Increased Expression of T-Box Transcription Factor Protein 21 (TBX21) in Skin Cutaneous Melanoma Predicts Better Prognosis: A Study Based on The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) Databases

Zhang, Xingying; Wen, Xin; Feng, Ning; Chen, Aoxing; Yao, Senbang; Ding, Xin; Zhang, Longzhen

doi:10.12659/msm.923087

Cited by 12 publications

(10 citation statements)

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“…In addition, RNA-sequencing profiles of PNO1 expression in 653 normal samples were obtained from the Genotype-Tissue Expression (GTEx) database ( ), which is a database that provides information on normal samples from healthy participants. Both the 653 samples in GTEx database and 11 normal samples in TCGA database were used as normal samples ( 8 , 9 ). The differentially expressed genes (DEGs) between control and cancerous samples were identified using the Limma package of R software ( ) ( 10 ).…”

Section: Methodsmentioning

confidence: 99%

Knockdown of PNO1 inhibits esophageal cancer progression

Wang

et al. 2021

Oncol Rep

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The present study aimed to investigate the role of partner of NOB1 homolog (PNO1) in esophageal cancer (EC). The expression levels of PNO1 in EC were primarily analyzed using data obtained from databases. PNO1 expression was also knocked down in EC cells (Eca-109 and TE1) to determine the biological effects of PNO1 on tumorigenesis in vitro and in vivo. In addition, possible downstream targets of PNO1 in EC were identified. The expression levels of PNO1 were upregulated in the tumor tissues compared with that noted in normal tissues. Moreover, the knockdown (KD) of PNO1 suppressed cell proliferation, migration and invasion, and promoted cell apoptosis (P<0.05). Furthermore, the protein expression levels of AKT1, Twist, Myc, mTOR, matrix metalloproteinase 2 (MMP2), nuclear factor (NF)-κB p65 and β-catenin 1 (CTNNB1) were downregulated following the KD of PNO1 in Eca-109 cells (P<0.05). In addition, the overexpression of CTNNB1 reversed the effects of PNO1 KD in Eca-109 cells (P<0.05). In conclusion, the findings of the present study suggest that PNO1 promotes EC progression by regulating AKT1, Twist, Myc, mTOR, MMP2, NF-κB p65 and CTNNB1 expression.Construction of stable PNO1-knockdown (KD) and β-catenin (CTNNB1)-overexpressing cells. PNO1 was stably knocked down in Eca-109 and TE-1 cells using short hairpin RNA (sh), and CTNNB1 was stably overexpressed in Eca-109 cells only. sh-PNO1-KD, sh-PNO1-negative control (NC), sh-CTNNB1-OE and sh-CTNNB1-negative control (NC)

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Section: Methodsmentioning

confidence: 99%

Knockdown of PNO1 inhibits esophageal cancer progression

Wang

et al. 2021

Oncol Rep

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“… Immune cell type Gene markers Spearman’s correlation p -value Ref. General T-cell activation CD3D 0.521 1.34e-26 [ 55 ] CD3E 0.539 8.58e-29 [ 56 ] CD4 + T cells (Th1 and Th2) TBX21 0.509 2.44e-25 [ 57 ] HLA-DMB 0.595 3.77e-36 [ 46 ] HLA-DRA 0.567 2.58e-32 [ 47 ] TGF- β 0.499 3.32e-24 [ 48 ] CRTAM 0.524 5.46e-27 IL12A 0.237 5.083e-6 IL12B 0.381 5.11e-14 Dendritic cells (DCs) VEGFC 0.517 3.36e-25 [ 58 ] CCL4 0.536 2.15e-28 [ 36 ] CCL5 0.536 2.08e-28 CD40L 0.455 6.18e-20 [ 59 ] CD40 0.585 1.15e-34 Neutrophils (N1 population) CXCL5 0.329 1.26e-10 [ 60 ] CSF2 0.391 9.82e-15 [ 61 ] <...…”

