Cellular Protein Metabolism Research Articles

A preliminary study of differentially expressed genes of the scallop Chlamys farreri against acute viral necrobiotic virus (AVNV)

The scallop Chlamys farreri is one of the most important aquaculture species in northern coastal provinces. However, the sustainable development of scallop industry is currently threatened by a notorious pathogen named as acute viral necrobiotic virus (AVNV), which often causes mass mortality of the animals. Despite that great attention has been focused on this novel pathogen, little knowledge about the host–virus interactions is available. In this study, suppression subtractive hybridization (SSH) was employed to identify the up-regulated differentially expressed genes in the hemocytes of C. farreri challenged by AVNV. A forward subtracted cDNA library was finally constructed and 288 positive colonies representing differentially genes were screened to perform sequencing. A total of 275 ESTs were used for further analysis using bioinformatics tools after vector screening, among which 167 ESTs could be finally identified, with significant match (E values <1 × 10−3) to the deposited genes (proteins) in the corresponding databases. These genes could be classified into ten categories according to their Gene Ontology annotations of biological processes and molecular functions, i.e. cell defense and homeostasis (13.82%), cellular protein metabolic process (14.90), cellular metabolism (13.09%), cytoskeletal or cellular component (5.82%), transcription regulation or RNA processing (2.18%), cell division (meiosis)/apoptosis (2.18%), DNA metabolic process and repair (1.45%), cell adhesion/signaling (1.09%), microsatellite (0.73%), and ungrouped or unknown functions (6.88). The possible biological significance of some novel genes (mainly immune and homeostasis related genes) in the host response to AVNV were discussed. This study is the first global analysis of differentially expressed genes in hemocytes from AVNV-infected C. farreri, and in addition to increasing our understanding of the molecular pathogenesis of this virus-associated scallop disease, the results presented here should provide new insights into the molecular basis of host–pathogen interactions in C. farreri.

Characterization of Clostridium acetobutylicum Protein Interaction Network from Butanol Fermentation

Successful industrial production of butanol requires an in depth knowledge of Clostridium acetobutylicum. Development of computational approaches for protein interaction studies enabled us to generate a predicted protein interaction network of C. acetobutylicum ATCC 824. In this study, over 400 proteins from C. acetobutylicum were identified during butanol fermentation using shotgun proteomics and from only 217 proteins, we predicted 1947 interactions. This analysis showed that C. acetobutylicum proteins form a highly interconnected network and the main represented functions were found to be protein synthesis, carbohydrate metabolism and butanoate metabolism. We further used this interaction data to analyse the enrichment of gene ontology terms and pathways in C. acetobutylicum. Our analysis revealed that biological processes such as translation, cellular protein metabolic process, biosynthetic process, and pathways including glycolysis, butanoate metabolism were significantly enriched in C. acetobutylicum during butanol fermentation. This study provides a novel insight into the functional mechanisms of C. acetobutylicum at the network level complementing the current knowledge in relation to this industrially important organism.

Revealing the Underlying Mechanism of Ischemia Reperfusion Injury Using Bioinformatics Approach

Background/Aims: To reveal the potential pathogenesis of ischemia/reperfusion (I/R) injury. Methods: GSE9943 were downloaded from Genome Expression Omnibus database, including I/R and control samples for both Brown Norway (BN) and Sprague Dawley (SD) rats (3 rats/each group). Then differentially expressed genes (DEGs) were identified by limma package. miRNA-target gene network pairs were predicted using WebGestalt, and protein-protein interactions (PPI) were identified based on STRING database, followed by the networks construction using Cytoscape. Next, ClusterONE was used for modules screening. Furthermore, functional analyses were performed to common DEGs and genes. Results: Totally, 23 common DEGs of BR and SD rats were screened, enriched in functions, such as regulation of cellular protein metabolic process, response to wounding, proteinaceous extracellular matrix, and Enzyme inhibitor activity. MIR-29A, MIR-29B and MIR-29C were discovered both in up- and down-regulated miRNA-target gene networks. Genes in the PPI network were significantly disturbed in p53 signaling, complement and coagulation cascades pathway. Four modules were found significantly disturbed cytochrome P450, Serine/threonine protein kinase, calcium binding and Transient receptor potential channel protein domains. Conclusion: During I/R injury, many genes mutated, interrupting several biological functions, pathways and protein domains. MIR-29C and TRPC6 were suggested to be potential novel targets for this disease.

