Novel target genes and a valid biomarker panel identified for cholangiocarcinoma

Cholangiocarcinoma is notoriously difficult to diagnose, and the mortality rate is high due to late clinical presentation. CpG island promoter methylation is frequently seen in cancer development. In the present study, we aimed at identifying novel epigenetic biomarkers with the potential to improve the diagnostic accuracy of cholangiocarcinoma. Microarray data analyses of cholangiocarcinoma cell lines treated with epigenetic drugs and their untreated counterparts were compared with previously published gene expression profiles of primary tumors and with non-malignant controls. Genes responding to the epigenetic treatment that were simultaneously downregulated in primary cholangiocarcinoma compared with controls (n = 43) were investigated for their promoter methylation status in cancer cell lines from the gastrointestinal tract. Genes commonly methylated in cholangiocarcinoma cell lines were subjected to quantitative methylation-specific polymerase chain reaction in a total of 93 clinical samples (cholangiocarcinomas and non-malignant controls). CDO1, DCLK1, SFRP1 and ZSCAN18, displayed high methylation frequencies in primary tumors and were unmethylated in controls. At least one of these four biomarkers was positive in 87% of the tumor samples, with a specificity of 100%. In conclusion, the novel methylation-based biomarker panel showed high sensitivity and specificity for cholangiocarcinoma. The potential of these markers in early diagnosis of this cancer type should be further explored.     

Novel target genes and a valid biomarker panel identified for cholangiocarcinoma

Cholangiocarcinoma is notoriously difficult to diagnose, and the mortality rate is high due to late clinical presentation. CpG island promoter methylation is frequently seen in cancer development. In the present study, we aimed at identifying novel epigenetic biomarkers with the potential to improve the diagnostic accuracy of cholangiocarcinoma. Microarray data analyses of cholangiocarcinoma cell lines treated with epigenetic drugs and their untreated counterparts were compared with previously published gene expression profiles of primary tumors and with non-malignant controls. Genes responding to the epigenetic treatment that were simultaneously downregulated in primary cholangiocarcinoma compared with controls (n = 43) were investigated for their promoter methylation status in cancer cell lines from the gastrointestinal tract. Genes commonly methylated in cholangiocarcinoma cell lines were subjected to quantitative methylation-specific polymerase chain reaction in a total of 93 clinical samples (cholangiocarcinomas and non-malignant controls). CDO1, DCLK1, SFRP1 and ZSCAN18, displayed high methylation frequencies in primary tumors and were unmethylated in controls. At least one of these four biomarkers was positive in 87% of the tumor samples, with a specificity of 100%. In conclusion, the novel methylation-based biomarker panel showed high sensitivity and specificity for cholangiocarcinoma. The potential of these markers in early diagnosis of this cancer type should be further explored.     

DNA microarray analysis of rheumatoid arthritis susceptibility genes identified by genome-wide association studies

