Dissecting positive selection events and immunological drives during the evolution of adeno-associated virus lineages.

Adeno-associated virus (AAV) serotypes from primates are being developed and clinically used as vectors for human gene therapy. However, the evolutionary mechanism of AAV variants is far from being understood, except that genetic recombination plays an important role. Furthermore, little is known about the interaction between AAV and its natural hosts, human and nonhuman primates. In this study, natural AAV capsid genes were subjected to systemic evolutionary analysis with a focus on selection drives during the diversification of AAV lineages. A number of positively selected sites were identified from these AAV lineages with functional relevance implied by their localization on the AAV structures. The selection drives of the two AAV2 capsid sites were further investigated in a series of biological experiments. These observations did not support the evolution of the site 410 of the AAV2 capsid driven by selection pressure from the human CD4+ T-cell response. However, positive selection on site 548 of the AAV2 capsid was directly related to host humoral immunity because of the profound effects of mutations at this site on the immune evasion of AAV variants from human neutralizing antibodies at both the individual and population levels. Overall, this work provides a novel interpretation of the genetic diversity and evolution of AAV lineages in their natural hosts, which may contribute to their further engineering and application in human gene therapy.

DRdriver: identifying drug resistance driver genes using individual-specific gene regulatory network.

Drug resistance is one of principal limiting factors for cancer treatment. Several mechanisms, especially mutation, have been validated to implicate in drug resistance. In addition, drug resistance is heterogeneous, which makes an urgent need to explore the personalized driver genes of drug resistance. Here, we proposed an approach DRdriver to identify drug resistance driver genes in individual-specific network of resistant patients. First, we identified the differential mutations for each resistant patient. Next, the individual-specific network, which included the genes with differential mutations and their targets, was constructed. Then, the genetic algorithm was utilized to identify the drug resistance driver genes, which regulated the most differentially expressed genes and the least non-differentially expressed genes. In total, we identified 1202 drug resistance driver genes for 8 cancer types and 10 drugs. We also demonstrated that the identified driver genes were mutated more frequently than other genes and tended to be associated with the development of cancer and drug resistance. Based on the mutational signatures of all driver genes and enriched pathways of driver genes in brain lower grade glioma treated by temozolomide, the drug resistance subtypes were identified. Additionally, the subtypes showed great diversity in epithelial-mesenchyme transition, DNA damage repair and tumor mutation burden. In summary, this study developed a method DRdriver for identifying personalized drug resistance driver genes, which provides a framework for unlocking the molecular mechanism and heterogeneity of drug resistance.

Molecular epidemiology of Mycoplasma pneumoniae pneumonia in children, Wuhan, 2020-2022.

BACKGROUND: Mycoplasma pneumoniae (M. pneumoniae) is an important pathogen of community-acquired pneumonia in children. The factors contributing to the severity of illness caused by M. pneumoniae infection are still under investigation. We aimed to evaluate the sensitivity of common M. pneumoniae detection methods, as well as to analyze the clinical manifestations, genotypes, macrolide resistance, respiratory microenvironment, and their relationship with the severity of illness in children with M. pneumoniae pneumonia in Wuhan. RESULTS: Among 1,259 clinical samples, 461 samples were positive for M. pneumoniae via quantitative polymerase chain reaction (qPCR). Furthermore, we found that while serological testing is not highly sensitive in detecting M. pneumoniae infection, but it may serve as an indicator for predicting severe cases. We successfully identified the adhesin P1 (P1) genotypes of 127 samples based on metagenomic and Sanger sequencing, with P1-type 1 (113/127, 88.98%) being the dominant genotype. No significant difference in pathogenicity was observed among different genotypes. The macrolide resistance rate of M. pneumoniae isolates was 96% (48/50) and all mutations were A2063G in domain V of 23S rRNA gene. There was no significant difference between the upper respiratory microbiome of patients with mild and severe symptoms. CONCLUSIONS: During the period of this study, the main circulating M. pneumoniae was P1-type 1, with a resistance rate of 96%. Key findings include the efficacy of qPCR in detecting M. pneumoniae, the potential of IgM titers exceeding 1:160 as indicators for illness severity, and the lack of a direct correlation between disease severity and genotypic characteristics or respiratory microenvironment. This study is the first to characterize the epidemic and genomic features of M. pneumoniae in Wuhan after the COVID-19 outbreak in 2020, which provides a scientific data basis for monitoring and infection prevention and control of M. pneumoniae in the post-pandemic era.

eHSP90α in front-line therapy in EGFR exon 19 deletion and 21 Leu858Arg mutations in advanced lung adenocarcinoma.

