Integrated Bioinformatics Analysis Identifies Crucial Biochemical Processes Shared between Pancreatitis and Pancreatic Ductal Adenocarcinoma

Background: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy associated with rapid progression and an abysmal prognosis. Previous research has shown that chronic pancreatitis can significantly increase the risk of developing PDAC. The overarching hypothesis is that some of the biological processes disrupted during the inflammatory stage tend to show significant dysregulation, even in cancer. This might explain why chronic inflammation increases the risk of carcinogenesis and uncontrolled proliferation. Here, we try to pinpoint such complex processes by comparing the expression profiles of pancreatitis and PDAC tissues. Methods: We analyzed a total of six gene expression datasets retrieved from the EMBL-EBI ArrayExpress and NCBI GEO databases, which included 306 PDAC, 68 pancreatitis and 172 normal pancreatic samples. The disrupted genes identified were used to perform downstream analysis for ontology, interaction, enriched pathways, potential druggability, promoter methylation, and the associated prognostic value. Further, we performed expression analysis based on gender, patient’s drinking habit, race, and pancreatitis status. Results: Our study identified 45 genes with altered expression levels shared between PDAC and pancreatitis. Over-representation analysis revealed that protein digestion and absorption, ECM-receptor interaction, PI3k-Akt signaling, and proteoglycans in cancer pathways as significantly enriched. Module analysis identified 15 hub genes, of which 14 were found to be in the druggable genome category. Conclusion: In summary, we have identified critical genes and various biochemical processes disrupted at a molecular level. These results can provide valuable insights into certain events leading to carcinogenesis, and therefore help identify novel therapeutic targets to improve PDAC treatment in the future.     

Down-regulation of BRCA1 in chronic pancreatitis and sporadic pancreatic adenocarcinoma.

PURPOSE: BRCA1 and BRCA2 are considered to be breast cancer susceptibility genes that may also contribute to pancreatic cancer development because family studies revealed mutation carriers to have an increased risk of developing pancreatic cancer. However, as demonstrated for breast and ovarian cancer, inactivation of BRCA in sporadic diseases is based on alteration in gene expression or functional alteration. EXPERIMENTAL DESIGN: To study a potential correlation of BRCA1 and BRCA2 to chronic pancreatitis and development of sporadic pancreatic adenocarcinoma, we have analyzed the expression of these genes by quantitative PCR and performed immunohistochemical analyses in normal pancreatic tissues, chronic pancreatitis, and pancreatic cancer specimens. RESULTS: BRCA1 expression was down-regulated in chronic alcoholic pancreatitis, in particular on the RNA level. Furthermore, our data indicate suppressed BRCA1 expression in pancreatic cancer on both the RNA and protein levels. Quantitative analysis of BRCA1 protein expression demonstrated regular staining in 50% of tumor specimens tested and reduced staining in 50% of tumor specimens tested. Correlation with the clinical outcome revealed a significantly better 1-year overall survival for patients with BRCA1-regular as compared with BRCA1-reduced or BRCA1-absent tumors. In contrast, no substantial differences in BRCA2 expression were found in chronic pancreatitis and pancreatic cancer samples. CONCLUSIONS: Our data demonstrate alteration of BRCA1 expression in chronic pancreatitis and sporadic pancreatic adenocarcinoma. We, for the first time, provide evidence for a role of BRCA1 in pancreatic carcinogenesis of noninherited tumors and for clinical outcome.     

Construction of a Protein-Protein Interaction Network for Chronic Myelocytic Leukemia and Pathway Prediction of Molecular Complexes

Background: Chronic myelocytic leukemia is a disease that threatens both adults and children. Great progress has been achieved in treatment but protein-protein interaction networks underlining chronic myelocytic leukemia are less known. Objective: To develop a protein-protein interaction network for chronic myelocytic leukemia based on gene expression and to predict biological pathways underlying molecular complexes in the network. Materials and Methods: Genes involved in chronic myelocytic leukemia were selected from OMIM database. Literature mining was performed by Agilent Literature Search plugin and a protein-protein interaction network of chronic myelocytic leukemia was established by Cytoscape. The molecular complexes in the network were detected by Clusterviz plugin and pathway enrichment of molecular complexes were performed by DAVID online. Results and Discussion: There are seventy-nine chronic myelocytic leukemia genes in the Mendelian Inheritance In Man Database. The protein-protein interaction network of chronic myelocytic leukemia contained 638 nodes, 1830 edges and perhaps 5 molecular complexes. Among them, complex 1 is involved in pathways that are related to cytokine secretion, cytokine-receptor binding, cytokine receptor signaling, while complex 3 is related to biological behavior of tumors which can provide the bioinformatic foundation for further understanding the mechanisms of chronic myelocytic leukemia.     

