EYA2 suppresses the progression of hepatocellular carcinoma via SOCS3-mediated blockade of JAK/STAT signaling.

BACKGROUND: Somatic mutations are involved in hepatocellular carcinoma (HCC) progression, but the genetic mechanism associated to hepatocarcinogenesis remains poorly understood. We report that Eyes absent homolog 2 (EYA2) suppresses the HCC progression, while EYA2(A510E) mutation identified by exome sequencing attenuates the tumor-inhibiting effect of EYA2. METHODS: Whole-exome sequencing was performed on six pairs of human HCC primary tumors and matched adjacent tissues. Focusing on EYA2, expression level of EYA2 in human HCC samples was evaluated by quantitative real-time PCR, western blot and immunohistochemistry. Loss- and gain-of-function studies, hepatocyte-specific deletion of EYA2 (Eya2-/-) in mice and RNA sequencing analysis were used to explore the functional effect and mechanism of EYA2 on HCC cell growth and metastasis. EYA2 methylation status was evaluated using Sequenom MassARRAY and publicly available data analysis. RESULTS: A new somatic mutation p.Ala510Glu of EYA2 was identified in HCC tissues. The expression of EYA2 was down-regulated in HCC and associated with tumor size (P = 0.001), Barcelona Clinic Liver Cancer stage (P = 0.016) and tumor differentiation (P = 0.048). High level of EYA2 was correlated with a favorable prognosis in HCC patients (P = 0.003). Results from loss-of-function and gain-of-function experiments suggested that knockdown of EYA2 enhanced, while overexpression of EYA2 attenuated, the proliferation, clone formation, invasion, and migration of HCC cells in vitro. Delivery of EYA2 gene had a therapeutic effect on inhibition of orthotopic liver tumor in nude mice. However, EYA2(A510E) mutation led to protein degradation by unfolded protein response, thus weakening the inhibitory function of EYA2. Hepatocyte-specific deletion of EYA2 in mice dramatically promoted diethylnitrosamine-induced HCC development. EYA2 was also down-regulated in HCC by aberrant CpG methylation. Mechanically, EYA2 combined with DACH1 to transcriptionally regulate SOCS3 expression, thus suppressing the progression of HCC via SOCS3-mediated blockade of the JAK/STAT signaling pathway. CONCLUSIONS: In our study, we identified and validated EYA2 as a tumor suppressor gene in HCC, providing a new insight into HCC pathogenesis.

Application of electrochemical methods for the detection of abiotic stress biomarkers in plants.

Abiotic stress is the main cause of low productivity in plants. Therefore, it is important to detect stress and respond to it in a timely manner to avoid irreversible damage to plant productivity and health. The application of traditional methods in agriculture is limited by expensive equipment and cumbersome sample processing. More effective detection methods are urgently needed due to the trace amounts and low stabilities of plant biomarkers. Electrochemical detection methods have the unique advantages of high accuracy, a low detection limit, fast response and easy integration with systems. In this review, the application of three types of electrochemical methods to phytohormone assessment is highlighted including direct electrochemical, immunoelectrochemical, and photoelectrochemical methods. Research on electrochemical methods for detecting abiotic stress biomarkers, including various phytohormones, is also summarized with examples. To date, the detection limit of exogenous plant hormones can reach pg/mL or even lower. Nevertheless, more efforts need to be made to develop a portable instrument for in situ online detection if electrochemical sensors are to be applied to the detection of the endogenous hormones or the physiological state of plants. Additionally, plant-wearable sensors that can be directly attached to or implanted into plants for continuous, noninvasive and real-time monitoring are emphasized. Finally, rational summaries of the considered methods and present challenges and future prospects in the field of abiotic stress detection-based electrochemical biosensors are thoroughly discussed.

Development of a novel autophagy-related gene prognostic signature for gastric cancer.

