduction reaction in acidic electrolyte. Our catalyst exhibits superior oxygen reduction reaction performance, with comparable onset potential (Eonset, 1.06 vs 1.03 V) and half-wave potential (E1/2, 0.863 vs 0.858 V) than commercial Pt/C. The fuel cell test reveals (Fe,Co)/N-C outperforms most reported Pt-free catalysts in H2/O2 and H2/air. In addition, this cathode catalyst with dual metal sites is stable in a long-term operation with 50 000 cycles for electrode measurement and 100 h for H2/air single cell operation. Density functional theory calculations reveal the dual sites is favored for activation of O-O, crucial for four-electron oxygen reduction.

Amber from northern Myanmar has been commercially exploited for millennia, and it also preserves the most diverse palaeobiota among the worlds' seven major deposits of Cretaceous amber. Recent estimated ages vary from Albian to Cenomanian, based on palynology, an ammonoid, and Mesozoic insect taxa preserved within the amber. The burmite-bearing rock is sedimentary and consists mainly of rounded lithic clasts (0.03 ∼ 0.15 mm in diameter), with minor fragments of quartz and feldspar. Among the lithic clasts are mostly volcanic rocks. Zircons separated from the amber matrix form two groups: Group-I zircons are overgrown and have variable CL patterns, experienced slight geological disturbances after they formed, and their Ion microprobe 206Pb/238U ages fall into a very narrow range of ∼102 Ma–∼108 Ma; Group-II zircons are typical magmatic ones with rhythmically flat zones, inferred to be derived from volcanic rock clasts, and yielded a concordia 206Pb/238U age of 98.79 ± 0.62 Ma. The dating on Group-I zircons is only for their interiors, thus hiding what age excursion might come from the overgrowth. Considering the nearshore marine environment and 1-m thickness of the burmite-bearing sediments, and the syn- and post-eruption deposition of volcanic clasts, the age of 98.79 ± 0.62 Ma therefore can be used as a maximum limit for the burmite (either at or after), establishing an earliest Cenomanian age for the fossilized inclusions. The age also indicates that volcanic eruption occurred at 98.79 ± 0.62 Ma in the vicinity of the Hukawng Valley.

<h2>Summary</h2> Early detection and effective treatment of severe COVID-19 patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control individuals. We then trained a machine learning model using proteomic and metabolomic measurements from a training cohort of 18 non-severe and 13 severe patients. The model was validated using 10 independent patients, 7 of which were correctly classified. Targeted proteomics and metabolomics assays were employed to further validate this molecular classifier in a second test cohort of 19 COVID-19 patients, leading to 16 correct assignments. We identified molecular changes in the sera of COVID-19 patients compared to other groups implicating dysregulation of macrophage, platelet degranulation, complement system pathways, and massive metabolic suppression. This study revealed characteristic protein and metabolite changes in the sera of severe COVID-19 patients, which might be used in selection of potential blood biomarkers for severity evaluation.

MoS(2) nanosheet-coated TiO(2) nanobelt heterostructures--referred to as TiO(2)@MoS(2)--with a 3D hierarchical configuration are prepared via a hydrothermal reaction. The TiO(2) nanobelts used as a synthetic template inhibit the growth of MoS(2) crystals along the c-axis, resulting in a few-layer MoS(2) nanosheet coating on the TiO(2) nanobelts. The as-prepared TiO(2)@MoS(2) heterostructure shows a high photocatalytic hydrogen production even without the Pt co-catalyst. Importantly, the TiO(2)@MoS(2) heterostructure with 50 wt% of MoS(2) exhibits the highest hydrogen production rate of 1.6 mmol h(-1) g(-1). Moreover, such a heterostructure possesses a strong adsorption ability towards organic dyes and shows high performance in photocatalytic degradation of the dye molecules.

The genomic region encoding the miR-17-92 microRNA (miRNA) cluster is often amplified in lymphoma and other cancers, and cancer cells carrying this amplification have higher expression of miRNA in this cluster. Retroviral expression of miR-17-92 accelerates c-Myc-induced lymphoma development, but precisely how higher expression of miR-17-92 promotes lymphomagenesis remains unclear. Here we generated mice with higher expression of miR-17-92 in lymphocytes. These mice developed lymphoproliferative disease and autoimmunity and died prematurely. Lymphocytes from these mice showed more proliferation and less activation-induced cell death. The miR-17-92 miRNA suppressed expression of the tumor suppressor PTEN and the proapoptotic protein Bim. This mechanism probably contributed to the lymphoproliferative disease and autoimmunity of miR-17-92-transgenic mice and contributes to lymphoma development in patients with amplifications of the miR-17-92 coding region.

Single-atom catalysts often exhibit unexpected catalytic activity for many important chemical reactions because of their unique electronic and geometric structures with respect to their bulk counterparts. Herein we adopt metal–organic frameworks (MOFs) to assist the preparation of a catalyst containing single Ni sites for efficient electroreduction of CO2. The synthesis is based on ionic exchange between Zn nodes and adsorbed Ni ions within the cavities of the MOF. This single-atom catalyst exhibited an excellent turnover frequency for electroreduction of CO2 (5273 h–1), with a Faradaic efficiency for CO production of over 71.9% and a current density of 10.48 mA cm–2 at an overpotential of 0.89 V. Our findings present some guidelines for the rational design and accurate modulation of nanostructured catalysts at the atomic scale.

Abstract KRAS is the most common oncogenic driver in lung adenocarcinoma (LUAC). We previously reported that STK11/LKB1 (KL) or TP53 (KP) comutations define distinct subgroups of KRAS-mutant LUAC. Here, we examine the efficacy of PD-1 inhibitors in these subgroups. Objective response rates to PD-1 blockade differed significantly among KL (7.4%), KP (35.7%), and K-only (28.6%) subgroups (P &amp;lt; 0.001) in the Stand Up To Cancer (SU2C) cohort (174 patients) with KRAS-mutant LUAC and in patients treated with nivolumab in the CheckMate-057 phase III trial (0% vs. 57.1% vs. 18.2%; P = 0.047). In the SU2C cohort, KL LUAC exhibited shorter progression-free (P &amp;lt; 0.001) and overall (P = 0.0015) survival compared with KRASMUT;STK11/LKB1WT LUAC. Among 924 LUACs, STK11/LKB1 alterations were the only marker significantly associated with PD-L1 negativity in TMBIntermediate/High LUAC. The impact of STK11/LKB1 alterations on clinical outcomes with PD-1/PD-L1 inhibitors extended to PD-L1–positive non–small cell lung cancer. In Kras-mutant murine LUAC models, Stk11/Lkb1 loss promoted PD-1/PD-L1 inhibitor resistance, suggesting a causal role. Our results identify STK11/LKB1 alterations as a major driver of primary resistance to PD-1 blockade in KRAS-mutant LUAC. Significance: This work identifies STK11/LKB1 alterations as the most prevalent genomic driver of primary resistance to PD-1 axis inhibitors in KRAS-mutant lung adenocarcinoma. Genomic profiling may enhance the predictive utility of PD-L1 expression and tumor mutation burden and facilitate establishment of personalized combination immunotherapy approaches for genomically defined LUAC subsets. Cancer Discov; 8(7); 822–35. ©2018 AACR. See related commentary by Etxeberria et al., p. 794. This article is highlighted in the In This Issue feature, p. 781

High absorption efficiency is particularly desirable at present for various microtechnological applications including microbolometers, photodectors, coherent thermal emitters, and solar cells. Here we report the design, characterization, and experimental demonstration of an ultrathin, wide-angle, subwavelength high performance metamaterial absorber for optical frequencies. Experimental results show that an absorption peak of 88% is achieved at the wavelength of ∼1.58 μm, though theoretical results give near perfect absorption.

Self-monitoring is the centerpiece of behavioral weight loss intervention programs. This article presents a systematic review of the literature on three components of self-monitoring in behavioral weight loss studies: diet, exercise, and self-weighing. This review included articles that were published between 1993 and 2009 that reported on the relationship between weight loss and these self-monitoring strategies. Of the 22 studies identified, 15 focused on dietary self-monitoring, one on self-monitoring exercise, and six on self-weighing. A wide array of methods was used to perform self-monitoring; the paper diary was used most often. Adherence to self-monitoring was reported most frequently as the number of diaries completed or the frequency of log-ins or reported weights. The use of technology, which included the Internet, personal digital assistants, and electronic digital scales were reported in five studies. Descriptive designs were used in the earlier studies whereas more recent reports involved prospective studies and randomized trials that examined the effect of self-monitoring on weight loss. A significant association between self-monitoring and weight loss was consistently found; however, the level of evidence was weak because of methodologic limitations. The most significant limitations of the reviewed studies were the homogenous samples and reliance on self-report. In all but two studies, the samples were predominantly white and women. This review highlights the need for studies in more diverse populations, for objective measures of adherence to self-monitoring, and for studies that establish the required dose of self-monitoring for successful outcomes.