The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data

Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched. Cytoscape software was for the construction of protein–protein interaction (PPI) network and module analysis to find the hub genes and key pathways. Finally, weighted correlation network analysis (WGCNA) was conducted to further screen critical gene modules with similar expression pattern and explore their biological significance. Significance analysis identified 1230 DEGs with fold change >2, including 632 significantly down-regulated DEGs and 598 significantly up-regulated DEGs. GO term enrichment analysis suggested that up-regulated DEG significantly enriched in immune response, cell adhesion, cell migration, type I interferon signaling pathway, and cell proliferation, and the down-regulated DEG mainly enriched in response to endoplasmic reticulum stress and endoplasmic reticulum unfolded protein response. KEGG pathway analysis found DEGs significantly enriched in five pathways including complement and coagulation cascades, focal adhesion, ECM–receptor interaction, antigen processing and presentation, and protein processing in endoplasmic reticulum. The top 10 hub genes in HCC were separately GMPS, ACACA, ALB, TGFB1, KRAS, ERBB2, BCL2, EGFR, STAT3, and CD8A, which resulted from PPI network. The top 3 gene interaction modules in PPI network enriched in immune response, organ development, and response to other organism, respectively. WGCNA revealed that the confirmed eight gene modules significantly enriched in monooxygenase and oxidoreductase activity, response to endoplasmic reticulum stress, type I interferon signaling pathway, processing, presentation and binding of peptide antigen, cellular response to cadmium and zinc ion, cell locomotion and differentiation, ribonucleoprotein complex and RNA processing, and immune system process, respectively. In conclusion, we identified some key genes and pathways closely related with HCC initiation and progression by a series of bioinformatics analysis on DEGs. These screened genes and pathways provided for a more detailed molecular mechanism underlying HCC occurrence and progression, holding promise for acting as biomarkers and potential therapeutic targets.     

Expression of epidermal and transforming growth factors in pancreatic cancer

Pancreatic cancer continues to be a major clinical problem and little is known of the various cellular and molecular events associated with this malignancy. Growth factors and their receptors have important functions in the process of tumor progression. We have examined by immunocytochemistry, the expression of epidermal growth factor (EGF), its receptor (EGFR) and the transforming growth factors alpha and beta (TGF alpha and beta) in various grades of pancreatic adenocarcinoma. Expression of the growth factors was compared to their distribution in apparently normal pancreas and chronic pancreatitis. EGF, TGF alpha and TGF beta was expressed in normal pancreatic tissue while the expression of EGFR was slight and restricted. In chronic pancreatitis, this expression of EGFR increased and was found to be moderate in intensity. Expression of EGF, TGF alpha and TGF beta was similar to that seen in normal pancreas. Moderate to intense expression of EGF and TGF alpha was evident in all grades of pancreatic cancer. Expression of EGFR was intense in all these lesions. However, the most significant finding was the absence of TGF beta in all pancreatic cancer lesions. These results may have significant implications for pancreatic tumor progression. EGF and TGF alpha are growth promoters influencing the expression of EGFR. TGF beta, on the other hand exerts an anti-proliferative effect and favours differentiation. It therefore appears that the balance between EGF and TGF alpha on the one hand and TGF beta on the other may be critical in the process of tumor progression, especially if one considers chronic pancreatitis as a pre-malignant condition and the growth factor expression associated with it.     

The MUC gene family: Their role in diagnosis and early detection of pancreatic cancer

The early diagnosis of pancreatic cancer, as well as distinguishing between chronic pancreatitis and malignant pancreatic disease, remains still a clinical problem. Presently, there is no specific tumor marker for diagnosing pancreatic cancer. Mucin-associated marker like CA 19-9 are the most widely available pancreatic cancer tumor marker, but its value as a screening marker is limited by its reduced specificity.Mucins (MUCs) are heavily glycosylated, high molecular weight glycoproteins with an aberrant expression profile in various malignancies.This review considers briefly the potential use of the mucin expression pattern in diagnosis of pancreatic neoplasm. The overview will point out the present knowledge about changes in the mucin gene expression in pancreatic intraepithelial neoplasia (PanINs) as precursor lesions and in pancreatic adenocarcinoma, compared to normal pancreas and chronic pancreatitis and the potential role for differentiating chronic pancreatitis from pancreatic cancer.Furthermore, the potential use of MUCs in the diagnosis and differentiation of intraductal papillary-mucinous neoplasm's (IPMNs) will be discussed.     