BACKGROUND: A growing number of evidence has revealed the vital role of autophagy in pathological processes of cancer, including gastric cancer (GC). However, many previous studies only focused on exploring single pathway or limited genes of interest in GC, which only reflected partial functions of autophagy. The present study aimed to construct an autophagy-related risk signature for GC. METHODS: Differentially expressed autophagy-related genes (ARGs) in GC and non-tumor samples were screened through The Cancer Genome Atlas (TCGA) database, followed by bioinformatics analysis using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) platforms. Prognosis-related ARGs were generated by univariate and multivariate Cox regression test. RESULTS: A total of seven prognosis-related ARGs (HSPB8, NRG2, GABARAPL1, TMEM74, DLC1, MAP1LC3C and NRG3) were determined to establish a prognostic index (PI) model, which was demonstrated to be an independent prognostic indicator for patients with GC. More importantly, it was successfully validated in an external cohort of patients from the GSE15460 dataset, indicating the useful reproducibility of this signature. In addition, the PI model was associated with immune cell infiltration estimates in GC. CONCLUSIONS: Taken together, the present study suggested that the seven ARGs-related signature could serve as an independent prognostic indicator for patients with GC.

Metallophosphoesterase 1, a novel candidate gene in hepatocellular carcinoma malignancy and recurrence.

BACKGROUND: There is an unmet need to identify novel mechanism-based prognostic genes associated with hepatocellular carcinoma (HCC) recurrence that can predict patient outcomes and provide therapeutic targets. This study aims to identify potential novel driver genes and mutations in HCC. METHODS: Single nucleotide variations (SNVs) contributing to HCC recurrence were identified using whole-exome sequencing of 5 DNA samples extracted from a single HCC patient with HBV-induced cirrhosis. SNVs were verified in primary HCC (n = 87), recurrent HCC (n = 34), and benign liver disease with cirrhosis tissues (n = 43). A candidate gene was identified, and its association and function in HCC development and recurrence were examined. RESULTS: 177 SNVs were identified and 70 SNVs were verified. A MPPE1 missense mutation on chr18_11897016 was the most frequent mutation (16.5%) in primary and recurrent HCC tissues, occurring with a higher frequency in recurrent HCC than primary HCC or benign liver tumor tissues. The MPPE1 mutation was significantly associated with HCC recurrence (P = .003), TNM stage (P = .002), and Child-Pugh classification (P = .039), and was an independent risk factor for HCC recurrence (HR = 1.969; 95%CI = 1.043-3.714, P = .037). Analysis of publically available data deposited in the GEO and TCGA showed MPPE1 expression levels were significantly increased in HCC tumor samples compared to adjacent nontumor tissues. The knockdown of MPPE1 in HCC cell lines significantly inhibited cell proliferation, migration and invasion, induced cell cycle arrest and apoptosis in vitro, and inhibited xenograft tumor growth in nude mice in vivo (P < .05). CONCLUSIONS: MPPE1 is a novel gene associated with HCC malignancy and recurrence.

Expression of Integrin ß6 and HAX-1 Correlates with Aggressive Features and Poor Prognosis in Esophageal Squamous Cell Carcinoma.

PURPOSE: The development of esophageal squamous cell carcinoma (ESCC) is a complicated process in which cell adhesion and motility, mediated by integrins, are involved through connecting the cytoskeleton to extracellular matrix. Different mechanisms via which integrin ß6 participates in cancer invasion and metastasis have been described by numerous studies; however, the expression and clinical significance of integrin ß6 in ESCC remain unknown. METHODS: To investigate the differential expression of integrin ß6 in ESCC, qPCR and immunohistochemistry assays were performed in 10 paired human samples. A total of 137 ESCC samples were further enrolled to evaluate the expression levels of integrin ß6 and its endocytic trafficking regulator HS1-associated protein X-1 (HAX-1), followed by the evaluation of their correlation with clinicopathological parameters. The overall survival was analyzed using the Kaplan-Meier method, with significant variables further evaluated by multivariate Cox regression analyses. RESULTS: The expression of integrin ß6 was markedly increased in ESCC compared with matched adjacent normal tissues. Among the ESCC samples, positive expression of integrin ß6 was observed in 41.6% tumors, which was associated with histological differentiation, lymph node metastasis and TNM stage. High expression of HAX-1 was detected in 47.4% tumors, and there was a positive relationship between the expression levels of integrin ß6 and HAX-1. Furthermore, the expression of integrin ß6 and HAX-1 were independent unfavorable indicators for prognosis. Patients with positive integrin ß6 and high HAX-1 expression demonstrated worst outcomes. CONCLUSION: The present findings suggested the predictive value of integrin ß6 and HAX-1 as independent indicators of poor prognosis for patients with ESCC, both of which may contribute to the tumor proliferation and metastasis, leading to ESCC progression. Therefore, combined targeting of integrin ß6 and HAX-1 may provide a potential novel approach for the treatment of ESCC.

