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Uveal melanoma (UM) is an uncommon but highly aggressive ocular malignancy. Poor overall survival is associated with deleterious BAP1 alterations, which frequently occur with monosomy 3 (LOH3) and a characteristic gene expression profile. Tumor DNA from a cohort of 100 UM patients from Moorfields Biobank (UK) that had undergone enucleation were sequenced for known UM driver genes (BAP1, SF3B1, EIF1AX, GNAQ, and GNA11). Immunohistochemical staining of BAP1 and interphase FISH for chromosomes 3 and 8 was performed, and cellular localization of BAP1 was correlated with BAP1 mutations. Wildtype (WT) BAP1 staining was characterized by nBAP1 expression with 10% cBAP1.

Background/aim Patients with stage IIIA (N2) non-small cell lung cancer (NSCLC) with no progression after induction chemotherapy are usually selected for surgery. Nowadays, response to chemotherapy is not predictable. We aimed to identify genomic predictive markers for response to induction chemotherapy in stage IIIA (N2) NSCLC patients. Patients and methods Whole-exome sequencing (WES) was performed on samples from 11 patients with no response after induction chemotherapy and 6 patients with documented pathological response, admitted to the Hotel Dieu Hospital, Paris or Allegemeines Krakenhaus University, Vienna. Results A higher alternative allele frequency was found on SENP5, rs63736860, rs1602 and NCBP2, rs553783 in the non-responder group, and on RGP1, rs1570248, SLFN12L, rs2304968, rs9905892, and GBA2, rs3833700 in the responder group. Conclusion These polymorphisms contribute to inter-individual sensibility to chemotherapy response. Interrogation of these genetic variations may have potential applicability when deciding the treatment strategy for patients with stage III NSCLC (N2).

Background: Survival rates among non-small cell lung cancer (NSCLC) stage IIIA (N2) patients are generally low and depend on the treatment. Patients and methods: We aimed to identify predictive markers for long term survival in responders and non-responders to chemotherapy, analyzing tumour and non-tumour samples by microarray (n=35) and whole exome sequencing (WES, n=25). Results: WES data showed correlation of overall survival of all patients with rs9905892 in the SLFN12L gene. High frequency of mutations (4/6, 66.7%) was identified in members of SWI/SNF complex in responder patients and in patients that were alive after seven years. Microarray data for immune components showed that VISTA (VSIR) was down-regulated in tumoral tissue. Conclusion: Our research suggests that mutations in SWI/SNF complex associate with long term survival after multimodal treatment, while down-regulation of VISTA might indicate its immunomodulatory role in NSCLC stage III (N2) patients.

Recently long non‐coding RNAs were identified as new factors involved in gene expression regulation. To gain insight into expression pattern of these factors related to E7 HPV18 oncogene, this study uses HeLa cell culture transfected with E7‐siRNA. Gene expression profile was investigated using microarray analysis. After analysing the microarray results, we identified 15,387 RNA species differentially expressed in E7‐siRNA‐transfected cells compared with controls (fold change >2). The expression profiles of lncRNA species highlighted 731 lncRNAs and 203 lincRNAs. We selected two lincRNAs (LINC01101 and LINC00277) and we evaluated the expression profile in HPV‐induced neoplasia. Both lincRNAs investigated display a significantly reduced pattern of expression in cervical lesions and cancer, associated with clinical parameters. A connection between HPV presence and lincRNAs was noted. hrHPV‐positive samples exhibit significantly reduced LINC01101 and LINC00277 expression level (P < 0.05). These results provide new insights into involvement of lncRNA in HPV‐induced cervical cancer, enriching our understanding of their potential role in this pathology.