Section: Resultsmentioning

confidence: 99%

Promising prognostic value of Transglutaminase type 2 and its correlation with tumor-infiltrating immune cells in skin cutaneous melanoma

et al. 2022

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Tissue Transglutaminases (TGs) are crosslinking enzymes with pleiotropic functions that have been linked to the development and progression of numerous cancers, with a recent focus on their ability to remodel the tumor microenvironment. Although several pieces of evidence demonstrated their importance in the regulation of the major signaling pathways that control oncogenesis, the correlation between TGs with clinical and pathological features remains controversial and to be further explored. Moreover, an assessment of the TGs alterations together with a functional analysis associated with clinical features and prognostic values are still lacking and would help to understand these intricacies, particularly in human cancers. In the present study, we processed data from numerous public datasets to investigate TGs distribution and prognostic signature in cancer patients. Here, we found that skin cutaneous melanoma (SKCM) shows the highest abundance of TGs mutations among the other human cancers. Interestingly, among all the TGs, TG2 is the only member whose expression is associated with a better overall survival in SKCM, although its expression increases with the worsening of the tumor phenotype. Our analysis revealed a strong positive association between TG2 expression and anti-tumoral immune response, which would explain the relationship between high mRNA levels and better overall survival. Our data suggest that TG2 may be presented as a new promising immune biomarker of prognosis in SKCM, which may contribute to identifying patients who would benefit the most from adjuvant immunotherapy.

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“…Among them, 472 samples were downloaded from the TCGA database, 1 including 1 normal and 471 tumor samples. To increase the normal sample size, we collected the expression profiles of 812 normal skin samples in the GTEx data downloaded through UCSC Xena 2 [ 20 , 22 ]. Subsequently, an expression matrix file (GSE65904) from the GEO Database 3 was used as external verification.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of ferroptosis-related genes and prognosis of cutaneous melanoma

Liu

et al. 2022

BMC Med Genomics

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Background Cutaneous Melanoma (CM) is a malignant disease with increasing incidence and high mortality. Ferroptosis is a new kind of cell death and related to tumor blood and lymphatic metastasis. This study aims at using bioinformatics technology to construct a prognostic signature and identify ferroptosis-related biomarkers to improve the prognosis and treatment of cutaneous melanoma. Methods We used bioinformatics tools to analyze RNA sequencing expression data with clinical information from multiple databases, utilized varieties of statistical methods to construct a ferroptosis-related prognostic signature of cutaneous melanoma and screened out specific genes with independent prognostic ability. Results We obtained 22 ferroptosis-related (P < 0.05) prognostic DEGs in the uniCox regression analysis, among which 10 high-expressed genes (ATG5, CHAC1, FANCD2, FBXL5, HMOX2, HSPB1, NQO1, PEBP1, PRNP, SLC3A2) were screened out by LASSO regression analysis to establish a predictive model. Meanwhile, the ferroptosis-related signature and the nomogram we drew performed an excellent performance based on Kaplan–Meier (K–M), Receiver operating characteristic (ROC) and calibration curves. Univariate and multivariable cox analyses displayed that our model was greater than other prognostic features. GO and KEGG analyses revealed that 10-biomarker signature was mainly related to epidermis differentiation and immunity. ssGSEA analysis indicated that the immune status between the two risk groups was highly different. Besides, we found that two genes (CP, ZEB1) had independent prognostic ability and can be applied for drug research. Both genes were highly related to immunity. GSEA illustrated that ZEB1 may be involved in cellular functions such as proliferation, apoptosis, and migration, while CP was closely connected to immune cell related functions. Conclusion The present study suggested a 10-biomarker signature can be clinically used to predict the prognosis of cutaneous melanoma, which was better than conventional factors. CP and ZEB1 were independent prognostic genes and can be applied to guide treatment. In addition, ZEB1 mutation was highly related to overall survival in cutaneous melanoma, while CP may be associated with tumor progression. Our study comprehensively analyzed the relationship between iron metabolism, ferroptosis-related genes, and the prognosis of cutaneous melanoma, provided new insight for molecular mechanisms and treatment of ferroptosis and cutaneous melanoma.

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Increased Expression of T-Box Transcription Factor Protein 21 (TBX21) in Skin Cutaneous Melanoma Predicts Better Prognosis: A Study Based on The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) Databases

Cited by 12 publications

References 0 publications

Knockdown of PNO1 inhibits esophageal cancer progression

Knockdown of PNO1 inhibits esophageal cancer progression

Promising prognostic value of Transglutaminase type 2 and its correlation with tumor-infiltrating immune cells in skin cutaneous melanoma

Comprehensive analysis of ferroptosis-related genes and prognosis of cutaneous melanoma

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