Interleukin-6 Promotes Epithelial-Mesenchymal Transition and Cell Invasion through Integrin ß6 Upregulation in Colorectal Cancer.

The metastatic potential of colorectal cancer (CRC) is intensively promoted by the tumor microenvironment (TME) in a paracrine manner. As a pleiotropic inflammatory cytokine, Interleukin-6 (IL-6) is produced and involved in CRC, the same scenario where integrin αvß6 also becomes upregulated. However, the relationship between IL-6 and integrin αvß6 as well as their involvement in the crosstalk between CRC and TME remains largely unclear. In the present study, we demonstrated a positive correlation between the expression of IL-6 and integrin ß6 in CRC samples. The mutually promotive interaction between CRC and TME was further determined by an indirect coculture system. CRC cells could augment the secretion of IL-6 from fibroblasts, which in return induced invasion and integrin ß6 expression of CRC cells. Through the classic IL-6 receptor/STAT-3 signaling pathway, IL-6 mediated the upregulation of integrin ß6, which was involved in the invasion and epithelial-mesenchymal transition of CRC cells induced by IL-6. Taken together, our results reveal a paracrine crosstalk between IL-6 signals originating from the TME and increased the integrin ß6 level of CRC. IL-6 induces CRC invasion via upregulation of integrin ß6 through the IL-6 receptor/STAT-3 signaling pathway. Combined inhibition of IL-6 along with integrin ß6-targeted strategy may indicate new directions for antitumor strategies for CRC.

Integrin αvß6 predicts poor prognosis and promotes resistance to cisplatin in hilar cholangiocarcinoma.

OBJECTIVE: Integrin αvß6 is associated with an extremely aggressive cancer phenotype. However, little is known about the clinicopathological significance and prognostic value of integrin αvß6 in human hilar cholangiocarcinoma. METHODS: In the present study, bioinformatics analysis demonstrated a significant increase of integrin ß6 gene expression in cholangiocarcinoma tissues compared to non-tumorous tissues, which was further validated in clinical samples through RT-qPCR and western blotting analyses. Integrin αvß6 was observed to be expressed in 48.6% of tumors, and its expression was related to a poor tumor differentiation (p = 0.002), lymph node metastasis (p<0.001) and advanced TNM stage (p=0.001). Furthermore, patients who were αvß6-positive showed a significantly shorter overall survival period than those who were αvß6-negative (p=0.004). Multivariate analysis confirmed that integrin αvß6 was an independent prognostic factor (p=0.002). In addition, loss- and gain-of-function assays showed integrin αvß6 not only played an important role in colony formation, but also protected cholangiocarcinoma cells from cisplatin-induced growth inhibition and apoptosis. ERK/MAPK signaling pathway was involved in integrin αvß6-mediated resistance of cholangiocarcinoma cells to cisplatin. CONCLUSIONS: Taken together, the present findings revealed that integrin αvß6 could serve as a potential prognostic predictor and contribute to cisplatin resistance, which might prove to be a promising target candidate for the clinical intervention of human hilar cholangiocarcinoma.

Gamma-secretase complex-dependent intramembrane proteolysis of CD147 regulates the Notch1 signaling pathway in hepatocellular carcinoma.

