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1.  The inhibitory effect of rapamycin on the oval cell response and development of preneoplastic foci in the rat 
Oval cell activation occurs under conditions of severe liver injury when normal hepatocyte proliferation is blocked. Recent studies have shown that a subset of hepatocellular carcinomas expresses oval cell markers, suggesting that these cells are targets of hepatocarcinogens. However, the signaling pathways that control oval cell activation and proliferation are not well characterized. Based on the role of the nutrient signaling kinase complex, mTORC1, in liver development, we investigated the role of this pathway in oval cell activation. Oval cell proliferation was induced in male Fisher rats by a modification of the traditional choline deficient plus ethionine model (CDE) or by 2-acetylaminoflourene treatment followed by 2/3 partial hepatectomy with or without initiation by diethylnitrosamine. To assess the role of mTOR in the oval cell response and development of preneoplastic foci, the effect of the mTORC1 inhibitor, rapamycin, was studied in all models. Rapamycin induced a significant suppression of the oval cell response in both models, an effect that coincided with a decrease in oval cell proliferation. Rapamycin administration did not affect the abundance of neutrophils or natural killer cells in CDE-treated liver or the expression of key cytokines. Gene expression studies revealed the fetal hepatocyte marker MKP-4 to be expressed in oval cells. In an experimental model of hepatic carcinogenesis, rapamycin decreased the size of preneoplastic foci and the rate of cell proliferation within the foci. mTORC1 signaling plays a key role in the oval cell response and in the development of preneoplastic foci. This pathway may be a target for the chemoprevention of hepatocellular carcinoma.
doi:10.1016/j.yexmp.2012.04.002
PMCID: PMC3612884  PMID: 22525806
Hepatic progenitor cells; Liver regeneration; Liver injury; mTOR; Hepatocellular carcinoma
2.  Phosphoproteomic Analysis of Liver Homogenates 
Summary
Regulation of protein function via reversible phosphorylation is an essential component of cell signaling. Our ability to understand complex phosphorylation networks in the physiological context of a whole organism or tissue remains limited. This is largely due to the technical challenge of isolating serine/threonine phosphorylated peptides from a tissue sample. In the present study, we developed a phosphoproteomic strategy to purify and identify phosphopeptides from a tissue sample by employing protein gel filtration, protein SAX (strong anion exchange) and SCX (strong cation exchange) chromatography, peptide SCX chromatography and TiO2 affinity purification. By applying this strategy to the mass spectrometry-based analysis of rat liver homogenates, we were able to identify with high confidence and quantify over four thousand unique phosphopeptides. Finally, the reproducibility of our methodology was demonstrated by its application to analysis of the mammalian Target of Rapamycin (mTOR) signaling pathways in liver samples obtained from rats in which hepatic mTOR was activated by refeeding following a period of fasting.
doi:10.1007/978-1-61779-959-4_11
PMCID: PMC3581044  PMID: 22903715
Signal transduction; liver; mass spectrometry; phosphoproteins; ion exchange chromatography; metal oxide chromatography
3.  The physiology and pathophysiology of rapamycin resistance 
Cell Cycle  2011;10(7):1050-1058.
Rapamycin is an inhibitor of the mammalian Target of Rapamycin, mTOR, a nutrient-sensing signaling kinase and a key regulator of cell growth and proliferation. While rapamycin and related compounds have anti-tumor activity, a prevalent characteristic of cancer cells is resistance to their anti-proliferative effects. Our studies on nutrient regulation of fetal development showed that hepatocyte proliferation in the late gestation fetal rat is resistant to rapamycin. Extension of these studies to other tissues in the fetal and neonatal rat indicated that rapamycin resistance is a characteristic of normal cell proliferation in the growing organism. In hepatic cells, ribosomal biogenesis and cap-dependent protein translation were found to be relatively insensitive to the drug even though mTOR signaling was highly sensitive. Cell cycle progression was also resistant at the level of cyclin E-dependent kinase activity. Studies on the effect of rapamycin on gene expression in vitro and in vivo demonstrated that mTOR-mediated regulation of gene expression is independent of effects on cell proliferation and cannot be accounted for by functional regulation of identifiable transcription factors. Genes involved in cell metabolism were overrepresented among rapamycin-sensitive genes. We conclude that normal cellular proliferation in the context of a developing organism can be independent of mTOR signaling, that cyclin E-containing complexes are a critical locus for rapamycin sensitivity, and that mTOR functions as a modulator of metabolic gene expression in cells that are resistant to the anti-proliferative effects of the drug.
doi:10.4161/cc.10.7.15230
PMCID: PMC3100882  PMID: 21389767
mTOR; mammalian target of rapamycin; cell cycle; translation control; gene expression; cell signaling; protein phosphorylation
4.  Postnatal liver growth and regeneration are independent of c-myc in a mouse model of conditional hepatic c-myc deletion 
BMC Physiology  2012;12:1.
