Beyond monotherapy: An era ushering in combinations of PARP inhibitors with immune checkpoint inhibitors for solid tumors.

The introduction of PARP inhibitors (PARPis) and immune checkpoint inhibitors (ICIs) has marked a significant shift in the treatment landscape for solid tumors. Emerging preclinical evidence and initial clinical trials have indicated that the synergistic application of PARPis and ICIs may enhance treatment efficacy and potentially improve long-term patient outcomes. Nonetheless, how to identify specific tumor types and molecular subgroups most likely to benefit from this combination remains an area of ongoing research. This review thoroughly examines current studies on the co-administration of PARPis and ICIs across various solid tumors. It explores the underlying mechanisms of action, evaluates clinical efficacy, identifies potential responder populations, and delineates common adverse events alongside strategic management approaches. The aim is to offer a detailed understanding of this combination therapy, potentially guiding future therapeutic strategies for solid tumors.

Comparison of poly (ADP-ribose) polymerase inhibitors (PARPis) as maintenance therapy for newly-diagnosed and platinum-sensitive recurrent ovarian cancer with BRCA mutational status: a systematic review and network meta-analysis.

BACKGROUND: Poly(adenosine diphosphate [ADP]-ribose) polymerase inhibitors (PARPi) treatment for ovarian cancer (OC) are ever-changing. This study aimed to compare the efficacy and overall safety of available PARPi as maintenance therapy for BRCA mutation status in patients with newly diagnosed and platinum-sensitive recurrent (PSR) OC patients. RESEARCH DESIGN AND METHODS: Relevant RCTs were systematically retrieved from PubMed and Embase until 31 May 2022. Progression-free survival (PFS) and overall survival (OS) based on BRCA mutation status and adverse events (AEs) regardless of mutation were efficacy and safety endpoints. RESULTS: In newly diagnosed BRCAm-OC patients, olaparib (HR: 0.33; 95% confidence interval [CI]: 0.25, 0.43) and other PARPis [niraparib (HR: 0.40; 95% CI: 0.29, 0.55), rucaparib (HR: 0.40; 95% CI: 0.21, 0.76) and veliparib (HR: 0.44; 95% CI: 0.28, 0.69)] had a statistically significant effect on PFS versus placebo. In BRCAm-PSROC patients, Olaparib exhibited significant benefit (HR: 0.69; 95% CI: 0.54, 0.88) for OS compared to other PARPis. In BRCAwt-PSR OC patients, Olaparib showed a favorable OS benefit than other PARPis (HR: 0.84; 95% CI: 0.57,1.22). Overall, safety profile of all PARPis was acceptable. CONCLUSION: All PARPis showed significant benefit, with olaparib showing greater benefit in newly diagnosed and PSR OC women. REGISTRATION: CRD42021288932.

Clinical characteristics and serum CA19-9 combined with HE4 are valuable in diagnosing endometriosis-associated ovarian cancer.

OBJECTIVE: Endometriosis-associated ovarian cancer (EAOC) is difficult to diagnose because of its low incidence, uncertain risk factors, and the absence of effective markers. This study aimed to investigate the clinical characteristics of EAOC and identify useful serological markers. METHODS: We retrospectively studied the clinical characteristics of patients with EAOC and ovarian endometriosis, obtained between January 1, 2011 and October 31, 2021. Univariate and multivariate logistic regression analyses were used to explore the relationship between clinical characteristics and EAOC. Receiver operating characteristic curves were applied to access the diagnostic value of serological markers in EAOC. RESULTS: In total, the clinical characteristics of 220 patients were obtained; 44 with EAOC and 176 with ovarian endometriosis. EAOC patients were older (46.20 vs. 36.26 years, P < 0.001) and had larger tumors (9.10 vs. 6.73 cm, P = 0.003) together with higher CA19-9 (21.44 vs. 4.72 U/mL, P < 0.001) and HE4 levels (62.35 vs. 44.19 pmol/L, P < 0.001) when compared with ovarian endometriosis patients. Multivariate analysis showed that HE4 greater than 59.7 pmol/L, CA19-9 greater than 8.5 U/mL, age 42 years or older, and tumor length 9.2 cm or longer were independent risk factors for EAOC. Significantly, CA19-9 combined with HE4 had high sensitivity (72.73%) and specificity (78.41%) in diagnosing EAOC. CONCLUSION: Age over 42 years, large ovarian tumor, serum CA19-9 and HE4 are valuable in the diagnosis of EAOC.

