MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation

We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted as well as untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC-MS). The two main objectives in developing version 6.0 are to support tandem MS (MS2) data processing and annotation, as well as to support the analysis of data from exposomics studies and related experiments. Key features of MetaboAnalyst 6.0 include: (i) a significantly enhanced Spectra Processing module with support for MS2 data and the asari algorithm; (ii) a MS2 Peak Annotation module based on comprehensive MS2 reference databases with fragment-level annotation; (iii) a new Statistical Analysis module dedicated for handling complex study design with multiple factors or phenotypic descriptors; (iv) a Causal Analysis module for estimating metabolite - phenotype causal relations based on two-sample Mendelian randomization, and (v) a Dose-Response Analysis module for benchmark dose calculations. In addition, we have also improved MetaboAnalyst's visualization functions, updated its compound database and metabolite sets, and significantly expanded its pathway analysis support to around 130 species. MetaboAnalyst 6.0 is freely available at https://www.metaboanalyst.ca.

Web-based multi-omics integration using the Analyst software suite

The growing number of multi-omics studies demands clear conceptual workflows coupled with easy-to-use software tools to facilitate data analysis and interpretation. This protocol covers three key components involved in multi-omics analysis, including single-omics data analysis, knowledge-driven integration using biological networks and data-driven integration through joint dimensionality reduction. Using the dataset from a recent multi-omics study of human pancreatic islet tissue and plasma samples, the first section introduces how to perform transcriptomics/proteomics data analysis using ExpressAnalyst and lipidomics data analysis using MetaboAnalyst. On the basis of significant features detected in these workflows, the second section demonstrates how to perform knowledge-driven integration using OmicsNet. The last section illustrates how to perform data-driven integration from the normalized omics data and metadata using OmicsAnalyst. The complete protocol can be executed in ~2 h. Compared with other available options for multi-omics integration, the Analyst software suite described in this protocol enables researchers to perform a wide range of omics data analysis tasks via a user-friendly web interface.

Comparison of Pulmonary and Extrapulmonary Models of Sepsis-Associated Acute Lung Injury

To compare different rat models of sepsis at different time points, based on pulmonary or extrapulmonary injury mechanisms, to identify a model which is more stable and reproducible to cause sepsis-associated acute lung injury (ALI). Adult male Sprague-Dawley rats were subjected to (1) cecal ligation and puncture (CLP) with single (CLP1 group) or two repeated through-and-through punctures (CLP2 group); (2) tail vein injection with lipopolysaccharide (LPS) of 10mg/kg (IV-LPS10 group) or 20 mg/kg (IV-LPS20 group); (3) intratracheal instillation with LPS of 10mg/kg (IT-LPS10 group) or 20mg/kg (IT-LPS20 group). Each of the model groups had a sham group. 7-day survival rates of each group were observed (n=15 for each group). Moreover, three time points were set for additional experimental studying in each model group: 4 hours, 24 hours and 48 hours after modeling (every time point, n=8 for each group). Rats were sacrificed to collect BALF and lung tissue samples at different time points for detection of IL-6, TNF-alpha, total protein concentration in BALF and MPO activity, HMGB1 protein expression in lung tissues, as well as the histopathological changes of lung tissues. More than 50 % of the rats died within 7 days in each model group, except for the IT-LPS10 group. In contrast, the mortality rates in the two IV-LPS groups as well as the IT-LPS20 group were significantly higher than that in IT-LPS10 group. Rats received LPS by intratracheal instillation exhibited evident histopathological changes and inflammatory exudation in the lung, but there was no evidence of lung injury in CLP and IV-LPS groups. Rat model of intratracheal instillation with LPS proved to be a more stable and reproducible animal model to cause sepsis-associated ALI than the extrapulmonary models of sepsis.

Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non-Model Organisms

ExpressAnalyst is a web-based platform that enables intuitive, end-to-end transcriptomics and proteomics data analysis. Users can start from FASTQ files, gene/protein abundance tables, or gene/protein lists. ExpressAnalyst will perform read quantification, gene expression table processing and normalization, differential expression analysis, or meta-analysis with complex study designs. The results are presented via various interactive visualizations such as volcano plots, heatmaps, networks, and ridgeline charts, with built-in functional enrichment analysis to allow flexible data exploration and understanding. ExpressAnalyst currently contains built-in support for 29 common organisms. For non-model organisms without good reference genomes, it can perform comprehensive transcriptome profiling directly from RNA-seq reads. These common tasks are covered in 11 Basic Protocols. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: RNA-seq count table uploading, processing, and normalization Basic Protocol 2: Differential expression analysis with linear models Basic Protocol 3: Functional analysis with volcano plot, enrichment network, and ridgeline visualization Basic Protocol 4: Hierarchical clustering analysis of transcriptomics data using interactive heatmaps Basic Protocol 5: Cross-species gene expression analysis based on ortholog mapping results Basic Protocol 6: Proteomics and microarray data processing and normalization Basic Protocol 7: Preparing multiple gene expression tables for meta-analysis Basic Protocol 8: Statistical and functional meta-analysis of gene expression data Basic Protocol 9: Functional analysis of transcriptomics signatures Basic Protocol 10: Dose-response and time-series data analysis Basic Protocol 11: RNA-seq reads processing and quantification with and without reference transcriptomes.

mGWAS-Explorer 2.0: Causal Analysis and Interpretation of Metabolite-Phenotype Associations

Metabolomics-based genome-wide association studies (mGWAS) are key to understanding the genetic regulations of metabolites in complex phenotypes. We previously developed mGWAS-Explorer 1.0 to link single-nucleotide polymorphisms (SNPs), metabolites, genes and phenotypes for hypothesis generation. It has become clear that identifying potential causal relationships between metabolites and phenotypes, as well as providing deep functional insights, are crucial for further downstream applications. Here, we introduce mGWAS-Explorer 2.0 to support the causal analysis between >4000 metabolites and various phenotypes. The results can be interpreted within the context of semantic triples and molecular quantitative trait loci (QTL) data. The underlying R package is released for reproducible analysis. Using two case studies, we demonstrate that mGWAS-Explorer 2.0 is able to detect potential causal relationships between arachidonic acid and Crohn's disease, as well as between glycine and coronary heart disease.

ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species

The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst ( www.expressanalyst.ca ), a web-based platform for processing, analyzing, and interpreting RNA-sequencing data from any eukaryotic species. ExpressAnalyst contains a series of modules that cover from processing and annotation of FASTQ files to statistical and functional analysis of count tables or gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst allows researchers to obtain global expression profiles and gene-level insights from raw RNA-sequencing reads within 24 h. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-sequencing data from multiple non-model salamander species, including two that do not have a reference transcriptome.

MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data

Microbiome studies have become routine in biomedical, agricultural and environmental sciences with diverse aims, including diversity profiling, functional characterization, and translational applications. The resulting complex, often multi-omics datasets demand powerful, yet user-friendly bioinformatics tools to reveal key patterns, important biomarkers, and potential activities. Here we introduce MicrobiomeAnalyst 2.0 to support comprehensive statistics, visualization, functional interpretation, and integrative analysis of data outputs commonly generated from microbiome studies. Compared to the previous version, MicrobiomeAnalyst 2.0 features three new modules: (i) a Raw Data Processing module for amplicon data processing and taxonomy annotation that connects directly with the Marker Data Profiling module for downstream statistical analysis; (ii) a Microbiome Metabolomics Profiling module to help dissect associations between community compositions and metabolic activities through joint analysis of paired microbiome and metabolomics datasets; and (iii) a Statistical Meta-Analysis module to help identify consistent signatures by integrating datasets across multiple studies. Other important improvements include added support for multi-factor differential analysis and interactive visualizations for popular graphical outputs, updated methods for functional prediction and correlation analysis, and expanded taxon set libraries based on the latest literature. These new features are demonstrated using a multi-omics dataset from a recent type 1 diabetes study. MicrobiomeAnalyst 2.0 is freely available at microbiomeanalyst.ca.

Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity

Several perturbations in the number of peripheral blood leukocytes, such as neutrophilia and lymphopenia associated with Coronavirus disease 2019 (COVID-19) severity, point to systemic molecular cell cycle alterations during severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the landscape of cell cycle alterations in COVID-19 remains primarily unexplored. Here, we performed an integrative systems immunology analysis of publicly available proteome and transcriptome data to characterize global changes in the cell cycle signature of COVID-19 patients. We found significantly enriched cell cycle-associated gene co-expression modules and an interconnected network of cell cycle-associated differentially expressed proteins (DEPs) and genes (DEGs) by integrating the molecular data of 1469 individuals (981 SARS-CoV-2 infected patients and 488 controls [either healthy controls or individuals with other respiratory illnesses]). Among these DEPs and DEGs are several cyclins, cell division cycles, cyclin-dependent kinases, and mini-chromosome maintenance proteins. COVID-19 patients partially shared the expression pattern of some cell cycle-associated genes with other respiratory illnesses but exhibited some specific differential features. Notably, the cell cycle signature predominated in the patients' blood leukocytes (B, T, and natural killer cells) and was associated with COVID-19 severity and disease trajectories. These results provide a unique global understanding of distinct alterations in cell cycle-associated molecules in COVID-19 patients, suggesting new putative pathways for therapeutic intervention.

Genetic polymorphisms in MIR1208 and MIR5708 are associated with susceptibility to COPD in the Chinese population

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by limited airflow and is influenced by genetic and environmental factors. The purpose of this study was to investigate the effects of gene polymorphisms in MIR5708 and MIR1208 on COPD risk.

METHODS

Four single nucleotide polymorphisms (SNPs) in MIR5708 (rs6473227 and rs16907751) and MIR1208 (rs2608029 and rs13280095) were selected and genotyped among 315 COPD patients and 314 healthy controls using the Agena MassARRAY platform. SPSS 18.0 was used for statistical analysis and data processing. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the association between genetic variants of MIR1208 and MIR5708 and COPD risk.

RESULTS

The results suggested that rs16907751 variants in MIR5708 contributed to an increased susceptibility to COPD in the allelic (P = 0.001), co-dominant (homozygous) (P = 0.001), dominant (P = 0.017), recessive (P = 0.002), and additive (P = 0.002) models. The effects of MIR5708 and MIR1208 gene polymorphisms on the risk of COPD were age-, sex-, smoking status-, and BMI-related. Furthermore, the C-A and G-A haplotypes of rs2608029 and rs13280095 in MIR1208 were identified as risk factors for COPD in the population over 70 years (P = 0.029) and in women (P = 0.049), respectively. Finally, significant associations between rs16907751genotypes with pulse rate and forced expiratory volume in 1 s were found among COPD patients.

CONCLUSION

Genetic polymorphisms in MIR5708 and MIR1208 are associated with increased risk of COPD in China.

Targeting a Conserved Lysine in the Hydrophobic Pocket of HIV-1 gp41 Improves Small Molecule Antiviral Activity

Human Immunodeficiency virus (HIV-1) fusion is mediated by glycoprotein-41, a protein that has not been widely exploited as a drug target. Small molecules directed at the gp41 ectodomain have proved to be poorly drug-like, having moderate efficacy, high hydrophobicity and/or high molecular weight. We recently investigated conversion of a fairly potent hydrophobic inhibitor into a covalent binder, by modifying it to react with a lysine residue on the protein. We demonstrated a 10-fold improvement in antiviral efficacy. Here, we continue this study, utilizing instead molecules with better inherent drug-like properties. Molecules possessing low to no antiviral activity as equilibrium binders were converted into µM inhibitors upon addition of an electrophilic warhead in the form of a sulfotetrafluorophenyl (STP) activated ester. We confirmed specificity for gp41 and for entry. The small size of the inhibitors described here offers an opportunity to expand their reach into neighboring pockets while retaining drug-likeness. STP esterification of equilibrium binders is a promising avenue to explore for inhibiting HIV-1 entry. Many gp41 targeting molecules studied over the years possess carboxylic acid groups which can be easily converted into the corresponding STP ester. It may be worth the effort to evaluate a library of such inhibitors as a way forward to small molecule inhibition of fusion of HIV and possibly other enveloped viruses.

