Upregulation of miR-194-5p or silencing of PRC1 enhances radiotherapy sensitivity in esophageal squamous carcinoma cells.

Background: To investigate the possible molecular mechanism of miR-194-5p/PRC1/Wnt/ß-catenin signaling axis that regulates the invasive metastatic ability and radiotherapy sensitivity of esophageal squamous cell carcinoma (ESCC) cells. Methods: ESCC-related differentially expressed miRNAs were identified by microarray analysis, followed by the identification of a putative target. The targeting relationship between miR-194-5p and PRC1 was assayed. A series of mimic and shRNA were transfected into ESCC cells to find out the mechanism of miR-194-5p in ESCC by regulating PRC1 through Wnt/ß-catenin signaling pathway and their effect on cell proliferation, migration, invasion, and radiosensitivity as well as xenograft tumor growth and metastasis in nude mice. Results: We demonstrated low miR-194-5p expression and high PRC1 expression in ESCC tissues and cells. PRC1 was confirmed as a putative target for miR-194-5p. High miR-194-5p or silenced PRC1 enhanced ESCC cell radiosensitivity but reduced proliferation, invasion, and migration via PRC1 through modulation of the Wnt/ß-catenin signaling pathway. Animal experiments also validated that overexpression of miR-194-5p suppressed tumorigenesis and in vivo metastasis in nude mice.Conclusion: miR-194-5p can inhibit the Wnt/ß-catenin signaling pathway through down-regulation of the PRC1 gene, thereby enhancing the sensitivity of ESCC cells to radiotherapy and attenuating the invasion and metastasis ability of ESCC cells.

Liquid tumor microenvironment enhances WNT signaling pathway of peritoneal metastasis of gastric cancer.

Gastric cancer remains one of the most prevalent tumors worldwide and peritoneal metastasis is responsible for approximately 60% of death in advanced gastric cancer patients. However, the underlying mechanism of peritoneal metastasis is poorly understood. We have established organoids derived from malignant ascites (MA) of gastric cancer patients and noticed that MA supernatant could strongly increase the colony formation of organoids. Thus, we realized the interaction between exfoliated cancer cells (ECCs) and liquid tumor microenvironment contributes to peritoneal metastasis. Further, we designed a medium component control test which proved that exosomes derived from MA could not enhance the growth of organoids. Using Immunofluorescence and confocal imaging as well as dual-luciferase reporter assay, our data showed WNT signaling pathway was upregulated by high concentrations of WNT ligands (wnt3a and wnt5a), which was verified by ELISA. Besides, suppressing WNT signaling pathway diminished the growth promoting function of MA supernatant. This result implicated WNT signaling pathway as a potential therapeutic target for peritoneal metastasis of gastric cancer.

An immune-related signature for optimizing prognosis prediction and treatment decision of hepatocellular carcinoma.

BACKGROUND: An immune-related gene signature (IGS) was established for discriminating prognosis, predicting benefit of immunotherapy, and exploring therapeutic options in hepatocellular carcinoma (HCC). METHODS: Based on Immune-related hub genes and The Cancer Genome Atlas (TCGA) LIHC dataset (n = 363), an immune-related gene signature (IGS) was established by least absolute shrinkage and selection operator (LASSO) analysis. The prognostic significance and clinical implications of IGS were verified in International Cancer Genome Consortium (ICGC) and Chinese HCC (CHCC) cohorts. The molecular and immune characteristics and the benefit of immune checkpoint inhibitor (ICI) therapy in IGS-defined subgroups were analyzed. In addition, by leveraging the Cancer Therapeutics Response Portal (CTRP) and PRISM Repurposing datasets, we determined the potential therapeutic agents for high IGS-risk patients. RESULTS: The IGS was constructed based on 8 immune-related hub genes with individual coefficients. The IGS risk model could robustly predict the survival of HCC patients in TCGA, ICGC, and CHCC cohorts. Compared with 4 previous established immune genes-based signatures, IGS exhibited superior performance in survival prediction. Additionally, for immunological characteristics and enriched pathways, a low-IGS score was correlated with IL-6/JAK/STAT3 signaling, inflammatory response and interferon α/γ response pathways, low TP53 mutation rate, high infiltration level, and more benefit from ICI therapy. In contrast, high IGS score manifested an immunosuppressive microenvironment and activated aggressive pathways. Finally, by in silico screening potential compounds, vindesine, ispinesib and dasatinib were identified as potential therapeutic agents for high-IGS risk patients. CONCLUSIONS: This study developed a robust IGS model for survival prediction of HCC patients, providing new insights into integrating tailored risk stratification with precise immunotherapy and screening potentially targeted agents.

