Integrated analysis of lncRNA-associated ceRNA network identified potential regulatory interactions in osteosarcoma.

This study aimed to identify potential therapeutic targets in osteosarcoma (OS) through the network analysis of competing endogenous RNAs (ceRNAs). The differentially expressed miRNAs (DEMIs) and mRNAs (DEMs) were identified between OS cell lines and human mesenchymal stem cells (hMSCs) from the data deposited under GSE70415 using limma package. Functional analysis of DEMs was performed using DAVID and clusterProfiler to identify significantly enriched Gene Ontology biological processes and KEGG pathways, respectively. The DEMI-DEM interaction network was constructed using Cytoscape. LncRNA-miRNA interactions were predicted using starBase database. The ceRNA regulatory network was constructed by integrating mRNAs, miRNAs, and lncRNAs, and functional enrichment analysis was performed for the genes involved. The analysis revealed a total of 326 DEMs and 54 DEMIs between OS cells and hMSCs. We identified several novel therapeutic targets involved in the progression and metastasis of OS, such as CBX7, RAD9A, SNHG7 and miR-34a-5p. The miRNA, miR-543 (target gene: CBX7) was found to be associated with the pathway Mucin type O-glycan biosynthesis. Using the ceRNA network, we established the following regulatory interactions: NEAT1/miR-543/CBX7, SNHG7/miR-34a-5p/RAD9A, and XIST/miR-34a-5p/RAD9A. CBX7, RAD9A, lncRNA SNHG7, miR-543, and miR-34a-5p may be explored as novel therapeutic targets for treatment of OS.

[Effects of dioscornin tablet containing serum on NF-kappaB p65, STAT3, and VEGF mRNA expressions in rats' synovial cell strain RSC-364 induced by IL-17 and TNF-alpha].

OBJECTIVE: To observe the effects of Dioscornin Tablet (DT) containing serum on nuclear factor of kappa B (NF-kappaB) p65, signal transducer and activator of transcription 3 (STAT3), and vascular endothelial growth factor (VEGF) mRNA expressions in rats' synovial cell strain 364 (RSC-364) induced by interleukin-17 (IL-17) and tumor necrosis factor-alpha (TNF-alpha), and to investigate the underlying mechanisms for DT to inhibit angiogenesis of rheumatoid arthritis (RA). METHODS: In this experiment, the vehicle control group, the cell model group, the DT containing serum group, and the positive control group (Tripterygium containing serum) were set up. The DT containing serum and the Tripterygium containing serum were prepared. The RA cell model was established by IL-17 combined TNF-alpha induced injury in RSC-364. The RA cells were intervened by DT containing serum and Tripterygium containing serum respectively. The DNA binding activity of NF-kappaB p65 was detected using TransAM NF-kappaB p65. The expression of STAT3 was observed using Western blot. The VEGF mRNA expressions were detected by real-time quantitative PCR. RESULTS: Compared with the vehicle control group, the NF-kappaB p65 activity, the expressions of STAT3 and VEGF mRNA increased significantly in RSC-364 induced by IL-17 +TNF-alpha (P < 0.01, P < 0.05). Compared with the model group, the NF-kappaB p65 activity, the expressions of STAT3 and VEGF mRNA decreased significantly in the DT containing serum group and the positive control group (P < 0.01, P < 0.05). There was no statistical difference between the two groups (P > 0.05). CONCLUSION: DT inhibited the VEGF mRNA expression through inhibiting the NF-kappaB p65 activity and the STAT3 protein expression in the Janus kinase (JAK)-signal transducer and activating transcription factor pathway, thus inhibiting the angiogenesis of RA.

Identification of key genes related to immune infiltration in cirrhosis via bioinformatics analysis.

Cirrhosis is the most common subclass of liver disease worldwide and correlated to immune infiltration. However, the immune-related molecular mechanism underlying cirrhosis remains obscure. Two gene expression profiles GSE89377 and GSE139602 were investigated to identify differentially expressed genes (DEGs) related to cirrhosis. Enrichment analysis for DEGs was conducted. Next, the immune infiltration of DEGs was evaluated using CIBERSORT algorithm. The hub DEGs with tight connectivity were identified using the String and Cytoscape databases, and the expression difference of these hub genes between normal liver and cirrhosis samples was determined. Moreover, in order to evaluate the discriminatory ability of hub genes and obtained the area under the receiver operating characteristic curve values in the GSE89377 and GSE139602 datasets. Finally, the association between hub DEGs and immune cell infiltration was explored by Spearman method. Among the 299 DEGs attained, 136 were up-regulated and 163 were down-regulated. Then the enrichment function analysis of DEGs and CIBERSORT algorithm showed significant enrichment in immune and inflammatory responses. And four hub DEGs (ACTB, TAGLN, VIM, SOX9) were identified, which also showed a diagnostic value in the GSE89377 and GSE 139,602 datasets. Finally, the immune infiltration analysis indicated that, these hub DEGs were highly related to immune cells. This study revealed key DEGs involved in inflammatory immune responses of cirrhosis, which could be used as biomarkers for diagnosis or therapeutic targets of cirrhosis.

