Transcriptome analysis reveals the mechanism of common carp brain injury after exposure to lead

Zhang, Yue; Zhang, Peijun; Yu, Peng; Shang, Xinchi; Lu, Yuting; Li, Yuehong

doi:10.1016/j.scitotenv.2020.140796

Cited by 18 publications

(8 citation statements)

References 35 publications

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“…Pathway annotations of DEGs were acquired using the KEGG database. GO enrichment analysis of DEGs was evaluated using the GOseq R package (Release 2.12) 58 . We used KOBAS v2.0 software to test the statistical enrichment of DEGs in KEGG pathway analysis 59 .…”

Section: Methodsmentioning

confidence: 99%

“…Thermal cycling was performed at 95 °C for 10 s, followed by 40 cycles at 95 °C for 5 s, and 60 °C for 20 s. Melting curve analyses was used to judge the specificity of the primers. The relative expression ratio of target genes versus β-actin was calculated using the 2 −∆∆Ct method 58 . Relative mRNA expression levels were statistically analyzed using SPSS 22.0 software.…”

Section: Methodsmentioning

confidence: 99%

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Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Huang

et al. 2022

Sci Rep

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Yellow mutant rainbow trout (YR), an economically important aquaculture species, is popular among consumers due to its excellent meat quality and attractive appearance. Skin color is a key economic trait for YR, but little is known about the molecular mechanism of skin color development. In this study, YR skin transcriptomes were analyzed to explore temporal expression patterns of pigmentation-related genes in three different stages of skin color development. In total, 16,590, 16,682, and 5619 genes were differentially expressed between fish at 1 day post-hatching (YR1d) and YR45d, YR1d and YR90d, and YR45d and YR90d. Numerous differentially expressed genes (DEGs) associated with pigmentation were identified, and almost all of them involved in pteridine and carotenoid synthesis were significantly upregulated in YR45d and YR90d compared to YR1d, including GCH1, PTS, QDPR, CSFIR1, SLC2A11, SCARB1, DGAT2, PNPLA2, APOD, and BCO2. Interestingly, many DEGs enriched in melanin synthesis pathways were also significantly upregulated, including melanogenesis (MITF, MC1R, SLC45A2, OCA2, and GPR143), tyrosine metabolism (TYR, TYRP1, and DCT), and MAPK signaling (KITA) pathways. Using short time-series expression miner, we identified eight differential gene expression pattern profiles, and DEGs in profile 7 were associated with skin pigmentation. Protein–protein interaction network analysis showed that two modules were related to xanthophores and melanophores. In addition, 1,812,329 simple sequence repeats and 2,011,334 single-nucleotide polymorphisms were discovered. The results enhance our understanding of the molecular mechanism underlying skin pigmentation in YR, and could accelerate the molecular breeding of fish species with valuable skin color traits and will likely be highly informative for developing new therapeutic approaches to treat pigmentation disorders and melanoma.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Huang

et al. 2022

Sci Rep

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“…PCR amplification procedure for all experiments were carried out at 95°C for 30 s, followed by 40 cycles at 95°C for 5 s and 60°C for 30 s. Target specificity was determined by melting curve analysis, and RNA expression levels of target genes versus β-actin or U6 were calculated using the 2 -ΔΔCt method. All results are expressed as means ± SD, and statistical analyses were performed using one-way ANOVA followed by Dunn’s test in SPSS (version 22.0) ( 42 ), and Pearson correlation analysis was used to calculate the correlation value between qRT-PCR and RNA-seq results. All primers are included in Table S1 .…”

Section: Methodsmentioning

confidence: 99%

Integrated Analysis of lncRNA and circRNA Mediated ceRNA Regulatory Networks in Skin Reveals Innate Immunity Differences Between Wild-Type and Yellow Mutant Rainbow Trout (Oncorhynchus mykiss)

Huang

et al. 2022

Front. Immunol.