The γ-secretase complex is a presenilin-dependent aspartyl protease involved in the intramembranous cleavage of various type I transmembrane proteins. As a type I transmembrane protein, CD147 is highly expressed in hepatoma cells and promotes cell proliferation, migration, and invasion. However, the direct underlying mechanism of how CD147 promotes cancer cell proliferation is unknown. Here, we demonstrated that CD147 undergoes an intramembranous cleavage by the γ-secretase at lysine 231 to release its intracellular domains (ICDs). The nuclear translocation of the CD147ICD regulated Notch1 expression by directly binding to the NOTCH1 promoter and promoted the activation of the Notch signaling pathway. Simultaneously, overexpression of CD147ICD promoted cancer cell proliferation via Notch1 signaling. In 102 cases of human hepatocellular carcinoma (HCC) tissues, patients with a high positive rate of nuclear CD147ICD expression had a significantly poor overall survival compared with patients with a low positive rate of nuclear CD147ICD expression. We confirmed that nuclear CD147ICD predicted a poor prognosis in human HCC. The combined therapy of the γ-secretase complex inhibitor and CD147-directed antibody showed better efficacy than monotherapy in orthotopic transplantation HCC mouse models. In conclusion, CD147 is cleaved by the γ-secretase and releases CD147ICD to the cell nucleus, promoting Notch1 expression via direct binding to the NOTCH1 promoter. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Systems analysis of key genes and pathways in the progression of hepatocellular carcinoma.

The carcinogenesis of hepatocellular carcinoma (HCC) is a complex process, starting from a chronically altered hepatic microenvironment due to liver cirrhosis and ultimately progressing to HCC. However, the sequential molecular alterations driving the malignant transformation in liver cirrhosis are not clearly defined.In this study, we obtained gene expression profiles of HCC, including 268 tumor tissues, 243 adjacent tumor tissues, and 40 cirrhotic tissues (GSE25097) from Gene Expression Omnibus (GEO), to comprehensively define changes in the transcriptome of HCC during the sequential evolution of liver cirrhosis into HCC.We showed that changes in the molecular profiles of cirrhotic and adjacent tumor samples were small and quite uniform, whereas there was a striking increase in the heterogeneity of tumors in HCC tissues at the mRNA level. A massive deregulation of key oncogenic molecules and pathways was observed from cirrhosis to HCC tumors. In addition, we focused on FOXO1 and DCN, 2 critical tumor suppressor genes that play an important role in liver cirrhosis and HCC development. FOXO1 and DCN expression levels were significantly reduced in tumor tissues compared with adjacent tumor tissues in HCC. Kaplan-Meier analysis revealed that FOXO1 and DCN expression was positively correlated with overall survival, defining FOXO1 and DCN as adverse prognostic biomarkers for HCC.This system-level research provided new insights into the molecular mechanisms of HCC carcinogenesis. FOXO1 and DCN may be applied as potential targets for HCC treatment in the future.

System analysis of the regulation of the immune response by CD147 and FOXC1 in cancer cell lines.

CD147, encoded by BSG, is a highly glycosylated transmembrane protein that belongs to the immunological superfamily and expressed on the surface of many types of cancer cells. While CD147 is best known as a potent inducer of extracellular matrix metalloproteinases, it can also function as a key mediator of inflammatory and immune responses. To systematically elucidate the function of CD147 in cancer cells, we performed an analysis of genome-wide profiling across the Cancer Cell Line Encyclopedia (CCLE). We showed that CD147 mRNA expression was much higher than that of most other genes in cancer cell lines. CD147 varied widely across these cell lines, with the highest levels in the ovary (COLO704) and stomach (SNU668), intermediate levels in the lung (RERFLCKJ, NCIH596 and NCIH1651) and lowest levels in hematopoietic and lymphoid tissue (UT7, HEL9217, HEL and MHHCALL3) and the kidney (A704 and SLR20). Genome-wide analyses showed that CD147 expression was significantly negatively correlated with immune-related genes. Our findings implicated CD147 as a novel regulator of immune-related genes and suggest its important role as a master regulator of immune-related responses in cancer cell lines. We also found a high correlation between the expression of CD147 and FOXC1, and proved that CD147 was a direct transcriptional target of FOXC1. Our findings demonstrate that FOXC1 is a novel regulator of CD147 and confirms its role as a master regulator of the immune response.

Basolateral CD147 induces hepatocyte polarity loss by E-cadherin ubiquitination and degradation in hepatocellular carcinoma progress.