[A multicenter cross-sectional study of quality of life and nonsurgical treatment in patients with knee osteoarthritis]

Objective: To explore the influencing factors of health-related quality of life (HRQoL) in patients with knee osteoarthritis, and to analyze the non-surgical treatment of knee osteoarthritis. Methods: Demographic variables, treatment modalities, imaging data, and 12-item short form health survey (SF-12) scores of patients with knee osteoarthritis in orthopedic outpatient departments of five hospitals in Beijing from December 2017 to November 2018 were collected to analyze influencing factors of HRQoL and non-surgical treatment. Results: A total of 2 034 patients were included. There were 530 males (26.1%) and 1 504 females (73.9%), with a mean age of (59.17±10.22) years. In terms of physical quality of life, female patients with knee osteoarthritis had lower physical components summary (PCS) compared with male patients (β=-0.521, P=0.036); patients aged ≥64 years had lower PCS than those aged<55 years (β=-0.636, P=0.026). Patients with an education of more than 12 years had higher PCS than those with less than 10 years (β=1.063, P<0.001). Compared to patients with mild clinical symptoms, the PCS of patients with moderate clinical symptoms was lower (β=-0.860, P=0.002), while the PCS of those with severe clinical symptoms was much lower (β=-1.126, P<0.001). Patients treated with combination therapy had higher PCS than untreated patients (β=0.731, P=0.005). In terms of mental quality of life, compared to patients engaged in sedentary work, the mental components summary (MCS) of patients engaged in mild manual labor jobs was lower (β=-0.712, P=0.015); Compared to patients with a Charson comorbidity index of 0, patients with a Charlson comorbidity index ≥ 2 had lower MCS (β=-1.183, P=0.007). In the past 12 months, 648 (31.9%), 143 (7.0%), 406 (20.0%), 680 (33.4%), 343 (16.9%), 681 (33.5%), 170 (8.4%) patients had used non-steroid anti-inflammatory drugs (NSAIDs), acetaminophen, glucosamine/chondroitin formulations, physical therapy, articular cavity puncture injection, traditional Chinese medicine treatment and exercise therapy, respectively. Total of 451 patients (22.2%) received monotherapy and 889 patients (43.7%) received combination therapy. Conclusions: The major non-surgical treatment methods for patients with knee osteoarthritis in Beijing are NSAIDs, physiotherapy and traditional Chinese medicine. Combination therapy is used more frequently than monotherapy. Physical quality of life is related to gender, age, education, severity of symptoms and treatment, while mental quality of life is related to occupational labor and comorbidities.

Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical barriers to the wider adoption of this technology. To help the user community overcome these barriers, we have made major updates to the well-established MetaboAnalyst platform ( www.metaboanalyst.ca ). This protocol extends the previous 2011 Nature Protocol by providing stepwise instructions on how to use MetaboAnalyst 5.0 to: optimize parameters for LC-HRMS spectra processing; obtain functional insights from peak list data; integrate metabolomics data with transcriptomics data or combine multiple metabolomics datasets; conduct exploratory statistical analysis with complex metadata. Parameter optimization may take ~2 h to complete depending on the server load, and the remaining three stages may be executed in ~60 min.

OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics

Researchers are increasingly seeking to interpret molecular data within a multi-omics context to gain a more comprehensive picture of their study system. OmicsNet (www.omicsnet.ca) is a web-based tool developed to allow users to easily build, visualize, and analyze multi-omics networks to study rich relationships among lists of ‘omics features of interest. Three major improvements have been introduced in OmicsNet 2.0, which include: (i) enhanced network visual analytics with eleven 2D graph layout options and a novel 3D module layout; (ii) support for three new ‘omics types: single nucleotide polymorphism (SNP) list from genetic variation studies; taxon list from microbiome profiling studies, as well as liquid chromatography–mass spectrometry (LC–MS) peaks from untargeted metabolomics; and (iii) measures to improve research reproducibility by coupling R command history with the release of the companion OmicsNetR package, and generation of persistent links to share interactive network views. We performed a case study using the multi-omics data obtained from a recent large-scale investigation on inflammatory bowel disease (IBD) and demonstrated that OmicsNet was able to quickly create meaningful multi-omics context to facilitate hypothesis generation and mechanistic insights.