胰腺癌危险因素的病例对照研究

目的:探讨与胰腺癌发病可能有关的各种危险因素。方法:回顾性分析2000年6月-2010年6月收治的290例胰腺癌患者和同期312例非肿瘤来源、非代谢性疾病患者的性别、年龄、高血压、吸烟史、肿瘤家族疾病史、消化系统手术史、胆系疾病史、慢性胰腺疾病史、总胆固醇、三酰甘油、乙型肝炎病毒表面抗原(hepatitis B surface antigen,HBsAg)、丙型肝炎病毒抗体(hepatitis C virus antibody,anti-HCV)和糖尿病等资料,进行单因素和多因素logistic分析。结果:单因素分析表明,糖尿病、高血压、吸烟史、肿瘤家族疾病史、消化系统手术史、胆系疾病史、慢性胰腺疾病史、总胆固醇水平和三酰甘油水平在2组间的差异有统计学意义(P<0.05);多因素logistic分析表明,吸烟[比数比(odds ratio,OR)=1.66,95%可信区间(confidence interval,CI)=1.08～2.56)]、糖尿病(OR=11.14,95%CI=5.07～24.49)、高血压(OR=1.64,95%CI=1.07～2.51)、胆系疾病史(OR=4.19,95%CI=2.74～6.40)和三酰甘油水平(OR=1.83,95%CI=1.44～2.32)是胰腺癌独立的高危因素(P<0.05)。结论:吸烟、糖尿病、高血压、胆系疾病史和三酰甘油水平可能是胰腺癌独立的高危因素。     

胰头癌与胰头慢性胰腺炎的MR诊断与鉴别诊断

目的探讨胰头癌及胰头慢性胰腺炎的MR诊断与鉴别诊断。方法回顾性分析24例胰头癌及3例胰头慢性胰腺炎的MR表现。全部27例病人均行常规及压脂SET1WI序列、常规及压脂FSET2WI序列扫描。8例胰头癌及3例胰头慢性炎症患者行压脂SET1WI序列增强扫描。T2WI序列发现胰管扩张时行MRCP共24例,其中胰头癌23例,慢性胰腺炎1例。结果24例胰头癌于常规SET1WI序列呈低(n=8)或稍低(n=16)信号,于常规FSET2WI序列可表现为高(n=8)、稍高(n=5)、等(n=10)或低(n=1)信号,于压脂FSET2WI序列可表现为高(n=11)、等(n=11)或稍低(n=2)信号,于压脂SET1WI序列均呈低信号。23例胰头癌于MRCP均可见典型的“双管征”、胆总管扩张及远端截断。8例胰头癌无明显强化。3例胰头慢性胰腺炎于常规SET1WI序列呈稍低或等信号,于常规FSET2WI序列均呈高信号。2例于压脂SET1WI及FSET2WI序列分别呈等信号及稍高信号,另1例则分别呈低信号及混杂信号,MRCP可见胆总管轻度扩张伴胰管近端不规则扩张。3例慢性胰炎均呈不同程度强化。结论胰头癌与胰头慢性胰腺炎均于多个序列表现出信号的多样性,均可见异常强化,绝大多数胰头癌及部分胰头慢性胰腺炎有异常的MRCP表现。联合使用多种序列特别是平扫及增强压脂SET1WI序列及MRCP,可能鉴别胰头癌与胰头慢     

Challenges of drug resistance in the management of pancreatic cancer

The current treatment of choice for metastatic pancreatic cancer involves single-agent gemcitabine or a combination of gemcitabine with capecitabine or erlotinib (a tyrosine kinase inhibitor). Only 25–30% of patients respond to this treatment and patients who do respond initially ultimately exhibit disease progression. Median survival for pancreatic cancer patients has reached a plateau due to inherent and acquired resistance to these agents. Key molecular factors implicated in this resistance include: deficiencies in drug uptake, alteration of drug targets, activation of DNA repair pathways, resistance to apoptosis and the contribution of the tumor microenvironment. Moreover, for newer agents including tyrosine kinase inhibitors, overexpression of signaling proteins, mutations in kinase domains, activation of alternative pathways, mutations of genes downstream of the target and/or amplification of the target represent key challenges for treatment efficacy. Here we will review the contribution of known mechanisms and markers of resistance to key pancreatic cancer drug treatments.     