Genome-wide identification and analysis of early heat stress responsive genes in rice

To overcome the challenges presented by predicted climate change, it is important to understand how crops perceive and respond to high temperatures. In this paper, we performed genome-wide transcriptome analysis of rice to identify immediate early genes strongly induced by high temperature. We compared the effects of high temperature (37°C) treatments (for 0.5 or 1h) of seedlings relative to untreated controls (28°C) using the NSF45K array. We then identified 710 genes exhibiting at least 2-fold up-regulation at both time points. From the comparison of this dataset with other publicly available rice datasets under heat stress [i.e., for 10 and 30 min (early heat response), and 10 h at 42°C (late heat response)], we identified 244 genes and 238 genes at least 2 fold upregulated during the early and late heat responses, respectively. We defined 244 genes as early heat stress responsive group and 238 genes as prolonged heat stress responsive group. Gene ontology (GO) enrichment analysis revealed that a chaperone-mediated protein folding cofactor was the most significantly over-represented GO term associated with the prolonged heat response. Processes involved in cellular protein metabolism, protein folding, response to stress, small GTPase mediated signal transduction, and glycolysis are enriched in both early and prolonged heat responses, suggesting a role for these genes in the general heat stress response. Enrichment of processes involved in cell redox homeostasis, intracellular protein transport, electron transport chain, and regulation of transcription (DNA-dependent) were only identified in the early heat response. In addition, we observed that a large portion of the genes relating to the prolonged heat response were also associated with responses to other abiotic stresses such as drought, salt, cold, and submergence. Our data contribute to a better understanding the molecular mechanism of heat stress response in rice.

Role of AMPK in UVB-induced DNA damage repair and growth control

Skin cancer is the most common cancer in the U.S., while DNA-damaging UVB radiation from the sun remains the major environmental risk factor. Reducing skin cancer incidence is becoming an urgent issue. The energy-sensing enzyme 5’-AMP-activated protein kinase (AMPK) plays a key role in the regulation of cellular lipid and protein metabolism in response to stimuli such as exercise and changes in fuel availability. However, the role AMPK in the response of skin cells to UVB damage and in skin cancer prevention remains unknown. Here we show that AMPK activation is reduced in human and mouse squamous cell carcinoma as compared with normal skin, and by UVB irradiation, suggesting that AMPK is a tumor suppressor. At the molecular level, AMPK deletion reduced the expression of the DNA repair protein xeroderma pigmentosum C (XPC) and UVB-induced DNA repair. AMPK activation by its activators AICAR (5-aminoimidazole-4-carboxamide ribonucleoside) and metformin (N’,N’-dimethylbiguanide), the most widely used anti-diabetic drug, increased the expression of XPC expression and UVB-induced DNA repair in mouse skin, normal human epidermal keratinocytes, and AMPK wild-type cells but not in AMPK deficient cells, indicating an AMPK-dependent mechanism. Topical treatment with AICAR and metformin not only delayed onset of UVB-induced skin tumorigenesis but also reduced tumor multiplicity. Furthermore, AMPK deletion increased ERK activation and cell proliferation, while AICAR and metformin inhibited ERK activation and cell proliferation in keratinocytes, mouse skin, AMPK wild-type and AMPK deficient cells, suggesting an AMPK-independent mechanism. Finally, in UVB-damaged tumor-bearing mice, both topical and systemic metformin prevented the formation of new tumors and suppressed growth of established tumors. Our findings not only suggest that AMPK is a tumor suppressor in the skin by promoting DNA repair and controlling cell proliferation, but also demonstrate previously unknown mechanisms by which the AMPK activators prevent UVB-induced skin tumorigenesis.

Proteomic Analysis Identifies Dysfunction in Cellular Transport, Energy, and Protein Metabolism in Different Brain Regions of Atypical Frontotemporal Lobar Degeneration

Frontotemporal lobar degeneration (FTLD) is an umbrella term for a heterogeneous group of young-onset dementias of uncertain prevalence and incidence worldwide. Atypical cases of FTLD with fused in sarcoma inclusions (aFTLD-U) have been described recently, but their molecular characterization is still due. Using shotgun mass spectrometry, we identified a total of 107 differentially expressed proteins in the prefrontal cortex, cerebellum and occipital lobe from aFTLD-U patients compared to controls. These proteins are involved in a range of biological pathways such as cellular transport in the prefrontal cortex, energy metabolism in the cerebellum, and protein metabolism in the occipital lobe. In addition, they were validated by selective reaction monitoring (SRM). Comparison of the aFTLD-U proteomic findings with similar studies of Alzheimer's disease and schizophrenia led to identification of proteins that may be related to dementias and psychoses, respectively. Further studies of aFTLD-U and other FTLD subtypes are warranted, although this will require intensive biobanking efforts.