ALKBH5 activates FAK signaling through m6A demethylation in ITGB1 mRNA and enhances tumor-associated lymphangiogenesis and lymph node metastasis in ovarian cancer.

Background: Lymph node (LN) metastasis is common in patients with epithelial ovarian cancer (EOC) and is associated with poor prognosis. Tumor-associated lymphangiogenesis is the first stage of LN metastasis. Research on lymphangiogenesis and lymph node metastases can help develop new anti-LN-targeted therapies. Aberrant N6-methyladenosine (m6A) modifications have been reported to be linked to LN metastasis in several cancers, however, their role in EOC lymphangiogenesis and LN metastasis remains unclear. Methods: m6A levels in EOC tissues with or without LN metastases were evaluated by dot blot analysis. Real-time polymerase chain reaction (PCR) and immunofluorescence were used to examine the expression of m6A-related enzymes. Additionally, in vitro and in vivo functional studies were performed to discover the importance of the AlkB homolog 5 (ALKBH5) gene in EOC lymphatic metastasis. To identify the downstream target genes regulated by ALKBH5, we performed RNA pulldown, RNA-binding protein immunoprecipitation-quantitative PCR, co-immunoprecipitation, m6A-modified RNA immunoprecipitation-quantitative PCR, and luciferase reporter assays. Results: m6A modification was reduced in ovarian cancers with LN metastases. ALKBH5 overexpression increased tumor-associated lymphangiogenesis and LN metastasis both in vitro and in vivo. ALKBH5 overexpression also reversed the m6A modification in ITGB1 mRNA and suppressed the YTHDF2 protein-mediated m6A-dependent ITGB1 mRNA degradation, which resulted in increased expression of ITGB1 and phosphorylation of the focal adhesion kinase (FAK) and Src proto-oncogene proteins, thereby increasing LN metastasis. Furthermore, hypoxia induced the expression of hypoxia inducible factor 1 subunit alpha, which increased ALKBH5 expression and enhanced LN metastasis in EOC. Conclusions: The ALKBH5/m6A-ITGB1/FAK signalling axis is important in ovarian cancer lymphangiogenesis and LN metastasis. Antibodies that block ITGB1 and FAK kinase-inhibitors are promising anti-metastatic agents.

A Low Dose of Ouabain Alters the Metabolic Profile of Adult Rats Experiencing Intrauterine Growth Restriction in a Sex-Specific Manner.

Intrauterine growth restriction (IUGR) increases the risk of type 2 diabetes mellitus (T2DM) and metabolic diseases. The pancreas of fetuses with IUGR is usually characterized by pancreatic dysplasia and reduced levels of insulin secretion caused by the diminished replication of ß-cells. Previous studies showed that a low dose of ouabain could reduce the apoptosis of embryonic nephric cells during IUGR and partially restore the number of nephrons at birth. The rescued kidneys functioned well and decreased the prevalence of hypertension. Thus, we hypothesized that ouabain could rescue pancreatic development during IUGR and reduce the morbidity of T2DM and metabolic diseases. Maternal malnutrition was used to induce the IUGR model, and then a low dose of ouabain was administered to rats with IUGR during pregnancy. Throughout the experiment, we monitored the pattern of weight increase and evaluated the metabolic parameters in the offspring in different stages. Male, but not female, offspring in the IUGR group presented catch-up growth. Ouabain could benefit the impaired glucose tolerance of male offspring; however, this desirable effect was eliminated by aging. The insulin sensitivity was significantly impaired in male offspring with IUGR, but it was improved by ouabain, even during old age. However, in the female offspring, low birth weight appeared to be a beneficial factor even in old age; administering ouabain exacerbated these favorable effects. Our data suggested that IUGR influenced glucose metabolism in a sex-specific manner and ouabain treatment during pregnancy exerted strongly contrasting effects in male and female rats.

