Gene Expression Profiling Interactive Analysis Research Articles

A meta-analysis and bioinformatics analysis of P4HB expression levels in the prognosis of cancer patients.

P4HB (prolyl 4-hydroxylase, beta polypeptide) is a human chromosomal gene that encodes an endoplasmic reticulum (ER) molecular chaperone protein with oxidoreductase, chaperone and isomerase activities. Recent studies indicated that P4HB may have clinical significance, with elevated P4HB expression reported in cancer patients, but its impact on tumor prognosis is not yet clear. To our knowledge, this is the first meta-analysis to show an association between P4HB expression and the prognosis of various cancers. We conducted a systematic literature search in the PubMed, PubMed Central, Web of Science, Embase, CNKI, Wanfang and Weipu databases, followed by a quantitative meta-analysis using Stata SE14.0 and R statistics software 4.2.1. The hazard ratio (HR) and relative risk (RR) were analyzed to evaluate the relationships of P4HB expression levels with overall survival (OS), disease-free survival (DFS), and clinicopathological parameters of cancer patients. Subsequently, P4HB expression in various cancer types was validated using the Gene Expression Profiling Interactive Analysis (GEPIA) online database. Ten articles containing the data of 4121 cancer patients were included in the analysis, and a significant correlation of high P4HB expression with apparently shorter OS was found (HR, 1.90; 95% CI, 1.50-2.40; P<0.01), while there was no significant correlation with gender (RR, 1.06; 95% CI, 0.91-1.22; P=0.084), or age. Additionally, GEPIA online analysis revealed significant upregulation of P4HB in 13 types of cancer. Among them, P4HB overexpression was associated with shorter OS in 9 and worse DFS in 11 cancer types. Upregulation of P4HB is correlated with worse prognosis in various cancers, which could provide new ideas for the development of P4HB-related diagnostic biomarkers and new therapeutic targets.

Elevated Expression of ADAM10 Induced by HPV E6 Influences the Prognosis of Cervical Cancer.

Objective: To explore the abnormal expression of ADAM10, its cause, and its clinical value in the prognosis of cervical lesions. Methods: The abnormal expression of ADAM10 was explored using the Gene Expression Profiling Interactive Analysis database, and the abnormal expression in cervical lesions was verified using immunohistochemistry (IHC). The transfection effect of shRNA was evaluated using real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The expression of ADAM10 in cells was analyzed using western blotting. Results: ADAM10 was highly expressed in multiple cancers. As the disease progressed, the expression of ADAM10 gradually increased (p < 0.05). Patients with higher expression of ADAM10 had poorer survival outcomes than those with lower expression levels (p < 0.05). The expression levels of ADAM10 decreased after expression levels of E6 was inhibited. Conclusion: ADAM10 is highly expressed in cervical cancer; the higher the expression levels, the worse the survival outcome. HPV E6 is the critical driver of the elevated expression of ADAM10 in cervical cancer.

High Expression of Triggering Receptor Expressed on Myeloid Cells 1 Predicts Poor Prognosis in Glioblastoma.

Glioblastoma (GBM) is a highly malignant tumor with poor prognosis, and new treatment strategies are urgently needed. Currently, the role of triggering receptor expressed on myeloid cells 1 (TREM-1) in tumors has been studied, but the role of TREM-1 in GBM remains unclear. Immunohistochemical staining for TREM-1 was performed in 91 patients diagnosed with GBM. Clinicopathological characteristics and survival times were recorded. TREM-1 expression and its effect on prognosis were analyzed using online Gene Expression Profiling Interactive Analysis (GEPIA), The Cancer Genome Atlas (TCGA), and Chinese Glioma Genome Atlas (CGGA) databases. The expression profile of TCGA-GBM cohort was used to perform functional enrichment analysis. The CIBERSORT method and Tumor Immune Estimation Resource (TIMER) database were used to estimate the tumor-infiltrating immune cells (TIICs). The ESTIMATE algorithm was used to estimate the immune-stromal scores. Finally, the relationships of TREM-1 with TIICs, immune-stromal score, and immune checkpoint genes (ICGs) were analyzed. The expression of TREM-1 was upregulated in GBM, and high TREM-1 expression predicted a poor prognosis. TREM-1, surgical resection, postoperative radiotherapy, and temozolomide (TMZ) chemotherapy were associated with the survival time of patients with GBM, but only surgical resection and TREM-1 expression were independent prognostic factors. GBM with high TREM-1 expression exhibited increased neutrophil and macrophage infiltration. TREM-1 was positively associated with the immune-stromal score and multiple ICGs, and most of which were involved in immunosuppressive responses. The present study revealed that high expression of TREM-1 in GBM is an independent poor prognosis factor and that TREM-1 is associated with the immunosuppressive microenvironment. Thus, blocking TREM-1 may be a strategy for enhancing the GBM immune response.

A novel prognostic biomarker: GINS3 is correlated with methylation and immune escape in liver hepatocellular carcinoma.