Retraction notice: Effect of educational interventions on health in childhood: a meta-analysis of randomized controlled trials [Public Health Volume 164, November 2018, Pages 134-147]

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). The article is a duplicate of a paper that has already been published in Medicine, 97 (2018) e11849 https://doi.org/10.1097/MD.0000000000011849. Redundant publications overweigh the relative importance of published findings and distort the academic record of the authors. One of the conditions of submission of a paper for publication is therefore that authors declare explicitly that the paper has not been previously published and is not under consideration for publication elsewhere. As such this article represents a misuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

Characterization of genetic fundamentals for piglet mortality at birth in Yorkshire, Landrace, and Duroc sows

Piglet mortality is an economically important complex trait that impacts sow prolificacy. Genetic analyses for piglet mortality at weaning have been reported in dozens of studies, but not for piglet mortality at birth. In this study, we used multi-breed data sets from Yorkshire, Landrace, and Duroc sows to characterize the genetic fundamentals of piglet mortality at birth. The heritabilities from parity I to III were estimated to be 0.0630, 0.1031, and 0.1140 respectively. By using a combined strategy, a total of 21 SNPs were detected in three parities, of which six were observed in parity I, five in parity II and 10 in parity III. Genome annotation revealed that these SNPs were harbored within or close to 19 candidate genes. The candidate genes were found to associate with the reproductive system and embryonic development in the tissue expression database, which are reasonably related to piglet mortality. These findings are expected to provide much information for understanding the genetic and genomic fundamentals of farrowing mortality.

A comparison of meat composition, tenderness and the fatty acid profile of three muscles from Holstein-Friesian bulls from production system resulting in final ages of either <16 or 19 months

Context The increased number of male dairy origin calves in Ireland due to the abolition of European Union milk quotas is a potential resource for the beef industry. Rearing these animals as bulls rather than steers is more efficient from a production perspective. Ensuring satisfactory quality of bull beef from dairy origin is essential. Aim To determine the effect of two production systems and three muscle types on physico-chemical characteristics and fatty acid (FA) profile of beef from Holstein-Friesian (HF) bulls. Methods Thirty HF bulls were equally assigned to two production systems, namely, slaughter at under 16 months of age or slaughter at 19 months of age. Longissimus thoracis (LT), Semitendinosus (ST) and Gluteus medius (GM) muscles were excised post-slaughter for determination of pH, colour, Warner–Bratzler (WB) variables, cook loss, chemical composition [intramuscular fat (IMF), moisture, protein, ash], collagen characteristics and FA profile. Results WB variables and cook loss after 14 days postmortem ageing, and insoluble and total collagen contents were higher, while IMF content, redness and saturation at 24 h post-blooming were lower for muscles from the 19-month production system. Muscles from the under 16-month production system had a higher saturated fatty acid (SFA) proportion and n-6:n-3 polyunsaturated fatty acid (PUFA) ratio, while muscle from the 19-month production system had a higher PUFA proportion, n-3 PUFA proportion and PUFA:SFA ratio. The GM muscle had the lowest L* value, followed by LT and ST. Yellowness, saturation and hue angle were greater in ST. LT had lower WB variables, cook loss, moisture, and a higher IMF content than ST and GM. The PUFA proportion and PUFA:SFA ratio were highest in ST, followed by GM and LT. IMF, total FA, SFA and monounsaturated fatty acid (MUFA) concentrations were higher in LT from the under 16-month production system bulls (the interaction). Conclusions Beef from the under 16-month production system compared with beef from the 19-month production system, and LT compared with ST and GM muscles had better quality characteristics. Implications Dairy bulls can produce beef of acceptable quality. The findings will guide selection of the combination of production system and muscle type most appropriate to specific market requirements.

The Siberian pine growth dynamics in Altai Mountains, China

Climatic factors play an essential role in the growth of tree ring width. In this study, we aimed to evaluate the correlation between climatic variables and tree-ring growth characteristics of Pinus sibirica in Altai mountains, northwestern China. This study being is first of its kind on climate growth analysis of Pinus sibirica in northwestern China. The study showed great potential to understand the species growing under the specific climatic conditions. Total of 70 tree cores collected from three sites in the sampling area, out of which 63 tree cores considered for this study. The effect of climatic variables which was studied include precipitation, temperature and PDSI. Our results showed that Tree Ring Width chronology has a significantly positive correlation with the late winter (March) temperature and significant negative correlation with the July temperatures. A significant correlation was observed with the late summer precipitation whereas no significant relation found with the Palmer Drought Severity Index. These significant correlations with temperature and precipitation suggested that this tree species had the potential for the reconstruction of the past climate in the area.

OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data

Data analysis and interpretation remain a critical bottleneck in current multi-omics studies. Here, we introduce OmicsAnalyst, a user-friendly, web-based platform that allows users to perform a wide range of well-established data-driven approaches for multi-omics integration, and visually explore their results in a clear and meaningful manner. To help navigate complex landscapes of multi-omics analysis, these approaches are organized into three visual analytics tracks: (i) the correlation network analysis track, where users choose among univariate and multivariate methods to identify important features and explore their relationships in 2D or 3D networks; (ii) the cluster heatmap analysis track, where users apply several cutting-edge multi-view clustering algorithms and explore their results via interactive heatmaps; and (iii) the dimension reduction analysis track, where users choose among several recent multivariate techniques to reveal global data structures, and explore corresponding scores, loadings and biplots in interactive 3D scatter plots. The three visual analytics tracks are equipped with comprehensive options for parameter customization, view customization and targeted analysis. OmicsAnalyst lowers the access barriers to many well-established methods for multi-omics integration via novel visual analytics. It is freely available at https://www.omicsanalyst.ca.

Era-like GTP protein gene expression in rice

The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

Since its first release over a decade ago, the MetaboAnalyst web-based platform has become widely used for comprehensive metabolomics data analysis and interpretation. Here we introduce MetaboAnalyst version 5.0, aiming to narrow the gap from raw data to functional insights for global metabolomics based on high-resolution mass spectrometry (HRMS). Three modules have been developed to help achieve this goal, including: (i) a LC-MS Spectra Processing module which offers an easy-to-use pipeline that can perform automated parameter optimization and resumable analysis to significantly lower the barriers to LC-MS1 spectra processing; (ii) a Functional Analysis module which expands the previous MS Peaks to Pathways module to allow users to intuitively select any peak groups of interest and evaluate their enrichment of potential functions as defined by metabolic pathways and metabolite sets; (iii) a Functional Meta-Analysis module to combine multiple global metabolomics datasets obtained under complementary conditions or from similar studies to arrive at comprehensive functional insights. There are many other new functions including weighted joint-pathway analysis, data-driven network analysis, batch effect correction, merging technical replicates, improved compound name matching, etc. The web interface, graphics and underlying codebase have also been refactored to improve performance and user experience. At the end of an analysis session, users can now easily switch to other compatible modules for a more streamlined data analysis. MetaboAnalyst 5.0 is freely available at https://www.metaboanalyst.ca.

A targeted covalent small molecule inhibitor of HIV-1 fusion

We describe a low molecular weight covalent inhibitor targeting a conserved lysine residue within the hydrophobic pocket of HIV-1 glycoprotein-41. The inhibitor bound selectively to the hydrophobic pocket and exhibited an order of magnitude enhancement of anti-fusion activity against HIV-1 compared to its non-covalent counterpart. The findings represent a significant advance in the quest to obtain non-peptide fusion inhibitors.

Comprehensive Meta-Analysis of COVID-19 Global Metabolomics Datasets

The novel coronavirus SARS-CoV-2 has spread across the world since 2019, causing a global pandemic. The pathogenesis of the viral infection and the associated clinical presentations depend primarily on host factors such as age and immunity, rather than the viral load or its genetic variations. A growing number of omics studies have been conducted to characterize the host immune and metabolic responses underlying the disease progression. Meta-analyses of these datasets have great potential to identify robust molecular signatures to inform clinical care and to facilitate therapeutics development. In this study, we performed a comprehensive meta-analysis of publicly available global metabolomics datasets obtained from three countries (United States, China and Brazil). To overcome high heterogeneity inherent in these datasets, we have (a) implemented a computational pipeline to perform consistent raw spectra processing; (b) conducted meta-analyses at pathway levels instead of individual feature levels; and (c) performed visual data mining on consistent patterns of change between disease severities for individual studies. Our analyses have yielded several key metabolic signatures characterizing disease progression and clinical outcomes. Their biological interpretations were discussed within the context of the current literature. To the best of our knowledge, this is the first comprehensive meta-analysis of global metabolomics datasets of COVID-19.

