Benzo[a]pyrene is associated with dysregulated myelo-lymphoid hematopoiesis in asthmatic children

Children's exposure to polycyclic aromatic hydrocarbon (PAHs): a review on urinary 1-hydroxypyrene and associated health effects

This article reviewed the published studies on the environmental exposure to polycyclic aromatic hydrocarbons (PAHs) among children and assessed the urinary 1-hydroxypyrene (1-OHP) level as a biomarker of exposure to PAHs. The current knowledge of the potential health effects of increased 1-OHP in children was reviewed. Additionally, the influence of genetic polymorphism on the urinary 1-OHP level was discussed in this review. The assembled data showed that children who are attending schools or living close to industrial and polluted urban areas might have greater exposure to higher concentrations of PAHs with a higher level of urinary 1-OHP when compared to those children living in rural areas. Urinary 1-OHP may be a reliable biomarker for determining the genotoxic effects, oxidative stress and inflammation caused by exposure to PAHs. Strong research evidence indicated that the total body burden of PAHs should be evaluated by biomonitoring of 1-OHP in line with other urinary PAHs metabolites (with 2-3 rings) to evaluate recent total exposure to PAHs. Overall, the study suggests implementing a mitigation plan to combat air pollution to provide a cleaner environment for children.

A scoping review of asthma and machine learning

OBJECTIVE

The objective of this study was to determine the extent of machine learning (ML) application in asthma research and to identify research gaps while mapping the existing literature.

DATA SOURCES

We conducted a scoping review. PubMed, ProQuest, and Embase Scopus databases were searched with an end date of September 18, 2020.

STUDY SELECTION

DistillerSR was used for data management. Inclusion criteria were an asthma focus, human participants, ML techniques, and written in English. Exclusion criteria were abstract only, simulation-based, not human based, or were reviews or commentaries. Descriptive statistics were presented.

RESULTS

A total of 6,317 potential articles were found. After removing duplicates, and reviewing the titles and abstracts, 102 articles were included for the full text analysis. Asthma episode prediction (24.5%), asthma phenotype classification (16.7%), and genetic profiling of asthma (12.7%) were the top three study topics. Cohort (52.9%), cross-sectional (20.6%), and case-control studies (11.8%) were the study designs most frequently used. Regarding the ML techniques, 34.3% of the studies used more than one technique. Neural networks, clustering, and random forests were the most common ML techniques used where they were used in 20.6%, 18.6%, and 17.6% of studies, respectively. Very few studies considered location of residence (i.e. urban or rural status).

CONCLUSIONS

The use of ML in asthma studies has been increasing with most of this focused on the three major topics (>50%). Future research using ML could focus on gaps such as a broader range of study topics and focus on its use in additional populations (e.g. location of residence).

Supplemental data for this article is available online at http://dx.doi.org/ .

Microarray and Bioinformatics Analysis of Differential Gene and lncRNA Expression during Erythropoietin Treatment of Acute Spinal Cord Injury in Rats

Purpose

We performed a genome-wide analysis of long noncoding RNA (lncRNA) expression to identify novel targets for the further study of recombinant human erythropoietin (rhEPO) treatment of acute spinal cord injury (SCI) in rats.

Methods

Nine rats were randomly divided into 3 groups. No operation was performed in group 1. In groups 2 and 3, a laminectomy was performed at the 10th thoracic vertebra, and a contusion injury was induced by extradural application of an aneurysm clip. Group 1 rats did not receive any treatment, group 2 rats received a single intraperitoneal injection of normal saline, and group 3 rats received rhEPO. Three days after injury, spinal cord tissues were collected for RNA-Seq, microarray, differentially expressed genes (DEGs), Gene Ontology (GO) function enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) analyses.

Results

Compared with group 1, 4,446 genes were found to be differentially expressed in group 2. Furthermore, 99 lncRNAs were found to be changed in the injury group. The data indicate that 2,471 mRNAs were upregulated, and 1,975 mRNAs were downregulated in group 2 as compared with group 1. In addition, 45 of the lncRNAs were upregulated, and the other 44 lncRNAs were downregulated. The top 5 upregulated and top 5 downregulated lncRNAs that were different between group 2 and group 1 are shown. The top 5 downregulated and the top 5 upregulated lncRNAs that were different between group 3 and group 2 are shown.

Conclusion

RhEPO treatment alters the expression profiles of the differentially expressed lncRNAs and genes beneficial to the development of new treatments.

