P53 regulation of osteoblast differentiation is mediated through specific microRNAs.

In order to understand the role of the p53 tumor suppressor gene in microRNA expression during osteoblast differentiation, we used a screen to identify microRNAs that were altered in a p53-dependent manner. MicroRNAs from MC3T3-E1 preosteoblasts were isolated from day 0 (undifferentiated) and day 4 (differentiating) and compared to a p53 deficient MC3T3-E1 line treated similarly. Overall, one fourth of all the microRNAs tested showed a reduction of 0.6 fold, and a similar number of them were increased 1.7 fold with differentiation. P53 deficiency caused 40% reduction in expression of microRNAs in differentiating cells, while a small percent (0.03%) showed an increase. Changes in microRNAs were validated using real-time PCR and two microRNAs were selected for further analysis (miR-34b and miR-140). These two microRNAs were increased significantly during differentiation but showed a dramatic reduction in expression in a p53 deficient state. Stable expression of miR-34b and miR-140 in MC3T3-E1 cells resulted in decreases in cell proliferation rates when compared to control cells. There was a 4-fold increase in p53 levels with miR-34b expression and a less dramatic increase with miR-140. Putative target binding sites for bone specific transcription factors, Runx2 and Osterix, were found for miR-34b, while Runx2, beta catenin and type 1 collagen were found to be miR-140 targets. Western blot analyses and functional assays for the transcription factors Runx2, Osterix and Beta-catenin confirmed microRNA specific interactions. These studies provide evidence that p53 mediated regulation of osteoblast differentiation can also occur through specific microRNAs such as miR-34b and miR-140 that also directly target important bone specific genes.

Gene expression profiles resulting from stable loss of p53 mirrors its role in tissue differentiation.

The tumor suppressor gene p53 is involved in a variety of cellular activities such as cellular stress responses, cell cycle regulation and differentiation. In our previous studies we have shown p53's transcription activating role to be important in osteoblast differentiation. There is still a debate in the literature as to whether p53 inhibits or promotes differentiation. We have found p53 heterozygous mice to show a p53 dependency on some bone marker gene expression that is absent in knockout mice. Mice heterozygous for p53 also show a higher incidence of osteosarcomas than p53 knockout mice. This suggests that p53 is able to modify the environment within osteoblasts. In this study we compare changes in gene expression resulting after either a transient or stable reduction in p53. Accordingly we reduced p53 levels transiently and stably in C2C12 cells, which are capable of both myoblast and osteoblast differentiation, and compared the changes in gene expression of candidate genes regulated by the p53 pathway. Using a PCR array to assay for p53 target genes, we have found different expression profiles when comparing stable versus transient knockdown of p53. As expected, several genes with profound changes after transient p53 loss were related to apoptosis and cell cycle regulation. In contrast, stable p53 loss produced a greater change in MyoD and other transcription factors with tissue specific roles, suggesting that long term loss of p53 affects tissue homeostasis to a greater degree than changes resulting from acute loss of p53. These differences in gene expression were validated by measuring promoter activity of different pathway specific genes involved in differentiation. These studies suggest that an important role for p53 is context dependent, with a stable reduction in p53 expression affecting normal tissue physiology more than acute loss of p53.

Vitamin D directly regulates Mdm2 gene expression in osteoblasts.

While Mdm2 is an important negative regulator of the p53 tumor suppressor, it also possesses p53-independent functions in cellular differentiation processes. Mdm2 expression is alternatively regulated by two P1 and P2 promoters. In this study we show that the P2-intiated transcription of Mdm2 gene is activated by 1,25-dihydroxy vitamin D3 in MC3T3 cells. By using P1 and P2-specific reporters, we demonstrate that only the P2-promoter responds to vitamin D treatment. We have further identified a potential vitamin D receptor responsive element proximal to the two p53 response elements within the Mdm2 P2 promoter. Using cell lines that are p53-temperature sensitive and p53-null, we show requirement of p53 for VDR-mediated up regulation of Mdm2 expression. Our results indicate that 1,25-dihydroxy vitamin D3 and its receptor have a role in the regulation of P2-initiated Mdm2 gene expression in a p53-dependent way.

