Label-free quantification of protein expression in the rainbow trout (Oncorhynchus mykiss) in response to short-term exposure to heat stress

High-temperature stress response: Insights into the molecular regulation of American shad (Alosa sapidissima) using a multi-omics approach

High temperature is an important abiotic stressor that limits the survival and growth of aquatic organisms. American shad (Alosa sapidissima), a migratory fish suitable for culturing at low temperatures, is known for its delicious taste and thus has high economic value. Studies concerning changes in A. sapidissima under high temperature are limited, especially at the gene expression and protein levels. High-temperature stress significantly reduced the survival rates and increased vacuolar degeneration and inflammatory infiltration in the gills and liver. High temperature increased the activities of SOD, CAT, and cortisol, with a trend of initial increase followed by decreases in MDA, ALP, and LDH, and irregular changes in T-AOC and Na-K-ATPase. Comprehensive analysis of the transcriptome, proteome, and metabolome of gills from fish treated with different culture temperatures (24, 27, and 30 °C) revealed that differentially expressed genes, proteins, and metabolites were highly enriched in pathways involved in protein digestion and absorption, protein processing in endoplasmic reticulum, metabolic pathways, and purine metabolism. Gene expression and protein profiles indicated that genes coding for antioxidants (i.e., cat and alpl) and members of the heat shock protein (i.e., HSP70, HSP90AA1, and HSP5) were significantly upregulated. Additionally, a conjoint analysis revealed that several key enzymes, including nucleoside diphosphate kinase 2, adenosine deaminase, and ectonucleoside triphosphate diphosphohydrolase 5/6 were altered, thereby affecting the metabolism of guanosine, guanine, and inosine. An interaction network further confirmed that levels of the essential amino acids DL-arginine and L-histidine were significantly reduced, and corticosterone levels were significantly increased, suggesting that A. sapidissima may be more dependent on amino acids for energy in vivo. Overall, this work suggests that living in a high-temperature environment leads to differential defense responses in fishes. The results provide novel perspectives for studying the molecular basis of adaptation to climate change in A. sapidissima and for genetic selection.

FoxO signaling and mitochondria-related apoptosis pathways mediate tsinling lenok trout (Brachymystax lenok tsinlingensis) liver injury under high temperature stress

Tsinling lenok trout (Brachymystax lenok tsinlingensis) is a typical cold water fish. High temperature has been shown to damage the liver of fish. However, few studies have investigated the liver apoptosis induced by high temperature stress in fish from the perspective of gene expression and metabolic function. Therefore, we investigated the changes caused by high temperature stress (24 °C) on the liver tissue structure, antioxidant capacity, liver gene expression, and the metabolome of tsinling lenok trout. The transcriptomic results showed that genes associated with apoptosis, such as CASP8, CASP3, PERK, Bcl-6 and TRAIL, were upregulated under high temperature stress. Metabolomic analysis showed that the metabolic pathway of nucleotide synthesis was significantly downregulated, while that of oxygen radical synthesis was significantly upregulated. Integrated analysis showed that after high temperature stress, immune-related signaling pathways in trout were activated and their apoptosis level increased, which might be related to hepatopancreas injury. In addition, abnormalities in the tricarboxylic acid cycle and mitochondrial function were observed, suggesting that functional hypoxia caused by high temperature might be involved fish cell apoptosis. These results provide new insights into the process of cell apoptosis in fish under high temperature stress.

Ecological Monitoring and Omics: A Comprehensive Comparison of Workflows for Mass Spectrometry-Based Quantitative Proteomics of Fish (Labeo rohita) Liver Tissue

Introduction: The liver is highly sensitive to the environmental factors. Liver tissue, particularly from fish, is often used as a biological target in ecological monitoring, disease research, and stress response studies. Labeo rohita (rohu) is a fish with a significant role in the global aquaculture economy. Methods: Bottom-up proteomics relies on efficient sample preparation for performing mass spectrometric analysis of the liver tissue. Optimization of protein solubilization and digestion strategies is the key step to obtain reliable data for a successful proteomics experiment. Because the goal of extraction is to acquire the optimum protein quality and yield, the first step should be to choose an appropriate extraction method based on the type of sample. Solubilization buffers containing sodium dodecyl sulfate (SDS) or urea, and digestion methods such as filter-aided sample preparation (FASP), suspension trap (S-Trap) and in-solution are often used in proteomics but are in need of comparative evaluation with an eye to protocol optimization. Experiment: We applied two different solubilization buffers (one containing SDS, and other containing urea) and three digestion methods (FASP, S-Trap, and in-solution) to the proteomic analysis of the fish (L. rohita) liver tissue. Label-free quantification analysis was performed to analyze the similarities and differences in the results with each method. Gene ontology-based functional analysis was performed for the identified proteome across the experimental conditions to overview their protein classes, molecular functions, and biological processes. Results: SDS lysis followed by S-Trap digestion outperformed the other combinations of lysis and digestion in terms of higher protein coverage, consistency in the results and repeatability. Filter-based methods provided comparatively better results than in-solution digestion. Discussion: This protocol presents new insights on ways to optimize discovery and targeted proteomic analyses of liver tissue using the fish L. rohita as a case study. Other tissues can also be evaluated in the future drawing from the results in this study. This would help the scientific community with hypothesis-driven studies on topics ranging from basic biology to applied aquaculture research and ecological monitoring. This is particularly relevant in the current era of ecological crises and environmental pollution, where advances and optimization in research protocols can contribute to in-depth studies of ecosystems and planetary health.