Complete mitochondrial genomes of Thyreophagus entomophagus and Acarus siro (Sarcoptiformes: Astigmatina) provide insight into mitogenome features, evolution, and phylogeny among Acaroidea mites.

Mites from the Acaroidea (Sarcoptiformes: Astigmatina) are important pests of various stored products, posing potential threats to preserved foods. In addition, mites can cause allergic diseases. Complete mitochondrial genomes (mitogenomes) are valuable resources for different research fields, including comparative genomics, molecular evolutionary analysis, and phylogenetic inference. We sequenced and annotated the complete mitogenomes of Thyreophagus entomophagus and Acarus siro. A comparative analysis was made between mitogenomic sequences from 10 species representing nine genera within Acaroidea. The mitogenomes of T. entomophagus and A. siro contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region. In Acaroidea species, mitogenomes have highly conserved gene size and order, and codon usage. Among Acaroidea mites, most PCGs were found to be under purifying selection, implying that most PCGs might have evolved slowly. Our findings showed that nad4 evolved most rapidly, whereas cox1 and cox3 evolved most slowly. The evolutionary rates of Acaroidea vary considerably across families. In addition, selection analyses were also performed in 23 astigmatid mite species, and the evolutionary rate of the same genes in different superfamilies exhibited large differences. Phylogenetic results are mostly consistent with those identified by previous phylogenetic studies on astigmatid mites. The monophyly of Acaroidea was rejected, and the Suidasiidae and Lardoglyphidae appeared to deviate from the Acaroidea branch. Our research proposed a review of the current Acaroidea classification system.

Spatial differentiation and driving mechanism of rural water security in typical "engineering water depletion" of karst mountainous area-A lesson of Guizhou, China.

Southwest China gets abundant rainfall, but in its rural areas, there is a severe shortage of water resources for irrigation and drinking. A case study was conducted in the Guizhou Province, which has the most concentrated karst distribution worldwide. The rural water security index was constructed, and Geodetector and ArcGIS were employed to systematically analyze the status quo, spatial differentiation, and driving mechanism of water security in rural areas of Guizhou in 2016. The results showed that (1) there was obvious spatial variation in the rural water security index in the study area, with only 3.85% of areas being maximally safe, and 20.51%, 35.89%, 15.38%, and 24.36% being sub-optimally safe, moderately safe, unsafe, and extremely unsafe, respectively. The spatial distribution of the rural water security index, it generally coincides with a gradual decay from the economically developed areas to the periphery. The water security of the geographical environment is inferior to those of domestic water and water for agricultural production. (2) For Guizhou Province, economic and social factors, such as the disposable income of rural residents and the incidence of impoverishment, were critical factors influencing rural water security. The critical influencing factors vary greatly among prefectures; however, there are some common factors that affect rural water security, such as the incidence of impoverishment, the penetration rate of rural piped water, the percentage of primary industry, and the percentage of karst area. The maximum value of the interactive driver of the percentage of groundwater and the disposable income of rural residents was 0.812, indicating that the interaction between the high percentage of groundwater caused by karst development and the low disposable income of rural residents was the primary reason for the low rural water security. (3) Rural water security was largely influenced by poor socioeconomic development, resulting in a low level of security and the availability of public water facilities and domestic water in rural areas. Significant improvements in rural water security depend on ameliorating the water security of agricultural production and domestic water, rather than improving the geo-environmental conditions of water resources at extremely high costs.

The complete mitochondrial genome of Scatoglyphus polytrematus (Acari: Acaridae).

We assembled and annotated the complete mitochondrial genome of Scatoglyphus polytrematus. It is the first complete mitochondrial genome sequence from the genus Scatoglyphus. The mitogenome was 13,966 bp in length and contains 37 genes (including 13 protein-coding genes, 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA)), and one largest non-coding region. The gene arrangement of S. polytrematus is consistent with the pattern of possible common ancestor of astigmatid mites. In the present study, phylogenetic analysis shows that genus Scatoglyphus was clustered into one branch with other Acaridae species.

