Gene Expression Profiling Interactive Analysis Research Articles

Multi‑dimensional analysis reveals NCKAP5L is a promising biomarker for the diagnosis and prognosis of human cancers, especially colorectal cancer.

The Nck-associated protein 5-like (NCKAP5L) gene, also known as Cep169, is associated with certain cancers. However, the diagnosis and prognosis value of NCKAP5L in several types of human cancer, including colorectal cancer, is not fully understood. In the present study, a comprehensive pan-cancer analysis of NCKAP5L was performed using several approaches, including gene expression and alteration, protein phosphorylation, immune infiltration, survival prognosis analyses and gene enrichment using the following: The University of California Santa Cruz Genome Browser Human Dec. 2013 (GRCh38/hg38) Assembly, Tumor Immune Estimation Resource (version 2), Human Protein Atlas, Gene Expression Profiling Interactive Analysis (version 2), University of Alabama at Birmingham Cancer Data Analysis portal, the Kaplan-Meier Plotter, cBioportal, Search Tool for the Retrieval of Interacting Genes/Proteins, Jvenn and the Metascape server. The role of NCKAP5L in colorectal cancer was further assessed by reverse transcription-quantitative PCR. The results demonstrated that NCKAP5L was upregulated in the majority of cancer types, including colorectal cancer. The high expression of NCKAP5L was significantly correlated with patient survival prognosis and immune infiltration of cancer-associated fibroblasts in numerous types of cancer, including colorectal cancer. Furthermore, Gene Ontology analysis identified that NCKAP5L may serve an important role in metabolic and cellular processes in human cancers. In summary, the data from the present study demonstrate that NCKAP5L is a potential tumor biomarker for the diagnosis and prognosis of human cancers, especially colorectal cancer.

NDUFA8 is transcriptionally regulated by EP300/H3K27ac and promotes mitochondrial respiration to support proliferation and inhibit apoptosis in cervical cancer

Cervical cancer, a common malignancy in women, poses a significant health burden worldwide. In this study, we aimed to investigate the expression, function, and potential mechanisms of NADH: ubiquinone oxidoreductase subunit A8 (NDUFA8) in cervical cancer. The Gene Expression Profiling Interactive Analysis (GEPIA) database and immunohistochemical scoring were used to analyze NDUFA8 expression in cervical cancer tissues and normal tissues. Quantitative real-time PCR and Western blot analyses were performed to assess the expression level of NDUFA8 in cervical cancer cell lines. NDUFA8 knockdown or overexpression experiments were conducted to evaluate its impact on cell proliferation and apoptosis. The mitochondrial respiratory status was analyzed by measuring cellular oxygen consumption, adenosine triphosphate (ATP) levels, and the expression levels of Mitochondrial Complex I activity, and Mitochondrial Complex IV-associated proteins Cytochrome C Oxidase Subunit 5B (COX5B) and COX6C. NDUFA8 exhibited high expression levels in cervical cancer tissues, and these levels were correlated with reduced survival rates. A significant upregulation of NDUFA8 expression was observed in cervical cancer cell lines compared to normal cells. Silencing NDUFA8 hindered cell proliferation, promoted apoptosis, and concurrently suppressed cellular mitochondrial respiration, resulting in decreased levels of available ATP. Conversely, NDUFA8 overexpression induced the opposite effects. Herein, we also found that E1A Binding Protein P300 (EP300) overexpression facilitated Histone H3 Lysine 27 (H3K27) acetylation enrichment, enhancing the activity of the NDUFA8 promoter region. NDUFA8, which is highly expressed in cervical cancer, is regulated by transcriptional control via EP300/H3K27 acetylation. By promoting mitochondrial respiration, NDUFA8 contributes to cervical cancer cell proliferation and apoptosis. These findings provide novel insights into NDUFA8 as a therapeutic target in cervical cancer.

Unraveling dedifferentiation and metastasis traces in pancreatic ductal adenocarcinoma ductal cells: Insights from single-cell RNA sequencing analysis of ITGB4 and C19orf33

Pancreatic Ductal Adenocarcinoma (PDAC) ranks among the most prevalent gastrointestinal malignancies, with risk factors including smoking, alcohol abuse, diabetes mellitus, obesity, age, family history, and genetic predisposition. Extensive research has focused on unraveling biomarkers and molecular intricacies associated with PDAC. Leveraging data from the Gene Expression Omnibus microarray and single-cell RNA sequencing datasets, our study identified ITGB4 and C19orf33 as potentially differentially expressed genes in PDAC samples when contrasted with non-malignant tissues. Notably, these genes exhibited a strong correlative expression pattern, primarily within ductal cells. Gene Expression Profiling Interactive Analysis corroborated our findings, further confirming the correlation between ITGB4 and C19orf33. Additionally, we conducted experiments involving two pivotal PDAC-related cell lines, MIA PaCa-2 and PANC-1, treated with oxaliplatin and 5-Fluorouracil. We also assessed the expression of these candidate genes in PDAC samples in comparison to adjacent normal tissues. Our findings revealed that C19orf33 is upregulated in PDAC samples, and treatment of PDAC cells with chemotherapeutic agents led to a correlated decrease in the expression of both ITGB4 and C19orf33. These co-expressed and correlated genes are implicated in relevant signaling pathways, suggesting shared biological activities that may contribute to the promotion of metastasis within malignant ductal cells. This study identifies ITGB4 and C19orf33 as key genes potentially shedding light on the molecular mechanisms driving tumorigenesis and metastasis in PDAC. These genes hold promise as potential diagnostic and therapeutic targets, offering valuable insights into the management of this challenging disease.