Tumor Organoid Model and Its Pharmacological Applications in Tumorigenesis Prevention.

Cancer is a leading cause of death and a severe threat to global public health. Organoid, as a novel 3D in vitro model, has been applied in various tumor related studies due to its apparent advantages. The organoid is mainly constructed by Matrigel-depended 3D culture system, Air-Liquid Interface (ALI) culture, and Microfluidic culture or Organ-on-chips platform. For the application in carcinogenesis studies, the organoid model may favor depicting initiative hallmarks and identifying potential intervening targets, investigating driver genes of carcinogenesis, and identifying known or unknown risk or protective factors. In this review, we discussed different organoid construction methods and their properties. We also noted that tumor organoids can portray initiative hallmarks and identify possible intervening targets, as well as explore carcinogenesis driver genes and uncover known or unknown risks or protective factors. Organoid systems have been used to identify tumor-preventive drugs such as oligomeric proanthocyanidins, Vitamin D, n-3 PUFAs, and pomegranate. The current evidence underscores the organoid model's potential importance in developing innovative tumorprevention techniques.

Effects of mFOLFOX6 regimen combined with carrelizumab on immune function and prognosis in patients with microsatellite instability colorectal cancer.

This study aimed to investigate the effect of the mFOLFOX6 regimen combined with SHR-1210 on immune function and prognosis in patients with microsatellite instability CRC. For this purpose, 60 patients with microsatellite instability CRC in our hospital from January 2019 to October 2020 were randomly divided into control and observation groups. The control group was treated with the mFOLFOX6 regimen, and the observation group was treated with s SHR-1210. After continuous treatment for 3 months, the clinical effects of the two groups were compared; CD4+, CD8+, CD4+/CD8+; IgA, IgG, IgM; Incidence of adverse reactions and PFS. The results showed that compared with the control group (30.00%), the total clinical effective rate in the observation group (53.33%) was significantly higher (P < 0.05). After treatment, CD4+, CD4+/ CD8+ decreased significantly and CD8+ increased significantly, and the change range of the observation group was significantly less than the control group (P < 0.05. The levels of IgA, IgG and IgM in the two groups decreased significantly after treatment, and the decrease in the observation group was significantly less than the control group (P < 0.05). There was no significant difference in the incidence of abnormal liver function, bleeding, proteinuria, neurotoxicity, gastrointestinal reaction, leucopenia and hypertension between the two groups (P > 0.05). PFS in the observation group was significantly prolonged after treatment (P < 0.05). In general, the mFOLFOX6 regimen combined with SHR-1210 is effective in the treatment of microsatellite instability CRC. It can not only improve the immune function, but also not increase adverse reactions, prolong the survival time, and has a high clinical reference value.

Identification of metabolism-related long non-coding RNA (lncRNA) signature predicts prognosis and immune infiltrates in hepatocellular carcinoma.

Background: Cancer-associated metabolic reprogramming promotes cancer cell differentiation, growth, and influences the tumor immune microenvironment (TIME) to promote hepatocellular carcinoma (HCC) progression. However, the clinical significance of metabolism-related lncRNA remains largely unexplored. Methods: Based on The Cancer Genome Atlas (TCGA) Liver hepatocellular carcinoma (LIHC) dataset, we identified characteristic prognostic long non-coding RNAs (lncRNAs) and construct metabolism-related lncRNA prognostic signature for HCC. Gender, age, grade, stage and TP53 status were used as covariates were used to assess the prognostic capacity of the characteristic lncRNA signature. Subsequently, the molecular and immune characteristics and drug sensitivity in metabolism-related lncRNA signature defined subgroups were analyzed. Results: We identified 34 metabolism-related lncRNAs significantly associated with the prognosis of HCC (P<0.05). Subsequently, we constructed a multigene signature based on 9 characteristics prognostic lncRNAs and classified HCC patients into high- and low-risk groups based on cutoff values. We found the lncRNA signature [hazard ratio (HR) =3.55 (2.44-5.15), P<0.001] to be significantly associated with survival. The receiver operating characteristic curve (ROC) curves area under the curve (AUC) values for 1-, 3-, and 5-year survival were 0.811, 0.773, and 0.753, respectively. In univariate and multivariate Cox regression analyses, prognostic characteristic lncRNAs were the most crucial prognostic factor besides the stage. The prognostic signature was subsequently validated in the test set. In addition, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) analyses revealed potential biological features and signaling pathways associated with the prognostic signature. We constructed a nomogram including risk groups and clinical parameters (age, gender, grade, and stage). Calibration plots and decision curve analysis (DCA) showed that our nomogram had a good predictive performance. Finally, we found reduced expression of immune-activated cells in the high-risk group. Conclusions: The metabolism-related lncRNA signature is a promising biomarker to distinguish the prognosis and an immune characteristic in HCC.

