RNA seq- and DEG-based comparison of developmental toxicity in fish embryos of two species exposed to Iranian heavy crude oil

Water-accommodated fractions of crude oil and its mixture with chemical dispersant impairs oxidase stress and energy metabolism disorders in Oryzias melastigma embryos

In this study, marine medaka (Oryzias melastigma) embryos were exposed to different concentrations of water-accommodated fractions (WAFs) and chemically enhanced water-accommodated fractions (CEWAFs) of Oman crude oil for 14 d by semi-static exposure methods. The effects on growth and development and energy metabolism process were evaluated. Results showed that embryo survival and hatchability were decreased in a dose-dependent manner with an increase in the concentration of petroleum hydrocarbon compounds, whereas the malformation exhibited a dose-dependent increase. Compared to the control, the adenosine triphosphate (ATP) content and Na+-K+-ATPase (NKA) activities of embryos exposed to both WAFs and CEWAFs were reduced, while intracellular reactive oxygen species (ROS) levels and NADH oxidase (NOX) activities were increased. Our study demonstrated that exposure to crude oil dispersed by chemical dispersant affected the growth and development of marine medaka embryos, caused oxidative stress while produced a series of malformations in the body and dysregulation in energy metabolism. In comparison, the toxic effects of chemically dispersed crude oil might be more severe than the oil itself in the equivalent diluted concentration treatment solution. These would provide more valuable and reliable reference data for the use of chemical dispersants in oil spills.

Predicting novel biomarkers for early diagnosis and dynamic severity monitoring of human ulcerative colitis

Background

Ulcerative colitis is an emerging global health concern that poses a significant threat to human health and can progress to colorectal cancer if not diagnosed and treated promptly. Currently, the biomarkers used clinically for diagnosis and dynamic severity monitoring lack disease specificity.

Methods

Mouse models induced with 2%, 2.5%, and 3% DSS were utilized to simulate human UC with varying severities of inflammation. Transcriptome sequencing technology was employed to identify differentially expressed genes (DEGs) between the control group and each treatment group. Functional enrichment analysis of the KEGG database was performed for shared DEGs among the three treatment groups. DEGs that were significantly and strongly correlated with DSS concentrations were identified using Spearman correlation analysis. Human homologous genes of the interested DEGs were searched in the HomoloGene database, and their regulation patterns in UC patients were validated using the GSE224758 dataset. These genes were then submitted to the DisGeNET database to identify their known associations with human diseases. Online tools, including SignalP 6.0 and DeepTMHMM 1.0, were used to predict signal peptides and transmembrane helices in the amino acid sequences of human genes homologous to the DEGs of interest.

Results

A total of 1,230, 995, and 2,214 DEGs were identified in the 2%, 2.5%, and 3% DSS-induced groups, respectively, with 668 DEGs common across all three groups. These shared DEGs were primarily associated with signaling transport, pathogenesis, and immune response. Through extensive screening, LGI2 and PRSS22 were identified as potentially novel biomarkers with higher specificity and ease of detection for the early diagnosis and dynamic severity monitoring of human UC, respectively.

Conclusion

We have identified two potentially novel biomarkers, LGI2 and PRSS22, which are easy of detection and more specific for human UC. These findings provide new insights into the accurate diagnosis and dynamic monitoring of this persistent disease.

A Comprehensive Bioinformatics Approach to Identify Molecular Signatures and Key Pathways for the Huntington Disease

Huntington disease (HD) is a degenerative brain disease caused by the expansion of CAG (cytosine-adenine-guanine) repeats, which is inherited as a dominant trait and progressively worsens over time possessing threat. Although HD is monogenetic, the specific pathophysiology and biomarkers are yet unknown specifically, also, complex to diagnose at an early stage, and identification is restricted in accuracy and precision. This study combined bioinformatics analysis and network-based system biology approaches to discover the biomarker, pathways, and drug targets related to molecular mechanism of HD etiology. The gene expression profile data sets GSE64810 and GSE95343 were analyzed to predict the molecular markers in HD where 162 mutual differentially expressed genes (DEGs) were detected. Ten hub genes among them (DUSP1, NKX2-5, GLI1, KLF4, SCNN1B, NPHS1, SGK2, PITX2, S100A4, and MSX1) were identified from protein-protein interaction (PPI) network which were mostly expressed as down-regulated. Following that, transcription factors (TFs)-DEGs interactions (FOXC1, GATA2, etc), TF-microRNA (miRNA) interactions (hsa-miR-340, hsa-miR-34a, etc), protein-drug interactions, and disorders associated with DEGs were predicted. Furthermore, we used gene set enrichment analysis (GSEA) to emphasize relevant gene ontology terms (eg, TF activity, sequence-specific DNA binding) linked to DEGs in HD. Disease interactions revealed the diseases that are linked to HD, and the prospective small drug molecules like cytarabine and arsenite was predicted against HD. This study reveals molecular biomarkers at the RNA and protein levels that may be beneficial to improve the understanding of molecular mechanisms, early diagnosis, as well as prospective pharmacologic targets for designing beneficial HD treatment.