The impact of different carcinogenic exposures on the specific patterns of somatic mutation in human tumors remains unclear. To address this issue, we profiled 209 cholangiocarcinomas (CCAs) from Asia and Europe, including 108 cases caused by infection with the liver fluke Opisthorchis viverrini and 101 cases caused by non-O. viverrini-related etiologies. Whole-exome sequencing (n = 15) and prevalence screening (n = 194) identified recurrent somatic mutations in BAP1 and ARID1A, neither of which, to our knowledge, has previously been reported to be mutated in CCA. Comparisons between intrahepatic O. viverrini-related and non-O. viverrini-related CCAs demonstrated statistically significant differences in mutation patterns: BAP1, IDH1 and IDH2 were more frequently mutated in non-O. viverrini CCAs, whereas TP53 mutations showed the reciprocal pattern. Functional studies demonstrated tumor suppressive functions for BAP1 and ARID1A, establishing the role of chromatin modulators in CCA pathogenesis. These findings indicate that different causative etiologies may induce distinct somatic alterations, even within the same tumor type.

Despite the reduced incidence of gastric cancer in the developed world, a diagnosis of stomach carcinoma still carries a poor prognosis due to the asymptomatic nature of the disease in the early stages, subsequent advanced stage diagnosis, and a low 5 year survival rate. Endoscopy remains the primary standard for diagnosis of stomach carcinoma and the current marker, carbohydrate antigen 19-9 (CA19-9) lacks the levels of sensitivity and specificity required in order to make it clinically useful for diagnostic monitoring. Therefore, there is a current need for additional markers to improve the diagnostic accuracy for the early stages of stomach cancer. Together, glycomic, proteomic, and glycoproteomic analyses of serum have the potential to identify such probable markers. A discovery study is reported here using preoperative serum from 80 stomach cancer patients, 10 patients bearing benign stomach disease, and 20 matched controls. Glycomic analysis of the total and immunoaffinity depleted serum revealed statistically significant increases in the levels of sialyl Lewis X epitopes (SLe(X)) present on triantennary glycans accompanied by increased levels of core fucosylated agalactosyl biantennary glycans present on IgG (referred to as the IgG G0 glycoform) which are associated with increasing disease pathogenesis. Protein expression analysis using 2D-DiGE returned a number of differentially expressed protein candidates in the depleted serum, many of which were shown to carry triantennary SLe(X) during subsequent glycomic investigations. Biological pathway analysis of the experimental data returned complement activation and acute phase response signaling as the most significantly altered pathways in the stomach cancer patient serum. Upon the basis of these findings, it is suggested that increased expression of IgG G0 and complement activation are a host response to the presence of the stomach tumor while the increased expression of SLe(X) and acute phase response proteins is a result of pro-inflammatory cytokine signaling, including IL-6, during carcinogenesis. The approach presented herein provides an insight into the underlying mechanisms of disease and the resulting changes in the glycome and glycoproteome offer promise as potential markers for diagnosis and prognostic monitoring in stomach cancer.

The aim of the study was to determine the pathways and expression profile of the genes that might predict response to neoadjuvant chemotherapy in patients with stage IIIA non-small cell lung cancer (NSCLC).We evaluated, by microarray, the gene-expression profile of tumoral mediastinal lymph node samples surgically removed from 27 patients with stage IIIA NSCLC before neoadjuvant chemotherapy treatment. Depending on the response to the induction treatment, the patients were divided in two groups: group A: patients whose disease evolved, stabilized or who had minor response to chemotherapy, and group B: patients whose disease stabilized or had major response to chemotherapy.The microarray experiments identified 1,127 genes with a modified expression in the tumoral tissue compared to normal tissue with p≤0.05 and 44 genes with p≤0.01. The identified up-regulated genes between tumoral versus normal tissue included collagen, type I, alpha 1 (COL1A1), inhibin beta A (INHBA) and thioredoxin interacting protein (TXNIP). Pathways identified with a false-discovery rate of0.005 included: cytokine pathways, focal adhesion or extracellular matrix receptor interaction.Our approach identified important characteristics of NSCLC and pointed-out molecular differences between sub-groups of patients based on their response to therapy.