Lead halide perovskite solar cells with the high efficiencies typically use high-temperature processed TiO2 as the electron transporting layers (ETLs). Here, we demonstrate that low-temperature solution-processed nanocrystalline SnO2 can be an excellent alternative ETL material for efficient perovskite solar cells. Our best-performing planar cell using such a SnO2 ETL has achieved an average efficiency of 16.02%, obtained from efficiencies measured from both reverse and forward voltage scans. The outstanding performance of SnO2 ETLs is attributed to the excellent properties of nanocrystalline SnO2 films, such as good antireflection, suitable band edge positions, and high electron mobility. The simple low-temperature process is compatible with the roll-to-roll manufacturing of low-cost perovskite solar cells on flexible substrates.

In a magnetic topological insulator, nontrivial band topology conspires with magnetic order to produce exotic states of matter that are best exemplified by quantum anomalous Hall (QAH) insulators and axion insulators. Up till now, such magnetic topological insulators are obtained by doping topological insulators with magnetic atoms. The random magnetic dopants, however, inevitably introduce disorders that hinder further exploration of quantum effects in the material. Here, we resolve this dilemma by probing quantum transport in MnBi$_2$Te$_4$ thin flake - a topological insulator with intrinsic magnetic order. In this layered van der Waals crystal, the ferromagnetic layers couple anti-parallel to each other, so MnBi$_2$Te$_4$ is an antiferromagnet. A magnetic field, however, aligns all the layers and induces an interlayer ferromagnetic order; we show that a quantized anomalous Hall response emerges in atomically thin MnBi$_2$Te$_4$ under a moderate magnetic field. MnBi$_2$Te$_4$ therefore becomes the first intrinsic magnetic topological insulator exhibiting quantized anomalous Hall effect. The result establishes MnBi$_2$Te$_4$ as an ideal arena for further exploring various topological phenomena.

We report a draft sequence for the genome of the domesticated silkworm (Bombyx mori), covering 90.9% of all known silkworm genes. Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content.

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages BA.2.12.1, BA.4 and BA.5 exhibit higher transmissibility than the BA.2 lineage 1 . The receptor binding and immune-evasion capability of these recently emerged variants require immediate investigation. Here, coupled with structural comparisons of the spike proteins, we show that BA.2.12.1, BA.4 and BA.5 (BA.4 and BA.5 are hereafter referred collectively to as BA.4/BA.5) exhibit similar binding affinities to BA.2 for the angiotensin-converting enzyme 2 (ACE2) receptor. Of note, BA.2.12.1 and BA.4/BA.5 display increased evasion of neutralizing antibodies compared with BA.2 against plasma from triple-vaccinated individuals or from individuals who developed a BA.1 infection after vaccination. To delineate the underlying antibody-evasion mechanism, we determined the escape mutation profiles 2 , epitope distribution 3 and Omicron-neutralization efficiency of 1,640 neutralizing antibodies directed against the receptor-binding domain of the viral spike protein, including 614 antibodies isolated from people who had recovered from BA.1 infection. BA.1 infection after vaccination predominantly recalls humoral immune memory directed against ancestral (hereafter referred to as wild-type (WT)) SARS-CoV-2 spike protein. The resulting elicited antibodies could neutralize both WT SARS-CoV-2 and BA.1 and are enriched on epitopes on spike that do not bind ACE2. However, most of these cross-reactive neutralizing antibodies are evaded by spike mutants L452Q, L452R and F486V. BA.1 infection can also induce new clones of BA.1-specific antibodies that potently neutralize BA.1. Nevertheless, these neutralizing antibodies are largely evaded by BA.2 and BA.4/BA.5 owing to D405N and F486V mutations, and react weakly to pre-Omicron variants, exhibiting narrow neutralization breadths. The therapeutic neutralizing antibodies bebtelovimab 4 and cilgavimab 5 can effectively neutralize BA.2.12.1 and BA.4/BA.5, whereas the S371F, D405N and R408S mutations undermine most broadly sarbecovirus-neutralizing antibodies. Together, our results indicate that Omicron may evolve mutations to evade the humoral immunity elicited by BA.1 infection, suggesting that BA.1-derived vaccine boosters may not achieve broad-spectrum protection against new Omicron variants.

Immune-checkpoint blockade is able to achieve durable responses in a subset of patients; however, we lack a satisfying comprehension of the underlying mechanisms of anti-CTLA-4- and anti-PD-1-induced tumor rejection. To address these issues, we utilized mass cytometry to comprehensively profile the effects of checkpoint blockade on tumor immune infiltrates in human melanoma and murine tumor models. These analyses reveal a spectrum of tumor-infiltrating T cell populations that are highly similar between tumor models and indicate that checkpoint blockade targets only specific subsets of tumor-infiltrating T cell populations. Anti-PD-1 predominantly induces the expansion of specific tumor-infiltrating exhausted-like CD8 T cell subsets. In contrast, anti-CTLA-4 induces the expansion of an ICOS+ Th1-like CD4 effector population in addition to engaging specific subsets of exhausted-like CD8 T cells. Thus, our findings indicate that anti-CTLA-4 and anti-PD-1 checkpoint-blockade-induced immune responses are driven by distinct cellular mechanisms.

A Ni3S2 nanorods/Ni foam composite electrode is prepared as a high-performance catalyst for the oxygen evolution reaction (OER), which exhibits excellent OER activity with a small overpotential of ∼157 mV based on the onset of catalytic current.

Size effect has been regularly utilized to tune the catalytic activity and selectivity of metal nanoparticles (NPs). Yet, there is a lack of understanding of the size effect in the electrocatalytic reduction of CO2, an important reaction that couples with intermittent renewable energy storage and carbon cycle utilization. We report here a prominent size-dependent activity/selectivity in the electrocatalytic reduction of CO2 over differently sized Pd NPs, ranging from 2.4 to 10.3 nm. The Faradaic efficiency for CO production varies from 5.8% at −0.89 V (vs reversible hydrogen electrode) over 10.3 nm NPs to 91.2% over 3.7 nm NPs, along with an 18.4-fold increase in current density. Based on the Gibbs free energy diagrams from density functional theory calculations, the adsorption of CO2 and the formation of key reaction intermediate COOH* are much easier on edge and corner sites than on terrace sites of Pd NPs. In contrast, the formation of H* for competitive hydrogen evolution reaction is similar on all three sites. A volcano-like curve of the turnover frequency for CO production within the size range suggests that CO2 adsorption, COOH* formation, and CO* removal during CO2 reduction can be tuned by varying the size of Pd NPs due to the changing ratio of corner, edge, and terrace sites.

Abstract The design of active, selective, and stable CO 2 reduction electrocatalysts is still challenging. A series of atomically dispersed Co catalysts with different nitrogen coordination numbers were prepared and their CO 2 electroreduction catalytic performance was explored. The best catalyst, atomically dispersed Co with two‐coordinate nitrogen atoms, achieves both high selectivity and superior activity with 94 % CO formation Faradaic efficiency and a current density of 18.1 mA cm −2 at an overpotential of 520 mV. The CO formation turnover frequency reaches a record value of 18 200 h −1 , surpassing most reported metal‐based catalysts under comparable conditions. Our experimental and theoretical results demonstrate that lower a coordination number facilitates activation of CO 2 to the CO 2 .− intermediate and hence enhances CO 2 electroreduction activity.

Mesoporous silica-coated gold nanorods (Au@SiO(2)) are developed as a promising and versatile theranostic platform for cancer treatment. Intracellular localization of Au@SiO(2) is visualized through two-photon imaging. With doxorubicin hydrochloride loaded, Au@SiO(2)-DOX show two light-mediated therapeutic modes: low power density laser-triggered drug release for chemotherapy, and high power density laser-induced hyperthermia, which suggest the potential for in-vivo applications.

Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships but require efficient methods for cell capture and mRNA sequencing. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths, the limitations of shallow sequencing have not been investigated directly. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing (~50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In the developing cortex, we identify diverse cell types, including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.

BRD4, a bromodomain and extraterminal domain (BET) family member, is an attractive target in multiple pathological settings, particularly cancer. While BRD4 inhibitors have shown some promise in MYC-driven malignancies such as Burkitt's lymphoma (BL), we show that BRD4 inhibitors lead to robust BRD4 protein accumulation, which may account for their limited suppression of MYC expression, modest antiproliferative activity, and lack of apoptotic induction. To address these limitations we designed ARV-825, a hetero-bifunctional PROTAC (Proteolysis Targeting Chimera) that recruits BRD4 to the E3 ubiquitin ligase cereblon, leading to fast, efficient, and prolonged degradation of BRD4 in all BL cell lines tested. Consequently, ARV-825 more effectively suppresses c-MYC levels and downstream signaling than small-molecule BRD4 inhibitors, resulting in more effective cell proliferation inhibition and apoptosis induction in BL. Our findings provide strong evidence that cereblon-based PROTACs provide a better and more efficient strategy in targeting BRD4 than traditional small-molecule inhibitors.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

<h2>Summary</h2> DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including <i>TP53</i> and <i>BRCA1/2</i>. Other prevalent alterations included epigenetic silencing of the direct repair genes <i>EXO5</i>, <i>MGMT</i>, and <i>ALKBH3</i> in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious <i>TP53</i> mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.

