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1.
Medicina (Kaunas) ; 58(12)2022 Dec 07.
Article En | MEDLINE | ID: mdl-36557005

Background and Objectives: Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, is the leading cause of cancer-related mortality. It arises and progresses against fibrotic or cirrhotic backgrounds mainly due to infection with hepatitis viruses B (HBV) or C (HCV) or non-viral causes that lead to chronic inflammation and genomic changes. A better understanding of molecular and immune mechanisms in HCC subtypes is needed. Materials and Methods: To identify transcriptional changes in primary HCC tumors with or without hepatitis viral etiology, we analyzed the transcriptomes of 24 patients by next-generation sequencing. Results: We identified common and unique differentially expressed genes for each etiological tumor group and analyzed the expression of SLC, ATP binding cassette, cytochrome 450, cancer testis, and heat shock protein genes. Metascape functional enrichment analysis showed mainly upregulated cell-cycle pathways in HBV and HCV and upregulated cell response to stress in non-viral infection. GeneWalk analysis identified regulator, hub, and moonlighting genes and highlighted CCNB1, ACTN2, BRCA1, IGF1, CDK1, AURKA, AURKB, and TOP2A in the HCV group and HSF1, HSPA1A, HSP90AA1, HSPB1, HSPA5, PTK2, and AURKB in the group without viral infection as hub genes. Immune infiltrate analysis showed that T cell, cytotoxic, and natural killer cell markers were significantly more highly expressed in HCV than in non-viral tumors. Genes associated with monocyte activation had the highest expression levels in HBV, while high expression of genes involved in primary adaptive immune response and complement receptor activity characterized tumors without viral infection. Conclusions: Our comprehensive study underlines the high degree of complexity of immune profiles in the analyzed groups, which adds to the heterogeneous HCC genomic landscape. The biomarkers identified in each HCC group might serve as therapeutic targets.


Carcinoma, Hepatocellular , Hepatitis C , Liver Neoplasms , Male , Humans , Carcinoma, Hepatocellular/pathology , Liver Neoplasms/pathology , Transcriptome/genetics , Hepatitis B virus/genetics , Hepatitis C/complications , Hepatitis C/genetics , RNA
2.
Cancers (Basel) ; 14(17)2022 Aug 25.
Article En | MEDLINE | ID: mdl-36077643

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% cytoplasmic BAP1 (cBAP1). Tumors exhibited heterogeneity with respect to BAP1 staining with different percentages of nBAP1 loss: ≥25% loss of nuclear BAP1 (nBAP1) was superior to chr8q and LOH3 as a prognostic indicator. Of the successfully sequenced UMs, 38% harbored oncogenic mutations in GNA11 and 48% harbored mutations in GNAQ at residues 209 or 183. Of the secondary drivers, 39% of mutations were in BAP1, 11% were in EIF1AX, and 20% were in the SF3B1 R625 hotspot. Most tumors with SF3B1 or EIF1AX mutations retained nuclear BAP1 (nBAP1). The majority of tumor samples with likely pathogenic BAP1 mutations, regardless of mutation class, displayed ≥25% loss of nBAP1. This included all tumors with truncating mutations and 80% of tumors with missense mutations. In addition, 60% of tumors with truncating mutations and 82% of tumors with missense mutations expressed >10% cBAP1.

4.
Cancer Genomics Proteomics ; 19(1): 94-104, 2022.
Article En | MEDLINE | ID: mdl-34949662

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.


Biomarkers, Tumor/genetics , Carcinoma, Non-Small-Cell Lung/mortality , Lung Neoplasms/mortality , Adult , Aged , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , B7 Antigens/genetics , Carcinoma, Non-Small-Cell Lung/diagnosis , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/therapy , Chemoradiotherapy , Chemotherapy, Adjuvant , Drug Resistance, Neoplasm/genetics , Female , Follow-Up Studies , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Kaplan-Meier Estimate , Lung/pathology , Lung/surgery , Lung Neoplasms/diagnosis , Lung Neoplasms/genetics , Lung Neoplasms/therapy , Male , Middle Aged , Neoadjuvant Therapy , Neoplasm Staging , Oligonucleotide Array Sequence Analysis , Pneumonectomy , Retrospective Studies , Risk Assessment/methods , Survival Rate , Treatment Outcome , Exome Sequencing
5.
Sci Rep ; 11(1): 19138, 2021 09 27.
Article En | MEDLINE | ID: mdl-34580349