Hepatocytes are epithelial cells with highly specialized polarity. The disorder and loss of hepatocyte polarity leads to a weakness of cell adhesion and connection, the induction of epithelial-mesenchymal transition, and eventually the occurrence of hepatocellular carcinoma (HCC). Cluster of differentiation 147 (CD147), a tumor-related glycoprotein, promotes epithelial-mesenchymal transition and the invasion of HCC. However, the function of CD147 in hepatocyte depolarization is unknown. Here we identified that CD147 was basolaterally polarized in hepatocyte membrane of liver tissues and HepG2 cells. CD147 not only promoted transforming growth factor-ß1-mediated hepatocyte polarity loss but also directly induced endocytosis and down-regulation of E-cadherin which contributed to hepatocyte depolarization. Overexpression of CD147 induced Src activation and subsequently recruited ubiquitin ligase Hakai for E-cadherin ubiquitination and lysosomal degradation, leading to decreases of partitioning defective 3 expression and ß-catenin nuclear translocation. This signal transduction was initiated by competitive binding of CD147 with integrin ß1 that interrupted the interaction between the Arg-Gly-Asp motif of fibronectin and integrin ß1. The specific antibodies targeting integrin α5 and ß1 reversed the decrease of E-cadherin and partitioning defective 3 levels induced by CD147 overexpression. In human liver tissues, CD147 polarity rates significantly declined from liver cirrhosis (71.4%) to HCC (10.4%). CD147-polarized localization negatively correlated with Child-Pugh scores in human liver cirrhosis (r = -0.6092, P < 0.0001) and positively correlated with differentiation grades in HCC (r = 0.2060, P = 0.004). HCC patients with CD147-polarized localization had significantly better overall survival than patients with CD147 nonpolarity (P = 0.021). CONCLUSION: The ectopic CD147-polarized distribution on basolateral membrane promotes hepatocyte depolarization by activation of the CD147-integrin α5ß1-E-cadherin ubiquitination-partitioning defective 3 decrease and ß-catenin translocation signaling cascade, replenishing a molecular pathway in hepatic carcinogenesis. (Hepatology 2018;68:317-332).

Integrated genomic analyses of lung squamous cell carcinoma for identification of a possible competitive endogenous RNA network by means of TCGA datasets.

The etiology of cancer includes aberrant cellular homeostasis where a compromised RNA regulatory network is a prominent contributing factor. In particular, noncoding RNAs including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were recently shown to play important roles in the initiation, progression, and metastasis of human cancers. Nonetheless, a mechanistic understanding of noncoding RNA functions in lung squamous cell carcinoma (LUSC) is lacking. To fill this critical gap in knowledge, we obtained mRNA, miRNA, and lncRNA expression data on patients with LUSC from the updated Cancer Genome Atlas (TCGA) database (2016). We successfully identified 3,366 mRNAs, 79 miRNAs, and 151 lncRNAs as key contributing factors of a high risk of LUSC. Furthermore, we hypothesized that the lncRNA-miRNA-mRNA regulatory axis positively correlates with LUSC and constructed a competitive endogenous RNA (ceRNA) network of LUSC by targeting interrelations with significantly aberrant expression data between miRNA and mRNA or lncRNA. Six ceRNAs (PLAU, miR-31-5p, miR-455-3p, FAM83A-AS1, MIR31HG, and MIR99AHG) significantly correlated with survival (P < 0.05). Finally, real-time quantitative PCR analysis showed that PLAU is significantly upregulated in SK-MES-1 cells compared with 16-BBE-T cells. Taken together, our findings represent new knowledge for a better understanding the ceRNA network in LUSC biology and pave the way to improved diagnosis and prognosis of LUSC.

Promoter mutations and cellular distribution of telomerase in non-clear cell and clear cell hepatocellular carcinoma.

