Hypoxia causes sex-specific hepatic toxicity at the transcriptome level in marine medaka (Oryzias melastigma)

Multi-omics analysis identifies sex-specific hepatic protein-metabolite networks in yellow catfish (Pelteobagrus fulvidraco) exposed to chronic hypoxia

Hypoxia disrupts the endocrine system of teleosts. The liver plays important roles in the endocrine system, energy storage, and metabolic processes. The aim of this study was to investigate the sex-specific hepatic response of yellow catfish under chronic hypoxia at the multi-omics level. Common hepatic responses in both sexes included the HIF-1 signaling pathway, glycolysis/gluconeogenesis, and steroid biosynthesis. Hypoxia dysregulated primary bile acid biosynthesis, lipid metabolism, and vitellogenin levels in female fish. Endoplasmic reticulum function in females also tended to be disrupted by hypoxia, as evidenced by significantly enriched pathways, including ribosome, protein processing in the endoplasmic reticulum, and RNA degradation. Other pathways, including the TCA cycle, oxidative phosphorylation, and Parkinson's and Huntington's disease, were highly enriched by hypoxia in male fish, suggesting that mitochondrial function was dysregulated. In both sexes of yellow catfish, the cell cycle was arrested and apoptosis was inhibited under chronic hypoxia. Multi-omics suggested that SLC2A5, CD209, LGMN, and NEDD8 served as sex-specific markers in these fish under chronic hypoxia. Our results provide insights into hepatic adaptation to chronic hypoxia and facilitate our understanding of sex-specific responses in fish.

Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.

New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data

International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH ) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.

Effects of lipophilic phycotoxin okadaic acid on the early development and transcriptional expression of marine medaka Oryzias melastigma

The lipophilic okadaic acid (OA)-group toxins produced by some species of Dinophysis spp. and Prorocentrum spp. marine dinoflagellates have been frequently and widely detected in natural seawater environments, e.g. 2.1∼1780 ng/L in Spanish sea and 5.63∼27.29 ng/L in the Yellow Sea of China. The toxicological effects of these toxins dissolved in seawater on marine fish is still unclear. Effects of OA on the embryonic development and 1-month old larvae of marine medaka (Oryzias melastigma) were explored and discussed in this study. Significantly increased mortality and decreased hatching rates occurred for the medaka embryos exposed to OA at 1.0 μg/mL. Diverse malformations including spinal curvature, dysplasia and tail curvature were also observed in the embryos exposed to OA and the heart rates significantly increased at 11 d post fertilization. The 96 h LC₅₀ of OA for 1-month old larvae was calculated at 3.80 μg/mL. The reactive oxygen species (ROS) was significantly accumulated in medaka larvae. Catalase (CAT) enzyme activity was significantly increased in 1-month old larvae. Acetylcholinesterase (AChE) activity significantly increased with a dose-dependent pattern in 1-month old larvae. Differentially expressed genes (DEGs) were enriched in 11 KEGG pathways with Q value < 0.05 in 1-month old medaka larvae exposed to OA at 0.38 μg/mL for 96 h, which were mainly related to cell division and proliferation, and nervous system. Most of DEGs involved in DNA replication, cell cycle, nucleotide excision repair, oocyte meiosis, and mismatch repair pathways were significantly up-regulated, while most of DEGs involved in synaptic vesicle cycle, glutamatergic synapse, and long-term potentiation pathways were markedly down-regulated. This transcriptome analysis demonstrated that a risk of cancer developing was possibly caused by OA due to DNA damage in marine medaka larvae. In addition, the neurotoxicity of OA was also testified for marine fish, which potentially cause major depressive disorder (MDD) via the up-regulated expression of NOS1 gene. The genotoxicity and neurotoxicity of OA to marine fish should be paid attention to and explored further in the future.

The effects of sustained and diel-cycling hypoxia on high-latitude fish Phoxinus lagowskii

High-latitude fish are subjected to sustained and diel-cycling hypoxia. Oxygen deficiency could pose a serious threat to fish, but little information is available regarding the response mechanisms employed by high-latitude fish to sustained and diel-cycling hypoxia. In this study, a combination of transcriptomics and metabolomics were used to examine the molecular response mechanisms actioned by sustained and diel-cycling hypoxia in the high-latitude fish, Phoxinus lagowskii. P. lagowskii was divided into normoxic control (6.0-7.0 mg/L dissolved oxygen), sustained (1.5 mg/L dissolved oxygen), and diel-cycling hypoxic treatment (6.0-7.0 mg/L between 07:00-21:00, and 3.0-4.0 mg/L between 21:00-07:00) tanks for 28 days. Differentially expressed genes (DEGs) and significantly different metabolites (DMs) related to digestive proteases, lipid metabolism, estrogen signaling pathway, steroid hormone biosynthesis, glutathione metabolism, and tryptophan metabolism were identified from comparative metabolomic and transcriptomic data expression profiles within the liver. The current study found that P. lagowskii had significantly different responses between sustained and diel-cycling hypoxia. P. lagowskii faced with sustained hypoxia may enhance their tolerance capacity through phospholipid and glutathione metabolism. Our data provide new insights into the high latitude fish coping with changes in hypoxia and warrants further investigation into these potentially important genes and metabolites.

