Discovery and validation of prognostic markers in gastric cancer by genome-wide expression profiling

A Comprehensive Review on the Importance of MiRNA-206 in the Animal Model and Human Diseases

MicroRNA-206 (miR-206) is a microRNA that is involved in many human diseases, such as myasthenia gravis, osteoarthritis, depression, cancers, etc. Both inhibition effects and progression roles of miR-206 have been reported for the past few years. High expression of miR-206 was observed in patients with osteoarthritis, gastric cancer and epithelial ovarian cancer compared to normal people. The study also showed that miR-206 promotes cancer progression in breast cancer patients and avascular necrosis of the femoral head. Meanwhile, several studies have shown that expression levels of miR-206 were down-regulated in laryngeal carcinoma cell multiplication, as well as in hepatocellular carcinoma, non-small lung cancer and infantile hemangioma. Moreover, miR-206 was up-regulated in the mild stage of amyotrophic lateral sclerosis patients and then down-regulated in the moderate and severe stages, indicating that miR-206 has the double effects of starting and aggravating the disease. In neuropsychiatric disorders, such as depression, miR-206 also plays an important role in the progression of the disease; the level of miR-206 is most highly expressed in the brains of patients with depression. In the current review, we summarize the role of miR-206 in various diseases, and miR-206 may be developed as a new biomarker for diagnosing diseases in the near future.

Circular RNA 0001789 sponges miR-140-3p and regulates PAK2 to promote the progression of gastric cancer

BACKGROUND

Gastric cancer (GC) is the third-leading cause of cancer-associated mortalities globally. The deregulation of circular RNAs (circRNAs) and microRNAs (miRNAs or miRs) is widely implicated in the pathogenesis and progression of different cancer types.

METHODS

The expression profiling of circRNAs in GC is required to identify crucial circRNAs as biomarkers or therapeutic targets. In the present study, a published circRNA microarray dataset was used to identify differentially expressed circRNAs between GC tissues and normal gastric mucosa tissues. Reverse transcription-quantitative PCR was performed to validate the expression of circ_0001789. Fisher's exact test, receiver operating characteristic curve and Kaplan-Meier plots were employed to analyze the clinical significance of circ_0001789. The miRNA targets of circ_0001789 were predicted using an online database, and their functional interaction was further confirmed by RNA pull-down, RNA immunoprecipitation and dual luciferase reporter assays. Transwell assays were conducted to investigate the biological functions of circ_0001789, miR-140-3p and p21 activated kinase 2 (PAK2) in the migration and invasion of GC cells. A xenograft mouse model was established to validate the role of circ_0001789 in the tumorigenesis of GC cells.

RESULTS

circ_0001789 was identified as a highly expressed circRNA in GC tissues versus normal gastric mucosa tissues. Silencing circ_0001789 attenuated the malignancy of GC cells, and exosomal circ_0001789 was sufficient to regulate the malignant phenotype of GC cells. miR-140-3p was further identified as a downstream target of circ_0001789, which showed a negative correlation with circ_0001789 expression in GC tissues. Overexpression of miR-140-3p suppressed cell migration, invasion and epithelial-mesenchymal transition in GC cells. PAK2 was identified as the target of miR-140-3 to mediate the malignant phenotype of GC cells.

CONCLUSION

The present data suggested that the upregulation of circ_0001789 was associated with the progression of GC and with poor prognosis in patients with GC, and that miR-140-3p/PAK2 served as the downstream axis to mediate the oncogenic effect of circ_0001789.

Identification of three immune subtypes characterized by distinct tumor immune microenvironment and therapeutic response in stomach adenocarcinoma

BACKGROUND

In primary stomach adenocarcinoma (STAD), the tumor immune microenvironment (TIME) is important for cancer occurrence and progression; however, its clinical significance remains unclear. This study investigated the association between patient survival, TIME, and therapeutic response to STAD.

METHODS

Gene expression profiles of STAD cases were collected from the Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus. Molecular subtypes were explored with consistent clustering methods according to 119 immune signatures and the infiltrating scores of 22 immune cells using the Multi-Omics Immuno-Oncology Biological Research algorithm. We determined IFNγ scores and immune cytolytic activity (CYT) scores on the basis of corresponding gene signatures via single-sample Gene Set Enrichment Analysis. Comparisons of survival, TIME, 10 immunity-related oncogenic pathways, immune checkpoint expression, and therapeutic response were conducted among the three subtypes. We further applied linear discriminant analysis to construct a characteristic index to classify the subtypes, and the Pearson correlation coefficient for the relationship between the index and immune checkpoint genes. Weighted Correlation Network Analysis (WGCNA) was used to mine the associated modules and specific genes.

RESULTS

We collected gene expression profiles from 352 STAD cases in the TCGA database, 300 in GSE62254, and 344 in GSE84437. Three STAD subtypes (IS1-IS3) were established according to the TIME signatures. The IS3 subtype had the highest immune score and the best prognosis, as well as markedly increased immune T-cell CYT, Th1/IFNγ scores, and immune checkpoint gene expression, compared to the other two subtypes. It was highly similar to the PD-1 response group in the previous study samples of GSE91061. The established TIME classification index performed well in classifying subtypes and was directly proportional to immune checkpoint-related gene expression levels. WGCNA explored 6 modules and 14 genes, namely DYSF, MAN1C1, HTRA3, EMCN, RFLNB, KANK3, MAGEH1, CD93, PCAT19, FUT11, BMP1, FOSB, DCHS1, and TCF3, which were associated with the established TIME classification index and STAD patient prognosis.

CONCLUSION

TIME phenotypes of STAD patients could be divided into three different molecular subtypes, which displayed different prognoses, immune features, and therapeutic responses. Our results shed new light on predicting patient outcomes and the discovery of new anti-STAD therapeutic strategies according to the TIME.