Comprehensive analysis and immunohistochemistry localization of NRP1 expression in pancancer and normal individual tissues in relation to SARS‑CoV‑2 susceptibility.

Neuropilin 1 (NRP1/CD304) is a typical membrane-bound co-receptor for vascular endothelial growth factor, semaphorin family members and viral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, NRP1 expression levels across cancer types and the potential role of SARS-CoV-2 infection in patients with cancer are not clear. Online databases, such as The Cancer Genome Atlas database of Human Protein Atlas, Gene Expression Profiling Interactive Analysis and cBioPortal were used for the expression analysis in this study. Immunohistochemical (IHC) staining for NRP1 was performed in the tissues of patients with non-small cell carcinoma. As a result, it was found that NRP1 mRNA and protein expression levels were highest in the female reproductive tissues and the respiratory system, specifically in the nasopharynx, bronchus and fallopian tube, as well as in adipocytes, hepatic stellate cells, Sertoli cells, endothelial cells and dendritic cells. IHC showed that the NRP1 protein was mainly localized to the cytoplasm and membrane in the tissues of patients with non-small cell carcinoma, demonstrating its role in lung infection by SARS-CoV-2, due to invasion of cell membranes by the virus. Levels of NRP1 mRNA were significantly increased in lymphoid neoplasm diffuse large B-cell lymphoma, esophageal carcinoma, glioblastoma multiforme, head and neck squamous cell carcinoma, kidney renal clear cell carcinoma (KIRC), pancreatic adenocarcinoma, stomach adenocarcinoma and thymoma, and significantly decreased in cervical squamous cell carcinoma and endocervical adenocarcinoma, kidney chromophobe, lung squamous cell carcinoma, ovarian serous cystadenocarcinoma, uterine corpus endometrial carcinoma and uterine carcinosarcoma, compared with corresponding healthy tissues in pancancer, indicating roles for viral invasion in most cancer types. Moreover, low NRP1 expression was significantly associated with long overall survival (OS) time in adrenocortical carcinoma, brain lower grade glioma, stomach adenocarcinoma and uveal melanoma, but with short OS time in KIRC only. The ENST00000374867.6 (NRP1-202) isoform is most highly expressed in most cancer types and thus could be involved in tumorigenesis and SARS-CoV-2 invasion in cancer patients. NRP1 may be involved in SARS-CoV-2 invasion in patients with cancer, including those with lung cancer.

Identification of the function of FOSB in cholangiocarcinoma using bioinformatics analysis.

Exploring the potential mechanism of cholangiocarcinoma (CCA) metabolic reprogramming is significant for guiding clinical treatment. However, related research and exploration are still lacking. Therefore, we aimed to identify a reliable metabolism-related gene or biomarker of CCA using bioinformatics analysis. The GSE26566, GSE45001, and GSE132305 datasets were obtained from the Gene Expression Omnibus (GEO) database. Differently expressed genes (DEGs) between CCA tissues and adjacent tissues were screened out. The key gene was identified through enrichment and functional analysis, and its immune and clinical correlation was investigated utilizing the Tumor Immune Evaluation Resource (TIMER2.0), the Tumor-Immune System Interactions Database (TISIDB), the Gene Expression Profiling Interactive Analysis (GEPIA2), and the Kaplan-Meier Plotter. Finally, immunohistochemistry (IHC) was performed to validate the results. By analysis, the expression of FBJ murine osteosarcoma viral oncogene homolog B (FOSB) was significantly downregulated in CCA tissues when compared with adjacent tissues. Moreover, the expression levels of FOSB positively correlated with tumor-infiltrating immune cells in most tumors, and patients with high FOSB expression tended to have a better prognosis. The FOSB and SIRT3/HIF1A axes have similar expression trends and metabolic functions in CCA cells, and the correlation between of them was preliminarily explored by IHC experiments. The expression levels of FOSB are closely related to the prognosis of CCA patients, which may be a predictive indicator for prognosis and immunotherapy.

Spleen-Derived CCL9 Recruits MDSC to Facilitate Tumor Growth in Orthotopic Hepatoma Mice.

Objectives Spleen is involved in multiple diseases, the role of the spleen and spleen-derived factors in hepatocellular carcinoma (HCC) is still not clarified. Methods In the current study, a murine H22 orthotopic hepatoma model was established. Three groups were divided: normal mice, tumor-bearing mice with spleen-preserving, and tumor-bearing mice with splenectomy. Spleen and tumor weights were recorded by weeks 1 and 2. The proportion of myeloid-derived suppressor cell (MDSC) in peripheral blood and tumor tissue was detected using flow cytometry. Protein chip assay was used to compare the differential cytokines between normal liver supernatant and tumor supernatant. The common upregulated cytokines both in spleen and tumor were focused and analyzed using gene expression profiling interactive analysis (GEPIA) database. Enzyme-linked immunosorbent assay was performed to verify the chip result, and to examine CCL9 expression before and after splenectomy. Spleen MDSC was sorted using flow cytometry, and chemotaxis assay was performed to demonstrate whether CCL9 attracted spleen MDSC. Results The spleen enlarged during tumor progression, and compared with splenectomy group, there were faster tumor growth, shorter survival time, and higher proportions of MDSC in spleen-preserving group. Protein chip assay and GEPIA database revealed CCL9 was the most promising chemokine involved in HCC upregulated both in spleen and tumor tissue. CCL9 attracted MDSC in vitro, the level of CCL9 in tumor tissue was downregulated, and the percentage of MDSC was decreased after splenectomy. Conclusion The results demonstrate that CCL9 may be derived from spleen; it facilitated HCC growth via the chemotaxis of MDSC, targeting CCL9 may be a promising strategy in HCC treatment.

