Effect of L-carnitine on the hepatic transcript profile in piglets as animal model
© Keller et al; licensee BioMed Central Ltd. 2011
Received: 25 August 2011
Accepted: 31 October 2011
Published: 31 October 2011
Carnitine has attracted scientific interest due to several health-related effects, like protection against neurodegeneration, mitochondrial decay, and oxidative stress as well as improvement of glucose tolerance and insulin sensitivity. The mechanisms underlying most of the health-related effects of carnitine are largely unknown.
To gain insight into mechanisms through which carnitine exerts its beneficial metabolic effects, we fed piglets either a control or a carnitine supplemented diet, and analysed the transcriptome in the liver.
Transcript profiling revealed 563 genes to be differentially expressed in liver by carnitine supplementation. Clustering analysis of the identified genes revealed that most of the top-ranked annotation term clusters were dealing with metabolic processes. Representative genes of these clusters which were significantly up-regulated by carnitine were involved in cellular fatty acid uptake, fatty acid activation, fatty acid β-oxidation, glucose uptake, and glycolysis. In contrast, genes involved in gluconeogenesis were down-regulated by carnitine. Moreover, clustering analysis identified genes involved in the insulin signaling cascade to be significantly associated with carnitine supplementation. Furthermore, clustering analysis revealed that biological processes dealing with posttranscriptional RNA processing were significantly associated with carnitine supplementation.
The data suggest that carnitine supplementation has beneficial effects on lipid and glucose homeostasis by inducing genes involved in fatty acid catabolism and glycolysis and repressing genes involved in gluconeogenesis.
Keywordscarnitine pig microarray gene expression liver
Carnitine (3-hydroxy-4-N, N, N-trimethylaminobutyric acid) belongs to the class of conditionally essential nutrients and has a number of indispensable functions in intermediary metabolism. Carnitine is necessary for fatty acid metabolism due to its role in the transfer of long-chain fatty acids (acyl groups) from the cytosol into the mitochondrial matrix for subsequent β-oxidation . Moreover, carnitine facilitates the transport of peroxisomal β-oxidation products to the mitochondria, the export accumulating acyl-groups and acts as a CoA buffer in mammalian cells . Carnitine in the body originates from intestinal absorption from dietary sources, especially meat, fish and dairy products  and enzyme catalyzed endogenous synthesis , which involves five enzymatic steps. Given that the last enzyme required for carnitine synthesis, γ-butyrobetaine hydroxylase, is only active in liver and kidney, other tissues than liver and kidney are dependent on the active uptake of carnitine from blood into tissues which is catalyzed by novel organic cation transporters (OCTN), particularly OCTN2 which is the physiologically most important carnitine transporter .
In livestock animal nutrition, supplementation with L-carnitine has attracted great interest due to its ability to improve performance characteristics, such as growth rate, feed conversion ratio, protein:fat accretion [6–8]. However, L-carnitine is also of interest for human nutrition because recent studies indicated that L-carnitine exerts several other effects which may be useful for the treatment of degenerative and metabolic disorders. For instance, supplementation of L-carnitine or acyl-carnitines has been associated with protecting against neurodegeneration , age-dependent mitochondrial decay , and oxidative stress . In addition, L-carnitine was shown to improve glucose tolerance and insulin sensitivity in animals as well as in healthy and diabetic patients [12, 13]. Moreover, L-carnitine supplementation was shown to be useful for the treatment of hepatic steatosis induced by total parenteral nutrition in rodents  and nonalcoholic steatohepatitis in humans [15, 16]. Furthermore, L-carnitine was reported to reduce hepatic inflammation and plasma levels of cytokines and acute phase proteins in patients with chronic hepatitis C . The mechanisms underlying many of these beneficial effects of L-carnitine are largely unknown. Therefore, the present study was designed to gain insight into mechanisms and pathways influenced by L-carnitine. For this end, we used piglets, indicating many genetical and physiological similarities with humans, making it an optimal species to study the effect of L-carnitine on transcript profile.