Liver cancer remains one of the tricky malignancies nowadays. GINS complex subunit 3 (GINS3), part of the GINS tetrameric complex, is significantly upregulated in many cancers, including liver hepatocellular carcinoma (LIHC). With the development of liver cancer treatment, immune and molecular targeted therapy gradually becomes a promising treatment. However, the key target for liver cancer is still indistinct. Herein, the underneath mechanism of GINS3 was investigated to verify its role as a biomarker in LIHC. Genomic expression, genetic alteration, and methylation analyses were obtained from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), The University of Alabama at Birmingham CANcer (UALCN), and Human Protein Atlas (HPA), cBioPortal, and MethSurv databases. Subsequently, the diagnostic and prognostic role of GINS3 in LIHC were analyzed based on data from receiver operating characteristic (ROC), Kaplan-Meier plotter (KM-plotter), and univariate and multivariate cox regression analyses. The functional analyses were conducted with GeneMANIA and STRING databases, gene-gene, and protein-protein interaction (PPI) networks, Gene Ontology (GO) term, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Tumor Immune Estimation Resource (TIMER), Tumor-Immune System Interaction Database (TISIDB), and Gene Expression Profiling Interactive Analysis (GEPIA) were utilized to explore the internal connection with the immune escape. Through the analyses of genomic expression, GINS3 was significantly upregulated in LIHC and positively correlated with higher T classification. ROC analysis indicated GINS3 as a potential biomarker in the diagnosis of LIHC. KM-plotter, univariate and multivariate cox regression analyses both associated GINS3 with poor prognosis in LIHC patients. GINS3 genetic alteration, gene-gene interaction, PPI networks, and enrichment analysis further revealed that GINS3 played a pivotal role in the progression of LIHC. Furthermore, hypermethylation of GINS3 at different cytosine-guanine (CpG) sites was correlated with better or worse overall survival (OS) in LIHC and GINS3 was also closely correlated with m6A modification. Moreover, results supported that GINS3 could influence the tumor microenvironment and relate to the immune checkpoints. Taken together, comprehensive analyses from this study supported GINS3 as a novel targeted biomarker in LIHC.

Hub genes and pathways in gastric cancer: A comparison between studies that used normal tissues adjacent to the tumour and studies that used healthy tissues as calibrator.

Several bioinformatics studies have been performed on high-throughput expression data to determine the cellular pathways and hub genes affected by Gastric cancer (GC). However, these studies differ in using a healthy tissue or normal tissue adjacent to the tumour (NAT) as calibrator tissues. This study was designed to find how using healthy or NAT tissues as calibrator tissues could affect pathway enrichment data and hub genes in GC. Two gene expression datasets with NAT tissues (GSE79973 and GSE118916) and one dataset with healthy tissues (GSE54129) were downloaded and processed by the limma package to screen the differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analysis were performed by the Enrichr online tool. Protein-protein interaction network construction, module analysis, and hub genes selection were performed by Cytoscape software, Molecular Complex Detection plugin, and cytoHubba plugin, respectively. The gene expression profiling interactive analysis web server was used to analyse RNA sequencing expression data from The Cancer Genome Atlas Program. The Kaplan-Meier plotter was used to perform survival analysis. Our results showed that some KEGG and GO pathways were shared between studies with NAT and the study with healthy tissues. However, some terms, especially inflammation-related terms, were missed when NAT tissues were used as calibrator tissues. Also, only FN1 and COL1A1 are common hub genes between DEGs of the studies with NAT and healthy tissues. Since hub genes are usually extracted and suggested as candidate targets for GC diagnosis, prognosis, or treatment, selecting healthy or NAT tissues may affect the hub genes selection.

Aberrant serum and tissue levels of Beclin1 and mechanistic target of rapamycin (mTOR) proteins in epithelial ovarian cancer.

Beclin1 and mechanistic target of rapamycin (mTOR) can be used as tumor markers of epithelial ovarian cancer. This study aimed to assess the association of Beclin1 and mTOR expression with clinicopathological and prognostic data in epithelial ovarian cancer patients. Serum and tissue samples from 45 epithelial ovarian cancer patients and 20 controls were analyzed by enzyme-linked immunosorbent assay and immunohistochemistry for Beclin1 and mTOR expression. The online datasets from gene expression profiling interactive analysis (n = 426), Kaplan-Meier plotter (n = 398), cBioPortal (n = 585), and UALCAN (n = 302) were also analyzed. Beclin1 expression was associated with low-grade differentiation (P = .003), earlier clinical stage (P = .013), fewer local lymph node metastases (P = .02) and lower serum Beclin1 level (P = .001). mTOR expression was associated with high-grade differentiation (P = .013), advanced clinical stage (P = .021), ascites (P = .028), and higher serum mTOR level (P = .001). The online datasets showed that a high mTOR expression level (HR = 1.44; 95% CI = 1.08-1.92; P = .013) was associated with a poor overall survival of 426 patients. Beclin1 was mutated in 1.8% and mTOR was mutated in 5% of epithelial ovarian cancer patients. Serum Beclin1 and mTOR levels were able to predict tumor differentiation, clinical stage, lymph node metastasis, and ascites in epithelial ovarian cancer patients.