Speciation-specific Cr bioaccumulation, morphologic and transcriptomic response in liver of Plectropomus leopardus exposed to dietary Cr(III) and Cr(VI)

Trivalent chromium (Cr(III)) and hexavalent chromium (Cr(VI)) are the two mainly stable oxidation states of Cr in aquatic environments, while the difference of their bioavailability and toxicity by dietary exposure has been rarely known in aquatic organisms. Using juvenile coral trout (Plectropomus leopardus), Cr(III) and Cr(VI) as model system, this study tested the hypothesis that the dietary Cr bioaccumulation and toxicity in fish were highly dependent on Cr speciation. The fish were chronically exposed to 200 mg kg^-1 of dietary Cr(III) and Cr(VI) for 8 weeks, and then the Cr bioaccumulation, morphologic change, and RNA-Seq in fish liver were determined. The results showed that dietary Cr(III) and Cr(VI) exposure significantly induced fish weight gain, while 1.17 folds and 1.26 folds increased in relation to Control group, respectively. Cr contents in liver was increased significantly in dietary Cr(VI) but not in Cr(III) groups. Both Cr treatment induced lipid deposition in liver tissue structure, moreover, pancreatic part was increased in dietary Cr(III) but its reduced in Cr(VI) exposure. RNA-Seq in fish liver were significantly different as well. Specifically, there were 138 differentially expressed genes (DEGs) in dietary Cr(III) group, including 76 up-regulated and 62 down-regulated, and these DEGs were mainly involved in lipid metabolism, while there were 175 DEGs in dietary Cr(VI) group, including 85 up-regulated and 90 down-regulated, and these DEGs were mainly involved in immune system. The qRT-PCR confirmed the RNA-seq data were reliable. Overall, these results supported our hypothesis that the chronic dietary Cr(III) and Cr(VI) exposure resulted in apparently different Cr bioaccumulation and toxicity in fish. Our findings here help us to fill in a big gap in our knowledge of speciation-specific Cr bioavailability and toxicity in aquatic organisms, which has been largely unclear previously. CAPSULE: Dietary Cr(III) increased lipid metabolism and dietary Cr(VI) activated immune system in liver of coral trout at transcription levels.

Comparative toxicity study of waterborne two booster biocides (CuPT and ZnPT) on embryonic flounder (Paralichthys olivaceus)

A new generation of booster biocides that include metal pyrithiones (PTs) such as copper pyrithione (CuPT) and zinc pyrithione (ZnPT) are being used as tributyltin alternatives. In the marine environment, ZnPT can easily transchelate Cu to form CuPT, and the environmental fate and persistence of these two metal pyrithiones are closely related. Although some data on the toxicity of biocides on marine fish are available, little is known about their toxicity and toxic pathway. We thus compared the toxic effects of CuPT and ZnPT on embryonic olive flounder (Paralichthys olivaceus) by investigating their adverse effects based on developmental morphogenesis and transcriptional variation. In our study, the toxic potency of CuPT was greater with respect to developmental malformation and mortality than ZnPT. Consistent with the developmental effects, the expression of genes related to tail fin malformation (including plod2, furin, and wnt3a) was higher in embryonic flounder exposed to CuPT than in those exposed to ZnPT. Genes related to muscle and nervous system development exhibited significant changes on differential gene expression profiles using RNA sequencing (cutoff value P < 0.05). Gene ontology analysis of embryos exposed to CuPT revealed affected cellular respiration and kidney development, whereas genes associated with cell development, nervous system development and heart development showed significant variation in embryonic flounder exposed to ZnPT. Overall, our study clarifies the common and unique developmental toxic effects of CuPT and ZnPT through transcriptomic analyses in embryonic flounder.

