WITHDRAWN: Prognostic Values of COL4As Transcriptional Expressions in Clear Cell Renal Cell Carcinoma Patients

Tu, Bizhi; Zhang, Yiqun; Jia, Yaya; Xiong, Cheng; Gao, Fei; Sha, Qi; Qian, Jun

doi:10.2174/1386207325666220707113100

Cited by 5 publications

(5 citation statements)

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“…Knockdown of COL4A3 significantly increased the invasion and migration ability of nasopharyngeal carcinoma cancer cells [26]. The diminished expression of COL4A4 is associated with poorer prognosis, while the downregulation of COL4A6 promotes prostate cancer progression and invasion [15,27].…”

Section: Discussionmentioning

confidence: 99%

“…The COL4 family, consisting of six genes-COL4A1, COL4A2, COL4A3, COL4A4, COL4A5, and COL4A6, is a group of subtypes in the COL family. Tu et al discovered that clear cell renal cell carcinoma (ccRCC) tissue exhibited significantly diminished expression of COL4A3/4/5/6 in comparison to normal renal tissue, while showing markedly elevated expression of COL4A1/2 [15]. Patients with negative COL4A2 and COL4A6 in extrahepatic bile duct cancer exhibited notably poorer prognoses than those with positive COL4A2 and COL4A6 [16].…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive analysis of the expression, prognostic, and immune infiltration for COL4s in stomach adenocarcinoma

Xu,

Jin,

Chen

et al. 2024

BMC Med Genomics

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Background Collagen (COL) genes, play a key role in tumor invasion and metastasis, are involved in tumor extracellular matrix (ECM)-receptor interactions and focal adhesion pathways. However, studies focusing on the diagnostic value of the COL4 family in stomach adenocarcinoma (STAD) are currently lacking. Methods The TCGA database was employed to retrieve the clinical features and RNA sequencing expression profiles of patients with STAD. We conducted an investigation to examine the expression disparities between STAD and adjacent normal tissues. Kaplan-Meier survival analysis was utilized to assess their prognostic significance, while Spearman correlation analysis was employed to determine their association with immune checkpoint genes and immunomodulatory molecules. Furthermore, GO and KEGG analyses were performed on the COL4s-related genes, revealing potential biological pathways through gene set enrichment analysis (GSEA). Subsequently, we explored the extent of immune infiltration of the COL4 family in STAD using the TIMER database. Lastly, the expression levels of the COL4 family in STAD were further validated through quantitative PCR (qPCR) and western blot techniques. Results The expression levels of COL4A1/2 were significantly upregulated, while COL4A5/6 were conspicuously downregulated in STAD. The survival analysis revealed that the upregulated COL4s indicated poorer overall survival, first progression and post-progression survival outcomes. Additionally, our findings demonstrated a positive correlation between the expressions of COL4A1/2/3/4 and the infiltration of immune cells, including CD8 + T cells, dendritic cells, macrophages, neutrophils and CD4 + T cells. Further correlation analysis uncovered a favorable association between the expression of COL4A1/2/3/4 and various crucial immunomodulatory molecules, immunological checkpoint molecules, and chemokines. Quantitative PCR analysis confirmed that the expression patterns of COL4A1/3/4/6 genes aligned with the finding from the TCGA database. However, gastric cancer cells exhibited downregulation of COL4A2. Consistently, the protein level of COL4A1 was elevated, whereas the protein level of COL4A2 was reduced in the gastric cancer cell lines. Conclusion COL4s could potentially serve as biomarkers for diagnosing and predicting the prognosis of STAD.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of the expression, prognostic, and immune infiltration for COL4s in stomach adenocarcinoma

Xu,

Jin,

Chen

et al. 2024

BMC Med Genomics

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“…It has been reported that deletion of COL15A1 modulates the tumor ECM and leads to increased tumor growth in the mouse mammary carcinoma model [ 29 ]. The transcript levels of COL4A4 and 6 could act as potential indicators for early disease progression in ccRCC [ 30 ]. Yongcan et al defined that DCN deficiency promotes RCC growth and metastasis through the downregulation of P21 and E-cadherin [ 19 ].…”

Section: Discussionmentioning

confidence: 99%

A 20-Gene Signature Predicting Survival in Patients with Clear Cell Renal Cell Carcinoma Based on Basement Membrane