Integrated transcriptome, proteome and single-cell sequencing uncover the prognostic and immunological features of colony-stimulating factor 3 receptor in pan-cancer.

Colony-stimulating factor 3 receptor (CSF3R) has been demonstrated to be associated with various hematological tumors, especially chronic neutrophilic leukemia; however, the detailed roles of CSF3R in other cancers remain to be explored. In the present study, we systematically analyzed the expression profiles of CSF3R in pan-cancer by comprehensive bioinformatics databases, such as Tumor Immune Estimation Resource, version 2 (TIMER2.0), Gene Expression Profiling Interactive Analysis, version 2 (GEPIA2.0), etc. GEPIA2.0 was also used to analyze the relationship between CSF3R expression and patients' survival prognosis. We found that the high expression of CSF3R was associated with a poor prognosis in the brain tumor patients, such as brain lower grade glioma and glioblastoma multiforme. In addition, we further investigated the genetic mutation and DNA methylation level of CSF3R in multiple cancers. Immune infiltration analysis showed that CSF3R expression was positively correlated with a variety of tumor-infiltrating immune cells in most cancers. Single cell sequencing indicated that CSF3R levels were correlated with several cancer-associated pathways, such as DNA damage, cell invasion, and stemness. Taken together, the role of CSF3R in multiple cancers might reveal its potential as a novel prognostic biomarker and therapeutic target for cancer patients.

SPTBN2 regulates endometroid ovarian cancer cell proliferation, invasion and migration via ITGB4‑mediated focal adhesion and ECM receptor signalling pathway.

Ovarian cancer is as a major contributor to gynaecologic death globally. The present study aimed to investigate the regulatory role of spectrin β non-erythrocytic 2 gene (SPTBN2) in endometroid ovarian cancer and its mechanism of action. According to the Gene Expression Profiling Interactive Analysis (GEPIA) database, SPTBN2 expression is elevated in ovarian cancer tissues and higher SPTBN2 expression indicated a worse prognosis. The present study assessed SPTBN2 mRNA and protein expression levels by reverse transcription-quantitative PCR and western blotting, respectively. Cell viability, proliferation, migration and invasion were assessed with Cell Counting Kit-8, 5-ethynyl-2'-deoxyuridine incorporation, wound healing and Transwell assays, respectively. SPTBN2 expression was notably enhanced in ovarian cancer cell lines, especially in A2780 cells compared with HOSEPiC cells (P<0.001). Following transfection with small interfering (si)RNA targeting SPTBN2, the viability, proliferation, migration and invasion of A2780 cells were decreased compared with those of A2780 cells transfected with siRNA-NC (P<0.001). Gene Set Enrichment Analysis database revealed that SPTBN2 was primarily enriched in 'focal adhesion' and 'extracellular matrix (ECM)-receptor interaction', whereas SPTBN2 was significantly associated with integrin β4 (ITGB4) in the GEPIA database. In addition, rescue experiments were performed to determine the mechanism of SPTBN2 in endometroid ovarian cancer. ITGB4 overexpression reversed the inhibitory effects of the SPTBN2 knockdown on viability, proliferation, migration and invasion of A2780 cells (P<0.05). The impacts of SPTBN2 on the expression of focal adhesion and downstream ECM receptor signalling-related proteins, including Src and p-FAK/FAK, were significantly reversed by ITGB4 overexpression (P<0.01). Collectively, SPTBN2 may regulate endometroid ovarian cancer cell proliferation, invasion and migration through the ITGB4-mediated focal adhesion and ECM receptor signalling pathway.

Integrated bioinformatics approach to unwind key genes and pathways involved in colorectal cancer.