To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival. Specific protein acetylations associated with homologous recombination deficiency suggest a potential means for stratifying patients for therapy. In addition to providing a valuable resource, these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC. VIDEO ABSTRACT.

Immunosuppression of tumour-infiltrating lymphocytes (TIL) is a common feature of advanced cancer, but its biological basis has remained obscure. We demonstrate here a molecular link between epithelial-to-mesenchymal transition (EMT) and CD8+ TIL immunosuppression, two key drivers of cancer progression. We show that microRNA-200 (miR-200), a cell-autonomous suppressor of EMT and metastasis, targets PD-L1. Moreover, ZEB1, an EMT activator and transcriptional repressor of miR-200, relieves miR-200 repression of PD-L1 on tumour cells, leading to CD8+ T-cell immunosuppression and metastasis. These findings are supported by robust correlations between the EMT score, miR-200 levels and PD-L1 expression in multiple human lung cancer datasets. In addition to revealing a link between EMT and T-cell dysfunction, these findings also show that ZEB1 promotes metastasis through a heretofore unappreciated cell non-autonomous mechanism, and suggest that subgroups of patients in whom malignant progression is driven by EMT activators may respond to treatment with PD-L1 antagonists. Tumour-infiltrating lymphocytes (TILs) can be suppressed by the tumour, but how this occurs is not clear. Here the authors show that the miR-200 family, which suppresses epithelial–mesenchymal transition, also targets tumour cell PD-L1 and thereby intratumoral immunosuppression and metastasis.

Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was anti-correlated with expression of immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss of chromosome arm 3p in squamous cancers. We applied genome engineering to delete 3p in lung cells, causing decreased proliferation rescued in part by chromosome 3 duplication. This study defines genomic and phenotypic correlates of cancer aneuploidy and provides an experimental approach to study chromosome arm aneuploidy.

In phase 2 trials, treatment with the combination of the nucleotide polymerase inhibitor sofosbuvir and the NS5A inhibitor velpatasvir resulted in high rates of sustained virologic response in patients chronically infected with hepatitis C virus (HCV) genotype 2 or 3.We conducted two randomized, phase 3, open-label studies involving patients who had received previous treatment for HCV genotype 2 or 3 and those who had not received such treatment, including patients with compensated cirrhosis. In one trial, patients with HCV genotype 2 were randomly assigned in a 1:1 ratio to receive sofosbuvir-velpatasvir, in a once-daily, fixed-dose combination tablet (134 patients), or sofosbuvir plus weight-based ribavirin (132 patients) for 12 weeks. In a second trial, patients with HCV genotype 3 were randomly assigned in a 1:1 ratio to receive sofosbuvir-velpatasvir for 12 weeks (277 patients) or sofosbuvir-ribavirin for 24 weeks (275 patients). The primary end point for the two trials was a sustained virologic response at 12 weeks after the end of therapy.Among patients with HCV genotype 2, the rate of sustained virologic response in the sofosbuvir-velpatasvir group was 99% (95% confidence interval [CI], 96 to 100), which was superior to the rate of 94% (95% CI, 88 to 97) in the sofosbuvir-ribavirin group (P=0.02). Among patients with HCV genotype 3, the rate of sustained virologic response in the sofosbuvir-velpatasvir group was 95% (95% CI, 92 to 98), which was superior to the rate of 80% (95% CI, 75 to 85) in the sofosbuvir-ribavirin group (P<0.001). The most common adverse events in the two studies were fatigue, headache, nausea, and insomnia.Among patients with HCV genotype 2 or 3 with or without previous treatment, including those with compensated cirrhosis, 12 weeks of treatment with sofosbuvir-velpatasvir resulted in rates of sustained virologic response that were superior to those with standard treatment with sofosbuvir-ribavirin. (Funded by Gilead Sciences; ASTRAL-2 ClinicalTrials.gov number, NCT02220998; and ASTRAL-3, NCT02201953.).

H5N1 avian influenza virus (AIV) has emerged as a pathogenic entity for a variety of species, including humans, in recent years. Here we report an outbreak among migratory birds on Lake Qinghaihu, China, in May and June 2005, in which more than a thousand birds were affected. Pancreatic necrosis and abnormal neurological symptoms were the major clinical features. Sequencing of the complete genomes of four H5N1 AIV strains revealed them to be reassortants related to a peregrine falcon isolate from Hong Kong and to have known highly pathogenic characteristics. Experimental animal infections reproduced typical highly pathogenic AIV infection symptoms and pathology.

Abstract The molecular underpinnings that drive the heterogeneity of KRAS-mutant lung adenocarcinoma are poorly characterized. We performed an integrative analysis of genomic, transcriptomic, and proteomic data from early-stage and chemorefractory lung adenocarcinoma and identified three robust subsets of KRAS-mutant lung adenocarcinoma dominated, respectively, by co-occurring genetic events in STK11/LKB1 (the KL subgroup), TP53 (KP), and CDKN2A/B inactivation coupled with low expression of the NKX2-1 (TTF1) transcription factor (KC). We further revealed biologically and therapeutically relevant differences between the subgroups. KC tumors frequently exhibited mucinous histology and suppressed mTORC1 signaling. KL tumors had high rates of KEAP1 mutational inactivation and expressed lower levels of immune markers, including PD-L1. KP tumors demonstrated higher levels of somatic mutations, inflammatory markers, immune checkpoint effector molecules, and improved relapse-free survival. Differences in drug sensitivity patterns were also observed; notably, KL cells showed increased vulnerability to HSP90-inhibitor therapy. This work provides evidence that co-occurring genomic alterations identify subgroups of KRAS-mutant lung adenocarcinoma with distinct biology and therapeutic vulnerabilities. Significance: Co-occurring genetic alterations in STK11/LKB1, TP53, and CDKN2A/B—the latter coupled with low TTF1 expression—define three major subgroups of KRAS-mutant lung adenocarcinoma with distinct biology, patterns of immune-system engagement, and therapeutic vulnerabilities. Cancer Discov; 5(8); 860–77. ©2015 AACR. This article is highlighted in the In This Issue feature, p. 783

Network embedding, aiming to learn the low-dimensional representations of nodes in networks, is of paramount importance in many real applications. One basic requirement of network embedding is to preserve the structure and inherent properties of the networks. While previous network embedding methods primarily preserve the microscopic structure, such as the first- and second-order proximities of nodes, the mesoscopic community structure, which is one of the most prominent feature of networks, is largely ignored. In this paper, we propose a novel Modularized Nonnegative Matrix Factorization (M-NMF) model to incorporate the community structure into network embedding. We exploit the consensus relationship between the representations of nodes and community structure, and then jointly optimize NMF based representation learning model and modularity based community detection model in a unified framework, which enables the learned representations of nodes to preserve both of the microscopic and community structures. We also provide efficient updating rules to infer the parameters of our model, together with the correctness and convergence guarantees. Extensive experimental results on a variety of real-world networks show the superior performance of the proposed method over the state-of-the-arts.

Modulating cholesterol metabolism can improve CD8+ T-cell-mediated immunity against tumours; genetic or pharmacological inhibition of the cholesterol esterification enzyme ACAT1 led to higher plasma membrane cholesterol levels, better T-cell receptor clustering and signalling, improved immunological synapse maturation, and enhanced antitumour activity in mice. This study reports a new approach to cancer immunotherapy through the modulation of T cell cholesterol metabolism. Chenqi Xu and colleagues demonstrate that inhibition of the cellular cholesterol esterification pathway in mice, either by genetic ablation or by pharmacological inhibition of acetyl-CoA acetyltransferase 1 (ACAT1) and ACAT2, increases plasma membrane cholesterol levels, T-cell receptor clustering and signalling, and significantly potentiates the antitumour response of CD8+ T cells in mice. To test the potential of ACAT1 as a drug target for cancer immunotherapy, the authors treated melanoma-bearing mice with avasimibe, an ACAT inhibitor that has been used to treat atherosclerosis in clinical trials. An antitumour effect was observed and a combination of avasimibe and anti-PD-1 antibody was more effective than either alone. CD8+ T cells have a central role in antitumour immunity, but their activity is suppressed in the tumour microenvironment1,2,3,4. Reactivating the cytotoxicity of CD8+ T cells is of great clinical interest in cancer immunotherapy. Here we report a new mechanism by which the antitumour response of mouse CD8+ T cells can be potentiated by modulating cholesterol metabolism. Inhibiting cholesterol esterification in T cells by genetic ablation or pharmacological inhibition of ACAT1, a key cholesterol esterification enzyme5, led to potentiated effector function and enhanced proliferation of CD8+ but not CD4+ T cells. This is due to the increase in the plasma membrane cholesterol level of CD8+ T cells, which causes enhanced T-cell receptor clustering and signalling as well as more efficient formation of the immunological synapse. ACAT1-deficient CD8+ T cells were better than wild-type CD8+ T cells at controlling melanoma growth and metastasis in mice. We used the ACAT inhibitor avasimibe, which was previously tested in clinical trials for treating atherosclerosis and showed a good human safety profile6,7, to treat melanoma in mice and observed a good antitumour effect. A combined therapy of avasimibe plus an anti-PD-1 antibody showed better efficacy than monotherapies in controlling tumour progression. ACAT1, an established target for atherosclerosis, is therefore also a potential target for cancer immunotherapy.

