Using RNAseq for identifying hepatic genes involved in multi- (F1 generation) and transgenerational (F2 generation) responses to chronic benzo[a]pyrene exposure (F0 generation) in Xenopus tropicalis
Ontology highlight
ABSTRACT:
ORGANISM(S): Xenopus tropicalis
PROVIDER: GSE150911 | GEO | 2021/01/01
REPOSITORIES: GEO
Similar Datasets
Project description:We investigated the multi- and transgenerational impact of BaP and TCS mixture on Xenopus females following F0 generation exposure from the tadpole to the mature adult stage at a concentration (50 ng.L-1 each). 5 females from F1 and F2 generations by parentale exposure conditions (control vs Mixture) were used for studying liver transcriptome by RNAseq. RNA-seq libraries were sequenced on an illumina GAIIx sequencer as 75bp single reads
2021-10-30 | GSE179257 | GEO
Project description:Persistent and ubiquitous organic pollutants, such as the polycyclic aromatic hydrocarbon benzo[⍺]pyrene (BaP), represent a major threat to aquatic organisms and human health. Beside some well-documented adverse effects on the development and reproduction of aquatic organisms, BaP was recently shown to affect fish bone formation and skeletal development through mechanisms that remain poorly understood. In this work, several bone-related in vivo assays were used in zebrafish to evaluate the osteotoxic effects of BaP during bone development and regeneration. Exposure to BaP for 3 days induced a dose-dependent reduction of the size of the opercular bone in 6 days post-fertilization (dpf) larvae, and affected osteoblast maturation as observed by the expression of the mature marker, osteocalcin. Exposure to BaP for 27 days affected the development of the axial skeleton and increased the incidence and severity of skeletal deformities. During bone regeneration, BaP affected the mineralization of newly formed fin rays and scales, while it impaired fin ray patterning and scale shape, through mechanisms that may involve an imbalance of bone remodeling. Transcriptomic and gene expression analyses indicate that BaP induced the activation of xenobiotic and metabolic pathways, while negatively impacting extracellular matrix formation and organization. Interestingly, BaP exposure positively regulated inflammation markers in 6 dpf larvae and increased neutrophil recruitment. A direct interaction between neutrophils and bone extracellular matrix or bone forming cells was observed in vivo, suggesting a role for neutrophils in the mechanisms underlying BaP osteotoxicity. Our work provides novel data on the cellular and molecular players involved in BaP osteotoxicity and brings new insights into a possible role for neutrophils in inflammatory bone reduction.
2024-04-29 | GSE174529 | GEO
Project description:People are exposed to polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP), via inhalation of particulate matter air pollution and ingestion of grilled and smoked foods. Prenatal exposure to BaP destroys germ cells in ovaries, causing earlier onset of ovarian senescence post-natally. Developing testes are affected at higher doses than ovaries. However, it is not known if adverse effects are transmitted to subsequent generations. We orally dosed pregnant female mice (F0) with 0.033, 0.2, or 2 mg/kg-day BaP or vehicle from embryonic day (E) 6.5-11.5 (F1 offspring) or E6.5-15.5 (F2 and F3). Ovarian germ cell and follicle numbers were significantly decreased in F3 females at all doses of BaP; testicular germ cells were not affected. E13.5 germ cell RNA-sequencing revealed significantly increased expression of male-specific genes in female germ cells across generations and BaP doses. Our study demonstrated that F0 BaP exposure partially disrupted sexual identity of female germ cells transgenerationally.
2023-06-07 | GSE213946 | GEO
Project description:People are exposed to polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP), via inhalation of particulate matter air pollution and ingestion of grilled and smoked foods. Prenatal exposure to BaP destroys germ cells in ovaries, causing earlier onset of ovarian senescence post-natally. Developing testes are affected at higher doses than ovaries. However, it is not known if adverse effects are transmitted to subsequent generations. We orally dosed pregnant female mice (F0) with 0.033, 0.2, or 2 mg/kg-day BaP or vehicle from embryonic day (E) 6.5-11.5 (F1 offspring) or E6.5-15.5 (F2 and F3). Ovarian germ cell and follicle numbers were significantly decreased in F3 females at all doses of BaP; testicular germ cells were not affected. E13.5 germ cell RNA-sequencing revealed significantly increased expression of male-specific genes in female germ cells across generations and BaP doses. Our study demonstrated that F0 BaP exposure partially disrupted sexual identity of female germ cells transgenerationally.