Upregulated PARP1 confers breast cancer resistance to CDK4/6 inhibitors via YB-1 phosphorylation

BackgroundCyclic-dependent kinase (CDK) 4/6 kinases, as the critical drivers of the cell cycle, are involved in the tumor progression of various malignancies. Pharmacologic inhibitors of CDK4/6 have shown significant clinical prospects in treating hormone receptor-positive and human epidermal growth factor receptor-negative (HR + /HER2-) breast cancer (BC) patients. However, acquired resistance to CDK4/6 inhibitors (CDK4/6i), as a common issue, has developed rapidly. It is of great significance that the identification of novel therapeutic targets facilitates overcoming the CDK4/6i resistance. PARP1, an amplified gene for CDK4/6i-resistant patients, was found to be significantly upregulated during the construction of CDK4/6i-resistant strains. Whether PARP1 drives CDK4/6i resistance in breast cancer is worth further study.MethodPARP1 and p-YB-1 protein levels in breast cancer cells and tissues were quantified using Western blot (WB) analysis, immunohistochemical staining (IHC) and immunofluorescence (IF) assays. Bioinformatics analyses of Gene Expression Profiling Interactive Analysis (GEPIA), Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE) datasets were applied to explore the relationship between YB-1/PARP1 protein levels and CDK4/6i IC50. Cell Counting Kit-8 (CCK-8) and crystal violet staining assays were performed to evaluate cell proliferation rates and drug killing effects. Flow cytometry assays were conducted to assess apoptosis rates and the G1/S ratio in the cell cycle. An EdU proliferation assay was used to detect the DNA replication ratio after treatment with PARP1 and YB-1 inhibitors. A ChIP assay was performed to assess the interaction of the transcription factor YB-1 and associated DNA regions. A double fluorescein reporter gene assay was designed to assess the influence of WT/S102A/S102E YB-1 on the promoter region of PARP1. Subcutaneous implantation models were applied for in vivo tumor growth evaluations.ResultsHere, we reported that PARP1 was amplified in breast cancer cells and CDK4/6i-resistant patients, and knockdown or inhibition of PARP1 reversed drug resistance in cell experiments and animal models. In addition, upregulation of transcription factor YB-1 also occurred in CDK4/6i-resistant breast cancer, and YB-1 inhibition can regulate PARP1 expression. p-YB-1 and PARP1 were upregulated when treated with CDK4/6i based on the WB and IF results, and elevated PARP1 and p-YB-1 were almost simultaneously observed during the construction of MCF7AR-resistant strains. Inhibition of YB-1 or PAPR1 can cause decreased DNA replication, G1/S cycle arrest, and increased apoptosis. We initially confirmed that YB-1 can bind to the promoter region of PARP1 through a ChIP assay. Furthermore, we found that YB-1 phosphorylated at S102 was crucial for PARP1 transcription according to the double fluorescein reporter gene assay. The combination therapy of YB-1 inhibitors and CDK4/6i exerted a synergistic antitumor effect in vitro and in vivo. The clinical data suggested that HR + /HER2- patients with low expression of p-YB-1/PARP1 may be sensitive to CDK4/6i in breast cancer.ConclusionThese findings indicated that a ‘‘YB-1/PARP1’’ loop conferred resistance to CDK4/6 inhibitors. Furthermore, interrupting the loop can enhance tumor killing in the xenograft tumor model, which provides a promising strategy against drug resistance in breast cancer.

Value of TMEM115 as a Potential Prognostic Biomarker in Liver Hepatocellular Carcinoma

Transmembrane protein 115 (TMEM115) is a membrane protein; considering the potential of membrane proteins as biomarkers for various pathological conditions, we aimed to examine the value of TMEM115 as a potential biomarker for improving the prognosis and treatment of liver hepatocellular carcinoma (LIHC) in this study. Online databases including the Tumor Immune Estimation Resource, UALCAN, Gene Expression Profiling Interactive Analysis version 2, OSlihc, and human Protein Atlas were used. The analysis suggested that TMEM115 expression in LIHC was higher compared to normal tissues; further, TMEM115 expression was confirmed to be related with poor prognosis in LIHC. Higher protein expression levels of TMEM115 were observed in LIHC tissues than in normal tissues. Tumor infiltration by immune cells was confirmed to be correlated with the expression of TMEM115. High TMEM115 expression and immune cell infiltration were further related to poor prognosis in LIHC. We also confirmed a correlation between TMEM115 and TP53 mutations. In conclusion, we confirmed that TMEM115 expression is correlated with tumor-infiltrating immune cells and poor prognosis in LIHC and that TMEM115 shows potential as a prognostic biomarker in LIHC.

Impact of curcumin on ferroptosis-related genes in colorectal cancer: Insights from in-silico and in-vitro studies.

