Differences In mRNA Expression Levels Research Articles

DNA methyltransferase expression and DNA methylation in human hepatocellular carcinoma and their clinicopathological correlation

Aberrant DNA methylation on CpG islands is one of the most consistent epigenetic changes in human cancers, and the methylation process is catalyzed by DNA methyltransferase (DNMT). We evaluated i) the mRNA levels of three DNMTs; DNMT1, DNMT3a and DNMT3b, in 25 hepatocellular carcinomas (HCCs), in their corresponding non-cancerous liver tissues and in 7 normal livers by using real-time reverse transcriptase-polymerase chain reaction; ii) nuclear expression of DNMT1 and DNMT3a proteins in the HCCs by immunohistochemistry, iii) the methylation status of 5 genes; p16, p15, E-cadherin, HIC-1 and RASSF1A in the same tissues, and iv) the relationships between the above results and the clinicopathological characteristics, including prognosis. The differences in mRNA expression levels for DNMT1, DNMT3a and DNMT3b were statistically significant between HCC and normal livers (p<0.001), HCC and chronic hepatitis (p<0.001) and HCC and cirrhosis (p<0.001). An increase in mRNA expression levels of >4-fold for DNMT3b in HCCs was significantly associated with a poorer overall survival (p=0.027) and shorter metastasis-free survival (p=0.0299). A poorer recurrence-free survival was noted in HCCs with a >4-fold increase in DNMT3a mRNA (p=0.0120). The average numbers of methylated genes were 0, 1.27, 1.38 and 2.72 for normal livers, chronic hepatitis, cirrhosis and HCCs, respectively, and this progressive increase from normal livers to chronic hepatitis/cirrhosis through HCC may suggest that tumor suppressor gene methylation is an early event in hepatocarcinogenesis. These results first suggest that hepatocarcinogenesis involves an increased expression of DNMT1, DNMT3a and DNMT3b mRNA and a progressive increase in the number of methylated genes from normal liver, chronic hepatitis/cirrhosis to HCC and secondly that an increase in the DNMT3a and DNMT3b mRNA levels in HCCs relative to their non-cancerous tissues may be a predictor of poor survival.

Effects of interleukin-12p40 gene transfer on rat corneal allograft survival

Purpose Despite the immunologically privileged nature of the cornea, graft rejection remains the major cause of human corneal allograft failure. Gene therapy is an interesting approach to introduce immunoregulatory molecules into the graft or the recipient to prevent rejection. In this study we investigated the immmunomodulatory effects of adenovirus-mediated gene transfer of a Th1 antagonist, interleukin-12p40 (IL-12p40), in vitro and on allogeneic graft survival in a rat experimental keratoplasty model. Methods Donor corneas were transduced with an E1/E3 deleted adenoviral (Ad) vector encoding the IL-12p40 gene (AdIL-12p40) and assayed for the expression of the therapeutic gene. Cell culture supernatants containing IL-12p40 protein were generated by transducing human corneal endothelial cells with AdIL-12p40 and analysed for their capacity to inhibit production of IFN-γ by naive T cells. The effect of both local ( ex vivo Ad-mediated gene transfer) and systemic (i.p.-injection) over-expression of IL-12p40 was investigated by analysing the survival of corneal allografts transplanted from Wistar–Furth rats to fully MHC-class I/II incompatible Lewis rats. Moreover, the intra-graft mRNA-expression profile of cytokines and T cell markers was investigated at different time points after gene transfer. Results Adenovirus-mediated gene transfer in cultured corneas led to significant IL-12p40 protein expression as determined by specific ELISA. Moreover we could show that IL-12p40 protein containing supernatants significantly inhibited the production of IFN-γ by alloreactive naive T cells. Interestingly, neither ex vivo genetic modification of cultured corneas before transplantation nor systemic AdIL-12p40 treatment of recipients receiving allogeneic corneas did improve corneal allograft survival. Real-time RT-PCR analysis of ex vivo modified cornea allografts on day 7 after transplantation showed significantly higher IL-4 mRNA-expression levels in the AdIL-12p40 group compared to the control group. Other significant differences in mRNA-expression levels of intra-graft CD3, CD25, IFN-γ, TNF-α, and IL-10 could not be detected, neither on day 7 nor on the day of rejection. Conclusions Despite the capacity of IL-12p40 protein to inhibit the production of IFN-γ of naive T cells in vitro and some Th1/Th2 shift in vivo, no prolongation of allogeneic graft survival of both AdIL-12p40 modified rat corneas and systemically treated rats could be obtained after transplantation. The possible binding of Ad-mediated IL-12p40 with ubiquitously expressed IL-12p35 in vivo might therefore limit the application of IL-12p40 for the prevention of transplant rejection.