Single-Cell RNA-Seq Analysis Reveals Lung Epithelial Cell Type-Specific Responses to HDM and Regulation by Tet1

Tet1 protects against house dust mite (HDM)-induced lung inflammation in mice and alters the lung methylome and transcriptome. In order to explore the role of Tet1 in individual lung epithelial cell types in HDM-induced inflammation, we established a model of HDM-induced lung inflammation in Tet1 knockout and littermate wild-type mice, then studied EpCAM+ lung epithelial cells using single-cell RNA-seq analysis. We identified eight EpCAM+ lung epithelial cell types, among which AT2 cells were the most abundant. HDM challenge altered the relative abundance of epithelial cell types and resulted in cell type-specific transcriptomic changes. Bulk and cell type-specific analysis also showed that loss of Tet1 led to the altered expression of genes linked to augmented HDM-induced lung inflammation, including alarms, detoxification enzymes, oxidative stress response genes, and tissue repair genes. The transcriptomic regulation was accompanied by alterations in TF activities. Trajectory analysis supports that HDM may enhance the differentiation of AP and BAS cells into AT2 cells, independent of Tet1. Collectively, our data showed that lung epithelial cells had common and unique transcriptomic signatures of allergic lung inflammation. Tet1 deletion altered transcriptomic networks in various lung epithelial cells, which may promote allergen-induced lung inflammation.

Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application

Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through  GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.

Organic matter composition, BaP biodegradation and microbial communities at sites near and far from the bioanode in a soil microbial fuel cell

Bioanodes in a soil microbial fuel cell (SMFC) can serve as sustainable electron acceptors in microbial metabolism processes; thus, SMFCs are considered a promising in situ bioremediation technology. Most related studies have focused on the removal efficiency of contaminants. Relatively few efforts have been made to comprehensively investigate the organic matter composition and biodegradation metabolites of organic contaminants and microbial communities at various distances from the bioanode. In this study, the level and composition of dissolved organic matter (DOM), biodegradation metabolites of benzo[a]pyrene (BaP), and microbial communities at two sites with different distances (S_1cm and S_11cm) to the bioanode were investigated in an SMFC. The consumption efficiency of dissolved organic carbon (R_DOC) and removal efficiency of BaP (R_BaP) at S_1cm were slightly higher than those at S_11cm after 100 days (R_DOC 47.82 ± 5.77% at S_1cm and 44.98 ± 10.76% at S_11cm; R_BaP 72.52 ± 1.88% at S_1cm and 68.50 ± 4.34% at S_11cm). More fulvic acid-like components and more low-molecular-weight metabolites (indicating a higher biodegradation degree) of BaP were generated at S_1cm than at S_11cm. The microbial community structures were similar at the two sites. Electroactive bacteria (EAB) and some polycyclic aromatic hydrocarbon degraders were both enriched at the bioanode. Energy metabolism at the bioanode could be upregulated to generate more adenosine triphosphate (ATP). In conclusion, the bioanode could modulate the metabolic pathways in the adjacent soil by strengthening the contact between the EAB and BaP degraders, and providing more ATP to the BaP degraders.

Genotoxic Activity of Particulate Matter and In Vivo Tests in Children Exposed to Air Pollution

The aim of this paper was to investigate the relationship between micronuclei and DNA damage in children's buccal mucosa cells and the genotoxicity and mutagenicity of the different sized fractions of particulate matter as well as the concentration of PAHs (polycyclic aromatic hydrocarbons) and metals in particulate matter. Air particulate matter was collected by high volume samplers located near the schools attended by the children on the same days of biological samplings. The mutagenic activity was assessed in different cells in in vitro tests (Ames test on bacteria and comet test on leukocytes). Our study showed weak positive correlations between (a) the mutagenicity of the PM_0.5 fraction and PAHs and (b) the micronuclei test of children's buccal cells and PAHs detected in PM_0.5 and PM_0.5-3 fractions. A positive correlation was also found between in vitro comet test on leukocytes and PAHs in the PM_3-10 fraction. No correlation was observed for metal concentrations in each PM fraction.

Airborne Benzo[a]Pyrene may contribute to divergent Pheno-Endotypes in children

BACKGROUND

Asthma represents a syndrome for which our understanding of the molecular processes underlying discrete sub-diseases (i.e., endotypes), beyond atopic asthma, is limited. The public health needs to characterize etiology-associated endotype risks is becoming urgent. In particular, the roles of polyaromatic hydrocarbon (PAH), globally distributed combustion by-products, toward the two known endotypes - T helper 2 cell high (Th2) or T helper 2 cell low (non-Th2) - warrants clarification.