The bandgaps of monolayer and bulk molybdenum sulfide (MoS2) result in that they are far from suitable for application as a saturable absorption device. In this paper, the operation of a broadband MoS2 saturable absorber is demonstrated by the introduction of suitable defects. It is believed that the results provide some inspiration in the investigation of two-dimensional optoelectronic materials.

<h2>Abstract</h2> <i>XRCC4</i> was identified via a complementation cloning method that employed an ionizing radiation (IR)-sensitive hamster cell line. By gene-targeted mutation, we show that XRCC4 deficiency in primary murine cells causes growth defects, premature senescence, IR sensitivity, and inability to support V(D)J recombination. In mice, XRCC4 deficiency causes late embryonic lethality accompanied by defective lymphogenesis and defective neurogenesis manifested by extensive apoptotic death of newly generated postmitotic neuronal cells. We find similar neuronal developmental defects in embryos that lack DNA ligase IV, an XRCC4-associated protein. Our findings demonstrate that differentiating lymphocytes and neurons strictly require the XRCC4 and DNA ligase IV end-joining proteins and point to the general stage of neuronal development in which these proteins are necessary.

Telomere maintenance has been proposed as an essential prerequisite to human tumor development. The telomerase enzyme is itself a marker for tumor cells, but the genetic alterations that activate the enzyme during neoplastic transformation have remained a mystery. Here, we show that Myc induces telomerase in both normal human mammary epithelial cells (HMECs) and normal human diploid fibroblasts. Myc increases expression of hEST2 (hTRT/TP2), the limiting subunit of telomerase, and both Myc and hEST2 can extend the life span of HMECs. The ability of Myc to activate telomerase may contribute to its ability to promote tumor formation.

Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects alternative splicing events and tumor variants by reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more alternative splicing events than normal samples. Association analysis of somatic variants with alternative splicing events confirmed known trans associations with variants in SF3B1 and U2AF1 and identified additional trans-acting variants (e.g., TADA1, PPP2R1A). Many tumors have thousands of alternative splicing events not detectable in normal samples; on average, we identified ≈930 exon-exon junctions ("neojunctions") in tumors not typically found in GTEx normals. From Clinical Proteomic Tumor Analysis Consortium data available for breast and ovarian tumor samples, we confirmed ≈1.7 neojunction- and ≈0.6 single nucleotide variant-derived peptides per tumor sample that are also predicted major histocompatibility complex-I binders ("putative neoantigens").

Significance We describe the development of a small molecule that mediates the degradation of bromodomain and extra-terminal (BET) proteins and its application in the treatment of castration-resistant prostate cancer (CRPC). Few therapeutic options exist to treat CRPC, especially CRPC tumors expressing constitutively active androgen receptor (AR) splice variants that lack the ligand-binding domain and can effect androgen-independent transactivation of target genes. Importantly, we demonstrate that targeted degradation of BET proteins using proteolysis-targeting chimera (PROTAC) technology causes cell death in cultured prostate cancer cells and results in tumor growth inhibition or regression in mouse models of CRPC, including models that express high levels of AR splice variant 7. Our work thus contains a significant potential therapeutic advance in the treatment of this cancer.

How do you like your eggs? Amphiphilic carbon dots (CDs) with intense blue fluorescence have been produced from chicken eggs by treatment with plasma. They are used as effective “fluorescent carbon inks” for multicolor luminescent inkjet and silk-screen printing (see image).

Topological states of quantum matter have attracted great attention in condensed matter physics and materials science. The study of time-reversal-invariant topological states in quantum materials has made tremendous progress. However, the study of magnetic topological states falls much behind due to the complex magnetic structures. Here, we predict the tetradymite-type compound ${\mathrm{MnBi}}_{2}{\mathrm{Te}}_{4}$ and its related materials host topologically nontrivial magnetic states. The magnetic ground state of ${\mathrm{MnBi}}_{2}{\mathrm{Te}}_{4}$ is an antiferromagetic topological insulator state with a large topologically nontrivial energy gap ($\ensuremath{\sim}0.2\text{ }\text{ }\mathrm{eV}$). It presents the axion state, which has gapped bulk and surface states, and the quantized topological magnetoelectric effect. The ferromagnetic phase of ${\mathrm{MnBi}}_{2}{\mathrm{Te}}_{4}$ might lead to a minimal ideal Weyl semimetal.

Abstract While thermo‐chemotherapy has proved to be effective in optimizing the efficacies of cancer treatments, traditional chemotherapy is subject to adverse side effects and heat delivery is often challenging in operation. Some photothermal inorganic nanoparticles responsive to near infrared light provide new opportunities for simultaneous and targeted delivery of heat and chemotherapeutics to the tumor sites in pursuit of synergistic effects for efficacy enhancement. The state of the art of nanoparticle‐induced thermo‐chemotherapy is summarized and the advantages and challenges of the major nanoplatforms based on gold nanoparticles, carbon nanomaterials, palladium nanosheets, and copper‐based nanocrystals are highlighted. In addition, the optical‐imaging potentials of the nanoplatforms that may endow them with imaging‐guided therapy and therapeutic‐result‐monitoring capabilities are also briefly discussed.

Although the prevalence and incidence of diabetes have increased in the United States in recent decades, no studies have systematically examined long-term, national trends in the prevalence and incidence of diagnosed diabetes.To examine long-term trends in the prevalence and incidence of diagnosed diabetes to determine whether there have been periods of acceleration or deceleration in rates.We analyzed 1980-2012 data for 664,969 adults aged 20 to 79 years from the National Health Interview Survey (NHIS) to estimate incidence and prevalence rates for the overall civilian, noninstitutionalized, US population and by demographic subgroups (age group, sex, race/ethnicity, and educational level).The annual percentage change (APC) in rates of the prevalence and incidence of diagnosed diabetes (type 1 and type 2 combined).The APC for age-adjusted prevalence and incidence of diagnosed diabetes did not change significantly during the 1980s (for prevalence, 0.2% [95% CI, -0.9% to 1.4%], P = .69; for incidence, -0.1% [95% CI, -2.5% to 2.4%], P = .93), but each increased sharply during 1990-2008 (for prevalence, 4.5% [95% CI, 4.1% to 4.9%], P < .001; for incidence, 4.7% [95% CI, 3.8% to 5.6%], P < .001) before leveling off with no significant change during 2008-2012 (for prevalence, 0.6% [95% CI, -1.9% to 3.0%], P = .64; for incidence, -5.4% [95% CI, -11.3% to 0.9%], P = .09). The prevalence per 100 persons was 3.5 (95% CI, 3.2 to 3.9) in 1990, 7.9 (95% CI, 7.4 to 8.3) in 2008, and 8.3 (95% CI, 7.9 to 8.7) in 2012. The incidence per 1000 persons was 3.2 (95% CI, 2.2 to 4.1) in 1990, 8.8 (95% CI, 7.4 to 10.3) in 2008, and 7.1 (95% CI, 6.1 to 8.2) in 2012. Trends in many demographic subpopulations were similar to these overall trends. However, incidence rates among non-Hispanic black and Hispanic adults continued to increase (for interaction, P = .03 for non-Hispanic black adults and P = .01 for Hispanic adults) at rates significantly greater than for non-Hispanic white adults. In addition, the rate of increase in prevalence was higher for adults who had a high school education or less compared with those who had more than a high school education (for interaction, P = .006 for <high school and P < .001 for high school).Analyses of nationally representative data from 1980 to 2012 suggest a doubling of the incidence and prevalence of diabetes during 1990-2008, and a plateauing between 2008 and 2012. However, there appear to be continued increases in the prevalence or incidence of diabetes among subgroups, including non-Hispanic black and Hispanic subpopulations and those with a high school education or less.

External stimuli, such as ultrasound, magnetic field, and light, can be applied to activate in vivo tumor targeting. Herein, we fabricated polymer encapsulated gold nanorods to couple the photothermal properties of gold nanorods and the thermo- and pH-responsive properties of polymers in a single nanocomposite. The activation mechamism was thus transformed from heat to near-infrared (NIR) laser, which can be more easily controlled. Doxorubicin, a clinical anticancer drug, can be loaded into the nanocomposite through electrostatic interactions with high loading content up to 24%. The nanocomposite’s accumulation in tumor post systematic administration can be significantly enhanced by NIR laser irradiation, providing a prerequisite for their therapeutic application which almost completely inhibited tumor growth and lung metastasis. Since laser can be manipulated very precisely and flexibly, the nanocomposite provides an ideally versatile platform to simultaneously deliver heat and anticancer drugs in a laser-activation mechanism with facile control of the area, time, and dosage. The NIR laser-induced targeted cancer thermo-chemotherapy without using targeting ligands represents a novel targeted anticancer strategy with facile control and practical efficacy.