Background
The transcription factor c-myc regulates genes involved in hepatocyte growth, proliferation, metabolism, and differentiation. It has also been assigned roles in liver development and regeneration. In previous studies, we made the unexpected observation that c-Myc protein levels were similar in proliferating fetal liver and quiescent adult liver with c-Myc displaying nucleolar localization in the latter. In order to investigate the functional role of c-Myc in adult liver, we have developed a hepatocyte-specific c-myc knockout mouse, c-mycfl/fl;Alb-Cre.
Results
Liver weight to body weight ratios were similar in control and c-myc deficient mice. Liver architecture was unaffected. Conditional c-myc deletion did not result in compensatory induction of other myc family members or in c-Myc's binding partner Max. Floxed c-myc did have a negative effect on Alb-Cre expression at 4 weeks of age. To explore this relationship further, we used the Rosa26 reporter line to assay Cre activity in the c-myc floxed mice. No significant difference in Alb-Cre activity was found between control and c-mycfl/fl mice. c-myc deficient mice were studied in a nonproliferative model of liver growth, fasting for 48 hr followed by a 24 hr refeeding period. Fasting resulted in a decrease in liver mass and liver protein, both of which recovered upon 24 h of refeeding in the c-mycfl/fl;Alb-Cre animals. There was also no effect of reducing c-myc on recovery of liver mass following 2/3 partial hepatectomy.
Conclusions
c-Myc appears to be dispensable for normal liver growth during the postnatal period, restoration of liver mass following partial hepatectomy and recovery from fasting.
doi:10.1186/1472-6793-12-1
PMCID: PMC3353165  PMID: 22397685
5.  Resveratrol Inhibits Protein Translation in Hepatic Cells 
PLoS ONE  2011;6(12):e29513.
Resveratrol is a plant-derived polyphenol that extends lifespan and healthspan in model organism. Despite extensive investigation, the biological processes mediating resveratrol's effects have yet to be elucidated. Because repression of translation shares many of resveratrol's beneficial effects, we hypothesized that resveratrol was a modulator of protein synthesis. We studied the effect of the drug on the H4-II-E rat hepatoma cell line. Initial studies showed that resveratrol inhibited global protein synthesis. Given the role of the mammalian Target of Rapamycin (mTOR) in regulating protein synthesis, we examined the effect of resveratrol on mTOR signaling. Resveratrol inhibited mTOR self-phosphorylation and the phosphorylation of mTOR targets S6K1 and eIF4E-BP1. It attenuated the formation of the translation initiation complex eIF4F and increased the phosphorylation of eIF2α. The latter event, also a mechanism for translation inhibition, was not recapitulated by mTOR inhibitors. The effects on mTOR signaling were independent of effects on AMP-activated kinase or AKT. We conclude that resveratrol is an inhibitor of global protein synthesis, and that this effect is mediated through modulation of mTOR-dependent and independent signaling.
doi:10.1371/journal.pone.0029513
PMCID: PMC3248458  PMID: 22242130
6.  Phosphoproteomic Profiling of In Vivo Signaling in Liver by the Mammalian Target of Rapamycin Complex 1 (mTORC1) 
PLoS ONE  2011;6(6):e21729.
Background
Our understanding of signal transduction networks in the physiological context of an organism remains limited, partly due to the technical challenge of identifying serine/threonine phosphorylated peptides from complex tissue samples. In the present study, we focused on signaling through the mammalian target of rapamycin (mTOR) complex 1 (mTORC1), which is at the center of a nutrient- and growth factor-responsive cell signaling network. Though studied extensively, the mechanisms involved in many mTORC1 biological functions remain poorly understood.
