Regulation of Gene Expression in Fish

Pollution of the aquatic environment has become a severe global concern due to rising levels of toxins connected with human activities, such as industry, mining, agriculture, and domestic waste generation [1]. Aquatic organisms, including fish, accumulate pollutants directly from contaminated water and indirectly through the food chain, while the bio-concentration of potentially harmful substances in aquatic organisms, primarily heavy metals, pesticides, polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs), poses a major threat to human health. Fish are extensively used as a bio-indicator to evaluate the health of aquatic ecosystems since they are at the top of the aquatic food chain [2].

Additionally, because cells control certain genes to preserve cellular structures and repair damage after exposure to toxicants, gene expression analysis has evolved into the preferred method for many toxicological research [3]. Analyses of gene expression data can reveal details about pollutant exposure and possible impacts at various biological levels [4]. In light of this, gene expression profile offers a sensitive, quantifiable endpoint for toxicity and can act as a precursor to a particular biological endpoint.

In fact, quantitative reverse transcription PCR (RT-qPCR) is the method of choice for assessing gene expression of a limited number of genes in hundreds or thousands of samples [5]. The advent of microarrays and next-generation sequencing (NGS) technology in recent decades has opened the way for a paradigm shift, from selected set of genes analysis to whole-genome screening of possibly all expressed genes [4]. Bioinformatics techniques are employed in the new era of toxicogenomics to find chemical classes, hazardous effects of novel chemicals, and pathways influenced by chemical stressors. Bioinformatics tools are also frequently utilized to deduce hazardous response pathways [5].

Climate change has lately sparked renewed interest, as it is already harming numerous types of life in aquatic habitats [6]. Temperature anomalies are the most apparent and harmful components of climate change, and because most aquatic species are poikilothermic, the ecosystem temperature has a direct effect on their body temperature. Changes in species distribution, abundance, and phenology have already been related to rising mean temperatures [7]. Coastal ecosystems, for example, are sensitive to minor mean temperature changes, ocean acidification, or sea level rise over decades, which have generally been the focus of studies on climate change’s effects on marine life [8].

In recent years, the increasing scenario of climatic variation has impacted the survival of inhabitants in water [9], where significant pollutants and heavy metal toxicants are also present. Several biomarkers are being researched to determine their effects in aquatic organisms. The majority of the research [10,11,12] found that these pollutants are to blame for human health risks as well as terrestrial or aquatic flora and fauna [13]. This means that biomarkers are important factors in environmental monitoring, potentially causing changes in biological organization and biodiversity.

In different fish species, molecular marker analysis revealed stressors’ complexity and effects in a particular niche [14]. For instance, gilthead seabream [15], tilapia [16], goldfish [17], bluegill sunfish—Lepomis macrochirus [18], Korean spotted barbel—Hemibarbus mylodon [19] represent just some of notable bioindicators in different aquatic habitats. Fish have also been used to evaluate the stress response to heavy metals [20], microplastics [21], and chemical toxicants [22] in the environment [23].

In general, these stressors can affect living organisms in two ways: debilitation and eventually death, or at non-lethal levels of exposure by affecting normal life processes, also known as ‘capacity’ effects [24,25]. Recent climate changes, particularly temperature changes, have impacted ecological processes across a wide range of taxa [26,27]. Ectotherms in aquatic systems, in particular, are influenced by thermal profiles and climate regimes in terms of distribution, physiology, and behavior [28].

Transcriptional analysis is a valuable tool for studying the physiological responses of non-model organisms [29] and species of conservation concern [30]. While some biomarkers, such as heat shock proteins and cortisol, are associated with a wide range of stressors, different individual stressors elicit more specific responses by stimulating different biological pathways. High water temperature stress, for example, increases the expression of molecular chaperones, heat shock proteins, and genes involved in RNA stabilization, transcriptional regulation, and immunity [31]. Transcriptomic responses have been easily evaluated during the last 15 years utilizing qRT-PCR, microarrays and RNA-sequencing (RNA-seq), with the technique of choice depending on the number of markers and individuals to be analyzed [32].

For example, ref. [32] used a molecular approach to develop specific biomarkers for thermal stress in salmonids, knowing that temperature influences growth, feeding, metabolism, embryo and alevins development, timing of life history events such as upstream migration, spawning, freshwater rearing, and seaward migration, and food availability [33]. Independent qRT-PCR validation of biomarkers identified through meta-analysis of microarray data resulted in a panel of eight genes involved in chaperoning and protein rescue, protein biosynthesis, and oxidative stress that were differentially activated in Pacific salmon gill tissue in response to elevated temperatures [32]. According to [32], all of these genes have the potential to be reliable unique thermal stress biomarkers. While some of these indicators may respond to other stressors or biological processes on their own, when co-expressed, these genes may provide a reliable technique for detecting the existence of a thermal stress response in field-caught salmon [32].

Finally, ref. [32] revealed that assessing groups of genes linked with a specific response is a more powerful approach for analyzing the effects of environmental stressors across species [30]. The next step in the other upcoming studies (by various authors in the Special Issue) will be to demonstrate the specificity of biomarkers in a multi-stressor test, as well as to identify the smallest number of genes required to predict a thermal stress response or other environmental stress stimuli.