Smooth Muscle α-Actin Deficiency in Myofibroblasts Leads to Enhanced Renal Tissue Fibrosis

Myofibroblasts are a major source of proinflammatory cytokines and extracellular matrix in progressive tissue fibrosis leading to chronic organ failure. Myofibroblasts are characterized by de novo expression of smooth muscle alpha-actin (SMalphaA), which correlates with the extent of disease progression, although their exact role is unknown. In vitro cultured myofibroblasts from kidney of SMalphaA knock-out mice demonstrate significantly more prominent cell motility, proliferation, and type-I procollagen expression than those of wild-type myofibroblasts. These pro-fibrotic properties are suppressed by adenovirus-mediated SMalphaA re-expression, accompanied by down-regulation of focal adhesion proteins. In interstitial fibrosis model, tissue fibrosis area, proliferating interstitial cell number, and type-I procollagen expression are enhanced under SMalphaA deficiency. In mesangioproliferative glomerulonephritis model, cell proliferation in the mesangial area is also enhanced in SMalphaA knock-out mice. Adenoviral SMalphaA introduction into renal interstitium obviously ameliorates tissue fibrosis in interstitial fibrosis model. These results indicate that SMalphaA suppresses the pro-fibrotic properties of myofibroblasts, highlighting the significance of smooth muscle-related proteins in moderating chronic organ fibrosis under pathological conditions.

Identification of clinically-informative biomarkers for risk stratification within the spectrum of gastro-esophageal reflux disease in the South African population

Background : Barrett's esophagus is the precursor of esophageal adenocarcinoma with a 5-year survival rate of 25-30%. Objective : To define clinically useful biomarkers for transcriptional profiling in South African patients with Barrett's esophagus in order to identify those patients with an increased cancer risk necessitating intensified surveillance intervals. Materials and method : One-hundred and two patients were recruited for the study. COX-2, c-myb and c-myc mRNA expression were measured using a quantitative PCR method in endoscopically obtained specimens of Barrett's metaplasia (BM, n=26) or dysplasia (BD, n=14) and matching squamous esophageal tissue (n=40), squamous esophageal tissue of patients with erosive esophagitis (n=20), non-erosive esophagitis (n=20) and normal controls (n=20). Two patients with Barrett's adenocarcinoma (BAC) were also studied. Results : Demographic data of the groups were comparable. No significant differences in m-RNA expression levels were observed between ethnic groups for the genes analyzed. In the BD/BAC group 69% (11/16) showed increased c-myb m-RNA expression compared with 35% (9/26) in the BM group (p = 0.03). In the BD patients 19% (3/16) had increased c-myc m-RNA expression compared to none in those with BM and BAC. One patient each with BM and BAC had increased COX-2 m-RNA levels. No significant associations were observed for COX-2 in any of the other study groups. Conclusion : In the South African study cohort c-myb appears to be a clinically useful molecular marker for Barrett's esophagus and increased cancer risk, since m-RNA levels are progressively more over expressed in the metaplasia-dysplasia-adenocarcinoma sequence. Further studies are required to clarify the potential significance c-myc and COX-2 in South African patients with Barrett's esophagus. South African Gastroenterology Review Vol. 3(1) 2005: 5-9

A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus

The recent sequencing of a large number of Xenopus tropicalis expressed sequences has allowed development of a high-throughput approach to study Xenopus global RNA gene expression. We examined the global gene expression similarities and differences between the historically significant Xenopus laevis model system and the increasingly used X.tropicalis model system and assessed whether an X.tropicalis microarray platform can be used for X.laevis. These closely related species were also used to investigate a more general question: is there an association between mRNA sequence divergence and differences in gene expression levels? We carried out a comprehensive comparison of global gene expression profiles using microarrays of different tissues and developmental stages of X.laevis and X.tropicalis. We (i) show that the X.tropicalis probes provide an efficacious microarray platform for X.laevis, (ii) describe methods to compare interspecies mRNA profiles that correct differences in hybridization efficiency and (iii) show independently of hybridization bias that as mRNA sequence divergence increases between X.laevis and X.tropicalis differences in mRNA expression levels also increase.

Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia

Through a genome survey and phylogenetic analysis, we have identified and sequenced 14 new coding regions for alpha-giardins in Giardia lamblia. These proteins are related to annexins and comprise a multi-gene family with 21 members. Many alpha giardins are highly expressed proteins that are very immunogenic during acute giardiasis in humans. However, little is known about the function of these proteins. By using PCR with different combinations of gene-specific primers, we demonstrated that several of the genes localised to the same chromosomal fragment. These data point towards a molecular evolution through gene duplication and subsequent functional divergence. Semi-quantitative reverse transcriptase-PCR analysis of the Giardia life cycle revealed large differences in mRNA expression levels of the alpha giardins. Epitope tagging of the alpha-giardins localised them to different cytoskeletal components, such as the flagella and the adhesive disc, but also to the plasma membrane. These localisation experiments suggest alpha-giardins play a role in cell motility, attachment and membrane stability.

Analysis of Candidate Genes for Prostate Cancer

Considerable evidence demonstrates that genetic factors are important in the development and aggressiveness of prostate cancer. To identify genetic variants that predispose to prostate cancer we tested candidate SNPs from genomic regions that show linkage to prostate cancer susceptibility and/or aggressiveness, as well as genes that show a significant difference in mRNA expression level between tumor and normal tissue. Cases had histologically verified prostate cancer. Controls were at least 65 years old, never registered a PSA above 2.5 ng/ml, always had digital rectal examinations that were not suspicious for cancer, and have no known family history of prostate cancer. Thirty-nine coding SNPs and nine non-coding SNPs were tested in up to 590 cases and 556 controls resulting in over 40,000 SNP genotypes. Significant differences in allele frequencies between cases and controls were observed for ID3 (inhibitor of DNA binding), p = 0.05, HPN (hepsin), p = 0.009, BCAS1 (breast carcinoma amplified sequence 1), p = 0.007, CAV2 (caveolin 2), p = 0.007, EMP3 (epithelial membrane protein 3), p < 0.0001, and MLH1 (mutL homolog 1), p < 0.0001. SNPs in three of these genes (BCAS1, EMP3 and MLH1) remained significant in an age-matched subsample.

Phlorizin treatment prevents the decrease in plasma insulin levels but not the progressive histopathological changes in the pancreatic islets during aging of Zucker diabetic fatty rats.

A hallmark of Type 2 diabetes mellitus (T2DM) is chronic hyperglycemia, which is thought to play a role in pancreatic beta-cell failure. Here we investigated whether treatment of Zucker diabetic fatty (ZDF) rats, an animal model for T2DM, with the renal glucose transport inhibitor phlorizin could prevent alterations in the pancreatic islets. ZDF rats were treated with phlorizin or vehicle for 13 weeks starting with 6-week-old rats and before the onset of hyperglycemia. During the treatment, blood glucose levels in sham-treated ZDF rats increased rapidly from 7.7 +/- 0.3 to 24.8 +/- 0.6 mmol/l, whereas those in phlorizin-treated ZDF rats increased only slightly, but significantly, from 7.0 +/- 0.2 to 8.9 +/- 0.6 mmol/l. Phlorizin prevented the decrease in plasma insulin levels and caused a higher increase in body weight of the ZDF rats. Compared to 6-week-old untreated ZDF rats, in 19-week-old sham- and phlorizin-treated ZDF rats similar changes were found in islet architecture (more irregular boundaries and a disrupted mantle of peripheral islet cells) and in the mitochondria at the ultrastructural level (swelling of the matrix and disruption of the cristae). Using reverse transcriptase-polymerase chain reaction, no differences in mRNA expression levels were found for insulin, islet amyloid polypeptide (IAPP), and the prohormone convertase (PC) 1 and PC2 between 6-week-old untreated ZDF rats and 19-week-old sham- and phlorizin-treated ZDF rats. However, immunohistochemistry revealed similar decreases in insulin and IAPP protein expression in 19-week-old sham- and phlorizin-treated ZDF rats compared to those in 6-week-old untreated ZDF rats. These observations indicate that during aging of ZDF rats phlorizin treatment does not prevent the decreases in insulin and IAPP protein expression and the progressive histopathological changes in the pancreatic islets. Therefore, it is highly unlikely that these changes are caused by chronic hyperglycemia.