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Fish skin is a vital immune organ that forms the first protective barrier preventing entry of external pathogens. Rainbow trout is an important aquaculture fish species that is farmed worldwide. However, our knowledge of innate immunity differences between wild-type (WR_S) and yellow mutant rainbow trout (YR_S) remains limited. In this study, we performed whole transcriptome analysis of skin from WR_S and YR_S cultured in a natural flowing water pond. A total of 2448 mRNAs, 1630 lncRNAs, 22 circRNAs and 50 miRNAs were found to be differentially expressed (DE). Among these DEmRNAs, numerous key immune-related genes, including ifih1, dhx58, trim25, atp6v1e1, tap1, tap2, cd209, hsp90a.1, nlrp3, nlrc3, and several other genes associated with metabolism (gstp1, nampt, naprt and cd38) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEmRNAs revealed that many were significantly enriched in innate immune-related GO terms and pathways, including NAD+ADP-ribosyltransferase activity, complement binding, immune response and response to bacterium GO terms, and RIG-I-like receptor signaling, NOD-like receptor signaling and phagosome KEGG pathways. Furthermore, the immune-related competing endogenous RNA networks were constructed, from which we found that lncRNAs MSTRG.11484.2, MSTRG.32014.1 and MSTRG.29012.1 regulated at least three immune-related genes (ifih1, dhx58 and irf3) through PC-5p-43254_34, PC-3p-28352_70 and bta-miR-11987_L-1R-1_1ss8TA, and tap2 was regulated by two circRNAs (circRNA5279 and circRNA5277) by oni-mir-124a-2-p5_1ss13GA. The findings expand our understanding of the innate immune system of rainbow trout, and lay the foundation for further study of immune mechanisms and disease resistance breeding.

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“…In some studies on RNA expression profiles, researchers have used a similarly small number of research samples, and these studies have nevertheless been valuable in giving insight into the mechanism of the disease. [39][40][41] Admittedly, it is difficult to perform any statistical test at n = 3, but the use of model animals should reduce the within-population variation due to their similar genetics and environment which improves the likelihood of achieving statistical power. Nevertheless, we believe that the whole transcriptome data generated in this study provide novel and diverse ideas for future mechanistic explorations.…”

Section: Discussionmentioning

confidence: 99%

“…A larger sample size helps to make the data more consistent with a normal distribution and may therefore be more robust in verifying its results, especially when using t ‐tests. In some studies on RNA expression profiles, researchers have used a similarly small number of research samples, and these studies have nevertheless been valuable in giving insight into the mechanism of the disease 39–41 . Admittedly, it is difficult to perform any statistical test at n = 3, but the use of model animals should reduce the within‐population variation due to their similar genetics and environment which improves the likelihood of achieving statistical power.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic analysis of bladder tissue in a rat model of ketamine‐induced bladder fibrosis

Zhu

et al. 2022

Neurourology and Urodynamics

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Introduction Ketamine‐induced cystitis (KIC) is a disease caused by ketamine that can cause lower urinary tract symptoms (LUTS). Its end‐stage is bladder contracture, which is related to bladder fibrosis and poses a serious burden to patient lives. Methods We established a KIC model in female Sprague Dawley rats and verified bladder fibrosis in the model by Masson trichrome staining and western blot analysis. The bladders of the rats from the ketamine and control groups were used to perform transcriptome analysis. In particular, association analysis with metabolomics was also used to determine the potential mechanisms of ketamine‐induced bladder fibrosis. Results A total of 685 differentially expressed messenger RNAs, 71 differentially expressed long noncoding RNAs, 23 differentially expressed microRNAs, and 68 differentially expressed circular RNAs were identified. We found that ribosome, Wnt signaling, vascular endothelial growth factor signaling, cytoskeleton organization, and cytoskeletal protein binding may be potential pathways in ketamine‐induced bladder fibrosis as identified by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. In addition, the mitogen‐activated protein kinase pathway appeared to be closely related to the development of ketamine‐induced bladder fibrosis according to association analysis. Conclusions In this study, using transcriptomic and correlation analyses of metabolomics, we identified pathways that may be potential targets for the prevention and treatment of ketamine‐induced bladder fibrosis.

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Transcriptome analysis reveals the mechanism of common carp brain injury after exposure to lead

Cited by 18 publications

References 35 publications

Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Integrated Analysis of lncRNA and circRNA Mediated ceRNA Regulatory Networks in Skin Reveals Innate Immunity Differences Between Wild-Type and Yellow Mutant Rainbow Trout (Oncorhynchus mykiss)

Transcriptomic analysis of bladder tissue in a rat model of ketamine‐induced bladder fibrosis

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