ARIP: A Tool for Precise Interatomic Contact Area and Volume Calculation in Proteins.

The interplay patterns of amino acid residues are pivotal in determining the tertiary structure and flexibility of proteins, which in turn are intricately linked to their functionality and interactions with other molecules. Here, we introduce ARIP, a novel tool designed to identify contact residues within proteins. ARIP employs a modified version of the dr_sasa algorithm and an atomic overlap weighted algorithm to directly calculate the contact area and volume between atoms based on their van der Waals radius. It also allows for the selection of solvent radii, recognizing that not every atom in proteins can interact with water molecules. The solvent parameters were derived from the analysis of approximately 5000 protein and nucleic acid structures with water molecules determined using X-ray crystallography. One advantage of the modified algorithm is its capability to analyze multiple models within a single PDB file, making it suitable for molecular dynamic capture. The contact volume is symmetrically distributed between the interacting atoms, providing more informative results than contact area for the analysis of intra- and intermolecular interactions and the development of scoring functions. Furthermore, ARIP has been applied to four distinct cases: capturing key residue-residue contacts in NMR structures of P4HB, protein-drug binding of CYP17A1, protein-DNA binding of SPI1, and molecular dynamic simulations of BRD4.

The relationship between GLIM-malnutrition, post-operative complications and long-term prognosis in elderly patients undergoing colorectal cancer surgery.

Background: Elderly people and patients with colorectal cancer (CRC) are both at high risk of malnutrition. Therefore, it is of great significance to explore suitable malnutrition screening and diagnostic indicators for elderly patients with CRC. Recently, the Global Leadership Initiative on Malnutrition (GLIM) proposed new diagnostic criteria for malnutrition. The aim of this article was to evaluate the diagnostic value of GLIM criteria for malnutrition in elderly colorectal patients. We explored the relationship between GLIM-malnutrition, post-operative complications and the long-term prognosis of elderly colorectal patients. Methods: Elderly patients (aged ≥65 years) who underwent CRC surgery from January 2015 to December 2018 were included. Malnutrition was diagnosed based on the GLIM criteria. The relationships between GLIM-malnutrition and clinical characteristics were analyzed by t-tests, Mann-Whitney U tests, and chi-squared tests. The relationships between GLIM-malnutrition and post-operative complications were analyzed by chi-squared tests, and logistic regression analyses. The relationships between GLIM-malnutrition and the long-term prognosis were analyzed by Kaplan-Meier analyses and logistic and Cox regression analyses. Results: A total of 385 elderly patients were included in this study, and 118 patients (30.65%) were diagnosed with malnutrition according to the GLIM criteria. GLIM-malnutrition was significantly associated with older age, lower body mass index (BMI), lower grip strength, tumor location, higher Nutrition Risk Screening 2002 (NRS-2002), and lower levels of albumin and hemoglobin. GLIM-malnutrition was an independent risk factor [odds ratio (OR): 1.753, 95% confidence interval (CI): 1.100-2.795, P=0.018] for post-operative complications. Cox regression analysis showed that GLIM-malnutrition was an independent risk factor for overall survival in elderly patients with CRC. Conclusions: The GLIM criteria are feasible diagnostic criteria for malnutrition of elderly patients with CRC. GLIM-malnutrition is significantly associated with post-operative complications and overall survival in elderly patients with CRC.

Rare and undiagnosed diseases: From disease-causing gene identification to mechanism elucidation.

Rare and undiagnosed diseases substantially decrease patient quality of life and have increasingly become a heavy burden on healthcare systems. Because of the challenges in disease-causing gene identification and mechanism elucidation, patients are often confronted with difficulty obtaining a precise diagnosis and treatment. Due to advances in sequencing and multiomics analysis approaches combined with patient-derived iPSC models and gene-editing platforms, substantial progress has been made in the diagnosis and treatment of rare and undiagnosed diseases. The aforementioned techniques also provide an operational basis for future precision medicine studies. In this review, we summarize recent progress in identifying disease-causing genes based on GWAS/WES/WGS-guided multiomics analysis approaches. In addition, we discuss recent advances in the elucidation of pathogenic mechanisms and treatment of diseases with state-of-the-art iPSC and organoid models, which are improved by cell maturation level and gene editing technology. The comprehensive strategies described above will generate a new paradigm of disease classification that will significantly promote the precision and efficiency of diagnosis and treatment for rare and undiagnosed diseases.