Systematic analysis of ferroptosis-related long non-coding RNA predicting prognosis in patients with lung squamous cell carcinoma.

Background: Ferroptosis is a novel iron-dependent cell death, and an increasing number of studies have shown that long non-coding RNA (lncRNAs) are involved in the ferroptosis process. However, studies on ferroptosis-related lncRNAs in lung squamous cell carcinoma (LUSC) are limited. In addition, the prognostic role of ferroptosis-related lncRNAs and their relationship with the immune microenvironment and methylation of LUSC is unclear. This study aimed to investigate the potential prognostic value of ferroptosis-related lncRNAs and their involved biological functions in LUSC. Methods: The Cancer Genome Atlas (TCGA) database and the FerrDb website were used to obtain ferroptosis-related genes for LUSC. The "limma" R package and Pearson analysis were used to find ferroptosis-related lncRNAs. The biological functions of the characterized lncRNAs were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We evaluated the prognostic power of this model using Kaplan-Meier analysis, receiver operating characteristic (ROC), and decision curve analysis (DCA). Univariate and multifactor Cox (proportional-hazards) risk model and a nomogram were produced using risk models and clinicopathological parameters for further verification. In addition, the relationship between characterized lncRNAs and tumor immune infiltration and methylation was also discussed. Results: We identified 29 characterized lncRNAs to produce prognostic risk models. Kaplan-Meier analysis revealed the high-risk group was associated with poor prognosis in LUSC (P<0.001), and ROC (AUC =0.658) and DCA suggested that risk models could predict prognosis. Univariate and multifactorial Cox as well as nomogram further validated the prognostic model (P<0.001). Gene set enrichment analysis (GSEA) showed that the high-risk group was associated with pro-tumor pathways and high-frequency mutations in TP53 were present in both groups. Single sample gene set enrichment analysis (ssGSEA) showed significant differences in immune cell infiltration subtypes and corresponding functions between the two groups. Some immune checkpoint and methylation-related genes were significantly different between the two groups (P<0.05). Conclusions: We investigated the potential mechanisms of LUSC development from the perspective of ferroptosis-related lncRNAs, providing new insights into LUSC research, and identified 29 lncRNAs as biomarkers to predict the prognosis of LUSC patients.

CD8+ T-cell exhaustion in the tumor microenvironment of head and neck squamous cell carcinoma determines poor prognosis.

Background: The occurrence of head and neck squamous cell carcinoma (HNSCC) is closely related to the immune system. The integration of traditional treatment methods and immunotherapy will be the future development direction of cancer treatment. But immunotherapy also has its limitations: a lot of basic research is going on, but the translation from basic to clinical is still not enough, and there are still few drugs approved for use.This study aimed to explore the clinical significance of the tumor immune microenvironment in HNSCC. Methods: Six clinically obtained postoperative cases were analyzed using multiplex immunohistochemistry (mIHC) to observe the tumor immune microenvironment and analyze infiltrating immune cells. Correlations between infiltrating immune cells from The Cancer Genome Atlas (TCGA) database and clinicopathological features of 510 HNSCC patients were then analyzed. Kaplan-Meier survival analysis was used to detect the relationship between the expression of different immune cells and the prognosis of HNSCC patients, and univariate and multivariate Cox regression analyses were used to analyze the prognostic factors associated with HNSCC patients. We validated the prognostic and predictive accuracy based on the expression of CD8+ T-cells in an independent group of 510 patients. Results: We detected infiltration of CD8+ T cells, NK cells, and macrophages in patients with laryngeal squamous cell carcinoma by multiplex immunofluorescence. The infiltration of the three types of immune cells in the tumor stroma was significantly higher than in the tumor parenchyma. Our results also showed the infiltration of CD8+ T cells was associated with prognosis, and the COX regression model showed CD8+ T cells were an independent prognostic factor in HNSCC patients. The higher density of infiltrating CD8+ T cells had the better prognosis. In addition, we developed a nomogram for clinical use that integrated the CD8+ T-cells-based classifier and three clinicopathological risk factors to predict the prognosis of HNSCC patients. Conclusions: CD8+ T-cell exhaustion in the tumor microenvironment of HNSCC determines poor prognosis and can be combined with the tumor stage to improve the accuracy of prognosis assessment in HNSCC patients.

MiR-448 suppresses cell proliferation and glycolysis of hepatocellular carcinoma through inhibiting IGF-1R expression.