Colorectal cancer (CRC)is responsible for a significant number of cancer-related fatalities worldwide. Researchers are investigating the therapeutic potential of ferroptosis, a type of iron-dependent controlled cell death, in the context of CRC. Curcumin, a natural compound found in turmeric, exhibits anticancer properties. This study explores the effects of curcumin on genes related to ferroptosis (FRGs)in CRC. To gather CRC data, we used the Gene Expression Profiling Interactive Analysis (GEPIA)and Gene Expression Omnibus (GEO)databases, while FRGs were obtained from the FerrDb database and PubMed. We identified 739 CRC differentially expressed genes (DEGs)in CRC and discovered 39 genes that were common genes between FRGs and CRC DEGs. The DEGs related to ferroptosis were enriched with various biological processes and molecular functions, including the regulation of signal transduction and glucose metabolism. Using the Drug Gene Interaction Database (DGIdb),we predicted drugs targeting CRC-DEGsand identified 17 potential drug targets. Additionally, we identified eight essential proteins related to ferroptosis in CRC, including MYC, IL1B, and SLC1A5. Survival analysis revealed that alterations in gene expression of CDC25A, DDR2, FABP4, IL1B, SNCA, and TFAM were associated with prognosis in CRC patients. In SW480 human CRC cells, treatment with curcumin decreased the expression of MYC, IL1B, and EZH2 mRNA, while simultaneously increasing the expression of SLCA5 and CAV1. The findings of this study suggest that curcumin could regulate FRGs in CRC and have the potential to be utilized as a therapeutic agent for treating CRC.

Casein Kinase II Inhibitor Sensitizes the Anti-Tumor Effect of EZH2 Inhibitor By Suppressing FOSL1 Expression in Acute Myeloid Leukemia

Background More effective combination therapy is emerging needed owing to the high mortality and poor outcome in acute myeloid leukemia (AML). The genomic amplification and overexpression of Enhancer of zeste homolog 2 (EZH2) occur in AML patients, and high expression of the Casein kinase 2 (CK2) is associated with poor survival in AML patients. Both EZH2 inhibitor and CK2 inhibitors are reported to inhibit cell proliferation and induce apoptosis in AML, however, the anti-leukemia effect of EZH2 inhibitor in combination with CK2 inhibitor has not been reported. The present study aims to investigate the effect of the combination of the EZH2 inhibitor DZNeP with CK2 inhibitor CX4945 in AML and possible underlying mechanisms. Methods A total of 40 newly diagnosed AML patients and 40 bone marrow control from healthy donors were obtained from our institute with the approval of the Ethics Committee. Cell Counting Kit-8 assay (CCK8), Cell cycle assay, and apoptosis assays were applied in THP-1 AML cells treated with control, DZNeP, CX4945, and CX4945+DZNeP. Global transcriptome analysis by RNA-seq was performed in U937 cells treated with 2μM DZNeP; 12.5μM CX4945 or vehicle for 48 hours. FOSL1 mRNA level was examined by qPCR; R2 genomics analysis and visualization application were used for comparison of the expression difference and the Kaplan-Meier overall survival analysis was conducted by the Gene Expression Profiling Interactive Analysis (GEPIA) platform. Results DZNeP only has little effect on cell proliferation arrest in THP-1 cells, but it significantly sensitized the effect of CX4945, and CalcuSyn analysis showed the synergistic effect of the CX4945+DZNeP (Fig.1A). The treatment of CX4945+DZNeP combination induced the G0/G1 phase arrest in THP-1 cells versus single-drug control (Fig. 1B). The combination also significantly increased the % of the apoptotic cells in THP-1 cells as well as the AML-5b primary cells from the patient compared to single-drug controls (p<0.0001) (Fig.1C). These data indicate the synergistic anti-tumor effect of CX4945+DZNep combination in AML. To understand the molecular mechanism underlying the synergy, the global transcriptome was identified in U937 cells. The significantly different expression genes (DEGs) were identified upon CX4945 treatment (∣log2FC∣>1.5, FDR<0.05), or DZNeP treatment (∣log2FC∣>1.0, FDR<0.05) versus vehicle-control; and 1908 overlapped DEGs are identified upon either drug treatment, in which 596 were intersected (429 genes changed in the same direction but 167 changed in the opposite (Fig. 1D). KEGG enrichment analyses showed the overlapped DEGs upon the drug treatment mainly involved in cell cycle, DNA replication, and MAPK signaling pathway. (Fig.1E). It is worth noting that FOSL1 is dramatically downregulated in U937 cells upon treatment of either DZNeP or CX4945 (Fig1.D); and qPCR data showed that the mRNA level of FOSL1 is significantly downregulated by CX4945+DZNeP, DZNeP or CX4945 compared to the vehicle control (p<0.0001) in THP-1 cells (Fig. 1F). These data indicated that the combination exerts its anti-tumor effect by down-regulation of FOSL1 expression in AML. FOSL1 is a key component of the AP-1 transcriptional complex, and overexpression of FOSL1 is associated with invasion, migration, proliferation, and stemness in human solid cancers. We also examined the FOSL1 mRNA level in 40 newly diagnosed patients with AML versus 40 normal bone marrow controls. Results showed the mRNA level of FOSL1 is significantly higher in AML patients than that of normal controls (p<0.001) (Fig1.G). Metadata analysis showed that FOSL1 high expression is associated with short overall survival (p=0.033) (Fig.1H). These results not only suggested the oncogenic role of FOSL1 in AML but also further supported the CX4945+DZNeP combination-induced anti-tumor effect mediated by suppressing FOSL1 expression in AML. The mechanism model is summarized in Fig. 1E. Conclusion The combination of EZH2 inhibitor DZNeP and CK2 inhibitor CX4945 exerts a potent synergistic effect on proliferation arrest, cell cycle arrest, and apoptosis in AML by suppressing FOSL1 expression. Our results reveal the oncogenic role of FOSL1 in AML. Our data also provide experimental hints for the potential clinical trial of the novel combination in AML patients.

The New Role of HNF1A-NAS1/miR-214/INHBA Signaling Axis in Colorectal Cancer.