Pleural mesothelioma is an aggressive malignancy with limited effective therapies. In order to identify therapeutic targets, we integrated SNP genotyping, sequencing and transcriptomics from tumours and low-passage patient-derived cells. Previously unrecognised deletions of SUFU locus (10q24.32), observed in 21% of 118 tumours, resulted in disordered expression of transcripts from Hedgehog pathways and the T-cell synapse including VISTA. Co-deletion of Interferon Type I genes and CDKN2A was present in half of tumours and was a predictor of poor survival. We also found previously unrecognised deletions in RB1 in 26% of cases and show sub-micromolar responses to downstream PLK1, CHEK1 and Aurora Kinase inhibitors in primary mesothelioma cells. Defects in Hippo pathways that included RASSF7 amplification and NF2 or LATS1/2 mutations were present in 50% of tumours and were accompanied by micromolar responses to the YAP1 inhibitor Verteporfin. Our results suggest new therapeutic avenues in mesothelioma and indicate targets and biomarkers for immunotherapy.


Biomarkers, Tumor/genetics , Gene Expression Regulation, Neoplastic/immunology , Hippo Signaling Pathway/genetics , Mesothelioma, Malignant/genetics , Pleural Neoplasms/genetics , Aged , Aged, 80 and over , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Biomarkers, Tumor/antagonists & inhibitors , Biopsy , DNA Copy Number Variations , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic/drug effects , Genomics , Hippo Signaling Pathway/drug effects , Hippo Signaling Pathway/immunology , Humans , Male , Mesothelioma, Malignant/drug therapy , Mesothelioma, Malignant/immunology , Mesothelioma, Malignant/pathology , Middle Aged , Mutation , Pleura/pathology , Pleural Neoplasms/drug therapy , Pleural Neoplasms/immunology , Pleural Neoplasms/pathology , Primary Cell Culture , Whole Genome Sequencing
6.
Cancer Genomics Proteomics ; 17(5): 587-595, 2020.
Article En | MEDLINE | ID: mdl-32859637

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).


Antineoplastic Combined Chemotherapy Protocols/pharmacology , Biomarkers, Tumor/genetics , Carcinoma, Non-Small-Cell Lung/therapy , Lung Neoplasms/therapy , Lymphatic Metastasis/therapy , Aged , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Carboplatin/pharmacology , Carboplatin/therapeutic use , Carcinoma, Non-Small-Cell Lung/diagnosis , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Chemotherapy, Adjuvant/methods , Cisplatin/pharmacology , Cisplatin/therapeutic use , Drug Resistance, Neoplasm/genetics , Female , Humans , Induction Chemotherapy/methods , Lung/diagnostic imaging , Lung/drug effects , Lung/pathology , Lung/surgery , Lung Neoplasms/diagnosis , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Lymph Nodes/diagnostic imaging , Lymph Nodes/pathology , Lymphatic Metastasis/diagnosis , Lymphatic Metastasis/pathology , Male , Mediastinum/diagnostic imaging , Mediastinum/pathology , Middle Aged , Neoadjuvant Therapy/methods , Neoplasm Staging , Pneumonectomy , Polymorphism, Single Nucleotide , Precision Medicine/methods , Prospective Studies , Thoracoscopy , Tomography, X-Ray Computed , Treatment Outcome , Exome Sequencing
7.
J Gastrointestin Liver Dis ; 26(3): 253-259, 2017 Sep.
Article En | MEDLINE | ID: mdl-28922437

BACKGROUND: The biliary complications (BC) have been always considered the "Achilles' heel" of liver transplantation (LT), being one of the leading causes of postoperative morbidity. AIM: To analyse predictors of BC, by monitoring in the peripheral blood the biomarkers involved in the inflammation and hepatic fibrosis, such as the matrix metalloproteinases (MMP 2, 9) and their tissue inhibitors (TIMP1), the interleukins (IL 2, 8), alfa-TNF, the endothelins and their receptors. METHODS: Thirty LT patients were followed-up prospectively for 5 years. The mRNA for the following biomarkers was quantified in the peripheral blood by qRTPCR and protein expression investigated by ELISA: MMP 2, 9, TIMP1, IL 2, IL 8, TNF-alfa, and endothelins and their receptors. RESULTS: Five patients developed anastomotic stenosis (AS). There was no difference regarding mRNA levels for all studied genes between AS and non-AS patients. Two cytokines were significantly different: pre-LT TNF alpha was higher in the non-AS group and post-LT endothelin-1 at day 7 and month 3 were higher in the AS group. There was a trend for lower levels of serum cytokines for patients without AS compared to patients with AS. CONCLUSION: BC play an important role in the patients' postoperative morbidity and molecular biomarkers prediction should improve their early recognition and treatment.