Functional genomics unique to week 20 post wounding in the deep cone/fat dome of the Duroc/Yorkshire porcine model of fibroproliferative scarring.

BACKGROUND: Hypertrophic scar was first described over 100 years ago; PubMed has more than 1,000 references on the topic. Nevertheless prevention and treatment remains poor, because 1) there has been no validated animal model; 2) human scar tissue, which is impossible to obtain in a controlled manner, has been the only source for study; 3) tissues typically have been homogenized, mixing cell populations; and 4) gene-by-gene studies are incomplete. METHODOLOGY/PRINCIPAL FINDINGS: We have assembled a system that overcomes these barriers and permits the study of genome-wide gene expression in microanatomical locations, in shallow and deep partial-thickness wounds, and pigmented and non-pigmented skin, using the Duroc(pigmented fibroproliferative)/Yorkshire(non-pigmented non-fibroproliferative) porcine model. We used this system to obtain the differential transcriptome at 1, 2, 3, 12 and 20 weeks post wounding. It is not clear when fibroproliferation begins, but it is fully developed in humans and the Duroc breed at 20 weeks. Therefore we obtained the derivative functional genomics unique to 20 weeks post wounding. We also obtained long-term, forty-six week follow-up with the model. CONCLUSIONS/SIGNIFICANCE: 1) The scars are still thick at forty-six weeks post wounding further validating the model. 2) The differential transcriptome provides new insights into the fibroproliferative process as several genes thought fundamental to fibroproliferation are absent and others differentially expressed are newly implicated. 3) The findings in the derivative functional genomics support old concepts, which further validates the model, and suggests new avenues for reductionist exploration. In the future, these findings will be searched for directed networks likely involved in cutaneous fibroproliferation. These clues may lead to a better understanding of the systems biology of cutaneous fibroproliferation, and ultimately prevention and treatment of hypertrophic scarring.

Detection of gene orthology from gene co-expression and protein interaction networks.

BACKGROUND: Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes across different pathways, and understanding the evolution of gene families. RESULTS: We exploit features derived from the alignment of protein-protein interaction networks and gene-coexpression networks to reconstruct KEGG orthologs for Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository and Mus musculus and Homo sapiens and Sus scrofa gene coexpression networks extracted from NCBI's Gene Expression Omnibus using the decision tree, Naive-Bayes and Support Vector Machine classification algorithms. CONCLUSIONS: The performance of our classifiers in reconstructing KEGG orthologs is compared against a basic reciprocal BLAST hit approach. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit.

Gene expression in hypothalamus, liver, and adipose tissues and food intake response to melanocortin-4 receptor agonist in pigs expressing melanocortin-4 receptor mutations.

Transcriptional profiling was used to identify genes and pathways that responded to intracerebroventricular injection of melanocortin-4 receptor (MC4R) agonist [Nle(4), d-Phe(7)]-α-melanocyte stimulating hormone (NDP-MSH) in pigs homozygous for the missense mutation in the MC4R, D298 allele (n = 12), N298 allele (n = 12), or heterozygous (n = 12). Food intake (FI) was measured at 12 and 24 h after treatment. All pigs were killed at 24 h after treatment, and hypothalamus, liver, and back-fat tissue was collected. NDP-MSH suppressed (P < 0.004) FI at 12 and 24 h in all animals after treatment. In response to NDP-MSH, 278 genes in hypothalamus (q ≤ 0.07, P ≤ 0.001), 249 genes in liver (q ≤ 0.07, P ≤ 0.001), and 5,066 genes in fat (q ≤ 0.07, P ≤ 0.015) were differentially expressed. Pathway analysis of NDP-MSH-induced differentially expressed genes indicated that genes involved in cell communication, nucleotide metabolism, and signal transduction were prominently downregulated in the hypothalamus. In both liver and adipose tissue, energy-intensive biosynthetic and catabolic processes were downregulated in response to NDP-MSH. This included genes encoding for biosynthetic pathways such as steroid and lipid biosynthesis, fatty acid synthesis, and amino acid synthesis. Genes involved in direct energy-generating processes, such as oxidative phosphorylation, electron transport, and ATP synthesis, were upregulated, whereas TCA-associated genes were prominently downregulated in NDP-MSH-treated pigs. Our data also indicate a metabolic switch toward energy conservation since genes involved in energy-intensive biosynthetic and catabolic processes were downregulated in NDP-MSH-treated pigs.

Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency.

Residual feed intake (RFI) is a measure of feed efficiency, in which low RFI denotes improved feed efficiency. Caloric restriction (CR) is associated with feed efficiency in livestock species and to human health benefits, such as longevity and cancer prevention. We have developed pig lines that differ in RFI, and we are interested in identifying the genes and pathways that underlie feed efficiency. Prepubertal Yorkshire gilts with low RFI (n = 10) or high RFI (n = 10) were fed ad libitum or fed at restricted intake of 80% of maintenance energy requirements for 8 days. We measured serum metabolites and hormones and generated transcriptional profiles of liver and subcutaneous adipose tissue on these animals. Overall, 6,114 genes in fat and 305 genes in liver were differentially expressed (DE) in response to CR, and 311 genes in fat and 147 genes in liver were DE due to RFI differences. Pathway analyses of CR-induced DE genes indicated a dramatic switch to a conservation mode of energy usage by down-regulating lipogenesis and steroidogenesis in both liver and fat. Interestingly, CR altered expression of genes in immune and cell cycle/apoptotic pathways in fat, which may explain part of the CR-driven lifespan enhancement. In silico analysis of transcription factors revealed ESR1 as a putative regulator of the adaptive response to CR, as several targets of ESR1 in our DE fat genes were annotated as cell cycle/apoptosis genes. The lipid metabolic pathway was overrepresented by down-regulated genes due to both CR and low RFI. We propose a common energy conservation mechanism, which may be controlled by PPARA, PPARG, and/or CREB in both CR and feed-efficient pigs.

ANEXdb: an integrated animal ANnotation and microarray EXpression database.

To determine annotations of the sequence elements on microarrays used for transcriptional profiling experiments in livestock species, currently researchers must either use the sparse direct annotations available for these species or create their own annotations. ANEXdb ( http://www.anexdb.org ) is an open-source web application that supports integrated access of two databases that house microarray expression (ExpressDB) and EST annotation (AnnotDB) data. The expression database currently supports storage and querying of Affymetrix-based expression data as well as retrieval of experiments in a form ready for NCBI-GEO submission; these services are available online. AnnotDB currently houses a novel assembly of approximately 1.6 million unique porcine-expressed sequence reads called the Iowa Porcine Assembly (IPA), which consists of 140,087 consensus sequences, the Iowa Tentative Consensus (ITC) sequences, and 103,888 singletons. The IPA has been annotated via transfer of information from homologs identified through sequence alignment to NCBI RefSeq. These annotated sequences have been mapped to the Affymetrix porcine array elements, providing annotation for 22,569 of the 23,937 (94%) porcine-specific probe sets, of which 19,253 (80%) are linked to an NCBI RefSeq entry. The ITC has also been mined for sequence variation, providing evidence for up to 202,383 SNPs, 62,048 deletions, and 958 insertions in porcine-expressed sequence. These results create a single location to obtain porcine annotation of and sequence variation in differently expressed genes in expression experiments, thus permitting possible identification of causal variants in such genes of interest. The ANEXdb application is open source and available from SourceForge.net.

Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant.