Phenotypic and transcriptomic consequences in zebrafish early-life stages following exposure to crude oil and chemical dispersant at sublethal concentrations

To further understand the underlying mechanisms involved in the developmental toxicity of crude oil and chemically dispersed crude oil on fish early-life stages (ELS), zebrafish (Danio rerio) embryos were exposed to GM-2 chemical dispersant (DISP), low-energy water-accommodated fractions (LEWAF), and chemically enhanced WAF (CEWAF) of Merey crude oil at sublethal concentrations for 120 h. We employed the General Morphology Score (GMS) and General Teratogenic Score (GTS) systems in conjunction with high-throughput RNA-Seq analysis to evaluate the phenotypic and transcriptomic responses in zebrafish ELS. Results showed that ΣPAHs concentrations in LEWAF and CEWAF solutions were 507.63 ± 80.95 ng·L^-1 and 4039.51 ± 241.26 ng·L^-1, respectively. The GMS and GTS values indicated that CEWAF exposure caused more severe developmental delay and higher frequencies of teratogenic effects than LEWAF exposure. Moreover, no significant change in heart rate was observed in LEWAF treatment, while CEWAF exposure caused a significant reduction in heart rate. LEWAF and CEWAF exposure exhibited an overt change in eye area, with a reduction of 4.0% and 25.3% (relative to the control), respectively. Additionally, no obvious impact on phenotypic development was observed in zebrafish embryo-larvae following DISP exposure. Significant changes in gene expression were detected in LEWAF and CEWAF treatments, with a total of 957 and 2062 differentially expressed genes (DEGs), respectively, while DISP exposure altered only 91 DEGs. Functional enrichment analysis revealed that LEWAF and CEWAF exposure caused significant perturbations in the pathways associated with phototransduction, retinol metabolism, metabolism of xenobiotics by cytochrome P450, and immune response-related pathways. Our results provide more valid evidence to corroborate the previous suggestion that ocular impairment is an equal or possibly more sensitive biomarker than cardiotoxicity in fish ELS exposed to oil-derived PAHs. All these findings could gain further mechanistic insights into the effects of crude oil and chemical dispersant on fish ELS.

Activation of the nucleotide excision repair pathway by crude oil exposure: A translational study from model organisms to the Hebei Spirit Oil Spill Cohort

In order to gain insight into the human health implications of the Hebei Spirit Oil Spill (HSOS), the mechanism of toxicity of the Iranian heavy crude (IHC), the main oil component in the HSOS was investigated in Caenorhabditis elegans and zebrafish. The identified mechanism was translated to humans using blood samples from Taean residents, who experienced HSOS with different levels of exposure to the spill. C. elegans TF RNAi screening with IHC oil revealed the nucleotide excision repair (NER) pathway as being significantly involved by oil exposure. To identify the main toxicity contributors within the chemical mixture of the crude oil, further studies were conducted on C. elegans by exposure to C3-naphthalene, an alkylated polycyclic aromatic hydrocarbon (PAH), which constitutes one of the major components of IHC oil. Increased expression of NER pathway genes was observed following exposure to the IHC oil, C3-naphthalene enriched fraction and C3-naphthalene. As the NER pathway is conserved in fish and humans, the same experiment was conducted in zebrafish, and the data were similar to what was seen in C. elegans. Increased expression of NER pathway genes was observed in human samples from the high exposure group, which suggests the involvement of the NER pathway in IHC oil exposure. Overall, the study suggests that IHC oil may cause bulk damage to DNA and activation of the NER system and Alkylated PAHs are the major contributor to DNA damage. Our study provides an innovative approach for studying translational toxicity testing from model organisms to human health.

Cellular, humoral and molecular responses in rainbow trout (Oncorhynchus mykiss) exposed to a herbicide and subsequently infected with infectious hematopoietic necrosis virus

Aquatic ecosystems are now chronically polluted by a cocktail of many chemical substances. There is now clear evidence of associations between exposure to pollutants and greater susceptibility to pathogens. The aim of the present study was to characterize the defense capacities of rainbow trout (Oncorhynchus mykiss), chronically exposed to pendimethalin (PD), to subsequent experimental challenge with the infectious hematopoietic necrosis virus (IHNV). Immunological responses were examined at different organizational levels, from individuals to gene expression. No negative effects of PD were noted on the Fulton index nor on the liver or spleen somatic indices (LSI; SSI) before viral infection, but the infectious stress seems to generate a weak but significant decrease in Fulton and LSI values, which could be associated with consumption of energy reserves. During the viral challenges, the distribution of cumulative mortality was slightly different between infected groups. The impact of the virus on fish previously contaminated by PD started earlier and lasted longer than controls. The proportion of seropositive fish was lower in the fish group exposed to PD than in the control group, with similar quantities of anti-IHNV antibodies secreted in positive fish, regardless of the treatment. While no significant differences in C3-1 expression levels were detected throughout the experiment, TNF1&2, TLR3, Il-1β and IFN expression levels were increased in all infected fish, but the difference was more significant in fish groups previously exposed to herbicide. On the other hand, β-def expression was decreased in the pendimethalin-IHNV group compared to that in fish only infected by the virus (control-IHNV group).