Site-specific protein cleavage in vivo by an intein-derived protease

Site-specific protein cleavage is a ubiquitous process in cellular protein metabolism, yet molecular tools to provide control of protein cleavage inside living cells remain scarce. Here, we show that the C-terminal intein fragment of the non-canonical Ssp ( Synechocystis sp. PCC6803) DnaB S1 split-intein can be used as a site-specific protease for in vivo protein cleavage both in bacterial and eukaryotic cells. Mutagenesis data indicate a broad tolerance of the intein-derived protease (IP) toward the amino acid upstream of the cleavage site. Furthermore, deletion studies reveal that the recognition sequence for the IP can be as short as ten amino acids. The structural features underlying the cleavage reaction preclude unintended proteolysis of endogenous proteins, thus ensuring that negative effects on cell viability are minimal.

Apigenin, a chemopreventive bioflavonoid, induces AMP‐activated protein kinase activation in human keratinocytes

AMP-activated protein kinase (AMPK) is a cellular energy sensor that is conserved in eukaryotes. Although AMPK is traditionally thought to play a major role in the regulation of cellular lipid and protein metabolism, recent discoveries reveal that AMPK inhibits mammalian target of rapamycin (mTOR) signaling and connects with several tumor suppressors such as liver kinase B1 (LKB1), p53, and tuberous sclerosis complex 2 (TSC2), indicating that AMPK may be a potential target for cancer prevention and treatment. For the first time, we demonstrated that apigenin, a naturally occurring nonmutagenic flavonoid, induced AMPK activation in human keratinocytes (both cultured HaCaT cell line and primary normal human epidermal keratinocytes). Through experiments with over-expression of constitutively active Akt and knockdown of LKB1 expression by siRNAs, we further found that the activation of AMPK by apigenin was not dependent on its inhibition of Akt, and was independent of the activation of upstream kinase LKB1. Instead, another upstream kinase of AMPK, calcium/calmodulin-dependent protein kinase kinase-β (CaMKKβ), was required for apigenin-induced AMPK activation. We have demonstrated that knockdown of CaMKKβ expression by siRNA or inhibition of CaMKKβ activity by either CaMKK inhibitor STO-609 or BAPTA-AM (1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid acetoxymethyl ester; a chelator of intracellular Ca(2+)) prevented apigenin-induced AMPK activation. Apigenin-induced AMPK activation inhibited mTOR signaling and further induced autophagy in human keratinocytes. These results suggest that one of the mechanisms by which apigenin exerts its chemopreventive action may be through activation of AMPK and induction of autophagy in human keratinocytes.

Convergence of Logic of Cellular Regulation in Different Premalignant Cells by an Information Theoretic Approach

BackgroundSurprisal analysis is a thermodynamic-like molecular level approach that identifies biological constraints that prevents the entropy from reaching its maximum. To examine the significance of altered gene expression levels in tumorigenesis we apply surprisal analysis to the WI-38 model through its precancerous states. The constraints identified by the analysis are transcription patterns underlying the process of transformation. Each pattern highlights the role of a group of genes that act coherently to define a transformed phenotype.ResultsWe identify a major transcription pattern that represents a contraction of signaling networks accompanied by induction of cellular proliferation and protein metabolism, which is essential for full transformation. In addition, a more minor, "tumor signature" transcription pattern completes the transformation process. The variation with time of the importance of each transcription pattern is determined. Midway through the transformation, at the stage when cells switch from slow to fast growth rate, the major transcription pattern undergoes a total inversion of its weight while the more minor pattern does not contribute before that stage.ConclusionsA similar network reorganization occurs in two very different cellular transformation models: WI-38 and the cervical cancer HF1 models. Our results suggest that despite differences in a list of transcripts expressed in different cancer models the rationale of the network reorganization remains essentially the same.