We considered the liver as the target organ because it plays a central role in whole body metabolism by regulating glucose and lipid homeostasis as well as protein synthesis. In this sense, we used liver samples taken from a previous experiment with piglets  which were fed a either a control diet with a low native carnitine content or a diet supplemented with 500 mg/kg diet L-carnitine and performed genome-wide transcript profiling in the liver of these piglets.
The animal experiment was approved by the local Animal Care and Use Committee. As described recently in more detail , the experiment was performed with sixteen male crossbred pigs [(German Landrace × Large White) × Pietrain] with an average body weight of 10 ± 1 (mean ± SD) kg. The pigs were assigned to two groups (control group and carnitine group) and fed experimental diets for a period of 21 days. The control group received a basal diet with a low native carnitine concentration (< 5 mg/kg) which was nutritionally adequate for growing pigs in a body weight range between 10 and 20 kg, according to the recommendations of the German Society for Nutrition Physiology (Gesellschaft für Ernährungsphysiologie, 2006). The carnitine group received the same diet supplemented with 500 mg L-carnitine (obtained from Lohmann Animal Health, Cuxhaven, Germany) per kg. Blood was collected and plasma obtained by centrifugation of the blood, and liver was excised. Plasma and liver samples were immediately stored at -80°C until analysis. A full description of diet composition, feeding regime, sample collection and carnitine analysis of diets and tissues can be found in our recent publication .
Concentrations of free carnitine, acetyl carnitine and propionyl carnitine in liver of pigs fed either a control diet or a diet supplemented with 500 mg/kg carnitine for 20 days were determined by tandem mass spectrometry using deuterated carnitine-d3 (Larodane Fine Chemicals, Malmö, Sweden) as internal standard as described recently in detail . Concentration of total carnitine represents the sum of free carnitine, acetyl carnitine and propionyl carnitine.
RNA isolation and quality control
Total RNA was prepared from 20-30 mg of frozen liver tissue using the RNeasy Minikit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Afterwards, the RNA concentration and purity were estimated from the optical density at 260 and 280 nm, respectively. The A260/280 ratio of all individual samples was 1.98 ± 0.02 (mean ± SD). The integrity of the total RNA was checked by 1% agarose gel electrophoresis. RNA was judged as suitable for array hybridization only if the samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits.
For microarray analyses, two RNA pools for each group (control, n = 2; carnitine group, n = 2) were prepared, with RNA from 4 animals contributing to each RNA pool. Hybridization to the Affymetrix GeneChip porcine genome arrays (Affymetrix) containing 23,937 probe sets that represent approximately 23,256 porcine transcripts and quality assessment of the hybridization process were performed at the Center of Excellence for Fluorescent Bioanalytics (KFB) at the University of Regensburg for hybridization to the Affymetrix GeneChip porcine genome arrays (Affymetrix, UK). The microarray data related to all samples have been deposited in NCBI's Gene Expression Omnibus (GEO) public repository (GEO accession number GSE22931) . Data analyses and functional interpretation of microarray data using the bioinformatic tools from the Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatic resource  were performed as described recently in detail .
Quantitative real-time RT-PCR (qPCR)
Characteristics of porcine primer pairs used for validation of microarray analysis using RT-PCR
Primer sequence (5'-3')
Product size (bp)
Values presented in the text are means ± SD. Data were analyzed by one factorial analysis of variance with dietary carnitine concentration as factor using the Minitab statistical software (Release 13, Minitab Inc., State College, PA, USA). For statistical significant F-values (P < 0.05), means of both groups were compared by Fisher's multiple range test.
Feed intake, final body weight and feed conversion ratio
Feed intake, final body weights and feed conversion ratio of piglets were not different between both groups .
