Figure 6. Parallel evolution in cavefish exhibits profound alteration of cholesterol / cholesteryl ester metabolism.
Cavefish possess a significant reduction in certain long-chain fatty acid cholesteryl esters (A–C) and cholesterol itself (D), particular in peripheral tissues (muscle). Values on the y–axis are mTIC-normalized peak intensities for each lipid species. Asterisks indicate significance at the 0.05 level according to an O-PLS / Bayesian logistic regression (Methods) for Pachón vs surface, Tinaja vs surface, and Pachón vs Tinaja.
Figure 6—figure supplement 1. Metabolic themes of A. mexicanus cave adaptation revealed by three independent RNA-Seq experiments.
To determine whether transcriptomic signatures support the notion of altered antioxidant metabolism in A. mexicanus cave populations, we compare here liver transcriptomic profiles of genes related to antioxidant metabolism in three different studies: adult (unpublished), juvenile (age-matched for this study Xiong et al., 2018), and wild vs lab (Krishnan et al., 2020) populations. Data are shown as -fold change. While age-related differences do exist, important patterns emerge between surface and cave. Notably, glutathione S-transferase rho (gstr), a key mediator of glutathione antioxidant activity, is consistently upregulated in Pachòn cavefish. Other genes such as prdx3 (perodiredoxin 3) and gpx4a (glutathione peroxidase) are also elevated in cavefish, whereas gpx1a, another glutathione peroxidase is upregulated in surface (but this difference disappears in wild populations). The latter could indicate the presence of additional stress in the lab environment for surface fish.
Figure 6—figure supplement 2. Profile of sugar / energy metabolism-related gene expression.
Focusing on sugar and energy metabolites reveals interesting although somewhat less concerted patterns of gene expression in surface and cave. Phosphoenolpyruvate carboxykinase (pck1/pck2), which catalyzes an irreversible step in gluconeogenesis, is generally upregulated in cavefish (although wild populations do not follow this pattern), whereas lactate dehydrogenase A (ldha) is upregulated in surface. However, Ldha is a bifunctional enzyme, and can be difficult to interpret as a proxy for gluconeogenesis activity. The signature of wild populations appears to deviate considerably from lab-raised populations.