alteration in cancer and its potential as tumoural biomarker.

Genetic information, in the form of DNA, must be protected for expression within the cell and transfer between generations. While a number of mechanisms have been developed to allow for genetic diversity, multiple and redundant mechanisms work to avoid errors during DNA synthesis before cell duplication and/or to avoid the impact of mutagens from endogenous or exogenous sources. The DNA sequence can be changed as the result of copying errors introduced by DNA polymerases during replication and by environmental agents such as mutagenic chemicals and certain types of radiation. If DNA sequence changes, whatever their cause, are left uncorrected, both growing and nongrowing somatic cells could accumulate so many mutations that they could no longer function. Thus, the correction of DNA sequence errors in all types of cells is important for survival (1).

Genetic information, in the form of DNA, must be protected for expression within the cell and transfer between generations. While a number of mechanisms have been developed to allow for genetic diversity, multiple and redundant mechanisms work to avoid errors during DNA synthesis before cell duplication and/or to avoid the impact of mutagens from endogenous or exogenous sources. The DNA sequence can be changed as the result of copying errors introduced by DNA polymerases during replication and by environmental agents such as mutagenic chemicals and certain types of radiation. If DNA sequence changes, whatever their cause, are left uncorrected, both growing and nongrowing somatic cells could accumulate so many mutations that they could no longer function. Thus, the correction of DNA sequence errors in all types of cells is important for survival (1).

BACKGROUND: Genomic datasets accompanying scientific publications show a surprisingly high rate of gene name corruption. This error is generated when files and tables are imported into Microsoft Excel and certain gene symbols are automatically converted into dates. RESULTS: We have developed Truke, a fexible Web tool to detect, tag and fix, if possible, such misconversions. Aside, Truke is language and regional locale-aware, providing file format customization (decimal symbol, field sepator, etc.) following user's preferences. CONCLUSIONS: Truke is a data format conversion tool with a unique corrupted gene symbol detection utility. Truke is freely available without registration at http://maplab.cat/truke .

Organochlorine compounds have been linked to increased risk of several cancers. Despite reductions in their use and fugitive release, they remain one of the most important groups of persistent pollutants to which humans are exposed, primarily through dietary intake. We designed a case-control study to assess the risk of colorectal cancer with exposure to these chemicals, and their potential interactions with genetic alterations in the tumors. A subsample of cases (n = 132) and hospital controls (n = 76) was selected from a larger case-control study in Barcelona, Catalonia, Spain. We measured concentrations in serum of several organochlorines by gas chromatography. We assessed point mutations in K-ras and p53 genes in tissue samples by polymerase chain reaction/single-strand conformation polymorphism and assessed expression of p53 protein by immunohistochemical methods. An elevated risk of colorectal cancer was associated with higher serum concentrations of mono-ortho polychlorinated biphenyl (PCB) congeners 28 and 118. The odds ratio for these mono-ortho PCBs for middle and higher tertile were, respectively, 1.82 [95% confidence interval (CI), 0.90-3.70] and 2.94 (95% CI, 1.39-6.20). Alpha-hexachlorocyclohexane, hexachlorobenzene, and p,p'-DDE (4,4'-dichlorodiphenyltrichloroethene) showed nonsignificant increases in risk. Risk associated with mono-ortho PCBs was slightly higher for tumors with mutations in the p53 gene but was not modified by mutations in K-ras. Mono-ortho PCBs were further associated with transversion-type mutations in both genes. These results generate the hypothesis that exposure to mono-ortho PCBs contributes to human colorectal cancer development. The trend and magnitude of the association, as well as the observation of a molecular fingerprint in tumors, raise the possibility that this finding may be causal.

Regional distribution of immunoreactive somatostatin (IRS) and melatonin were investigated in the bovine pineal gland. The total IRS and melatonin content ranged from 0.26 to 2.28 pmol, and from 19.4 to 42.7 pmol, respectively, per bovine pineal. Reverse phase liquid chromatography of pineal extracts demonstrated that more than 90% of IRS coeluted with synthetic somatostatin-14 and somatostatin-28. While the IRS content was shown to vary considerably throughout the gland, with a constant and marked maximal concentration at the proximal end of the pineal, the maximal melatonin concentration appeared in the central part of the gland, coinciding with the total protein distribution. The existence of the highest levels of pineal IRS near the habenular commissure, where the afferent fibers of the central pinealopetal innervation enter the gland, suggests that pineal somatostatin may be, at least in part, of neural origin.

