RTP4 is a novel prognosis-related hub gene in cutaneous melanoma

Li, Yiqi; Qi, Jue; Yang, Jiankang

doi:10.1186/s41065-021-00183-z

Cited by 10 publications

(8 citation statements)

References 36 publications

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“…Previous studies have suggested that RTP4 helps the GPCR oligomer properly assemble in the endoplasmic reticulum, promotes the dimerization of receptors in the Golgi apparatus, and decreases the ubiquitination of the heterodimers [ 29 ]. Other studies have shown that the RTP4 was overexpressed in some connective tissue disorders and parasitic infections [ 30 , 31 ] and correlated with some cancers [ 32 , 33 ]. That RTP4 induced by IFN-I could explain this phenomenon and is associated with immune responses.…”

Section: Discussionmentioning

confidence: 99%

“…For example, methylated RTP4 can be considered as a new biomarker for precise diagnosis and treatment of prostate cancer [ 37 ] and RTP4 can be considered as an independent indicator to judge the prognosis of oral cancer [ 38 ]. RTP4 has also been reported that it is significantly associated with immune cell infiltration and immune checkpoint encoding genes (PDCD1, TIM-3, and LAG3) in melanoma [ 33 ].…”

Section: Discussionmentioning

confidence: 99%

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RTP4, a Biomarker Associated with Diagnosing Pulmonary Tuberculosis and Pan-Cancer Analysis

Zhou

Ding

et al. 2023

Mediators of Inflammation

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Background. Pulmonary tuberculosis (PTB) is a global epidemic of infectious disease; the purpose of our study was to explore new potential biomarkers for the diagnosis of pulmonary tuberculosis and to use the biomarkers for further pan-cancer analysis. Methods. Four microarray gene expression sets were downloaded from the GEO public databases and conducted for further analysis. Healthy control (HC) samples and samples of pulmonary tuberculosis (PTB) were calculated with enrichment scores in folate biosynthesis pathways. The scores acted as a new phenotype combined with clinical information (control or PTB) for subsequent analysis. Weight gene coexpression network analysis (WGCNA) was used to seek the modules mostly related to PTB and folate biosynthesis in training sets. Twenty-nine coexistence genes were screened by intersecting the genes in the green-yellow module of GSE28623 and the brown module of GSE83456. We used the protein-protein interaction network analysis to narrow the gene range to search for hub genes. Then, we downloaded the unified and standardized pan-cancer data set from the UCSC database for correlations between biomarkers and prognosis and tumor stage differences. Results. Eventually, RTP4 was selected as a biomarker. To verify the reliability of this biomarker, an area under the ROC (AUC) was calculated in gene sets (GSE28623, GSE83456, and GSE34608). Lastly, to explore the difference in RTP4 expression before and after antituberculosis treatment, the GSE31348 gene set was enrolled to compare the expressions in weeks 0 and 26. The results showed significant differences between these two time points ( p < 0.001 ). RTP4 was significantly upregulated in the pulmonary tuberculosis group compared to the healthy control group in three gene sets and downregulated after antituberculosis therapy in one gene set. These results suggest that RTP4 can be used as a potential biomarker in diagnosing tuberculosis. The results of pan-cancer analysis showed that high expression of RTP4 in 4 tumor types was positively correlated with poor prognosis and high expression of RTP4 in 6 tumor types was negatively correlated with poor prognosis. We found significant differences in the expression of the RTP4 gene at different stages in 5 types of tumors. Conclusion. RTP4 might be a new potential biomarker for diagnosing pulmonary tuberculosis.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

RTP4, a Biomarker Associated with Diagnosing Pulmonary Tuberculosis and Pan-Cancer Analysis

Zhou

Ding

et al. 2023

Mediators of Inflammation

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“…Recent documents have revealed 4 key genes as guardians who actively participate in the protective immunity of various inflammatory diseases and cancer ( Li et al, 2021a ). IFI44 is found on human chromosome 1p31.1 ad belongs to the interferon-stimulated gene (ISG), which plays a significant role in immunoregulation and tumor cell recognition ( Lukhele et al, 2019 ; Wang et al, 2020 ; Li et al, 2021b ).…”

Section: Discussionmentioning

confidence: 99%

“…RTP4 (Receptor Transporter Protein 4) is a member of the RTPs family that is directly involved in modulating the expression of cell-surface G-coupled protein receptors ( Saito et al, 2004 ; Boys et al, 2020 ). Several studies have found that RTP4 is strongly linked to a virus defense response and cancer prognosis ( Li et al, 2021a ). Following Lipinski’s rule-of-five for drug likeliness, a protein’s druggability is solely determined by its affinity and specificity for small molecules ( Abi et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Integrated bioinformatic analyses investigate macrophage-M1-related biomarkers and tuberculosis therapeutic drugs

Deng

Shen²,

Liu³

et al. 2023

Front. Genet.