Concentration of carnitine in the liver
Identification of differentially expressed genes
The 15 most strongly up- and down-regulated genes in the liver of growing piglets fed with or without L-carnitine
Probe set ID
Gene name (Gene symbol)
Probe set ID
Gene name (Gene symbol)
Glutathione S-transferase A3-3 (GSTA3)
Kelch-like protein 8 (KLHL8)
Hexokinase D (GCK)
Homeobox protein Meis1 (MEIS1)
Apolipoprotein A-IV precursor (ApoA4)
Mannose-binding protein C precursor (MBP-C)
Sentrin-specific protease 6 (SENP6)
Insulin-like growth factor binding protein 1 precursor (IGFBP-1)
Sprouty homolog 3 (SPRY3)
Phosphoenolpyruvate carboxykinase, cytosolic (PCK1)
R3H domain protein 1 (R3HDM)
estrogen-related receptor gamma isoform 2 (ESRRG)
Telomerase-binding protein p23 (TEPB)
Synaptic vesicular amine transporter (SLC18A2)
Cytochrome P450 2J2 (CYP2J2)
Serine/threonine-protein kinase (ULK1)
SPARC related modular calcium-binding protein 1 precursor (SMOC1)
DRE1 protein (DRE1)
Ubiquitin carboxyl-terminal hydrolase 1 (USP1)
Cyclin G2 (CCNG2)
Heterogeneous nuclear ribonucleoprotein M (hnRNP M)
T-cell lymphoma breakpoint-associated target 1 (TCBA1)
cell adhesion molecule with homology to L1CAM precursor (CHL1)
oxidation resistance 1 (OXR1)
Metabotropic glutamate receptor 5 precursor GRM5)
Ephrin-A1 precursor (EFNA1)
Serine/threonine-protein kinase (Nek7)
Glutaminase, kidney isoform, mitochondrial precursor (GLS)
Testican-1 precursor (SPOCK)
Real-time RT-PCR verification of microarray data
qPCR and microarray gene expression analyses of liver tissue
Mean fold changes
Identification of overrepresented annotation terms
563 genes identified to be differentially expressed were used for gene-term enrichment analysis using the DAVID Functional Annotation Chart tool. The analyses were based on the GO category biological process. The GO analysis assigned the 563 differentially expressed genes to 21 biological processes (p-value < 0.01). Most genes were allocated to the annotation terms cellular process (357 genes), metabolic process (262 genes), and cellular metabolic process (239 genes). The most significantly enriched annotation terms were (top-ranked: lowest p-values): cellular process (P = 2.0E-04), ribosome biogenesis (P = 3.8E-04), developmental process (P = 4.0E-04), ribonucleoprotein complex biogenesis (P = 4.6E-04), cellular metabolic process (P = 6.5E-04), multicellular organismal development (P = 1.5E-03), cellular protein metabolic process (P = 1.9E-03), rRNA processing (P = 2.1E-03), and rRNA metabolic process (P = 2.8E-03). The annotation terms with the highest fold enrichment were triglyceride metabolic process (4.5-fold), rRNA processing (3.5-fold), ribosome biogenesis (3.4-fold), and rRNA metabolic process (3.4-fold).