Delineation of gastric tumors with activated ERK/MAPK signaling cascades for the development of targeted therapeutics

The ERK/MAPK signaling pathway is activated in various cancers including gastric cancer. Targeting the ERK/MAPK/MEK pathway has been considered as a promising strategy for cancer therapy. However, MEK inhibition leads to a series of resistance mechanisms due to mutations in MEK, elevated expression of RAS or RAF proteins and activation of the associated signaling pathways. In the present study, ERK/MAPK pathway specific gene signatures were identified to be highly activated in intestinal subtype gastric tumors. Inhibition of ERK/MAPK pathway with the inhibitor PD98059 in gastric cancer cell lines by in vitro signaling pathway and genome-wide expression profiling revealed the associated signaling pathways. Functional genomic investigation of the ERK/MAPK regulated genes reveals the association of ERK/MAPK pathway with E2F, Myc, SOX-2, TGF-β, OCT4 and Notch pathways in gastric cancer cells. Of these, E2F, Myc and SOX-2 pathways are activated in intestinal subtype gastric tumors and TGF-β, OCT4, Notch pathways are activated in diffuse subtype gastric tumors. Further, the mutational load of gastric tumors was found to have association and correlation with the activation pattern of ERK/MAPK pathways across gastric tumors. ERK/MAPK activation was also found to represent the EBV and MSI activated subtypes of gastric tumors. Identification of potent drug candidates inhibiting the ERK/MAPK and associated pathways would pave a way for developing the targeted therapeutics for a subset of gastric tumors with activated ERK/MAPK signaling cascade.

BAIAP2L2 promotes the progression of gastric cancer via AKT/mTOR and Wnt3a/β-catenin signaling pathways

INTRODUCTION

Gastric cancer is third leading cause of cancer-related deaths worldwide and remarkably threatens human health and life. BAIAP2L2 is an epithelial-specific BAR domain protein that considered to be closely related to cell migration. In this study, we explored the specific role of BAIAP2L2 in human gastric cancer.

METHODS

BAIAP2L2 expression was analyzed via online database and immunohistochemistry. The proliferation was detected using CCK8 and colony formation assay. The migration and invasion was confirmed by transwell assay, and the apoptosis of gastric cancer cells was detected by flow cytometry.

RESULTS

BAIAP2L2 was highly expressed in tumour tissues and its expression significantly correlated with tumor diameter, T stage, pTNM stage and lymph node metastasis, respectively. Compared with GES-1 cells, SGC7901, MKN28, MKN45, AGS and BGC-823 tumor cells were all presented a high-expression of BAIAP2L2. The in vitro results showed that knockdown of BAIAP2L2 inhibited the proliferation, migration and invasion, and induced the apoptosis of gastric cancer cell. Further, knockdown of BAIAP2L2 inhibited the expression of the related proteins of AKT/mTOR and Wnt3a/β-catenin signaling pathways.

CONCLUSION

BAIAP2L2 is upregulated in gastric cancer, and knockdown of BAIAP2L2 inhibited the proliferation and metastasis through the inactivation of AKT/mTOR and Wnt3a/β-catenin signaling pathways.

Evaluation of predictive role of carcinoembryonic antigen and salivary mRNA biomarkers in gastric cancer detection

We explored the potential of combining carcinoembryonic antigen (CEA) and salivary mRNAs for gastric cancer (GC) detection.This study included 2 phases of study: a biomarker discovery phase and an independent validation phase. In the discovery phase, we measured CEA levels in blood samples and expression level of messenger RNAs (SPINK7, PPL, SEMA4B, SMAD4) in saliva samples of 140 GC patients and 140 healthy controls. We evaluated the clinical performance of each biomarker and developed a predictive model using machine-learning algorithm to differentiate GC patients and healthy controls.Our biomarker panel successfully discriminated GC patients from healthy controls with both high sensitivity (0.94) and high specificity (0.91). We next applied our biomarker panel in the independent validation phase, in which we recruited a new patient cohort of 60 GC patients and 60 healthy controls. Using our biomarker panel, the GC patients were discriminated from healthy controls in the validation phase, with sensitivity of 0.92 and specificity of 0.87.A combination of blood CEA and salivary messenger RNA could be a promising approach to detect GC.

CDK12 and PAK2 as novel therapeutic targets for human gastric cancer

Background: Gastric cancer remains the second leading cause of cancer-related death, and the third in mortality due to lack of effective therapeutic targets for late stage cancer patients. This study aims to identify potential druggable target biomarkers as potential therapeutic options for patients with gastric cancer.

Methods: Immunohistochemistry of human gastric tumor tissues was conducted to determine the expression level of cyclin-dependent kinase 12 (CDK12). Multiple in vitro and in vivo assays such as RNAi, mass spectrometry, computer docking models, kinase assays, cell xenograft NU/NU mouse models (CDXs) and patient-derived xenograft NOD/SCID mouse models (PDXs) were conducted to study the function and molecular interaction of CDK12 with p21 activated kinase 2 (PAK2), as well as to find CDK12 inhibitors as potential treatment options for human gastric cancer.

Results: Here we identified that CDK12 is a driver gene in human gastric cancer growth. Mechanistically, CDK12 directly binds to and phosphorylates PAK2 at T134/T169 to activate MAPK signaling pathway. We further identified FDA approved clinical drug procaterol can serve as an effective CDK12 inhibitor, leading to dramatic restriction of cancer cell proliferation and tumor growth in human gastric cancer cells and PDXs.

Conclusions: Our data highlight the potential of CDK12/PAK2 as therapeutic targets for patients with gastric cancer, and we propose procaterol treatment as a novel therapeutic strategy for human gastric cancer.

Oncogenic role of LYN in human gastric cancer via the Wnt/β-catenin and AKT/mTOR pathways

LYN kinase (LYN) is a member of the Src tyrosine kinase family, which plays an important role in multiple tumor-related functions. The current study demonstrated that LYN functions as a pro-oncogene in AGS gastric cancer cells. It was found that LYN expression levels were significantly raised in gastric cancer tissue and were significantly associated with the pathological grades of patients with gastric cancer. This was accomplished by knocking down LYN in AGS cells using short hairpin RNA (shRNA) plasmid transfection, with reverse transcription-quantitative PCR detection verifying the effectiveness of RNA interference. It was found that the cell proliferation and colony formation abilities of AGS cells were significantly inhibited, using CCK-8 and clone formation assays, respectively. Furthermore, LYN knockdown was found to induce apoptosis and inhibit both migration and invasion in AGS cells, using flow cytometry and Transwell assays, respectively. A mechanical investigation further suggested that LYN knockdown resulted in the activation of the mitochondrial apoptotic pathway. Likewise, the Wnt/β-catenin pathway was inactivated by LYN knockdown, including decreased levels of Wnt3a, β-catenin, snail family transcriptional repressor (Snail)1 and Snail2. Epithelial-mesenchymal transition mesenchymal markers (including N-cadherin and vimentin) were also found to be downregulated, and E-cadherin was upregulated in LYN-silenced AGS cells. Finally, the AKT/mTOR pathway was found to be downregulated by LYN knockdown in AGS cells, including decreased levels of phosphorylated (p)-AKT (Ser473), p-mTOR (Ser2448), and the down-stream effector p70S6 kinase (p70S6K). Furthermore, the AKT pathway activator, insulin like growth factor-1 (IGF-1), was found to reverse the inhibitory effects of LYN knockdown on the proliferation, migration and invasion of AGS cells. In conclusion, the current study demonstrated that LYN plays an oncogenic role in the proliferation, survival and movement of human gastric cancer cells by activating the mitochondrial apoptotic pathway, and downregulating the Wnt/β-catenin and AKT/mTOR pathways. The current research provides a comprehensive insight into the regulation of LYN in gastric cancer and may help with the development of new tumor treatment strategies.