L-Tyrosine Limits Mycobacterial Survival in Tuberculous Granuloma.

Caused by the intracellular pathogen Mycobacterium tuberculosis (Mtb), tuberculosis (TB) remains a massive global public health issue. A well-known and key TB trait is caseous necrotic granuloma, which allows mycobacteria to reactivate and disseminate, thus confounding TB eradication programs. Amino acid (AA) metabolism is key to regulating immune responses in Mtb infections; however, it is currently unclear if AAs can be used to treat tuberculous granulomas. Here, we screened 20 proteinogenic AAs using a Mycobacterium marinum-infected zebrafish granuloma model. Only L-tyrosine simultaneously reduced Mycobacterium marinum (M. marinum) levels in zebrafish larvae and adults and inhibited intracellular pathogen survival levels. Mechanistically, L-tyrosine significantly upregulated interferon-γ (IFN-γ) expression in M. marinum -infected zebrafish adults but not in larvae. Using N-acetylcysteine (NAC) to inhibit reactive oxygen species (ROS), L-tyrosine appeared to inhibit Mtb intracellular survival by promoting ROS production. Thus, L-tyrosine as a non-essential AA may reduce mycobacterial survival in both macrophages and tuberculous granulomas. Our research provides a platform for the clinical development of AAs for active or latent TB patients infected with drug-sensitive or drug-resistant Mtb.

In vitro Synergism of Six Antituberculosis Agents Against Drug-Resistant Mycobacterium tuberculosis Isolated from Retreatment Tuberculosis Patients.

BACKGROUND: Retreatment tuberculosis (TB) has become a major source of drug-resistant TB. In contrast to the combination of isoniazid (INH) and rifampicin (RIF), that of pasiniazid (Pa) and rifabutin (RFB) or rifapentine (RFP) appears to have better activity in vitro against drug-resistant Mycobacterium tuberculosis (MTB), especially when combined with moxifloxacin (MXF). However, there has been limited study of potential synergism among Pa, RFB, RFP, and MXF, or simultaneous comparison with the standard INH and RIF combination. METHODS: In vitro synergism of four two-drug combinations (INH and RIF, Pa and RFB, Pa and RFP, MXF and Pa) and two three-drug combinations (MXF and Pa combined with RFB or RFP) was evaluated against 90 drug-resistant MTB strains isolated from retreatment TB patients by the checkerboard method. The fractional inhibitory concentration index (FICI) was calculated for each combination. RESULTS: The synergistic activity of the combination of Pa with RFB or RFP was higher than that of INH and RIF or MXF and Pa, and the synergistic activity of Pa in combination with RFP was even higher than that of RFB, although RFP yielded an MIC90 of 64 mg/liter, higher than that of RFB of 8 mg/liter against 90 drug-resistant MTB strains. Meanwhile, for three-drug combinations, the synergistic effects of MXF and Pa combined with RFB or RFP were similar. Further stratification analysis showed that, for XDR-MTB strains, the synergistic effect of the Pa and RFP combination was also better than those of other two-drug combinations. CONCLUSION: The combination of Pa with RFP shows better in vitro synergism than Pa with RFB and standard INH with RIF combinations, which can provide a reference for new regimens for retreatment TB patients.

Re-Clustering and Profiling of Digestive System Tumors According to Microenvironment Components.

BACKGROUND: Immunotherapy has become the most promising therapy in digestive system tumors besides conventional chemotherapy and radiotherapy. But only a few patients can benefit from different types of immunotherapies, such as immune checkpoint blockade (ICB). To identify these ICB-susceptible patients, methods are urgently needed to screen and profile subgroups of patients with different responsiveness to ICB. METHODS: This study carried out analysis on patients with digestive system tumors that were obtained from Cancer Genome Atlas (TCGA) cohorts. The analyses were mainly performed using GraphPad Prism 7 and R language. RESULTS: We have quantified the microenvironmental components of eight digestive system tumor patients in TCGA cohorts and evaluated their clinical value. We re-clustered patients based on their microenvironment composition and divided these patients into six clusters. The differences between these six clusters were profiled, including survival conditions, enriched biological processes, genomic mutations, and microenvironment traits. Cluster 3 was the most immune-related cluster, exhibiting a high infiltration of non-tumor components and poor survival status, along with an inhibitory immune status, and we found that patients with high stromal score indicated a poor response in ICB cohort. CONCLUSIONS: Our research provides a new strategy based on the microenvironment components for the reclassification of digestive system tumors, which could provide guidance for prognosis judgment and treatment response prediction like ICB.