PURPOSE: Extracellular heat shock protein 90 AA1(eHSP90α) is intricately linked to tumor progression and prognosis. This study aimed to investigate the difference in the value of eHSP90α in post-treatment response assessment and prognosis prediction between exon 19 deletion(19DEL) and exon 21 Leu858Arg(L858R) mutation types in lung adenocarcinoma(LUAD). METHODS: We analyzed the relationship between the expression of eHSP90α and clinicopathological features in 89 patients with L858R mutation and 196 patients with 19DEL mutation in LUAD. The Kaplan-Meier survival curve was used to determine their respective cut-off values and analyze the relationship between eHSP90α expression and the survival time of the two mutation types. The area under the curve (AUC) was used to evaluate the diagnostic performance of biomarkers. Then, the prognostic model was developed using the univariate-Cox multivariate-Cox and LASSO-multivariate logistic methods. RESULTS: In LUAD patients, eHSP90α was positively correlated with carcinoembryonic antigen(CEA), carbohydrate antigen 125(CA125), and carbohydrate antigen 153(CA153). The truncated values of eHSP90α in L858R and 19DEL patients were 44.5 ng/mL and 40.8 ng/mL, respectively. Among L858R patients, eHSP90α had the best diagnostic performance (AUC = 0.765), and higher eHSP90α and T helper cells(Th cells) expression were significantly related to shorter overall survival(OS) and worse treatment response. Also, high eHSP90a expression and short progression-free survival(PFS) were significantly correlated. Among 19DEL patients, CEA had the best diagnostic efficacy (AUC = 0.734), and CEA and Th cells were independent prognostic factors that predicted shorter OS. Furthermore, high CA125 was significantly associated with short PFS and poor curative effect. CONCLUSIONS: eHSP90α has a better prognostic value in LUAD L858R patients than 19DEL, which provides a new idea for clinical diagnosis and treatment.

Dichloramine Hydrolysis in Membrane Desalination Permeate: Mechanistic Insights and Implications for Oxidative Capacity in Potable Reuse Applications.

Dichloramine (NHCl2) naturally exists in reverse osmosis (RO) permeate due to its application as an antifouling chemical in membrane-based potable reuse treatment. This study investigated mechanisms of background NHCl2 hydrolysis associated with the generation of oxidative radical species in RO permeate, established a kinetic model to predict the oxidative capacity, and examined its removal efficiency on trace organic contaminants in potable reuse. Results showed that NHCl2 hydrolysis generated transient peroxynitrite (ONOO-) and subsequently dissociated into hydroxyl radical (HO•). The maximal HO• exposure was observed at an RO permeate pH of 8.4, higher than that from typical ultraviolet (UV)-based advanced oxidation processes. The HO• exposure during NHCl2 hydrolysis also peaked at a NH2Cl-to-NHCl2 molar ratio of 1:1. The oxidative capacity rapidly degraded 1,4-dioxane, carbamazepine, atenolol, and sulfamethoxazole in RO permeate. Furthermore, background elevated carbonate in fresh RO permeate can convert HO• to carbonate radical (CO3•-). Aeration of the RO permeate removed total carbonate, significantly increased HO• exposure, and enhanced the degradation kinetics of trace organic contaminants. The kinetic model of NHCl2 hydrolysis predicted well the degradation of contaminants in RO permeate. This study provides new mechanistic insights into NHCl2 hydrolysis that contributes to the oxidative degradation of trace organic contaminants in potable reuse systems.

Promotive Effects of Chloride and Sulfate on the Near-Complete Destruction of Perfluorocarboxylates (PFCAs) in Brine via Hydrogen-tuned 185-nm UV Photolysis: Mechanisms and Kinetics.