Influence of mitochondria on gene expression in a citrus cybrid

The production of cybrids, combining nucleus of a species with alien cytoplasmic organelles, is a valuable method used for improvement of various crops. Several citrus cybrids have been created by somatic hybridization. These genotypes are interesting models to analyze the impact of cytoplasmic genome change on nuclear genome expression. Herein, we report genome-wide gene expression analysis in leaves of a citrus cybrid between C. reticulata cv 'Willowleaf mandarin' and C. limon cv 'Eureka lemon' compared with its lemon parent, using a Citrus 20K cDNA microarray. Molecular analysis showed that this cybrid possesses nuclear and chloroplast genomes of Eureka lemon plus mitochondria from Willowleaf mandarin and, therefore, can be considered as a lemon bearing foreign mitochondria. Mandarin mitochondria influenced the expression of a large set of lemon nuclear genes causing an over-expression of 480 of them and repression of 39 genes. Quantitative real-time RT-PCR further confirmed the credibility of microarray data. Genes over-expressed in cybrid leaves are predominantly attributed to the functional category "cellular protein metabolism" whereas in the down-regulated none functional category was enriched. Overall, mitochondria replacement affected different nuclear genes including particularly genes predicted to be involved in mitochondrial retrograde signaling. Mitochondria regulate all cell structures even chloroplast status. These results suggest that nuclear gene expression is modulated with respect to new information received from the foreign organelle, with the final objective to suit specific needs to ensure better cell physiological balance.

Intracellular molecular effects of insulin resistance in patients with metabolic syndrome

Aim of the studyPatients with metabolic syndrome (MetS) have an increased risk of cardiovascular disease. Data obtained from muscle biopsies have demonstrated altered insulin signaling (IS) in patients with MetS. The IS regulates critical cell functions including molecular-regulated cellular metabolite fluxes, protein and energetic metabolism, cell proliferation and apoptosis with consequent regulation of cell life including endothelial homeostasis and blood coagulation. However, little is known about blood cell IS in MetS patients. The aim of this study was to develop a method to evaluate IS in peripheral lymphocytes to identify altered intracellular molecules in patients with MetS to use as risk biomarkers of vascular thrombosis.Patients and MethodsWe investigated 40 patients with MetS and 20 controls. MetS was defined according to guidelines from the US National Cholesterol Education Program Adult Treatment Panel III. Blood samples were taken from all participants. Total mononuclear cells were isolated from peripheral blood using density gradient centrifugation. IS molecules were evaluated using Western blot analysis followed by computer-assisted densitometer evaluation.ResultsLymphocytes of MetS patients showed a reduced mTOR expression (the mammalian target of rapamycin) which is a fundamental molecule of IS. Major impairment of IS was confirmed by reduced upstream and downstream mTOR molecules which regulate fundamental cells metabolic functions.ConclusionsIn patients with MetS, we found a reduction of mTOR and other mTOR-related molecules involved in insulin resistance, cell repair, coagulation and vasculogenesis. A reduced expression of mTOR may reflect an increased risk of vascular thrombosis.

Identification of Water Deficit Stress Upregulated Genes in Sugarcane

Sugarcane represents an important renewable source among biofuel crops with high capability to assimilate carbon among the C4 plants. Limited availability of freshwater renders this crop uneconomical, warranting the necessity for the development of varieties with higher water use efficiency and tolerant to water deficiency stress. Sugarcane variety cv. Co740 was subjected to varied levels of water deficiency stress to isolate transcripts differentially expressed to the imposed stress. The leaf relative water content was used as a measure to estimate the stress response. PCR-based cDNA suppression subtractive hybridization technique was applied to construct forward subtracted library for differentially expressed genes under stress. Dot blot-selected 158 clones showing elevated response were sequenced, of which 62% resembled similarity with known functional genes, 12% with hypothetical proteins of plant origin, while 26% represented new unknown sequences. Annotation of these differentially expressed sequence tags (ESTs) in the moderately water deficit stress-tolerant cultivar predicted that most of them encoded proteins involved in cellular organization, protein metabolism, signal transduction, and transcription. Further, semi-quantitative reverse transcriptase PCR carried out for five genes projected the involvement of these ESTs in stress alleviation/tolerance. Results from this study may help in targeting useful genes for improving drought tolerance in sugarcane and other grasses.