LncRNA PCAT6 predicts poor prognosis in hepatocellular carcinoma and promotes proliferation through the regulation of cell cycle arrest and apoptosis

Long noncoding RNAs have been proved in regulating tumourigenesis, including hepatocellular carcinoma (HCC). However, up to date, the role of PCAT6 in HCC is rare to be reported. In current study, bioinformatics analysis and quantitative real-time PCR were applied to examine the expression of PCAT6 in HCC. The role of PCAT6 in cell proliferation, cell cycle arrest, apoptosis, and metastasis were detected in both gain- and loss-of-function studies by cell biological assays. Bioinformatics analysis was employed to investigate the PCAT6-related genes and pathways in HCC. And we found that PCAT6 was significantly upregulated in HCC tissues and correlated with poor overall survival and disease-free survival in HCC patients. Furthermore, elevated PCAT6 promoted cell proliferation, inhibited cell cycle arrest and cell apoptosis while deficiency of PCAT6 impaired cell proliferation, caused cell cycle arrest and induced cell apoptosis of HCC. Moreover, as for bioinformatics analysis, a total of 389 PCAT6-related genes were found in both HCC tissue and cell lines, and these promising target genes were highly enriched in various key pathways, such as Wnt, HIF-1 signalling pathway, and metabolic pathways. Additionally, among these genes, DCAF13, SNRPB2, RPS8, and FKBP1A were revealed to be overexpressed in HCC and predicted poor prognosis. Taken together, our findings illustrate that PCAT6 contributes to HCC progression and might be a potential target for HCC therapy. Bioinformatics analysis may present a new way for assessing the underlying mechanism of PCAT6 in HCC. SIGNIFICANCE OF THE STUDY: Hepatocellular carcinoma (HCC) is one of the most common and malignant tumours all over the world. In this study, we observed that PCAT6 was upregulated in HCC and correlated with poor prognosis of HCC patients. PCAT6 could promote cell proliferation, inhibit cell cycle arrest and cell apoptosis of HCC, suggesting PCAT6 exerts tumorigenic role in HCC. Moreover, bioinformatics analysis revealed a total of 389 PCAT6-related genes in both HCC tissue and cell lines, and these promising target genes were highly enriched in various key pathways, such as Wnt, HIF-1 signalling pathway, and metabolic pathways. These finding provided evidence that PACT6 may be identified as a strategy to treat HCC in the future.

Prediction of gastric cancer prognosis in the next-generation sequencing era

Gastric cancer (GC) is one of the most commonly diagnosed malignancies worldwide, and is caused by complex interactions of multiple risk factors such as environmental (Helicobacter pylori and Epstein–Barr Virus), hereditary (genetic alterations and epigenetic modifications), as well as dietary and lifestyle factors. GC is usually detected at an advanced stage, with a dismal prognosis. Even for patients with similar clinical or pathologic stage receiving similar treatment, the outcomes are still uneven and unpredictable. To better incorporate genetic and epigenetic profiles into GC prognostic predication, gene expression signatures have been developed to predict GC outcomes. More recently, the advancement of high-throughput sequencing technology, also known as next-generation sequencing (NGS) technology, and analysis has provided the basis for accurate molecular classification of GC tumors. Here, we summarized and updated the literature related to NGS studies of GC, including whole-genome sequencing, whole-exome sequencing, RNA sequencing, and targeted sequencing, and discussed current progresses. NGS has facilitated the identification of genetic/epigenetic targets for screening as well as development of targeted agent therapy, thus enabling individualized patient management and treatment.

Identification of key regulators in prostate cancer from gene expression datasets of patients

Identification of key regulators and regulatory pathways is an important step in the discovery of genes involved in cancer. Here, we propose a method to identify key regulators in prostate cancer (PCa) from a network constructed from gene expression datasets of PCa patients. Overexpressed genes were identified using BioXpress, having a mutational status according to COSMIC, followed by the construction of PCa Interactome network using the curated genes. The topological parameters of the network exhibited power law nature indicating hierarchical scale-free properties and five levels of organization. Highest degree hubs (k ≥ 65) were selected from the PCa network, traced, and 19 of them was identified as novel key regulators, as they participated at all network levels serving as backbone. Of the 19 hubs, some have been reported in literature to be associated with PCa and other cancers. Based on participation coefficient values most of these are connector or kinless hubs suggesting significant roles in modular linkage. The observation of non-monotonicity in the rich club formation suggested the importance of intermediate hubs in network integration, and they may play crucial roles in network stabilization. The network was self-organized as evident from fractal nature in topological parameters of it and lacked a central control mechanism.

Integrative machine learning analysis of multiple gene expression profiles in cervical cancer

Although most of the cervical cancer cases are reported to be closely related to the Human Papillomavirus (HPV) infection, there is a need to study genes that stand up differentially in the final actualization of cervical cancers following HPV infection. In this study, we proposed an integrative machine learning approach to analyse multiple gene expression profiles in cervical cancer in order to identify a set of genetic markers that are associated with and may eventually aid in the diagnosis or prognosis of cervical cancers. The proposed integrative analysis is composed of three steps: namely, (i) gene expression analysis of individual dataset; (ii) meta-analysis of multiple datasets; and (iii) feature selection and machine learning analysis. As a result, 21 gene expressions were identified through the integrative machine learning analysis which including seven supervised and one unsupervised methods. A functional analysis with GSEA (Gene Set Enrichment Analysis) was performed on the selected 21-gene expression set and showed significant enrichment in a nine-potential gene expression signature, namely PEG3, SPON1, BTD and RPLP2 (upregulated genes) and PRDX3, COPB2, LSM3, SLC5A3 and AS1B (downregulated genes).