Yin

Zhao

Zhou

et al. 2023

Journal of Oncology

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Objectives. The most common subtype of renal cell carcinoma, clear cell renal cell carcinoma (ccRCC), has a high heterogeneity and aggressive nature. The basement membrane (BM) is known to play a vital role in tumor metastasis. BM-related genes remain untested in ccRCC, however, in terms of their prognostic significance. Methods. BM-related genes were gleaned from the most recent cutting-edge research. The RNA-seq and clinical data of the ccRCC were obtained from TCGA and GEO databases, respectively. The multigene signature was constructed using the univariate Cox regression and the LASSO regression algorithm. Then, clinical features and prognostic signatures were combined to form a nomogram to predict individual survival probabilities. Using functional enrichment analysis and immune-correlation analysis, we investigated potential enrichment pathways and immunological characteristics associated with BM-related-gene signature. Results. In this study, we built a model of 20 BM-related genes and classified them as high-risk or low-risk, with each having its anticipated risk profile. Patients in the high-risk group showed significantly reduced OS compared with patients in the low-risk group in the TCGA cohort, as was confirmed by the testing dataset. Functional analysis showed that the BM-based model was linked to cell-substrate adhesion and tumor-related signaling pathways. Comparative analysis of immune cell infiltration degrees and immune checkpoints reveals a central role for BM-related genes in controlling the interplay between the immune interaction and the tumor microenvironment of ccRCC. Conclusions. We combined clinical characteristics known to predict the prognosis of ccRCC patients to create a gene signature associated with BM. Our findings may also be useful for forecasting how well immunotherapies would work against ccRCC. Targeting BM may be a therapeutic alternative for ccRCC, but the underlying mechanism still needs further exploration.

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“…recently reported that the HMCN1 mutations are frequently detected in patients with ccRCC and are correlated with a higher tumor mutation burden and dismal clinical consequences, and may correlate with anti-tumor immunity and cell metabolism ( 42 ). In addition, COL4A4 has been identified as an unfavorable prognostic factor for ccRCC ( 43 ). The functions of other genes in ccRCC currently remain unknown and require further exploration.…”

Section: Discussionmentioning

confidence: 99%

Expression of basement membrane genes and their prognostic significance in clear cell renal cell carcinoma patients

Tao

Liang

et al. 2022

Front. Oncol.

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BackgroundClear cell renal cell carcinoma (ccRCC) is a malignant tumor with limited treatment options. A recent study confirmed the involvement of basement membrane (BM) genes in the progression of many cancers. Therefore, we studied the role and prognostic significance of BM genes in ccRCC.MethodsCo-expression analysis of ccRCC-related information deposited in The Cancer Genome Atlas database and a BM geneset from a recent study was conducted. The differentially expressed BM genes were validated using quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Least absolute shrinkage and selection operator regression and univariate Cox regression analyses were performed to identify a BM gene signature with prognostic significance for ccRCC. Multivariate Cox regression, time-dependent receiver operating characteristic, Kaplan–Meier, and nomogram analyses were implemented to appraise the prognostic ability of the signature and the findings were further verified using a Gene Expression Omnibus dataset. Additionally, immune cell infiltration and and pathway enrichment analyses were performed using ImmuCellAI and Gene Set Enrichment Analysis (GSEA), respectively. Finally, the DSIGDB dataset was used to screen small-molecule therapeutic drugs that may be useful in treating ccRCC patients.ResultsWe identified 108 BM genes exhibiting different expression levels compared to that in normal kidney tissues, among which 32 genes had prognostic values. The qRT-PCR analyses confirmed that the expression patterns of four of the ten selected genes were the same as the predicted ones. Additionally, we successfully established and validated a ccRCC patient prediction model based on 16 BM genes and observed that the model function is an independent predictor. GSEA revealed that differentially expressed BM genes mainly displayed significant enrichment of tumor and metabolic signaling cascades. The BM gene signature was also associated with immune cell infiltration and checkpoints. Eight small-molecule drugs may have therapeutic effects on ccRCC patients.ConclusionThis study explored the function of BM genes in ccRCC for the first time. Reliable prognostic biomarkers that affect the survival of ccRCC patients were determined, and a BM gene-based prognostic model was established.

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WITHDRAWN: Prognostic Values of COL4As Transcriptional Expressions in Clear Cell Renal Cell Carcinoma Patients

Cited by 5 publications

References 0 publications

Comprehensive analysis of the expression, prognostic, and immune infiltration for COL4s in stomach adenocarcinoma

Comprehensive analysis of the expression, prognostic, and immune infiltration for COL4s in stomach adenocarcinoma

A 20-Gene Signature Predicting Survival in Patients with Clear Cell Renal Cell Carcinoma Based on Basement Membrane

Expression of basement membrane genes and their prognostic significance in clear cell renal cell carcinoma patients

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