Dysfunction of liver-gut axis in marine medaka exposed to hypoxia and perfluorobutanesulfonate

With objectives to explore the interactive mode on the function of liver-gut axis, adult marine medaka were exposed for 7 days to environmentally realistic concentrations of perfluorobutanesulfonate (PFBS) (0 and 10 μg/L) under normoxia or hypoxia condition. Furthermore, PFBS exposure was extended to 21 days to reveal the temporal progression in toxicity. The results showed that hypoxia exposure significantly disturbed lipid metabolism, caused oxidative damage, and induced inflammation in the livers of medaka. The composition of gut microbiota was also drastically shifted by hypoxia acute exposure. In contrast, the effect of PFBS was much milder. Hypoxia was thus the determinant of the combined toxicity. Depending on the exposure duration, a time-course recovery from PFBS innate toxicity was generally noted. Overall, the present study underlines the hypoxic and temporal variation in the dysregulation of liver-gut axis by PFBS, which is expected to support a comprehensive ecological risk assessment.

Dissolved oxygen gradient on three dimensionally printed microfluidic platform for studying its effect on fish at three levels: cell, embryo, and larva

A simple and low-cost dissolved oxygen gradient platform of three dimensionally (3D) printed microfluidic chip was developed for cultivating cells, embryos, and larvae of fish. "Christmas tree" structure channel networks generated a dissolved oxygen gradient out of two fluids fed to the device. Polydimethylsiloxane (PDMS) membrane with high biocompatibility was used as the substrate for cell culture in the 3D-printed microfluidic chip, which made the cell analysis easy. The embryos and larvae of fish could be cultured directly in the chip, and their development can be observed in real time with a microscope. Using zebrafish as a model, we assessed the effect of different dissolved oxygen on its cells, embryos, and larvae. Hypoxia induced production of reactive oxygen species (ROS) in zebrafish cells, embryos, and larvae, eventually leading to cell apoptosis and developmental impairment. Hypoxia also increased nitric oxide content in zebrafish cells, which might be a defensive strategy to overcome the adverse effect of hypoxia in fish cells. This is the first platform that could comprehensively investigate the effects of different dissolved oxygen on fish at the cell, embryo, and larva levels, which has great potential in studying the responses of aquatic organisms under different oxygen concentrations.

Multi-omics responses in tree swallow (Tachycineta bicolor) nestlings from the Maumee Area of Concern, Maumee River, Ohio

A multi-omics approach was utilized to identify altered biological responses and functions, and to prioritize contaminants to assess the risks of chemical mixtures in the Maumee Area of Concern (AOC), Maumee River, OH, USA. The Maumee AOC is designated by the United States Environmental Protection Agency as having significant beneficial use impairments, including degradation of fish and wildlife populations, bird or animal deformities or reproduction problems, and loss of fish and wildlife habitat. Tree swallow (Tachycineta bicolor) nestlings were collected at five sites along the Maumee River, which included wastewater treatment plants (WWTPs) and industrial land-use sites. Polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo p dioxins and furans (PCDD/Fs), and chlorinated pesticide concentrations were elevated in Maumee tree swallows, relative to a remote reference site, Star Lake, WI, USA. Liver tissue was utilized for non-targeted transcriptome and targeted metabolome evaluation. A significantly differentially expressed gene cluster related to a downregulation in cell growth and cell cycle regulation was identified when comparing all Maumee River sites with the reference site. There was an upregulation of lipogenesis genes, such as PPAR signaling (HMGCS2, SLC22A5), biosynthesis of unsaturated fatty acids (FASN, SCD, ELOVL2, and FADS2), and higher lipogenesis related metabolites, such as docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (AA) at two industrial land-use sites, Ironhead and Maumee, relative to WWTP sites (Perrysburg and SideCut), and the reference site. Toledo Water, in the vicinity of the other two industrial sites and also adjacent to a WWTP, showed a mix of signals between industrial land-use and WWTP land-use. PAHs, oxychlordane, and PBDEs were determined to be the most likely causes of the differentiation in biological responses, including de novo lipogenesis and biosynthesis of unsaturated fatty acids.