The Effects of Two Different Ganoderma Species (Lingzhi) on Gene Expression in Human Monocytic THP-1 Cells

Lingzhi (ganoderma) is an important woody mushroom that is known for its medicinal benefits in China since ancient times. The mode of action in humans is still not clear. Using microarray technology, we have compared the ethanol extracts of two different lingzhi (red lingzhi, G. lucidum; and purple lingzhi, G. sinense) for their effects on gene expression profile in human monocytic cells. Our results suggest that at best ≈25% of target genes are common to the two lingzhi: functionally ranging from cell development, negative regulation of cellular process, and cellular protein metabolic process to signal transduction and transcription. The pathways mediated by purple lingzhi focus on inflammation and immune response, whereas red lingzhi modestly increases levels of expression for genes involved in macromolecule metabolism. Furthermore, our ethanolic extracts of both red and purple lingzhi do not inhibit monocytic cell growth. The extract of red lingzhi does not have significant effect on the genes in the nuclear factor kappa B (NFκB) pathway (an important inflammation pathway), whereas the extract of purple lingzhi can increase multiple key genes in the NFκB pathway. Altogether, our results suggest that the common mode of action for lingzhi is complex; and different species of Ganoderma can modulate different pathways in human cells.

Proteomic analysis of brain proteins of rats exposed to high fluoride and low iodine

Epidemiological investigations reveal that high fluoride and low iodine have strong adverse effects on the intelligence quotient (IQ) of children. Studies also report that in some high fluoride areas, iodine deficiency also exists, especially in China. Here, with the proteomic techniques, we first report on the proteomic changes in brain proteins in offspring rats at postnatal day 20 exposed to high fluoride and/or low iodine. To investigate molecular mechanisms of central neural system injury induced by the above two elements, proteins were isolated and profiled by two-dimensional gel electrophoresis (2DE). By the analysis of Image-Master 2D Elite software, 71 protein spots in 2DE gels of treatment groups were gained and up- or down-regulated by two folds, and 5 proteins were regulated by five folds, with the comparison to the control group. The proteins changed by five folds were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The identified proteins are mainly related with cellular signaling, energy metabolism, and protein metabolism and provide a valuable clue to explore the mechanism underlining the neurotoxicity of high fluoride and low iodine. Moreover, these results could provide potential biomarkers for hazards caused by excessive fluoride and low iodine.

Crystallization and preliminary X-ray crystallographic analysis of Lon fromThermococcus onnurineusNA1

Lon is an oligomeric ATP-dependent protease that degrades defective or denatured proteins as well as some folded proteins for the control of cellular protein quality and metabolism. Lon from Thermococcus onnurineus NA1 was purified and crystallized at 295 K. A 2.0 A resolution data set was collected using synchrotron radiation. The crystals belonged to space group P6(3), with unit-cell parameters a = 121.45, b = 121.45, c = 195.24 A. Assuming the presence of two monomers in the asymmetric unit, the solvent content was estimated to be about 60.7%.

Quantitative proteomic analysis of ribosomal protein L35b mutant of Saccharomyces cerevisiae

Recent studies have revealed that in higher eukaryotes, several ribosomal proteins are involved in some pathological events or developmental defects, indicating that ribosomal proteins perform unconventional functions other than protein biosynthesis. To obtain an insight into the novel roles of ribosomal proteins, we aimed to analyze the changes in proteome expression in ribosomal protein mutants by using Saccharomyces cerevisiae as a model system. We introduced the rpl35bΔ mutation into the 4159 green fluorescent protein (GFP)-tagged yeast strains by using the synthetic genetic array (SGA) method, and performed quantitative proteomic analysis by using a multilabel microplate reader and flow cytometer. We identified 22 upregulated and 20 downregulated proteins in the rpl35bΔ mutant. These proteins were primarily classified into the Gene Ontology (GO) categories of cellular biosynthetic process, translation, protein or nucleotide metabolic process, cell wall organization and biogenesis, and hyperosmotic response. We also investigated the correlation between the mRNA and protein levels of the identified proteins. Our results show that a ribosomal protein mutation can lead to perturbation in the expression of several proteins, including some other ribosomal proteins. Furthermore, our approach of combining a library of GFP-tagged yeast strains and the SGA method provides an effective and highly sensitive method for dynamic analysis of the effects of various mutations on proteome expression.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) interaction with 3' ends of Japanese encephalitis virus RNA and colocalization with the viral NS5 protein