Identification of clusters of functionally related annotation terms
Identification of functionally related annotation groups (GO category biological process)
RNA splicing, via transesterification reactions
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
nuclear mRNA splicing, via spliceosome
ribosomal RNA processing
ribosomal RNA metabolic process
non-coding RNA processing
triglyceride metabolic process
acylglycerol metabolic process
neutral lipid metabolic process
glycerol ether metabolic process
organic ether metabolic process
triglyceride biosynthetic process
neutral lipid biosynthetic process
acylglycerol biosynthetic process
glycerol ether biosynthetic process
positive regulation of glucose import
positive regulation of glucose transport
regulation of glucose import
regulation of glucose transport
mitotic metaphase plate congression
metaphase plate congression
Establishment of chromosome localization
chaperone mediated protein folding requiring cofactor
'de novo' posttranslational protein folding
'de novo' protein folding
hexose biosynthetic process
monosaccharide biosynthetic process
alcohol biosynthetic process
cellular carbohydrate biosynthetic process
carbohydrate biosynthetic process
carboxylic acid metabolic process
oxoacid metabolic process
organic acid metabolic process
modification-dependent protein catabolic process
modification-dependent macromolecule catabolic process
proteolysis involved in cellular protein catabolic process
cellular protein catabolic process
protein catabolic process
In the present study we aimed to get insight into potential mechanisms of L-carnitine by applying genome-wide transcript profiling in the liver of piglets. After feeding carnitine supplemented diets for 3 weeks, concentrations of free and total carnitine in the liver of the piglets were markedly increased (approximately 10-fold) compared to piglets fed diets without supplemental L-carnitine, indicating that the supplemental L-carnitine significantly improved the carnitine status of the piglets. As a main result we observed that 563 genes were differentially expressed by L-carnitine. This shows that supplemental L-carnitine influences gene expression in the liver of piglets and indicates that at least some of the biological effects of L-carnitine are mediated by altering gene transcription. To extract biological meaning from the observed alterations in gene expression we performed gene term enrichment analysis and functional clustering analysis with the 563 differentially expressed genes. Gene term enrichment analysis revealed that the most frequent biological processes associated with L-carnitine supplementation were dealing with metabolic processes. This was not surprising considering that the main function of L-carnitine is to stimulate energy metabolism by acting as shuttling molecule for long-chain fatty acids which also enhances the metabolic flux of glucose through the glycolytic chain. This was also confirmed by clustering analysis showing that 6 out of the 10 top-ranked clusters were dealing with metabolic processes. Representative genes from one of these clusters dealing with metabolic processes (carboxylic acid metabolic process, oxoacid metabolic process, organic acid metabolic process) encoded proteins or enzymes involved in cellular fatty acid uptake (SLC27A6, solute carrier family 27/fatty acid transporter, member 6), fatty acid activation (ACSL3, Long-chain-fatty-acid-CoA ligase 3) and fatty acid β-oxidation (ACADSB, Acyl-CoA dehydrogenase, short/branched chain specific), and most of these genes including SLC27A6, ACSL3 and ACADSB were found to be significantly up-regulated by L-carnitine supplementation by microarray analysis and confirmed by qPCR, a more sensitive method for gene expression analysis. Thus, our data indicate that the well-known stimulatory effect of carnitine on fatty acid β-oxidation [22, 23] is at least partially mediated by stimulating the transcription of genes involved in cellular fatty acid uptake, fatty acid activation and β-oxidation.
Clustering analysis further revealed that L-carnitine supplementation was significantly associated with biological processes involved in glucose metabolism, like glucose transport, conversion of glucose into glucose 6-phosphate, and glycolysis, and hexose biosynthetic processes, like gluconeogenesis. Representative genes included GLUT8 (glucose transporter type 8), GCK (Hexokinase D), GPD1 (Glycerol-3-phosphate dehydrogenase), PCK1 (Phosphoenolpyruvate carboxykinase), and FBP2 (Fructose-1,6-bisphosphatase isozyme 2). Moreover, the tandem enzyme PFKFB3 (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3) which is responsible for maintaining the cellular levels of fructose-2,6-biphosphate, the most potent allosteric activator