Although pancreatic ductal adenocarcinoma (PDAC) remains a major challenge for therapy, biomarkers for early detection are lacking. Epigenetic silencing of tumor suppressor genes is a majorcontributor to neoplastic transformation. The aim of this study was to identify new factors involved in PDAC progression. The GNMT gene possesses CpG islands in the promoter region and is important in methyl-group metabolism and in maintaining a normal methylation status of the genome.To test the hypothesis whether GNMT is epigenetically regulated in PDAC, we evaluated the GNMT gene expression and promoter methylation status in 30 paired samples of PDAC and normal pancreatic tissue.We found significantly higher methylation frequencies (p0.001) in PDACs (2.82-100%; median, 36.05%) than in controls (0.28-14.02%; median, 4.39%). The GNMT gene expression was decreased in PDACs compared to normal pancreatic tissues in 26/30 cases (86.67%). Furthermore, we showed that treatment with 5-aza-2-deoxycytidine (5-aza-dC) increased GNMT mRNA expression and decreased viability in PDAC cells.Collectively, these data indicate that GNMT is aberrantly methylated in PDAC representing, thus, a potential major mechanism for gene silencing. Methylation of GNMT gene is directly correlated with disease stage and with tumor grade indicating that these epigenetic effects may be important regulators of PDAC progression.

Background: The objective of this study is to assess the outcome of the patients treated for hepatocellular carcinoma (HCC) in a General Surgery and Liver Transplantation Center. Methods: This retrospective study includes 844 patients diagnosed with HCC and surgically treated with curative intent methods. Curative intent treatment is mainly based on surgery, consisting of liver resection (LR), liver transplantation (LT). Tumor ablation could become the choice of treatment in HCC cases not manageable for surgery (LT or LR). 518 patients underwent LR, 162 patients benefited from LT and in 164 patients radiofrequency ablation (RFA) was performed. 615 patients (73%) presented liver cirrhosis. Results: Mordidity rates of patient treated for HCC was 30% and mortality was 4,3% for the entire study population. Five year overall survival rate was 39 % with statistically significant differences between transplanted, resected, or ablated patients (p 0.05) with better results in case of LT followed by LR and RFA. Conclusions: In HCC patients without liver cirrhosis, liver resection is the treatment of choice. For early HCC occurred on cirrhosis, LT offers the best outcome in terms of overall and disease free survival. RFA colud be a curative method for HCC patients not amenable for LT of LR.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies with a dismal prognostic. KRAS is a well-recognized driver gene in PDAC, detected in the earliest stages of pancreatic tumor transformation. To establish the frequency of KRAS mutations in a cohort of Romanian patients, we performed Sanger sequencing for exon 2 and exon 3 of the gene on 31 PDACs pairs. We further examined correlation of the mutational status with clinico-pathologic data of the patients and evaluated the prognostic implication of KRAS mutations. Ten out of 31 patients (32%) had KRAS missense mutations, all were detected in exon 2, and codon 12 only. Among patients with KRAS mutations, the majority (7/10, 70%) had c.35G>A (p.G12D) substitutions. Patients with p.G12D mutations had a marginally worse survival (p=0.07) and a shorter disease-free survival (p=0.04) when compared to KRAS wild-type patients. Correlation between patients age and recurrence was seen in KRAS wild-type cohort (p=0.096, r=-0.6). In summary, evaluation of KRAS mutational status is a