OBJECTIVES

To explain ambient B[a]P association with non-atopic asthma (i.e., a proxy of non-Th2 endotype) is markedly different from that with atopic asthma (i.e., a proxy for Th2-high endotype).

METHODS

In a case-control study, we compare the non-atopic as well as atopic asthmatic boys and girls against their respective controls in terms of the ambient Benzo[a]pyrene concentration nearest to their home, plasma 15-Ft2-isoprostane (15-Ft2-isoP), urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), and lung function deficit. We repeated the analysis for i) dichotomous asthma outcome and ii) multinomial asthma-overweight/obese (OV/OB) combined outcomes.

RESULTS

The non-atopic asthma cases are associated with a significantly higher median B[a]P (11.16 ng/m3) compared to that in the non-atopic controls (3.83 ng/m3; P-value < 0.001). In asthma-OV/OB stratified analysis, the non-atopic girls with lean and OV/OB asthma are associated with a step-wisely elevated B[a]P (median,11.16 and 18.00 ng/m3, respectively), compared to the non-atopic lean control girls (median, 4.28 ng/m3, P-value < 0.001). In contrast, atopic asthmatic children (2.73 ng/m3) are not associated with a significantly elevated median B[a]P, compared to the atopic control children (2.60 ng/m3; P-value > 0.05). Based on the logistic regression model, on ln-unit increate in B[a]P is associated with 4.7-times greater odds (95% CI, 1.9-11.5, P = 0.001) of asthma among the non-atopic boys. The same unit increase in B[a]P is associated with 44.8-times greater odds (95% CI, 4.7-428.2, P = 0.001) among the non-atopic girls after adjusting for urinary Cotinine, lung function deficit, 15-Ft2-isoP, and 8-oxodG.

CONCLUSIONS

Ambient B[a]P is robustly associated with non-atopic asthma, while it has no clear associations with atopic asthma among lean children. Furthermore, lung function deficit, 15-Ft2-isoP, and 8-oxodG are associated with profound alteration of B[a]P-asthma associations among the non-atopic children.

Network models of primary melanoma microenvironments identify key melanoma regulators underlying prognosis

Melanoma is the most lethal skin malignancy, driven by genetic and epigenetic alterations in the complex tumour microenvironment. While large-scale molecular profiling of melanoma has identified molecular signatures associated with melanoma progression, comprehensive systems-level modeling remains elusive. This study builds up predictive gene network models of molecular alterations in primary melanoma by integrating large-scale bulk-based multi-omic and single-cell transcriptomic data. Incorporating clinical, epigenetic, and proteomic data into these networks reveals key subnetworks, cell types, and regulators underlying melanoma progression. Tumors with high immune infiltrates are found to be associated with good prognosis, presumably due to induced CD8+ T-cell cytotoxicity, via MYO1F-mediated M1-polarization of macrophages. Seventeen key drivers of the gene subnetworks associated with poor prognosis, including the transcription factor ZNF180, are tested for their pro-tumorigenic effects in vitro. The anti-tumor effect of silencing ZNF180 is further validated using in vivo xenografts. Experimentally validated targets of ZNF180 are enriched in the ZNF180 centered network and the known pathways such as melanoma cell maintenance and immune cell infiltration. The transcriptional networks and their critical regulators provide insights into the molecular mechanisms of melanomagenesis and pave the way for developing therapeutic strategies for melanoma.

While the molecular profiling of melanoma progression has been extensively characterised by large-scale studies, there is still need for the comprehensive integration of such datasets. Here the authors construct predictive gene network models for prognostic and therapeutic purposes.

Organic and inorganic model soil fractions instigate the formation of distinct microbial biofilms for enhanced biodegradation of benzo[a]pyrene

This study conducted the sorption and biodegradation of benzo[a]pyrene (BaP) by microbial biofilm communities developed on proxies for materials typically found in soils. The half-life of BaP was 4.7 and 2.3 weeks for biofilms on the inorganic carrier (BC_INOR, montmorillonite) and on the organic carrier (BC_OR, humic acid), respectively. In contrast, the half-life was 7.0 weeks for specialized planktonic cultures (PK). The exposure to BaP caused the development of lipid inclusion bodies inside the bacteria of the PK systems and biofilms of the BC_INOR, but not on the biofilms of the BC_OR system. Interestingly, the BC_OR displayed not only the greatest BaP sorption capacity but also the greatest bacterial density and membrane integrity and the shortest bacteria-to-bacteria distances, which were consistent with the increased production of cell surface extracellular polymeric substances on the BC_OR. Both carriers caused a noticeable shift in the bacterial genera during the biodegradation of the BaP. The BC_INOR selected for Rhodococcus, Brucella, Chitinophaga, and Labrys, whereas the BC_OR favored Rhodococcus and Dokdonella. It indicated that ultra-structure and BaP degradation within the organic carrier-attached biofilms differed from the inorganic ones, and suggested that the microstructural heterogeneity and microbial biodiversity from biofilms on the organic carrier promoted biodegradation.

Asthma genomics and pharmacogenomics

In this review, we summarize recent published work interrogating the relationship between genetic variation or gene expression regulation across the genome and asthma or asthma treatment outcomes. This includes 11 genome-wide association studies of asthma phenotypes that collectively identified 64 novel loci; transcriptome-wide asthma association studies which identified genes involved in virus recognition, bacterial infection, lung tissue remodeling, eosinophilic and neutrophilic inflammation and genes in the chromosome 17q12 asthma susceptibility locus; and three epigenome-wide studies of asthma that had robust sample sizes and replicated findings. We also highlight pharmacogenomic studies of corticosteroids, bronchodilator response to albuterol and zileuton, although finding from these studies may still be preliminary due to their relatively small sample sizes and limited availability of replication cohorts.

Comparison of polycyclic aromatic hydrocarbon metabolite concentrations in urine of mothers and their newborns

Polycyclic aromatic hydrocarbons (PAHs) are environmental contaminants produced during incomplete combustion of organic matter. Humans can be exposed to them via several pathways (inhalation, digestion, dermal exposure). The aim of this study was to assess the concentration of 11 monohydroxylated metabolites of PAHs (OH-PAHs) in 660 urine samples collected from mothers and their newborns residing in two localities of the Czech Republic - Most and Ceske Budejovice - in 2016 and 2017. After enzymatic hydrolysis, the target analytes were extracted from the urine samples using liquid-liquid extraction, with extraction solvent ethyl acetate and a clean-up step using dispersive solid-phase extraction (d-SPE) with the Z-Sep sorbent. For identification and quantification, ultra-high performance liquid chromatography coupled with tandem mass spectrometry was applied. 2-OH-NAP was the compound present in all of the measured samples and it was also the compound at the highest concentration in both mothers' and newborns' urine samples (median concentration 5.15 μg/g creatinine and 3.58 μg/g creatinine). The total concentrations of OH-PAHs in urine samples collected from mothers were 2 times higher compared to their children. The most contaminated samples were collected in Most in the period October 2016-March 2017 from both mothers (12.59 μg/g creatinine) and their newborns (8.29 μg/g creatinine). The concentrations of OH-PAHs in urine samples, which were collected from both mothers and their newborns as presented in this study, are comparable with those found in our previous study between 2013 and 2014. In addition, they are slightly lower or comparable to other studies from Poland, USA, Germany, China, and Australia. The results might indicate that the population in the previously highly air-polluted mining districts carries some long-term changes (maybe existing changes in genetic information), which also affect the metabolism of PAHs. It could be related to the long-lasting effect, and thus corresponding to the shortened life expectancy.

Polycyclic aromatic hydrocarbons in infant formulae, follow-on formulae, and baby foods in Iran: An assessment of risk

Twenty-seven samples of infant formulae and follow-on formulae and fifteen samples of baby food from Iranian markets were analyzed for concentrations of four polycyclic aromatic hydrocarbons (PAH4) determined by use of gas chromatography coupled to mass spectrophotometry. An assessment of risks posed to infants and toddlers was conducted by calculating the margin of exposure and incremental lifetime cancer risk (ILCR) by use of the Monte Carlo Simulation Method. Benzo (a) anthracene, was not detected in any of the samples, while approximately 64.3% samples contained detectable amounts of benzo (a) pyrene, while chrysene was observed in three samples and benzo (b) fluoranthene was detected in one sample. One of the samples contained 1.43 μg PAH4/kg, which was greater than the maximum tolerable limit (MTL; 1 μg/kg) stated in Commission Regulation (EU) 2015/1125. Accordingly, the 95% ILCRs in the infants/toddlers due to ingestion of milk powder and baby foods were determined to be 1.3 × 10^-6 and 7.3 × 10^-7, respectively. Also, the 95th centiles of the MOEs, due to ingesting milk powder or baby foods by infants/toddlers were estimated to be 3.6 × 10⁴ and 7.2 × 10⁴, respectively. In Iran, infants and toddlers are not at serious health risk (MOE ≥ 1 × 10⁴ and ILCR < 1 × 10^-4).