Background: Microribonucleic acids (miRNAs) have been shown to play important roles in hepatocellular carcinoma (HCC) progression. MiR-448 has frequently been shown to be a tumor suppressor, and is abnormally expressed in HCC tumor tissues. However, little is known about the role of miR-448 in HCC development. In this article, the regulatory role of miR-448 on insulin-like growth factor 1 receptor (IGF-1R) in modulating hepatoma cell viability and glycolysis was investigated. Methods: The expression of miR-448 profiles in clinical tumor tissues and cell lines was examined using quantitative real-time polymerase chain reaction (qRT-PCR). HepG2 and Huh7 cells were transfected with miR-448 mimics, inhibitors, and scramble sequences. Cell viability and apoptosis were determined by a Cell Counting Kit-8 assay and a flow cytometry analysis. IGF-1R, a potential target of miR-448, was selected following a bioinformatic analysis, and the regulatory effects of miR-448 on IGF-1R expression was confirmed by luciferase reporter assay, qRT-PCR, and western blot. Glucose uptake, lactate production, and adenosine triphosphate (ATP) generation were detected by corresponding kits. Results: Decreased miR-448 expression was observed in both HCC patients' tumor tissues and hepatoma cells in vitro. The overexpression of miR-448 in HepG2 and Huh7 cells decreased cell viability and increased apoptosis. Additionally, the overexpression of miR-448 or the knockdown of IGF-1R lowered the level of glucose uptake, lactate production, and ATP generation, while the knockdown of miR-448 increased glycolysis. Further, aberrantly expressed miR-448 downregulated IGF-1R levels, while the inhibition of miR-448 resulted in the upregulation of IGF-1R in both HepG2 and Huh7 cells. In addition, miR-448 interacted with the wild-type 3'untranslated regions (3'UTRs) of IGF-1R, but had no effect on the mutant 3'UTRs. The expression of IGF-1R was increased in HCC patients' tumor tissues and serum, and was inversely correlated with miR-448 expression. Conclusions: The increased expression of miR-448 appears to downregulate the expression of IGF-1R by interacting with the 3'UTR in HCC progression. These findings highlight its role as a potential target for HCC therapy.

CCR4 is a prognostic biomarker and correlated with immune infiltrates in head and neck squamous cell carcinoma.

BACKGROUND: Increased evidence has indicated that the tumour microenvironment plays an essential in the development, treatment and prognosis of head and neck squamous cell carcinoma (HNSC). Recent studies have indicated CC chemokine receptor 4 (CCR4) plays an essential role in tumor invasion and other adverse biological behavior. This study used data from the Cancer Genome Atlas (TCGA) database to explore the role of CCR4 in HNSC and its clinical significance. METHODS: The gene expression and clinical data of HNSC patients in the TCGA database were extracted. Gene Expression Profiling Interactive Analysis (GEPIA) was used to analyze the expression of CCR4 in tumor and non-tumor tissue. Kaplan-Meier survival analysis was used to analyze the relationship between CCR4 expression and overall survival rate (OS), disease-specific survival (DSS), and progression-free interval (PFI) in HNSC. A logistic regression model was used to analyze the relationships between various clinical factors and CCR4 expression. Gene Set Enrichment Analysis (GSEA) was used to explore the potential role of CCR4 in HNSC. Additionally, we explored the relationship between CCR4 and immune infiltration. RESULTS: The expression of CCR4 in HNSC was not significantly different from that in normal tissue. The expression level of CCR4 in wild-type TP53 was higher than that in mutant TP53. Cox regression analysis showed the expression level of CCR4 was related to the patient's tumor grade and Tumor-Node-Metastasis (TNM) stage. CCR4 expression level is an independent prognostic factor. CCR4 is positively correlated with immune infiltration and immune checkpoints expression levels. The results of GSEA revealed that the high CCR4 expression group genes were enriched in allograft rejection, inflammatory response, IL-6/JAK/STAT3 signaling, interferon gamma response, and KRAS signaling up. Low CCR4 expression group genes were enriched in oxidative phosphorylation, MYC targets v1, DNA repair, reactive oxygen species pathway, and P53 pathway. Further, our study indicated CCR4 can also predict the prognosis of radiotherapy patients. CONCLUSIONS: Our study found that CCR4 was a prognostic marker related to HNSC immune infiltration, and patients with high expression of CCR4 had a better prognosis.

Identification of m6A methyltransferase-related genes predicts prognosis and immune infiltrates in head and neck squamous cell carcinoma.

BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) accounts for 90% of head and neck malignant tumors. As the early symptoms of HNSCC are not obvious, and it is prone to recurrence and metastasis, making the overall survival (OS) rate of patients very low. Existing studies have shown m6A methylation plays a crucial role in various cancers, but it is rarely studied in HNSCC. This study aimed to explore the expression of m6A methylation-related genes in HNSCC and its correlation with prognosis, and to explore its relationship with immune infiltration. METHODS: The gene expression data of HNSCC patient tumor samples (tumor =510) and adjacent normal tissue samples (normal =50) were extracted from The Cancer Genome Atlas (TCGA) database, and the expression characteristics of m6A regulatory factors were described. Kaplan-Meier survival analysis was used to analyze the relationship between m6A regulatory factors and OS and disease-specific survival (DSS). Least absolute shrinkage and selection operator (LASSO) regression was used to construct the m6A regulatory factor-HNSCC risk prediction model. In addition, the relationship between m6A methylation-related genes and tumor immune infiltration were discussed. RESULTS: The differential expression of 20 genes were identified by TCGA, and 18 genes (IGF2BP2, IGF2BP1, IGF2BP3, VIRMA, YTHDF1, YTHDF2, YTHDF3, ZC3H13, METTL14, ALKBH5, METTL3, RBMX, WTAP, YTHDC1, FTO, HNRNPC, HNRNPA2B1, and RBM15) were overexpressed in HNSCC. The survival rate of different gene expression levels was different. The high expression of YTHDC1 and YTHDC2 indicated better OS. Furthermore, for DSS, increased expression of YTHDC2 was also correlated with better clinical outcomes (P<0.05). At the same time, we drew a 3-gene risk score model in the TCGA-HNSCC cohort, and the survival curve showed compared with low-risk patients, high-risk patients had significantly worse OS (P<0.05). Gene enrichment analysis showed EPITHELIAL_MESENCHYMAL_TRANSITIO, MTORC1_SIGNALING, MYC_TARGETS_V1, MYC_TARGETS_V2, MYOGENESIS pathways, high TP53 mutations, and suppressive immunity were related to the high-risk group. The low-risk group was related to ALLOGRAFT_REJECTION, COMPLEMENT, IL6_JAK_STAT3_SIGNALING, INTERFERON_ALPHA_RESPONSE, INTERFERON_GAMMA_RESPONSE pathways, low TP53 mutations, and active immunity. CONCLUSIONS: The m6A methyltransferase-related genes can predict the prognosis of HNSCC and are related to immune infiltration.

Correlation of the AKT/mTOR signaling pathway with the clinicopathological features and prognosis of nasopharyngeal carcinoma.

The primary aim of this study was to examine the correlation of the AKT/mTOR signaling pathway with the clinicopathological features and prognostic significance in nasopharyngeal carcinoma (NPC). The study tissues were collected from 285 patients with NPC and normal mucosal tissues were obtained from 289 individuals with normal nasopharynxes. Immunohistochemical staining was used to detected the expression of the AKT, mTOR, and p70 ribosomal S6 kinase (P70S6K) proteins. Follow-up was performed for between 8 and 60 months. Spearman's rank correlation analysis was performed to evaluate the correlation of the expression of the AKT, mTOR, and P70S6K proteins in NPC tissues. Kaplan-Meier curves were plotted to show the survival of patients with NPC. A Cox proportional hazards model was used to explore the independent risk factors for prognosis. The expression of the AKT, mTOR, and P70S6K proteins in NPC tissues was higher than that in healthy nasopharyngeal mucosal tissues, and was correlated with T-staging, N-staging, clinical stage, distant metastasis, and differentiation. The positive expression of the AKT, mTOR, and P70S6K proteins was higher in patients with stage III/IV NPC, low differentiation, and metastasis. The survival rates of patients with NPC with AKT-positive, mTOR-positive, and P70S6K-positive expression were considerably lower than those without the expression of these proteins. Distant metastasis and the overexpression of the AKT, mTOR, and P70S6 proteins were independent risk factors for the prognosis of patients with NPC. The results obtained from this study indicated an association between the AKT/mTOR signaling pathway and the progression of NPC. The upregulation of the AKT/mTOR pathway in patients with NPC is a predictor of poor prognosis.