Methodology/Principal Findings
We developed a phosphoproteomic strategy to purify, enrich and identify phosphopeptides from rat liver homogenates. Using the anticancer drug rapamycin, the only known target of which is mTORC1, we characterized signaling in liver from rats in which the complex was maximally activated by refeeding following 48 hr of starvation. Using protein and peptide fractionation methods, TiO2 affinity purification of phosphopeptides and mass spectrometry, we reproducibly identified and quantified over four thousand phosphopeptides. Along with 5 known rapamycin-sensitive phosphorylation events, we identified 62 new rapamycin-responsive candidate phosphorylation sites. Among these were PRAS40, gephyrin, and AMP kinase 2. We observed similar proportions of increased and reduced phosphorylation in response to rapamycin. Gene ontology analysis revealed over-representation of mTOR pathway components among rapamycin-sensitive phosphopeptide candidates.
Conclusions/Significance
In addition to identifying potential new mTORC1-mediated phosphorylation events, and providing information relevant to the biology of this signaling network, our experimental and analytical approaches indicate the feasibility of large-scale phosphoproteomic profiling of tissue samples to study physiological signaling events in vivo.
doi:10.1371/journal.pone.0021729
PMCID: PMC3125343  PMID: 21738781
7.  DDisorders of the Growth Plate 
Purpose of the review
To summarize the recent advances in our understanding of the majors genes involved in chondrogenesis and their molecular mechanisms.
Recent findings
Disorders of the growth plate and the resulting skeletal dysplasias are a consequence of defects in genes involved in various stages of the chondrocyte proliferation and differentiation process. Recent identification of disease genes has provided insights into the pathophysiology of many skeletal dysplasias.
Summary
This knowledge enhances our understanding of the physiology and pathophysiology of the growth plate. Many skeletal dysplasias can now be characterized at the molecular level, allowing clinicians to provide accurate molecular diagnoses and counseling. Further research in this area will likely provide insights into possible therapeutic options for disorders of the growth plate.
doi:10.1097/MED.0b013e328331dca2
PMCID: PMC2894809  PMID: 19770649
chondrocyte; growth plate; skeletal dysplasia; chondrocyte-specific transcription; extracellular matrix
8.  The Effect of Rapamycin on Bone Growth in Rabbits 
mTOR is a nutrient-sensing protein kinase that regulates numerous cellular processes. Our prior studies using the mTOR inhibitor, rapamycin, indicate an important role for mTOR in chondrogenesis. We extended our observations to a physiological, in vivo model of bone growth, direct infusion of rapamycin into the proximal tibial growth plates of rabbits. Rapamycin or DMSO vehicle was infused directly into growth plates by an osmotic minipump for 8 weeks. Tibial growth was followed radiographically. At the end of the experiment, growth plates were recovered for histological analysis. Six animals were studied. No untoward effects of rapamycin infusion were found. Bone growth of limbs exposed to rapamycin was slower than control limbs, particularly during the period of most rapid growth. Histological analysis revealed that growth plate height in the rapamycin-infused limbs was reduced. Both the hypertrophic and proliferative zones were significantly smaller in the rapamycin-infused limbs. Direct infusion of rapamycin into proximal tibial growth plates decreased the size of the growth plate and inhibited overall long bone growth. Rapamycin appears to affect both the proliferative and hypertrophic zones of the tibial growth plate. Our results indicate that nutrients may exert a direct effect on long bone growth via mTOR-mediated modulation of chondrogenesis at the growth plate. and suggest that the possible inhibitory effects of rapamycin on skeletal growth warrant further attention before its use in children.
doi:10.1002/jor.20894
PMCID: PMC2894807  PMID: 19382193
growth plate; chondrocytes; mTOR; cell proliferation; cell differentiation
9.  Regulation of Gene Expression in Hepatic Cells by the Mammalian Target of Rapamycin (mTOR) 
PLoS ONE  2010;5(2):e9084.
Background
We investigated mTOR regulation of gene expression by studying rapamycin effect in two hepatic cell lines, the non-tumorigenic WB-F344 cells and the tumorigenic WB311 cells. The latter are resistant to the growth inhibitory effects of rapamycin, thus providing us with an opportunity to study the gene expression effects of rapamycin without confounding effects on cell proliferation.
Methodology/Principal Findings
The hepatic cells were exposed to rapamycin for 24 hr. Microarray analysis on total RNA preparations identified genes that were affected by rapamycin in both cell lines and, therefore, modulated independent of growth arrest. Further studies showed that the promoter regions of these genes included E-box-containing transcription factor binding sites at higher than expected rates. Based on this, we tested the hypothesis that c-Myc is involved in regulation of gene expression by mTOR by comparing genes altered by rapamycin in the hepatic cells and by c-Myc induction in fibroblasts engineered to express c-myc in an inducible manner. Results showed enrichment for c-Myc targets among rapamycin sensitive genes in both hepatic cell lines. However, microarray analyses on wild type and c-myc null fibroblasts showed similar rapamycin effect, with the set of rapamycin-sensitive genes being enriched for c-Myc targets in both cases.