MicroRNA-139 inhibits the proliferation, migration and invasion of gastric cancer cells by directly targeting ρ-associated protein kinase 1

The expression, function and underlying mechanisms of microRNA-139 (miR-139) in gastric cancer were investigated in the present study. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to detect miR-139 expression in gastric cancer tissues and cell lines. The effects of miR-139 overexpression on gastric cancer cell proliferation, migration and invasion were evaluated. ρ-associated protein kinase 1 (ROCK1) was predicted as a downstream target of miR-139 and its role in gastric cancer was assessed by bioinformatics analysis, luciferase reporter assay, RT-qPCR and western blot analysis. ROCK1 overexpression was established to investigate if the effects of miR-139 on gastric cancer cells may be attenuated. The results indicated that miR-139 was aberrantly downregulated in gastric cancer tissues and cell lines. Increased miR-139 expression reduced gastric cancer cell proliferation, migration and invasion. ROCK1 was demonstrated to be a direct target of miR-139 in gastric cancer and ROCK1 overexpression reversed the suppressive effects on gastric cancer cell proliferation, migration and invasion induced by miR-139 overexpression. The present study provides clear evidence demonstrating the anti-oncogenic activity of miR-139 in human gastric cancer, as mediated by the targeted downregulation of ROCK1.

PSMB8 and PBK as potential gastric cancer subtype-specific biomarkers associated with prognosis

Gastric adenocarcinoma is a common form of cancer associated with a poor prognosis. We analyzed microarray profiling data from 48 patients with gastric adenocarcinoma to characterize gastric cancer subtypes and identify biomarkers associated with prognosis. We identified two major subtypes of gastric adenocarcinoma differentially associated with overall survival (P = 0.025). Genes that were differentially expressed were identified using specific criteria (P < 0.001 and >1.5-fold); expression of 294 and 116 genes was enriched in good and poor prognosis subtypes, respectively. Genes related to translational elongation and cell cycle were upregulated in the poor prognosis group. Of these genes, upregulation of proteasome subunit beta type 8 PSMB8 and PDZ binding kinase PBK was confirmed by real-time reverse transcription-PCR analysis. PSMB8 or PBK knockdown had no effect on gastric cancer cell proliferation but suppressed cell migration and invasion, respectively. Furthermore, immunohistochemistry analysis of 385 gastric cancer patients revealed that increased nuclear expression of PSMB8 and PBK was correlated with depth of invasion, lymph node metastasis, and lower survival rates. Taken together, two gastric adenocarcinoma subtypes were predictive of prognosis. PSMB8 and PBK were predictive of gastric cancer prognosis and could be potential gastric cancer subtype-specific biomarkers.

Prognostic value of microRNA-126 and CRK expression in gastric cancer

Background

MicroRNA (miR)-126, acting as a tumor suppressor, has been reported to inhibit the invasion of gastric cancer cells in part by targeting v-crk sarcoma virus CT10 oncogene homologue (CRK). The aim of this study was to investigate the clinical significance of miR-126/CRK axis in gastric cancer.

Methods

miR-126 and CRK mRNA expression levels were detected by real-time quantitative reverse transcription polymerase chain reaction in 220 self-pairs of gastric cancer and adjacent noncancerous tissues.

Results

Expression levels of miR-126 and CRK mRNA in gastric cancer tissues were, respectively, lower and higher than those in adjacent noncancerous tissues (both P<0.001). Low miR-126 expression and high CRK expression, alone or in combination, were all significantly associated with positive lymph node and distant metastases and advanced TNM stage of human gastric cancer (all P<0.05). We also found that the overall survival rates of the patients with low miR-126 expression and high CRK expression were, respectively, shorter than those with high miR-126 expression and low CRK expression. Interestingly, miR-126-low/CRK-high expression was associated with a significantly worse overall survival of all miR-126/CRK groups (P<0.001). Moreover, multivariate analysis identified miR-126 and/or CRK expression as independent prognostic factors for patients with gastric cancer. Notably, the prognostic relevance of miR-126 and/or CRK expression was more obvious in the subgroup of patients with TNM stage IV.

Conclusion

Dysregulation of miR-126/CRK axis may promote the malignant progression of human gastric cancer. miR-126 and CRK combined expression may serve as an independent predictor of overall survival in patients with advanced gastric cancer.

How does epidemiological and clinicopathological features affect survival after gastrectomy for gastric cancer patients-single Egyptian center experience

AIM: To investigate the clinicopathological features and the significance of different prognostic factors which predict surgical overall survival in patients with gastric carcinoma.

METHODS: This retrospective study includes 80 patients diagnosed and treated at gastroenterology surgical center, Mansoura University, Egypt between February 2009 to February 2013. Prognostic factors were assessed by cox proportional hazard model.

RESULTS: There were 57 male and 23 female. The median age was 57 years (24-83). One, 3 and 5 years survival rates were 71%, 69% and 46% respectively. The median survival was 69.96 mo. During the follow-up period, 13 patients died (16%). Hospital morbidity was reported in 10 patients (12.5%). The median number of lymph nodes removed was 22 (4-41). Lymph node (LN) involvement was found in 91% of cases. After R0 resection, depth of wall invasion, LN involvement and the number (> 15) of retrieved LN, LN ratio and tumor differentiation predict survival. In multivariable analysis, tumor differentiation, curability of resection and a number of resected LN superior to 15 were found to be independent prognostic factors.

CONCLUSION: Surgery remains the cornerstone of treatment. Tumor differentiation, curability of resection and a number of resected LN superior to 15 were found to be independent prognostic factors. Extended LN dissection does not increase the morbidity or mortality rate but markedly improves long term survival.