NSUN2 modified by SUMO-2/3 promotes gastric cancer progression and regulates mRNA m5C methylation.

The 5-methylcytosine (m5C) RNA methyltransferase NSUN2 is involved in the regulation of cell proliferation and metastasis formation and is upregulated in multiple cancers. However, the biological significance of NSUN2 in gastric cancer (GC) and the modification of NSUN2 itself have not been fully investigated. Here, we analyzed the expression level of NSUN2 in tissue microarrays containing 403 GC tissues by immunohistochemistry. NSUN2 was upregulated in GC, and that it was a predictor of poor prognosis. NSUN2 promotes the proliferation, migration, and invasion of GC cells in vitro. We also demonstrated that small ubiquitin-like modifier (SUMO)-2/3 interacts directly with NSUN2 by stabilizing it and mediating its nuclear transport. This facilitates the carcinogenic activity of NSUN2. Furthermore, m5C bisulfite sequencing (Bis-seq) in NSUN2-deficient GC cells showed that m5C-methylated genes are involved in multiple cancer-related signaling pathways. PIK3R1 and PCYT1A may be the target genes that participate in GC progression. Our findings revealed a novel mechanism by which NSUN2 functions in GC progression. This may provide new treatment options for GC patients.

Establishment of the Radiologic Tumor Invasion Index Based on Radiomics Splenic Features and Clinical Factors to Predict Serous Invasion of Gastric Cancer.

BACKGROUND: Currently, there are shortcomings in diagnosing gastric cancer with or without serous invasion, making it difficult for patients to receive appropriate treatment. Therefore, we aimed to develop a radiomic nomogram for preoperative identification of serosal invasion. METHODS: We selected 315 patients with gastric cancer, confirmed by pathology, and randomly divided them into two groups: the training group (189 patients) and the verification group (126 patients). We obtained patient splenic imaging data for the training group. A p-value of <0.05 was considered significant for features that were selected for lasso regression. Eight features were chosen to construct a serous invasion prediction model. Patients were divided into high- and low-risk groups according to the radiologic tumor invasion risk score. Subsequently, univariate and multivariate regression analyses were performed with other invasion-related factors to establish a visual combined prediction model. RESULTS: The diagnostic accuracy of the radiologic tumor invasion score was consistent in the training and verification groups (p<0.001 and p=0.009, respectively). Univariate and multivariate analyses of invasion risk factors revealed that the radiologic tumor invasion index (p=0.002), preoperative hemoglobin <100 (p=0.042), and the platelet and lymphocyte ratio <92.8 (p=0.031) were independent risk factors for serosal invasion in the training cohort. The prediction model based on the three indexes accurately predicted the serosal invasion risk with an area under the curve of 0.884 in the training cohort and 0.837 in the testing cohort. CONCLUSIONS: Radiological tumor invasion index based on splenic imaging combined with other factors accurately predicts serosal invasion of gastric cancer, increases diagnostic precision for the most effective treatment, and is time-efficient.

The Human Cytomegalovirus US31 Gene Predicts Favorable Survival and Regulates the Tumor Microenvironment in Gastric Cancer.

Human cytomegalovirus (HCMV) is an oncogenic virus associated with tumorigenesis. Our previous study revealed that the HCMV US31 gene interacted with NF-κB2 and mediated inflammation through macrophages. However, there are few reports on the role of US31 in gastric cancer (GC). The aim of this study was to investigate the expression of the US31 gene in GC tissue and assess its role in the occurrence and development of GC. US31 expression in 573 cancer tissues was analyzed using immunohistochemistry. Results showed that US31 was significantly associated with tumor size (P = 0.005) and distant metastasis (P < 0.001). Higher US31 expression indicated better overall survival in GC patients. Overexpression of US31 significantly inhibited the proliferation, migration, and invasion of GC cells in vitro (P < 0.05). Furthermore, expression levels of CD4, CD66b, and CD166 were positively correlated with US31, suggesting that it was involved in regulating the tumor immune microenvironment of GC. RNA sequencing, along with quantitative real-time polymerase chain reaction, confirmed that the expression of US31 promoted immune activation and secretion of inflammatory cytokines. Overall, US31 inhibited the malignant phenotype and regulated tumor immune cell infiltration in GC; these results suggest that US31 could be a potential prognostic factor for GC and may open the door for a new immunotherapy strategy.