Outcomes following emergency colorectal cancer presentation in the elderly

AIM

Colorectal cancer is predominantly a disease of the elderly and up to 30% of these patients will present as an emergency. We compared the outcomes of 'elderly' patients presenting to our unit with a colorectal cancer emergency over a 10-year period with those of a 'younger' cohort.

METHODS

A single centre retrospective review of colorectal cancer emergencies between 1 April 2007 and 1 April 2017 was performed. Patients were separated into two cohorts: 'young' (< 75 years) and 'elderly' (≥ 75 years). Data collected included demographics, disease status, treatment and outcomes.

RESULTS

A total of 341 patients (< 75 years: n = 154; ≥ 75 years: n = 187) presented as a colorectal cancer emergency. Significantly fewer 'elderly' patients underwent curative surgical procedures (72% vs 49%, P < 0.0001) or received adjuvant chemotherapy (56% vs 21%, P < 0.0001). 'Elderly' patients had significantly more postoperative cardio-respiratory complications (7% vs 36%, P < 0.0001), but despite this there was no significant difference in 30-day mortality (7% vs 12%) and survival rates at 1 year (75% vs 74%) or 3 years (56% vs 49%). Elderly patients treated with best supportive care had a median overall survival of just 62 (range 1-955) days.

CONCLUSION

Patients ≥ 75 years presenting as a colorectal cancer emergency were significantly less likely to undergo emergency curative surgery or receive adjuvant chemotherapy than those < 75 years. However, the 30-day mortality, 1- and 3-year survival rates for patients undergoing curative surgery were comparable.

Obesity prevalence and risks among Chinese adults: findings from China PEACE Million Persons Project, 2014–2018

Background

With demographic and epidemiologic transitions, China has become home to the greatest number of obese individuals in the world. Effective policy intervention requires a contemporary assessment of obesity across broad socio-demographic subgroups.

Purpose

We aim to assess the prevalence of overall and abdominal obesity by socio-demographic characteristics and the associations of these characteristics with obesity in China.

Methods

Using the data of 2.7-million community-dwelling participants aged 35–75 years in the China PEACE Million Persons Project, a nationwide cross-sectional screening project from 2014 to 2018, we calculated the prevalence of overall and abdominal obesity based on national guideline definitions (body mass index ≥28 kg/m2, waist circumference ≥85/90 cm for women/men). We examined 12 available socio-demographic variables that are potentially associated with obesity, in addition to self-reported co-morbidities, and quantified the associations of these socio-demographic characteristics with obesity using multivariable mixed models.

Results

The prevalence of overall and abdominal obesity were 15.8% and 37.6% in women and 15.0% and 36.3% in men (Figure). Compared to individuals with normal weight, those with overall obesity had a higher prevalence of hypertension, dyslipidemia, and diabetes (in women: by 30.4, 16.1, and 6.0 percent points; in men, by 29.9, 31.2, and 5.8 percent points). A similar pattern was observed with abdominal obesity. In women, those aged 55–64 years constituted the largest age group with overall and abdominal obesity (33.7% and 35.0%), while in men, those aged 45–54 and 55–64 years constituted the largest age group with overall obesity (30.4%) and abdominal obesity (30.5%), respectively. Older women were at substantially higher risk for obesity (e.g., adjusted relative risk [95% CI] of women aged 65–75 vs. 35–44 years: 1.29 [1.27–1.31] for overall obesity and 1.76 [1.74–1.77] for abdominal obesity) while older men were not. Higher education was associated with lower risk in women (e.g., those with college or university education vs. less than primary school: 0.47 [0.46–0.48] for overall obesity and 0.61 [0.60–0.62] for abdominal obesity) but higher risk in men (1.07 [1.05–1.10] and 1.17 [1.16–1.19]). In both women and men, current smoking was associated with lower risk for obesity, and current drinking was associated with higher risk, but the magnitude of associations was smaller in women than men.