Molecular classification and prediction in gastric cancer

Gastric cancer, a highly heterogeneous disease, is the second leading cause of cancer death and the fourth most common cancer globally, with East Asia accounting for more than half of cases annually. Alongside TNM staging, gastric cancer clinic has two well-recognized classification systems, the Lauren classification that subdivides gastric adenocarcinoma into intestinal and diffuse types and the alternative World Health Organization system that divides gastric cancer into papillary, tubular, mucinous (colloid), and poorly cohesive carcinomas. Both classification systems enable a better understanding of the histogenesis and the biology of gastric cancer yet have a limited clinical utility in guiding patient therapy due to the molecular heterogeneity of gastric cancer. Unprecedented whole-genome-scale data have been catalyzing and advancing the molecular subtyping approach. Here we cataloged and compared those published gene expression profiling signatures in gastric cancer. We summarized recent integrated genomic characterization of gastric cancer based on additional data of somatic mutation, chromosomal instability, EBV virus infection, and DNA methylation. We identified the consensus patterns across these signatures and identified the underlying molecular pathways and biological functions. The identification of molecular subtyping of gastric adenocarcinoma and the development of integrated genomics approaches for clinical applications such as prediction of clinical intervening emerge as an essential phase toward personalized medicine in treating gastric cancer.

Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas

BACKGROUND

Classifiers based on molecular criteria such as gene expression signatures have been developed to distinguish Burkitt lymphoma and diffuse large B cell lymphoma, which help to explore the intermediate cases where traditional diagnosis is difficult. Transfer of these research classifiers into a clinical setting is challenging because there are competing classifiers in the literature based on different methodology and gene sets with no clear best choice; classifiers based on one expression measurement platform may not transfer effectively to another; and, classifiers developed using fresh frozen samples may not work effectively with the commonly used and more convenient formalin fixed paraffin-embedded samples used in routine diagnosis.

METHODS

Here we thoroughly compared two published high profile classifiers developed on data from different Affymetrix array platforms and fresh-frozen tissue, examining their transferability and concordance. Based on this analysis, a new Burkitt and diffuse large B cell lymphoma classifier (BDC) was developed and employed on Illumina DASL data from our own paraffin-embedded samples, allowing comparison with the diagnosis made in a central haematopathology laboratory and evaluation of clinical relevance.

RESULTS

We show that both previous classifiers can be recapitulated using very much smaller gene sets than originally employed, and that the classification result is closely dependent on the Burkitt lymphoma criteria applied in the training set. The BDC classification on our data exhibits high agreement (~95 %) with the original diagnosis. A simple outcome comparison in the patients presenting intermediate features on conventional criteria suggests that the cases classified as Burkitt lymphoma by BDC have worse response to standard diffuse large B cell lymphoma treatment than those classified as diffuse large B cell lymphoma.

CONCLUSIONS

In this study, we comprehensively investigate two previous Burkitt lymphoma molecular classifiers, and implement a new gene expression classifier, BDC, that works effectively on paraffin-embedded samples and provides useful information for treatment decisions. The classifier is available as a free software package under the GNU public licence within the R statistical software environment through the link http://www.bioinformatics.leeds.ac.uk/labpages/softwares/ or on github https://github.com/Sharlene/BDC.

Expression and significance of annexin A2 in patients with gastric adenocarcinoma and the association with E-cadherin

Annexin A2 is a calcium-dependent phospholipid-binding protein, involved in invasion, angiogenesis and migration in cancer cells. The aims of the present study were to evaluate the expression levels of annexin A2 and E-cadherin in gastric adenocarcinoma (GAC), and to investigate the association between the expression of annexin A2 and that of E-cadherin and Ki67, in addition to various clinicopathological factors. This study included 126 patients that were histopathologically diagnosed with GAC. Tissue samples were acquired by surgical resection, and annexin A2 mRNA expression levels were determined using reverse transcription-quantitative polymerase chain reaction. Annexin A2, E-cadherin and Ki67 protein expression levels were detected using western blot analysis and/or immunohistochemical staining. The expression of annexin A2 mRNA and protein was significantly upregulated in the GAC tissues. Annexin A2 expression was detected in 52/126 cases (41.3%) of gastric cancer (GC), and correlations were identified between annexin A2 expression and Tumor, Node, Metastasis (TNM) stage (P=0.002), lymph node metastasis (P=0.016) and distal metastasis (P=0.005). The positive expression rates of E-cadherin and Ki67 in the tumor tissue of patients with GAC were 27.8% (35/126) and 56.2% (71/126), respectively. A negative correlation was observed between the expression of annexin A2 and E-cadherin (P<0.001). No significant association was detected between the expression levels of annexin A2 and Ki67 (P=0.801). In conclusion, upregulated annexin A2 expression was associated with lymph node metastasis, distal metastasis, advanced TNM stage and E-cadherin expression in patients with GAC. The association between the expression of annexin A2 and that of E-cadherin may indicate an underlying mechanism by which annexin A2 contributes to the metastasis in GC, and thus annexin A2 may represent a potential target for the treatment of GAC.

Prognostic significance of combined microRNA-206 and CyclinD2 in gastric cancer patients after curative surgery: A retrospective cohort study

AIM

To investigate associations of microRNA (miR)-206 and CyclinD2 (CCND2) expression, alone or in combination, with clinicopathological characteristics and patients' prognosis in gastric cancer.

METHODS

MiR-206 and CCND2 mRNA expression levels were detected by real-time quantitative RT-PCR in 220 self-pairs of gastric cancer and adjacent non-cancerous tissues.

RESULTS

Compared with the adjacent non-cancerous tissues, the expression levels of miR-206 and CCND2 mRNA were respectively reduced and elevated in gastric cancer tissues dramatically (both P<0.001). Notably, the expression levels of miR-206 in gastric cancer tissues were negatively correlated with those of CCND2 mRNA significantly (r=-0.463, P<0.001). Then, statistical analysis showed that low miR-206 expression and high CCND2 expression, alone or in combination, were all significantly associated with great depth of invasion, positive lymph node and distant metastases, and advanced TNM stage of human gastric cancer (all P<0.05). After that, we also found that the overall survivals of the patients with low miR-206 expression and high CCND2 expression were respectively shorter than those with high miR-206 expression and low CCND2 expression. More interestingly, miR-206-low/CCND2-high expression was associated with a significantly worst overall survival of all miR-206/CCND2 groups (P<0.001). Furthermore, multivariate analysis identified miR-206 and/or CCND2 expression as independent prognostic factors for overall survival in patients with gastric cancer.