<h2>Summary</h2> Inhibiting protein function selectively is a major goal of modern drug discovery. Here, we report a previously understudied benefit of small molecule proteolysis-targeting chimeras (PROTACs) that recruit E3 ubiquitin ligases to target proteins for their ubiquitination and subsequent proteasome-mediated degradation. Using promiscuous CRBN- and VHL-recruiting PROTACs that bind >50 kinases, we show that only a subset of bound targets is degraded. The basis of this selectivity relies on protein-protein interactions between the E3 ubiquitin ligase and the target protein, as illustrated by engaged proteins that are not degraded as a result of unstable ternary complexes with PROTAC-recruited E3 ligases. In contrast, weak PROTAC:target protein affinity can be stabilized by high-affinity target:PROTAC:ligase trimer interactions, leading to efficient degradation. This study highlights design guidelines for generating potent PROTACs as well as possibilities for degrading undruggable proteins immune to traditional small-molecule inhibitors.

An unbiased screen for genes that can immortalize mouse embryonic fibroblasts identified the glycolytic enzyme phosphoglycerate mutase (PGM). A 2-fold increase in PGM activity enhances glycolytic flux, allows indefinite proliferation, and renders cells resistant to ras-induced arrest. Glucosephosphate isomerase, another glycolytic enzyme, displays similar activity and, conversely, depletion of PGM or glucosephosphate isomerase with short interfering RNA triggers premature senescence. Immortalized mouse embryonic fibroblasts and mouse embryonic stem cells display higher glycolytic flux and more resistance to oxidative damage than senescent cells. Because wild-type p53 down-regulates PGM, mutation of p53 can facilitate immortalization via effects on PGM levels and glycolysis.

A three-dimensional graphene network (3DGN) grown on nickel foam is an excellent template for the synthesis of graphene-based composite electrodes for use in supercapacitors. Ni(OH)2nanosheets coated onto single-crystal Ni3S2nanorods grown on the surface of the 3DGN (referred to as the Ni3S2@Ni(OH)2/3DGN) are synthesized using a one-step hydrothermal reaction. SEM, TEM, XRD and Raman spectroscopy are used to investigate the morphological and structural evolution of the Ni3S2@Ni(OH)2/3DGN. Detailed electrochemical characterization shows that the Ni3S2@Ni(OH)2/3DGN exhibits high specific capacitance (1277 F g−1 at 2 mV s−1 and 1037.5 F g−1 at 5.1 A g−1) and areal capacitance (4.7 F cm−2 at 2 mV s−1 and 3.85 F cm−2 at 19.1 mA cm−2) with good cycling performance (99.1% capacitance retention after 2000 cycles).

Reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert the results that have been analyzed according to old assemblies to newer versions, or vice versa, to facilitate meta-analysis, direct comparison, data integration and visualization. Several useful conversion tools can convert genome interval files in browser extensible data or general feature format, but none have the functionality to convert files in sequence alignment map or BigWig format. This is a significant gap in computational genomics tools, as these formats are the ones most widely used for representing high-throughput sequencing data, such as RNA-seq, chromatin immunoprecipitation sequencing, DNA-seq, etc.Here we developed CrossMap, a versatile and efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format.CrossMap is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://crossmap.sourceforge.net/.

Lithium is commonly used to treat bipolar disorder, which is associated with altered circadian rhythm. Lithium is a potent inhibitor of glycogen synthase kinase 3 (GSK3), which regulates circadian rhythm in several organisms. In experiments with cultured cells, we show here that GSK3beta phosphorylates and stabilizes the orphan nuclear receptor Rev-erbalpha, a negative component of the circadian clock. Lithium treatment of cells leads to rapid proteasomal degradation of Rev-erbalpha and activation of clock gene Bmal1. A form of Rev-erbalpha that is insensitive to lithium interferes with the expression of circadian genes. Control of Rev-erbalpha protein stability is thus a critical component of the peripheral clock and a biological target of lithium therapy.

Phosphatidylinositol 4 phosphate [PI(4)P] is essential for secretion in yeast, but its role in mammalian cells is unclear. Current paradigms propose that PI(4)P acts primarily as a precursor to phosphatidylinositol 4,5 bisphosphate (PIP2), an important plasma membrane regulator. We found that PI(4)P is enriched in the mammalian Golgi, and used RNA interference (RNAi) of PI4KIIalpha, a Golgi resident phosphatidylinositol 4 kinase, to determine whether PI(4)P directly regulates the Golgi. PI4KIIalpha RNAi decreases Golgi PI(4)P, blocks the recruitment of clathrin adaptor AP-1 complexes to the Golgi, and inhibits AP-1-dependent functions. This AP-1 binding defect is rescued by adding back PI(4)P. In addition, purified AP-1 binds PI(4)P, and anti-PI(4)P inhibits the in vitro recruitment of cytosolic AP-1 to normal cellular membranes. We propose that PI4KIIalpha establishes the Golgi's unique lipid-defined organelle identity by generating PI(4)P-rich domains that specify the docking of the AP-1 coat machinery.

Ag2O/TiO2 heterostructure with high photocatalytic activity both in ultraviolet and visible-light region was synthesized via a simple and practical coprecipitation method by using surface-modified TiO2 nanobelts as substrate materials. The as-prepared heterostructure composite included Ag2O nanoparticles assembled uniformly on the rough surface of TiO2 nanobelts. Comparing with pure TiO2 nanobelts and Ag2O nanoparticles, the composite photocatalyst with a wide weight ratio between TiO2 and Ag2O exhibited enhanced photocatalytic activity under ultraviolet and visible light irradiation in the decomposition of methyl orange (MO) aqueous solution. On the basis of the characterization by X-ray diffraction, photoluminescence and UV−vis diffuse reflectance spectroscopies, two mechanisms were proposed to account for the photocatalytic activity of Ag2O/TiO2 nanobelts’ heterostructure.

The relationship between severe myoclonic epilepsy of infancy (SMEI or Dravet syndrome) and the related syndrome SMEI-borderland (SMEB) with mutations in the sodium channel alpha 1 subunit gene SCN1A is well established. To explore the phenotypic variability associated with SCN1A mutations, 188 patients with a range of epileptic encephalopathies were examined for SCN1A sequence variations by denaturing high performance liquid chromatography and sequencing. All patients had seizure onset within the first 2 years of life. A higher proportion of mutations were identified in patients with SMEI (52/66; 79%) compared to patients with SMEB (25/36; 69%). By studying a broader spectrum of infantile epileptic encephalopathies, we identified mutations in other syndromes including cryptogenic generalized epilepsy (24%) and cryptogenic focal epilepsy (22%). Within the latter group, a distinctive subgroup designated as severe infantile multifocal epilepsy had SCN1A mutations in three of five cases. This phenotype is characterized by early onset multifocal seizures and later cognitive decline. Knowledge of an expanded spectrum of epileptic encephalopathies associated with SCN1A mutations allows earlier diagnostic confirmation for children with these devastating disorders.

Thermally reduced graphene nanoplatelets were covalently functionalised via Bingel reaction to improve their dispersion and interfacial bonding with an epoxy resin. Functionalised graphene were characterized by microscopic, thermal and spectroscopic techniques. Thermal analysis of functionalised graphene revealed a significantly higher thermal stability compared to graphene oxide. Inclusion of only 0.1 wt% of functionalised graphene in an epoxy resin showed 22% increase in flexural strength and 18% improvement in storage modulus. The improved mechanical properties of nanocomposites is due to the uniform dispersion of functionalised graphene and strong interfacial bonding between modified graphene and epoxy resin as confirmed by microscopy observations.

Developing low-cost, efficient, and bifunctional electrocatalysts for both the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) is an appealing yet challenging task. Herein, for the first time, a NiS microsphere film was grown in situ on Ni foam (NiS/Ni foam) via a sulfurization reaction as an efficient bifunctional electrocatalyst for overall water splitting with superior activity and good durability. This NiS/Ni foam electrode delivers 20 mA cm(-2) at an overpotential of 158 mV for the HER and 50 mA cm(-2) at an overpotential of 335 mV for the OER in 1.0 M KOH. This bifunctional electrode also enables a high-efficiency alkaline water electrolyzer with 10 mA cm(-2) at a cell voltage of only 1.64 V, which could be promising in water splitting devices for large-scale hydrogen production.

The survival of patients with oral squamous cell carcinoma (OSCC) has not changed significantly in several decades, leading clinicians and investigators to search for promising molecular targets. To this end, we conducted comprehensive genomic analysis of gene expression, copy number, methylation, and point mutations in OSCC. Integrated analysis revealed more somatic events than previously reported, identifying four major driver pathways (mitogenic signaling, Notch, cell cycle, and TP53) and two additional key genes (FAT1, CASP8). The Notch pathway was defective in 66% of patients, and in follow-up studies of mechanism, functional NOTCH1 signaling inhibited proliferation of OSCC cell lines. Frequent mutation of caspase-8 (CASP8) defines a new molecular subtype of OSCC with few copy number changes. Although genomic alterations are dominated by loss of tumor suppressor genes, 80% of patients harbored at least one genomic alteration in a targetable gene, suggesting that novel approaches to treatment may be possible for this debilitating subset of head and neck cancers.