Reactivation of telomerase is a critical step in the development of hepatocellular carcinoma (HCC). Here we identified the frequency of mutations in telomerase reverse transcriptase (TERT) promoter was 34% in non-clear cell HCC (NCCHCC, n = 259) and 26.3% in clear cell HCC (CCHCC, n = 57). The mutations were independently associated with poor recurrence-free survival of HCCs. Interestingly immunohistochemical analysis demonstrated a higher positive rate of TERT cytoplasmic localization (95%) than nuclear localization (64%) in HCCs. In NCCHCCs, the mutations correlated with higher TERT nuclear expression and increased telomere-dependent telomerase activity. Higher cytoplasmic expression was found in adjacent tissues compared to tumor tissues, and was associated with tumor well-differentiation and lower level of α-fetoprotein. NCCHCCs with low nuclear as well as high cytoplasmic expression correlated with better prognosis. In CCHCCs, elevated TERT cytoplasmic expression was observed in CCHCCs harboring mutations. Higher TERT cytoplasmic expression was found in tumor tissues compared to adjacent tissues, and was associated with multiple numbers of tumors and poor prognosis of CCHCCs. In conclusion, mutations in TERT promoter disclose the significance of both nuclear and cytoplasmic TERT in HCC. Cytoplasmic TERT should also be considered when determining prognosis and treatment of HCCs.

A three-caller pipeline for variant analysis of cancer whole-exome sequencing data.

Rapid advancements in next generation sequencing (NGS) technologies, coupled with the dramatic decrease in cost, have made NGS one of the leading approaches applied in cancer research. In addition, it is increasingly used in clinical practice for cancer diagnosis and treatment. Somatic (cancer­only) single nucleotide variants and small insertions and deletions (indels) are the simplest classes of mutation, however, their identification in whole exome sequencing data is complicated by germline polymorphisms, tumor heterogeneity and errors in sequencing and analysis. An increasing number of software and methodological guidelines are being published for the analysis of sequencing data. Usually, the algorithms of MuTect, VarScan and Genome Analysis Toolkit are applied to identify the variants. However, one of these algorithms alone results in incomplete genomic information. To address this issue, the present study developed a systematic pipeline for analyzing the whole exome sequencing data of hepatocellular carcinoma (HCC) using a combination of the three algorithms, named the three­caller pipeline. Application of the three­caller pipeline to the whole exome data of HCC, improved the detection of true positive mutations and a total of 75 tumor­specific somatic variants were identified. Functional enrichment analysis revealed the mutations in the genes encoding cell adhesion and regulation of Ras GTPase activity. This pipeline provides an effective approach to identify variants from NGS data for subsequent functional analyses.

CD147 promotes reprogramming of glucose metabolism and cell proliferation in HCC cells by inhibiting the p53-dependent signaling pathway.

BACKGROUND & AIMS: Cancer cells exhibit the reprogrammed metabolism characterized by high level of glycolysis even in the presence of oxygen. Aerobic glycolysis, known as the Warburg effect, supplies cancer cells with the substrates required for biomass generation. To date, several intracellular signaling mediators have been identified in metabolic regulation of cancer cells. However, it remains largely ambiguous how molecules on the cell surface are involved in regulation of cancer metabolism. METHODS: In the current study, we established several HCC cell lines differing in their CD147 (a typical transmembrane glycoprotein) expression status by zinc-finger nuclease and RNAi techniques. Then, we systematically investigated the role of CD147 in the regulation of the Warburg effect in HCC cells and explored the underlying mechanism. RESULTS: We found that CD147 significantly contributed to the reprogramming of glucose metabolism in HCC cells through a p53-dependent way. CD147 facilitated the cell surface expression of MCT1 and lactate export, which led to activation of the PI3K/Akt/MDM2 pathway and thus increased p53 degradation. The gain/loss-of-function studies demonstrated that while CD147 promoted glycolysis, mediated by p53-dependent upregulation of GLUT1 and activation of PFKL, it inhibited mitochondrial biogenesis and functions, mediated by p53-dependent downregulation of PGC1α, TFAM, and p53R2. Additionally, proliferation of HCC cells was suppressed by blocking CD147 and/or MCT1, which resulted in down-regulation of glucose metabolism. CONCLUSIONS: We demonstrate that CD147 is a crucial regulator of glucose metabolism.

A meta-analysis of array-CGH studies implicates antiviral immunity pathways in the development of hepatocellular carcinoma.