Development and validation of a novel nomogram to predict cancer-specific survival in patients with uterine cervical adenocarcinoma.

BACKGROUND: The treatment strategies and prognostic factors for uterine cervical adenocarcinoma (UAC) primarily refer to that for squamous cell carcinoma (SCC). However, the biological behavior, treatment outcomes of UAC differ from that of SCC. This study aimed to develop and validate a prognostic nomogram for predicting the probability of 3- and 5-year cancer-specific survival (CSS) in patients with UAC. METHODS: A total of 8,991 UAC patients from the Surveillance, Epidemiology, and End Results (SEER) database were included in this study. Patients diagnosed between 1988 and 2010 (n=5,655) were enrolled for model development and internal validation, and those diagnosed between 2011 and 2016 (n=3,336) were used for temporal validation. The least absolute shrinkage and selection operator (LASSO) regression analysis was used to select predictors of CSS. Cox hazard regression analysis was used to construct the model, which was presented as a static nomogram and web-based dynamic nomogram. The nomogram was internally validated using the bootstrap resampling method and underwent temporal validation. RESULTS: Tumor grade, stage T, stage N, stage M, tumor size, and surgery of the primary site were identified as independent prognostic factors for CSS and subsequently incorporated into construction of the nomogram. The nomogram could accurately predict 3- and 5-year CSS with an optimism adjusted c-statistic of 0.90 [95% confidence intervals (CI): 0.89-0.91] and 0.89 (95% CI: 0.88-0.91) after internal validation, respectively; while, after temporal validation, the statistics were 0.89 (95% CI: 0.87-0.91) and 0.88 (95% CI: 0.83-0.94), respectively. The internal and temporal calibration plots demonstrated good consistency between the predicted and observed values of CSS. Based on the model, the cases were stratified into high- and low-risk groups. The Kaplan-Meier plot showed that high-risk patients exhibited significantly poorer survival than those at low risk (P<0.0001). The prediction model exhibited a good discriminative ability and an optimal accuracy. CONCLUSIONS: In the form of a static nomogram or an online calculator, an effective and convenient nomogram was developed and validated to help clinicians quantify the risk of mortality, make personalized survival assessments, and create optimal treatment plans for UAC patients.

Ouabain Protects Nephrogenesis in Rats Experiencing Intrauterine Growth Restriction and Partially Restores Renal Function in Adulthood.

Intrauterine growth restriction (IUGR) is, in general, accompanied by a reduction of the nephron number, which increases the risk of hypertension and renal dysfunction. Studies have revealed that ouabain can partially restore the number of nephrons during IUGR. However, there is limited information regarding the melioration of nephric structure and function. We used maternal malnutrition to induce an IUGR model in rats. Subsequently, we used a mini-pump to administer ouabain to IUGR rats during pregnancy. Male offspring were divided randomly into two groups. One group was fed a normal diet, whereas the other was fed an isocaloric 8% high-salt diet. Maternal malnutrition led to a reduction in the birth weight and number of nephrons in offspring. At the end of a 40-week follow-up period, offspring from the IUGR group had high blood pressure and abnormal excretion of urinary protein; these parameters were exacerbated in offspring fed a high-salt diet. However, ouabain administration during pregnancy could partially restore the number of nephrons in IUGR offspring, normalize blood pressure, and reduce urinary protein excretion, even when challenged with a high-salt diet. Pathology findings revealed that IUGR, particularly following feeding of a high-salt diet, damaged the ultrastructure of glomeruli, but these harmful effects were ameliorated in offspring treated with ouabain. Collectively, our data suggest that ouabain could rescue nephrogenesis in IUGR newborns and protect (at least in part) the structure and function of the kidney during adulthood even when encountering unfavorable environmental challenges in subsequent life.

LINC00294 induced by GRP78 promotes cervical cancer development by promoting cell cycle transition.