Biomarkers/blood , Cholestasis/blood , Liver Transplantation/adverse effects , Reperfusion Injury/blood , Adolescent , Adult , Cholestasis/diagnosis , Cholestasis/genetics , Enzyme-Linked Immunosorbent Assay , Female , Follow-Up Studies , Genetic Markers , Humans , Male , Middle Aged , Polymerase Chain Reaction , Predictive Value of Tests , Prognosis , Prospective Studies , Reperfusion Injury/diagnosis , Reperfusion Injury/genetics , Risk Factors , Time Factors , Treatment Outcome , Young Adult
8.
J Cell Mol Med ; 21(12): 3787-3794, 2017 Dec.
Article En | MEDLINE | ID: mdl-28767188

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.


DNA-Binding Proteins/genetics , Host-Pathogen Interactions , Human papillomavirus 18/genetics , Oncogene Proteins, Viral/genetics , Papillomavirus Infections/genetics , RNA, Long Noncoding/genetics , Uterine Cervical Neoplasms/genetics , Adult , Aged , Case-Control Studies , DNA-Binding Proteins/metabolism , Female , Gene Expression Regulation , HeLa Cells , Human papillomavirus 18/growth & development , Human papillomavirus 18/pathogenicity , Humans , Middle Aged , Oncogene Proteins, Viral/metabolism , Papillomavirus Infections/metabolism , Papillomavirus Infections/pathology , Papillomavirus Infections/virology , RNA, Long Noncoding/metabolism , Signal Transduction , Uterine Cervical Neoplasms/metabolism , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/virology
9.
Chirurgia (Bucur) ; 112(3): 289-300, 2017.
Article En | MEDLINE | ID: mdl-28675364

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.


Carcinoma, Hepatocellular/surgery , Catheter Ablation , Hepatectomy , Liver Neoplasms/surgery , Liver Transplantation , Carcinoma, Hepatocellular/etiology , Carcinoma, Hepatocellular/mortality , Carcinoma, Hepatocellular/pathology , Catheter Ablation/methods , Female , General Surgery , Hepatectomy/methods , Humans , Liver Cirrhosis/complications , Liver Neoplasms/etiology , Liver Neoplasms/mortality , Liver Neoplasms/pathology , Liver Transplantation/methods , Male , Middle Aged , Neoplasm Staging , Retrospective Studies , Romania/epidemiology , Survival Rate , Treatment Outcome
10.
Am J Cancer Res ; 7(3): 484-502, 2017.
Article En | MEDLINE | ID: mdl-28401006

AT rich interactive domain 1A (ARID1A) is one of the most commonly mutated genes in a broad variety of tumors. The mechanisms that involve ARID1A in ampullary cancer progression remains elusive. Here, we evaluated the frequency of ARID1A and KRAS mutations in ampullary adenomas and adenocarcinomas and in duodenal adenocarcinomas from two cohorts of patients from Singapore and Romania, correlated with clinical and pathological tumor features, and assessed the functional role of ARID1A. In the ampullary adenocarcinomas, the frequency of KRAS and ARID1A mutations was 34.7% and 8.2% respectively, with a loss or reduction of ARID1A protein in 17.2% of the cases. ARID1A mutational status was significantly correlated with ARID1A protein expression level (P=0.023). There was a significant difference in frequency of ARID1A mutation between Romania and Singapore (2.7% versus 25%, P=0.04), suggestive of different etiologies. One somatic mutation was detected in the ampullary adenoma group. In vitro studies indicated the tumor suppressive role of ARID1A. Our results warrant further investigation of this chromatin remodeller as a potential early biomarker of the disease, as well as identification of therapeutic targets in ARID1A mutated ampullary cancers.

11.
Cancer Genomics Proteomics ; 12(5): 231-42, 2015.
Article En | MEDLINE | ID: mdl-26417026

BACKGROUND/AIM: 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). MATERIALS AND METHODS: 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. RESULTS: 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 of <0.005 included: cytokine pathways, focal adhesion or extracellular matrix receptor interaction. CONCLUSION: Our approach identified important characteristics of NSCLC and pointed-out molecular differences between sub-groups of patients based on their response to therapy.


Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Gene Expression Profiling , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Lymph Nodes/pathology , Mediastinum/pathology , Adult , Aged , Carcinoma, Non-Small-Cell Lung/mortality , Carcinoma, Non-Small-Cell Lung/therapy , Cluster Analysis , Combined Modality Therapy , Female , Gene Expression Regulation, Neoplastic , Humans , Lung Neoplasms/mortality , Lung Neoplasms/therapy , Lymphatic Metastasis , Male , Middle Aged , Models, Biological , Neoplasm Staging , Prognosis , Signal Transduction , Transcriptome , Treatment Outcome
12.
Oncotarget ; 6(8): 5666-77, 2015 Mar 20.
Article En | MEDLINE | ID: mdl-25686840

The complex regulation of tumor suppressive gene and its pseudogenes play key roles in the pathogenesis of hepatocellular cancer (HCC). However, the roles played by pseudogenes in the pathogenesis of HCC are still incompletely elucidated. This study identifies the putative tumor suppressor INTS6 and its pseudogene INTS6P1 in HCC through the whole genome microarray expression. Furthermore, the functional studies - include growth curves, cell death, migration assays and in vivo studies - verify the tumor suppressive roles of INTS6 and INTS6P1 in HCC. Finally, the mechanistic experiments indicate that INTS6 and INTS6P1 are reciprocally regulated through competition for oncomiR-17-5p. Taken together, these findings demonstrate INTS6P1 and INTS6 exert the tumor suppressive roles through competing for oncomiR-17-5p. Our investigation of this regulatory circuit reveals novel insights into the underlying mechanisms of hepatocarcinogenesis.


Carcinoma, Hepatocellular/genetics , Liver Neoplasms/genetics , MicroRNAs/genetics , Pseudogenes , Ribosomal Proteins/genetics , Tumor Suppressor Proteins/genetics , Animals , Binding, Competitive , Carcinoma, Hepatocellular/metabolism , Cell Line, Tumor , Cell Proliferation , Genes, Tumor Suppressor , Heterografts , Humans , Liver Neoplasms/metabolism , Mice , MicroRNAs/metabolism , RNA-Binding Proteins , Ribosomal Proteins/metabolism , Transfection , Tumor Suppressor Proteins/metabolism
13.
Cancer Genomics Proteomics ; 12(1): 21-30, 2015.
Article En | MEDLINE | ID: mdl-25560641

BACKGROUND/AIM: 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. MATERIALS AND METHODS: 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. RESULTS: We found significantly higher methylation frequencies (p<0.001) 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. CONCLUSION: 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.


Adenocarcinoma/genetics , Carcinoma, Pancreatic Ductal/genetics , Cell Line, Tumor , Epigenesis, Genetic , Gene Expression Regulation, Neoplastic , Gene Silencing , Humans , Middle Aged , Prognosis
14.
Rom J Anaesth Intensive Care ; 21(2): 134-138, 2014 Oct.
Article En | MEDLINE | ID: mdl-28913446

Severe sepsis and septic shock are associated with an inflammatory cascade that is primarily responsible for multiple organ dysfunction. To date, there are no specific treatments designed to modulate and rebalance inflammatory cytokines levels. We present a case of a 50 years old man with postoperative septic shock after undergoing cephalic pancreatectomy for a pancreatic cystic tumor. The use of a haemoadsorbtion device (CytoSorb®) in combination with continuous veno-venous haemofiltration was associated with a decrease in TNFα, IL-1ß and IFNγ and an increase in IL-10 levels measured before and after two consecutive procedures. The effect of CytoSorb® on inflammatory cytokines translated into a more stable haemodynamic profile with a stable cardiac output and normalization of systemic vascular resistance index and decreased vasopressor requirements. Further prospective large clinical trials are required in order to determine the indications for CytoSorb® and to evaluate the overall outcome.

15.
Nat Genet ; 45(12): 1474-8, 2013 Dec.
Article En | MEDLINE | ID: mdl-24185513

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.