of one of the key regulatory enzymes of glycolysis, 6-phosphofructo-1-kinase, was also identified to be differentially expressed by L-carnitine. All the genes dealing with glucose metabolism like GLUT8, GCK and GPD1 were markedly up-regulated, at least 4-fold, by the supplemental L-carnitine. These strongly up-regulation could also observed by qPCR, supporting microarray analysis. GCK which is the predominant hexokinase isoenzyme in the liver phosphorylating glucose for subsequent metabolism by either glycolysis, pentose phosphate shunt or glycogen synthesis was even induced 27-fold by L-carnitine supplementation - indicating that L-carnitine has a dramatic effect on glucose metabolism. Several studies have already shown that carnitine supplementation increases glucose disposal and glucose oxidation in animals as well as in healthy and diabetic patients [12, 24, 25] due to activation of the pyruvate dehydrogenase complex . Besides allosteric regulation of the activity of enzymes of the glycolytic pathway, it is also well known that the flux through the glycolytic pathway can be increased by induction of the rate-limiting enzymes of this pathway, GCK and PFK1 (6-phosphofructo-1-kinase). Thus, our observations suggest that up-regulation of genes involved in glucose uptake, glucose phosphorylation and glycolysis also contributes to increased glucose oxidation by supplemental L-carnitine. In contrast to the genes involved in glucose metabolism, genes involved in gluconeogenesis, like PCK1 and FBP2 were significantly down-regulated in the liver of piglets by L-carnitine supplementation. This indicates that the positive effect of carnitine on glucose utilization is explained not only by stimulation of glycolysis but also suppression of gluconeogenesis in the liver. It has been recently shown in rats that dietary L-carnitine is capable of restoring an increase in the activity of the gluconeogenic enzymes PCK1, FBP2 and glucose 6-phosphatase caused by feeding fructose , which increases the availability of the gluconeogenic substrates pyruvate, lactate and glycerol. The present findings suggest that inhibition of transcription of gluconeogenic genes by L-carnitine also contributes to the suppression of gluconeogenesis by carnitine, which has not been demonstrated yet. The exact reason for this effect of L-carnitine remains to be established. However, it has been suggested that the inhibitory effect of L-carnitine on gluconeogenic enzyme activities is the consequence of an improvement in the action of insulin [12, 28], which is a known repressor of expression of gluconeogenic genes. Supportive of this assumption is also the identification of another annotation term cluster dealing with positive regulation of glucose import. Considering that insulin is the most important regulator of glucose import, it was not surprising that genes belonging to this cluster were involved in insulin signaling, like IRS2 (Insulin receptor substrate-2), PIK3R1 (Phosphatidylinositol 3-kinase regulatory alpha subunit), and ERBB3 (Receptor protein-tyrosine kinase erbB-3 precursor). Besides regulation by insulin action, key gluconeogenic enzymes such as FBP2 are also known to be subject to complex allosteric regulation. Noteworthy, one of the allosteric inhibitors of FBP2 is fructose-2,6-biphosphate whose cellular levels are controlled by the abovementioned tandem enzyme PFKFB3. Thus, the activity of gluconeogenic enzymes may be influenced by L-carnitine through regulating the cellular availability of allosteric enzyme regulators as well.
Two other identified annotation term clusters were dealing with triglyceride metabolic and triglyceride biosynthetic processes. Representative genes were GPAT, which esterifies acyl-groups from acyl-ACP to the sn-1 position of glycerol-3-phosphate, an essential step in glycerolipid biosynthesis, and MTTP, which catalyses the transport of triglyceride, cholesteryl ester, and phospholipid between phospholipid surfaces, and is required for the secretion of apolipoprotein B containing lipoproteins from the liver. In rodents, L-carnitine administration was demonstrated to decrease liver lipids and hepatic steatosis after administration of a high fat diet, after parenteral nutrition, or after alcohol intoxication [14, 29, 30], with the mechanisms of action being largely unknown. Our observations that GPAT was down-regulated whereas MTTP and genes involved in fatty acid catabolism (SLC27A6, ACSL3, ACADSB) were up-regulated by L-carnitine supplementation in the liver of the piglets, confirmed by qPCR. Thus, our data indicates that inhibition of glycerolipid biosynthesis and stimulation of lipoprotein secretion and fatty acid catabolism may contribute to the decreased liver lipids in rodents fed L-carnitine.