Cervical cancer is one of the most common gynecological malignancies, and it has become a crucial public health problem. In the present study, the expression profiles of cervical cancer and normal cervical tissues were downloaded from the Gene Expression Omnibus and The Cancer Genome Atlas databases. Subsequently, the dysregulated long non-coding RNAs (lncRNAs) in cervical cancer were identified using R software Differentially expressed lncRNAs in cervical cancer that were associated with glucose-regulated protein 78 (GRP78) were screened out and the results demonstrated that eight lncRNAs were strongly positively correlated with GRP78. In order to confirm the relationship between GRP78 and candidate lncRNAs, GRP78 small interfering RNA (siRNA) was transfected into HeLa cells. The target lncRNAs that were regulated by GRP78 were then identified by reverse transcription-quantitative PCR and it was revealed that LINC00294 was significantly downregulated following GRP78-knockdown. Subsequently, Gene Set Enrichment Analysis demonstrated that LINC00294 was mainly enriched in regulating the cell cycle and the Hedgehog pathway. Following transfection of HeLa and SiHa cells with LINC00294 siRNA, the cell cycle was arrested at the G0/G1 phase. Western blotting suggested that LINC00294-knockdown downregulated the expression of cell cycle-associated factors (cyclin D, cyclin E and cyclin Dependent kinase 4) and upregulated cell cycle inhibitory factors (p16 and p21). The Hedgehog pathway was inhibited following knockdown of LINC00294 in HeLa and SiHa cells. In summary, LINC00294 induced by GRP78 promoted the progression of cervical cancer by regulating the cell cycle via Hedgehog pathway.

Center-Line Velocity Change Regime in a Parallel-Flow Square Exhaust Hood.

A parallel-flow exhaust hood is an effective ventilation device to control dust and toxic pollutants and protect the occupational health of workers, whether it is used alone or combined with a uniform air supply hood in a push-pull ventilation system. Some scholars have studied the outside air flow characteristics of the conventional exhaust hood with non-uniform air speed at the hood face, but the law of velocity variation outside the parallel-flow exhaust hood is not clear at present. Therefore, this paper uses the dimensionless method to study the center-line velocity change regime in a parallel-flow square exhaust hood based on simulation and experimental data. The results show that the dimensionless center-line velocity has a good change law with the characteristic length of exhaust hood in a parallel-flow square exhaust hood, which can eliminate the influence of hood face velocity and the hood size on the velocity change regime; and the experimental data is basically consistent with the calculated data, which shows that the regression equation method is reliable.

Exploration of a novel prognostic risk signatures and immune checkpoint molecules in endometrial carcinoma microenvironment.

In this study, we devoted to investigate immune-related genes and tumor microenvironment (TME) in EC based on The Cancer Genome Atlas (TCGA) database. In total 799 up-regulated and 139 down-regulated immune-related and differentially expressed genes in EC were investigated for functional annotations and prognosis. By a conjoint Cox regression analysis, we built two risk models for OS and DFS, as well as the consistent nomograms. Immune-related pathways were revealed mostly enriched in the low-risk group. By further analyzing TME based on the risk signatures, the higher immune cell infiltration and activation, lower tumor purity and higher tumor mutational burden were found in low-risk group, which presented a better prognosis. Both the expression and immunophenoscore of immune checkpoints PD-1, CTLA4, PD-L1 and PD-L2 increased significantly in low-risk group. These findings may provide new ideas for novel biomarkers and immunotherapy targets in EC.

RNA demethylase ALKBH5 promotes ovarian carcinogenesis in a simulated tumour microenvironment through stimulating NF-κB pathway.