Patients with Helicobacter pylori-positive gastric cancer with human cytomegalovirus infection have a low tendency of advanced lymphatic metastasis in a Chinese population.

Recognized as a group I carcinogen for gastric cancer (GC) and a factor involved in the development of GC, Helicobacter pylori serves a major part in GC research. However, most studies have focused on H. pylori itself, ignoring the complicated pathogenic microbiological environment of GC and neglecting the synergistic or antagonistic effects of H. pylori with other pathogenic microorganisms. Increasing evidence has revealed that the human cytomegalovirus (HCMV) is present in several types of tumors and serves an important role in the neoplastic process of certain human malignant tumors, including GC. The aim of the present study was to explore the role of HCMV and H. pylori co-infection in GC. HCMV and H. pylori infection was analyzed in paired gastric tumor and peri-tumoral tissues from 134 (98 male and 36 female) patients using PCR. The results revealed that a total of 74 (55.2%) patients had H. pylori infection, 58 patients (43.3%) had HCMV infection, and 34 (25.4%) patients had both HCMV and H. pylori infection. Univariate and multivariate analyses demonstrated that H. pylori infection was independently associated with advanced lymphatic metastasis [P=0.007; odds ratio (OR)=3.51]. Furthermore, compared with HCMV-/H. pylori -, neither HCMV+/H. pylori - nor HCMV+/H. pylori + were associated with metastasis, but HCMV-/H. pylori + co-infection status was an independent risk factor for advanced lymphatic metastasis (P=0.005; OR=6.00). In conclusion, GC co-infected with HCMV and H. pylori exhibited a low tendency of lymph node metastasis. HCMV may interact with H. pylori to inhibit the process of lymphatic metastasis, and the mechanism requires further investigation.

Laparoscopic gastrectomy reduces adverse postoperative outcomes and decreases morbidity for gastric cancer patients with visceral obesity: a propensity score-matched analysis.

Background: Laparoscopic gastrectomy for gastric cancer shortens the recovery period without decreasing long-term survival. However, clinical evidence on whether laparoscopic radical gastrectomy reduces the surgical stress and improves the short- and long-term outcomes of obese patients with gastric cancer is lacking. We compared the short- and long-term outcomes of gastric cancer patients with visceral obesity (VO) who underwent laparoscopic gastrectomy (LG) or open gastrectomy (OG). Methods: We prospectively collected data from 578 patients who underwent radical gastrectomy in two centers between January 2014 and December 2016. The visceral fat area (VFA) was measured on the umbilicus level, and VFA ≥100 cm2 was defined as VO. The section bias was reduced by conducting a propensity score matching analysis. The short- and long-term outcomes were further compared between patients who underwent OG and those who underwent LG. Results: Overall, 245 patients (42.61%) were classified as having VO, of whom 102 were included for further analysis after matching. There were no significant differences in clinical characteristics between the two groups in the matched cohort. The LG group had significantly fewer overall complications (P<0.001) and shorter postoperative hospital stays (P<0.001). Subgroup analysis of postoperative complications also showed that the incidence of surgical complications was lower in the LG group (P=0.002). Further survival analysis showed the LG group had significantly better long-term overall survival (P=0.017). Conclusions: Compared with open radical gastrectomy, laparoscopy would reduce the rate of postoperative complications in patients with VO, as well as prolong their overall survival.

Sarcopenia in Patients With Normal Body Mass Index Is an Independent Predictor for Postoperative Complication and Long-Term Survival in Gastric Cancer.

Malnutrition in patients with gastric cancer (GC) with normal body mass index (BMI) is often ignored. This study aimed to explore the role of sarcopenia in predicting postoperative complication and long-term survival in patients with GC with normal BMI. We included patients with normal BMI (18.5 kg/m2  ≤ BMI < 23 kg/m2 ) who underwent radical gastrectomy between July 2014 and December 2016. Sarcopenia was assessed by muscle mass, handgrip strength, and gait speed. Kaplan-Meier survival analysis was used to analyze the association between sarcopenia and the prognosis of patients with GC. Univariate and multivariate analyses were used to identify risk factors contributing to postoperative complications and long-term survival. Overall, 267 patients with GC with normal BMI were included in this study; of which 49 (18.35%) patients were diagnosed with sarcopenia. Patients with sarcopenia had higher incidence of a major postoperative complication, longer postoperative hospital stays, and greater hospital costs. The Kaplan-Meier survival analysis showed that patients with sarcopenia had poorer overall survival than non-sarcopenia patients. Univariate and multivariate analyses showed that sarcopenia was an independent predictor for postoperative complication and long-term survival in such patients. Sarcopenia is an independent predictor for postoperative complications and long-term survival in patients with normal BMI after radical gastrectomy for GC. We recommend that patients with normal BMI should perform nutritional risk screening by sarcopenia.