Besides metabolic processes, clustering analysis revealed that biological processes dealing with posttranscriptional RNA processing (mRNA splicing, ribosomal RNA processing, non-coding RNA processing) were significantly associated with L-carnitine supplementation. Noteworthy, almost all of these genes were significantly up-regulated in the liver of the piglets by the supplemental L-carnitine indicating that the biological functions exerted by the encoded proteins are stimulated by L-carnitine. Posttranscriptional RNA processing, which includes precursor-mRNA splicing, is one of the main regulatory mechanisms of gene expression which results in a repertoire of mRNAs, and consequently of proteins, much larger than expected from the number of genes. This process contributes substantially to cell-specific and tissue-specific gene expression, and it is estimated that over 60% of human genes are alternatively spliced . Although the exact biological meaning of the up-regulation of genes dealing with posttranscriptional RNA processing by L-carnitine is unclear, it is obvious that L-carnitine supplementation has a stimulatory effect on this important regulatory mechanism of gene expression. It is therefore possible that the alterations in gene expression observed with L-carnitine supplementation are mediated, at least partially, by modulating posttranscriptional RNA processing.
As far as the physiological relevance of the carnitine dose (500 mg/kg) used in this study is concerned, it has to be noted that omnivorous humans are reported to generally ingest 0.3-1.9 mg of carnitine per day and kg of body weight . Based on a daily feed consumption of approximately 500 g per day and a final body weight of the piglets of about 17 kg this relates to 15 mg of carnitine/kg body weight indicating that the carnitine dose applied to the piglets was at least 8-fold higher than achieved in humans by a normal diet. However, when compared to several clinical trials in which free carnitine was supplemented up to 3 g per day and subject [33–35], which relates to 40 mg carnitine/kg body weight for a human weighing 70 kg, the dose applied in our study can be regarded as low. Therefore, the beneficial effects of carnitine supplementation on several metabolic parameters observed in the abovementioned clinical trials may be at least partially explained by the alterations in gene expression found in our pig model. In several clinical trials, carnitine supplementation was shown to improve glucose homeostasis and insulin sensitivity in obese, insulin resistant and diabetic subjects [36, 37]. Due to theses effects carnitine supplementation has gained significant attention as a tool for the treatment or prevention of insulin resistance and type 2 diabetes mellitus . The improvement of glucose tolerance has been explained by a normalization of mitochondrial fuel metabolism, which is perturbed during insulin resistance due to an intracellular accumulation of acyl-CoA derivatives. Recent evidence indicates that carnitine supplementation corrects these mitochondrial perturbations through an increased efflux of acyl-carnitine out of mitochondria and cells into the blood . Based on our transcriptomic data it cannot be evaluated whether or not acyl-carnitine efflux and mitochondrial function was stimulated by carnitine in the piglets of this study. However, since convincing evidence from both human and animal studies suggests that carnitine lowers "mitochondrial stress" and improves mitochondrial function, in particular in the face of energy surplus, we suggest that carnitine also improved mitochondrial function in our pig model.
In conclusion, results of the present study show that supplemental L-carnitine influences gene expression in the liver of growing piglets. Our data suggest that L-carnitine supplementation has beneficial effects on lipid and glucose homeostasis by inducing genes involved in fatty acid catabolism and glycolysis and repressing genes involved in gluconeogenesis. In addition, the data indicate that the effects of L-carnitine on transcription of glycolytic and gluconeogenic genes are mediated by potentiating the action of insulin and that at least some of the alterations in gene expression observed with L-carnitine supplementation are mediated by modulating posttranscriptional RNA processing. Regarding the strong similarities between pigs and humans with regard to metabolism, our data obtained in piglets can be considered as relevant for humans. Future studies employing both, transcriptomics and metabolomics are required to confirm a correlation between alterations in gene expression and modulation of carbon fluxes through metabolic pathways.
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