Transcriptional profiling coupled with blood metabolite analyses were used to identify porcine genes and pathways that respond to a fasting treatment or to a D298N missense mutation in the melanocortin-4 receptor (MC4R) gene. Gilts (12 homozygous for D298 and 12 homozygous for N298) were either fed ad libitum or fasted for 3 days. Fasting decreased body weight, backfat, and serum urea concentration and increased serum nonesterified fatty acid. In response to fasting, 7,029 genes in fat and 1,831 genes in liver were differentially expressed (DE). MC4R genotype did not significantly affect gene expression, body weight, backfat depth, or any measured serum metabolite concentration. Pathway analyses of fasting-induced DE genes indicated that lipid and steroid synthesis was downregulated in both liver and fat. Fasting increased expression of genes involved in glucose sparing pathways, such as oxidation of amino acids and fatty acids in liver, and in extracellular matrix pathways, such as cell adhesion and adherens junction in fat. Additionally, we identified DE transcription factors (TF) that regulate many DE genes. This confirms the involvement of TF, such as PPARG, SREBF1, and CEBPA, which are known to regulate the fasting response, and implicates additional TF, such as ESR1. Interestingly, ESR1 controls several fasting induced genes in fat that are involved in cell matrix morphogenesis. Our findings indicate a transcriptional response to fasting in two key metabolic tissues of pigs, which was corroborated by changes in blood metabolites, and the involvement of novel putative transcriptional regulators in the immediate adaptive response to fasting.

Identification of differential gene expression during porcine conceptus rapid trophoblastic elongation and attachment to uterine luminal epithelium.

Early embryonic development in the pig is characterized by a rapid elongation of the conceptus trophectoderm on days 11-12 of gestation. Initially, the conceptus trophoblast is morphologically rearranged from a 10-mm sphere into a tubular shape, transitioning into a thin filamentous form >150 mm in length in 2-3 h, followed by continued expansion within the uterine lumen for several days. Conceptus elongation is critical for establishing adequate placental surface area needed for embryo and fetal survival throughout gestation. The objective of this study was to characterize conceptus gene expression during trophoblastic elongation and the early attachment to the uterine endometrium on days 11-14 of gestation with the GeneChip Porcine Genome Array. In all, 3,759 different probe sets were statistically different in at least one comparison [spherical vs. tubular, spherical vs. day 12 filamentous (D12F), spherical vs. day 14 filamentous (D14F), tubular vs. D12F, tubular vs. D14F, and D12F vs. D14F]. When restricted to the spherical vs. D12F and D12F vs. D14F comparisons, 482 and 232 genes, respectively, were statistically different with greater than twofold change in expression. Utilization of k-means clustering, in addition to the Database for Annotation, Visualization, and Integrated Discovery (DAVID), identified genes of interest. Quantitative RT-PCR expression profiles for interferon-gamma (IFNG), heat shock protein 27 kDa (HSPB1), angiomotin, B-cell linker (BLNK), chemokine ligand 14 (CXCL14), parathyroid hormone-like hormone (PTHLH), and maspin were supportive of the GeneChip Porcine Genome Array data.

Analysis of porcine transcriptional response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the mesenteric lymph node.

BACKGROUND: Specific knowledge of the molecular pathways controlling host-pathogen interactions can increase our understanding of immune response biology as well as provide targets for drug development and genetic improvement of disease resistance. Toward this end, we have characterized the porcine transcriptional response to Salmonella enterica serovar Choleraesuis (S. Choleraesuis), a Salmonella serovar that predominately colonizes swine, yet can cause serious infections in human patients. Affymetrix technology was used to screen for differentially expressed genes in pig mesenteric lymph nodes (MLN) responding to infection with S. Choleraesuis at acute (8 hours (h), 24 h and 48 h post-inoculation (pi)) and chronic stages (21 days (d) pi). RESULTS: Analysis of variance with false discovery rate control identified 1,853 genes with significant changes in expression level (p-value < 0.01, q-value < 0.26, and fold change (FC) > 2) during infection as compared to un-inoculated control pigs. Down-regulation of translation-related genes at 8 hpi and 24 hpi implied that S. Choleraesuis repressed host protein translation. Genes involved in the Th1, innate immune/inflammation response and apoptosis pathways were induced significantly. However, antigen presentation/dendritic cell (DC) function pathways were not affected significantly during infection. A strong NFkappaB-dependent response was observed, as 58 known NFkappaB target genes were induced at 8, 24 and/or 48 hpi. Quantitative-PCR analyses confirmed the microarray data for 21 of 22 genes tested. Based on expression patterns, these target genes can be classified as an "Early" group (induced at either 8 or 24 hpi) and a "Late" group (induced only at 48 hpi). Cytokine activity or chemokine activity were enriched within the Early group genes GO annotations, while the Late group was predominantly composed of signal transduction and cell metabolism annotated genes. Regulatory motif analysis of the human orthologous promoters for both Early and Late genes revealed that 241 gene promoters were predicted to contain NFkappaB binding sites, and that of these, 51 Early and 145 Late genes were previously not known to be NFkappaB targets. CONCLUSION: Our study provides novel genome-wide transcriptional profiling data on the porcine response to S. Choleraesuis and expands the understanding of NFkappaB signaling in response to Salmonella infection. Comparison of the magnitude and timing of porcine MLN transcriptional response to different Salmonella serovars, S. Choleraesuis and S. Typhimurium, clearly showed a larger but later transcriptional response to S. Choleraesuis. Both microarray and QPCR data provided evidence of a strong NFkappaB-dependent host transcriptional response during S. Choleraesuis infection. Our data indicate that a lack of strong DC-mediated antigen presentation in the MLN may cause S. Choleraesuis infected pigs to develop a systemic infection, and our analysis predicts nearly 200 novel NFkappaB target genes which may be applicable across mammalian species.