A metabolism-related gene signature for predicting the prognosis and therapeutic responses in patients with hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) often has an insidious onset and rapid progression. Often, when the disease is first diagnosed, the opportune time for surgical intervention has already lapsed. In addition, the effects of systemic treatment is relatively unsatisfactory. Metabolic reprogramming is one of the hallmarks of cancer. This study aimed to identify a set of genes related to metabolism to construct a predictive model for the prognosis of HCC. METHODS: The transcriptomic and clinical data of 352 HCC patients were obtained from The Cancer Genome Atlas (TCGA) Liver Hepatocellular Carcinoma (LIHC) dataset and divided into a training cohort (n=212) and a testing cohort (n=140) at a ratio of 6:4. Univariate Cox regression analysis and the LASSO Cox regression model were used to identify 5 genes to establish a risk score for predicting the prognosis of HCC patients. Subsequently, the molecular characteristics of the model were assessed and the ability of the model to predict the tumor immune microenvironment and patient response to immunotherapy and chemotherapy was also examined. RESULTS: The risk score model was constructed based on the five genes, methyltransferase-like protein 6 (METTL6), RNA polymerase III subunit G (POLR3G), phosphoribosyl pyrophosphate amidotransferase (PPAT), SET Domain Bifurcated 2 (SETDB2), and suppressor of variegation 3-9 homolog 2 (SUV39H2). The Kaplan-Meier survival analysis and time-dependent receiver operating characteristic (ROC) curves demonstrated that high-risk patients had a poorer overall survival (OS) compared to low-risk patients. he nomogram score had a better predictive ability compared to the common factors. Our results finally showed that high-risk cases were associated with cell proliferation and cell cycle related gene sets, high tumor protein P53 (TP53) mutation rate, suppressive immunity and increased sensitivity to cisplatin, gemcitabine and docetaxel. Meanwhile, low-risk cases were associated with cell cycle and immune response related pathways, low TP53 mutation rate, active immunity and more benefit from immunotherapy. CONCLUSIONS: This study provided novel insights into the role of metabolism-related genes in HCC, and demonstrated that our model could be a promising prognostic biomarker for distinguishing the molecular and immune characteristics and inferring the potential response to chemotherapy and immunotherapy.

IFI30 as a prognostic biomarker and correlation with immune infiltrates in glioma.

BACKGROUND: Increased evidence indicates that the tumour microenvironment (TME) plays an essential role in the development, treatment and prognosis of glioma. High expression of interferon-gamma-inducible protein 30 (IFI30) is associated with the malignant phenotype, but the effect of IFI30 on the tumour immune microenvironment and its potential role in the carcinogenesis of glioma remain unknown. METHODS: The RNA sequencing (RNA-seq) data of 33 types of human cancer were obtained from The Cancer Genome Atlas (TCGA) Genomic Data Commons (GDC). R software was used to perform analyses, such as the expression of IFI30 in pan-cancer, evaluation of IFI30 as a prognostic biomarker in glioma, the relationship between IFI30 expression and clinical characteristics, and immune checkpoint. TIMER was used to analyse the correlation of IFI30 expression level with immune cell infiltration, and also to conduct survival analysis for immune cells and IFI30 in low grade glioma (LGG). DAVID was used for Gene Ontology (GO) functional annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway analysis of the genes similar to IFI30 in glioma. The differentially expressed genes (DEGs) between the high- and low-IFI30 expression groups were determined by DESeq2. Gene set enrichment analysis (GSEA) was then conducted to identify IFI30-related functional significance based on the hallmark gene set. RESULTS: Dysregulated expression of IFI30 was associated with human cancers. High IFI30 expression was associated with poor overall survival (OS), disease-specific survival (DSS) and progression-free interval (PFI). Univariate and multivariate analyses identified IFI30 as an independent predictor for glioma. Meanwhile, IFI30 overexpression significantly correlated with high-grade tumours, poor OS, and immune infiltration. In addition, IFI30-associated genes significantly enriched the hallmark tumour progression-related clusters and cancer pathways. CONCLUSIONS: IFI30 is a prognostic biomarker correlated with immune infiltrates and acts as an oncogene in glioma.

Identification of critical radioresistance genes in esophageal squamous cell carcinoma by whole-exome sequencing.

BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancer due to insufficient actionable molecules. Radiotherapy (RT) plays a vital role in the treatment of ESCC, while radioresistance is a significant challenge to RT and results in locoregional and distant failure. METHODS: Radioresistance is a complex involving confounding factors, and its genetic mechanism is challenging to study. Postoperative recurrence after RT is more likely to be due to genetic causes than recurrence in unoperated patients. Therefore, two independent cohorts of ESCC patients who had received postoperative radiotherapy (PORT) and had opposite prognoses were set up, and whole-exome sequencing (WES) technology was applied. We compared the differences in the mutant spectra between the two groups. RESULTS: The mutation rate was slightly higher in the relapsed group than in the stable group [average mutation rate, 1.15 vs. 0.73 mutations per megabyte (Mb)], while the mutation types and proportions in the two groups were not significantly different. In particular, three mutated genes (TTN, MUC19, and NPIPA5) and two copy number alterations (CNAs) (1q amplification and 14q deletion) were identified to be associated with poor RT prognosis, while MUC4 was a favorable factor. CONCLUSIONS: These radioresistance biomarkers may supply insight into predicting the radioresponse. Further, these findings offer the first data on the mutational landscape of ESCC radioresistance.