Colorectal cancer (CRC) is the third most common cancer and one of the leading causes of death worldwide. Seriously threatens human life and health. Previous studies have identified that inhibin βA (INHBA) could induce tumorgenesis and progression of CRC through the regulation of the TGF-β/Smad signal axis. The abnormal expression of INHBA is related to the poor prognosis of patients. The aim of this study was to identify the molecular mechanism of HNF1A-AS1 and miR-214 regulating INHBA and carcinogenesis through bioinformatics combined with experiments. The expression of HNF1A-AS1, miRNA-214-5p, INHBA in pan-cancer and CRC were investigated in the Cancer Genome Atlas (TCGA). The correlation between HNF1A-AS1 and immune-related genes or miRNAs was explored via the Gene Expression Profiling Interactive Analysis (GEPIA) and volcano plots, respectively. The association between HNF1A-AS1 and differentially expressed miRNAs was constructed by TargetScan. The miRDB, miRWalk, and TargetScan databases were utilized to predict the target genes of hsa-miR-214. The expression of INHBA in tissues and cell lines of CRC was examined by RT-qPCR and western blot assay. The INHBA and HNF1A-AS1 expressions were increased in Colon adenocarcinoma (COAD) and Rectum adenocarcinoma (READ) of the TCGA database. Hsa-miR-214 was relatively less expressed in CRC tissues compared with para-cancer tissues. The expression of HNF1A-AS1 was negatively correlated with hsa-miR-214. INHBA was one of the target genes of hsa-miR-214 based on miRDB, miRWalk, and TargetScan databases. The specific binding sites of INHBA-3'UTR and miR-214-5p were identified by starBase. The expression level of INHBA was positively correlated with the T stage of tumor and negatively correlated with overall survival (OS) and disease-free survival (DFS) in CRC patients. The results of RT-qPCR and western blot indicated that the expression of INHBA in tissues and cell lines in CRC was higher than those in para-carcinoma tissues and normal colon cell lines, respectively. These findings suggested that HNF1A-AS1 and miRNA-214-5p were key upstream non-coding RNAs of INHBA. The HNF1A-AS1/miR-214/INHBA signal axis plays a significant role in the tumorgenesis and progression of CRC. By interfering with HNF1A-AS1 and INHBA genes on HT29 and SW480 cells, it was found that HNF1A-AS1 and INHBA genes may be important target genes in CRC.

A pan-cancer analysis of the role of argininosuccinate synthase 1 in human tumors.

There is accumulating evidence indicating that ASS1 is closely related to tumors. No pan-cancer analysis of ASS1 was available. Here we explored the gene expression and survival analysis of ASS1 across thirty-three tumors based on the datasets of the TCGA (Cancer Genome Atlas), the GEO (Gene Expression Omnibus), and the GEPIA2 (Gene Expression Profiling Interactive Analysis, version 2). ASS1 is highly expressed in most normal tissues and is related to the progression of some tumors. We also report ASS1 genetic alteration and their association with tumor prognosis and report differences in ASS1 phosphorylation sites between tumors and control normal tissues. ASS1 expression was associated with the infiltration of cancer-associated fibroblasts (CAFs) for the TCGA tumors of BRCA (Breast invasive carcinoma), CESC (Cervical squamous cell carcinoma and endocervical adenocarcinoma), COAD (Colon adenocarcinoma), ESCA (Esophageal carcinoma), SKCM (Skin cutaneous melanoma), SKCM-Metastasis, TGCT (Testicular germ cell tumors), and endothelial cell for the tumors of BRCA, BRCA-Basal, CESC, ESCA, KIRC (Kidney renal clear cell carcinoma), LUAD (Lung adenocarcinoma), LUSC (Lung squamous cell carcinoma), SKCM, SKCM-Metastasis, SKCM-Primary, STAD (Stomach adenocarcinoma), and TGCT. The KEGG and GO analysis were used to analyze ASS1-related signaling pathways. Finally, we used Huh7 cell line to verify the function of ASS1 in vitro. After ASS1 knockdown using small interfering RNA (siRNA), the proliferation and invasion of Huh7 were enhanced, cyclin D1 was up-regulated, and anti-apoptotic protein bax was down-regulated, suggesting that ASS1 is a tumor suppressor gene in hepatocellular carcinoma. Our first pan-cancer study offers a relatively comprehensive understanding of the roles of ASS1 in different tumors.

Cancer-associated fibroblast-associated gene IGFBP2 promotes glioma progression through induction of M2 macrophage polarization.