Wilson's disease (WD) is a rare autosomal recessive disease. More than 500 mutations have been described so far, out of which 29 in exon 14. H1069Q mutation in the exon 14 of ATP7B gene is the most frequently encountered in Europe. The aim of the present study was to evaluate the incidence of mutations occurring in exon 14 of ATP7B gene in Romanian patients referred to a tertiary gastroenterology center, with known or suspected WD and in asymptomatic first degree relatives of index cases.93 patients were included in the study. Exon 14 of ATP7B gene has been amplified by PCR from genomic DNA and mutations identified by sequencing.Only H1069Q missense mutation was detected in our study group. In patients with an established diagnosis of WD (38 cases), 34.2% were heterozygous for H1069Q and 21.1% were homozygous, with an allelic frequency of 38.1%. In paediatric WD patients (12 cases) 25% were heterozygous and 16.7% were homozygous (not significant versus adult population). Among asymptomatic first degree relatives of patients with WD (12 siblings, 25 parents) there were 40.5% cases heterozygous for H1069Q. In patients with suspected WD (17 cases), only 5.9% were heterozygous and no homozygous patient was identified. In our study group, H1069Q screening alone could not raise the Leipzig score to confirm diagnosis in patients with suspected WD or in asymptomatic first degree relatives.H1069Q mutation is highly prevalent in Romanian WD patients and first degree relatives, similar to other central and continental western European populations.

Molecular events responsible for the onset and progression of peripheral occlusive arterial disease (POAD) are incompletely understood. Gene expression profiling may point out relevant features of the disease.Tissue samples were collected as operatory waste from a total of 36 patients with (n = 18) and without (n = 18) POAD. The tissues were histologically evaluated, and the patients with POAD were classified according to Leriche-Fontaine (LF) classification: 11% with stage IIB, 22% with stage III, and 67% with stage IV. Total RNA was isolated from all samples and hybridized onto Agilent 4×44K Oligo microarray slides. The bioinformatic analysis identified genes differentially expressed between control and pathologic tissues. Ten genes with a fold change ≥ 2 (1 with a fold change ≥ 1.8) were selected for quantitative polymerase chain reaction validation (GPC3, CFD, GDF10, ITLN1, TSPAN8, MMP28, NNMT, SERPINA5, LUM, and FDXR). C-reactive protein (CRP) was assessed with a specific assay, while nicotinamide N-methyltransferase (NNMT) was evaluated in the patient serum by enzyme-linked immunosorbent assay.A multiple regression analysis showed that the level of CRP in the serum is correlated with the POAD LF stages (r(2) = 0.22, P = 0.046) and that serum NNMT is higher in IV LF POAD patients (P = 0.005). The mRNA gene expression of LUM is correlated with the LF stage (r(2) = 0.45, P = 0.009), and the mRNA level of ITLN1 is correlated with the ankle-brachial index (r(2) = 0.42, P = 0.008).Our analysis shows that NNMT, ITLN1, LUM, CFD, and TSPAN8 in combination with other known markers, such as CRP, could be evaluated as a panel of biomarkers of POAD.

This study aimed to understand gradual biological variations during gastric tumorigenesis, and to identify the candidate genes that are involved in tumor progression and metastasis.cDNA microarray data were obtained from 10 pair of cancerous and normal adjacent tissue from gastric adenocarcinoma patients. The samples were divided in primary and advanced gastric adenocarcinoma with lymph node metastasis. Validation of the microarray data was accomplished by quantitative RT-PCR on additional 41 samples. The significantly modified genes were grouped in clusters according to their functional annotation, and comparison was done regarding molecular mechanisms involved tumor progression.A total of 136 genes were up-regulated and 96 genes were down-regulated by at least fourfold in tumor tissue. The analysis of gene clusters revealed a complex remodelling of normal gastric epithelium morphology and function associated with the tumorigenesis and metastasis. A large number of proteases are being overexpressed, together with keratins, genes associated with morphogenesis and anti-apoptosis. Between the most significant down-regulated genes, there were genes involved in gastric motility and synthesis and genes related to metabolic and pro-apoptotic processes. We also report, the identification of seven genes, significant up-regulated, that seem to be associated with tumor progression: KRT17, COL10A2, KIAA1199, SPP1, IL11, S100A2, and MMP3.Our cDNA microarray study identified several genes that appeared to meet the criteria of a good biomarker, and may therefore be especially useful for the development of diagnostic tools, for the early detection, or for the prediction of tumor progression.