BACKGROUND: The development and progression of hepatocellular carcinoma (HCC) is significantly correlated to the accumulation of genomic alterations. Array-based comparative genomic hybridization (array CGH) has been applied to a wide range of tumors including HCCs for the genome-wide high resolution screening of DNA copy number changes. However, the relevant chromosomal variations that play a central role in the development of HCC still are not fully elucidated. METHODS: In present study, in order to further characterize the copy number alterations (CNAs) important to HCC development, we conducted a meta-analysis of four published independent array-CGH datasets including total 159 samples. RESULTS: Eighty five significant gains (frequency ≥ 25%) were mostly mapped to five broad chromosomal regions including 1q, 6p, 8q, 17q and 20p, as well as two narrow regions 5p15.33 and 9q34.2-34.3. Eighty eight significant losses (frequency ≥ 25%) were most frequently present in 4q, 6q, 8p, 9p, 13q, 14q, 16q, and 17p. Significant correlations existed between chromosomal aberrations either located on the same chromosome or the different chromosomes. HCCs with different etiologies largely exhibited surprisingly similar profiles of chromosomal aberrations with only a few exceptions. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the genes affected by these chromosomal aberrations were significantly enriched in 31 canonical pathways with the highest enrichment observed for antiviral immunity pathways. CONCLUSIONS: Taken together, our findings provide novel and important clues for the implications of antiviral immunity-related gene pathways in the pathogenesis and progression of HCC.

Global risk transformative prioritization for prostate cancer candidate genes in molecular networks.

Understanding the pathogenesis of complex diseases is aided by precise identification of the genes responsible. Many computational methods have been developed to prioritize candidate disease genes, but coverage of functional annotations may be a limiting factor for most of these methods. Here, we introduce a global candidate gene prioritization approach that considers information about network properties in the human protein interaction network and risk transformative contents from known disease genes. Global risk transformative scores were then used to prioritize candidate genes. This method was introduced to prioritize candidate genes for prostate cancer. The effectiveness of our global risk transformative algorithm for prioritizing candidate genes was evaluated according to validation studies. Compared with ToppGene and random walk-based methods, our method outperformed the two other candidate gene prioritization methods. The generality of our method was assessed by testing it on prostate cancer and other types of cancer. The performance was evaluated using standard leave-one-out cross-validation.

Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks.

BACKGROUND: Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions. RESULTS: Here, we weighted edges of a human protein interaction network and a transcriptional regulatory network to construct an integrated network, and introduce a probabilistic model and a bipartite graph framework to exploit human co-regulated modules and uncover their specific features in packaging different biological entities (genes, protein complexes or metabolic pathways). Finally, we identified 96 human co-regulated modules based on this method, and evaluate its effectiveness by comparing it with four other methods. CONCLUSIONS: Dysfunctions in co-regulated interactions often occur in the development of cancer. Therefore, we focussed on an example co-regulated module and found that it could integrate a number of cancer-related genes. This was extended to causal dysfunctions of some complexes maintained by several physically interacting proteins, thus coordinating several metabolic pathways that directly underlie cancer.

Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways.

MOTIVATION: Complex diseases are generally thought to be under the influence of one or more mutated risk genes as well as genetic and environmental factors. Many traditional methods have been developed to identify susceptibility genes assuming a single-gene disease model ('single-locus methods'). Pathway-based approaches, combined with traditional methods, consider the joint effects of genetic factor and biologic network context. With the accumulation of high-throughput SNP datasets and human biologic pathways, it becomes feasible to search for risk pathways associated with complex diseases using bioinformatics methods. By analyzing the contribution of genetic factor and biologic network context in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, we proposed an approach to prioritize risk pathways for complex diseases: Prioritizing Risk Pathways fusing SNPs and pathways (PRP). A risk-scoring (RS) measurement was used to prioritize risk biologic pathways. This could help to demonstrate the pathogenesis of complex diseases from a new perspective and provide new hypotheses. We introduced this approach to five complex diseases and found that these five diseases not only share common risk pathways, but also have their specific risk pathways, which is verified by literature retrieval.