Colorectal cancer (CRC) is the fifth leading cause of death in India. Until now, the exact pathogenesis concerning CRC signaling pathways is largely unknown; however, the diseased condition is believed to deteriorate with lifestyle, aging, and inherited genetic disorders. Hence, the identification of hub genes and therapeutic targets is of great importance for disease monitoring. Identification of hub genes and targets for identification of candidate hub genes for CRC diagnosis and monitoring. The present study applied gene expression analysis by integrating two profile datasets (GSE20916 and GSE33113) from NCBI-GEO database to elucidate the potential key candidate genes and pathways in CRC. Differentially expressed genes (DEGs) between CRC (195 CRC tissues) and healthy control (46 normal mucosal tissue) were sorted using GEO2R tool. Further, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed using Cluster Profiler in Rv. 3.6.1. Moreover, protein-protein interactions (PPI), module detection, and hub gene identification were accomplished and visualized through the Search Tool for the Retrieval of Interacting Genes, Molecular Complex Detection (MCODE) plug-in of Cytoscape v3.8.0. Further hub genes were imported into ToppGene webserver for pathway analysis and prognostic expression analysis was conducted using Gene Expression Profiling Interactive Analysis webserver. A total of 2221 DEGs, including 1286 up-regulated and 935down-regulated genes mainly enriched in signaling pathways of NOD-like receptor, FoxO, AMPK signalling and leishmaniasis. Three key modules were detected from PPI network using MCODE. Besides, top 20 high prioritized hub genes were selected. Further, prognostic expression analysis revealed ten of the hub genes, namely IL1B, CD44, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, MMP9, CREB1, STAT1, vascular endothelial growth factor (VEGFA), CDC5 L, Ataxia-telangiectasia mutated (ATM + and CDH1 to be differently expressed in normal and cancer patients. The present study proposed five novel therapeutic targets, i.e., ATM, GAPDH, CREB1, VEGFA, and CDH1 genes that might provide new insights into molecular oncogenesis of CRC.

Upregulation of ENKD1 disrupts cellular homeostasis to promote lymphoma development.

Diffuse large B cell lymphoma (DLBCL) is a common and aggressive form of B cell lymphoma. Approximately 40% of DLBCL patients are incurable despite modern therapeutic approaches. To explore the molecular mechanisms driving the growth and progression of DLBCL, we analyzed genes with differential expression in DLBCL using the Gene Expression Profiling Interactive Analysis database. Enkurin domain-containing protein 1 (ENKD1), a centrosomal protein-encoding gene, was found to be highly expressed in DLBCL samples compared with normal samples. The phylogenetic analysis revealed that ENKD1 is evolutionarily conserved. Depletion of ENKD1 in cultured DLBCL cells induced apoptosis, suppressed cell proliferation, and blocked cell cycle progression in the G2/M phase. Moreover, ENKD1 expression positively correlates with the expression levels of a number of cellular homeostatic regulators, including Sperm-associated antigen 5, a gene encoding an important mitotic regulator. These findings thus demonstrate a critical function for ENKD1 in regulating the cellular homeostasis and suggest a potential value of targeting ENKD1 for the treatment of DLBCL.

A comprehensive analysis of the expression and the prognosis for LOX-1 in multiple cancer types

ABSTRACT Lectin-likeoxidized low-density lipoprotein receptor (LOX-1) has been identified to beinvolved in the development of atherosclerosis. There is an increasing experimental evidence which indicated that LOX-1 was implicated in cancer tumorigenesis. However, the expression and the prognostic value of LOX-1 in multiple cancers still require the further analysis. Pubmed, Embase and the Cochrane Library were used for the literature review collection with the confined date up to 31 December 2021. Ten studies including 1982 patients were performed in meta-analysis according to the inclusion and exclusion criteria. Oncomine, Gene Expression Profiling Interactive Analysis(GEPIA), Kaplan-Meier plotter and Tumor Immune Estimation Resource (TIMER) were utilized to analyze the differential expression and the prognostic value of LOX-1 in different cancers. Records from Gene Expression Omnibus (GEO) database were applied for the verification test. The meta-pooled result demonstrated that elevated LOX-1 predicted a poor survival in some cancers (HR = 1.95, 95%CI 1.46–2.44, P < 0.001). In this sense, further analysis using databases found the expression of LOX-1 was higher in breast cancer, colorectal cancer, gastric cancer and pancreatic cancer while the lower expression in lung squamous cell carcinoma was observed. Moreover, the expression of LOX-1 was related to the tumor stages of colorectal cancer, gastric cancer and pancreatic cancer. The survival analysis revealed that LOX-1 was a potential prognostic factor for the patients with colorectal cancer, gastric cancer, pancreatic cancer and lung squamous cell carcinoma. Consequently, this study may provide a novel insight for the expression and the prognostic value of LOX-1 in specific cancers.

Clinicopathological and prognostic significance of SPARC expression in gastric cancer: A meta‑analysis and bioinformatics analysis.