We elucidated the molecular mechanism of cancer-associated fibroblast (CAF)-associated gene insulin-like growth factor binding protein-2 (IGFBP2)-induced M2 macrophage polarization in the tumor microenvironment involved in glioma progression. The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) provided bulk RNA-sequencing datasets, ESTIMATE scores for glioma stromal cells, and overall survival-clinicopathological correlation analyses. TIMER provided CAF abundance in the TCGA glioma-related dataset, differential gene analysis was performed for high- and low-CAF groups, and weighted gene coexpression network analysis identified CAF-related genes. Univariate and multifactorial cyclooxygenase (COX) regression analyses created the CAF risk models single sample gene set enrichment analysis, CIBERSORT, and GSE84465. Mice were implanted with gliomas, and Western blot and RT-quantitative PCR showed IGFBP2 in tumor tissues. Adeno-associated virus (AAV) decreased IGFBP2, flow cytometry measured M1 and M2 macrophage ratios, and immunohistochemistry detected markers. TCGA and CGGA transcriptome data showed malignant gliomas had higher stromal cell scores and worse prognoses. Low- and high-CAF TCGA gliomas were detected, and differential expression, WGCNA, and multifactorial COX identified 132 CAF-related genes and seven high-risk genes (CPQ, EFEMP2, IGFBP2, RAB42, TNFRSF12A, and VASN). Neither CAF risk score, grade, nor 1p/19q affected glioma prognosis. CAF only enriched EFEMP2 and IGFBP2. Gene Expression Profiling Interactive Analysis compared EFEMP2 and IGFBP2 expression in normal brain tissue and gliomas. Low-grade glioma and malignant glioblastoma highly expressed IGFBP2 and EFEMP2. GSEA raised IGFBP2. CIBERSORT linked M2 macrophage infiltration to TCGA glioma immune cell subpopulation IGFBP2 expression. IGFBP2 knockdown stopped mouse glioma and M2 macrophage polarization. CAF plays a procarcinogenic role in glioma, and the CAF-related gene IGFBP2 could promote glioma progression by inducing M2 macrophage polarization.NEW & NOTEWORTHY The cancer-associated fibroblast (CAF)-related gene insulin-like growth factor binding protein-2 (IGFBP2) is highly expressed in gliomas and is associated with poor prognosis. CAF-related gene IGFBP2 promotes glioma progression by inducing polarization of M2 macrophages. This study provides a new basis for an in-depth investigation of the functional mechanisms of the glioma tumor microenvironment and the search for key genes involved in immune regulation in CAF.

Multi-omics analysis of the oncogenic role of optic atrophy 1 in human cancer.

To investigate the prognostic significance of optic atrophy 1 (OPA1) in pan-cancer and analyze the relationship between OPA1 and immune infiltration in cancer. OPA1 exhibited high expression levels or mutations in various types of tumor cells, and its expression levels were significantly correlated with the survival rate of tumor patients. In different tumor tissues, there was a notable positive correlation between OPA1 expression levels and the infiltration of cancer-associated fibroblasts in the immune microenvironment. Additionally, OPA1 and its related genes were found to be involved in several crucial biological processes, including protein phosphorylation, protein import into the nucleus, and protein binding. OPA1 is highly expressed or mutated in numerous tumors and is strongly associated with protein phosphorylation, patient prognosis, and immune cell infiltration. OPA1 holds promise as a novel prognostic marker with potential clinical utility across various tumor types. We examined OPA1 expression in pan-cancer at both the gene and protein levels using various databases, including Tumor Immune Estimation Resource 2.0 (TIMER 2.0), Gene Expression Profiling Interactive Analysis (GEPIA2), UALCAN, and The Human Protein Atlas (HPA). We utilized the Kaplan-Meier plotter and GEPIA datasets to analyze the relationship between OPA1 expression levels and patient prognosis. Through the cBioPortal database, we detected OPA1 mutations in tumors and examined their relationship with patient prognosis. We employed the TIMER 2.0 database to explore the correlation between OPA1 expression levels in tumor tissue and the infiltration of cancer-associated fibroblasts in the immune microenvironment. Furthermore, we conducted a gene search associated with OPA1 and performed enrichment analysis to identify the main signaling pathways and biological processes linked to them.

The gene RAD51AP1 promotes the progression of pancreatic cancer via the PI3K/Akt/NF-κB signaling pathway.

Pancreatic cancer is one of the most lethal tumors due to its rapid proliferation and aggressiveness. RAD51AP1 is a protein-coding gene with critical functions in many cancers but few studies have assessed RAD51AP1 in pancreatic cancer. Bioinformatics methods and cell function experiments were performed to reveal the functions of RAD51AP1 in vitro. Gene Expression Profiling Interactive Analysis (GEPIA) was used to explore key proteins and their relationships with RAD51AP1 in the PI3K/AKT/NF-κB signaling pathways. Western blotting (WB) was conducted to detect the expression of key proteins after the downregulation of RAD51AP1. Co-Immunoprecipitation (Co-IP) was applied to confirm the binding of RAD51AP1 and PI3K. In addition, the lentivirus was used to construct subcutaneous tumors in nude mice to verify the function of RAD51AP1 in vivo. The Kaplan-Meier curves illustrated that elevated expression levels of RAD51AP1 were significantly correlated with reduced overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in pancreatic cancer patients. The results of WB showed that several key proteins in the PI3K/AKT/NF-κB signaling pathway (including PI3K, AKT, IKK1, IKK2, P65, P50, C-FLIP, and XIAP) exhibited a significant knockdown upon reducing the expression of RAD51AP1. Co-IP suggested that RAD51AP1 could directly bind to PI3K. In vitro, CCK-8, wound healing, and Transwell assays revealed that high RAD51AP1 expression was significantly correlated with increased cell proliferation, migration, and invasion. In vivo, mouse tumor formation experiments showed that RAD51AP1 inhibition significantly inhibited tumor growth. RAD51AP1 plays an important role in fostering cellular proliferation, invasion, metastasis, and tumor enlargement via the PI3K/AKT/NF-κB signaling pathway.