Unexpected role for HO-1 in the clinical heart transplant setting

Oxidative stress is an important factor that can trigger the process of transplant coronary artery disease (TCAD). Animal studies have shown that induction of the anti-oxidant enzyme heme oxygenase (HO)-1 prior to or shortly after transplantation, protects the donor organ from TCAD by its anti-inflammatory and anti-apoptotic properties.To investigate the role of HO-1 in TCAD after clinical heart transplantation we measured intragraft mRNA expression of HO-1, TGF-β, FLIP, the anti-apoptotic marker of the FasL induced apoptosis route, and the balance of Bcl-2/Bax, the anti- and pro-apoptotic markers of the mitochondrial apoptosis pathway. We analyzed biopsies that were taken at the end of graft implantation, at one week and at one year after transplantation of patients (n = 46) with and without signs of TCAD diagnosed by coronary angiography at one year. In time zero biopsies, no differences in mRNA expression levels for any of the measured parameters were found between patients with (n = 18) or without (n = 28) TCAD at one year. However, in one week biopsies, the expression levels of TGF-β and HO-1 were associated with the development of TCAD. For both mediators the mRNA expression level was significantly higher in grafts with signs of TCAD (p = 0.0002 and p = 0.001). In the biopsies taken at one year, elevated expression of TGF-β and HO-1 were still found in TCAD positive patients (p = 0.05 and p = 0.02). In the one week biopsies the high TGF-β and HO-1 levels were accompanied by a shifted Bcl-2/Bax balance, but not by a difference in FLIP mRNA levels, suggesting that cells from the graft are prone for apoptosis via the mitochondrial pathway.

Analysis of Differential Expression of Barley ESTs during Cold Acclimatization Using Microarray Technology

Abstract: Genomics adds a new dimension to genetic analysis, shifting the focus from the study of a single gene to the whole genome. We have successfully applied the genomics approach based on microarray to the study of genes involved in barley responses to cold stress. About 900 EST clones from barley were obtained from a cDNA library of cold acclimatized leaves of cv. Nure and arrayed, and gene expression analysis done on cold acclimatized vs. control plants. The system allowed for reliable detection of differences in mRNA expression levels, and was confirmed by the finding that numerous previously reported cold‐related genes were differentially expressed in treated and untreated plants when evaluated in our arrays. The expression profiles of a sample of genes analysed by the array were confirmed by quantitative RT‐PCR.Previously, identification of novel plant genes was achieved considering a few genes at a time; now many genes can be found as up‐ or down‐regulated based on a one step procedure. Many of the genes we found to be up‐ or down‐regulated do not have an assigned function. This includes 15 of the 78 up‐regulated and 8 of the 45 down‐regulated clones. Our results add new genes to the group of cold‐regulated genes and provide the opportunity to better understand the complex mechanism of stress tolerance.

Characterization of inhibitor-resistant histone deacetylase activity in plant-pathogenic fungi.

HC-toxin, a cyclic peptide made by the filamentous fungus Cochliobolus carbonum, is an inhibitor of histone deacetylase (HDAC) from many organisms. It was shown earlier that the HDAC activity in crude extracts of C. carbonum is relatively insensitive to HC-toxin as well as to the chemically unrelated HDAC inhibitors trichostatin and D85, whereas the HDAC activity of Aspergillus nidulans is sensitive (G. Brosch et al., Biochemistry 40:12855-12863, 2001). Here we report that HC-toxin-resistant HDAC activity was present in other, but not all, plant-pathogenic Cochliobolus species but not in any of the saprophytic species tested. The HDAC activities of the fungi Alternaria brassicicola and Diheterospora chlamydosporia, which also make HDAC inhibitors, were resistant. The HDAC activities of all C. carbonum isolates tested, except one non-toxin-producing isolate, were resistant. In a cross between a sensitive isolate and a resistant isolate, resistance genetically cosegregated with HC-toxin production. When fractionated by anion-exchange chromatography, extracts of resistant and sensitive isolates and species had two peaks of HDAC activity, one that was fully HC-toxin resistant and a second that was larger and sensitive. The first peak was consistently smaller in extracts of sensitive fungi than in resistant fungi, but the difference appeared to be insufficiently large to explain the differential sensitivities of the crude extracts. Differences in mRNA expression levels of the four known HDAC genes of C. carbonum did not account for the observed differences in HDAC activity profiles. When mixed together, resistant extracts protected extracts of sensitive C. carbonum but did not protect other sensitive Cochlibolus species or Neurospora crassa. Production of this extrinsic protection factor was dependent on TOXE, the transcription factor that regulates the HC-toxin biosynthetic genes. The results suggest that C. carbonum has multiple mechanisms of self-protection against HC-toxin.