Secreted protein acidic and rich in cysteine (SPARC) is a member of the extracellular matrix glycoprotein family that binds to calcium ions. It may bind to a variety of proteins in the extracellular matrix and also compete with cell membrane surface receptors for growth. In the present study, the relationship between SPARC expression in gastric cancer tissues and the clinicopathological characteristics and prognosis of patients with gastric cancer were systematically evaluated. A meta-analysis and bioinformatics analysis were performed using the PubMed, Chinese National Knowledge Infrastructure, Kaplan-Meier (KM)-plotter, The Cancer Genome Atlas (TCGA), Gene Expression Profiling Interactive Analysis (GEPIA), University of ALabama at Birmingham CANcer (UALCAN), Human Protein Atlas (HPA) and Timer databases. SPARC was mainly expressed in tumor mesenchymal cells. The meta-analysis indicated that SPARC expression was higher in gastric cancer tissues than in normal tissues. SPARC was associated with the degree of differentiation and distant metastasis. K-M plotter results indicated that high SPARC expression was negatively associated with overall survival, post-progression survival and progression-free survival rates of patients. According to the Oncomine, GEPIA, UALCAN and HPA databases, SPARC mRNA and protein expression was upregulated in gastric cancer vs. normal tissues and was negatively associated with poor patient prognosis. In the TCGA database, univariate analysis indicated that lymph node metastasis and distant metastasis were associated with the prognosis of patients with gastric cancer. Cox multifactorial analysis suggested that high SPARC expression, age and distant metastasis were important factors affecting the survival time of patients with gastric cancer. Analysis with the Timer database indicated that SPARC was closely associated with the proportion of 7 immune-cell infiltrates in gastric cancer. These findings indicated that high expression of SPARC may be a potential marker of tumorigenesis and metastasis in patients with gastric cancer.

Seven Immune-Related Genes' Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is a growing concern worldwide, due to its poor prognosis, low responsiveness to treatment, and drug resistance. Since immunotherapy effectively improves HNSCC patients' survival status, it is important to continuously explore new immune-related predictive factors to accurately predict the immune landscape and clinical outcomes of individuals suffering from HNSCC. The HNSCC transcriptome profiling of RNA-sequencing data was retrieved from TCGA database, and the microarray of GSE27020 was obtained from the GEO database for validation. The differentially expressed genes (DEGs) between HNSCC and normal samples were identified by multiple test corrections in TCGA database. The univariate and multivariate Cox analyses were performed to identify proper immune-related genes (IRGs) to construct a risk model. The Cox regression coefficient was employed for calculation of the risk score (RS) of IRG signature. The median value of RS was utilized as a basis to classify individuals with HNSCC into high- and low-risk groups. The Kaplan-Meier (K-M) survival analysis and receiver operating characteristic (ROC) curves were employed for the identification of the prognostic significance and precision of the IRG signature. The signature was also evaluated based on clinical variables, predictive nomogram, mutation analysis, infiltrating immune cells, immune-related pathways, and chemotherapeutic efficacy. The protein-protein interaction (PPI) network and functional enrichment pathway investigations were utilized to explore possible potential molecular mechanisms. Finally, the hub gene's differential mRNA expression levels were evaluated by means of the Gene Expression Profiling Interactive Analysis (GEPIA), and the Human Protein Atlas (HPA) was utilized for the validation of their translational levels. Collectively, 1593 DEGs between HNSCC and normal samples were identified, of which 136 IRGs were differentially expressed. Then, the 136 immune-related DEGs were mostly enriched in the cytokine-related signaling pathways by GO and KEGG analyses. After that, a valuable signature based on seven genes (DKK1, GAST, IGHM, IL12RB2, SLURP1, STC2, and TNFRSF4) was designed. The HNSCC patients into the low-risk group and the high-risk group were divided by using the median RS; the HNSCC patients in the high-risk group had a worse survival than those in the low-risk group. The risk signature was verified to be an independent predictive marker for HNSCC patients. Meanwhile, the RS had the largest contribution to survival of these patients based on the predictive nomogram. In addition, the low-risk HNSCC patients exhibited significantly enriched immune cells, along with an association with high chemosensitivity. The constructed gene signature can independently function as a predictive indicator for the clinical features of HNSCC patients. The low-risk HNSCC subjects might benefit from immunotherapy and chemotherapy.

RAD54L promotes progression of hepatocellular carcinoma via the homologous recombination repair pathway.

Hepatocellular carcinoma (HCC) is a malignant tumor with high incidence worldwide. The underlying mechanisms remain poorly understood. The DNA metabolic process of homologous recombination repair (HRR) has been linked to a high probability of tumorigenesis and drug resistance. This study aimed to determine the role of HRR in HCC and identify critical HRR-related genes that affect tumorigenesis and prognosis. A total of 613 tumor and 252 para-carcinoma tissue samples were collected from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) to obtain differentially expressed genes (DEGs). HRR-related genes were assessed using gene enrichment and pathway analyses. Survival analysis was performed using the Kaplan-Meier method in the Gene Expression Profiling Interactive Analysis portal. The levels of RAD54L in the HRR pathway were detected by RT-qPCR and western blotting in para-carcinoma and HCC tissues and in L02 normal human liver cells and Huh7 HCC cells. Immunohistochemistry (IHC) was performed on the clinical specimens to determine the connection between gene expression and clinical features. Bioinformatics analysis revealed that the HRR pathway was enriched in HCC tissues. Upregulation of HRR pathway DEGs in HCC tissues was positively correlated with tumor pathological staging and negatively associated with patient overall survival. RAD54B, RAD54L, and EME1 genes in the HRR pathway were screened as markers for predicting HCC prognosis. RT-qPCR identified RAD54L as the most significantly expressed of the three genes. Western blotting and IHC quantitative analyses further demonstrated that RAD54L protein levels were higher in HCC tissues. IHC analysis of 39 pairs of HCC and para-carcinoma tissue samples also revealed an association between RAD54L and Edmondson-Steiner grade and the proliferation-related gene Ki67. The collective findings positively correlate RAD54L in the HRR signaling pathway with HCC staging and implicate RAD54L as a marker to predict HCC progression.