Expression of collagen genes in the cones of skin in the Duroc/Yorkshire porcine model of fibroproliferative scarring.

During the past decades there has been minimal improvement in prevention and treatment of hypertrophic scarring. Reasons include the lack of a validated animal model, imprecise techniques to dissect scar into the histologic components, and limited methodology for measurement of gene expression. These problems have been addressed with the Duroc/Yorkshire model of healing, laser capture microdissection, and the Affymetrix Porcine GeneChip. Here we compared collagen gene expression in fibroproliferative healing in the Duroc breed to nonfibroproliferative healing in the Yorkshires. We made shallow and deep dorsal wounds, biopsied at 1, 2, 3, 12, and 20 weeks. We sampled the dermal cones by laser capture microdissection, extracted and amplified the RNA, and hybridized Affymetrix Porcine GeneChips. We also obtained samples of human hypertrophic scar approximately 20 weeks postinjury. Data were normalized and statistical analysis performed with mixed linear regression using the Bioconductor R/maanova package. Genes for further analysis were also restricted with four biologic criteria, including that the 20-week deep Duroc expression match the human samples. Eleven collagen genes and seven collagen types were differentially over expressed in deep Duroc wounds including 1a1, 1a2, 3a1, 4a1, 4a2, 5a1, 5a2, 5a3, 6a3 (transcript variant 5), 14a1 and 15a1. COL7a1 gene was differentially under expressed in deep Duroc wounds. The results suggest that collagens I, III, IV, V, VI, VII, XIV, and XV [corrected] are involved in the process of fibroproliferative scarring. With these clues, we will attempt to construct the regulatory pathway(s) of fibroproliferative healing.

Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium.

To elucidate the host transcriptional response to Salmonella enterica serovar Typhimurium, Affymetrix porcine GeneChip analysis of pig mesenteric lymph nodes was used to identify 848 genes showing differential expression across different times after inoculation or when compared to non-inoculated controls. Annotation analyses showed that a high proportion of these differentially expressed (DE) genes are involved in immune and inflammatory responses. T helper 1, innate/inflammatory, and antigen-processing pathways were induced at 24 h post-inoculation (hpi) and/or 48 hpi, while apoptosis and antigen presentation/dendritic cell function pathways were downregulated at 8 hpi. Cluster analyses revealed that most DE genes annotated as NFkappaB targets were grouped into a specific induced subcluster, while many translation-related DE genes were found in a repressed subcluster. Quantitative polymerase chain reaction analyses confirmed the Affymetrix results, revealing transcriptional induction of NFkappaB target genes at 24 hpi and suppression of the NFkappaB pathway from 24 to 48 hpi. We propose that such NFkappaB suppression in antigen-presenting cells may be the mechanism by which S. Typhimurium eludes a strong inflammatory response to establish a carrier status in pigs.

Advances in swine transcriptomics.

The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig.