Bioinformatics analysis of C3 and CXCR4 demonstrates their potential as prognostic biomarkers in clear cell renal cell carcinoma (ccRCC)

Quan, Jing; Bai, Yuchen; Yang, YunBei; Han, Er Lei; Bai, Hong; Zhang, Qi; Zhang, Dahong

doi:10.1186/s12885-021-08525-w

Cited by 5 publications

(5 citation statements)

References 32 publications

(34 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Chen et al concluded that the DEGs of ccRCC are also enriched in the nucleus ("nucleus" and "kinetochore"), this observation was similar to the findings of our study (Chen et al 2020). Similar to the results of Quan et al 2021, we found that the molecular functions of the DEGs in advanced ccRCC were associated with the binding function of proteins and metal ions (Quan et al 2021).…”

Section: Accepted Manuscript 11supporting

confidence: 92%

“…Regarding the cellular components, the DEGs were mainly associated with the membrane; this was also found by Wang et al (Wang et al 2020). The upregulated genes of ccRCC are mainly located on the plasma membrane (Quan et al 2021). Chen et al concluded that the DEGs of ccRCC are also enriched in the nucleus ("nucleus" and "kinetochore"), this observation was similar to the findings of our study (Chen et al 2020).…”

Section: Accepted Manuscript 11mentioning

confidence: 62%

See 1 more Smart Citation

Identification of Novel Genes and Associated Drugs in Advanced Clear Cell Renal Cell Carcinoma by Bioinformatic Methods

Lin

et al. 2022

Tohoku J. Exp. Med.

View full text Add to dashboard Cite

show abstract

Section: Accepted Manuscript 11supporting

confidence: 92%

Section: Accepted Manuscript 11mentioning

confidence: 62%

Identification of Novel Genes and Associated Drugs in Advanced Clear Cell Renal Cell Carcinoma by Bioinformatic Methods

Lin

et al. 2022

Tohoku J. Exp. Med.

View full text Add to dashboard Cite

show abstract

“…With regard to assessing the prognosis in ccRCC patients, the TNM staging system is widely used in clinical procedures ( Nakayama et al, 2014 ); however, these predictive frameworks are not always useful indicators for undertaking the prognosis in ccRCC victims ( Qin et al, 2013 ). The progression of ccRCC in patients is monitored by analyzing those molecules that possess tumorigenic properties ( Quan et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Prognostic significance of CKAP2L expression in patients with clear cell renal cell carcinoma

Zhang²,

Shen

et al. 2023

Front. Genet.

View full text Add to dashboard Cite

Background: Cytoskeleton-associated protein 2-like protein (CKAP2L) is thought to promote the progression of glioma, breast cancer, and ovarian cancer. However, the role of cytoskeleton-associated protein 2-like protein in clear cell renal cell carcinoma (ccRCC) is still unclear. The study aimed to investigate the roles and mechanisms of cytoskeleton-associated protein 2-like protein in clear cell renal cell carcinoma.Methods: The level of cytoskeleton-associated protein 2-like protein in tumors was explored by using UALCAN and Oncomine databases. Gene expression datasets of clear cell renal cell carcinoma from The Cancer Genome Atlas and Gene Expression Omnibus (GEO) were also used to validate the cytoskeleton-associated protein 2-like protein level in clear cell renal cell carcinoma. Survival analysis was performed to investigate the relationship between cytoskeleton-associated protein 2-like protein level and prognosis of clear cell renal cell carcinoma patients. Cox regression analysis was used for identifying the independent prognostic factors. Gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), protein–protein interaction analysis, co-expression analysis, and immune infiltration analysis were used to explore the potential mechanisms of cytoskeleton-associated protein 2-like protein in clear cell renal cell carcinoma. Moreover, the levels of cytoskeleton-associated protein 2-like protein in clinical clear cell renal cell carcinoma tissues were also measured using RT-PCR, immunohistochemical analysis, and Western blotting. M1 macrophages and CD4+ T cells were also detected by immunohistochemistry between tumor and normal tissues.Results: The level of cytoskeleton-associated protein 2-like protein was upregulated in clear cell renal cell carcinoma according to multiple databases and experimental verification. Upregulated cytoskeleton-associated protein 2-like protein is an independent prognostic factor, which might activate the JAK–STAT signaling pathway, the P53 signaling pathway, the TGF-β signaling pathway, the WNT signaling pathway, etc., in clear cell renal cell carcinoma. Protein–protein interaction analysis and co-expression analysis suggest that cytoskeleton-associated protein 2-like protein might interact with some proliferation proteins. Immune infiltration analysis indicates that cytoskeleton-associated protein 2-like protein may affect the level of activated CD4+ memory T cells, M1 macrophages, CD8+ T cells, and neutrophils in clear cell renal cell carcinoma. More M1 macrophage infiltrations in tumor tissues with higher cytoskeleton-associated protein 2-like protein were validated by clear cell renal cell carcinoma tumor tissues.Conclusion: Cytoskeleton-associated protein 2-like protein is upregulated in clear cell renal cell carcinoma tissues, which may promote progression of the disease. Cytoskeleton-associated protein 2-like protein is a potential target for prognostic markers and a potential treatment target in clear cell renal cell carcinoma.