CONCLUSION

Our data provide evidence that the dysregulation of miR-206-CCND2 axis may contribute to the aggressive progression and poor prognosis of human gastric cancer in clinical settings. Combined detection of their expression might be particularly helpful for surveillance of disease progression and treatment stratification.

Prognostic significance of the co-expression of nucleophosmin and trefoil factor 3 in postoperative gastric cancer patients

Although a number of studies have indicated that the positive expression of nucleophosmin (NPM) and trefoil factor 3 (TFF3) is associated with oncogenesis and poor prognosis in several tumor types, the prognostic value of the co-expression of NPM and TFF3 in gastric cancer (GC) has not been fully elucidated. Therefore, in this study, we aimed to investigate the role of NPM and TFF3 in GC and determine their prognostic value. We retrospectively reviewed 108 patients who had undergone radical gastric tumor resection. The expression of NPM and TFF3 was detected by immunohistochemistry and the association of NPM and TFF3 with clinicopathological characteristics was investigated using the Chi-square test. Furthermore, univariate and multivariate analyses were conducted to determine the prognostic value of these markers. Of the 108 samples, NPM was positive in 57 (53%) and TFF3 was positive in 54 samples (50%). The positive expression of NPM was correlated with advanced tumor stage and recurrence (P=0.0333 and P<0.0001, respectively), whereas the expression of TFF3 was associated with larger tumor size (P=0.0005), poor differentiation (P=0.0435), lymph node metastasis (P=0.0116), advanced tumor stage (P=0.0244) and recurrence (P=0.0116). The univariate analysis revealed that the expression of NPM, the expression of TFF3 and the co-expression of the two were associated with poor survival (P=0.0004, 0.0028 and 0.0020, respectively). By multivariate analysis, all three factors were identified as independent prognostic factors in postoperative GC patients (hazard ratio = 1.970, 2.021 and 2.339, respectively). In conclusion, the expression of NPM and TFF3 and, particularly, the co-expression of the two, may serve as independent prognostic factors in postoperative GC patients.

Helicobacter pylori and gastric cancer

Infection with Helicobacter pylori is established as the major risk factor for gastric cancer development. Damage of the mucosal barrier due to H. pylori-induced inflammation enhances the carcinogenic effect of other risk factors such as salt intake or tobacco smoking. The genetic disposition of both the bacterial strain and the host can increase the potential towards gastric cancer formation. Genetic variance of the bacterial proteins CagA and VacA is associated with a higher gastric cancer risk, as are polymorphisms and epigenetic changes in host gene coding for interleukins (IL1β, IL8), transcription factors (CDX2, RUNX3) and DNA repair enzymes. Application of high-throughput assays for genome-wide assessment of either genetic structural variance or gene expression patterns may lead to a better understanding of the pathobiological background of these processes, including the underlying signaling pathways. Understanding of the stepwise alterations that take place in the transition from chronic atrophic gastritis, via metaplastic changes, to invasive neoplasia is vital to define the 'point of no return' before which eradication of H. pylori has the potential to prevent gastric cancer. Currently, eradication as preventive strategy is only recommended for high-incidence regions in Asia; large population studies with an adequate follow-up are required to demonstrate the effectiveness of such an approach in Western populations.

Activation of P21-activated protein kinase 2 is an independent prognostic predictor for patients with gastric cancer

Objective

p21-activated kinase (PAK) 2, as a member of the PAK family kinases, is involved in a number of hallmark processes including cell proliferation, survival, mitosis, apoptosis, motility and angiogenesis. However, the clinical significance of the activation of PAK2 in human gastric cancer has not been fully elucidated. The aim of this study was to investigate whether PAK2 expression and its phosphorylation status are correlated with tumor progression and prognosis in gastric cancer.

Methods

Expression patterns and subcellular localizations of PAK2 and Ser20-phosphorylated PAK2 (pSer20PAK2) in 82 gastric cancer patients were detected by immunohistochemistry.

Results

Both PAK2 and pSer20PAK2 immunostainings were localized in the cytoplasm of tumor cells of gastric cancer tissues. Compared with the normal gastric mucosa, the expression levels of PAK2 and pSer20PAK2 proteins were both significantly increased (both P < 0.001). Additionally, the patients displaying the over-expression of PAK2 and pSer20PAK2 proteins were dramatically associated with unfavorable clinicopathologic variables including higher tumor depth (P = 0.022 and 0.036, respectively), greater extent of lymph node metastasis ((P = 0.022 and 0.036, respectively), positive distant metastasis (P = 0.025 and 0.038, respectively) and advanced tumor stage (P = 0.018 and 0.031, respectively). Moreover, the patients overexpressing PAK2 and pSer20PAK2 proteins have poor overall survival rates relative to those without overexpression of these proteins. Furthermore, cox multi-factor analysis showed that PAK2 (p = 0.012) and pSer20PAK2 (p = 0.010) were independent prognosis factors for human gastric cancer.

Conclusion

Our data suggest for the first time that PAK2 activation may be associated with advanced tumor progression and poor prognosis of gastric cancer.

Virtual slides

The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1236344107120406.

Expression characteristics of CDC20 in gastric cancer and its correlation with poor prognosis

The cell division cycle 20 homolog (CDC20) expression is increased in diverse human cancers and plays a vital role in tumorigenesis and progression. However, the clinical significance of CDC20 expression in gastric cancer (GC) remains largely unknown. The aim of this study was to investigate the clinicopathologic features and prognostic significance of CDC20 in GC. The CDC20 mRNA expression was measured by quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR). Immunohistochemistry (IHC) was used to detect the expression of CDC20 protein in 131 clinicopathologically characterized GC cases. The relationship between CDC20 expression and clinicopathological features was analyzed by appropriate statistics. Kaplan-Meier analysis and Cox proportional hazards regression models were used to investigate the correlation between CDC20 expression and prognosis of GC patients. The relative mRNA expression of CDC20 were significantly higher in GC tumor tissues than in the corresponding noncancerous tissues (P<0.001). Simultaneously, CDC20 protein expression was positively correlated with tumor size (P=0.02), histological grade (P=0.037), lymph node involvement (P=0.009), and TNM stage (P=0.015). Furthermore, Kaplan-Meier analysis indicated that patients with high CDC20 expression had poor overall survival (P<0.001). Multivariate analysis showed that high CDC20 expression was an independent predictor of overall survival. In conclusion, our data indicated that CDC20 upregulation was associated with aggressive progression and poor prognosis in GC. CDC20 was identified for the first time as an independent marker for predicting the clinical outcome of GC patients.