Wiskott-Aldrich syndrome gene as a prognostic biomarker correlated with immune infiltrates in clear cell renal cell carcinoma.

The abnormal expression of the Wiskott-Aldrich syndrome protein (WASP) encoded by the Wiskott-Aldrich syndrome (WAS) gene has been implicated in tumor invasion and immune regulation. However, prognostic implications of WAS and its correlation tumor infiltrating in renal clear cell carcinoma (ccRCC) is not clear cut. The correlation between WAS expression, clinicopathological variables and clinical outcomes were evaluated using The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Tumor Immune Estimation Resource (TIMER), UALCAN, Gene Expression Profiling Interaction Analysis (GEPIA), Kaplan-Meier (KM) plotter and other databases. Furthermore, we assessed the transcription expression of WAS in renal cancer tissues, various renal carcinoma cell lines and human renal tubular cells (HK2) using quantitative polymerase chain reaction (qPCR). A comprehensive analysis of multiple databases including TIMER, GEPIA, TISIDB, ESTIMATE algorithm, and CIBERSORT algorithm were performed to determine the correlation between WAS and tumor infiltrating immune cells in ccRCC. The results displayed an increase in WAS mRNA level in ccRCC compared to normal tissue. WAS protein level was found highly expressed in cancer tissues, particularly within renal tumor cells via the human protein atlas (HPA). Interestingly, we found that elevated WAS expression was significantly positively correlated with the infiltration of CD8+ T cells, B cells, Monocytes, Neutrophils, Macrophages, T cell regulation, NK cells, and Dendritic cells in ccRCC. Bioinformatics demonstrated a strong correlation between WAS expression and 42 immune checkpoints, including the T cell exhaustion gene PD-1, which is critical for exploring immunotherapy for ccRCC. We revealed that patients with high WAS expression were less sensitive to immunotherapy medications. In conclusion, our study identified that WAS was a prognostic biomarker and correlated with immune infiltrates in ccRCC.

Aquaporin-4 as a New Potential Molecular Biomarker for Prognosis of Low-Grade Glioma: Comprehensive Analysis Based on Online Platforms

Aquaporin-4 (AQP4) is a significant factor in transcellular and transepithelial water movement, and abnormal expression of AQP4 has been detected in many types of tumors. The purpose of this study was to explore its role in low-grade gliomas (LGG) using freely available online bioinformatics tools. OncoLnc database was used to analyze Cox coefficients and compare AQP4 expression between various types of tumors; Tumor Immune Estimation Resource database and Gene Expression Profiling Interactive Analysis were used to compare gene expression between LGG and normal tissues; University of California Santa Cruz Xena browser generated Kaplan-Meier survival curves in the LGG cohort in The Cancer Genome Atlas and subgroups; LinkedOmics database screened the most relevant genes based on Pearson correlation coefficient; Gene Ontology Biological Process and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed through gene set enrichment analysis to explore possible molecular mechanisms. LGG had higher AQP4 expression compared with normal tissues and ranked first among 21 different types of cancer (P < 0.05). The oligodendroglioma group had the lowest AQP4 expression and the longest overall survival (OS) (P < 0.05). LGG with astrocytoma, isocitrate dehydrogenase mutation, or 1p/19q codeletion had lower AQP4 expression and longer OS (P < 0.001). LGG with lower AQP4 expression, without 1p/19q codeletion, without chemotherapy, and with or without radiation therapy had longer OS (P < 0.05). AQP4 and coexpressed genes were involved in complex biological processes in LGG, including regulation of neurotransmitter level, peroxisome proliferator-activated receptor signaling pathway, cell adhesion molecules, and others. AQP4 is a prognostic marker in LGG and its subgroups. Patients with lower AQP4 expression may have longer OS.

Abstract 534: PRMT5 inhibition as a therapeutic strategy for KRAS mutant CRC: downstream mediators of the PRMT5-KRAS crosstalk