Identification of critical genes in gastric cancer to predict prognosis using bioinformatics analysis methods.

BACKGROUND: Ranking fourth in the world in tumor incidence and second in cancer-related death worldwide, gastric cancer (GC) is one of the major malignant tumors, and has a very complicated pathogenesis. In the present study, we aimed to identify new biomarkers to predict the survival rate of GC patients. METHODS: The differentially expressed genes (DEGs) between GC tissues and normal stomach tissues were obtained by using GEO2R, and overlapped DEGs were acquired with Venn diagrams. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted with R software. Then, the protein-protein interaction (PPI) of these DEGs was visualized by Cytoscape. Gene Expression Profiling Interactive Analysis (GEPIA) was used to verify the expression differences of hub genes in gastric adenocarcinoma tissues and normal tissues. Overall survival (OS) of hub genes was calculated by Kaplan-Meier plotter. RESULTS: There were a total of 128 consistently expressed genes in the two datasets: 85 upregulated genes were enriched in extra-cellular matrix (ECM)-receptor interaction, protein digestion and absorption, focal adhesion, gastric acid secretion, mineral absorption, systemic lupus erythematosus, amoebiasis, and PI3K-Akt signaling pathway, and 43 downregulated genes were enriched in palate development, blood coagulation, positive regulation of transcription from RNA polymerase II promoter, axonogenesis, receptor internalization, negative regulation of transcription from RNA polymerase II promoter, and in no significant signaling pathways. From the PPI network analyzed by Molecular Complex Detection (MCODE) plug-in, all 27 upregulated genes were selected. Furthermore, to analyze the OS among these genes, Kaplan-Meier analysis was conducted, and 25 genes were associated with remarkably worse survival. For validation in GEPIA, 11 of 25 genes were discovered to be highly expressed in GC tissues compared to normal OS tissues. Furthermore, in the re-analysis of the Database for Annotation, Visualization and Integrated Discovery (DAVID), three genes [G2/miotic-specific cyclin B1 (CCNB1), polo-like kinases 1 (PLK1), and pituitary tumor-transforming gene-1 (PTTG1)] were markedly enriched in the cell cycle pathway, particulary the G1-G1/S phase. CONCLUSIONS: Three remarkably upregulated DEGs with poor prognosis in GC were identified and may serve as new prognostic biomarkers and targets in GC therapy.

MGMT expression affects the gemcitabine resistance of pancreatic cancer cells.

Pancreatic cancer is a malignant cancer with poor prognosis. This study aimed to explore how O6-methylguanine-DNA methyltransferase (MGMT) affects the gemcitabine resistance of pancreatic cancer cells by the regulatory role of SHH/GLI signaling pathway. MGMT inhibition induced by lomeguatrib (LM) suppressed the proliferation, invasion, migration and autophagy, promoted the apoptosis of PanC-1/GEM cells and up-regulated the GEM inhibition rates for PanC-1/GEM cells. Moreover, MGMT inhibition increased the expression of Caspase-3 and Bax and decreased the expression of Bcl-2, Beclin1 and Atg5 in PanC-1/GEM cells. PVT1 silencing could also produce the similar effects of MGMT inhibition induced by LM on PanC-1/GEM cells. And, PVT1 silencing could inhibit the SHH/GLI signaling pathway in PanC-1/GEM cells by regulating the MGMT expression. miR-409 was demonstrated to be a potential target of PVT1 and SHH was demonstrated to be a potential target of miR-409. Furthermore, GLI overexpression could reverse the effects of PVT1 silencing. In the xenograft model of pancreatic cancer, nude mice were treated with GEM. MGMT inhibition suppressed the tumor growth and autophagy and promoted the apoptosis in tumor tissues. And, PVT1 silencing could inhibit the SHH/GLI signaling pathway in tumor tissues. In conclusion, MGMT inhibition could suppress the proliferation, invasion, migration and autophagy and promote the apoptosis of PanC-1/GEM cells in vitro and in vivo. PVT1 silencing may affect the PanC-1/GEM cells through changing the MGMT expression by inhibiting the SHH/GLI signaling pathway.

Investigation of Potential Mechanisms Associated with Non-small Cell Lung Cancer.

