Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

Abstract

Background: Because the cost of cereals is unstable and represents a large part of production charges for meat-type chicken, there is an urge to formulate alternative diets from more cost-effective feedstuff. We have recently shown that meat-type chicken source is prone to adapt to dietary starch substitution with fat and fiber. The aim of this study was to better understand the molecular mechanisms of this adaptation to changes in dietary energy sources through the fine characterization of transcriptomic changes occurring in three major metabolic tissues - liver, adipose tissue and muscle - as well as in circulating blood cells.

Results: We revealed the fine-tuned regulation of many hepatic genes encoding key enzymes driving glycogenesis and de novo fatty acid synthesis pathways and of some genes participating in oxidation. Among the genes expressed upon consumption of a high-fat, high-fiber diet, we highlighted CPT1A, which encodes a key enzyme in the regulation of fatty acid oxidation. Conversely, the repression of lipogenic genes by the high-fat diet was clearly associated with the down-regulation of SREBF1 transcripts but was not associated with the transcript regulation of MLXIPL and NR1H3, which are both transcription factors. This result suggests a pivotal role for SREBF1 in lipogenesis regulation in response to a decrease in dietary starch and an increase in dietary PUFA. Other prospective regulators of de novo hepatic lipogenesis were suggested, such as PPARD, JUN, TADA2A and KAT2B, the last two genes belonging to the lysine acetyl transferase (KAT) complex family regulating histone and non-histone protein acetylation. Hepatic glycogenic genes were also down-regulated in chickens fed a high-fat, high-fiber diet compared to those in chickens fed a starch-based diet. No significant dietary-associated variations in gene expression profiles was observed in the other studied tissues, suggesting that the liver mainly contributed to the adaptation of birds to changes in energy source and nutrients in their diets, at least at the transcriptional level. Moreover, we showed that PUFA deposition observed in the different tissues may not rely on transcriptional changes.

Conclusion: We showed the major role of the liver, at the gene expression level, in the adaptive response of chicken to dietary starch substitution with fat and fiber.

Keywords: Adaptation; Chicken; Fat diet; Gene expression; Lipid; PUFA; Regulation; SREBF1; TADA2A.

Fig. 1

Diet effect on growth performance, body composition and organ weight, Two divergent Fat (solid bars) and Lean (hatched bars) meat-type chicken lines selected for abdominal fat weight, were fed during 6 weeks between 21 and 63 days an iso-caloric diet either enriched in lipids and fiber (HF diet, orange bars) or in starch (LF diet, blue bars). The values are means ± standard deviation with n = 12. a Growth performance and body composition. b Organ weights. c Correlation between liver/body weight ration and FASN mRNA level. ***: p-value ≤0.001

Fig. 2

Overview of gene expression and differential expression between diets in liver, adipose tissue, muscle and PBMC. a. Number of genes expressed in the 4 tissues. b Number of genes differentially expressed between diets in the 4 tissues. c Pearson correlation between expression fold change in liver (log2(FC)) for 50 genes analyzed by microarray (x-axis) and RT-qPCR (y-axis) in the same experimental design; Significance of the DEG by microarray is indicated by the following color chart: brown dots = p-value ≤0.001, orange dots = p-value ≤0.01, yellow dots = p-value ≤0.05, black dots = node (p.value > 0.05)

Fig. 3

Hepatic expression of key genes involved in fatty acid and glucose metabolism. a List of genes up- and down-regulated in HF diet vs. LF diet. DEP: DE probes; DEG: DE genes. b GO term enrichment for these two up- and down-regulated gene lists. c Heatmap based on gene expression and depicting the main genes related to fatty acid and glucose metabolism. Glycog: glycogen synthesis, Glycol: glycolysis, FA.act: FA activation, FA.synt: FA synthesis, TG.synt: TG synthesis, FA.TF: transcription factor related to FA metabolism. Column annotations: F = fat line L = lean Line, fatWgt = fat weight (g). Row annotations: Exp = mean expression, FDR = corrected p-value (False Discovery Rate), FC = fold change between HF and LF diet (ratio HF/LF). d Hepatic UGP2 expression and Glycogen (μmol/g of tissue). E. Hepatic and blood CPT1A expression

Fig. 4

Hepatic fatty acid biosynthesis and secretion was the major metabolism altered in response to the dietary lipid source. a Lipid content in three tissues (% of tissue weight). b, c and d. MFA representations related to individuals (B) and variables (C and D). Blue color is related to transcriptomic data and red color to metabolic data. In D, genes in bold blue are known to be involved in FA and TG synthesis storage; grey genes have unknown function. e Effect of HF and LF diets on the three FA classes (in % of total FA). SFA: saturated FA (C14:0 + C16:0 + C18:0), MUFA: monounsaturated FA (MUFA (C16:1 + C18:1), PUFA: n-6 and n-3 polyunsaturated FA. n = 24 per diet (no effect of lines). f Effect of HF and LF diets on the activity of fatty acid synthase (FASN) enzyme and correlation between this activity and the FASN expression. n = 24 per diet. g Plasmatic cholesterol (mg/l), triglyceride (mg/l) and lipoproteins. **: p-value ≤0.01, ***: p-value ≤0.001, NS: No Significant

Fig. 5

Expression of DE transcription factors, nuclear hormones or transcriptional co-activators in liver of chickens fed HL or LF diets. a and b Differences in expression levels between HF and LF diets were significant for all genes except NR1H3 and MLXIPL. ***: p-value ≤0.001, **: p-value ≤0.01, *: p-value ≤0.05, NS: No Significant. C. Correlations between SREBF1, JUN or PPARD with different DE genes encoding key lipogenic enzymes

Fig. 6

A co-localized and co-expressed gene set containing ACACA and TADA2A. a Syntenic region conserved between chicken, human and mouse. b Hepatic expression of the syntenic genes in the two diets and genotypes for male broiler chickens. c Correlation between TADA2A hepatic expression (taken as reference) and hepatic expression of other co-localized genes in two chicken experimental designs. Top: male broilers analyzed in this study (n = 48); bottom: female layers analyzed by RNA-Seq (n = 40). Rpkm normalized expression are available in the Additional file 5. d Expression in liver (Liv) and brain (Br) of C57BL/6 J mice (n = 22) (GDS3232 in GEO profiles [31]. e Circle plot depicting the correlation between TADA2A and the 298 down-regulated genes in HF diet: red edges indicate genes which expressions are highly correlated to TADA2A expression (r > =0.8). Red names indicate genes involved in lipid metabolism. Correlations in bold in the Figure (r > 0.7) are highly significant with a p-value ≤0.001

Fig. 7

Putative mechanisms explaining hepatic impact of PUFA on genes encoding lipogenic enzymes and SREBF1 and NR1H3 transcription factors in HF diet vs. LF diet. 1- [46, 47]. 2-[–50]. 3- [51, 52]. 4- [53]. 5- [54, 60, 102]. 6- [60, 102]. 7- [103, 104]. 8- [105]. 9- [106]. 10: [56, 57, 107]