Abstract Despite decades of research, there are still no effective targeted treatments for the nearly 45% of colorectal cancer (CRC) patients harboring a mutation in their KRAS gene. Protein Arginine Methyltransferase 5 (PRMT5) is an epigenetic regulator undergoing clinical trials as a potential therapeutic target for cancer. Our group has previously reported that PRMT5 is overexpressed in KRAS mutant CRC when compared to KRAS wild-type (WT) CRC, and that PRMT5 inhibition exhibited greater therapeutic efficacy in KRAS mutant CRC when compared to KRAS WT CRC. We therefore proposed that PRMT5 may be a strong therapeutic target for KRAS mutant CRC, and that PRMT5 and KRAS may crosstalk. In this study, we investigated several key downstream signal transduction proteins that may be involved in mediating the potential crosstalk between PRMT5 and KRAS. This is important, as these key intermediate proteins may be strong therapeutic targets for inhibition, as well as valuable therapeutic targets for combination therapy along with PRMT5 inhibitors. We first conducted a literature review to determine which key downstream proteins may be involved in mediating the potential crosstalk between PRMT5 and KRAS. Our initial findings indicated that MYC, p65/RELA, TP53, P21/CDKN1A, ELF1, E2F1, and EIF4E may be key downstream proteins involved in mediating the potential crosstalk between PRMT5 and KRAS. We next used the STRING database to determine which of the aforementioned proteins have demonstrated interactions with PRMT5 and KRAS. We found that PRMT5 and KRAS both interact with MYC, p65/RELA, TP53, P21/CDKN1A, E2F1, and EIF4E with an interaction score &amp;gt; 0.150. We then used the Gene Expression Profiling Interactive Analysis (GEPIA) database to analyze the RNA-Seq data of CRC patients from The Cancer Genome Atlas (TCGA) database. We first used the GEPIA database to determine which proteins are overexpressed in CRC patient tumor samples compared to normal colon and rectum patient samples. We observed that MYC, TP53, E2F1, and EIF4E are all over 2-fold overexpressed in CRC patient tumor samples compared to normal colon and rectum patient samples (q &amp;lt; 0.01). We next used the GEPIA database to determine which proteins have an expressional correlation with PRMT5 and KRAS in CRC patient tumor samples. We found that MYC, E2F1, and EIF4E are all positively correlated with PRMT5 and KRAS with an R-Value &amp;gt; 0.70 and a P-Value &amp;lt; 0.01 in CRC patient tumor samples. Our study thus showcases the key downstream signal transduction proteins that may be involved in mediating the potential crosstalk between PRMT5 and KRAS. These findings are significant, as these key intermediate proteins may be strong therapeutic targets for inhibition, as well as strong therapeutic targets for a PRMT5 combination therapy. Additional research is currently underway to outline the molecular processes behind MYC, E2F1, and EIF4E’s interactions with both PRMT5 and KRAS. Citation Format: David Shifteh, Tzuriel Sapir, Moshe Pahmer, Sanjay Goel, Radhashree Maitra. PRMT5 inhibition as a therapeutic strategy for KRAS mutant CRC: downstream mediators of the PRMT5-KRAS crosstalk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 534.

Abstract 4914: Role of ClpP in the anti-cancer effects of imipridone ONC201 and ONC206

Abstract ONC201 is the first bitopic dopamine receptor D2 (DRD2) antagonist and allosteric mitochondrial protease ClpP agonist. Downstream of target engagement, ONC201 activates the integrated stress response pathway resulting in selective tumor cell death. ONC201 is well tolerated and induces durable tumor regressions in H3 K27M-mutant glioma patients. ONC206, a derivative of ONC201 currently in Phase I trials for adult and pediatric brain tumors, is also a bitopic DRD2 antagonist and ClpP agonist with nanomolar potency. We further evaluated in vitro efficacy and mechanism of action specific to ClpP for ONC206 and investigated acquired resistance to ONC201 and ONC206. FITC-casein and peptide degradation assays confirmed that ONC206 acts as an agonist of human ClpP with enhanced potency relative to ONC201. Broad efficacy in the nanomolar range for ONC206 (GI50 &amp;lt;78-889nM, 72h) was observed in 1,088 Genomics of Drug Sensitivity in Cancer (GDSC) cancer cell lines with increased sensitivity in cell lines exhibiting high ClpP mRNA expression. Among solid tumors, nervous system-related cell lines were particularly sensitive. Gene Expression Profiling Interactive Analysis (GEPIA) database analysis showed ClpP mRNA was overexpressed in glioblastoma cells relative to normal cells. GDSC observations were confirmed in glioblastoma (GBM) (T98G, A172, U87MG), H3.3 K27M mutant diffuse intrinsic pontine glioma (DIPG) (SF8628, SF7761) and astrocytoma (H4, U118MG) cell lines. ONC206 was more potent than ONC201 in cell viability assays for all glioma lines tested. SF8628 cells with a CRISPR-mediated ClpP knockout were shown to demonstrate resistance to both ONC201 and ONC206. Polyclonal resistant cell lines were generated through prolonged passaging in increasing concentrations of ONC201 or ONC206 (SF8628 and T98G cells). Cells with acquired resistance to ONC201 (ONC201Res) or ONC206 (ONC206Res) showed cross resistance to both imipridones. Time-stability of resistance was confirmed by removing drug for 2 to 4 weeks and retesting. RNAseq analysis revealed upregulation of the integrated stress response with imipridone treatment in T98G parental cells but not resistant clones. Whole genome sequencing revealed ClpP mutations in both ONC201Res and ONC206Res cells. Our results confirm the role of ClpP in the mechanism of action of ONC201 and ONC206 in tumor cells. Citation Format: Andrew Lee, Cristina Maranto, Scott Foster, Sara Morrow, Joshua E. Allen, Randall Lanier, Phiroze Sethna, Varun V. Prabhu. Role of ClpP in the anti-cancer effects of imipridone ONC201 and ONC206. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4914.