Hydrogen-tuned 185 nm vacuum ultraviolet (VUV/H2) photolysis is an emerging technology to destroy per- and polyfluoroalkyl substance (PFAS) in brine. This study discovered the promotive effects of two major brine anions, i.e., chloride and sulfate in VUV/H2 photolysis on the hydrated electron (eaq-) generation and perfluorocarboxylates (PFCAs) destruction and established a kinetics model to elucidate the promotive effects on the steady-state concentration of eaq- ([eaq-]ss). Results showed that VUV/H2 achieved near-complete defluorination of perfluorooctanoic acid (PFOA) in the presence of up to 1000 mM chloride or sulfate at pH 12. The defluorination rate constant (kdeF) of PFOA peaked with a chloride concentration at 100 mM and with a sulfate concentration at 500 mM. The promotive effects of chloride and sulfate were attributed to an enhanced generation of eaq- via their direct VUV photolysis and conversion of additionally generated hydroxyl radical to eaq- by H2, which was supported by a linear correlation between the predicted [eaq-]ss and experimentally observed kdeF. The kdeF value increased from pH 9 to 12, which was attributed to the speciation of the H·/eaq- pair. Furthermore, the VUV system achieved >95% defluorination and ≥99% parent compound degradation of a concentrated PFCAs mixture in a synthetic brine, without generating any toxic perchlorate or chlorate.

Scutellaria baicalensis enhances 5-fluorouracil-based chemotherapy via inhibition of proliferative signaling pathways.

Fluoropyridine-based chemotherapy remains the most widely used treatment for colorectal cancer (CRC). In this study, we investigated the mechanism by which the natural product Scutellaria baicalensis (Huang Qin; HQ) and one of its main components baicalin enhanced 5-fluorouracil (5-FU) antitumor activity against CRC. Cell proliferation assays, cell cycle analysis, reverse-phase protein array (RPPA) analysis, immunoblot analysis, and qRT-PCR were performed to investigate the mechanism(s) of action of HQ and its active components on growth of CRC cells. HQ exhibited in vitro antiproliferative activity against drug resistant human CRC cells, against human and mouse CRC cells with different genetic backgrounds and normal human colon epithelial cells. In vivo animal models were used to document the antitumor activity of HQ and baicalin. The mechanism of growth inhibitory activity of HQ is due to inhibition of proliferative signaling pathways including the CDK-RB pathway. In addition, HQ enhanced the antitumor effects of 5-FU and capecitabine in vivo. Furthermore, we identified baicalin as an active component of HQ. The combination of baicalin and 5-FU demonstrated synergistic activity against 5-FU-resistant RKO-R10 cells. The combination significantly inhibited in vivo tumor growth greater than each treatment alone. RPPA results showed that the signaling pathway alterations in CRC cells were similar following HQ and baicalin treatment. Together, these results indicate that HQ and its component baicalin enhance the effect of 5-fluorouracil-based chemotherapy via inhibition of CDK-RB pathway. These findings may provide the rational basis for developing agents that can overcome the development of cellular drug resistance. Video Abstract.

Inhibition of Hexavalent Chromium Release from Drinking Water Distribution Systems: Effects of Water Chemistry-Based Corrosion Control Strategies.

In drinking water distribution systems, the oxidation of zerovalent chromium, Cr(0), in iron corrosion scales by chlorine residual disinfectant is the dominant reaction to form carcinogenic hexavalent chromium, Cr(VI). This study investigates inhibitive corrosion control strategies through adjustments of chemical water parameters (i.e., pH, silicate, phosphate, calcium, and alkalinity) on Cr(VI) formation through oxidation of Cr(0)(s) by free chlorine under drinking water conditions. The results show that an increase in pH, silicate, alkalinity, and calcium suppressed Cr(VI) formation that was mainly attributed to in situ surface precipitation of new Cr(III) solids on the surface of Cr(0)(s), including Cr(OH)3(s), Cr2(SiO3)3(s), CrPO4(s), Cr2(CO3)3(s), and Cr10Ca(CO3)16(s). The Cr(III) surface precipitates were much less reactive with chlorine than Cr(0)(s) and suppressed the Cr redox reactivity. The concentration of surface Cr(III) solids was inversely correlated with the rate constant of Cr(VI) formation. Adding phosphate either promoted or inhibited the Cr(VI) formation, depending on the phosphate concentration. This study provides fundamental insight into the Cr(VI) formation mechanisms via Cr(0) oxidation by chlorine and the importance of surface precipitation of Cr(III) solids with different corrosion control strategies and suggests that increasing the pH/alkalinity and addition of phosphate or silicate can be effective control strategies to minimize Cr(VI) formation.

