Diagnostic and prognostic value of CEP55 in clear cell renal cell carcinoma as determined by bioinformatics analysis

Low ACADM expression predicts poor prognosis and suppressive tumor microenvironment in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) represents a highly frequent renal cancer subtype. However, medium-chain acyl-CoA dehydrogenase (ACADM) encodes an important enzyme responsible for fatty acid β-oxidation (FAO) and its association with prognosis and immunity in cancers has rarely been reported. Therefore, the present work focused on exploring ACADM's expression and role among ccRCC cases. We used multiple public databases and showed the hypo levels of ACADM protein and mRNA within ccRCC. Additionally, we found that ACADM down-regulation showed a remarkable relation to the advanced stage, high histological grade, as well as dismal prognostic outcome. As suggested by Kaplan-Meier curve analysis, cases showing low ACADM levels displayed shorter overall survival (OS) as well as disease-free survival (DFS). Moreover, according to univariate/multivariate Cox regression, ACADM-mRNA independently predicted the prognosis of ccRCC. In addition, this work conducted immunohistochemistry for validating ACADM protein expression and its prognostic role in ccRCC samples. KEGG and GO analyses revealed significantly enriched genes related to ACADM expression during fatty acid metabolism. The low-ACADM group with more regulatory T-cell infiltration showed higher expression of immune negative regulation genes and higher TIDE scores, which might contribute to poor response to immunotherapies. In conclusion, our results confirmed that downregulated ACADM predicted a poor prognosis for ccRCC and a poor response to immunotherapy. Our results provide important data for developing immunotherapy for ccRCC.

CEP55: an immune-related predictive and prognostic molecular biomarker for multiple cancers

BACKGROUND

Centrosomal protein 55 (CEP55) plays a significant role in specific cancers. However, comprehensive research on CEP55 is lacking in pan-cancer.

METHODS

In-house and multi-center samples (n = 15,823) were used to analyze CEP55 in 33 cancers. The variance of CEP55 expression levels among tumor and control groups was evaluated by the Wilcoxon rank-sum test and standardized mean difference (SMD). The clinical value of CEP55 in cancers was assessed using receiver operating characteristic (ROC) curves, Cox regression analysis, and Kaplan-Meier curves. The correlations between CEP55 expression and the immune microenvironment were explored using Spearman's correlation coefficient.

RESULTS

The data of clustered regularly interspaced short palindromic repeats confirmed that CEP55 was essential for the survival of cancer cells in multiple cancer types. Elevated CEP55 mRNA expression was observed in 20 cancers, including glioblastoma multiforme (p < 0.05). CEP55 mRNA expression made it feasible to distinguish 21 cancer types between cancer specimens and their control samples (AUC = 0.97), indicating the potential of CEP55 for predicting cancer status. Overexpression of CEP55 was correlated with the prognosis of cancer individuals for 18 cancer types, exhibiting its prognostic value. CEP55 expression was relevant to tumor mutation burden, microsatellite instability, neoantigen counts, and the immune microenvironment in various cancers (p < 0.05). The expression level and clinical relevance of CEP55 in cancers were verified in lung squamous cell carcinoma using in-house and multi-center samples (SMD = 4.07; AUC > 0.95; p < 0.05).

CONCLUSION

CEP55 may be an immune-related predictive and prognostic marker for multiple cancers, including lung squamous cell carcinoma.

CircRNF220 plays a pathogenic role to facilitate cell progression of AML in vitro via sponging miR-330-5p to induce upregulation of SOX4

BACKGROUND

Circular RNAs (circRNAs) are a specific family of non-coding RNAs (ncRNAs) with important function in disease progression. This research is performed to study circRNA Ring Finger Protein 220 (circRNF220) in acute myeloid leukemia (AML).

METHODS

CircRNF220, microRNA-330-5p (miR-330-5p) and sex-determining region Y-related high-mobility group box 4 (SOX4) were measured via quantitative real-time polymerase chain reaction (qRT-PCR). 3-(4, 5-dimethylthiazol-2-y1)-2, 5- diphenyl tetrazolium bromide (MTT) and EdU assays were used to assess cell proliferation. Cell cycle and apoptosis were detected using flow cytometry. Cell invasion was determined by transwell assay. Glycolytic metabolism was assessed by glucose consumption and lactate production. The target interaction was implemented via dual-luciferase reporter and RNA pull-down assays. SOX4 protein detection was conducted by western blot.

RESULTS

Expression detection identified that circRNF220 was overexpressed in AML. In vitro experiments showed that silence of circRNF220 promoted cell apoptosis but impeded proliferation, cell cycle progression, invasion and glycolytic metabolism in AML cells. Target analysis indicated that circRNF220 directly targeted miR-330-5p, and the effects of si-circRNF220 were abrogated by miR-330-5p inhibitor. Moreover, circRNF220 targeted miR-330-5p to increase the expression of SOX4 and SOX4 promoted cell progression of AML.

CONCLUSION

All these findings revealed that circRNF220 contributed to AML cell development in vitro via upregulating SOX4 expression by targeting miR-330-5p.

Circular RNA circSDHC (hsa_circ_0015004) regulates tumor growth and angiogenesis via regulating centrosomal protein 55 expression in renal cell carcinoma

BACKGROUND

Renal cell carcinoma (RCC) is the main aggressive subtype of kidney cancer. Circular RNAs have been shown to exert critical roles in RCC. However, little is known about the regulatory mechanism of hsa_circ_0015004 (circSDHC) in RCC.

METHODS

35 patients with RCC were recruited in the research. Expression changes of circSDHC were determined by real-time quantitative polymerase chain reaction (RT-qPCR). The effects of circSDHC inhibition on cell proliferation, apoptosis, angiogenesis, migration, and invasion were analyzed. The regulation mechanism of circSDHC was surveyed by bioinformatics analysis. The effect of circSDHC on tumorigenesis was validated by xenograft assay.

RESULTS

We observed an observable elevation in circSDHC expression in RCC tissues and cell lines. Functionally, circSDHC silencing decreased xenograft tumor growth and induced RCC cell apoptosis, repressed RCC cell proliferation, angiogenesis, migration, and invasion in vitro. Mechanically, circSDHC modulated centrosomal protein 55 (CEP55) expression by functioning as a miR-130a-3p sponge. Also, miR-130a-3p silencing offset circSDHC knockdown-mediated impacts on malignant phenotypes and angiogenesis of RCC cells. Furthermore, exogenetic expression of CEP55 counteracted miR-130a-3p overexpression-mediated effects on malignant phenotypes and angiogenesis of RCC cells.

CONCLUSION

Silencing of circSDHC restrained cell malignant phenotypes and angiogenesis via reducing CEP55 expression by releasing miR-130a-3p in RCC, providing a new mechanism for understanding the progression of RCC.

Identification and Validation of CYBB, CD86, and C3AR1 as the Key Genes Related to Macrophage Infiltration of Gastric Cancer

Gastric cancer (GC) is rampant around the world. Most of the GC cases are detected in advanced stages with poor prognosis. The identification of marker genes for early diagnosis is of great significance. Studying the tumor environment is helpful to acknowledge the process of tumorigenesis, development, and metastasis. Twenty-two kinds of immune cells were calculated by CIBERSORT from Gene Expression Omnibus (GEO) database. Subsequently, higher infiltration of macrophages M0 was discovered in GC compared with normal tissues. WGCNA was utilized to construct the network and then identify key modules and genes related to macrophages in TCGA. Finally, 18 hub genes were verified. In the PPI bar chart, the top 3 genes were chosen as hub genes involved in most pathways. On the TIMER and THPA websites, it is verified that the expression levels of CYBB, CD86, and C3AR1 genes in tumor tissues were higher than those in normal tissues. These genes may work as biomarkers or targets for accurate diagnosis and treatment of GC in the future. Our findings may be a new strategy for the treatment of GC.

Biomarkers for Renal Cell Carcinoma Recurrence: State of the Art

PURPOSE OF REVIEW

We aim to summarize the current state of art about the possible use of biomarkers for predicting renal cell carcinoma (RCC) recurrence after curative treatment. In addition, we aim to provide a snapshot about the clinical implication of biomarkers use for follow-up planification.

RECENT FINDINGS

A wide variety of biomarkers have been proposed. RCC biomarkers have been individuated in tumoral tissue, blood, and urine. A variety of molecules, including proteins, DNA, and RNA, warrant a good accuracy for RCC recurrence and progression prediction. Their use in prediction models might warrant a better patients' risk stratification. Future prognostic models will probably include a combination of classical features (tumor grade, stage, etc.) and novel biomarkers. Such models might allow a more accurate treatment and follow-up planification.

