Pan-Cancer Analysis of the TRP Family, Especially TRPV4 and TRPC4, and Its Expression Correlated with Prognosis, Tumor Microenvironment, and Treatment Sensitivity

Chen, Zhenghao; Zhao, Youquan; Tian, Ye; Cao, Rui; Shang, Donghao

doi:10.3390/biom13020282

Cited by 13 publications

(9 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Bekele et al specified in their investigation that bladder cancer cell lines are sensible to BRAFV600E inhibitor PLX4720 [54]. Also, Chen et al, determined Transient receptor potential (TRP) family gene expression in bladder and para-carcinoma tissues and TRP expression is associated with the sensibility to several drugs inclusive of PLX-4720 [55]. Otherwise, PLX4720 is applied for other cancer types such as melanoma [56,57] and colorectal carcinoma [58].…”

Section: Discussionmentioning

confidence: 99%

Drug repurposing analysis with co-expressed genes identifies novel drugs and small molecules for bladder cancer

Göv,

Kaynak Bayrak

2024

Journal of Scientific Reports-A

View full text Add to dashboard Cite

Bladder cancer (BC) is the fifth most common malignancy in humans and has poor survival rates. Although there is extensive research on the diagnosis and treatment of BC, novel molecular therapies are essential due to tumor recurrence. In this study, we aim to identify repurposed drugs or small molecules of BC with multi-omics systems biology perspective. Gene expression datasets were statistically analyzed by comparing bladder tumor and normal bladder tissues and differentially expressed genes (DEGs) were determined. Co-expression network of common DEGs for BC was constructed and co-expressed module was found by using tumors and control bladder tissues. Using independent data, we demonstrated the high prognostic capacity of the module genes. Moreover, repurposed drugs or small molecules were predicted by using L1000CDS2 gene expression based-search engine tool. We found numerous drug candidates as 480743.cdx, MK-2206, Geldanamycin, PIK-90, BRD-K50387473 (XMD8-92), BRD-K96144918 (mead acid), Vorinostat, PLX-4720, Entinostat, BIX-01294, PD-0325901 and Selumetinib, that may be used in BC therapy. We report 480743.cdx, BRD-K50387473 (XMD8-92) and mead acid as novel drugs or small molecules that offer crucial step in translational cancer research of BC.

show abstract

Section: Discussionmentioning

confidence: 99%

Drug repurposing analysis with co-expressed genes identifies novel drugs and small molecules for bladder cancer

Göv,

Kaynak Bayrak

2024

Journal of Scientific Reports-A

View full text Add to dashboard Cite

show abstract

“…Extensive research on the mechanisms driving cancer progression has elucidated the pivotal role played by interactions between genes and immune cells within the TME. Chen et al conducted a comprehensive analysis to elucidate the expression patterns of TRP family genes and their association with the tumor microenvironment (TME) across different types of cancer [50]. In a separate study, Feng et al demonstrated a signi cant positive correlation between CENPT and in ltration of myeloid-derived suppressor cells (MDSCs), while a signi cant negative correlation was observed between CENPT and in ltration of T-cell natural killer (NK) cells in the majority of cancer types [51].…”

Section: Discussionmentioning

confidence: 99%

SLC8A1, a novel prognostic biomarker and immunotherapy target in RSA and UCEC based on scRNA-seq and pan-cancer analysis