Enhancing Aqueous Chlorate Reduction Using Vanadium Redox Cycles and pH Control.

Chlorate (ClO3-) is a toxic oxyanion pollutant from industrial wastes, agricultural applications, drinking water disinfection, and wastewater treatment. Catalytic reduction of ClO3- using palladium (Pd) nanoparticle catalysts exhibited sluggish kinetics. This work demonstrates an 18-fold activity enhancement by integrating earth-abundant vanadium (V) into the common Pd/C catalyst. X-ray photoelectron spectroscopy and electrochemical studies indicated that VV and VIV precursors are reduced to VIII in the aqueous phase (rather than immobilized on the carbon support) by Pd-activated H2. The VIII/IV redox cycle is the predominant mechanism for the ClO3- reduction. Further reduction of chlorine intermediates to Cl- could proceed via VIII/IV and VIV/V redox cycles or direct reduction by Pd/C. To capture the potentially toxic V metal from the treated solution, we adjusted the pH from 3 to 8 after the reaction, which completely immobilized VIII onto Pd/C for catalyst recycling. The enhanced performance of reductive catalysis using a Group 5 metal adds to the diversity of transition metals (e.g., Cr, Mo, Re, Fe, and Ru in Groups 6-8) for water pollutant treatment via various unique mechanisms.

Accelerating Catalytic Oxyanion Reduction with Inert Metal Hydroxides.

Adding CrIII or AlIII salts into the water suspension of platinum group metal (PGM) catalysts accelerated oxyanion pollutant reduction by up to 600%. Our initial attempts of adding K2CrVIO4, K2CrVI2O7, or KCrIII(SO4)2 into Pd/C enhanced BrO3- reduction with 1 atm H2 by 6-fold. Instrument characterizations and kinetic explorations collectively confirmed the immobilization of reduced CrVI as CrIII(OH)3 on the catalyst surface. This process altered the ζ-potentials from negative to positive, thus substantially enhancing the Langmuir-Hinshelwood adsorption equilibrium constant for BrO3- onto Pd/C by 37-fold. Adding AlIII(OH)3 from alum at pH 7 achieved similar enhancements. The Cr-Pd/C and Al-Pd/C showed top-tier efficiency of catalytic performance (normalized with Pd dosage) among all the reported Pd catalysts on conventional and nanostructured support materials. The strategy of adding inert metal hydroxides works for diverse PGMs (palladium and rhodium), substrates (BrO3- and ClO3-), and support materials (carbon, alumina, and silica). This work shows a simple, inexpensive, and effective example of enhancing catalyst activity and saving PGMs for environmental applications.

Ginseng polysaccharides alter the gut microbiota and kynurenine/tryptophan ratio, potentiating the antitumour effect of antiprogrammed cell death 1/programmed cell death ligand 1 (anti-PD-1/PD-L1) immunotherapy.

OBJECTIVE: Programmed death 1 and its ligand 1 (PD-1/PD-L1) immunotherapy is promising for late-stage lung cancer treatment, however, the response rate needs to be improved. Gut microbiota plays a crucial role in immunotherapy sensitisation and Panax ginseng has been shown to possess immunomodulatory potential. In this study, we aimed to investigate whether the combination treatment of ginseng polysaccharides (GPs) and αPD-1 monoclonal antibody (mAb) could sensitise the response by modulating gut microbiota. DESIGN: Syngeneic mouse models were administered GPs and αPD-1 mAb, the sensitising antitumour effects of the combination therapy on gut microbiota were assessed by faecal microbiota transplantation (FMT) and 16S PacBio single-molecule real-time (SMRT) sequencing. To assess the immune-related metabolites, metabolomics analysis of the plasma samples was performed. RESULTS: We found GPs increased the antitumour response to αPD-1 mAb by increasing the microbial metabolites valeric acid and decreasing L-kynurenine, as well as the ratio of Kyn/Trp, which contributed to the suppression of regulatory T cells and induction of Teff cells after combination treatment. Besides, the microbial analysis indicated that the abundance of Parabacteroides distasonis and Bacteroides vulgatus was higher in responders to anti-PD-1 blockade than non-responders in the clinic. Furthermore, the combination therapy sensitised the response to PD-1 inhibitor in the mice receiving microbes by FMT from six non-responders by reshaping the gut microbiota from non-responders towards that of responders. CONCLUSION: Our results demonstrate that GPs combined with αPD-1 mAb may be a new strategy to sensitise non-small cell lung cancer patients to anti-PD-1 immunotherapy. The gut microbiota can be used as a novel biomarker to predict the response to anti-PD-1 immunotherapy.