Abstract Since December 2019, a newly identified coronavirus (2019 novel coronavirus, 2019-nCov) is causing outbreak of pneumonia in one of largest cities, Wuhan, in Hubei province of China and has draw significant public health attention. The same as severe acute respiratory syndrome coronavirus (SARS-CoV), 2019-nCov enters into host cells via cell receptor angiotensin converting enzyme II (ACE2). In order to dissect the ACE2-expressing cell composition and proportion and explore a potential route of the 2019-nCov infection in digestive system infection, 4 datasets with single-cell transcriptomes of lung, esophagus, gastric, ileum and colon were analyzed. The data showed that ACE2 was not only highly expressed in the lung AT2 cells, esophagus upper and stratified epithelial cells but also in absorptive enterocytes from ileum and colon. These results indicated along with respiratory systems, digestive system is a potential routes for 2019-nCov infection. In conclusion, this study has provided the bioinformatics evidence of the potential route for infection of 2019-nCov in digestive system along with respiratory tract and may have significant impact for our healthy policy setting regards to prevention of 2019-nCoV infection.

A new compilation of heat flow data for the continental area of China has been constructed using both published data (up to 1999) as well as previously unpublished data. The data set is composed of 862 observations from different sites. Within the continental area of China, heat flow values range from 23 to 319 mW/m2, with a mean of 63±24.2 mW/m2. If non-conductive values related to local hydrothermal systems are excluded, the representative average heat flow is 61±15.5 mW/m2 (n=823), with an associated range of 30–140 mW/m2. Heat flow analysis for each specific sub-tectonic province shows discernible trends within a tectonic province. The relationships between the heat flow and geological ages based on this new dataset indicate that surface heat flow is obviously more dependent on the last tectonothermal activity than the age of the orogeny. The overall heat flow pattern exhibits high values in the east and in the southwest, and low in the center and northwest parts of the continental area of China, and appears to be dominated largely by the Meso-Cenozoic tectonothermal evolution of the lithosphere. The Cenozoic collision between the Indian and Eurasian plates, and the subsequent thickening of the lithosphere; and the lithospheric thinning and volcano-magmatic activities during the Late Mesozoic in East China; can be seen clearly in the heat flow pattern.

Abstract STK11/LKB1 is among the most commonly inactivated tumor suppressors in non–small cell lung cancer (NSCLC), especially in tumors harboring KRAS mutations. Many oncogenes promote immune escape, undermining the effectiveness of immunotherapies, but it is unclear whether the inactivation of tumor suppressor genes, such as STK11/LKB1, exerts similar effects. In this study, we investigated the consequences of STK11/LKB1 loss on the immune microenvironment in a mouse model of KRAS-driven NSCLC. Genetic ablation of STK11/LKB1 resulted in accumulation of neutrophils with T-cell–suppressive effects, along with a corresponding increase in the expression of T-cell exhaustion markers and tumor-promoting cytokines. The number of tumor-infiltrating lymphocytes was also reduced in LKB1-deficient mouse and human tumors. Furthermore, STK11/LKB1–inactivating mutations were associated with reduced expression of PD-1 ligand PD-L1 in mouse and patient tumors as well as in tumor-derived cell lines. Consistent with these results, PD-1–targeting antibodies were ineffective against Lkb1-deficient tumors. In contrast, treating Lkb1-deficient mice with an IL6-neutralizing antibody or a neutrophil-depleting antibody yielded therapeutic benefits associated with reduced neutrophil accumulation and proinflammatory cytokine expression. Our findings illustrate how tumor suppressor mutations can modulate the immune milieu of the tumor microenvironment, and they offer specific implications for addressing STK11/LKB1–mutated tumors with PD-1–targeting antibody therapies. Cancer Res; 76(5); 999–1008. ©2016 AACR.

Advanced MaterialsVolume 23, Issue 26 p. 2915-2919 Communication Versatile Bifunctional Magnetic-Fluorescent Responsive Janus Supraballs Towards the Flexible Bead Display Su-Na Yin, Su-Na Yin State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorCai-Feng Wang, Cai-Feng Wang State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorZi-Yi Yu, Zi-Yi Yu State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorJing Wang, Jing Wang State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorSi-Si Liu, Si-Si Liu State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorSu Chen, Corresponding Author Su Chen [email protected] State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaState Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. China.Search for more papers by this author Su-Na Yin, Su-Na Yin State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorCai-Feng Wang, Cai-Feng Wang State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorZi-Yi Yu, Zi-Yi Yu State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorJing Wang, Jing Wang State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorSi-Si Liu, Si-Si Liu State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaSearch for more papers by this authorSu Chen, Corresponding Author Su Chen [email protected] State Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. ChinaState Key Laboratory of Materials-Oriented Chemical Engineering, and College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, P. R. China.Search for more papers by this author First published: 26 April 2011 https://doi.org/10.1002/adma.201100203Citations: 430Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat Graphical Abstract The first microfluidic synthesis of ionomer-based bifunctional Janus supraballs possessing two distinct magnetic-nanoparticle-dropped and quantum dots–polymer hemispheres within an anisotropic structure is reported. Based on such Janus supraballs with stable fluorescence and superparamagnetism, a magnetoresponsive fluorescent switch is developed to realize free-writing under a magnetic field. This is a promising, simple way to fabricate novel flexible bead displays. Supporting Information Detailed facts of importance to specialist readers are published as "Supporting Information". Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Filename Description adma_201100203_sm_suppl.pdf446.4 KB suppl Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. References 1 a) Z. Nie, W. Li, M. Seo, S. Xu, E. Kumacheva, J. Am. Chem. Soc. 2006, 128, 9408; b) A. Ghosh, N. K. Sheridon, P. Fischer, Small 2008, 4, 1956; c) T. Nisisako, T. 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Proteolysis targeting chimera (PROTAC) technology has emerged over the last two decades as a powerful tool for targeted degradation of endogenous proteins. Herein we describe the development of PROTACs for receptor tyrosine kinases, a protein family yet to be targeted for induced protein degradation. The use of VHL-recruiting PROTACs against this protein family reveals several advantages of degradation over inhibition alone: direct comparisons of fully functional, target-degrading PROTACs with target-inhibiting variants that contain an inactivated E3 ligase-recruiting ligand show that degradation leads to more potent inhibition of cell proliferation and a more durable and sustained downstream signaling response, and thus addresses the kinome rewiring challenge seen with many receptor tyrosine kinase inhibitors. Combined, these findings demonstrate the ability to target receptor tyrosine kinases for degradation using the PROTAC technology and outline the advantages of this degradation-based approach.

<h2>Summary</h2><h3>Background</h3> COVID-19 has spread globally. Epidemiological susceptibility to COVID-19 has been reported in patients with cancer. We aimed to systematically characterise clinical features and determine risk factors of COVID-19 disease severity for patients with cancer and COVID-19. <h3>Methods</h3> In this multicentre, retrospective, cohort study, we included all adult patients (aged ≥18 years) with any type of malignant solid tumours and haematological malignancy who were admitted to nine hospitals in Wuhan, China, with laboratory-confirmed COVID-19 between Jan 13 and March 18, 2020. Enrolled patients were statistically matched (2:1) with patients admitted with COVID-19 who did not have cancer with propensity score on the basis of age, sex, and comorbidities. Demographic characteristics, laboratory examinations, illness severity, and clinical interventions were compared between patients with COVID-19 with or without cancer as well as between patients with cancer with non-severe or severe COVID-19. COVID-19 disease severity was defined on admission on the basis of the WHO guidelines. Univariable and multivariable logistic regression, adjusted for age, sex, comorbidities, cancer type, tumour stage, and antitumour treatments, were used to explore risk factors associated with COVID-19 disease severity. This study was registered in the Chinese Clinical Trial Register, ChiCTR2000030807. <h3>Findings</h3> Between Jan 13 and March 18, 2020, 13 077 patients with COVID-19 were admitted to the nine hospitals in Wuhan and 232 patients with cancer and 519 statistically matched patients without cancer were enrolled. Median follow-up was 29 days (IQR 22–38) in patients with cancer and 27 days (20–35) in patients without cancer. Patients with cancer were more likely to have severe COVID-19 than patients without cancer (148 [64%] of 232 <i>vs</i> 166 [32%] of 519; odds ratio [OR] 3·61 [95% CI 2·59–5·04]; p<0·0001). Risk factors previously reported in patients without cancer, such as older age; elevated interleukin 6, procalcitonin, and D-dimer; and reduced lymphocytes were validated in patients with cancer. We also identified advanced tumour stage (OR 2·60, 95% CI 1·05–6·43; <i>p</i>=0·039), elevated tumour necrosis factor α (1·22, 1·01–1·47; <i>p</i>=0·037), elevated N-terminal pro-B-type natriuretic peptide (1·65, 1·03–2·78; p=0·032), reduced CD4+ T cells (0·84, 0·71–0·98; p=0·031), and reduced albumin–globulin ratio (0·12, 0·02–0·77; p=0·024) as risk factors of COVID-19 severity in patients with cancer. <h3>Interpretation</h3> Patients with cancer and COVID-19 were more likely to deteriorate into severe illness than those without cancer. The risk factors identified here could be helpful for early clinical surveillance of disease progression in patients with cancer who present with COVID-19. <h3>Funding</h3> China National Natural Science Foundation.