Replication of the Japanese encephalitis virus (JEV) genome depends on host factors for successfully completing their life cycles; to do this, host factors have been recruited and/or relocated to the site of viral replication. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a cellular metabolic protein, was found to colocalize with viral RNA-dependent RNA polymerase (NS5) in JEV-infected cells. Subcellular fractionation further indicated that GAPDH remained relatively constant in the cytosol, while increasing at 12 to 24 hours postinfection (hpi) and decreasing at 36 hpi in the nuclear fraction of infected cells. In contrast, the redistribution patterns of GAPDH were not observed in the uninfected cells. Co-immunoprecipitation of GAPDH and JEV NS5 protein revealed no direct protein-protein interaction; instead, GAPDH binds to the 3' termini of plus- and minus-strand RNAs of JEV by electrophoretic mobility shift assays. Accordingly, GAPDH binds to the minus strand more efficiently than to the plus strand of JEV RNAs. This study highlights the findings that infection of JEV changes subcellular localization of GAPDH suggesting that this metabolic enzyme may play a role in JEV replication.

Adipose tissue gene expression profiles of healthy young adult and geriatric dogs

Obesity is a major problem in today's dog population, with aged animals having an increased susceptibility to obesity-related comorbidities. A molecular approach to studying adipose tissue may enhance our understanding of its role in energy homeostasis and the disease process. Thus, the objective of this study was to use canine microarrays to compare gene expression profiles of adipose tissue from geriatric and young adult dogs. Adipose tissue samples were collected from six geriatric (12 year-old) and six young adult (one-year-old) female beagles after being fed one of two diets (animal protein-based vs. plant protein-based) for 12 months. RNA samples were hybridised to canine microarrays. Statistical analyses indicated that age had the greatest impact on gene expression, with 65 differentially expressed gene transcripts in geriatric dogs. Diet had a minor impact on gene expression, altering the expression of only 19 gene transcripts. In general, adipose tissue of geriatric dogs had increased expression of genes associated with cell cycle and growth, cell development and structure, cellular trafficking and protein processing, immune function, metabolism, and transcription and translation, as compared with that of young adults. Overall, our mRNA data suggest either an increased population of macrophages or increased inflammatory nature of adipocytes in adipose tissue of aged dogs.

New inhibitors of prion replication that target the amyloid precursor

At present, there is no effective therapy for any of the neurodegenerative amyloidoses, despite renewed efforts to identify compounds active against the various implicated pathogenetic molecules. We have screened a library of 2960 natural and synthetic compounds in two cell lines chronically infected with mouse prions, and have identified eight new inhibitors of prion replication in vitro. They belong to two distinct chemical families that have not previously been recognised as effective in the field of transmissible spongiform encephalopathies: seven are 3-aminosteroids and one is a derivative of erythromycin A with an oxime functionality. Our results suggest that these aminosteroids inhibit prion replication by triggering a common target, possibly implicated in the regulatory pathways of cellular prion protein metabolism. Furthermore, using a quantitative approach for the study of protein stability, it was shown that the erythromycin A derivative altered prion protein stability by direct interaction. Such direct targeting of this amyloid precursor might provide new clues for the understanding of prion diseases and, more importantly, help to define new molecules that are active against prion diseases.

Peripheral Blood Gene Expression Profile Associated with Sustained Virologic Response after Peginterferon Plus Ribavirin Therapy for Chronic Hepatitis-C Genotype 1

We investigated the relationship between global gene expression in peripheral blood mononuclear cells (PBMCs) during the first 4 weeks of peginterferon alfa and ribavirin therapy and long-term eradication of hepatitis-C genotype 1 infections in 23 patients. A sustained virologic response (SVR), defined as an undetected serum HCV ribonucleic acid (RNA) at week 72, was the virologic response endpoint. PBMC RNA was prepared at week 0 and week 4 from 23 patients (17 black and 6 white Americans), and hybridized to Affymetrix GeneChip HG-U133 plus 2.0 arrays. Compared to week 0, 269 genes were differentially expressed at week 4 of treatment, including many genes regulated by alpha interferons and associated with host immunity (p<0.0001), cell signal transduction (p<0.001) and cellular protein metabolism (p<0.001). Expression of these 269 genes at week 0 and week 4 did not differ significantly between patients with and without a SVR. In contrast, SVR was associated with differential expression of 98 genes at week 4 (false discovery rate <0.01). Many of the genes have been implicated in control of HCV lifecycle and thus may play important roles in HCV clearance during peginterferon and ribavirin therapy.