Carcinogenic effects of oil dispersants: A KEGG pathway-based RNA-seq study of human airway epithelial cells

Arsenic and UVR co-exposure results in unique gene expression profile identifying key co-carcinogenic mechanisms

Changes in gene expression underlie many pathogenic endpoints including carcinogenesis. Metals, like arsenic, alter gene expression; however, the consequences of co-exposures of metals with other stressors are less understood. Although arsenic acts as a co-carcinogen by enhancing the development of UVR skin cancers, changes in gene expression in arsenic UVR co-carcinogenesis have not been investigated. We performed RNA-sequencing analysis to profile changes in gene expression distinct from arsenic or UVR exposures alone. A large number of differentially expressed genes (DEGs) were identified after arsenic exposure alone, while after UVR exposure alone fewer genes were changed. A distinct increase in the number of DEGs was identified after exposure to combined arsenic and UVR exposure that was synergistic rather than additive. In addition, a majority of these DEGs were unique from arsenic or UVR alone suggesting a distinct response to combined arsenic-UVR exposure. Globally, arsenic alone and arsenic plus UVR exposure caused a global downregulation of genes while fewer genes were upregulated. Gene Ontology analysis using the DEGs revealed cellular processes related to chromosome instability, cell cycle, cellular transformation, and signaling were targeted by combined arsenic and UVR exposure, distinct from UVR alone and arsenic alone, while others were related to epigenetic mechanisms such as the modification of histones. This result suggests the cellular functions we identified in this study may be key in understanding how arsenic enhances UVR carcinogenesis and that arsenic-enhanced gene expression changes may drive co-carcinogenesis of UVR exposure.

LPCAT1 functions as an oncogene in cervical cancer through mediating JAK2/STAT3 signaling

Cervical cancer is a major gynecological tumor worldwide. Unfortunately, the molecular mechanisms involved in cervical cancer tumorigenesis still requires more clarification. Lysophosphatidylcholine acyltransferase 1 (LPCAT1), an enzyme involved in phosphatidylcholine metabolism, has been reported to regulate the proliferation, epithelial-mesenchymal transition (EMT) and recurrence of malignancies. Here in our study, we found that LPAT1 was over-expressed in clinical cervical cancer tissues, and its high expression was closely correlated with poor outcomes of patients. We further showed that LPCAT1 knockdown remarkably restrained the proliferation, migration and invasion of cervical cancer cells, while it significantly induced apoptosis. RNA-seq and bioinformatics assays initially showed that interleukin-6/signal transducer and activator of transcription 3 (IL-6/STAT3) pathway was a key mechanism for LPCAT1 to regulate cervical cancer progression. LPCAT1 silence strongly decreased IL-6, p-Janus kinase 2 (JAK2) and p-STAT3 expression levels in cervical cancer cells. Similarly, the expression levels of IL-6/STAT3 target genes were also highly down-regulated in cervical cancer cells with LPCAT1 deletion. Importantly, we found that human recombinant IL-6 addition considerably abolished the function of LPCAT1-knockdown to suppress the proliferation and EMT process in cervical cancer cells, accompanied with mitigated apoptotic cell death. Furthermore, our animal experiment results validated that stable LPCAT1 deletion efficiently reduced the tumor growth rates of xenograft mouse models and lung metastasis in vivo. Collectively, all our findings revealed that LPCAT1 may be a promising alternative prognostic biomarker and therapeutic target for cervical cancer through regulating JAK2/STAT3 signaling pathway.

Effect of Graphene and Graphene Oxide on Airway Barrier and Differential Phosphorylation of Proteins in Tight and Adherens Junction Pathways

Via inhalation we are continuously exposed to environmental and occupational irritants which can induce adverse health effects, such as irritant-induced asthma (IIA). The airway epithelium forms the first barrier encountered by these agents. We investigated the effect of environmental and occupational irritants on the airway epithelial barrier in vitro. The airway epithelial barrier was mimicked using a coculture model, consisting of bronchial epithelial cells (16HBE) and monocytes (THP-1) seeded on the apical side of a permeable support, and human lung microvascular endothelial cells (HLMVEC) grown on the basal side. Upon exposure to graphene (G) and graphene oxide (GO) in a suspension with fetal calf serum (FCS), ammonium persulfate (AP), sodium persulfate (SP) and hypochlorite (ClO⁻), the transepithelial electrical resistance (TEER) and flux of fluorescent labelled dextran (FD4-flux), was determined. Exposure to graphene nanoparticles (GNPs) induced an immediate negative effect on the epithelial barrier, whereas ClO⁻ only had a negative impact after 24 h of exposure. AP and SP did not affect the barrier properties. The tight junctions (TJ) network showed less connected zonula occludens 1 (ZO-1) and occludin staining in GNP-exposed cocultures. Functional analysis of the phosphoproteomic data indicated that proteins in the adherens junction (AJ) and TJ pathways showed an altered phosphorylation due to GNP exposure. To conclude, the negative effect of GNPs on the epithelial barrier can be explained by the slightly altered the TJ organization which could be caused by alterations in the phosphorylation level of proteins in the AJ and TJ pathway.

Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods

Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or inter-coordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired pathways, were highly mutually consistent among the five datasets. The combinatory list of 92 hub genes was generally multi-functional, suggesting their complex and dynamic roles in SCZ pathophysiology. In our constructed pathway crosstalk network, we found “Clostridium neurotoxicity” and “signaling events mediated by focal adhesion kinase” had the highest interactions. We further identified disconnected gene links underlying the disrupted pathway crosstalk. Among them, four gene pairs (PAK1:SYT1, PAK1:RFC5, DCTN1:STX1A, and GRIA1:MAP2K4) were normally correlated in universal contexts. In summary, we systematically identified rewired pathways, disrupted pathway crosstalk circuits, and critical genes and gene links in schizophrenia transcriptomes.

Transcriptome analysis of two structurally related flavonoids; Apigenin and Chrysin revealed hypocholesterolemic and ketogenic effects in mouse embryonic fibroblasts

There is no known single therapeutic drug for treating hypercholesterolemia that comes with negligible systemic side effects. In the current study, using next generation RNA sequencing approach in mouse embryonic fibroblasts we discovered that two structurally related flavonoid compounds. Apigenin and Chrysin exhibited moderate blocking ability of multiple transcripts that regulate rate limiting enzymes in the cholesterol biosynthesis pathway. The observed decrease in cholesterol biosynthesis pathway correlated well with an increase in transcripts involved in generation and trafficking of ketone bodies as evident by the upregulation of Bdh1 and Slc16a6 transcripts. The hypocholesterolemic potential of Apigenin and Chrysin at higher concentrations along with their ability to generate ketogenic substrate especially during embryonic stage is useful or detrimental for embryonic health is not clear and still debatable. Our study will serve as a steppingstone to further the investigation in whole animal studies and also in translating this knowledge to human studies.

A study on the pathogenesis of blood-heat psoriasis with transcriptome analysis

Background

Most existing studies on psoriasis' pathogenesis have focused on collecting epithelial cell gene sequences from psoriasis patients and normal subjects. In this paper, for the first time, high-throughput microarray was used to study the differential expression of genes in venous blood between patients with blood-heat psoriasis and normal subjects, providing theoretical support for studying the pathogenesis of blood-heat psoriasis.

Methods

Peripheral venous blood was collected from ten patients with blood-heat psoriasis and ten healthy volunteers for high-throughput microarray. The mRNAs, lncRNAs, and circRNAs related to blood-heat psoriasis were selected by analyzing the transcriptome microarray results. Then gene ontology (GO) analysis and KEGG signaling pathway analysis were used to explore further the biological functions of these mRNAs, lncRNAs, and circRNAs in blood-heat pathogenesis psoriasis. Network pharmacology was used to analyze the protein-protein interaction (PPI) network of the genes with differential expression, and the core genes to transmit information were obtained.

Results

A total of 205 circRNAs, 393 lncRNAs, and 157 mRNAs with differential expression associated with psoriasis were selected using high-throughput microarray. GO analysis showed these mRNAs, lncRNAs, and circRNAs were mainly enriched in cellular processes, biological regulation, ribosome formation, and negative regulation of protein binding. However, KEGG enrichment analysis suggested they were mainly enriched in autoimmunity pathways, lipid metabolism, translation, and signal transduction. PPI network analysis of mRNAs with significant difference revealed 11 core genes that transmitted information in psoriasis primarily.

Conclusions

The mRNAs, lncRNAs, and circRNAs with differential expression related to the pathogenesis of blood-heat psoriasis were found using high-throughput microarray for the first time. And the mRNAs, lncRNAs, and circRNAs with potential regulatory functions related to blood-heat psoriasis were then screened by bioinformatics analysis, effectively providing a new research entry point to the pathogenesis of blood-heat psoriasis.