Conclusions/Significance
There is considerable overlap in the regulation of gene expression by mTOR and c-Myc. However, regulation of gene expression through mTOR is c-Myc-independent and cannot be attributed to the involvement of specific transcription factors regulated by the rapamycin-sensitive mTOR Complex 1.
doi:10.1371/journal.pone.0009084
PMCID: PMC2816708  PMID: 20140209
10.  THE ROLE OF THE mTOR NUTRIENT SIGNALING PATHWAY IN CHONDROCYTE DIFFERENTIATION 
The mammalian Target of Rapamycin (mTOR) is a nutrient-sensing protein kinase that regulates numerous cellular processes. Physilogical fetal rat metatarsal explant cultures were used, to study the effect of mTOR inhibition on chondrogenesis. Insulin significantly enhanced bone growth. Rapamycin significantly diminished the growth response to insulin, selectively on hypertrophic zone. Cell proliferation (BrdU incorporation) was unaffected by rapamycin. Similar observation was noted in In vivo injection of rapamycin to E19 fetal rats. In ATDC5 chondrogenic cell line, rapamycin inhibited proteoglycan accumulation and collagen X expression. Rapamycin decreased Indian Hedgehog (Ihh) accumulation, a regulator of chondrocyte differentiation. Furthermore, addition of Ihh to culture media was able to reverse of effect of rapamycin. We conclude that modulation of mTOR signaling contributes to chondrocyte differentiation, perhaps through its ability to regulate Ihh expression. Our findings are consistent with the hypothesis that nutrients, acting through mTOR, directly influence chondrocyte differentiation and long bone growth.
doi:10.1002/dvdy.21464
PMCID: PMC2768549  PMID: 18265001
Chondrocyte; differentiation; mTOR; rapamycin; insulin; receptor; Indian hedgehog; collagen X
11.  Rapamycin Response in Tumorigenic and Non-Tumorigenic Hepatic Cell Lines 
PLoS ONE  2009;4(10):e7373.
Background
The mTOR inhibitor rapamycin has anti-tumor activity across a variety of human cancers, including hepatocellular carcinoma. However, resistance to its growth inhibitory effects is common. We hypothesized that hepatic cell lines with varying rapamycin responsiveness would show common characteristics accounting for resistance to the drug.
Methodology/Principal Findings
We profiled a total of 13 cell lines for rapamycin-induced growth inhibition. The non-tumorigenic rat liver epithelial cell line WB-F344 was highly sensitive while the tumorigenic WB311 cell line, originally derived from the WB-F344 line, was highly resistant. The other 11 cell lines showed a wide range of sensitivities. Rapamycin induced inhibition of cyclin E–dependent kinase activity in some cell lines, but the ability to do so did not correlate with sensitivity. Inhibition of cyclin E–dependent kinase activity was related to incorporation of p27Kip1 into cyclin E–containing complexes in some but not all cell lines. Similarly, sensitivity of global protein synthesis to rapamycin did not correlate with its anti-proliferative effect. However, rapamycin potently inhibited phosphorylation of two key substrates, ribosomal protein S6 and 4E-BP1, in all cases, indicating that the locus of rapamycin resistance was downstream from inhibition of mTOR Complex 1. Microarray analysis did not disclose a unifying mechanism for rapamycin resistance, although the glycolytic pathway was downregulated in all four cell lines studied.
Conclusions/Significance
We conclude that the mechanisms of rapamycin resistance in hepatic cells involve alterations of signaling downstream from mTOR and that the mechanisms are highly heterogeneous, thus predicting that maintaining or promoting sensitivity will be highly challenging.
doi:10.1371/journal.pone.0007373
PMCID: PMC2756589  PMID: 19816606
12.  The α4-Containing Form of Protein Phosphatase 2A in Liver and Hepatic Cells 
Journal of cellular biochemistry  2008;105(1):290-300.
