Immune-related biomarkers predict the prognosis and immune response of breast cancer based on bioinformatic analysis and machine learning

Zheng, Xuewei; Ma, Haodi; Dong, Y.; Fang, M.; Wang, Junxiang; Xiong, Xin; Liang, Jian; Meng, Haoyu; You, Aimin; Yin, Qinan; Huang, Wenbin

doi:10.1007/s10142-023-01124-x

Cited by 10 publications

(4 citation statements)

References 47 publications

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“…Immunotherapy has become a powerful clinical strategy for treating cancer patients, particularly those with metastatic spread (Kennedy and Salama 2020 ; Yu et al 2022 ; Zheng et al 2023 ). There has been significant progress in the treatment of patients with ccRCC, with improved knowledge of disease biology and the introduction of targeted agents and immunotherapies (Atkins and Tannir 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma

Wang,

You,

et al. 2023

Funct Integr Genomics

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Y box binding protein 3 (YBX3) is an indispensable factor for protein synthesis, cellular growth, and proliferation, and is intricately involved in the progression of diverse tumor types. The objective of the current study was to investigate the role of YBX3 in the prognosis, immune infiltration, and progression of clear cell renal clear cell carcinoma (ccRCC). The expression level of YBX3 in ccRCC tissues was compared using The Cancer Genome Atlas (TCGA) and analyzed using the Wilcoxon rank sum test. Logistic regression and multivariate Cox analyses were subsequently employed to scrutinize the association between YBX3 expression and the clinicopathological characteristics of patients. The TIMER 2.0 tool was also utilized to quantify the degree of immune cell infiltration of YBX3. Kaplan Meier analysis was performed to assess the correlation between YBX3 and the survival rate. A high expression level of YBX3 was significantly correlated with the tumor pathological stage, histological grade, TNM stage, and the abundance of aDC, pDC, Th1, and Treg immune cells. Higher expression of YBX3 in advanced ccRCC was found to be associated with a lower overall survival rate in the M0, N0, and T2 subgroups. In vitro, after the silencing of YBX3 in A498 cells and overexpression of YBX3 in ACHN cells, cell proliferation, colony formation, migration, invasion, cell cycle assays, and flow cytometric apoptotic analysis were performed to evaluate the role of YBX3 in the progression of ccRCC. YBX3 was found to be intricately associated with the progression and prognosis of ccRCC, and may serve as an effective treatment target for ccRCC or a biomarker for prognosis prediction.

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Section: Discussionmentioning

confidence: 99%

Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma

Wang,

You,

et al. 2023

Funct Integr Genomics

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“…In addition, several immune checkpoint genes exhibit a positive correlation with UBE2C [74]. Other studies have reported a correlation between UBE2C and immune cell infiltration [61,69,72,73,102]. Specifically in hepatocellular carcinoma, UBE2C is positively correlated with infiltration of regulatory T cells and T follicular helper cells while presenting a negative correlation with macrophage infiltration [69].…”

Section: Other Neoplasmsmentioning

confidence: 94%

Role of UBE2C in Brain Cancer Invasion and Dissemination

Domentean,

Paisana,

Cascão

et al. 2023

IJMS

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Glioblastoma (GB) and brain metastases (BM) are the most common brain tumors in adults and are invariably associated with a dismal outcome. These highly malignant tumors share common features including increased invasion and migration of the primary or metastatic brain cancer cells, whose triggering mechanisms are largely unknown. Emerging evidence has suggested that the ubiquitin-conjugating enzyme E2C (UBE2C), essential for controlling cell cycle progression, is overexpressed in diverse malignancies, including brain cancer. This review highlights the crucial role of UBE2C in brain tumorigenesis and its association with higher proliferative phenotype and histopathological grade, with autophagy and apoptosis suppression, epithelial-to-mesenchymal transition (EMT), invasion, migration, and dissemination. High expression of UBE2C has been associated with patients’ poor prognosis and drug resistance. UBE2C has also been proven as a promising therapeutic target, despite the lack of specific inhibitors. Thus, there is a need to further explore the role of UBE2C in malignant brain cancer and to develop effective targeted therapies for patients with this deadly disease.

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“…The preprocessing of the data referred to previous study. [ 14 ] In briefly, the data was firstly normalized using limma R package, and the gene whose expression data omitted more that 80% sample was excluded.…”

Section: Methodsmentioning

confidence: 99%

PLAU and GREM1 are prognostic biomarkers for predicting immune response in lung adenocarcinoma

Fu,

Hu,

et al. 2024

Medicine

Self Cite

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Lung adenocarcinoma (LUAD) is a common malignant tumor. Identification of biomarkers and understanding their potential functions will facilitate the treatment and diagnosis in LUAD patients. The yellow module (cor = 0.31, P = 2e-6) was selected as the core module based on weighted gene co-expression network analysis (WGCNA) by integrating RNA-seq data and tumor stage. Two upregulated genes (PLAU and GREM1) in yellow module were identified to be biomarkers. Kaplan–Meier curve analysis displayed that high expression levels of them had a poor overall survival (OS). And, their high expression levels revealed higher tumor stage and relapse possibility in LUAD patients, and could be a prognostic parameter. Both biomarkers showed similar immune cell expression profiles in low- and high-expression groups. Strongly positive correlation between both biomarkers and biomarkers of tumor-infiltrating lymphocytes were also clarified in TCGA-LUAD cohort. Importantly, single gene GSEA showed that transcriptional mis-regulation in cancer and microRNAs in cancer were enriched in LUAD patients. Therefore, a miRNA-mRNA-transcription factors (TFs) co-expression regulatory networks was constructed for each biomarker, various miRNAs and TFs were related to PLAU and GREM1. Among which, 6 downstream TFs were overlapped genes for both biomarkers. Notably, 2 of these TFs (FOXF1 and TFAP2A) exhibited significantly abnormal expression levels. Among which, FOXF1 was downregulated and TFAP2A was upregulated in TCGA-LUAD cohort. Both TFs showed a significantly positive correlation with the expression level of PLAU. In conclusion, we identified 2 biomarkers related to immune response and achieved a good accuracy in predicting OS in patients with LUAD.

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Immune-related biomarkers predict the prognosis and immune response of breast cancer based on bioinformatic analysis and machine learning

Cited by 10 publications

References 47 publications

Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma

Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma

Role of UBE2C in Brain Cancer Invasion and Dissemination

PLAU and GREM1 are prognostic biomarkers for predicting immune response in lung adenocarcinoma

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