Opposing biological functions of the cytoplasm and nucleus DAXX modified by SUMO-2/3 in gastric cancer.

Death domain-associated protein (DAXX) is a complex biological multifunctional protein and is involved in the tumorigenesis and progression of multiple cancers. The accumulation of DAXX in the nucleus is a common phenomenon in tumor cells. However, altering the subcellular localizations of DAXX results in different biological functions, and we also found that its nuclear/cytoplasmic ratio (NCR) was associated with poor prognosis in gastric cancer (GC). In this study, we investigated the effect of cytoplasmic and nuclear DAXX (cDAXX and nDAXX) in GC and the underlying mechanisms. Immunohistochemical detection performed in 323 GC tissues reveled that cDAXX was associated with a better survival, while high nDAXX expression suggested a poorer prognosis outcome. Upregulation of DAXX in the cytoplasm inhibited cell proliferation and promoted apoptosis, whereas downregulation of DAXX in the nucleus displayed opposite effects. Moreover, Transwell assays revealed that DAXX enhanced GC cell migration and invasion. Analysis from the Gene Expression Profile Interactive Analysis (GEPIA) database showed that the expression of DAXX was significantly associated with SUMO-2/3 in GC tissues. Co-immunoprecipitation combined with immunofluorescence analysis indicated that DAXX interacted directly with SUMO-2/3. Subsequently, down-regulating the expression of SUMO-2/3 resulted in altered subcellular localization of DAXX. Bioinformatics analysis showed that RanBP2 may act as SUMO E3 ligase to promote nuclear-plasma transport via combining with RanGAP1. Taken together, our results indicated that DAXX plays opposing roles in GC and suggest a new model whereby cDAXX, nDAXX, and SUMO-2/3 form a molecular network that regulates the subcellular localization of DAXX and thereby modulates its opposing biological effects. Thus, our findings provide a foundation for future studies of DAXX as a novel therapeutic target for patients with GC.

Upregulation of ZNF148 in SDHB-deficient gastrointestinal stromal tumor potentiates Forkhead box M1-mediated transcription and promotes tumor cell invasion.

Succinate dehydrogenase (SDH) deficiency is associated with gastrointestinal stromal tumor (GIST) oncogenesis, but the underlying molecular mechanism remains to be further investigated. Here, we show that succinate accumulation induced by SDHB loss of function increased the expression of zinc finger protein 148 (ZNF148, also named ZBP-89) in GIST cells. Meanwhile, ZNF148 is found to be phosphorylated by ERK at Ser306, and this phosphorylation results in ZNF148 binding to Forkhead box M1 (FOXM1). Through the complex formation at the promoter, ZNF148 facilitates Histone H3 acetylation and FOXM1-mediated Snail transcription, which eventually promotes cell invasion and tumor growth. The clinical analysis indicates that SDHB deficiency is associated with elevated ZNF148 levels, and ZNF148-S306 phosphorylation level displays a positive correlation with poor prognosis in GIST patients. These findings illustrate an unidentified molecular mechanism underlying FOXM1-regulated gene transcription related to GIST cell invasion, which highlights the physiological effects of SDHB deficiency on the invasiveness of GIST.

Three-Dimensional Ex Vivo Culture for Drug Responses of Patient-Derived Gastric Cancer Tissue.

Gastric cancer (GC) is one of the most common malignancies with high mortality and substantial morbidity. Although the traditional treatment strategies for GC revolve around surgery, radiotherapy, and chemotherapy, none have been able to optimally treat most affected patients. To improve clinical outcomes and overcome potential GC resistance, we established a three-dimensional (3D) culturing platform that accurately predicts drug responses in a time- and cost-effective manner. We collected tumor tissues from patients following surgeries and cultured them for 3 days using our protocol. We first evaluated cell proliferation, viability, and apoptosis using the following markers: Ki67 and cleaved caspase 3 (Cas3). We demonstrated that cell viability was maintained for 72 h in culture and that the tumor microenvironments and vascular integrities of the tissues were intact throughout the culture period. We then administered chemotherapeutics to assess drug responses and found differential sensitivity across different patient-derived tissues, enabling us to determine individualized medication plans. Overall, our study validated this rapid, cost-effective, scalable, and reproducible protocol for GC tissue culture that can be employed for drug response assessments. Our 3D culture platform paves a new way for personalized medication in GC and other tumors and can greatly impact future oncological research.