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Tuberculosis (TB) is a common infectious disease linked to host genetics and the innate immune response. It is vital to investigate new molecular mechanisms and efficient biomarkers for Tuberculosis because the pathophysiology of the disease is still unclear, and there aren’t any precise diagnostic tools. This study downloaded three blood datasets from the GEO database, two of which (GSE19435 and 83456) were used to build a weighted gene co-expression network for searching hub genes associated with macrophage M1 by the CIBERSORT and WGCNA algorithms. Furthermore, 994 differentially expressed genes (DEGs) were extracted from healthy and TB samples, four of which were associated with macrophage M1, naming RTP4, CXCL10, CD38, and IFI44. They were confirmed as upregulation in TB samples by external dataset validation (GSE34608) and quantitative real-time PCR analysis (qRT-PCR). CMap was used to predict potential therapeutic compounds for tuberculosis using 300 differentially expressed genes (150 downregulated and 150 upregulated genes), and six small molecules (RWJ-21757, phenamil, benzanthrone, TG-101348, metyrapone, and WT-161) with a higher confidence value were extracted. We used in-depth bioinformatics analysis to investigate significant macrophage M1-related genes and promising anti-Tuberculosis therapeutic compounds. However, more clinical trials were necessary to determine their effect on Tuberculosis.

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“…RTP4 (Receptor transporter protein 4) as an innate antiviral effector [ 33 ], it was related to the flavivirus replication, binds viral RNA, and inhibits viral genome amplification [ 34 ], and plays a role in diverse viral infections [ 35 ]. In addition, Li et al reported that RTP4 was associated with immune cell infiltration [ 36 ]. This suggests that RTP4 might be involved in immunity response process, while previous study indicated that activation of the immune response results in low feed efficiency due to increased maintenance requirements [ 26 , 37 ].…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of circular RNAs in association with the feed efficiency in Hu lambs

Zhang

et al. 2022

BMC Genomics

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Background Circular RNA (circRNA), as a new members of noncoding RNA family, have vital functions in many biological processes by as microRNA sponges or competing endogenous RNAs (ceRNAs). However, little has been reported about the genetic mechanism of circRNAs regulation of feed efficiency in sheep. Results This study aimed to explore the expression of circRNAs in the liver of Hu sheep with High-RFI (High residual feed intake) and Low-RFI (Low residual feed intake) using transcriptome sequencing. A total of 20,729 circRNAs were identified in two groups, in which 219 circRNAs were found as significantly differentially expressed. Several circRNAs were validated by using RT-PCR, sanger sequencing and RT-qPCR methods. These results demonstrated that the RNA-seq result and expression level of circRNAs identified are reliable. Subsequently, GO and KEGG enrichment analysis of the parental genes of the differentially expressed (DE) circRNAs were mainly involved in immunity response and metabolic process. Finally, the ceRNA regulatory networks analysis showed that the target binding sites for miRNA such as novel_41, novel_115, novel_171 and oar-miR-485-3p in the identified DE cirRNAs. Importantly, two metabolic (SHISA3 and PLEKHH2) and four (RTP4, CD274, OAS1, and RFC3) immune-related target mRNAs were identified from 4 miRNAs. Association analysis showed that the polymorphism (RTP4 c.399 A > G) in the target gene RTP4 were significantly associated with RFI (P < 0.05). Conclusions Analysis of sequencing data showed some candidate ceRNAs that may play key roles in the feed efficiency in sheep by regulating animal immune and metabolic. These results provide the basis data for further study of the biological functions of circRNAs in regulating sheep feed efficiency.

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RTP4 is a novel prognosis-related hub gene in cutaneous melanoma

Cited by 10 publications

References 36 publications

RTP4, a Biomarker Associated with Diagnosing Pulmonary Tuberculosis and Pan-Cancer Analysis

RTP4, a Biomarker Associated with Diagnosing Pulmonary Tuberculosis and Pan-Cancer Analysis

Integrated bioinformatic analyses investigate macrophage-M1-related biomarkers and tuberculosis therapeutic drugs

Identification and characterization of circular RNAs in association with the feed efficiency in Hu lambs

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