Prognostic and immunological role of Ras-related protein Rap1b in pan-cancer

Cui, Guoliang; Wang, Can; Lin, Zhenyan; Feng, Xiaoke; Wei, Mu-Xin; Miao, Zhengyue; Sun, Zilin; Wei, Fei

doi:10.1080/21655979.2021.1955559

Cited by 19 publications

(13 citation statements)

References 47 publications

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“…Future analysis of these pathways will help to further reveal the pathogenesis of primary OVC in M. fortis . The some DEGs in this study also were reported as marker genes associated with human OVC, such as CYR61 ( 44 ), RAP1B ( 45 ), RHOA ( 46 ), RAC1 ( 47 ) and BTG3 ( 48 ). Hence, M. fortis could be used to better understand human OVC.…”

Section: Discussionsupporting

confidence: 60%

De novo assembly and transcriptome characterization: Novel insights into the mechanisms of primary ovarian cancer in Microtus fortis

Gao²,

Du³

et al. 2021

Mol Med Rep

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The natural incidence of primary epithelial ovarian cancer (oVc) in adult female voles of some established strains of Microtus fortis is relatively high. M. fortis oVc has some pathological similarities to human epithelial oVc, therefore M. fortis represents the latest and most valuable animal model for studying human oVc. The lack of available genetic information for M. fortis limits the use of common immunological methods; thus, high-throughput sequencing technologies have been used to reveal the mechanisms of primary oVc in M. fortis. The individuals with cancer were diagnosed using histopathologic hematoxylin and eosin staining. The present study used rna-sequencing (rna-seq) technology to establish a de novo assembly of the M. fortis transcriptome produced 339,830 unigenes by the short reads assembly program Trinity. comparisons were made between oVc and healthy ovarian tissue (oV) and between fallopian tube cancer (FTc) and healthy fallopian tube (FT) tissues using rna-seq analysis. a total of 3,434 differentially expressed genes (deGs) were identified in oVc tissue compared with oV tissue using rna-Seq by Expectation-Maximization software, including 1,950 significantly upregulated and 1,484 significantly downregulated genes. There were 2,817 DEGs identified in the FTC tissues compared with the FT tissue, including 1,762 significantly upregulated and 1,055 significantly downregulated genes.Pathway enrichment analysis revealed that upregulated transcripts in the oVc vs. oV groups were involved in cell growth and proliferation-associated pathways, whereas the downregulated deGS in the oVc vs. oV groups were enriched in steroid biosynthesis-related pathways. Furthermore, the tumor suppressor gene, p53, was downregulated in the FTc and oVc compared with the FT and oV groups, respectively; whereas, genes that promoted cell migration, such as ras-related protein rap-1b, ras homolog family member a and rac1, were upregulated. in summary, to the best of our knowledge, the present study characterized the M. fortis de novo transcriptome of oV and FT tissues and to perform RNA-seq quantification to analyze the differences in healthy and cancerous oV and FT tissues. These results identified pathways that differed between cancerous and healthy M. fortis tissues. analysis of these pathways may help to reveal the pathogenesis of primary oVc in M. fortis in future work.

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Section: Discussionsupporting

confidence: 60%

De novo assembly and transcriptome characterization: Novel insights into the mechanisms of primary ovarian cancer in Microtus fortis

Gao²,

Du³

et al. 2021

Mol Med Rep

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“…Domain-containing protein 1 has been reported upregulated in most cancers and played oncogenic roles in pan-cancer by comprehensive bioinformatic analysis [ 85 ]. Ras-related Protein Rap1b expression was corelated with poor prognosis and tumor immune infiltration in pan-cancer [ 86 ]. A 12-gene signature related to iron metabolism was developed in lung cancer [ 87 ].…”

Section: Discussionmentioning

confidence: 99%

A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

Tang

Wang

et al. 2021

Bioengineered

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Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors was explored based on the datasets of gene expression omnibus and the cancer genome atlas. Differential expression of ACTB was found between cancer and adjacent normal tissues, and significant associations was found between ACTB expression and prognosis of tumor patients. In most cancers, ACTB expression was associated with immune cells infiltration, immune checkpoints and other immune modulators. Relevance between ACTB and metastasis and invasion was identified in various types of cancers by CancerSEA. Moreover, focal adhesion and actin regulation-associated pathways were included in the functional mechanisms of ACTB. The expression of ACTB was verified by quantitative real-time polymerase chain reaction. Knockdown of ACTB inhibited head and neck squamous carcinoma cell migration and invasion by NF-κB and Wnt/β-catenin pathways. Our first pan-cancer study of ACTB offers insight into the prognostic and immunological roles of ACTB across different tumors, indicating ACTB may be a potential biomarker for poor prognosis and immune infiltration in cancers, and the role of ACTB as a reference gene in cancers was challenged.

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“…MSI, TNB and TMB had been regarded as vital factors influencing cancer patients' prognosis and they could also be as characterized as biomarkers of immunotherapies [42][43][44]. Based on our results, MSI was significantly related to EXTL3 expression in TCGA-PRAD, while TMB and TNB did not have significant associations with EXTL3 expression.…”

Section: Discussionmentioning

confidence: 60%

EXTL3 could serve as a potential biomarker of prognosis and immunotherapy for prostate cancer and its potential mechanisms

et al. 2022

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Background Exostosin like glycosyltransferase 3 (EXTL3) had been reported to be associated with immune deficiency and play prognostic roles in various cancers. However, little is known about the associations between EXTL3 and prostate cancer (PCa). Hence, this article was designed to clarify their associations. Methods All original data were downloaded from The Cancer Genome Atlas (TCGA) database. Gene set enrichment analysis (GSEA) and CellMiner database was utilized, respectively, to identify EXTL3-related signaling pathways and drugs. We explored the relationships between EXTL3 expression and immunity to further evaluate the involvement of EXTL3 in response to immunotherapies. LncRNA/RBP/EXTL3 mRNA networks were also identified for its potential mechanism. Results Compared with normal prostate samples, EXTL3 was poorly expressed in PCa samples not only in mRNA expression levels, but also in protein expression levels, with worse overall survival (P < 0.05) and this gene could be an independent prognostic biomarker for PCa (both P < 0.05). EXTL3 was revealed to be markedly linked with seven signaling pathways in PCa by GSEA, including calcium, chemokine, ERBB, JAK STAT, MAPK, WNT, oxidative phosphorylation pathways. EXTL3 expression was also revealed to be significantly associated with MSI, immune cells, immune checkpoint molecules, tumor microenvironment and immune cells infiltration. We further predicted immune responses of EXTL3 gene to immunotherapies by TIDE database and the IMvigor210 cohort. A total of six LncRNA/RBP/EXTL3 mRNA networks were eventually identified for its potential mechanisms. Conclusions EXTL3 could serve as a potential biomarker of prognosis and immunotherapy for PCa and six LncRNA/RBP/EXTL3 mRNA networks were also identified for its potential mechanisms.

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Prognostic and immunological role of Ras-related protein Rap1b in pan-cancer

Cited by 19 publications

References 47 publications

De novo assembly and transcriptome characterization: Novel insights into the mechanisms of primary ovarian cancer in Microtus fortis

De novo assembly and transcriptome characterization: Novel insights into the mechanisms of primary ovarian cancer in Microtus fortis

A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

EXTL3 could serve as a potential biomarker of prognosis and immunotherapy for prostate cancer and its potential mechanisms

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