HP1α promotes the progression of prostate cancer.

Patients who have been diagnosed with prostate cancer (PCa) typically have a dismal outlook and few therapeutic choices available to them, because the precise pathogenesis of the disease is not yet fully understood. The presence of HP1α, also known as the heterochromatin protein 1α, is required for the creation of higher-order chromatin structures. However, little is known about HP1α that serves roles in the pathogenesis of PCa. The primary purpose of our research was to investigate alterations in the levels of HP1α expression and to plan a series of tests to validate the function of HP1α in PCa. Information on HP1α expression in PCa and benign prostatic hyperplasia (BPH) tissues were gathered using the Cancer Genome Atlas (TCGA) and Gene Expression Profiling Interactive Analysis (GEPIA) databases. RT-qPCR, western blotting, and immunohistochemistry (IHC) were used to assess HP1α mRNA and protein expression in several human PCa tissues and cell lines. The CCK8 assay, clone formation assay, and transwell assay were used to examine biological activities including cell proliferation, migration, and invasion. The expression of proteins connected to apoptosis and the epithelial-mesenchymal transition (EMT) was examined using Western blot. The tumorigenic effect of HP1α was also verified by in vivo experiments. HP1α expression was much higher in PCa than in BPH tissues and cells, and was positively correlated with the Gleason score of PCa. In vitro experiments showed that HP1α knockdown could inhibit the ability of proliferation, invasion, and migration of PC3 and LNCaP cells, and promote cell apoptosis and EMT. In vivo experiments showed that HP1α knockdown inhibited tumorigenesis in mice. Our findings indicate that HP1α expression promotes PCa development and might be a novel therapeutic target for the diagnosis or treatment of PCa.

Abstract 1406: Long non-coding RNA DUXAP10 is a putative determinant of anaplastic thyroid cancer

Abstract Anaplastic Thyroid Cancer (ATC) is one of the most aggressive forms of cancer, with only a 4% survival rate with metastatic disease. ATC is highly refractory and resistant to both traditional therapeutic modalities and recently discovered small molecule inhibitors. The elucidation of molecular mechanisms that contribute to ATC’s metastatic propensity, and the identification of molecular biomarkers for early diagnosis, prognosis, and therapeutic intervention are critical unmet clinical needs-highlighting the importance of novel avenues of intervention. Recently, long non-coding RNAs (lncRNA) have been described as regulators of gene expression and cancer cell phenotypes, exhibiting the importance of identifying non-coding profiles that potentially impact ATC behavior. Publicly available datasets provided by Gene Expression Omnibus (GSE33630, GSE85457) enabled investigation of gene expression profiles of ATC vs. normal thyroid patient tissue. Bioinformatic analyses with the GEO2R program identified the lncRNA, Double Homeobox A Pseudogene 10 (DUXAP10), to be highly upregulated in ATC patient-derived tissue samples when compared to normal thyroid tissue by about 5logFC. Analysis using Gene Expression Profiling Interactive Analysis shows that high DUXAP10 expression is correlated with decreased survival in thyroid cancer patients. To recapitulate this patient data in an in vitro model, we found that the expression of DUXAP10 is also upregulated in the ATC cell line, T238, in comparison to Nthy-ori-3-1, an immortalized “normal” thyroid cell line. To understand the consequences of DUXAP10 overexpression in ATC, we used CRISPRi technology to determine the phenotypic and genotypic effects of DUXAP10 downregulation. CRISPRi knockdown of DUXAP10 significantly reduces the migratory capabilities of T238 by 50%, invasiveness by 37%, clonogenicity by 70%, cell size by 34%, and proliferation by 28%, 45%, and 36% at 24, 48, and 72 hours, respectively. This provides evidence that elevated DUXAP10 expression may increase the probability and negative consequences of metastases. Thus, targeting DUXAP10 expression may have beneficial clinical outcomes. Identification of the molecular innervations of DUXAP10 that orchestrate these pro-metastatic phenotypic changes are currently in progress. Immediate next steps are aimed toward determining if DUXAP10 can be utilized as a potential biomarker for ATC diagnosis and prognosis, as well as elucidating the full range of interactions that DUXAP10 has in shaping the ATC phenotype. Citation Format: Nicole R. DeSouza, Michelle Carnazza, Danielle Quaranto, Tara Jarboe, Kaci Kopec, Sarnath Singh, Augustine Moscatello, Jan Geliebter, Raj K. Tiwari. Long non-coding RNA DUXAP10 is a putative determinant of anaplastic thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1406.