2023-06-07 | GSE213945 | GEO
Project description:Purpose: This study aimed to identify differentially expressed genes and transcripts in zebrafish embryos and larvae following benzo[a]pyrene (BaP) exposure. Methods: Adult zebrafish (2 males × 4 females, N=6 replicate tanks for each treatment) were acclimated for 7 days in an 818 Low Temp Illuminated Incubator (Precision Scientific, Chennai, India) at 28.5°C. Next, adult fish were waterborne exposed to control or 50 μg/L (ppb) BaP for 7 days; ethanol was used as vehicle solvent, and final ethanol concentration was 0.1 mL/L (100 ppm) in all treatment groups. This dose of ethanol is not teratogenic to zebrafish. Water was changed and/or re-dosed daily. From day 7 to 11 of the parental exposure, eggs were collected, counted, and raised in normal conditions (control) or continuously exposed to 50 μg/L BaP until 3.3 and 96 hours post fertilization (hpf). At 3.3 or 96 hpf, embryos (200/pool) or larvae (10/pool) were collected and pooled. Total RNA was isolated for transcriptomic RNA sequencing with Illumina HiSeq2000 (2X100bp). RNA-seq reads were uploaded to the galaxy platform https://main.g2.bx.psu.edu/. RNA-seq reads were trimmed, filtered, and aligned to the zebrafish genome (Danio_rerio.Zv9.68) with the Tophat for Illumina tool. Counting and annotation of RNA-seq reads were performed with Partek Genomics Suite version 6.11. Refseq Transcripts (2013-04-10) and Ensembl Transcripts release 70 databases were used for gene and transcript annotation. Differential expression of gene and transcript reads between treatments was analyzed with R package EdgeR. Genes/transcripts with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Differentially expressed genes were defined as genes with altered expression at either gene or transcript level. Results: Differential expression analysis with EdgeR revealed that gene expression was vastly different between 3.3 hpf zebrafish embryos and 96 hpf larvae. Using Refseq annotation, we found that 10644 out of 13950 transcribed zebrafish genes were differentially expressed between the two developmental time-points, with 5961 up-regulated genes and 4683 down-regulated genes in 96 hpf larvae compared with 3.3 hpf embryos. Similarly, using Ensembl annotation, 16529 out of 19886 transcribed zebrafish genes were differentially expressed, with 9318 up-regulated genes and 7211 down-regulated genes in 96 hpf larvae compared with 3.3 hpf embryos. In 3.3 hpf embryos, four genes and seven transcripts were differentially expressed after BaP exposure. In 96 hpf larvae, 447 and 484 zebrafish genes were significantly up- and down-regulated, respectively, by BaP exposure. Conclusions: Parental and developmental BaP exposure caused gene expression changes in zebrafish embryos and larvae. Illumina HiSeq2000 deep sequencing was used to generate transcriptomic profiles for BaP-exposed 3.3 hpf zebrafish embryos (n=3 for control, n=3 for BaP) and 96 hpf larvae (n=2 for control, n=2 for BaP).
2015-09-04 | E-GEOD-64198 | biostudies-arrayexpress
Project description:People are exposed to polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP), via inhalation of particulate matter air pollution and ingestion of grilled and smoked foods. Prenatal exposure to BaP destroys germ cells in ovaries, causing earlier onset of ovarian senescence post-natally. Developing testes are affected at higher doses than ovaries. However, it is not known if adverse effects are transmitted to subsequent generations. We orally dosed pregnant female mice (F0) with 0.033, 0.2, or 2 mg/kg-day BaP or vehicle from embryonic day (E) 6.5-11.5 (F1 offspring) or E6.5-15.5 (F2 and F3). Ovarian germ cell and follicle numbers were significantly decreased in F3 females at all doses of BaP; testicular germ cells were not affected. E13.5 germ cell RNA-sequencing revealed significantly increased expression of male-specific genes in female germ cells across generations and BaP doses. Our study demonstrated that F0 BaP exposure partially disrupted sexual identity of female germ cells transgenerationally.
2023-06-07 | GSE230356 | GEO
Project description:People are exposed to polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP), via inhalation of particulate matter air pollution and ingestion of grilled and smoked foods. Prenatal exposure to BaP destroys germ cells in ovaries, causing earlier onset of ovarian senescence post-natally. Developing testes are affected at higher doses than ovaries. However, it is not known if adverse effects are transmitted to subsequent generations. We orally dosed pregnant female mice (F0) with 0.033, 0.2, or 2 mg/kg-day BaP or vehicle from embryonic day (E) 6.5-11.5 (F1 offspring) or E6.5-15.5 (F2 and F3). Ovarian germ cell and follicle numbers were significantly decreased in F3 females at all doses of BaP; testicular germ cells were not affected. E13.5 germ cell RNA-sequencing revealed significantly increased expression of male-specific genes in female germ cells across generations and BaP doses. Our study demonstrated that F0 BaP exposure partially disrupted sexual identity of female germ cells transgenerationally.