Reconstructing low-dose X-ray computed tomography (CT) images is a noise problem. This work investigated a penalized weighted least-squares (PWLS) approach to address this problem in two dimensions, where the WLS considers first- and second-order noise moments and the penalty models signal spatial correlations. Three different implementations were studied for the PWLS minimization. One utilizes a Markov random field (MRF) Gibbs functional to consider spatial correlations among nearby detector bins and projection views in sinogram space and minimizes the PWLS cost function by iterative Gauss-Seidel algorithm. Another employs Karhunen-Loeve (KL) transform to de-correlate data signals among nearby views and minimizes the PWLS adaptively to each KL component by analytical calculation, where the spatial correlation among nearby bins is modeled by the same Gibbs functional. The third one models the spatial correlations among image pixels in image domain also by a MRF Gibbs functional and minimizes the PWLS by iterative successive over-relaxation algorithm. In these three implementations, a quadratic functional regularization was chosen for the MRF model. Phantom experiments showed a comparable performance of these three PWLS-based methods in terms of suppressing noise-induced streak artifacts and preserving resolution in the reconstructed images. Computer simulations concurred with the phantom experiments in terms of noise-resolution tradeoff and detectability in low contrast environment. The KL-PWLS implementation may have the advantage in terms of computation for high-resolution dynamic low-dose CT imaging

Small cell lung cancer (SCLC) is an aggressive malignancy distinct from non-small cell lung cancer (NSCLC) in its metastatic potential and treatment response. Using an integrative proteomic and transcriptomic analysis, we investigated molecular differences contributing to the distinct clinical behavior of SCLCs and NSCLCs. SCLCs showed lower levels of several receptor tyrosine kinases and decreased activation of phosphoinositide 3-kinase (PI3K) and Ras/mitogen-activated protein (MAP)/extracellular signal-regulated kinase (ERK) kinase (MEK) pathways but significantly increased levels of E2F1-regulated factors including enhancer of zeste homolog 2 (EZH2), thymidylate synthase, apoptosis mediators, and DNA repair proteins. In addition, PARP1, a DNA repair protein and E2F1 co-activator, was highly expressed at the mRNA and protein levels in SCLCs. SCLC growth was inhibited by PARP1 and EZH2 knockdown. Furthermore, SCLC was significantly more sensitive to PARP inhibitors than were NSCLCs, and PARP inhibition downregulated key components of the DNA repair machinery and enhanced the efficacy of chemotherapy.SCLC is a highly lethal cancer with a 5-year survival rate of less than 10%. To date, no molecularly targeted agents have prolonged survival in patients with SCLCs. As a step toward identifying new targets, we systematically profiled SCLCs with a focus on therapeutically relevant signaling pathways. Our data reveal fundamental differences in the patterns of pathway activation in SCLCs and NSCLCs and identify several potential therapeutic targets for SCLCs, including PARP1 and EZH2. On the basis of these results, clinical studies evaluating PARP and EZH2 inhibition, together with chemotherapy or other agents, warrant further investigation.

BackgroundMutations in the v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) play a critical role in cancer cell growth and resistance to therapy. Most mutations occur at codons 12 and 13. In colorectal cancer, the presence of any mutant KRas amino acid substitution is a negative predictor of patient response to targeted therapy. However, in non–small cell lung cancer (NSCLC), the evidence that KRAS mutation is a predictive factor is conflicting.

A targeted intracellular delivery system of paclitaxel (PTX) was successfully developed based on redox-sensitive hyaluronic acid-deoxycholic acid (HA-ss-DOCA) conjugates. The conjugates self-assembled into nano-size micelles in aqueous media and exhibited excellent drug-loading capacities (34.1%) and entrapment efficiency (93.2%) for PTX. HA-ss-DOCA micelles were sufficiently stable at simulated normal physiologic condition but fast disassembled in the presence of 20 mm reducing agent, glutathione. In vitro drug release studies showed that the PTX-loaded HA-ss-DOCA micelles accomplished rapid drug release under reducing condition. Intracellular release of fluorescent probe nile red indicated that HA-ss-DOCA micelles provide an effective approach for rapid transport of cargo into the cytoplasm. Enhanced cytotoxicity of PTX-loaded HA-ss-DOCA micelles further confirmed that the sensitive micelles are more potent for intracellular drug delivery as compared to the insensitive control. Based on flow cytometry and confocal microscopic analyses, observations revealed that HA-ss-DOCA micelles were taken up to human breast adenocarcinoma cells (MDA-MB-231) via HA-receptor mediated endocytosis. In vivo investigation of micelles in tumor-bearing mice confirmed that HA-ss-DOCA micelles possessed much higher tumor targeting capacity than the insensitive control. These results suggest that redox-sensitive HA-ss-DOCA micelles hold great potential as targeted intracellular delivery carriers of lipophilic anticancer drugs.

Background Across many observational studies, herpes simplex virus type 2 (HSV-2) infection is associated with two-fold to three-fold increased risk for HIV-1 infection. We investigated whether HSV-2 suppression with aciclovir would reduce the risk of HIV-1 acquisition. Methods We undertook a double-blind, randomised, placebo-controlled phase III trial in HIV-negative, HSV-2 seropositive women in Africa and men who have sex with men (MSM) from sites in Peru and the USA. Participants were randomly assigned by block randomisation to twice daily aciclovir 400 mg (n=1637) or matching placebo (n=1640) for 12–18 months, and were seen monthly for dispensation of study drug, adherence counselling and measurement by pill count and self-reporting, and risk reduction counselling, and every 3 months for genital examination and HIV testing. The primary outcome was HIV-1 acquisition and secondary was incidence of genital ulcers. Analysis was by intention to treat. This study is registered with ClinicalTrials.gov, number NCT00076232. Findings 3172 participants (1358 women, 1814 MSM) were included in the primary dataset (1581 in aciclovir group, 1591 in control group). The incidence of HIV-1 was 3·9 per 100 person-years in the aciclovir group (75 events in 1935 person-years of follow-up) and 3·3 per 100 person-years in the placebo group (64 events in 1969 person-years of follow-up; hazard ratio 1·16 [95% CI 0·83–1·62]). Incidence of genital ulcers on examination was reduced by 47% (relative risk 0·53 [0·46–0·62]) and HSV-2 positive genital ulcers by 63% (0·37 [0·31–0·45]) in the aciclovir group. Adherence to dispensed study drug was 94% in the aciclovir group and 94% in the placebo group, and 85% of expected doses in the aciclovir group and 86% in the placebo group. Retention was 85% at 18 months in both groups (1028 of 1212 in aciclovir group, 1030 of 1208 in placebo group). We recorded no serious events related to the study drug. Interpretation Our results show that suppressive therapy with standard doses of aciclovir is not effective in reduction of HIV-1 acquisition in HSV-2 seropositive women and MSM. Novel strategies are needed to interrupt interactions between HSV-2 and HIV-1. Funding US National Institute of Allergy and Infectious Diseases, US National Institute of Child Health and Human Development, US National Institute of Drug Abuse, US National Institute of Mental Health, US Office of AIDS Research, and GlaxoSmithKline.

Abstract Hard carbons (HCs) possess high lithium/sodium storage capacities, which however suffer from low electric conductivity and poor ion diffusion kinetics. An efficient structure design with appropriate heteroatoms doping and optimized graphitic/defective degree is highly desired to tackle these problems. This work reports a new design of N‐doped HC nanoshells (N‐GCNs) with homogeneous defective nanographite domains, fabricated through the prechelation between Ni 2+ and chitosan and subsequent catalyst confined graphitization. The as‐prepared N‐GCNs deliver a high reversible lithium storage capacity of 1253 mA h g −1 , with outstanding rate performance (175 mA h g −1 at a high rate of 20 A g −1 ) and good cycling stability, which outperforms most state‐of‐the‐art HCs. Meanwhile, a high reversible sodium storage capacity of 325 mA h g −1 is also obtained, which stabilizes at 174 mA h g −1 after 200 cycles. Density functional theory calculations are performed to uncover the coupling effect between heteroatom‐doping and the defective nanographitic domains down to the atomic scale. The in situ Raman analysis reveals the “adsorption mechanism” for sodium storage and the “adsorption–intercalation mechanism” for lithium storage of N‐GCNs.

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines—in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.

Oxidative stress and inflammation interact in the development of diabetic atherosclerosis. Intracellular hyperglycemia promotes production of mitochondrial reactive oxygen species (ROS), increased formation of intracellular advanced glycation end-products, activation of protein kinase C, and increased polyol pathway flux. ROS directly increase the expression of inflammatory and adhesion factors, formation of oxidized-low density lipoprotein, and insulin resistance. They activate the ubiquitin pathway, inhibit the activation of AMP-protein kinase and adiponectin, decrease endothelial nitric oxide synthase activity, all of which accelerate atherosclerosis. Changes in the composition of the gut microbiota and changes in microRNA expression that influence the regulation of target genes that occur in diabetes interact with increased ROS and inflammation to promote atherosclerosis. This review highlights the consequences of the sustained increase of ROS production and inflammation that influence the acceleration of atherosclerosis by diabetes. The potential contributions of changes in the gut microbiota and microRNA expression are discussed.