FAM107A as a tumor suppressor in esophageal squamous carcinoma inhibits growth and metastasis

BackgroundSequence similarity Family 107 member A (FAM107A) has been recognized as a tumor suppressor of various malignancies, which suppresses tumor proliferation and metastasis. Its specific role in esophageal squamous cell carcinoma (ESCC) remains unclear. MethodsPublic datasets including Gene Expression Profiling Interactive Analysis (GEPIA) and Gene Expression Omnibus (GEO), quantitative real-time PCR (qRT-PCR), and Western blot were utilized for comparative analysis of FAM107A expression between ESCC and normal tissues. The link between FAM107A and clinicopathological features, as well as prognosis determined through χ2-test, log-rank analysis, and univariate and multivariate analyses, respectively. The impact of FAM107A on ESCC cell malignant behavior was confirmed through in vitro assays, including cell counting using the Cell Counting Kit-8 (CCK-8), clonal formation, wound healing, and transwell assays. Western blot analysis was employed to assess the effects of FAM107A on tumor epithelial-mesenchymal transition (EMT) and cell cycle-related proteins. Finally, xenograft tumors were developed to investigate the influence of FAM107A on ESCC growth in vivo. ResultsFAM107A exhibited low expression in ESCC tissues. Reduced FAM107A expression was associated with a poorer prognosis and unfavorable clinicopathological characteristics, such as degree of differentiation, T-stage, and N-stage. Overexpression of FAM107A suppressed ESCC cell proliferation, invasion, migration, the EMT process, and cell cycle progression. Finally, FAM107A overexpression inhibited tumor development in vivo. ConclusionThe decreased expression of FAM107A is indicative of a worse prognosis for ESCC patients. FAM107A exerts inhibitory impacts on malignant behavior and may hold promise as a therapeutic target for ESCC.

DUSP22 suppresses tumor progression by directly dephosphorylating AKT in non-small cell lung cancer.

Protein kinase B (AKT) plays a pivotalin regulating cell migration, proliferation, apoptosis, and survival, making it a prominent target for anticancer therapy. While the kinase activity of AKT has been extensively explored, its dephosphorylation have largely remained uncharted. Herein, we aimed to unravel the molecular mechanisms governing AKT dephosphorylation, with a specific emphasis on dual-specificity phosphatases DUSP22. Our investigation sought to shed light on the potential of DUSP22 as a potential therapeutic target for non-small cell lung cancer (NSCLC). To determine the expression level of DUSP22 in NSCLC cell lines, the gene expression profiling interactive analysis (GEPIA) and Oncomine database were searched. Additionally, the effect of DUSP22 on patient survival was analyzed with Kaplan-Meier database. Antitumor effects of DUSP22 were tested in A549 and H1299 cell lines. Experiments are based on: (1) cell viability determined by the cell counting kit-8 assay and colony-formation assay; (2) cell migratory ability assessed throughthe scratch assay and the transwell migration assay; (3) the mechanism behind the antitumor effects of DUSP22 dissected with co-immunoprecipitation (Co-IP) and in vitro kinase assays. Our study revealed a significant downregulation ofDUSP22 in both NSCLC cell lines and tissues. Meanwhile, survival rate analysis results demonstratedthat reduced DUSP22 expression was correlated with pooreroverall survival in lung cancer patients. Moreover, DUSP22 exhibited an inhibitory effect on the cell viability and migratory capacity of A549 and H1299 cells. This inhibition was accompanied by the decrease in the phosphorylation of AKT and p38. Mechanistically, the phosphatase domain of DUSP22 interacted with AKT, resulting in theinhibitionof AKT phosphorylation. This inhibitory effect was contingent upon the phosphatase activity of DUSP22. These findings provide compelling evidence that DUSP22 directly interacted with AKT, leading to the dephosphorylation ofAKT at S473 and T308 residues, ultimately curbing the proliferation and migration of lung cancer cells. Additionally, our results also highlight a preclinical rationale for utilizing DUSP22 as a prognostic marker in NSCLC.

Pan‑cancer analysis identified ARHGAP23 as a potential biomarker for pancreatic adenocarcinoma.

Rho GTPASE-activating protein 23 (ARHGAP23) is known to activate RHO-GTPase and has an important role in the infiltration and metastasis of tumors. Although previous studies suggested its involvement in certain human cancers, its role in pan-cancer remains unclear. In the present study, the expression, prognosis and potential functions of ARHGAP23 in pan-cancer were evaluated through various public databases such as Human Protein Atlas, Tumor IMmune Estimation Resource, Gene Set Co-Expression Analysis, Gene Expression Profiling Interactive Analysis, cBio Cancer Genomics Portal, Tumor-Immune System Interactions Database (TISIDB) and others. Through these data combined with a variety of biological information analysis methods, the potential role of ARHGAP23 as a carcinogenic gene was explored in the present study. The present analysis revealed that ARHGAP23 expressed abnormalities in >10 tumors, which was associated with differences in prognosis. Furthermore, the findings of the present study indicated that ARHGAP23 is associated with DNA methylation and multiple immune cell infiltrations in these tumors. ARHGAP23 expression was related to clinical prognosis, DNA methylation and immune infiltration. These findings support the potential of ARHGAP23 as a prognostic biomarker and a molecular target for cancer treatment.

HDAC Inhibitor Synergizes with GL-V9, a Derivative of Wogonin, to Suppress Acute Myeloid Leukemia By Downregulating ESPL1 and PLK4