2023-06-07 | GSE213812 | GEO
Project description:Purpose: This study aimed to identify differentially expressed genes and transcripts in zebrafish embryos and larvae following benzo[a]pyrene (BaP) exposure. Methods: Adult zebrafish (2 males × 4 females, N=6 replicate tanks for each treatment) were acclimated for 7 days in an 818 Low Temp Illuminated Incubator (Precision Scientific, Chennai, India) at 28.5°C. Next, adult fish were waterborne exposed to control or 50 μg/L (ppb) BaP for 7 days; ethanol was used as vehicle solvent, and final ethanol concentration was 0.1 mL/L (100 ppm) in all treatment groups. This dose of ethanol is not teratogenic to zebrafish. Water was changed and/or re-dosed daily. From day 7 to 11 of the parental exposure, eggs were collected, counted, and raised in normal conditions (control) or continuously exposed to 50 μg/L BaP until 3.3 and 96 hours post fertilization (hpf). At 3.3 or 96 hpf, embryos (200/pool) or larvae (10/pool) were collected and pooled. Total RNA was isolated for transcriptomic RNA sequencing with Illumina HiSeq2000 (2X100bp). RNA-seq reads were uploaded to the galaxy platform https://main.g2.bx.psu.edu/. RNA-seq reads were trimmed, filtered, and aligned to the zebrafish genome (Danio_rerio.Zv9.68) with the Tophat for Illumina tool. Counting and annotation of RNA-seq reads were performed with Partek Genomics Suite version 6.11. Refseq Transcripts (2013-04-10) and Ensembl Transcripts release 70 databases were used for gene and transcript annotation. Differential expression of gene and transcript reads between treatments was analyzed with R package EdgeR. Genes/transcripts with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Differentially expressed genes were defined as genes with altered expression at either gene or transcript level. Results: Differential expression analysis with EdgeR revealed that gene expression was vastly different between 3.3 hpf zebrafish embryos and 96 hpf larvae. Using Refseq annotation, we found that 10644 out of 13950 transcribed zebrafish genes were differentially expressed between the two developmental time-points, with 5961 up-regulated genes and 4683 down-regulated genes in 96 hpf larvae compared with 3.3 hpf embryos. Similarly, using Ensembl annotation, 16529 out of 19886 transcribed zebrafish genes were differentially expressed, with 9318 up-regulated genes and 7211 down-regulated genes in 96 hpf larvae compared with 3.3 hpf embryos. In 3.3 hpf embryos, four genes and seven transcripts were differentially expressed after BaP exposure. In 96 hpf larvae, 447 and 484 zebrafish genes were significantly up- and down-regulated, respectively, by BaP exposure. Conclusions: Parental and developmental BaP exposure caused gene expression changes in zebrafish embryos and larvae.
2015-09-04 | GSE64198 | GEO
Project description:Benzo[a]pyrene (BaP) is a product of combustion and is an abundant constituent of wildfire derived smoke and particulate matter 2.5 (PM2.5). Although arrythmias are associated with wildfire, the mechanism remains unclear. We hypothesized that BaP might predispose individuals to arrhythmias and possibly sudden cardiac death. Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) from healthy donors (n=3) were used to investigate the cardiovascular toxicity of BaP. Across a broad concentration range, BaP did not affect iPSC-CM viability, and a 4-day exposure of BaP at 50 M did not affect contractility. After exposure to BaP at 50 M for 5 days, iPSC-CMs were subjected to bulk RNA sequencing, and analysis revealed markers of inflammation were upregulated, and ion channel expression was modulated. Because inflammation is associated with reactive oxygen species (ROS) production, iPSC-CMs exposed to BaP had a concentration-dependent increase in ROS production. Mitotracker fluorescent imaging revealed decreased mitochondrial membrane potentials after iPSC-CMs treatment with 50 μM BaP. Seahorse assays revealed that BaP exposure decreased oxygen consumption rate, basal respiration, and maximal respiration in a dose-dependent manner. Using multiple electrode array (MEA) assays, iPSC-CMs exposed to 50 M BaP for 3 days, had prolonged field potential duration (FPD) and increased beat period (BP). However, co-treatment with N-acetyl cysteine (NAC), a nucleophile that scavenges ROS and preserves glutathione, attenuated the effect of BaP on FPD and BP (p<0.001). In summary, BaP exposure upregulated inflammatory cytokines and increased ROS production by impairing mitochondrial function. BaP had proarrhythmic effects of increased BP and FPD and was abrogated by NAC. Thus, BaP inhalation from wildfire smoke may predispose individuals to QT prolongation, arrhythmia, and sudden cardiac death.
2024-08-25 | GSE244567 | GEO
Project description:Polycyclic aromatic hydrocarbons (PAHs) are abundant organic compounds and are anthropogenically produced by the incomplete combustion of organic matter (e.g. fossil fuels and tobacco smoke). One notable model PAH is benzo[a]pyrene (BaP), which is listed as a Group 1 human carcinogen by the International Agency of Research on Cancer (IARC). Although the mode of action for BaP is well known in higher organisms, limited knowledge is available regarding the consequence of BaP exposure in the model organism Caenorhabditis elegans. The objective of this study was to define the the global transcriptome of wild-type C. elegans exposed to BaP (0, 5 and 20 μM). The most responsive transcripts were linked to redox processes and xenobiotic responses, including P450 enzymes (CYPs) (mainly members of the CYP35 family), epoxide hydrolases (EHs), glutathione S-transferases (GSTs), and UDP-glucuronosyltransferases (UGTs), all of which are linked to the metabolism (phase I & II) of xenobiotic substances. In summary, although the dominant CYP1A1/2 & CYP1B1 metabolic pathway is absent in C. elegans, BaP still induced a strong transcriptomic response. This provides strong evidence that parallel pathway(s) are implicated in BaP metabolism, and possibly, in its detoxification.
2021-03-03 | GSE152257 | GEO