Highly uniform ruthenium (Ru) nanoparticles over N-doped carbon (Ru@CN) was designed and confirmed as a promising candidate for the hydrogen evolution reaction (HER) over a wide pH range.

<h2>Summary</h2> Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as <i>TMPRSS2</i>, <i>RET</i>, <i>FGFR3</i>, <i>ALK</i>, and <i>ESR1</i> in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy.

Bicuspid aortic valve (BAV) is the most common congenital cardiac abnormality. BAV aortic dilatation is associated with an increased risk of adverse aortic events and represents a potentially lethal disease and hence a considerable medical burden. BAV with aortic dilatation warrants frequent monitoring, and elective surgical intervention is the only effective method to prevent dissection or rupture. The predictive value of the aortic diameter is known to be limited. The aortic diameter is presently still the main reference standard for surgical intervention owing to the lack of a comprehensive understanding of BAV aortopathy progression. This article provides a brief comprehensive review of the current knowledge on BAV aortopathy regarding clinical definitions, epidemiology, natural course, and pathophysiology, as well as hemodynamic and clinically significant aspects on the basis of the limited data available.

Despite being promising substitutes for noble metal catalysts used in hydrogen evolution reaction (HER), the nonprecious metal catalysts (NPMCs) based on inexpensive and earth-abundant 3d transition metals (TMs) are still practically unfeasible due mainly to unsatisfactory activity and durability. Herein, a highly active and stable catalyst for HER has been developed on the basis of molybdenum-carbide-modified N-doped carbon vesicle encapsulating Ni nanoparticles (MoxC-Ni@NCV). This MoxC-Ni@NCV material was synthesized simply by the solid-state thermolysis of melamine-related composites of oxalate and molybdate with uniform Ni ions doping (Ni@MOM-com). Notably, the prepared MoxC-Ni@NCV was almost the most efficient NPMCs for HER in acidic electrolyte to date. Besides good long-term stability, MoxC-Ni@NCV exhibited a quiet low overpotential that was comparable to Pt/C. Thus, this work opens a new avenue toward the development of highly efficient, inexpensive HER catalysts.

Objective Since December 2019, a newly identified coronavirus (severe acute respiratory syndrome coronavirus (SARS-CoV-2)) has caused outbreaks of pneumonia in Wuhan, China. SARS-CoV-2 enters host cells via cell receptor ACE II (ACE2) and the transmembrane serine protease 2 (TMPRSS2). In order to identify possible prime target cells of SARS-CoV-2 by comprehensive dissection of ACE2 and TMPRSS2 coexpression pattern in different cell types, five datasets with single-cell transcriptomes of lung, oesophagus, gastric mucosa, ileum and colon were analysed. Design Five datasets were searched, separately integrated and analysed. Violin plot was used to show the distribution of differentially expressed genes for different clusters. The ACE2-expressing and TMPRRSS2-expressing cells were highlighted and dissected to characterise the composition and proportion. Results Cell types in each dataset were identified by known markers. ACE2 and TMPRSS2 were not only coexpressed in lung AT2 cells and oesophageal upper epithelial and gland cells but also highly expressed in absorptive enterocytes from the ileum and colon. Additionally, among all the coexpressing cells in the normal digestive system and lung, the expression of ACE2 was relatively highly expressed in the ileum and colon. Conclusion This study provides the evidence of the potential route of SARS-CoV-2 in the digestive system along with the respiratory tract based on single-cell transcriptomic analysis. This finding may have a significant impact on health policy setting regarding the prevention of SARS-CoV-2 infection. Our study also demonstrates a novel method to identify the prime cell types of a virus by the coexpression pattern analysis of single-cell sequencing data.

As one of the first defenders of innate immune response, neutrophils make a rapid and robust response against infection or harmful agents. While traditionally regarded as suicidal killers that cause collateral tissue damage, recent findings on neutrophil extracellular trap formation, heterogeneity and plasticity and novel reparative functions have expanded our understanding of their diverse roles in health and disease. This review summarizes our current understanding of neutrophil-associated tissue injury, highlighting the emerging roles of neutrophil extracellular traps. This review will also focus on scrutinizing the roles of neutrophils in tissue repair and regeneration and will examine data on unexpected aspects of involvement of neutrophils in regulating normal tissue homeostasis.

Resilient Hyperpolarization Despite constant exposure to all sorts of stressors, most people are resilient and do not develop depression, but we do not understand the neurophysiological underpinnings of stress resilience. Friedman et al. (p. 313 ) studied this phenomenon in a mouse model of social-defeat stress depression. In the mice they found that, despite apparently pathological levels of hyperpolarization and elevated potassium channel currents in the ventral tegmental area (a structure known to be involved in depression), resilient mice showed normal activity in dopaminergic neurons. Thus, if “depressed” mice were experimentally provoked into hyperpolarization—unexpectedly, they completely reversed depression-related behaviors.

Members of the HCN channel family generate hyperpolarization-activated cation currents (Ih) that are directly regulated by cAMP and contribute to pacemaker activity in heart and brain. The four HCN isoforms show distinct but overlapping patterns of expression in different tissues. Here, we report that HCN1 and HCN2, isoforms coexpressed in neocortex and hippocampus that differ markedly in their biophysical properties, coassemble to generate heteromultimeric channels with novel properties. When expressed in Xenopus oocytes, HCN1 channels activate 5-10-fold more rapidly than HCN2 channels. HCN1 channels also activate at voltages that are 10-20 mV more positive than those required to activate HCN2. In cell-free patches, the steady-state activation curve of HCN1 channels shows a minimal shift in response to cAMP (+4 mV), whereas that of HCN2 channels shows a pronounced shift (+17 mV). Coexpression of HCN1 and HCN2 yields Ih currents that activate with kinetics and a voltage dependence that tend to be intermediate between those of HCN1 and HCN2 homomers, although the coexpressed channels do show a relatively large shift by cAMP (+14 mV). Neither the kinetics, steady-state voltage dependence, nor cAMP dose-response curve for the coexpressed Ih can be reproduced by the linear sum of independent populations of HCN1 and HCN2 homomers. These results are most simply explained by the formation of heteromeric channels with novel properties. The properties of these heteromeric channels closely resemble the properties of I(h) in hippocampal CA1 pyramidal neurons, cells that coexpress HCN1 and HCN2. Finally, differences in Ih channel properties recorded in cell-free patches versus intact oocytes are shown to be due, in part, to modulation of Ih by basal levels of cAMP in intact cells.

Abstract Purpose: We previously demonstrated the association between epithelial-to-mesenchymal transition (EMT) and drug response in lung cancer using an EMT signature derived in cancer cell lines. Given the contribution of tumor microenvironments to EMT, we extended our investigation of EMT to patient tumors from 11 cancer types to develop a pan-cancer EMT signature. Experimental Design: Using the pan-cancer EMT signature, we conducted an integrated, global analysis of genomic and proteomic profiles associated with EMT across 1,934 tumors including breast, lung, colon, ovarian, and bladder cancers. Differences in outcome and in vitro drug response corresponding to expression of the pan-cancer EMT signature were also investigated. Results: Compared with the lung cancer EMT signature, the patient-derived, pan-cancer EMT signature encompasses a set of core EMT genes that correlate even more strongly with known EMT markers across diverse tumor types and identifies differences in drug sensitivity and global molecular alterations at the DNA, RNA, and protein levels. Among those changes associated with EMT, pathway analysis revealed a strong correlation between EMT and immune activation. Further supervised analysis demonstrated high expression of immune checkpoints and other druggable immune targets, such as PD1, PD-L1, CTLA4, OX40L, and PD-L2, in tumors with the most mesenchymal EMT scores. Elevated PD-L1 protein expression in mesenchymal tumors was confirmed by IHC in an independent lung cancer cohort. Conclusions: This new signature provides a novel, patient-based, histology-independent tool for the investigation of EMT and offers insights into potential novel therapeutic targets for mesenchymal tumors, independent of cancer type, including immune checkpoints. Clin Cancer Res; 22(3); 609–20. ©2015 AACR.

A major obstacle for successful axon regeneration in the adult central nervous system (CNS) arises from inhibitory molecules in CNS myelin, which signal through a common receptor complex on neurons consisting of the ligand-binding Nogo-66 receptor (NgR) and two transmembrane coreceptors, p75 and LINGO-1. However, p75 expression is only detectable in subpopulations of mature neurons, raising the question of how these inhibitory signals are transduced in neurons lacking p75. In this study, we demonstrate that TROY (also known as TAJ), a TNF receptor family member selectively expressed in the adult nervous system, can form a functional receptor complex with NgR and LINGO-1 to mediate cellular responses to myelin inhibitors. Also, both overexpressing a dominant-negative TROY or presence of a soluble TROY protein can efficiently block neuronal response to myelin inhibitors. Our results implicate TROY in mediating myelin inhibition, offering new insights into the molecular mechanisms of regeneration failure in the adult nervous system.