CD30L/CD30 signaling regulates the formation of the tumor immune microenvironment and inhibits intestinal tumor development of colitis-associated colon cancer in mice.

Inflammatory bowel disease is one of the major causes of colitis-associated colon cancer (CAC). Therefore, it is necessary to explore new therapies to prevent colon cancer (CRC) in view of the relationship between chronic inflammation and tumor development. Previous studies on the correlation between CD30L/CD30 and cancer were mostly limited to lymphoid or homogenous tumors, while there have been only a few reports on the role of CD30L/CD30 signal transduction in the pathogenesis of CAC. In this study, we established an AOM/DSS-induced CAC model with CD30LKO mice to explore the effect of CD30L/CD30 signal transduction on the formation of the intestinal tumor immune microenvironment (TIME) during the development of intestinal tumors. Our results revealed that CD30L deficiency promoted the accumulation of myeloid derived suppressor cells (MDSCs), increased the expression of PD-L1 on MDSCs and tumor associated macrophages (TAMs), and enhanced the secretion of various inflammatory and immunosuppressive factors in the intestinal mucosa of CAC mice. Furthermore, CD30L gene deletion could selectively promote the upregulation of PD-1 expression on CD4+ and CD8+ T cells and inhibit their activation, differentiation and secretion of effector cytokines, which led to an attenuation of antitumor immune responses mediated by TEM (CD44+CD62L-) cells. Thus, our data suggest that CD30L/CD30 signaling might be a potential candidate target for immunological therapy in CAC.

Development of an autophagy-related signature in pancreatic adenocarcinoma.

In recent years, autophagy has become a research hotspot in the field of pancreatic adenocarcinoma (PAAD) due to its ambiguous roles in pancreatic tumor progression. Hence, it is necessary to assess its clinical significance in a larger cohort of patients with PAAD. Here, we identified autophagy-related genes with prognostic value in PAAD and constructed a risk model based on these genes. We found that patients in high-risk group were significantly associated with poor prognosis. Genome mutation analysis suggested that KRAS and TP53 mutations were significantly higher in high-risk groups. In addition, functional enrichment analysis showed that high-risk groups were associated with immune cell infiltration and tumor-associated signaling pathways. We further performed CIBERSORT analysis and observed increased macrophage infiltration in high-risk group, but decreased B and T cell counts compared to that in low-risk group. Gene set enrichment analysis indicated that the Hippo pathway was enriched in the high-risk group. Further, using weighted gene co-expression network analysis, Yes-associated protein 1 (YAP1) was identified as a critical hub gene. Interestingly, we found that the autophagy status and YAP1 expression status could influence each other, thus creating a positive feedback loop. In conclusion, in this study, we highlighted the clinical significance of autophagy in pancreatic cancer, constructed an autophagy-related prognostic predictive system, and identified a promising target for autophagy regulation in pancreatic cancer.

TNF-like ligand 1A is associated with progression and prognosis of human gastric cancer.

PURPOSE: This study aimed to investigate the function of TNF-like ligand 1A (TL1A) in the tumorigenesis and progression of gastric cancer (GC). METHODS: RNA-seq gene expression and clinical information for GC patients were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) between GC tissue samples and normal controls were screened with the edgeR package. Identification of gene co-expression and functional enrichment analyses were performed with Pearson's correlation analysis and gene set enrichment analysis (GSEA), respectively. Lastly, survival analysis was performed using the Kaplan-Meier method with the log rank test. RESULTS: TL1A expression in GC tissue samples were significantly higher than that in normal controls (LogFC=1.07 and P=8.90E-07). Moreover, 215 genes, co-expressed with TL1A, and 21 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were obtained. Next, the miRNA-lncRNA/mRNA network, comprising 7 miRNAs, 27 lncRNAs, and 21 mRNAs, was constructed based on key genes from intersections between co-expression analysis and GSEA. In addition, survival analysis results demonstrated that TL1A (P=2.6e-07) was significantly associated with the overall survival (OS) of GC patients. CONCLUSION: TL1A was involved in the tumorigenesis and progression of GC, and was significantly associated with the OS of GC patients.

CD30 ligand deficiency accelerates glioma progression by promoting the formation of tumor immune microenvironment.