Methylation is the main form of RNA modification. N6-methyladenine (m6A) regulates the splicing and translation of mRNA. Alk B homologue 5 (ALKBH5) participates in the biological regulation of various cancers. However, its role in ovarian carcinogenesis has not been unveiled. In the present study, ALKBH5 showed higher expression in ovarian cancer tissue than in normal ovarian tissue, but lower expression in ovarian cancer cell lines than in normal ovarian cell lines. Interestingly, Toll-like receptor (TLR4), a molecular functioning in tumour microenvironment (TME), demonstrated the same expression trend. To investigate the effect of abnormal TME on ovarian carcinogenesis, we established an in vitro model in which macrophages and ovarian cancer cells were co-cultured. In the ovarian cancer cells co-cultured with M2 macrophages, the expression of ALKBH5 and TLR4 increased. We also verified that TLR4 up-regulated ALKBH5 expression via activating NF-κB pathway. Depending on transcriptome sequencing, m6A-Seq and m6A MeRIP, we found that NANOG served as a target in ALKBH5-mediated m6A modification. NANOG expression increased after mRNA demethylation, consequently enhancing the aggressiveness of ovarian cancer cells. In conclusion, highly expressed TLR4 activated NF-κB pathway, up-regulated ALKBH5 expression and increased m6A level and NANOG expression, all contributing to ovarian carcinogenesis. Our study revealed the role of m6A in ovarian carcinogenesis, providing a clue for inventing new target therapy.

Identification of aberrantly methylated differentially expressed genes and associated pathways in endometrial cancer using integrated bioinformatic analysis.

Endometrial cancer (EC) is a fatal female reproductive tumor. Bioinformatic tools are increasingly developed to screen out molecular targets related to EC. In this study, GSE17025 and GSE40032 were obtained from Gene Expression Omnibus (GEO). "limma" package and Venn diagram tool were used to identify hub genes. FunRich was used for functional analysis. Retrieval of Interacting Genes Database (STRING) was used to analyze protein-protein interaction (PPI) complex. Cancer Genome Atlas (TCGA), GEPIA, immunohistochemistry staining, and ROC curve analysis were carried out for validation. Univariate and multivariate regression analyses were performed to predict the risk score. Compound muscle action potential (CMap) was used to find potential drugs. GSEA was also done. We retrieved seven oncogenes which were upregulated and hypomethylated and 12 tumor suppressor genes (TSGs) which were downregulated and hypermethylated. The upregulated and hypomethylated genes were strikingly enriched in term "immune response" while the downregulated and hypermethylated genes were mainly focused on term "aromatic compound catabolic process." TCGA and GEPIA were used to screen out EDNRB, CDO1, NDN, PLCD1, ROR2, ESPL1, PRAME, and PTTG1. Among them, ESPL1 and ROR2 were identified by Cox regression analysis and were used to construct prognostic risk model. The result showed that ESPL1 was a negative independent prognostic factor. Cmap identified aminoglutethimide, luteolin, sulfadimethoxine, and maprotiline had correlation with EC. GSEA results showed that "hedgehog signaling pathway" was enriched. This research inferred potential aberrantly methylated DEGs and dysregulated pathways may participate in EC development and firstly reported eight hub genes, including EDNRB, CDO1, NDN, PLCD1, ROR2, ESPL1, PRAME, and PTTG1 that could be used to predict EC prognosis. Aminoglutethimide and luteolin may be used to fight against EC.

Co-expression network analysis identified atypical chemokine receptor 1 (ACKR1) association with lymph node metastasis and prognosis in cervical cancer.

Cervical cancer (CC) is one kind of female cancer. With the development of bioinformatics, targeted specific biomarkers therapy has become much more valuable. GSE26511 was obtained from gene expression omnibus (GEO). We utilized a package called "WGCNA" to build co-expression network and choose the hub module. Search Tool for the Retrieval of Interacting Genes Database (STRING) was used to analyze protein-protein interaction (PPI) information of those genes in the hub module. A Plug-in called MCODE was utilized to choose hub clusters of PPI network, which was visualized in Cytoscape. Clusterprofiler was used to do functional analysis. Univariate and multivariate cox proportional hazards regression analysis were both conducted to predict the risk score of CC patients. Kaplan-Meier curve analysis was done to show the overall survival. Receiver operating characteristic (ROC) curve analysis was utilized to evaluate the predictive value of the patient outcome. Validation of the hub gene in databases, Gene set enrichment analysis (GSEA) and GEPIA were completed. We built co-expression network based on GSE26511 and one CC-related module was identified. Functional analysis of this module showed that extracellular space and Signaling pathways regulating pluripotency of stem cells were most related pathways. PPI network screened GNG11 as the most valuable protein. Cox analysis showed that ACKR1 was negatively correlated with CC progression, which was validated in Gene Expression Profiling Interactive Analysis (GEPIA) and datasets. Survival analysis was performed and showed the consistent result. GSEA set enrichment analysis was also completed. This study showed hub functional terms and gene participated in CC and then speculated that ACKR1 might be tumor suppressor for CC.