show abstract

“…Currently, it remains difficult to identify the early symptoms of RCC, and the majority of patients are identified at an advanced stage or even with metastases. In addition, due to the complexity of its etiology and pathophysiology, RCC exhibits the clinical features of a high risk of recurrence and metastasis (74,75). Although the broader implementation of various diagnostic, screening techniques and advanced therapies, the risk of metastasis and recurrence for ccRCC shows a 5-year survival rate of 50%-69% for ccRCC patients and 10% for patients with metastasis (76).…”

Section: Discussionmentioning

confidence: 99%

Crosstalk of necroptosis and pyroptosis defines tumor microenvironment characterization and predicts prognosis in clear cell renal carcinoma

Fu¹,

Bao²,

Li³

et al. 2022

Front. Immunol.

View full text Add to dashboard Cite

Pyroptosis and necroptosis are two recently identified forms of immunogenic cell death in the tumor microenvironment (TME), indicating a crucial involvement in tumor metastasis. However, the characteristics of necroptosis and pyroptosis that define tumor microenvironment and prognosis in ccRCC patients remain unknown. We systematically investigated the transcriptional variation and expression patterns of Necroptosis and Pyroptosis related genes (NPRGs). After screening the necroptosis-pyroptosis clusters, the potential functional annotation for clusters was explored by GSVA enrichment analysis. The Necroptosis-Pyroptosis Genes (NPG) scores were used for the prognosis model construction and validation. Then, the correlations of NPG score with clinical features, cancer stem cell (CSC) index, tumor mutation burden (TMB), TME, and Immune Checkpoint Genes (ICGs) were also individually explored to evaluate the prognosis predictive values in ccRCC. Microarray screenings identified 27 upregulated and 1 downregulated NPRGs. Ten overall survival associated NPRGs were filtered to construct the NPG prognostic model indicating a better prognostic signature for ccRCC patients with lower NPG scores (P< 0.001), which was verified using the external cohort. Univariate and multivariate analyses along with Kaplan-Meier survival analysis demonstrated that NPG score prognostic model could be applied as an independent prognostic factor, and AUC values of nomogram from 1- to 5- year overall survival with good agreement in calibration plots suggested that the proposed prognostic signature possessed good predictive capabilities in ccRCC. A high-/sNPG score is proven to be connected with tumor growth and immune-related biological processes, according to enriched GO, KEGG, and GSEA analyses. Comparing patients with a high-NPG score to those with a low-NPG score revealed significant differences in clinical characteristics, growth and recurrence of malignancies (CSC index), TME cell infiltration, and immunotherapeutic response (P< 0.005), potentially making the NPG score multifunctional in the clinical therapeutic setting. Furthermore, AIM2, CASP4, GSDMB, NOD2, and RBCK1 were also found to be highly expressed in ccRCC cell lines and tumor tissues, and GASP4 and GSDMB promote ccRCC cells’ proliferation, migration, and invasion. This study firstly suggests that targeting the NPG score feature for TME characterization may lend novel insights into its clinical applications in the prognostic prediction of ccRCC.

show abstract

Bioinformatics analysis of C3 and CXCR4 demonstrates their potential as prognostic biomarkers in clear cell renal cell carcinoma (ccRCC)

Cited by 5 publications

References 32 publications

Identification of Novel Genes and Associated Drugs in Advanced Clear Cell Renal Cell Carcinoma by Bioinformatic Methods

Identification of Novel Genes and Associated Drugs in Advanced Clear Cell Renal Cell Carcinoma by Bioinformatic Methods

Prognostic significance of CKAP2L expression in patients with clear cell renal cell carcinoma

Crosstalk of necroptosis and pyroptosis defines tumor microenvironment characterization and predicts prognosis in clear cell renal carcinoma

Contact Info

Product

Resources

About