Metabolic syndrome predicts postoperative complications after gastrectomy in gastric cancer patients: Development of an individualized usable nomogram and rating model.

BACKGROUND: Metabolic syndrome (MetS), a public health problem, is reportedly related to an increased risk of postoperative complications after surgery. However, whether MetS have an effect on complications after gastric cancer (GC) surgery are unknown. This study aimed to investigate the effects of preoperative MetS on complications after gastrectomy. METHODS: Altogether, 718 gastric cancer patients who planned to receive radical gastrectomy between June 2014 and December 2016 were enrolled, demographic and clinicopathological characteristics were analyzed. Univariate and multivariate analyses were performed to identify potential risk factors for postoperative complications. A predictive model for postoperative complications was constructed in the form of a nomogram, and its clinical usefulness was assessed. RESULTS: Of the 628 patients ultimately included in the study (mean age 62.92 years, 450 men and 178 women), 84 were diagnosed with MetS preoperatively. Severe postoperative complications (Clavien-Dindo grade ≥II) were significantly more common in patients with MetS (41.7% versus 23.7%, P < .001). Predictors of postoperative complications included MetS (odds ratio [OR] = 1.800, P = .023), age (OR = 1.418, P = .050), Charlson score (OR = 1.787, P = .004 for 1-2 points) and anastomosis type (OR = 1.746, P = .007 for Billroth II reconstruction). The high-risk rating had a high AUC (ROC I = 0.503, ROC Ib = 0.544, ROC IIa = 0.601, ROC IIb = 0.612, ROC IIc = 0.638, ROC III = 0.735), indicating that the risk-rating model has good discriminative capacity and clinical usefulness. CONCLUSIONS: MetS was an independent risk factor for complications after gastrectomy. The nomogram and rating model incorporating MetS, Billroth II anastomosis, age, and Charlson score was useful for individualized prediction of postoperative complications.

Controlling Nutritional Status (CONUT) Score Is A Predictor Of Post-Operative Outcomes In Elderly Gastric Cancer Patients Undergoing Curative Gastrectomy: A Prospective Study.

PURPOSE: The Controlling Nutritional Status (CONUT) score is a recently developed measure that is calculated using the serum albumin level, total cholesterol level, and lymphocyte counts. The aim of this study was to examine whether the CONUT score can predict post-operative outcomes in elderly patients undergoing curative gastrectomy. PATIENTS AND METHODS: Pre-operative CONUT scores were evaluated from August 2014 to September 2016 in 357 gastric cancer patients who were scheduled to undergo curative gastrectomy. The patients were divided into three groups according to pre-operative CONUT scores: normal, light, moderate, and severe. We then calculated the association between the patient's CONUT score and post-operative complications. RESULTS: CONUT scores were statistically associated with age (P = 0.015), body mass index (P < 0.001), pre-operative hemoglobin level (P < 0.001), tumor-node-metastasis stage (P < 0.001), surgical method (P = 0.036), and post-operative complications (P < 0.001). Multivariate analysis showed that age and the CONUT score were independent predictors of post-operative complications and 1-year survival. CONCLUSION: CONUT scores can be used to predict post-operative complications and 1-year survival in elderly gastric cancer patients undergoing curative gastrectomy. They can also be used to classify the nutritional status of patients, which can be helpful for pre-and post-operative nutritional management.

Upregulation of long noncoding RNA LINC00152 promotes proliferation and metastasis of esophageal squamous cell carcinoma.