Eleven genes associated with progression and prognosis of endometrial cancer (EC) identified by comprehensive bioinformatics analysis.

BACKGROUND: Endometrial cancer (EC) is one of the female malignant tumors. Endometrial cancer predominately affects post-menopausal women. Bioinformatics analysis has been widely applied to screen and analyze genes in linkage to various types of cancer progression. METHODS: Download the gene expression profile from Gene Expression Omnibus (GEO). Calculate raw expression data according to pre-processing procedures. We performed the "limma" R language package to screen DEGs between Endometrial cancer tissue samples and normal uterus tissue samples. Enrichment of the functions and pathways was analyzed by using clusterprofiler. We utilized Search Tool for the Retrieval of Interacting Genes Database (STRING) to assess protein-protein interaction (PPI) information, and then we used plug-in Molecular Complex Detection (MCODE) to screen hub modules of PPI network in Cytoscape. We also performed functional analysis on the genes in the hub module by using clusterprofiler. Next, we utilized the "WGCNA" package in R to establish co-expression network for the DEGs. The Venn diagram was performed to overlap the gene in key module and hub PPI cluster. We validated the key genes in TCGA, GEPIA, UALCAN and Immunohistochemistry staining obtained from The Human Protein Atlas database. And then we did ROC curve analysis by SPSS. Gene set enrichment analysis (GSEA) and mutation analysis were also performed for hub genes. RESULTS: Functional and pathway enrichment analysis demonstrated that the upregulated differentially expressed genes (DEGs) were significantly enriched in CXCR chemokine receptor binding, chemokine activity, chemokine receptor binding, G-protein coupled receptor binding, RAGE receptor binding, cytokine activity, microtubule binding, receptor regulator activity and microtubule motor activity, and the down-regulated genes were highly enriched in collagen binding. After using STRING software to construct PPI network, 30 prominent proteins were identified and the first two significant modules were selected. In co-expression network, 5 EC-related modules were identified. Among them, the turquoise module has the highest correlation with the EC. We further analyzed the genes in the PPI and turquoise module, and selected eleven key genes related to EC after validation of TCGA database, GEPIA, UALCAN and immunohistochemistry. Six of them had mutation significance. CONCLUSIONS: In summary, these 11 genes may become new therapy targets for EC treatment.

Competing endogenous RNA network of endometrial carcinoma: A comprehensive analysis.

Competing endogenous RNA (ceRNA) network is dysregulated in the initiation and progression of tumors. In the present study, we explored the regulatory mechanism of ceRNA in endometrial carcinoma (EC) and the potential key molecules with potential value in the diagnosis, treatment, and prognosis of EC. The long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) expression profiles (552 EC tissues and 35 nontumor tissues) and microRNAs (miRNAs) expression profiles (546 EC tissues and 33 nontumor tissues) were downloaded from The Cancer Genome Atlas database to identify differentially expressed RNAs (DERNAs) in EC. An integrated bioinformatics analysis was used to construct an EC-specific ceRNA network and select key molecules. As a result, 96 differentially expressed lncRNAs (DElncRNAs), 29 differentially expressed miRNAs (DEmiRNAs), and 77 differentially expressed mRNAs (DEmRNAs) were identified. An EC-specific ceRNA network was built based on nine DElncRNAs significantly associated with overall survival. CCNB1 was found as a key gene in EC through the weighted gene coexpression network analysis and protein-protein interaction network analysis. Our ceRNA network showed C2orf48 and LINC00483 might upregulate CCNB1 via competing with miR-183. In addition, we found a subnetwork which contained survival-associated DERNAs (AC110491.1, LINC00483-miR-192-GRHL1). The results of reverse transcription quantitative polymerase chain reaction supported the relative expressions of C2orf48, LINC00483 were upregulated and that of AC110491.1 was downregulated in EC. We further found C2orf48 was upregulated in serous EC, endometrioid EC, and mixed serous and endometrioid EC. LINC00483 was upregulated in mixed serous and endometrioid EC compared with that in the normal tissues according to UALCAN database. In addition, candidate small molecular drugs were screened out by ConnectivityMap based on the 77 DEmRNAs in the ceRNA network. Eventually, C2orf48, LINC00483, and AC110491.1 were identified as three key lncRNAs in EC.

