Biomarker selection depends on gene function and organ: the case of the cytochrome P450 family genes in freshwater fish exposed to chronic pollution

Abstract

Pollution and its effects have been of major concern in recent decades. Many strategies and markers have been developed to assess their effects on biota. Cytochrome P450 (CYP) genes have received significant attention in this context because of their relationship with detoxification and activation of exogenous compounds. While their expression has been identified as a pollution exposure biomarker, in most cases, it has been tested only after acute exposures and for CYP genes associated with exogenous compounds. To elucidate CYP gene expression patterns under chronic pollution exposure, we have used the silverside Basilichthys microlepidotus as a model, which inhabits the Maipo River Basin, a freshwater system with different pollution levels. We performed next-generation RNA sequencing of liver and gill tissues from polluted and non-polluted populations. We found most CYP genes were not dysregulated by pollution, and the seven genes that were present and differentially expressed in liver and gill were mainly downregulated. Three CYP genes associated with exogenous compounds showed differential expression in the gill, while four CYP genes associated with endogenous compounds showed differential expression in the liver. The findings presented here highlight the importance of CYP genes, his family, tissues and his interaction in the context of pollution biomarkers use.

Genome scans reveal signals of selection associated with pollution in fish populations of Basilichthys microlepidotus, an endemic species of Chile

“…The second locus is located in the PEL and MEL sites and is involved in the biological processes of negative regulation of circadian rhythm and negative regulation of DNA-driven transcription. In 2018–2019, we identified two loci in our dataset that deviated significantly from the expected patterns and that, interestingly, also showed differential expression in the RNA-Seq study from 2016 (RNA-Seq data available in Cortés-Miranda et al 13 ). We found a correlation between one of the genetic markers and individuals from the MEL locus, while the other marker was associated with the PEL locus.…”

“…This finding suggests that metal contamination may play an important role at this particular site. Water quality degradation increased recently at the IM site 13 compared to the results of previous studies conducted in our laboratory 20 – 22 . The recent observed decline in water quality is consistent with the finding that this particular site had the lowest number of genes showing signs of selection pressure when compared with the sites with long term pollution, PEL and MEL.…”

“…Other sites, like Isla de Maipo (IM), have suffered considerable water quality deterioration in recent years. Using 36 environmental variables (22 from water and 14 from sediments) measured in 2016, the same study found a clear separation between SFM and the other sites, PEL, MEL and IM 13 . Recent studies have demonstrated the impact of this pollution on the biota, specifically on the endemic silverside fish Basilichthys microlepidotus a vulnerable insectivorous atherinid that inhabits lakes and rivers from 28° to 39°S 19 .…”

“…Chile's Maipo River, a heavily polluted catchment area, supplies 70% of the region's drinking water and irrigation needs. The river basin, spanning 15,304 km 2 , is primarily made up of watercourses drained from snowmelt from the Andes Mountain Range 13 , 14 . With 7.11 million human residents, it accounts for 40% of the Chilean population, living in 163 regions, including Santiago 15 .…”

“…Analyses of ten physicochemical parameters measured in 2007, 2011, and 2016 showed that some sites of the basin, such as Pelvin (PEL) and Melipilla (MEL), suffered chronic pollution, while others, such as San Francisco Mostazal (SFM), showed a consistently lower grade of pollution over time (Fig. 1 ) 13 . Other sites, like Isla de Maipo (IM), have suffered considerable water quality deterioration in recent years.…”