Bile Duct Neoplasms/genetics , Bile Duct Neoplasms/parasitology , Bile Ducts, Intrahepatic , Cholangiocarcinoma/genetics , Cholangiocarcinoma/parasitology , Exome/genetics , Fasciola hepatica , Fascioliasis/complications , Animals , Female , Gene Frequency , Genetic Predisposition to Disease , Humans , Isocitrate Dehydrogenase/genetics , Male , Mutation , Sequence Analysis, DNA , Tumor Cells, Cultured , Tumor Suppressor Proteins/genetics , Ubiquitin Thiolesterase/genetics
16.
J Gastrointestin Liver Dis ; 21(2): 181-5, 2012 Jun.
Article En | MEDLINE | ID: mdl-22720308

BACKGROUND AND AIM: 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. METHODS: 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. RESULTS: 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. CONCLUSION: H1069Q mutation is highly prevalent in Romanian WD patients and first degree relatives, similar to other central and continental western European populations.


Adenosine Triphosphatases/genetics , Cation Transport Proteins/genetics , Hepatolenticular Degeneration/genetics , Mutation, Missense , Adolescent , Adult , Copper-Transporting ATPases , DNA Mutational Analysis/methods , Female , Gene Frequency , Genetic Predisposition to Disease , Genetic Testing/methods , Hepatolenticular Degeneration/diagnosis , Heterozygote , Homozygote , Humans , Male , Young Adult
17.
Can J Cardiol ; 28(6): 712-20, 2012.
Article En | MEDLINE | ID: mdl-22721676

BACKGROUND: 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. METHODS: 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. RESULTS: 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). CONCLUSIONS: 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.


Arterial Occlusive Diseases/genetics , Chondroitin Sulfate Proteoglycans/genetics , Cytokines/genetics , Gene Expression Regulation , Keratan Sulfate/genetics , Lectins/genetics , RNA, Messenger/genetics , Ankle Brachial Index , Arterial Occlusive Diseases/diagnosis , Arterial Occlusive Diseases/metabolism , C-Reactive Protein/metabolism , Chondroitin Sulfate Proteoglycans/biosynthesis , Cytokines/biosynthesis , Enzyme-Linked Immunosorbent Assay , Female , Femoral Artery/metabolism , Femoral Artery/pathology , Follow-Up Studies , GPI-Linked Proteins/biosynthesis , GPI-Linked Proteins/genetics , Humans , Keratan Sulfate/biosynthesis , Lectins/biosynthesis , Lumican , Male , Middle Aged , Nicotinamide N-Methyltransferase/blood , Real-Time Polymerase Chain Reaction
18.
J Proteome Res ; 10(3): 1246-65, 2011 Mar 04.
Article En | MEDLINE | ID: mdl-21142185

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.


Biomarkers, Tumor/blood , Biomarkers, Tumor/chemistry , Glycomics/methods , Glycoproteins/blood , Glycoproteins/chemistry , Immune System/physiology , Stomach Neoplasms/metabolism , Adult , Aged , Blood Proteins/analysis , Female , Humans , Immunoglobulin G/blood , Male , Middle Aged , Proteome/analysis , Stomach Neoplasms/chemistry , Two-Dimensional Difference Gel Electrophoresis , Young Adult
19.
Hepatogastroenterology ; 57(104): 1453-64, 2010.
Article En | MEDLINE | ID: mdl-21443102

BACKGROUND/AIMS: 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. METHODOLOGY: 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. RESULTS: 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. CONCLUSIONS: 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.


Adenocarcinoma/genetics , Biomarkers, Tumor/genetics , Stomach Neoplasms/genetics , Adenocarcinoma/pathology , Chemotactic Factors/genetics , Collagen Type X/genetics , Gene Expression Regulation, Neoplastic , Humans , Hyaluronoglucosaminidase , Interleukin-11/genetics , Keratin-17/genetics , Lymphatic Metastasis , Matrix Metalloproteinase 3/genetics , Microarray Analysis , Neoplasm Staging , Osteopontin/genetics , Proteins/genetics , Reverse Transcriptase Polymerase Chain Reaction , S100 Proteins/genetics , Stomach Neoplasms/pathology
20.
Neuroreport ; 18(9): 921-4, 2007 Jun 11.
Article En | MEDLINE | ID: mdl-17515802

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.


Analgesia , Coffee , Pain/psychology , Smoking/psychology , Adult , Blood Pressure/drug effects , Blood Pressure/physiology , Cold Temperature , Drug Synergism , Female , Humans , Male , Pain Measurement/drug effects , Pain Threshold/drug effects , Pain Threshold/physiology , Pressure , Substance Withdrawal Syndrome/psychology
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