Chu,

Qin,

2023

Preprint

View full text Add to dashboard Cite

Purpose As the field of gynecological immunology increasingly focuses on reproduction, the importance of recurrent spontaneous abortion (RSA) is growing. The complex mechanisms underlying the interaction between RSA and cancer are still not well understood. This study seeks to identify a new prognostic biomarker for RSA and cancer. Methods Weighted Gene Co-Expression Network Analysis (WGCNA), single-cell RNA sequencing (scRNA-seq), and machine learning algorithms were utilized for the analysis of RSA decidua samples (GSE164449, GSE214607, GSE65099) to identify the hub gene. The expression and distribution of the hub gene were subsequently investigated using the pan-cancer database TCGA. Furthermore, a prognostic prediction was made to assess the hub gene's impact on cancer response, mutation burden, immunity microenvironment, immune checkpoint, and chemotherapy. Results SLC8A1 has been identified as a hub gene within the RAS. In pan-cancer analysis, SLC8A1 exhibited strong expression levels in UCEC. The efficacy of SLC8A1 as a predictive marker was substantiated by calibration curves and concordance index. The mutation rate of SLC8A1 was found to be 6% based on the waterfall plot. Immune analysis revealed notable differences in the fractions of T cells and macrophages between the high and low expression groups. The analysis of immune checkpoint has demonstrated notable associations with CD40positive immune checkpoints. Notably, patients classified in the low-risk group exhibited enhanced responsiveness to Osimertinib, Dasatinib, Sepantronium bromid, lbrutinib, and other treatments. Conclusion These findings suggest that SLC8A1 may serve as a promising prognostic biomarker and potential target for immunotherapy in the context of RSA and UCEC.

show abstract

“…To identify variations in the expression of TRAF family genes across different cancers, we utilized RNA sequencing data (FPKM format) along with clinical characteristics, survival information, immune subtypes, and stemness scores (based on DNA methylation and RNA) for 33 cancer types. This data was sourced from TCGA database and accessed via the University of California Santa Cruz (UCSC) Xena data set platform ( http://xena.ucsc.edu/ ) [ 16 ]. Comprehensive details of the 33 cancer types, encompassing abbreviations, full names, the quantity of cancerous and normal samples, and other relevant data, are presented in the Supplementary table (Table S1).…”

Section: Methodsmentioning

confidence: 99%

Pan-cancer analysis of the TRAF family genes and their correlation with prognosis, TME, immune and drug sensitivity

Yao,

Hu,

Chen

et al. 2024

Eur J Med Res

View full text Add to dashboard Cite

Background Tumor necrosis factor receptor-associated factors family genes play a pivotal role in tumorigenesis and metastasis, functioning as adapters or E3 ubiquitin ligases across various signaling pathways. To date, limited research has explored the association between tumor necrosis factor receptor-associated factors family genes and the clinicopathological characteristics of tumors, immunity, and the tumor microenvironment (TME). This comprehensive study investigates the relationship between tumor necrosis factor receptor-associated factors family and prognosis, TME, immune response, and drug sensitivity in a pan-cancer context. Methods Utilizing current public databases, this study examines the expression levels and prognostic significance of tumor necrosis factor receptor-associated factors family genes in a pan-cancer context through bioinformatic analysis. In addition, it investigates the correlation between tumor necrosis factor receptor-associated factors expression and various factors, including the TME, immune subtypes, stemness scores, and drug sensitivity in pan-cancer. Results Elevated expression levels of tumor necrosis factor receptor-associated factor 2, 3, 4, and 7 were observed across various cancer types. Patients exhibiting high expression of these genes generally faced a worse prognosis. Furthermore, a significant correlation was noted between the expression of tumor necrosis factor receptor-associated factors family genes and multiple dimensions of the TME, immune subtypes, and drug sensitivity.

show abstract

Pan-Cancer Analysis of the TRP Family, Especially TRPV4 and TRPC4, and Its Expression Correlated with Prognosis, Tumor Microenvironment, and Treatment Sensitivity

Cited by 13 publications

References 49 publications

Drug repurposing analysis with co-expressed genes identifies novel drugs and small molecules for bladder cancer

Drug repurposing analysis with co-expressed genes identifies novel drugs and small molecules for bladder cancer

SLC8A1, a novel prognostic biomarker and immunotherapy target in RSA and UCEC based on scRNA-seq and pan-cancer analysis

Pan-cancer analysis of the TRAF family genes and their correlation with prognosis, TME, immune and drug sensitivity

Contact Info

Product

Resources

About