Clinico-Pathological Particularities of the Shock-Related Pancreatitis

Acute pancreatitis can develop in patients with shock due to the underlying diseases, surgical interventions or because of severe hypoperfusion. The aim of our work was to study the histological alterations of the pancreas in patients dying after cardiogenic, hypovolemic or septic shock, to demonstrate the presence and severity of pancreatic injury. We performed a retrospective study which included patients who died and who were autopsied after different types of shock, hospitalized between 2007-2009 in general and cardiac intensive care units. We excluded the patients with known pancreatic diseases. From 223 patients included in our study 39 presented necrotising hemorrhagic alteration of the pancreatic tissue. There were no differences in histological and immunohistochemical findings between the different etiopathogenetic types of shock. None of the patients had characteristic clinical signs for acute pancreatitis. The digestive symptoms, they presented, could be related to the underlying disease or to postoperative state. The common findings in these patients were prolonged and severe hypotension, associated renal dysfunction, leucocytosis, hyperglycemia and hypocalcemia. Pancreatitis can occur in patients with shock, due to prolonged hypoperfusion of the pancreas. It is difficult to diagnose it because clinical signs are altered due to severity of underlying disease or analgo-sedation commonly used in intensive care. We therefore recommend in patients with shock to consider the possible development of ischemic pancreatitis for prompt and efficient treatment.     

Challenges of drug resistance in the management of pancreatic cancer

The current treatment of choice for metastatic pancreatic cancer involves single-agent gemcitabine or a combination of gemcitabine with capecitabine or erlotinib (a tyrosine kinase inhibitor). Only 25–30% of patients respond to this treatment and patients who do respond initially ultimately exhibit disease progression. Median survival for pancreatic cancer patients has reached a plateau due to inherent and acquired resistance to these agents. Key molecular factors implicated in this resistance include: deficiencies in drug uptake, alteration of drug targets, activation of DNA repair pathways, resistance to apoptosis and the contribution of the tumor microenvironment. Moreover, for newer agents including tyrosine kinase inhibitors, overexpression of signaling proteins, mutations in kinase domains, activation of alternative pathways, mutations of genes downstream of the target and/or amplification of the target represent key challenges for treatment efficacy. Here we will review the contribution of known mechanisms and markers of resistance to key pancreatic cancer drug treatments.     

COL1A2 is a Novel Biomarker to Improve Clinical Prediction in Human Gastric Cancer: Integrating Bioinformatics and Meta-Analysis

Gastric cancer is the third most common cause of cancer-related death in worldwide. It is crucial to target the key genes controlling pathogenesis in the early stage of gastric cancer. This study describes an integrated bioinformatics to identify molecular biomarkers for gastric cancer in patients’ cancer tissues. We reports differently expression genes in large gastric cancer cohorts from Gene Expression Ominus (GEO). Our findings revealed that 433 genes were significantly different expressed in human gastric cancer. Differently expression gene profile in gastric cancer was further validated by bioinformatic analyses, co-expression network construction. Based on the co-expression network and top-ranked genes, we identified collagen type I alpha 2 (COL1A2) which encodes the pro-alpha2 chain of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain, was the key gene in a 37-gene network that modulates cell motility by interacting with the cytoskeleton. Furthermore, the prognostic role of COL1A2 was determined by use of immunohistochemistry on human gastric cancer tissue. COL1A2 was highly expressed in human gastric cancer as compared with normal gastric tissues. Statistical analysis showed COL1A2 expression level was significantly associated with histological type and lymph node status. However, there were no correlations between COL1A2 expression and age, lymph node numbers, tumor size, or clinical stage. In conclusion, the novel bioinformatics used in this study has led to identification of improving diagnostic biomarkers for human gastric cancer and could benefit further analyses of the key alteration during its progression.     

Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses

Molecular mechanisms contributing to initiation and progression of head and neck squamous cell carcinoma are still poorly known. Numerous genetic alterations have been described, but molecular consequences of such alterations in most cases remain unclear. Here, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 20 laryngeal cancer cell lines and primary tumors. Our aim was to identify genetic alterations that play a key role in disease pathogenesis and pinpoint genes whose expression is directly impacted by these events. Integration of DNA level data from array-based comparative genomic hybridization with RNA level information from oligonucleotide microarrays was achieved with custom-developed bioinformatic methods. High-level amplifications had a clear impact on gene expression. Across the genome, overexpression of 739 genes could be attributed to gene amplification events in cell lines, with 325 genes showing the same phenomenon in primary tumors including FADD and PPFIA1 at 11q13. The analysis of gene ontology and pathway distributions further pinpointed genes that may identify potential targets of therapeutic intervention. Our data highlight genes that may be critically important to laryngeal cancer progression and offer potential therapeutic targets.     

Expression of connective tissue growth factor in pancreatic cancer cell lines

Connective tissue growth factor (CTGF/CCN2) is thought to play a role in normal wound repair and bone remodeling, but also promotes fibrosis in several disease processes including diabetic nephropathy, sclerodoma and pancreatitis. A contribution to desmoplasia associated with pancreatic cancer progression has also been proposed. CTGF is induced by TGFbeta in diverse cell types, but TGFbeta receptor mediated signaling is impaired in pancreatic cancers and cell lines, usually due to DPC4/Smad4 mutations which arise during the later stages of intraepithelial neoplastic progression. Therefore, in order to define signaling pathways that mediate basal and TGFbeta-induced CTGF expression in normal and transformed cells, we compared CTGF gene regulation in pancreatic cancer cells and fibroblasts by measuring the effects of small molecule inhibitors and dominant negative mutants of signaling proteins on CTGF promoter reporter activity, message, and protein expression. We determined that the previously identified TEF-1 cis element is essential for CTGF promoter reporter activity in pancreatic cancer cell lines. Whereas p38 mediated CTGF induction by TGFbeta in fibroblasts, MEK/ERK signaling mediated TGFbeta-induced CTGF expression in pancreatic cancer cells and was also responsible for basal CTGF expression in pancreatic cancer cell lines with defective Smad signaling. Since activating Ras mutations occur in the earliest stages of pancreatic cancer, CTGF may be induced independent of Smad4 in pancreatic cancer cells.     

survivin基因在胰腺癌组织中的表达及与HSP27表达的关系

目的:探讨胰腺癌组织中survivin基因的表达及其与热体克蛋白(HSP27)表达的关系。方法:用RT-PCR法检测62例胰腺癌、12例慢性胰腺炎及10例正常胰腺组织中survivinmRNA的表达,免疫组织化学法检测胰腺癌组织中HSP27的表达。结果:survivin在胰腺癌中的表达率为74.2%,而在慢性胰腺炎及正常胰腺组织中未见表达;survivin表达与胰腺癌的肿块大小、分化程度、临床分期及淋巴结转移无相关性;survivin与HSP27的表达有相关性。结论:survivin在胰腺癌中过度表达,提示其在胰腺癌的发生和发展中起重要作用;survivin和HSP27通过抗凋亡机制协同参与胰腺癌的发生。     

ErbB2 oncogene antibodies differentiate between the normal and diseased pancreas, and between chronic pancreatitis and pancreatic cancer

Histological differentiation between chronic pancreatitis and pancreatic cancer, especially in biopsy material, remains challenging and the frequent association of 'secondary' chronic pancreatitis (due to ductal obstruction) with pancreatic cancer causes additional diagnostic problems. Our study, using anti-ErbB2 antibodies from Santa Cruz and Dako in tissues from the normal pancreas, chronic pancreatitis and pancreatic cancer showed that these antibodies discriminate between primary chronic pancreatitis and 'secondary' chronic pancreatitis due to pancreatic cancer. Tissues from 28 pancreatic cancer patients, 15 chronic pancreatitis patients and 12 organ donors or early autopsy cases were subjected to immunohistochemical studies using polyclonal ErbB2 antibodies from Santa Cruz and Dako. The Santa Cruz antibody immunoreacted with islet cells in all tissues from the normal pancreas and pancreatic cancer but not in any chronic pancreatitis specimen. The Dako antibody showed a membrane staining of ductal and ductular cells only in chronic pancreatitis cases but in none of the normal or cancer specimens. Moreover, in chronic pancreatitis cases, ductular cells were stained with the Santa Cruz antibody only in the severe form, but not in the mild or moderate form of the disease. The utilized ErbB2 antibodies discriminate between the normal pancreas, chronic pancreatitis and pancreatic cancer. Hence, these antibodies seem to present an additional useful aid in the surgical pathology of pancreatic diseases.