Identification of EPHX2 and RMI2 as two novel key genes in cervical squamous cell carcinoma by an integrated bioinformatic analysis.

Cervical cancer is the fourth most common malignancy in women worldwide and cervical squamous cell carcinoma (CESC) is the most common histological type of cervical cancer. The dysregulation of genes plays a significant role in cancer. In the present study, we screened out differentially expressed genes (DEGs) of CESC in the GSE63514 data set from the Gene Expression Omnibus database. An integrated bioinformatics analysis was used to select hub genes, as well as to investigate their related prognostic signature, functional annotation, methylation mechanism, and candidate molecular drugs. As a result, a total of 1907 DEGs were identified (944 were upregulated and 963 were downregulated). In the protein-protein interaction network, three hub modules and 30 hub genes were identified. And two hub modules and 116 hub genes were screened out from four CESC-related modules by the weighted gene coexpression network analysis. The gene ontology term enrichment analysis and Kyoto encyclopedia of genes and genomes pathway analysis were performed to better understand functions and pathways. Genes with a significant prognostic value were found by prognostic signature analysis. And there were five genes (EPHX2, CHAF1B, KIAA1524, CDC45, and RMI2) identified as significant CESC-associated genes after expression validation and survival analysis. Among them, EPHX2 and RMI2 were noted as two novel key genes for the CESC-associated methylation and expression. In addition, four candidate small molecule drugs for CESC (camptothecin, resveratrol, vorinostat, and trichostatin A) were defined. Further studies are required to explore these significant CESC-associated genes for their potentiality in diagnosis, prognosis, and targeted therapy.

ITLNI identified by comprehensive bioinformatic analysis as a hub candidate biological target in human epithelial ovarian cancer.

BACKGROUND: Epithelial ovarian cancer (EOC) is a female malignant tumor. Bioinformatics has been widely utilized to analyze genes related to cancer progression. Targeted therapy for specific biological factors has become more valuable. MATERIALS AND METHODS: Gene expression profiles of GSE18520 and GSE27651 were downloaded from Gene Expression Omnibus. We used the "limma" package to screen differentially expressed genes (DEGs) between EOC and normal ovarian tissue samples and then used Clusterprofiler to do functional and pathway enrichment analyses. We utilized Search Tool for the Retrieval of Interacting Genes Database to assess protein-protein interaction (PPI) information and the plug-in Molecular Complex Detection to screen hub modules of PPI network in Cytoscape, and then performed functional analysis on the genes in the hub module. Next, we utilized the Weighted Gene Expression Network Analysis package to establish a co-expression network. Validation of the key genes in databases and Gene Expression Profiling Interactive Analysis (GEPIA) were completed. Finally, we used quantitative real-time PCR to validate hub gene expression in clinical tissue samples. RESULTS: We analyzed the DEGs (96 samples of EOC tissue and 16 samples of normal ovarian tissue) for functional analysis, which showed that upregulated DEGs were strikingly enriched in phosphate ion binding and the downregulated DEGs were significantly enriched in glycosaminoglycan binding. In the PPI network, CDK1 was screened as the most relevant protein. In the co-expression network, one EOC-related module was identified. For survival analysis, database and clinical sample validation of genes in the turquoise module, we found that ITLN1 was positively correlated with EOC prognosis and had lower level in EOC than in normal tissues, which was consistent with the results predicted in GEPIA. CONCLUSION: In this study, we exhibited the key genes and pathways involved in EOC and speculated that ITLN1 was a tumor suppressor which could be used as a potential biomarker for treating EOC, Gene Expression Omnibus, prognosis.