Dietary nanoselenium supplementation for heat-stressed rainbow trout: effects on organizational structure, lipid changes, and biochemical parameters as well as heat-shock-protein- and selenoprotein-related gene expression

Nanoselenium (nano-Se) shows unique protective effects against environmental heat stress in rainbow trout as a selenium source additive and free radical scavenger. Accordingly, we investigated the effects of supplementation with different levels of nano-Se (0, 5, and 10 mg/kg) and before and after heat stress (24°C) for different treatment times on the dynamic changes of rainbow trout liver tissue structure, lipid changes, biochemical properties, and gene expression. The results showed that, under heat stress, the fish supplementation of 5 mg/kg nano-Se significantly increased liver glutathione peroxidase (GPx) activity and upregulated expression levels of HSP70b, HSP90a1, GPx1a, and Trx mRNAs, while liver alanine aminotransferase (ALT), aspartate aminotransferase (AST), superoxide dismutase (SOD), and malondialdehyde (MDA) levels as well as tissue structure damage and lipid accumulation were decreased. Combining the trends for the above indicators indicated that stress began to increase significantly at 8 h. It can be concluded that supplementation with 5 mg/kg nano-Se effectively alleviates stress damage in rainbow trout. Furthermore, stress at 24°C for 8 h can be thought of as a critical time point for the study of heat stress in rainbow trout, with significant changes in response but no serious damage. Thus, these results provide a reference for the addition of nano-Se to rainbow trout feed and provide theoretical and practical guidance for enhancing the resistance of rainbow trout to heat stress.

Integrated analysis of the responses of a circRNA-miRNA-mRNA ceRNA network to heat stress in rainbow trout (Oncorhynchus mykiss) liver

BACKGROUND

With the intensification of global warming, rainbow trout (Oncorhynchus mykiss) suffer from varying degrees of thermal stimulation, leads to mass mortality, which severely restrict the development of aquaculture. Understanding the molecular regulatory mechanisms of rainbow trout under heat stress is useful to develop approaches to relieve symptoms.

RESULTS

Changes in nonspecific immune parameters revealed that a strong stress response was caused in rainbow trout at 24 °C, so we performed multiple transcriptomic analyses of rainbow trout liver under heat stress (HS, 24 °C) and control conditions (CG, 18 °C). A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified. A ceRNA regulatory network was constructed and a total of 301 circRNA-miRNA and 51 miRNA-mRNA negative correlation pairs were screened, and three regulatory correlation pairs were predicted: novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some target genes involved in metabolic processes, biological regulation or response to stimulus were highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as protein processing in the ER, the estrogen signaling pathway, and the HIF-1 signaling pathway.

CONCLUSIONS

These results extend our understanding of the molecular mechanisms of the heat stress response and provide novel insight for the development of strategies that relieve heat stress.

Proteome analysis of rainbow trout (Oncorhynchus mykiss) liver responses to chronic heat stress using DIA/SWATH

Aquaculture of rainbow trout (Oncorhynchus mykiss) is severely hampered by high temperatures in summer, and understanding the regulatory mechanisms controlling responses to chronic heat stress may assist the development of measures to relieve heat stress. In the present study, biochemical parameters revealed a strong stress response in rainbow trout at 24 °C, including activation of stress defence and immune systems. Liver proteome analysis under heat stress (24 °C) and control (18 °C) conditions using DIA/SWATH identified precursors (90,827), peptides (67,028), proteins (6770) and protein groups (5124), among which 460 differentially abundant proteins (DAPs; q-value < 0.05, fold change >1.5), 201 and 259 were up- and down-regulated, respectively. Many were related to heat shock proteins (HSPs), metabolism and immunity. Gene Ontology (GO) analysis showed that some DAPs induced at high temperature were involved in regulating cell homeostasis, metabolism, adaptive stress and stimulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified metabolic pathways, protein processing in endoplasmic reticulum, PPAR signalling, and complement and coagulation cascades. Protein-protein interaction (PPI) network analysis indicated that HSP90b1 and C3 may cooperative to affect cell membrane integrity under heat stress. Our findings assist the development of strategies to relieve heat stress in rainbow trout.

Multi-Omics Analysis Provides Novel Insight into Immuno-Physiological Pathways and Development of Thermal Resistance in Rainbow Trout Exposed to Acute Thermal Stress

In recent years, poikilothermic animals such as fish have increasingly been exposed to stressful high-temperature environments due to global warming. However, systemic changes in fish under thermal stress are not fully understood yet at both the transcriptome and proteome level. Therefore, the objective of this study was to investigate the immuno-physiological responses of fish under extreme thermal stress through integrated multi-omics analysis. Trout were exposed to acute thermal stress by raising water temperature from 15 to 25 °C within 30 min. Head-kidney and plasma samples were collected and used for RNA sequencing and two-dimensional gel electrophoresis. Gene enrichment analysis was performed: differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were identified to interpret the multi-omics results and identify the relevant biological processes through pathway analysis. Thousands of DEGs and 49 DEPs were identified in fish exposed to thermal stress. Most of these genes and proteins were highly linked to DNA replication, protein processing in the endoplasmic reticulum, cell signaling and structure, glycolysis activation, complement-associated hemolysis, processing of released free hemoglobin, and thrombosis and hypertension/vasoconstriction. Notably, we found that immune disorders mediated by the complement system may trigger hemolysis in thermally stressed fish, which could have serious consequences such as ferroptosis and thrombosis. However, antagonistic activities that decrease cell-free hemoglobin, heme, and iron might be involved in alleviating the side effects of thermally induced immuno-physiological disorders. These factors may represent the major thermal resistance traits that allow fish to overcome extreme thermal stress. Our findings, based on integration of multi-omics data from transcriptomics and proteomics analyses, provide novel insight into the pathogenesis of acute thermal stress and temperature-linked epizootics.