Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding

Abstract

Snakes provide a unique and valuable model system for studying the extremes of physiological remodeling because of the ability of some species to rapidly upregulate organ form and function upon feeding. The predominant model species used to study such extreme responses has been the Burmese python because of the extreme nature of postfeeding response in this species. We analyzed the Burmese python intestine across a time series, before, during, and after feeding to understand the patterns and timing of changes in gene expression and their relationship to changes in intestinal form and function upon feeding. Our results indicate that >2,000 genes show significant changes in expression in the small intestine following feeding, including genes involved in intestinal morphology and function (e.g., hydrolases, microvillus proteins, trafficking and transport proteins), as well as genes involved in cell division and apoptosis. Extensive changes in gene expression occur surprisingly rapidly, within the first 6 h of feeding, coincide with changes in intestinal morphology, and effectively return to prefeeding levels within 10 days. Collectively, our results provide an unprecedented portrait of parallel changes in gene expression and intestinal morphology and physiology on a scale that is extreme both in the magnitude of changes, as well as in the incredibly short time frame of these changes, with up- and downregulation of expression and function occurring in the span of 10 days. Our results also identify conserved vertebrate signaling pathways that modulate these responses, which may suggest pathways for therapeutic modulation of intestinal function in humans.

Keywords: RNA-Seq; hyperplasia; organ remodeling; physiological remodeling; small intestine.

Fig. 1.

Scatterplots comparing gene expression in intestinal mucosal and intestinal cross-section samples. A: mucosal and cross-sectional samples from individual AJ7. B: mucosal and cross-sectional samples from individual Ak25. C: mucosal samples from 2 different individuals (AJ7 and R27). It is clear that the 2 different types of samples (cross-sectional and mucosal) from the same individual (A and B) are more similar than the same type of sample from different individuals (C).

Fig. 2.

General trends in gene expression across postfed time-points in the Burmese python intestine analyzed with STEM time-series analyses. Generalized trends in gene expression that are significantly overrepresented in the python small intestine based upon cluster analysis of gene expression profiles and identification of statistically overpopulated profiles. The numbers of genes clustered and P value of these clusters is shown along with linear trends in expression.

Fig. 3.

General trends of gene expression and digestion across postfed time-points. A: heat-map of gene expression for 1,772 genes found to be significantly differentially expressed across time-points based on regression analysis. Each column represents a replicate, with time-points clearly delimited, and each row represents a gene, which are clustered by similarity using average linkage hierarchical clustering. B: percent of meal mass in stomach (filled circles and solid line) and small intestine (open circles and dashed line) across postfeeding time-points.

Fig. 4.

Patterns of expression for genes involved in cell cycling, apoptosis, and WNT signaling along with corresponding physiological changes in the small intestine. A: heat-map of genes involved in cell cycle progression and apoptosis that were shown to be significantly differentially expressed across time-points, identified from pairwise and regression analysis. B: change in small intestinal mass across time. C: change in mucosal thickness across time. D: change in serosa thickness across time. E: average expression values for Wnt signaling genes plotted across postfed time-points. F: heat-map of expression values for all replicates across postfed time-points, with each row representing a gene and each column representing an individual, which are manually clustered by time-points. This pathway is known to be important in development and processes such as asymmetric cell division.

Fig. 5.

Patterns of expression for genes involved with intestinal form and function alongside corresponding morphological or physiological changes in the small intestine. A: heat-map of genes involved in various intestinal functional processes that were shown to be significantly differentially expressed across time-points via pairwise or regression analysis. B: change in enterocyte volume through time. C: change in microvillus surface area across time postfeeding. D: change in absorption of d-glucose across postfed time-points. E: change in absorption of l-proline across postfed time-points. F: change in absorption of l-leucine across postfed time-points. G: change in activity of aminopeptidase N (APN) across postfed time-points.