Extensive Repertoire of Membrane-bound and Soluble Dendritic Cell-specific ICAM-3-grabbing Nonintegrin 1 (DC-SIGN1) and DC-SIGN2 Isoforms: INTER-INDIVIDUAL VARIATION IN EXPRESSION OF DC-SIGN TRANSCRIPTS

Expression in dendritic cells (DCs) of DC-SIGN, a type II membrane protein with a C-type lectin ectodomain, is thought to play an important role in establishing the initial contact between DCs and resting T cells. DC-SIGN is also a unique type of human immunodeficiency virus-1 (HIV-1) attachment factor and promotes efficient infection in trans of cells that express CD4 and chemokine receptors. We have identified another gene, designated here as DC-SIGN2, that exhibits high sequence homology with DC-SIGN. Here we demonstrate that alternative splicing of DC-SIGN1 (original version) and DC-SIGN2 pre-mRNA generates a large repertoire of DC-SIGN-like transcripts that are predicted to encode membrane-associated and soluble isoforms. The range of DC-SIGN1 mRNA expression was significantly broader than previously reported and included THP-1 monocytic cells, placenta, and peripheral blood mononuclear cells (PBMCs), and there was cell maturation/activation-induced differences in mRNA expression levels. Immunostaining of term placenta with a DC-SIGN1-specific antiserum showed that DC-SIGN1 is expressed on endothelial cells and CC chemokine receptor 5 (CCR5)-positive macrophage-like cells in the villi. DC-SIGN2 mRNA expression was high in the placenta and not detectable in PBMCs. In DCs, the expression of DC-SIGN2 transcripts was significantly lower than that of DC-SIGN1. Notably, there was significant inter-individual heterogeneity in the repertoire of DC-SIGN1 and DC-SIGN2 transcripts expressed. The genes for DC-SIGN1, DC-SIGN2, and CD23, another Type II lectin, colocalize to an approximately 85 kilobase pair region on chromosome 19p13.3, forming a cluster of related genes that undergo highly complex alternative splicing events. The molecular diversity of DC-SIGN-1 and -2 is reminiscent of that observed for certain other adhesive cell surface proteins involved in cell-cell connectivity. The generation of this large collection of polymorphic cell surface and soluble variants that exhibit inter-individual variation in expression levels has important implications for the pathogenesis of HIV-1 infection, as well as for the molecular code required to establish complex interactions between antigen-presenting cells and T cells, i.e. the immunological synapse.

Highest trkB mRNA expression in the entorhinal cortex among hippocampal subregions in the adult rat: contrasting pattern with BDNF mRNA expression

Brain-derived neurotrophic factor (BDNF) and its receptor, TrkB, regulate synaptic functions in the hippocampus of the adult rodent. In previous studies, in situ hybridization methods have been used to evaluate regional differences in BDNF and trkB mRNA expression levels in hippocampal subregions. However, these studies have failed to reach consensus regarding the regional differences in the mRNA expression levels. In the present study, we quantitated mRNA expression levels using two different methods, ribonuclease protection assays and a quantitative reverse-transcription polymerase chain reaction technique, in four hippocampal subregions: the entorhinal cortex, dentate gyrus (DG), CA3 and CA1. These two methods yielded the same results. We found that BDNF and trkB mRNA expression levels did not covary in the four subregions. BDNF and full length trkB ( trkB FL) mRNA in the entorhinal cortex and the DG show contrasting expression patterns. The expression level of BDNF mRNA was highest in the DG among the hippocampal subregions and low in the entorhinal cortex and the CA1, whereas the trkB FL mRNA expression level was highest in the entorhinal cortex, low in the DG and lowest in the CA3. These results suggest regional differences in BDNF/TrkB signaling for maintenance and modifiability of neuronal connections in the hippocampal formation.