Purpose: Esophageal cancer is a major cause of cancer-related mortality worldwide. The long noncoding RNA LINC00152 has been confirmed to play an oncogenic role in many cancers. However, the expression pattern and function of LINC00152 in human esophageal squamous cell carcinoma (ESCC) remain unclear. Materials and methods: We evaluated LINC00152 expression in ESCC by qPCR and in situ hybridization. Proliferation, apoptosis, cell cycle, migration and invasion were examined in ESCC cells knocked down for LINC00152 knockdown by siRNA. Furthermore, an mRNA microarray was performed in ESCC cells with LINC00152 knockdown. Results: LINC00152 was significantly upregulated in human ESCC clinical samples (P<0.001) and cell lines (P=0.008), and LINC00152 overexpression was related to lymphatic metastasis (P=0.03) and advanced pTNM classification (P=0.005). Furthermore, ESCC patients with LINC00152 overexpression had significantly shorter overall survival (P=0.007), and LINC00152 overexpression was an independent risk factor for overall survival of ESCC patients. LINC00152 knockdown inhibited the proliferation, migration and invasion of ESCC cells in vitro. In addition, mechanistic investigations through mRNA array and immunoblot analyses demonstrated that LINC00152 regulated the expression of several cell cycle-related proteins and SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) interactions in vesicular transport pathway proteins. Conclusion: Our research indicated that LINC00152 exhibits oncogenic functions in ESCC and may represent a potential new target for ESCC therapy.

microRNA-33a prevents epithelial-mesenchymal transition, invasion, and metastasis of gastric cancer cells through the Snail/Slug pathway.

Invasion and metastasis are responsible for the majority of deaths in gastric cancer (GC). microRNA-33a (miR-33a) might function as a tumor suppressor in multiple cancers. Here, we describe the regulation and function of miR-33a in GC and mechanisms involved in epithelial-mesenchymal transition (EMT) and metastasis. First, GC tissues and adjacent normal tissues were collected. miR-33a upregulation or SNAI2 depletion on GC cells were introduced to assess the detailed regulatory mechanism of them. We assessed the expression of miR-33a, SNAI2, Snail/Slug signaling pathway-related genes, and EMT-related markers in GC tissues and cells. miR-33a distribution in GC tissues and adjacent normal tissues was measured. Cell proliferation, migration and invasion, and cell cycle distribution were assessed. In nude mice, GC tumor growth and lymph node metastasis were observed. Furthermore, the predicative value of miR-33a in the prognosis of GC patients was evaluated. The obtained results indicated that lowly expressed miR-33a, highly expressed SNAI2, activated Snail/Slug, and increased EMT were identified in GC tissues. miR-33a was located mainly in the cytoplasm. miR-33a targeted and negatively regulated SNAI2. MKN-45 and MKN-28 cell lines were selected for in vitro experiments. Upregulated miR-33a expression or siRNA-mediated silencing of SNAI2 suppressed the activation of Snail/Slug, whereby GC cell proliferation, invasion and migration, EMT, tumor growth, and lymph node metastasis were inhibited. High expression of miR-33a was a protective factor influencing the prognosis of GC. This study suggests that miR-33a inhibited EMT, invasion, and metastasis of GC through the Snail/Slug signaling pathway by modulating SNAI2 expression.NEW & NOTEWORTHY miR-33a targets and inhibits the expression of SNAI2, overexpression of SNAI2 activates the Snail/Slug signaling pathway, the Snail/Slug signaling pathway promotes GC cell proliferation, invasion, and metastasis, and overexpression of miR-33a inhibits cell proliferation, invasion, and metastasis. This study provides a new therapeutic target for the treatment of GC.

Investigating Potential Molecular Mechanisms of Carcinogenesis and Genes as Biomarkers for Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis.

Gastric cancer, as the fifth most common malignancy worldwide, is a deadly disease afflicting nearly a million people. Researchers have devoted much to study the mechanisms of carcinogenesis and progression, but the exact information of tumor initiation and progression is remained largely unknown. Here, we hypothesized several differentially expressed genes and possible pathways by employing integrated bioinformatics analysis. We fully analyzed four gastric cancer-related microarray datasets to screen differentially expressed mRNAs (DEMs), miRNAs (DEMis) and lncRNAs (DELs). The functional enrichment analysis was deeply construed, PPI network and ceRNA regulatory network were constructed to investigate potential mechanisms of tumorigenesis and progression. Furthermore, survival analysis was performed to identify critical lncRNAs that may significantly affect pathogenesis of gastric cancer. QRT-PCR was applied to verify our result. We identified two hub subnetworks that may explain the progression, metastasis and poor prognosis of gastric cancer. Meanwhile, several potential significant lncRNAs were identified. In summary, we ascertained several significantly changed KEGG pathways in the tumor initiation and progression. We also hypothesized several lncRNAs that contribute to poor prognosis of gastric cancer via integrated bioinformatics, which deserve further investigation.

Low periostin expression predicts poor survival in intestinal type gastric cancer patients.