The Ser/Thr phosphatase PP2A is a set of multisubunit enzymes that regulate many cellular processes. In yeast, the PP2A regulatory subunit Tap42 forms part of the Target of Rapamycin (TOR) signaling pathway that links nutrient and energy availability to cell growth. The physiological intersection between the mammalian orthologs of Tap42 and TOR, α4 and mTOR, has not been fully characterized. We used two in vivo models of liver growth in the rat, late gestation fetal development and regeneration after partial hepatectomy, to explore the regulation of the α4-containing form of PP2A. The α4/PP2A catalytic subunit (α4/PP2A-C) complex was present in both fetal and adult liver extracts. There was a trend towards higher levels of α4 protein in fetal liver, but the complex was more abundant in adult liver. Fractionation of extracts by ion exchange chromatography and transient transfection of the AML12 mouse hepatic cell line indicated that α4 associates with PP2A-C but that these complexes have low catalytic activity with both peptide and protein substrates. α4 was able to associate with forms of PP2A-C that were both methylated and non-methylated at the carboxy-terminus. The mTOR inhibitor rapamycin did not block the formation of α4/PP2A-C in liver or hepatic cells, nor did it appear to modulate PP2A activity. Furthermore, sensitivity to the growth inhibitory effects of rapamycin among a panel of hepatic cell lines did not correlate with levels of α4 or α4/PP2A-C. Our results indicate that the yeast Tap42/TOR paradigm is not conserved in hepatic cells.
doi:10.1002/jcb.21830
PMCID: PMC2597445  PMID: 18543252
Protein phosphorylation; mTOR; rapamycin; regeneration; cell growth
13.  Subunit Composition and Developmental Regulation of Hepatic Protein Phosphatase 2A (PP2A) 
The prototypical form of the Ser/Thr phosphatase PP2A is a heterotrimeric complex consisting of catalytic subunit (C), A and B regulatory subunits. C-terminal methylation of PP2A-C influences holoenzyme assembly. Using late gestation development in the rat as an in vivo model of liver growth, we found that PP2A-C protein and activity levels were higher in fetal compared to adult liver extracts. However, unmethylated PP2A-C was much higher in the adult extracts. In MonoQ fractionation, unmethylated C eluted separately from methylated C, which was present predominantly in ABC heterotrimers. Gel filtration chromatography revealed that some unmethylated C was present as free catalytic subunit. In addition, a significant proportion of PP2A was in inactive forms that may involve novel regulatory subunits. Our results indicate that methylation of PP2A-C appears to be a primary determinant for the biogenesis of PP2A heterotrimers.
doi:10.1016/j.abb.2007.02.019
PMCID: PMC1868455  PMID: 17391644
Signal transduction; fetal development; liver; hepatocyte
14.  RAPAMYCIN INHIBITS LIVER GROWTH DURING REFEEDING IN THE RAT VIA CONTROL OF RIBOSOMAL PROTEIN TRANSLATION BUT NOT CAP-DEPENDENT TRANSLATION INITIATION1 
The Journal of nutrition  2006;136(1):27-33.
We have examined the role of the mammalian target of rapamycin (mTOR) in hepatic cell growth. In order to dissociate cell growth from cell proliferation, we employed an in vivo model of non-proliferative liver growth in the rat, refeeding following 48 h of food deprivation. Starvation resulted in a decrease in liver mass, liver protein and cell size, all of which were largely restored after 24 h of refeeding. Administration of the mTOR inhibitor, rapamycin, before the refeeding period partially inhibited the restoration of liver protein content. Refeeding was also associated with an increase in ribosomal protein S6 phosphorylation and phosphorylation of the eukaryotic initiation factor (eIF) 4E binding protein 1 (4E-BP1). 4E-BP1 phosphorylation was accompanied by a decrease in the abundance of the complex containing 4E-BP1 with eIF4E. These changes were prevented by rapamycin administration. However, association of eIF4E and eIF4G and eIF2α phosphorylation, both of which are stimulated by refeeding, were insensitive to rapamycin. The functional significance of these observations was confirmed by polysome fractionation, which showed that translation initiation of 5′ oligopyrimidine tract-containing mRNAs, which encode ribosomal proteins, was inhibited by rapamycin while translation of STAT1, a cap-dependent mRNA, was unaffected. The abundance of ribosomal proteins paralleled total protein content during refeeding in both control and rapamycin-injected rats. We conclude that accretion of liver protein during refeeding is dependent on mTOR-mediated activation of the translation of ribosomal proteins but not dependent on mTOR-mediated activation of cap-dependent translation initiation.
PMCID: PMC1386153  PMID: 16365054
Liver; hepatocyte; mammalian target of rapamycin; signal transduction; ribosome

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