Conclusions

In China, over one in seven individuals meet criteria for overall obesity, and one in three for abdominal obesity. Wide variation exists across socio-demographic subgroups. The associations of age and education with obesity are significant and differ by sex. Understanding obesity in contemporary China has broad domestic policy implications and provides a valuable international reference.

Figure 1

Funding Acknowledgement

Type of funding source: Other. Main funding source(s): The National Key Research and Development Program from the Ministry of Science and Technology of China, the CAMS Innovation Fund for Medical Science

miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology

miRNet is an easy-to-use, web-based platform designed to help elucidate microRNA (miRNA) functions by integrating users' data with existing knowledge via network-based visual analytics. Since its first release in 2016, miRNet has been accessed by >20 000 researchers worldwide, with ∼100 users on a daily basis. While version 1.0 was focused primarily on miRNA-target gene interactions, it has become clear that in order to obtain a global view of miRNA functions, it is necessary to bring other important players into the context during analysis. Driven by this concept, in miRNet version 2.0, we have (i) added support for transcription factors (TFs) and single nucleotide polymorphisms (SNPs) that affect miRNAs, miRNA-binding sites or target genes, whilst also greatly increased (>5-fold) the underlying knowledgebases of miRNAs, ncRNAs and disease associations; (ii) implemented new functions to allow creation and visual exploration of multipartite networks, with enhanced support for in situ functional analysis and (iii) revamped the web interface, optimized the workflow, and introduced microservices and web application programming interface (API) to sustain high-performance, real-time data analysis. The underlying R package is also released in tandem with version 2.0 to allow more flexible data analysis for R programmers. The miRNet 2.0 website is freely available at https://www.mirnet.ca.

Biophysical studies of HIV-1 glycoprotein-41 interactions with peptides and small molecules - Effect of lipids and detergents

BACKGROUND

The hydrophobic pocket (HP) of HIV-1 glycoprotein-41 ectodomain is defined by two chains of the N-heptad repeat trimer, within the protein-protein interface that mediates 6HB formation. It is a potential target for inhibitors of viral fusion, but its hydrophobic nature and proximity to membrane in situ has precluded ready analysis of inhibitor interactions.

METHODS

We evaluated the sensitivity of ¹⁹F NMR and fluorescence for detecting peptide and small molecule binding to the HP and explored the effect of non-denaturing detergent or phospholipid as cosolvents and potential mimics of the membrane environment surrounding gp41.

RESULTS

Chemical shifts of aromatic fluorines were found to be sensitive to changes in the hydrogen bonding network that occurred when inhibitors transitioned from solvent into the HP or into ordered detergent micelles. Fluorescence intensities and emission maxima of autofluorescent compounds responded to changes in the local environment.

CONCLUSIONS

Gp41 - ligand binding occurred under all conditions, but was diminished in the presence of detergents. NMR and fluorescence studies revealed that dodecylphosphocholine (DPC) was a poor substitute for membrane in this system, while liposomes could mimic the membrane surroundings.

GENERAL SIGNIFICANCE

Our findings suggest that development of high potency small molecule binders to the HP may be frustrated by competition between binding to the HP and binding to the bilayer membrane.

Recent progress on the Chinese space programme and radiation research

Manned space exploration was initiated in China in 1992, and substantial progress has been made. The next step is to build the Chinese Space Station (CSS), which is planned to be launched in 2020. The CSS will provide an on-orbit laboratory for experimental studies including space radiation research. The health risk of space radiation, especially carcinogenesis, is a major concern for long-term space exploration. Establishing a risk assessment system suitable for Chinese astronauts and developing effective countermeasures are major tasks for Chinese space radiobiologists. The Institute of Space Life Sciences, Soochow University has focused on these topics for years. We established cancer models with low-dose-rate exposure of alpha particles, and elucidated a microRNA-TGFβ network regulating bystander effects and a lncRNA-cytoskeleton network regulating genomic instability induced by ionising radiation. We also confirmed the radioresistance of quiescent cells, which inspires a potential strategy to improve individual radioresistance during long-term space travel. However, we believe that a multi-disciplinary strategy must be developed to protect astronauts from highly energised space radiation.