Decrease of miR-202-3p expression, a novel tumor suppressor, in gastric cancer

Emerging studies have indicated that microRNAs are involved in the development and progression of cancer. Here we found that miR-202-3p was frequently down-regulated in gastric cancer tissues. Overexpression of miR-202-3p in gastric cancer cells MKN-28 and BGC-823, markedly suppressed cell proliferation and induced cell apoptosis both in vitro and in vivo. Furthermore, Gli1 expression was frequently positive in gastric cancer tissues and inversely correlated with miR-133b expression. We demonstrate that the transcriptional factor Gli1 was a target of miR-202-3p and plays an essential role as a mediator of the biological effects of miR-202-3p in gastric cancer. MiR-202-3p also inhibited the expression of γ-catenin and BCL-2. Taken together, these findings suggest that miR-202-3p may function as a novel tumor suppressor in gastric cancer and its anti-tumor activity may attribute the direct targeting and inhibition of Gli1.

Prognostic role of human epidermal growth factor receptor in gastric cancer: a systematic review and meta-analysis

BACKGROUND AND AIMS

Human epidermal growth factor receptor (EGFR) and HER2 (ErbB2) both belong to EGFR family, which are overexpressed in a significant proportion of cases of gastric cancer (GC). Various studies have evaluated the prognostic value of EGFR or HER level in GC. However, the overall test performance remains unclear. We undertook this study to perform a systematic review and meta-analysis of prognostic cohort studies evaluating the use of EGFR or HER2 as a predictor of survival time in patients with GC.

METHODS

Eligible studies were identified through multiple search strategies. Studies were assessed for quality using the Newcastle-Ottawa Tool. Data were collected comparing overall survival (OS) in patients with high and low EGFR or HER2 level. Studies were pooled and summary hazard ratios were calculated.

RESULTS

Studies were listed twice if they provided overall survival data for both EGFR and HER2. Eight studies (seven for EGFR and eight for HER2) were included. Two distinct groups were pooled for analysis and revealed that high EGFR, HER2 levels predicted poor overall (HR = 1.66, 95% CI: 1.35-2.02) and (HR = 1.43, 95% CI: 1.09-1.88) survival. No publication bias was found.

CONCLUSIONS

This meta-analysis result suggested that EGFR or HER2 should have significant predictive ability for estimating overall survival in GC patients and may be useful for defining prognosis of GC patients.

Reduced expression of miR-22 in gastric cancer is related to clinicopathologic characteristics or patient prognosis

Objective

Involvements of microRNA-22 (miR-22) in cancer development have attracted much attention, but its role in tumorigenesis of gastric cancer is still largely unknown. Therefore, the aim of this study was to investigate the expression patterns and clinical implications of miR-22 in gastric cancer.

Methods

Quantitative RT-PCR was performed to evaluate the expression levels of miR-22 in 98 pairs of gastric cancer and normal adjacent mucosa.

Results

Compared with normal adjacent mucosa, miR-22 expression was significantly downregulated in gastric cancer tissues (P < 0.001). Of 98 patients with gastric cancer, 58 (59.2%) were placed in the low miR-22 expression group and 40 (40.8%) were placed in the high miR-22 expression group. In addition, tumors with low miR-22 expression had greater extent of lymph node metastasis (P = 0.02) and distant metastasis (P = 0.01), and were at a worse stage (P = 0.01) than the tumors with high miR-22 expression. Moreover, the gastric cancer patients with low miR-22 expression had shorter overall survival than those with high miR-22 expression (P = 0.03). MiR-22, determined by multivariate analysis, was an independent prognostic factor for patients with gastric cancer.

Conclusion

Our data offer the convincing evidence that the reduced expression of miR-22 was significantly associated with malignant development of gastric cancer and may be a novel prognostic marker of this disease. miR-22 might have potentials in the application of cancer therapy for patients with gastric cancer.

Genetics/genomics/proteomics of gastric adenocarcinoma

Hereditary diffuse gastric cancer can be caused by epithelial cadherin mutations for which genetic testing is available. Inherited cancer predisposition syndromes including Lynch, Li-Fraumeni, and Peutz-Jeghers syndromes, can be associated with gastric cancer. Chromosomal and microsatellite instability occur in gastric cancers. Several consistent genetic and molecular alterations including chromosomal instability, microsatellite instability, and epigenetic alterations have been identified in gastric cancers. Biomarkers and molecular profiles are being discovered with potential for diagnostic, prognostic, and treatment guidance implications.

Over-expression of Metastasis-associated in Colon Cancer-1 (MACC1) Associates with Better Prognosis of Gastric Cancer Patients

OBJECTIVE

The aim of this study was to detect metastasis-associated in colon cancer-1 (MACC1) expression in Chinese gastric cancer and analyze the relationship between MACC1 expression and postoperative survival.

METHODS

The expression of MACC1 and c-MET protein in a sample of 128 gastric cancer tissues was detected by immunohistochemistry. A retrospective cohort study on the prognosis was carried out and data were collected from medical records.

RESULTS

The positive rate of MACC1 protein expression in gastric cancer was 47.66%, higher than that in adjacent noncancerous mucosa (P<0.001). MACC1 protein expression was not related to the clinicopathological variables involved. Kaplan-Meier analysis revealed that the survival of MACC1 positive group tended to be better than that of MACC1 negative group, particularly in patients with stage III carcinoma (P=0.032). Cox regression analysis revealed that MACC1 protein over-expression in gastric cancer tended to be a protective factor with hazard ratio of 0.621 (P=0.057). Immunohistochemical analysis showed that the positive rate of c-MET protein expression was much higher in cases with positive MACC1 expression in gastric cancer (P=0.002), but P53 expression was not associated with MACC1 expression.

CONCLUSION

MACC1 over-expression implies better survival and may be an independent prognostic factor for gastric cancer in Chinese patients.