CD30 ligand (CD30L, CD153), belonging to the tumor necrosis factor superfamily, has been reported to act as an immune regulator mainly in several autoimmune diseases and Hodgkin's lymphoma. However, little is known about its regulation in the glioma microenvironment. In this study, using a GL261 mouse glioma model, we showed that CD30L deficiency in the host accelerated glioma growth and reduced mouse survival, which might be associated with the accumulation of tumor-infiltrating immune cells, especially tumor-associated macrophages, myeloid-derived suppressor cells and CD8+ PD-1+ T cells. Moreover, CD30L deficiency resulted in distinct subsets of tumor-associated macrophages compared with those of wild-type mice. Furthermore, compared with those of wild-type mice, tumor-associated macrophages and microglia in CD30L-deficient mice adopted a more pro-tumorigenic phenotype within tumors. CD8+ T cells in CD30L-deficient mice decreased the expression of ki-67. Therefore, these results suggest that CD30L deficiency promotes the exhaustion of CD8+ T cells and the infiltration of tumor-associated macrophages and microglia. Our findings provide evidence for a new potential immunotherapy for glioma targeting CD30/CD30L signaling.

Anti-angiogenic effect of total saponins of Rhizoma Dioscorea nipponica on collagen induced-arthritis in rats.

Rheumatoid arthritis (RA) is a common chronic autoimmune and incurable disease. The aim of the present study was to investigate the therapeutic effect and mechanism of the total saponins of Rhizoma Dioscorea nipponica (TSRDN) in RA. A collagen induced-arthritis (CIA) rat model was established. CIA rats were randomly divided into three groups and lavaged with an equal volume of solvent (CIA group), TSRDN (25 mg/kg/day, RDN group) and tripterygium (TP; 12 mg/kg/day, TP group) for 21 days, respectively. Normal rats served as a control group. Hematoxylin-eosin (HE) staining was used to observe the histopathological injury of synovial tissues. The level of CD31, which used for marking and counting, micro vessel density (MVD) and the expression levels of vascular endothelial growth factor (VEGF) and signal transducer and activator of transcription 3 (STAT3) were detected by immunohistochemical analysis. Additionally, the DNA-binding activity of nuclear factor-κB (NF-κB) was determined using an ELISA kit. HE staining showed obvious synovial hyperplasia, inflammatory cell infiltration, pannus formation, cartilage and bone erosion in the CIA group rats. In addition, compared with control group, the level of MVD, the expression of VEGF and STAT3, and the DNA-binding activity of NF-κB were all increased in CIA group rat synovial tissue (all P<0.01); however, TSRDN or tripterygium were able to inhibit these changes (all P<0.01). It was speculated that TSRDN may prevent angiogenesis by inhibiting the expression of STAT3 and the DNA-binding activity of NF-κB p65, thereby potentially improving CIA.

NPY1R is a novel peripheral blood marker predictive of metastasis and prognosis in breast cancer patients.

The aim of the current study was to evaluate a novel tumor marker, neuropeptide Y receptor Y1 (NPY1R), for the detection of circulating cancer cells and to investigate its clinical significance in breast cancer patients. The Digital Gene Expression Displayer tool of the Cancer Genome Anatomy Project was used to identify the marker gene NPY1R, which is able to detect circulating cancer cells. Nested quantitative polymerase chain reaction was performed to correlate the NPY1R expression levels with the clinicopathological features of 142 breast cancer patients. A follow-up study of 131 of the breast cancer patients was conducted for 38 months. Compared with the 60 normal control individuals, NPY1R was highly expressed in the cancer patients (P<0.01). These high levels of NPY1R expression were positively correlated with the clinical stage and lymph node metastasis status of the disease, as well as with the status of the estrogen and progesterone receptors (P<0.05). Breast cancer patients with circulating cancer cells that expressed NPY1R exhibited shorter tumor-specific survival when compared with those with no NPY1R expression (P<0.01). Additionally, the mortality rate was associated with HER2 expression in the NPY1R positive and negative groups. These results indicate that NPY1R may serve as a useful marker to predict breast cancer metastasis and to evaluate the prognosis of breast cancer patients.

A rapid nested polymerase chain reaction method to detect circulating cancer cells in breast cancer patients using multiple marker genes.

The aim of the present study was to develop a simple and rapid method for the detection of circulating cancer cells using multiple tumor markers and to investigate the clinical significance of circulating cancer cells in breast cancer patients. A novel rapid nested polymerase chain reaction (PCR) assay, with high sensitivity and specificity, was evaluated, which was considered to be suitable for clinical application. The rapid nested PCR method was used to detect the circulating cancer cells of 142 breast cancer patients, using a panel of marker genes (FAM83A, NPY1R and KRT19), which were identified by the Digital Gene Expression Displayer Tool of the National Cancer Institute-Cancer Genome Anatomy Project. In total, 79.6% of the 142 breast cancer patient blood samples were found to express at least one tumor marker. In addition, the number of positive markers was found to significantly correlate with the disease stage and presence of distant metastasis. Furthermore, positivity for more than one tumor marker appeared to predict a reduced survival time in breast cancer patients.