BACKGROUND AND AIM: Periostin is a protein from the Fascilin family. It is commonly present in normal tissues and is responsible for cell adhesion. Evidence has emerged showing that changes in periostin expression play an important role in tumor initiation, development, and progression. This study aims to investigate the effect of periostin in gastric cancer (GC) patients who underwent gastrectomy. Seven hundred and forty-seven GC patients who underwent gastrectomy between December 2006 and July 2011 were included in this study. METHODS: Seven hundred and forty-seven cancer tissues and 70 paired adjacent normal tissues were collected. Periostin expression was evaluated by immunohistochemistry. The Gene Expression Omnibus database was used to study the association between the mRNA level and patient's overall survival. The tumor microenvironment was also studied. RESULTS: Periostin expression in stroma was downregulated in tumor tissues but it was upregulated in the epithelial cells. After dividing the tissues according to the Lauren Classification, we found that periostin expression in stroma and epithelial cells was higher in intestinal type than in diffuse type (P<0.001 and P=0.010, respectively). Periostin was an independent predictor of lymph node (LN) metastasis in GC patients. The study of CD163(+) tumor-associated macrophages (TAMs) revealed that in diffuse type GC, periostin expression was associated with CD163(+) TAMs. CONCLUSION: We found that the periostin expression can predict LN metastasis in patients undergoing curative gastrectomy. Intestinal type GC patients with high periostin level had both a favorable survival and lesser LN metastasis.

Effects of downregulated expression of microRNA-187 in gastric cancer.

microRNAs (miRNAs) are involved in cancer development and progression, and have regulatory roles as tumor suppressors or oncogenes. Although aberrant expression of miR-187 has been observed in several types of cancer, its pathophysiological role and relevance to tumorigenesis in gastric cancer (GC) remains unknown. In the present study, the expression and biological role of miR-187 was investigated in 32 specimens of GC tissues and their adjacent non-tumorigenic controls, and the association between miR-187 expression and clinical features of GC were analyzed further. Kaplan-Meier survival curves determined the clinical significance of miR-187 expression in GC. Following transfection with miR-187 mimics, the biological functions of miR-187 were determined by cell proliferation and cell cycle assays. Moreover, following transfection with miR-187 mimics, the targets regulated by miR-187 were investigated using western blotting. Luciferase reporter assays confirmed whether miR-187 regulated MAD2 mitotic arrest deficient-like 2 (MAD2L2) and stomatin (EPB72)-like 2 (STOML2) expression. The data of the present study revealed that miR-187 was significantly downregulated in GC compared with adjacent non-tumorigenic counterparts. Furthermore, decreased expression of miR-187 correlated with cell differentiation (P<0.05), TNM staging (P<0.05) and poor prognosis in GC patients. Functional studies indicated that miR-187 overexpression evidently inhibited MGC-803 cell proliferation in vitro and altered the cell cycle by arresting cells in the G0/G1 phase. In addition, the luciferase assay and western blotting revealed that MAD2L2 and STOML2 were targeted by miR-187. In conclusion, it is suggested that miR-187 functions as a tumor suppressor in GC, and is important in the development and progression of GC. Moreover, miR-187 may be a potential biomarker and therapeutic target in GC.

Algae explosive growth mechanism enabling weather-like forecast of harmful algal blooms.

As a global problem in coastal environments, harmful algal blooms (HABs) have seriously affected the health of coastal ecosystems and regional economies. Here we report an aerosol-trigger mechanism for the occurrence of HABs based on long-term field data and laboratory experiments. The occurrence times of HABs and aerosol events had a significant correlation from 2005 to 2013 in the East China Sea, indicating that aerosol transport was probably an alternative trigger of HABs. HABs mostly occur in the transition time between winter and summer, during which northwest monsoon transport substantial aerosol (rich in phosphate, iron and other trace metals) to coastal waters, as revealed by chemical measurements, transmission electron microscope and electron microprober results. Such nutrients can stimulate algal growth in our incubation experiments, suggesting that such aerosol transport can be important nutrient sources for the East China Sea where phytoplankton growth is relatively phosphate limited. Air-borne nutrients are available for algal growth by rapid downward air flow, which additional results a clear weather condition, and thus adequate light intensity for algal growth. At last, the transition from northwest monsoon to warm southwest monsoon establishes favorable seawater temperature for algal blooms. Such weather-related aerosol-trigger mechanism suggests possibly forecast of HABs.