PURPOSE: The purpose of this study was to analyze the value of germline and tumor thymidylate synthase (TS) genotyping as a prognostic marker in a series of colorectal cancer patients receiving adjuvant fluorouracil (FU) -based treatment. PATIENTS AND METHODS: One hundred twenty-nine colorectal cancer patients homogeneously treated with FU plus levamisole or leucovorin in the adjuvant setting were included. TS enhancer region, 3R G > C single nucleotide polymorphism (SNP), and TS 1494del6 polymorphisms were assessed in both fresh-frozen normal mucosa and tumor. Mutational analyses of TS and allelic imbalances were studied in all primary tumors and in 18 additional metachronic metastases. TS protein immunostaining was assessed in an expanded series of 214 tumors. Multivariate Cox models were adjusted for stage, differentiation, and location. RESULTS: Tumor genotyping (frequency of allelic loss, 26%) showed that the 3R/3R genotype was associated with a better outcome (hazard ratio [HR] = 0.38; 95% CI, 0.16 to 0.93; P = .020 for the recessive model). 3R G > C SNP genotyping did not add prognostic information. Tumor TS 1494del6 allele (frequency of allelic loss, 36%) was protective (for each allele with the deletion, based on an additive model, HR = 0.42; 95% CI, 0.22 to 0.82; P = .0034). Both polymorphisms were in strong linkage disequilibrium (D' = 0.71, P < .001), and the 3R/-6 base pair (bp) haplotype showed a significant overall survival benefit compared with the most prevalent haplotype 2R/+6bp (HR = 0.42; 95% CI, 0.20 to 0.85; P = .017). No TS point mutation was detected in primary tumors or metastases. TS protein immunostaining was not associated with survival or any of the genotypes analyzed. CONCLUSION: Tumor TS 1494del6 genotype may be a prognostic factor in FU-based adjuvant treatment of colorectal cancer patients.

Supplementary Figure 4 from Epigenetic Deregulation Across Chromosome 2q14.2 Differentiates Normal from Prostate Cancer and Provides a Regional Panel of Novel DNA Methylation Cancer Biomarkers

Activation of hepatic stellate cells (HSC) is a major event in liver fibrogenesis. A typical feature of activated HSC is the expression of α-smooth muscle actin (SMA) and other smooth muscle cell (SMC) marker genes. The transcription of these genes is mainly regulated by the transcription factor ‘serum response factor’ (SRF) [1]. Less is known about transcriptional control of the SRF gene itself. We could recently demonstrate that TGF-β upregulates SRF in activated HSC [2]. Primary rat HSC or CFSC were treated with specific inhibitors against the ALK5 receptor and members of the MAPK pathways (ERK, JNK, p38). The rate of SRF expression was determined on RNA (semi-quantitative PCR) and protein (Western blot) levels. Additionally, expression of SRF target genes SMA, SM22α, or c-fos was analysed in parallel and by use of respective luciferase reporter gene constructs. Expression of SRF was not only inducible by TGF-β but also and more effective by PDGF-BB, while treatment of cells with dexamethasone resulted in a strong decrease of SRF expression. We found no relevant effect on SRF protein levels by use of the ALK5 inhibitor. In contrast, inhibition of MAPK pathways influenced SRF and SMC marker expression. Administration of TAK1 or p38 inhibitors led to increased SRF contents in TGF-β-treated cells, while JNK inhibition strongly decreased SRF in these cells. Interestingly, we found no relevant change of SRF expression after PDGF induction by additional treatment with these inhibitors. In parallel, respective effects of MAPK inhibitors onto expression of SRF target genes were observed. A number of publications described stimulatory or inhibitory effects of members of the MAPK family onto SMA expression as a classical indicator of HSC activation [3,4]. Our results link the transcription factor SRF to these observations and give a mechanical explanation for TGF-β-regulated but Smad-independent regulation of genes during HSC transdifferentiation.

Gene amplification is one of the most frequent manifestations of genomic instability in human tumors and plays an important role in tumor progression and acquisition of drug resistance. To better understand the factors involved in acquired resistance to cytotoxic drugs via gene amplification, we have analyzed the structure and dynamics of dihydrofolate reductase (DHFR) gene amplification in HT29 cells treated with methotrexate (MTX). Analysis of the DHFR gene amplification process shows that the amplicon exhibits a complex structure that is consistently reproduced in independent treatments. The cytogenetic manifestation of the amplification in advanced stages of the treatment may be in the form of double minutes or as a homogeneously stained region. To get insights into the mechanisms of resistance, we have also investigated the sensitization to MTX of MTX-resistant cells after drug withdrawal and reexposure to MTX. Passive loss of the DHFR amplicon by withdrawal of the drug results in MTX-sensitive cells exhibiting a substantial reduction of their capacity or even an incapacity to generate resistance when submitted to a second cycle of MTX treatment. On a second round of drug administration, the resistant cells generate a different amplicon structure, suggesting that the formation of the amplicon as in the first cycle of treatment is not feasible. These results indicate that DHFR gene amplification is a "wear and tear" process in HT29 cells and that MTX-resistant cells may become responsive to a second round of treatment if left untreated during a sufficient period of time.