Novel prognostic prediction model constructed through machine learning on the basis of methylation-driven genes in kidney renal clear cell carcinoma

Kidney renal clear cell carcinoma (KIRC) is a common tumor with poor prognosis and is closely related to many aberrant gene expressions. DNA methylation is an important epigenetic modification mechanism and a novel research target. Thus, exploring the relationship between methylation-driven genes and KIRC prognosis is important. The methylation profile, methylation-driven genes, and methylation characteristics in KIRC was revealed through the integration of KIRC methylation, RNA-seq, and clinical information data from The Cancer Genome Atlas. The Lasso regression was used to establish a prognosis model on the basis of methylation-driven genes. Then, a trans-omics prognostic nomogram was constructed and evaluated by combining clinical information and methylated prognosis model. A total of 242 methylation-driven genes were identified. The Gene Ontology terms of these methylation-driven genes mainly clustered in the activation, adhesion, and proliferation of immune cells. The methylation prognosis prediction model that was established using the Lasso regression included four genes in the methylation data, namely, FOXI2, USP44, EVI2A, and TRIP13. The areas under the receiver operating characteristic curve of 1-, 3-, and 5-year survival rates were 0.810, 0.824, and 0.799, respectively, in the training group and 0.794, 0.752, and 0.731, respectively, in the testing group. An easy trans-omics nomogram was successfully established. The C-indices of the nomogram in the training and the testing groups were 0.8015 and 0.8389, respectively. The present study revealed the overall perspective of methylation-driven genes in KIRC and can help in the evaluation of the prognosis of KIRC patients and provide new clues for further study.

Identification of novel prognostic biomarkers in renal cell carcinoma

Objective: To identify novel prognostic biomarkers in renal cell carcinoma (RCC).

Results: 12 coding genes and one miRNA were finally identified as prognostic biomarkers. All of them were related to a poor prognosis. Lower expression levels of the coding genes were observed in higher clinical stages. Prognostic signatures including 7 biomarkers were identified. Patients in the high-risk group had worse survival than those in the low-risk group. The areas under the curves in different years indicated that it was a valuable signature in prognosis. It was found that elevated WDR72 inhibited the survival and invasion of 786-O and 769P cells in vitro.

Conclusions: Thirteen prognostic biomarkers of RCC were identified. Among them, 7 biomarkers comprised a signature to evaluate the RCC prognosis. WDR72 was a cancer suppressor and a potential therapeutic target in RCC.

Methods: Differentially expressed genes/miRNAs (DEGs/DEMs) and prognosis-related genes/miRNAs were acquired from public database. Prognostic biomarkers were identified by overlapping the significant DEGs/DEMs and prognosis-related genes/miRNAs. The associations between these biomarkers and the clinical stages were analyzed. All of these prognostic biomarkers were further investigated with multi-variable Cox regression. Finally, the inhibitory effect of WDR72 on the growth and invasion of RCC cells was studied.

TYROBP is a potential prognostic biomarker of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) exhibits high recurrence and metastasis rates. Although target therapy has significantly improved the prognosis of some patients with ccRCC, the median survival rate remains poor. Thus, there remains a need for the identification of novel potential targets for diagnosis and therapy. Here, we screened differentially expressed genes between ccRCC and normal tissues through analyzing The Cancer Genome Atlas database. We identified 55 up‐regulated and 67 down‐regulated genes associated with poor prognosis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these genes were associated with glycometabolic process, complement and coagulation cascades. In addition, the eight down‐regulated genes (HRG, FABP1, ALDOB, PCK1, HAO2, CASR, PLG, and HMGCS2) and two up‐regulated genes (SERPINE1 and TYROBP) were filtered out. Finally, TYROBP was selected through repeated verification of various databases. High expression of TYROBP is associated with low survival rate in ccRCC, is closely related to immune cell infiltration and is coexpressed with Programmed cell death protein‐1(PD‐1) and Cytotoxic T lymphocyte‐associated antigen‐4(CTLA‐4). In conclusion, TYROBP may have potential for diagnosis and treatment of ccRCC.