The Impact of the Deepwater Horizon Oil Spill upon Lung Health-Mouse Model-Based RNA-Seq Analyses

We used a transcriptomic approach to interrogate the effects of a saline-accommodated fraction from the Macondo 252 well (MC252) oil and Corexit dispersants on lung tissue. Wild-type C57BL/6 male and female mice were exposed on days 0, 7 and 13 by oropharyngeal aspiration to saline accommodated fractions (SAF) of crude oil from the Macondo (MC252) well, Corexit 9500, Corexit 9527, 9500+oil and 9527+oil or a saline solution as the vehicle control. These treatments did not cause overt toxicity, with the exception of the Corexit exposures which caused brief weight loss after the first exposure. On day 14, total RNA was isolated from the left lung for RNA-seq analyses. KEGG-pathway-based differential expression revealed that Corexit 9527 elicited the strongest changes involving the upregulation of 19 KEGG pathways (FDR < 0.10), followed by Corexit 9500 with the upregulation of seven pathways (FDR < 0.10). As an important signature, pathways related to a response to DNA damage (e.g., p53 signaling and mismatch repair) dominate those upregulated by Corexit 9527 and Corexit 9500. In addition, pro-inflammatory pathways (e.g., cytokine-cytokine receptor interaction, IL-17 signaling pathway and TNF signaling pathways) were upregulated selectively in oil-treated male mice. Surprisingly, oil + dispersant combinations caused lesser effects than the individual treatments at the transcriptomic level. Overall, these findings support potential genotoxicity, inflammation and cell death due to dispersant or oil exposures. Similar exposures to lung tumor bearing K-Ras^LA1 mice provided evidence for tumor promotion by oil and Corexit dispersant treatments. Our mouse RNA-seq analyses may be relevant to the pulmonary health hazards of MC252 oil and dispersants experienced in exposed populations.

Current issues confounding the rapid toxicological assessment of oil spills

Oil spills of varying magnitude occur every year, each presenting a unique challenge to the local ecosystem. The complex, changeable nature of oil makes standardised risk assessment difficult. Our review of the state of science regarding oil's unique complexity; biological impact of oil spills and use of rapid assessment tools, including commercial toxicity kits and bioassays, allows us to explore the current issues preventing effective, rapid risk assessment of oils. We found that despite the advantages to monitoring programmes of using well validated standardised tests, which investigate impacts across trophic levels at environmentally relevant concentrations, only a small percentage of the available tests are specialised for use within the marine environment, or validated for the assessment of crude oil toxicity. We discuss the use of rapid tests at low trophic levels in addition to relevant sublethal toxicity assays to allow the characterisation of oil, dispersant and oil and dispersant mixture toxicity. We identify novel, passive dosing techniques as a practical and reproducible means of improving the accuracy and maintenance of nominal concentrations. Future work should explore the possibility of linking this tiered testing system with ecosystem models to allow the prediction and risk assessment of the entire ecosystem.

In vitro toxicity testing in hemocytes of the marine mussel Mytilus galloprovincialis (L.) to uncover mechanisms of action of the water accommodated fraction (WAF) of a naphthenic North Sea crude oil without and with dispersant

Dispersants used in oil spills could result toxic to marine organisms and could influence the toxicity of oil compounds. The aim of this work was to uncover the mechanisms of action of the water accommodated fraction (WAF) of a naphthenic North Sea crude oil produced at 10, 15 and 20 °C without and with the dispersant Finasol OSR52 (WAF and WAFD, respectively) using hemocytes of the marine mussel Mytilus galloprovincialis. Primary cultures of hemocytes were exposed in glass-coated microplates to different WAF or WAFD dilutions (0.25, 2.5, 25, 50 and 100%) and to the dispersant alone at the same concentrations present in the WAFD dilutions (1.25, 12.5, 125, 250 and 500 mg/L). Of the two in vitro approaches tested, the second one was selected which involved exposure of hemocytes for 4 h to unfiltered WAF, WAFD and dispersant dilutions without cell culture media. WAF decreased hemocytes viability only at the highest dilution whereas WAFD and the dispersant alone were cytotoxic at the three highest concentrations. Temperature of production of WAF, WAFD and dispersant did not influence their cytotoxicity to hemocytes. WAF increased ROS production and MXR transport activity in hemocytes. Exposure to WAFD and dispersant increased ROS production, provoked plasma membrane and actin cytoskeleton disruption and decreased phagocytic activity. In conclusion, the dispersant tested was toxic to mussel hemocytes and it greatly increased the toxicity of WAFD. The present data could be useful for the environmental risk assessment of oil spills and their remediation strategies in the marine environment.