Distinct metabolic shifts occur during the transition between normoxia and hypoxia in the hybrid and its maternal abalone

Due to anthropogenic activities that have increased global climate change and nutrient discharges, severe hypoxic events have frequently occurred in coastal waters in recent years. Relying on coastal waters, the aquaculture area has suffered ecological and economic losses caused by hypoxia, especially in summer. In this study, to investigate the stress resistance of the Pacific abalone Haliotis discus hannai (DD) and the hybrid H. discus hannai ♀ × H. fulgens ♂ (DF), a combination of physiological, biochemical, and metabolomic methods were used to compare the metabolic responses of these two abalones to acute hypoxia (~0.5 mg O₂/L, 12 h) and reoxygenation (~6.6 mg O₂/L, 10-20 h). Hemolymph characteristics and aerobic/anaerobic respiratory capacity changed significantly under hypoxia or reoxygenation conditions, and they were regulated in different trends in two abalones. The contents of hepatopancreas glycogen in two abalones reached the trough after 10 h recovery, implying that short-term hypoxia leads to a long-lasting (several hours) imprint on the energy storage of abalone. In response to dissolved oxygen fluctuation, metabolic profiles of two abalones changed in distinct ways both in the hypoxia group or the reoxygenation group. The conversion of carbohydrate metabolism and amino acid metabolism indicated that hypoxia prompts abalone to change the way of energy metabolism, which may also reflect the difference in the energy utilization of DD and DF abalones. In addition, 3 metabolites (L-glutamate, 2-hydroxy-butanoic acid, and 2-methyl-3-hydroxybutyric acid) as potential biomarkers for hypoxia and reoxygenation response in abalone were determined by operating characteristic analysis (ROC). Overall, this study provides information towards understanding the damage caused by frequent hypoxic events and implies the metabolic shifts that occur under hypoxia and reoxygenation conditions in DD and DF abalones.

Transcriptome analysis reveals that high temperatures alter modes of lipid metabolism in juvenile turbot (Scophthalmus maximus) liver

With the increase in farming density and the continuously high summer temperatures against the background of global warming, high temperature stress has become a major challenge in fish farming. In this study, we simulated the high temperature environments (20 °C, 24 °C, and 28 °C) that may occur during turbot culture. High-throughput sequencing was used to investigate the lipid metabolism response patterns in juvenile turbot liver under high temperature stress. A total of 2067 differentially expressed genes (DEGs) were identified. KEGG analysis revealed that the DEGs were mainly associated with glycerophospholipid metabolism, steroid biosynthesis, glycerolipid metabolism, fatty acid metabolic pathways, and the PPAR signaling pathway. A regulatory network was constructed to further elucidate the transcriptional regulation of lipid metabolism. We speculated that high temperature activates PPAR signaling pathway through interaction with ligands such as fatty acids. On the one hand, the HMGCS1 gene in this pathway can inhibit sterol synthesis by down-regulating the expression of key genes in steroid biosynthesis pathway (SQLE, EBP, and DHCR24). On the other hand, the expression of ACSL1 in this pathway is significantly increased under high temperature, which may play an important role in regulating fatty acid metabolism. Moreover, we collected blood and detected changes in serum lipid parameters; the variation patterns were also consistent with our results. These findings reveal that lipid metabolism has an important regulatory role in stress resistance when turbot is exposed to high temperatures.

Hypoxia-induced miR-92a regulates p53 signaling pathway and apoptosis by targeting calcium-sensing receptor in genetically improved farmed tilapia (Oreochromis niloticus)

miR-92a miRNAs are immune molecules that regulate apoptosis (programmed cell death) during the immune response. Apoptosis helps to maintain the dynamic balance in tissues of fish under hypoxia stress. The aim of this study was to explore the role and potential mechanisms of miR-92a in the liver of tilapia under hypoxia stress. We first confirmed that CaSR (encoding a calcium-sensing receptor) is a target gene of miR-92a in genetically improved farmed tilapia (GIFT) using luciferase reporter gene assays. In GIFT under hypoxia stress, miR-92a was up-regulated and CaSR was down-regulated in a time-dependent manner. Knocked-down CaSR expression led to inhibited expression of p53, TP53INP1, and caspase-3/8, reduced the proportion of apoptotic hepatocytes, and decreased the activity of calcium ions induced by hypoxia in hepatocytes. GIFT injected in the tail vein with an miR-92a agomir showed up-regulation of miR-92a and down-regulation of CaSR, p53, TP53INP1, and caspase-3/8 genes in the liver, resulting in lower serum aspartate aminotransferase and alanine aminotransferase activities under hypoxia stress. These findings suggest that stimulation of miR-92a interferes with hypoxia-induced apoptosis in hepatocytes of GIFT by targeting CaSR, thereby alleviating liver damage. These results provide new insights into the adaptation mechanisms of GIFT to hypoxia stress.