In a recent interesting review, Alex Clarke and Timothy Vyse described the genetics of rheumatic disease [1]. In the past several years, genome-wide association studies (GWAS) have led to the identification of six high-risk rheumatoid arthritis (RA) susceptibility genes - namely, CD244, PADI4, SLC22A2, PTPN22, CTLA4, and STAT4 (summarized in [2]). In vitro studies using mutant alleles and cultured cells have revealed the individual upregulation of CD244, PADI4, SLC22A2, and PTPN22 [2-6]; however, studies on the expression of RA susceptibility genes in RA patients are rare. We therefore investigated the expression of the above-mentioned six RA susceptibility genes in 112 RA patients using DNA microarray analysis. This study aims to clarify whether DNA microarray analysis and GWAS produce comparable results with respect to RA susceptibility genes.Total RNA extracted from total peripheral blood cells obtained from 112 RA patients and 45 healthy individuals was used to prepare aminoallyl RNA. As a reference, mixed RNA from 45 healthy individuals was used. The aminoallyl RNA of each individual and the reference was subjected to Cy3 and Cy5 labeling, respectively, and was hybridized with an oligonucleotide-based DNA microarray. The data obtained were analyzed by nonparametric statistical group comparison. The intensities of the noprobe spots were used as the background. The median and standard deviation of the background intensity were calculated. The genes with an intensity value that was less than the median plus 2 standard deviation of the background intensity were identified as null. The Cy3/Cy5 ratios of all spots on the DNA microarray were normalized using the global ratio median. Only gene expression data that were collected from at least 80% of samples from each group were selected for further analysis. The unpaired Mann-Whitney test was used to determine statistically significant differences in the mRNA expression levels between the RA and healthy groups. Statistical significance was set at P < 0.05.The results of our DNA microarray analysis showed that the expressions of four out of the six RA susceptibility genes were significantly higher in RA patients than in healthy individuals (1.0 × 10^-16 to 2.32 × 10^-5) (Table ​(Table1).1). As described above, the upregulation of these four genes (CD244, PADI4, SLC22A2, and PTPN22) has been previously confirmed in in vitro studies. We found, however, that CTLA4 expression levels were similar between the RA and control groups, whereas STAT4 expression was significantly downregulated in the RA group (1.38 × 10^-8). We investigated the expression of other RA susceptibility genes - namely, TRF1/C5 [7], CD40 [8], and CCL21 [8] - and found that their expressions were similar in both groups. The genetic risk factors for RA were recently reported to differ between Caucasian and Asian (Korean) populations [9]. The samples used in our microarray analysis were derived from the same Asian (Japanese) cohort. The expression profiles for these three genes may therefore not be consistent with the profiles determined by GWAS.

Table 1

Candidate genes identified from rheumatoid arthritis genome-wide association studies

Novel estrogen-related genes and potential biomarkers of ovarian endometriosis identified by differential expression analysis

In the search for novel biomarkers of endometriosis, we selected 152 genes from the GeneLogic database based on results of genome-wide expression analysis of ovarian endometriosis, plus 20 genes related to estrogen metabolism and action. We then performed low-density array analysis of these 172 genes on 11 ovarian endometriosis samples and 9 control endometrium samples. Principal component analysis of the gene expression levels showed clear separation between the endometriosis and control groups. We identified 78 genes as differentially expressed. Based on Ingenuity pathway analysis, these differentially expressed genes were arranged into groups according to biological function. These analyses revealed that 32 differentially expressed genes are estrogen related, 23 of which have not been reported previously in connection with endometriosis. Functional annotation showed that 25 and 22 genes are associated with the biological terms "secreted" and "extracellular region", respectively. Differential expression of 4 out of 5 genes related to estrogen metabolism and action (ESR1, ESR2, PGR and BGN) was also confirmed by immunohistochemistry. Our study thus reveals differential expression of several genes that have not previously been associated with endometriosis and that encode potential novel biomarkers and drug targets.     

Clofibrate causes an upregulation of PPAR-{alpha} target genes but does not alter expression of SREBP target genes in liver and adipose tissue of pigs

This study investigated the effect of clofibrate treatment on expression of target genes of peroxisome proliferator-activated receptor (PPAR)-alpha and various genes of the lipid metabolism in liver and adipose tissue of pigs. An experiment with 18 pigs was performed in which pigs were fed either a control diet or the same diet supplemented with 5 g clofibrate/kg for 28 days. Pigs treated with clofibrate had heavier livers, moderately increased mRNA concentrations of various PPAR-alpha target genes in liver and adipose tissue, a higher concentration of 3-hydroxybutyrate, and markedly lower concentrations of triglycerides and cholesterol in plasma and lipoproteins than control pigs (P < 0.05). mRNA concentrations of sterol regulatory element-binding proteins (SREBP)-1 and -2, insulin-induced genes (Insig)-1 and Insig-2, and the SREBP target genes acetyl-CoA carboxylase, 3-methyl-3-hydroxyglutaryl-CoA reductase, and low-density lipoprotein receptor in liver and adipose tissue and mRNA concentrations of apolipoproteins A-I, A-II, and C-III in the liver were not different between both groups of pigs. In conclusion, this study shows that clofibrate treatment activates PPAR-alpha in liver and adipose tissue and has a strong hypotriglyceridemic and hypocholesterolemic effect in pigs. The finding that mRNA concentrations of some proteins responsible for the hypolipidemic action of fibrates in humans were not altered suggests that there were certain differences in the mode of action compared with humans. It is also shown that PPAR-alpha activation by clofibrate does not affect hepatic expression of SREBP target genes involved in synthesis of triglycerides and cholesterol homeostasis in liver and adipose tissue of pigs.     