This study aimed at investigating the crucial mechanisms underlying non-small cell lung cancer (NSCLC). NSCLC-related microarray data GSE27262 were downloaded from Gene Expression Omnibus, including 7 NSCLC 1a samples, 18 NSCLC 1b samples, and their matched normal samples. The common differentially expressed genes (DEGs) between NSCLC 1a and NSCLC 1b samples were identified, followed by protein-protein interaction (PPI) network construction, functional enrichment analysis, and weighted gene co-expression network analysis (WGCNA). Further, the key DEGs were confirmed based on the lung adenocarcinoma (LUAD) data from the Cancer Genome Atlas (TCGA) database, followed by clinical prognostic analysis. There were 802 (NSCLC 1a) and 734 (NSCLC 1b) DEGs identified. By intersection analysis, we obtained 255 upregulated and 97 downregulated common DEGs. Upregulated DEGs were significantly enriched in the plasma membrane and extracellular region, whereas the downregulated DEGs were significantly enriched in the cytoskeleton and cell cycle process. Topoisomerase (DNA) II alpha (TOP2A) and cyclin B1 (CCNB1) were hub nodes in the PPI network. Based on WGCNA, 5 modules were obtained. In the module MEgreen, DEGs were significantly enriched in cytokine-cytokine receptor interaction and focal adhesion. Notably, 1797 DEGs were identified based on the LUAD data from the TCGA database; among them, 285 DEGs were common DEGs identified from GSE27262 data. Upregulation of TOP2A and CCNB1 was correlated with poor survival of patients. The hub genes and key pathways identified in this study are helpful for a comprehensive knowledge of the molecular mechanisms of NSCLC.

Circular RNA_LARP4 Sponges miR-1323 and Hampers Progression of Esophageal Squamous Cell Carcinoma Through Modulating PTEN/PI3K/AKT Pathway.

BACKGROUND: Emerged as important regulators in cancer progression, circular RNAs have been tested to participate in diverse biological processes. Former studies have suggested that circular RNA_LARP4 (circLARP4) exerts indispensable function on the development of different cancers such as gastric cancer and ovarian cancer. Nonetheless, the specific role of circLARP4 has not been discovered in ESCC. AIMS: The aim of this study is to explore the biological function and regulatory mechanism of circLARP4 in ESCC. METHODS: CircLARP4, miR-1323, and PTEN expression levels were quantified by RT-qPCR. CCK-8, EdU, caspase-3 activity, wound healing, transwell, and western blot assays were chosen to assess ESCC cell growth. Luciferase reporter, RIP, and RNA pull-down assays were performed to examine the interaction between miR-1323 and circLARP4 (or PTEN). RESULTS: CircLARP4 expression was observably downregulated in ESCC cell lines, and overexpressed circLARP4 restrained cell proliferation and migration whereas boosted cell apoptosis in ESCC. Molecular mechanism experiments revealed that circLARP4 could act as a sponge for miR-1323 and negatively modulated miR-1323 expression in ESCC. Interestingly, the repression of miR-1323 was correlated with inhibitive cell proliferation, migration, and promotive apoptosis. Besides, miR-1323 bound with PTEN, and PTEN expression was negatively regulated by miR-1323 whereas positively regulated by circLARP4 in ESCC. Moreover, rescue assays testified that miR-1323 overexpression or PTEN deficiency could countervail the function of circLARP4 overexpression on ESCC progression. More importantly, circLARP4 played an inhibitory role in PI3K/AKT pathway. CONCLUSIONS: CircLARP4 sponges miR-1323 and hampers tumorigenesis of ESCC through modulating PTEN/PI3K/AKT pathway.

Analysis of lncRNA-mRNA networks after MEK1/2 inhibition based on WGCNA in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDA) responds poorly to treatment. Efforts have been exerted to prolong the survival time of PDA, but the 5-year survival rates remain disappointing. Understanding the molecular mechanisms of PDA development is significant. MEK/ERK pathway signaling has been proven to be important in PDA. lncRNA-mRNA networks have become a vital part of molecular mechanisms in the MEK/ERK pathway. Herein, weighted gene coexpression network analysis was used to investigate the coexpressed lncRNA-mRNA networks in the MEK/ERK pathway based on GSE45765. Differently expressed long noncoding RNA (lncRNA) and messenger RNA (mRNA) were found and 10 modules were identified based on coexpression profiles. Gene ontology and Kyoto Encyclopedia of Genes and Genomes were then performed to analyze the coexpressed lncRNA and mRNA in different modules. PDA cells and tissues were used to validate the analysis results. Finally, we found that NONHSAT185150.1 and B4GALT6 were negatively correlated with MEK1/2. By analyzing GSE45765, the genome-wide profiles of lncRNA-mRNA network after MEK1/2 was established, which might aid the development of drug-targeting MEK1/2 and the investigation of diagnostic markers.