Background Developing more effective non-chemotherapy options is emerging needed for acute myeloid leukemia (AML). GL-V9, a newly synthetic flavonoid derivative, exhibits anticancer activities with low toxicity as its nature features, however, the anti-leukemia effect and molecular mechanism against AML remain elusive. HDACs inhibitors are promising effective therapies for cancers. Chidamide (CS055/HBI-8000) is a benzamide histone deacetylase (HDAC) inhibitor that induces growth inhibition, cell cycle arrest, and apoptosis in MDS and AML. Here, we sought to determine the potential synergistic anti-leukemia effect of Chidamide combined with GL-V9 in AML. Methods Cell proliferation assays were measured by Cell Counting Kit-8(CCK-8) in AML cells; CalcuSyn was used for synergy analysis. Cell cycle and apoptosis were measured by flow cytometry analysis. Transcriptome was analyzed by RNA-seq in U937 cells treated with 10μM Chidamide and in MV4-11 treated with 4μM GL-V9. qPCR was utilized for gene expression; R2 genomics analysis and visualization application were used for comparison of the expression difference and the Kaplan-Meier overall survival analysis was conducted by the Gene Expression Profiling Interactive Analysis (GEPIA) platform. Results GL-V9 had a dose-dependent effect on cell proliferation arrest in U937 and MV4-11 cells. Chidamide significantly sensitized this effect of GL-V9 versus single-drug controls, and CalcuSyn analysis showed the synergistic effect of the combination (Fig.1A). The combination also significantly increased the % of apoptotic cells versus single-drug controls (p<0.0001) (Fig1.B). Chidamide induced G0/G1-phase arrest and GL-V9 induced G2/M arrest, whereas the combination significantly decreased the % of S-phase cells (Fig.1C). These data indicate that Chidamide+GL-V9 combination results in the synergistic effect on cell growth inhibition, apoptosis and cell cycle arrest in AML. Next, the drug-induced change of the global transcriptome was analyzed. The significantly different expression genes (DEGs) were identified upon GL-V9 treatment and Chidamide treatment versus vehicle control. 1663 DEGs are identified upon GL-V9 treatment and 3756 DEGs upon Chidamide, in which 1405 were intersected regulated (1231 genes changed in the same direction but 174 changed in the opposite (Fig.2AB). The overlapped DEGs are mainly enriched in cell cycle regulation, DNA repair, chromosome segregation, spindle organization, DNA damage, etc. (Fig2.C). ESPL1 and PLK4 are at the top of the overlapped down-regulated DEGs; and qPCR results confirmed their mRNA levels are significantly downregulated by GL-V9+Chidamide, GL-V9, and Chidamide versus the vehicle control (p<0.0001) (Fig. 2D). ESPL1 encoded protein, Separase is an enzyme resolving sister chromatid cohesion, and plays a pivotal role in cell division and oncogenesis. PLK4 (polo-like kinase 4) is a key regulator of centrosome duplication and the substrate of histone acetyltransferases, and PLK4 overexpression leads to centrosome amplification in human cancer and contributes to multipolar spindle assembly. Our results not only indicated that the combination exerts its anti-tumor effect through down-regulation of ESPL1 and PLK4 expression but also reveal their oncogenic roles in AML. Indeed, the mRNA levels of ESPL1 and PLK4 are significantly high expressed in AML patients versus normal BM controls, and ESPL1 high expression is correlated with poor prognosis (Log-rank p=0.0039) (Fig2.E). In addition, our data showed that the expression of the anti-apoptosis genes BCL2 and BCL2L1 are significantly decreased, and the early apoptosis indicators, Caspase-3 and Casepase-9 increased by the combination versus the single-drug controls in U937 cells (Fig2.F). The proposed mechanism model is summarized in Fig. 2G. Conclusion Our data indicate that HDAC inhibitor Chidamide significantly synergizes GL-V9-induced cell growth inhibition, apoptosis, and cell cycle arrest in AML, and the underlying mechanism by suppressing the expression of ESPL1 and PLK4, the key regulators of cell division and proliferation. Our results also provide a potential chemotherapy-free option for AML patients.

Low OGDHL expression affects the prognosis and immune infiltration of kidney renal clear cell carcinoma.

Oxoglutarate dehydrogenase-like (OGDHL) modulates glutamine metabolism to influence tumor progression. Therefore, we aimed to explore the potential role of OGDHL in the prognosis of kidney renal clear cell carcinoma (KIRC) and its effect on immune infiltration. The Cancer Genome Atlas, Tumor Immune Estimation Resource, Gene Expression Profiling Interactive Analysis, Human Protein Atlas, and The University of Alabama at Birmingham Cancer databases and the GSE53757 dataset were utilized to analyze expression difference and prognosis of OGDHL in tumor and normal tissue; diagnostic value was assessed using receiver operating characteristic curves. Correlations with clinical features and survival prognosis were analyzed. Independent prognostic factors were identified using univariate and multifactorial Cox regression analysis. We used the CIBERSORT analysis tool to discover the proportion of tumor-infiltrating immune cells (TIICs) in KIRC patients. Next, the differences in the proportion of TIICs under different OGDHL expression were analyzed. Finally, we explored the potential mechanisms by which OGDHL expression affects patient survival using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). OGDHL expression was markedly downregulated in KIRC tissues compared to in normal tissues, and the downregulation of OGDHL expression was significantly associated with tumor progression (including tumor stage and grade) and poor prognosis. Cox regression analyses revealed OGDHL to be an independent prognostic factor for KIRC. CIBERSORT analysis showed that OGDHL expression is associated with differences in the proportion of several TIICs, particularly resting mast cells. Finally, GO and KEGG analysis showed that OGDHL was associated with extracellular matrix and epithelial cell differentiation involved in kidney development. GSEA indicated that low OGDHL was closely related to the activation of carcinogenic signaling pathways, including epithelial mesenchymal transition, tumor necrosis factor alpha and nuclear factor kappa B signaling pathway, negative regulation of apoptotic signaling, collagen formation, etc. OGDHL level can be monitored for diagnosing KIRC. Reduced expression is associated with poor prognosis and immune infiltration of KIRC. OGDHL is expected to become a new target for the treatment of KIRC.