Nicotine (from cigarette smoke) and caffeine (from coffee) have analgesic effects in humans and experimental animals. We investigated the combined effects of coffee drinking and cigarette smoking on pain experience in a group of moderate nicotine-dependent, coffee drinking, young smokers. Pain threshold and pain tolerance were measured during cold pressor test following the habitual nocturnal deprivation of smoking and coffee drinking. Smoking increased pain threshold and pain tolerance in both men and women. Coffee drinking, at a dose that had no independent effect, doubled the increase in pain threshold induced by smoking. The effect could not be explained by a cumulative raise in blood pressure. Our data suggest that caffeine enhances the analgesic effect of nicotine.

Standard cytotoxic chemotherapy is effective for certain type of cancer; however, as far as many other types are concerned, the available treatments only offer a limited survival benefit. Lung cancer represents one of these types of cancer. The development of specific therapies is the greatest promise for the successful treatment of this disease; nevertheless, an oriented approach depends on the understanding of the tumor cells genome. The exon sequencing of a large number of lung cancer samples has provided an initial insight of the somatic mutation profile of these tumors. These studies have confirmed the high frequency of TP53 and KRAS mutations in lung cancer. They have discovered mutational inactivation in some suppressor genes of known tumors that have not been previously associated with lung cancer. In addition, they have identified oncogene mutations of EGFR, which has led to the first targeted therapy in pulmonary adenocarcinoma. There are other oncogene candidates awaiting for functional validation. It is expected for the future sequencing of the entire exome and of the entire genome of lung cancer to reveal a more thorough view of somatic mutations that can be exploited for therapeutical purposes.

Background: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and has a good prognosis only when is treated curatively. The development of new systems that can predict the likelihood of recurrence after curative treatment, including molecular prognostic factors, is much needed. The liver enriched transcription factors (LETFs) are critical in inducing and maintaining hepatic phenotype during liver organogenesis and their expression level in HCC could have prognostic implications. The aim of our work was to investigate the expression profile of liver enriched transcription factors FoxA2, HNF6 (ONECUT1), C/Ebp-alpha and HNF1-beta in hepatocelullar carcinoma specimens from liver resections or liver explants after liver transplantations, in comparison to non-tumoral liver tissue from the same patients. Methods: The study group included 22 patients, 12 with liver resection and 10 with liver transplantation for HCC with a mean follow-up after treatment of 20 months. Total RNA was isolated from tumoral and non-tumoral tissue fragments and gene expression has been quantified by qRT-PCR, using beta-actin as reference gene. A higher than 5-fold change in relative gene expression has been considered significant. A statistical model for prediction of tumor recurrence has been developped by logistic regression using quantitative RT-PCR data. The clinical utility of the model has been evaluated by the C-statistic (equivalent of the area under the ROC curve). Results: In 14 patients (63.6%) a higher than 5-fold change in relative gene expression has been detected. A significat up-regulation of the studied liver enriched transcription factors has been found in 4 patients (18.1%). A significat down regulation has been identified in 11 patients (50%) out of which HNF6 down regulation was detected in 4 patients (18.1%) and HNF1beta down regulation in 8 patients (36.3%). Only in one patient (4.5%) dramatical changes in LETFs expression has been detected FoxA2 and HNF6 were not detectable and C/Ebp-alpha and HNF1beta expression had a 100 fold decrease. The patient had a tumor recurrence in 4 months after the treatment. Based on qRT-PCR data a statistical model to predict recurence after curative treatment has been generated. The significant variables in the model were HNF6 and FoxA2 expression. The model has a C-statistic of 0.98 suggesting an excelent clinical utility. A cut-off level of 0.67 of the prognostic score had a 80% sensitivity and a 94.1% specificity in predicting recurrence of HCC after curative treatment. Conclusions: A significant change in LETF gene expression has been identified in 63.6% of patients curatively treated for hepatocellular carcinoma. A prognostic score using HNF6 and FoxA2 quantitative expression could be proposed for prospective validation.