Novel methylotrophy genes of Methylobacterium extorquens AM1 identified by using transposon mutagenesis including a putative dihydromethanopterin reductase

Ten novel methylotrophy genes of the facultative methylotroph Methylobacterium extorquens AM1 were identified from a transposon mutagenesis screen. One of these genes encodes a product having identity with dihydrofolate reductase (DHFR). This mutant has a C(1)-defective and methanol-sensitive phenotype that has previously only been observed for strains defective in tetrahydromethanopterin (H(4)MPT)-dependent formaldehyde oxidation. These results suggest that this gene, dmrA, may encode dihydromethanopterin reductase, an activity analogous to that of DHFR that is required for the final step of H(4)MPT biosynthesis.     

Novel key genes in triple-negative breast cancer identified by weighted gene co-expression network analysis

Triple-negative breast cancer (TNBC) is a special subtype of breast cancer (BC) with poor prognosis. Although some molecular mechanisms of TNBC have been elucidated, the efficacy of current treatments is limited. Therefore, it is urgently demanded to screen for novel biomarkers and drug targets for TNBC. In this study, we obtained four independent data sets (GSE76250, GSE31448, GSE43358, and METABRIC) from the Gene Expression Omnibus (GEO) database and the cBioPortal website. In the GSE76250 data set, 890 differentially expressed genes were identified and weighted gene co-expression network analysis was performed based on them. Then, two preserved modules associated with the KI67 score were detected. Gene ontology and pathway enrichment analyses showed genes in the modules participated in some cancer-related biological processes or pathways. Non-SMC condensin I complex subunit G (NCAPG) and ATP-binding cassette subfamily A member 9 (ABCA9) were identified as hub genes of the modules, and the significance of hub genes was validated in the GSE43358 data set. Finally, their prognostic value was assessed by survival analysis. These findings suggested that NCAPG and ABCA9 may be the key genes of TNBC. Moreover, ABCA9 was first reported in TNBC. They deserved further studies.     

Novel putative protein tyrosine phosphatases identified by the polymerase chain reaction

Protein tyrosine phosphatases (PTPases) are a family of enzymes that specifically dephosphorylate phosphotyrosyl residues in selected protein substrates. To more fully understand the regulatory role of protein tyrosine phosphorylation and dephosphorylation in cellular signal transduction, characterization of PTPases is essential. Using the polymerase chain reaction and degenerate oligonucleotide primers corresponding to conserved amino acid sequences within the catalytic domain of PTPases, we have identified 11 PTPase-related human liver cDNA sequences. Five of these have not been described previously. These results indicate that, like protein tyrosine kinases, PTPases may also comprise a gene family with a large number of members.     

Novel persistence genes in Pseudomonas aeruginosa identified by high-throughput screening

Salmonella enterica polymyxin B (PM) resistance is modulated mainly by substitutions of the acyl chains and the phosphate groups on the lipid A moiety of lipopolysaccharide. These modifications are mediated by genes under the control of the PmrA/PmrB and PhoP/PhoQ two-component regulatory systems. In this study, a deletion in the gene encoding the alternative σ⁵⁴ factor, rpoN , was shown to increase PM resistance without affecting protamine sensitivity. The results presented here showed that the increased polymyxin resistance observed in the Δ rpoN mutant occurs through a PmrA/PhoP-independent pathway. Downregulation of one or more genes belonging to the RpoN regulon may provide an additional mechanism of defence against membrane-permeabilizing antimicrobial peptides that helps the pathogen to survive in different environments.