Identifying Japanese Encephalitis Virus Using Metatranscriptomic Sequencing, Xinjiang, China.

The treat of infectious disease epidemics has increased the critical need for continuous broad-ranging surveillance of pathogens with outbreak potential. Using metatranscriptomic sequencing of blood samples, we identified several cases of Japanese encephalitis virus infection from Xinjiang Uyghur Autonomous Region, China. This discovery highlights the risk for known viral diseases even in nonendemic areas.

RNA Sequencing Demonstrates That Circular RNA Regulates Avian Influenza Virus Replication in Human Cells.

Circular RNAs (circRNAs) are involved in diverse biological processes. Avian influenza virus (AIV) can cross the species barrier to infect humans. Here, we employed RNA sequencing technology to profile circRNA, microRNA, and mRNA expression in human lung carcinoma cells in response to AIV or human influenza A virus (IAV) infection at viral replication. The analysis revealed that the expression of 475 common circRNAs were significantly regulated. The 381 and 1163 up-regulated circRNAs were induced by AIV at 8 and 16 h, respectively. Subsequently, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were also conducted for the AIV-specific up-regulated circRNAs. Moreover, the circRNAs were characterized, of which six were verified by quantitative real-time PCR. We further confirmed that expression of the selected circRNAs only increased following AIV infection. Knocking down the selected circRNAs promoted AIV proliferation, and overexpression of three of the candidate circRNAs restricted AIV replication and proliferation. We further analyzed that AIV-specific up-regulated circRNA mechanisms might function through the ceRNA network to affect the "Endocytosis" pathway and the "Cell cycle process". These data provide the first expression profile of AIV-specific up-regulated circRNAs and shed new light on the pathogenesis of AIV infection. Our findings also suggest that these circRNAs serve an important role in AIV infection.

Comparative Circulation Dynamics of the Five Main HIV Types in China.

The HIV epidemic in China accounts for 3% of the global HIV incidence. We compared the patterns and determinants of interprovincial spread of the five most prevalent circulating types. HIV pol sequences sampled across China were used to identify relevant transmission networks of the five most relevant HIV-1 types (B and circulating recombinant forms [CRFs] CRF01_AE, CRF07_BC, CRF08_BC, and CRF55_01B) in China. From these, the dispersal history across provinces was inferred. A generalized linear model (GLM) was used to test the association between migration rates among provinces and several measures of human mobility. A total of 10,707 sequences were collected between 2004 and 2017 across 26 provinces, among which 1,962 are newly reported here. A mean of 18 (minimum and maximum, 1 and 54) independent transmission networks involving up to 17 provinces were identified. Discrete phylogeographic analysis largely recapitulates the documented spread of the HIV types, which in turn, mirrors within-China population migration flows to a large extent. In line with the different spatiotemporal spread dynamics, the identified drivers thereof were also heterogeneous but are consistent with a central role of human mobility. The comparative analysis of the dispersal dynamics of the five main HIV types circulating in China suggests a key role of large population centers and developed transportation infrastructures as hubs of HIV dispersal. This advocates for coordinated public health efforts in addition to local targeted interventions.IMPORTANCE While traditional epidemiological studies are of great interest in describing the dynamics of epidemics, they struggle to fully capture the geospatial dynamics and factors driving the dispersal of pathogens like HIV as they have difficulties capturing linkages between infections. To overcome this, we used a discrete phylogeographic approach coupled to a generalized linear model extension to characterize the dynamics and drivers of the across-province spread of the five main HIV types circulating in China. Our results indicate that large urbanized areas with dense populations and developed transportation infrastructures are facilitators of HIV dispersal throughout China and highlight the need to consider harmonized country-wide public policies to control local HIV epidemics.

Phylogenetics, Genomic Recombination, and NSP2 Polymorphic Patterns of Porcine Reproductive and Respiratory Syndrome Virus in China and the United States in 2014-2018.

Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen that affects the pig industry, is a highly genetically diverse RNA virus. However, the phylogenetic and genomic recombination properties of this virus have not been completely elucidated. In this study, comparative analyses of all available genomic sequences of North American (NA)-type PRRSVs (n = 355, including 138 PRRSV genomes sequenced in this study) in China and the United States during 2014-2018 revealed a high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and the GP2 to GP3 regions. Lineage 1 (L1) PRRSV was found to be susceptible to recombination among PRRSVs both in China and the United States. The recombinant major parent between the 1991-2013 data and the 2014-2018 data showed a trend from complex to simple. The major recombination pattern changed from an L8 to L1 backbone during 2014-2018 for Chinese PRRSVs, whereas L1 was always the major backbone for US PRRSVs. Intralineage recombination hot spots were not as concentrated as interlineage recombination hot spots. In the two main clades with differential diversity in L1, NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, NADC34-like PRRSVs have been relatively stable in population genetic diversity for years. Systematic analyses of insertion and deletion (indel) polymorphisms of NSP2 divided PRRSVs into 25 patterns, which could generate novel references for the classification of PRRSVs. The results of this study contribute to a deeper understanding of the recombination of PRRSVs and indicate the need for coordinated epidemiological investigations among countries.IMPORTANCE Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine diseases. However, the phylogenetic and genomic recombination properties of the PRRS virus (PRRSV) have not been completely elucidated. In this study, we systematically compared differences in the lineage distribution, recombination, NSP2 polymorphisms, and evolutionary dynamics between North American (NA)-type PRRSVs in China and in the United States. Strikingly, we found high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and in the GP2 to GP3 region. Also, intralineage recombination hot spots were scattered across the genome between Chinese and US strains. Furthermore, we proposed novel methods based on NSP2 indel patterns for the classification of PRRSVs. Evolutionary dynamics analysis revealed that NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, suggesting that a dominant population may occur and cause an outbreak. Our findings offer important insights into the recombination of PRRSVs and suggest the need for coordinated international epidemiological investigations.

Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.

Pathway enrichment analysis has been widely used to identify cancer risk pathways, and contributes to elucidating the mechanism of tumorigenesis. However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway. Here, we first reviewed the existing widely used pathway enrichment analysis approaches briefly, and then, we proposed a novel topology-based pathway enrichment analysis (TPEA) method, which integrated topological properties and global upstream/downstream positions of genes in pathways. We compared TPEA with four widely used pathway enrichment analysis tools, including database for annotation, visualization and integrated discovery (DAVID), gene set enrichment analysis (GSEA), centrality-based pathway enrichment (CePa) and signaling pathway impact analysis (SPIA), through analyzing six gene expression profiles of three tumor types (colorectal cancer, thyroid cancer and endometrial cancer). As a result, we identified several well-known cancer risk pathways that could not be obtained by the existing tools, and the results of TPEA were more stable than that of the other tools in analyzing different data sets of the same cancer. Ultimately, we developed an R package to implement TPEA, which could online update KEGG pathway information and is available at the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/TPEA/.

Immune landscape and prognostic immune-related genes in KRAS-mutant colorectal cancer patients.

BACKGROUND: KRAS gene is the most common type of mutation reported in colorectal cancer (CRC). KRAS mutation-mediated regulation of immunophenotype and immune pathways in CRC remains to be elucidated. METHODS: 535 CRC patients were used to compare the expression of immune-related genes (IRGs) and the abundance of tumor-infiltrating immune cells (TIICs) in the tumor microenvironment between KRAS-mutant and KRAS wild-type CRC patients. An independent dataset included 566 cases of CRC and an in-house RNA sequencing dataset were served as validation sets. An in-house dataset consisting of 335 CRC patients were used to analyze systemic immune and inflammatory state in the presence of KRAS mutation. An immue risk (Imm-R) model consist of IRG and TIICs for prognostic prediction in KRAS-mutant CRC patients was established and validated. RESULTS: NF-κB and T-cell receptor signaling pathways were significantly inhibited in KRAS-mutant CRC patients. Regulatory T cells (Tregs) was increased while macrophage M1 and activated CD4 memory T cell was decreased in KRAS-mutant CRC. Prognosis correlated with enhanced Tregs, macrophage M1 and activated CD4 memory T cell and was validated. Serum levels of hypersensitive C-reactive protein (hs-CRP), CRP, and IgM were significantly decreased in KRAS-mutant compared to KRAS wild-type CRC patients. An immune risk model composed of VGF, RLN3, CT45A1 and TIICs signature classified CRC patients with distinct clinical outcomes. CONCLUSIONS: KRAS mutation in CRC was associated with suppressed immune pathways and immune infiltration. The aberrant immune pathways and immune cells help to understand the tumor immune microenvironments in KRAS-mutant CRC patients.