Endo-sulfatase Sulf-1 protein expression is down-regulated in gastric cancer

In our recent report on gene expression in gastric cancer we identified the endo-sulfatase Sulf-1 gene to be up-regulated in gastric tumors relative to apparently normal (AN), and paired normal (PN) gastric tissue samples. In the present report we investigate the protein expression levels of Sulf-1 gene in gastric tumors, AN and PN samples using tissue microarray (TMA) and immunohistochemistry. Expression data was collected from two sets of TMA's containing replicate sections of tissue samples. Scoring data from TMA set-1 revealed a significant difference in Sulf-1 immunoreactivity between tumors and "normals" (PN and AN) (p-value = 0.001928). Also, Sulf-1 expression in tumors was also significantly different from either PN (p-value = 0.019) or AN (p-value = 0.006) samples. Similar results were obtained from analysis of scoring data from the second set of arrays. Comparison of mRNA expression and protein expression in gastric tumor tissues revealed that in 6/20 (30%) tumor samples showed up-regulated protein expression concordant with over-expression of mRNA. However, a discord with mRNA being over-expressed relative to down regulated protein expression was observed in majority 14/20 (70%) of tumor samples. Our study indicates down regulation of Sulf-1 protein expression in gastric tumors relative to PN and AN samples which is discordant with mRNA over-expression seen in tumors.

Analysis of whole genomic expression profiles and screening of the key signaling pathways associated with pancreatic cancer

The tumorigenesis of pancreatic cancer is thought to be a complex process. Investigation of the molecular mechanism of pancreatic cancer and exploring the specific markers for early diagnosis and specific targets of therapy is a key point to prevent and treat pancreatic cancer effectively and to improve their prognosis. In this study, expression profiles experiment was performed using Agilent human whole genomic oligonucleotide microarrays with 41,000 genes. Differentially expressed genes related with pancreatic cancer were screened, and analyzed further by GO term analysis and KEGG Pathway analysis. Our results showed that there were 1276 differentially expressed genes associated with pancreatic cancer. 691 genes were up regulated and 585 were down regulated in pancreatic cancer group. The present study confirmed that the occurrence of pancreatic cancer was involved in multiple-gene interaction. In addition, our study found that pancreatic cancer was related to an activation of the mTOR signaling pathway and renal cell carcinoma pathway.

Presence of S100A9-positive inflammatory cells in cancer tissues correlates with an early stage cancer and a better prognosis in patients with gastric cancer

Background

S100A9 was originally discovered as a factor secreted by inflammatory cells. Recently, S100A9 was found to be associated with several human malignancies. The purpose of this study is to investigate S100A9 expression in gastric cancer and explore its role in cancer progression.

Methods

S100A9 expression in gastric tissue samples from 177 gastric cancer patients was assessed by immunohistochemistry. The expression of its dimerization partner S100A8 and the S100A8/A9 heterodimer were also assessed by the same method. The effect of exogenous S100A9 on motility of gastric cancer cells AGS and BGC-823 was then investigated.

Results

S100A9 was specifically expressed by inflammatory cells such as macrophages and neutrophils in human gastric cancer and gastritis tissues. Statistical analysis showed that a high S100A9 cell count (> = 200) per 200x magnification microscopic field in cancer tissues was predictive of early stage gastric cancer. High S100A9-positive cell count was negatively correlated with lymph node metastasis (P = 0.009) and tumor invasion (P = 0.011). S100A9 was identified as an independent prognostic predictor of overall survival of patients with gastric cancer (P = 0.04). Patients with high S100A9 cell count were with favorable prognosis (P = 0.021). Further investigation found that S100A8 distribution in human gastric cancer tissues was similar to S100A9. However, the number of S100A8-positive cells did not positively correlate with patient survival. The inflammatory cells infiltrating cancer were S100A8/A9 negative, while those in gastritis were positive. Furthermore, exogenous S100A9 protein inhibited migration and invasion of gastric cancer cells.

Conclusions

Our results suggested S100A9-positive inflammatory cells in gastric cancer tissues are associated with early stage of gastric cancer and good prognosis.

Prognostic value of ADAM17 in human gastric cancer

A disintegrin and metalloproteinase-17 (ADAM17, also named as tumor necrosis factor-alpha-converting enzyme) is a member of the ADAM family. Of all ADAMs, the strongest evidence for a role in malignancy exists for ADAM17. Especially, it has been demonstrated that ADAM17 expression was significantly increased in human gastric cancer. The aim of this study was to investigate the association between ADAM17 expression and the clinicopathological features of patients with gastric cancer. The expression of ADAM17 was detected by real-time quantitative RT-PCR in gastric cancer and adjacent non-cancerous tissues. In addition, ADAM17 expression was analyzed by immunohistochemistry in 220 clinicopathologically characterized gastric cancer cases. The expression levels of ADAM17 mRNA and protein in gastric cancer tissues were both significantly higher than those in non-cancerous gastric mucosa. In addition, positive expression of ADAM17 correlated with the degree of tumor differentiation, depth of invasion, lymph node metastases, distant metastases, and TNM stage (all P<0.05). Furthermore, multivariate analysis suggested that lymph node metastases, distant metastases, TNM stage, and ADAM17 expression were independent prognostic indicators for gastric cancer. Our data suggest for the first time that the increased expression of ADAM17 in gastric cancer is associated significantly with aggressive progression and poor prognosis. ADAM17 may be an important molecular marker for predicting the carcinogenesis, progression, and prognosis of gastric cancer.

Decreased expression of Nedd4L correlates with poor prognosis in gastric cancer patient

The neural precursor cell expressed, developmentally down-regulated 4-like (Nedd4L) gene encodes an ubiquitin ligase that targets the epithelial sodium channel for degradation. Recent studies have demonstrated that Nedd4L plays a role in the progression of various cancers. However, the clinical implications of Nedd4L expression status in gastric cancer have remained unclear. We examined the Nedd4L expression in 82 gastric cancer patients by immunohistochemistry. The correlation between Nedd4L expression and clinicopathological factors, including prognosis, was evaluated. Cancerous Nedd4L expression was detectable in 36 of the 82 tumors (43.9%). Tumors with negative Nedd4L expression had greater extent of lymph node metastasis, lymphatic invasion, and venous invasion, and were at a worse stage than the tumors with positive Nedd4L expression. Additionally, the patients with negative Nedd4L expression had poor clinical outcomes. Furthermore, multivariate analysis indicated that Nedd4L expression was an independent prognostic factor for gastric cancer patients. Our results suggest for the first time that negative Nedd4L expression is strongly related to the invasion and metastasis of gastric cancer. Therefore, Nedd4L expression can be used as an independent prognostic marker of gastric cancer.