Oxidation of V(IV) by Birnessite: Kinetics and Surface Complexation.

Vanadium is a redox-active metal that has been added to the EPA's Contaminant Candidate List with a notification level of 50 µg L-1 due to mounting evidence that VV exposure can lead to adverse health outcomes. Groundwater V concentration exceeds the notification level in many locations, yet geochemical controls on its mobility are poorly understood. Here, we examined the redox interaction between VIV and birnessite (MnO2), a well-characterized oxidant and a scavenger of many trace metals. In our findings, birnessite quickly oxidized sparingly soluble VIV species such as häggite [V2O3(OH)2] into highly mobile and toxic vanadate (HnVO4(3-n)-) in continuously stirred batch reactors under neutral pH conditions. Synchrotron X-ray absorption spectroscopic (XAS) analysis of in situ and ex situ experiments showed that oxidation of VIV occurs in two stages, which are both rapid relative to the measured dissolution rate of the VIV solid. Concomitantly, the reduction of birnessite during VIV oxidation generated soluble MnII, which led to the formation of the MnIII oxyhydroxide feitknechtite (ß-MnOOH) upon back-reaction with birnessite. XAS analysis confirmed a bidentate-mononuclear edge-sharing complex formed between VV and birnessite, although retention of VV was minimal relative to the aqueous quantities generated. In summary, we demonstrate that Mn oxides are effective oxidants of VIV in the environment with the potential to increase dissolved V concentrations in aquifers subject to redox oscillations.

Discriminating Clonotypes of Influenza A Virus Genes by Nanopore Sequencing.

Influenza viruses still pose a serious threat to humans, and we have not yet been able to effectively predict future pandemic strains and prepare vaccines in advance. One of the main reasons is the high genetic diversity of influenza viruses. We do not know the individual clonotypes of a virus population because some are the majority and others make up only a small fraction of the population. First-generation (FGS) and next-generation sequencing (NGS) technologies have inherent limitations that are unable to resolve a minority clonotype's information in the virus population. Third-generation sequencing (TGS) technologies with ultra-long reads have the potential to solve this problem but have a high error rate. Here, we evaluated emerging direct RNA sequencing and cDNA sequencing with the MinION platform and established a novel approach that combines the high accuracy of Illumina sequencing technology and long reads of nanopore sequencing technology to resolve both variants and clonotypes of influenza virus. Furthermore, a new program was written to eliminate the effect of nanopore sequencing errors for the analysis of the results. By using this pipeline, we identified 47 clonotypes in our experiment. We conclude that this approach can quickly discriminate the clonotypes of virus genes, allowing researchers to understand virus adaptation and evolution at the population level.

ncRI: a manually curated database for experimentally validated non-coding RNAs in inflammation.

BACKGROUND: Inflammation has been considered to be central to the onset, progression, and outcome of infectious diseases, especially as one of the hallmarks of cancer. Non-coding RNAs (ncRNAs), such as miRNAs and lncRNAs, have emerged as vital regulators in control of immune and inflammatory processes, and also play important roles in the inflammatory disease and immunotherapy. RESULTS: In this study, we presented a database ncRI, which documented experimentally verified ncRNAs in inflammatory diseases, from published articles. Each entry contained the detailed information about ncRNA name, inflammatory diseases, mechanism, experimental techniques (e.g., microarray, RNA-seq, qRT-PCR), experimental samples (cell line and/or tissue), expression patterns of ncRNA (up-regulated or down-regulated), reference information (PubMed ID, year of publication, title of paper) and so on. Collectively, ncRI recorded 11,166 entries that include 1976 miRNAs, 1377 lncRNAs and 107 other ncRNAs across 3 species (human, mouse, and rat) from more than 2000 articles. All these data are free for users to search, browse and download. CONCLUSION: In summary, the presented database ncRI provides a relatively comprehensive credible repository about ncRNAs and their roles in inflammatory diseases, and will be helpful for research on immunotherapy. The ncRI is now freely available to all users at http://www.jianglab.cn/ncRI/.